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Recent Articles in Journal of Biology

Okubo T, Hogan BL
Hyperactive Wnt signaling changes the developmental potential of embryonic lung endoderm.
J Biol. 2004;3(3):11.
BACKGROUND: Studies in many model systems have shown that canonical signaling through the pathway downstream of ligands of the Wnt family can regulate multiple steps in organogenesis, including cell proliferation, differentiation, and lineage specification. In addition, misexpression of the Wnt-family member Wingless in Drosophila imaginal disc cells can lead to transdetermination of progenitors from one lineage to another. Conditional deletion of the beta-catenin component of the Wnt signaling pathway has indicated a role for Wnt signaling in mouse lung endoderm development. The full range of effects of this pathway, which includes the transcription factor Lef1, has not been explored, however. RESULTS: To explore this issue, we expressed a constitutively active beta-catenin-Lef1 fusion protein in transgenic embryos using a lung-endoderm-specific promoter from the surfactant protein C gene. Transgenic lungs appeared grossly normal, but internally they contained highly proliferative, cuboidal epithelium lacking fully differentiated lung cell types. Unexpectedly, microarray analysis and in situ hybridization revealed a mosaic of cells expressing marker genes characteristic of intestinal Paneth and goblet cells and other non-lung secretory cell types. In addition, there was strong ectopic expression of genes such as Cdx1 and Atoh1 that normally regulate gut development and early allocation of cells to intestinal secretory lineages. CONCLUSIONS: Our results show that hyperactive Wnt signaling in lung progenitors expressing a lung-specific gene can induce a dramatic switch in lineage commitment and the generation of intestinal cell types. We discuss the relevance of our findings to the poorly understood pathological condition of intestinal metaplasia in humans. [Abstract/Link to Full Text]

Slack JM
Intestine in the lung.
J Biol. 2004;3(3):10.
The phenomenon of metaplasia, in which one tissue type is converted into another, is beginning to be explained in molecular terms. The transformation of lung to intestinal tissue has not previously been described, but it is now reported that it can be brought about by prolonged Wnt signaling in late development. [Abstract/Link to Full Text]

Weihs D
The hydrodynamics of dolphin drafting.
J Biol. 2004;3(2):8.
BACKGROUND: Drafting in cetaceans is defined as the transfer of forces between individuals without actual physical contact between them. This behavior has long been surmised to explain how young dolphin calves keep up with their rapidly moving mothers. It has recently been observed that a significant number of calves become permanently separated from their mothers during chases by tuna vessels. A study of the hydrodynamics of drafting, initiated in the hope of understanding the mechanisms causing the separation of mothers and calves during fishing-related activities, is reported here. RESULTS: Quantitative results are shown for the forces and moments around a pair of unequally sized dolphin-like slender bodies. These include two major effects. First, the so-called Bernoulli suction, which stems from the fact that the local pressure drops in areas of high speed, results in an attractive force between mother and calf. Second is the displacement effect, in which the motion of the mother causes the water in front to move forwards and radially outwards, and water behind the body to move forwards to replace the animal's mass. Thus, the calf can gain a 'free ride' in the forward-moving areas. Utilizing these effects, the neonate can gain up to 90% of the thrust needed to move alongside the mother at speeds of up to 2.4 m/sec. A comparison with observations of eastern spinner dolphins (Stenella longirostris) is presented, showing savings of up to 60% in the thrust that calves require if they are to keep up with their mothers. CONCLUSIONS: A theoretical analysis, backed by observations of free-swimming dolphin schools, indicates that hydrodynamic interactions with mothers play an important role in enabling dolphin calves to keep up with rapidly moving adult school members. [Abstract/Link to Full Text]

Moore P
Examining dolphin hydrodynamics provides clues to calf-loss during tuna fishing.
J Biol. 2004;3(2):6. [Abstract/Link to Full Text]

Alexander RM
Hitching a lift hydrodynamically--in swimming, flying and cycling.
J Biol. 2004;3(2):7.
Swimming animals set the water around them moving, and flying animals generate air movements. Other animals traveling with them can save energy by exploiting these movements of the fluid medium; similarly, a cyclist can save energy by riding close behind another. A new study of dolphin mothers and calves exemplifies the advantages of moving in concert. [Abstract/Link to Full Text]

Martindale D
Budding viral hijackers co-opt the endocytic machinery to make a getaway.
J Biol. 2003;3(1):2. [Abstract/Link to Full Text]

Yap MW, Stoye JP
Bending out and breaking away: host-cell accomplices in retroviral escape.
J Biol. 2003;3(1):3.
Budding through the host-cell membrane is a key step in the life cycle of many viruses. Recent studies of retrovirus replication implicate a large number of cellular proteins in this process. [Abstract/Link to Full Text]

Wang MQ, Kim W, Gao G, Torrey TA, Morse HC, De Camilli P, Goff SP
Endophilins interact with Moloney murine leukemia virus Gag and modulate virion production.
J Biol. 2003;3(1):4.
BACKGROUND: The retroviral Gag protein is the central player in the process of virion assembly at the plasma membrane, and is sufficient to induce the formation and release of virus-like particles. Recent evidence suggests that Gag may co-opt the host cell's endocytic machinery to facilitate retroviral assembly and release. RESULTS: A search for novel partners interacting with the Gag protein of the Moloney murine leukemia virus (Mo-MuLV) via the yeast two-hybrid protein-protein interaction assay resulted in the identification of endophilin 2, a component of the machinery involved in clathrin-mediated endocytosis. We demonstrate that endophilin interacts with the matrix or MA domain of the Gag protein of Mo-MuLV, but not of human immunodeficiency virus, HIV. Both exogenously expressed and endogenous endophilin are incorporated into Mo-MuLV viral particles. Titration experiments suggest that the binding sites for inclusion of endophilin into viral particles are limited and saturable. Knock-down of endophilin with small interfering RNA (siRNA) had no effect on virion production, but overexpression of endophilin and, to a lesser extent, of several fragments of the protein, result in inhibition of Mo-MuLV virion production, but not of HIV virion production. CONCLUSIONS: This study shows that endophilins interact with Mo-MuLV Gag and affect virion production. The findings imply that endophilin is another component of the large complex that is hijacked by retroviruses to promote virion production. [Abstract/Link to Full Text]

Weitzman JB
RNAi and the shape of things to come.
J Biol. 2003;2(4):23. [Abstract/Link to Full Text]

Kyriakis JM
At the crossroads: AMP-activated kinase and the LKB1 tumor suppressor link cell proliferation to metabolic regulation.
J Biol. 2003;2(4):26.
The tumor suppressor kinase LKB1 has been identified as a physiologic activator of the key metabolic regulator 5'-AMP-activated protein kinase, establishing a possible molecular link between the regulation of metabolism and cell proliferation. [Abstract/Link to Full Text]

Pollard TD
Functional genomics of cell morphology using RNA interference: pick your style, broad or deep.
J Biol. 2003;2(4):25.
Several new studies have used RNA interference to screen for protein functions affecting cell shape, mitosis and cytokinesis of Drosophila cells in culture. One broad survey of nearly 1,000 proteins and three studies focused on cytoskeletal and motor proteins have identified key proteins essential for these processes in animal cells. [Abstract/Link to Full Text]

Kiger AA, Baum B, Jones S, Jones MR, Coulson A, Echeverri C, Perrimon N
A functional genomic analysis of cell morphology using RNA interference.
J Biol. 2003;2(4):27.
BACKGROUND: The diversity of metazoan cell shapes is influenced by the dynamic cytoskeletal network. With the advent of RNA-interference (RNAi) technology, it is now possible to screen systematically for genes controlling specific cell-biological processes, including those required to generate distinct morphologies. RESULTS: We adapted existing RNAi technology in Drosophila cell culture for use in high-throughput screens to enable a comprehensive genetic dissection of cell morphogenesis. To identify genes responsible for the characteristic shape of two morphologically distinct cell lines, we performed RNAi screens in each line with a set of double-stranded RNAs (dsRNAs) targeting 994 predicted cell shape regulators. Using automated fluorescence microscopy to visualize actin filaments, microtubules and DNA, we detected morphological phenotypes for 160 genes, one-third of which have not been previously characterized in vivo. Genes with similar phenotypes corresponded to known components of pathways controlling cytoskeletal organization and cell shape, leading us to propose similar functions for previously uncharacterized genes. Furthermore, we were able to uncover genes acting within a specific pathway using a co-RNAi screen to identify dsRNA suppressors of a cell shape change induced by Pten dsRNA. CONCLUSIONS: Using RNAi, we identified genes that influence cytoskeletal organization and morphology in two distinct cell types. Some genes exhibited similar RNAi phenotypes in both cell types, while others appeared to have cell-type-specific functions, in part reflecting the different mechanisms used to generate a round or a flat cell morphology. [Abstract/Link to Full Text]

Hawley SA, Boudeau J, Reid JL, Mustard KJ, Udd L, M�kel� TP, Alessi DR, Hardie DG
Complexes between the LKB1 tumor suppressor, STRAD alpha/beta and MO25 alpha/beta are upstream kinases in the AMP-activated protein kinase cascade.
J Biol. 2003;2(4):28.
BACKGROUND: The AMP-activated protein kinase (AMPK) cascade is a sensor of cellular energy charge that acts as a 'metabolic master switch' and inhibits cell proliferation. Activation requires phosphorylation of Thr172 of AMPK within the activation loop by upstream kinases (AMPKKs) that have not been identified. Recently, we identified three related protein kinases acting upstream of the yeast homolog of AMPK. Although they do not have obvious mammalian homologs, they are related to LKB1, a tumor suppressor that is mutated in the human Peutz-Jeghers cancer syndrome. We recently showed that LKB1 exists as a complex with two accessory subunits, STRAD alpha/beta and MO25 alpha/beta. RESULTS: We report the following observations. First, two AMPKK activities purified from rat liver contain LKB1, STRAD alpha and MO25 alpha, and can be immunoprecipitated using anti-LKB1 antibodies. Second, both endogenous and recombinant complexes of LKB1, STRAD alpha/beta and MO25 alpha/beta activate AMPK via phosphorylation of Thr172. Third, catalytically active LKB1, STRAD alpha or STRAD beta and MO25 alpha or MO25 beta are required for full activity. Fourth, the AMPK-activating drugs AICA riboside and phenformin do not activate AMPK in HeLa cells (which lack LKB1), but activation can be restored by stably expressing wild-type, but not catalytically inactive, LKB1. Fifth, AICA riboside and phenformin fail to activate AMPK in immortalized fibroblasts from LKB1-knockout mouse embryos. CONCLUSIONS: These results provide the first description of a physiological substrate for the LKB1 tumor suppressor and suggest that it functions as an upstream regulator of AMPK. Our findings indicate that the tumors in Peutz-Jeghers syndrome could result from deficient activation of AMPK as a consequence of LKB1 inactivation. [Abstract/Link to Full Text]

Neufeld TP
Shrinkage control: regulation of insulin-mediated growth by FOXO transcription factors.
J Biol. 2003;2(3):18.
The insulin signaling pathway regulates organismal growth in response to nutrient conditions by controlling a range of metabolic and biosynthetic processes. Recent studies in Drosophila have shown how transcriptional responses to reduced insulin and nutrient levels can act to inhibit growth. [Abstract/Link to Full Text]

Chu P, Pardo J, Zhao H, Li CC, Pali E, Shen MM, Qu K, Yu SX, Huang BC, Yu P, Masuda ES, Molineaux SM, Kolbinger F, Aversa G, de Vries J, Payan DG, Liao XC
Systematic identification of regulatory proteins critical for T-cell activation.
J Biol. 2003;2(3):21.
BACKGROUND: The activation of T cells, mediated by the T-cell receptor (TCR), activates a battery of specific membrane-associated, cytosolic and nuclear proteins. Identifying the signaling proteins downstream of TCR activation will help us to understand the regulation of immune responses and will contribute to developing therapeutic agents that target immune regulation. RESULTS: In an effort to identify novel signaling molecules specific for T-cell activation we undertook a large-scale dominant effector genetic screen using retroviral technology. We cloned and characterized 33 distinct genes from over 2,800 clones obtained in a screen of 7 x 108 Jurkat T cells on the basis of a reduction in TCR-activation-induced CD69 expression after expressing retrovirally derived cDNA libraries. We identified known signaling molecules such as Lck, ZAP70, Syk, PLC gamma 1 and SHP-1 (PTP1C) as truncation mutants with dominant-negative or constitutively active functions. We also discovered molecules not previously known to have functions in this pathway, including a novel protein with a RING domain (found in a class of ubiquitin ligases; we call this protein TRAC-1), transmembrane molecules (EDG1, IL-10R alpha and integrin alpha2), cytoplasmic enzymes and adaptors (PAK2, A-Raf-1, TCPTP, Grb7, SH2-B and GG2-1), and cytoskeletal molecules (moesin and vimentin). Furthermore, using truncated Lck, PLC gamma 1, EDG1 and PAK2 mutants as examples, we showed that these dominant immune-regulatory molecules interfere with IL-2 production in human primary lymphocytes. CONCLUSIONS: This study identified important signal regulators in T-cell activation. It also demonstrated a highly efficient strategy for discovering many components of signal transduction pathways and validating them in physiological settings. [Abstract/Link to Full Text]

Moore P
Controlling how many cells make a fly.
J Biol. 2003;2(3):16. [Abstract/Link to Full Text]

J�nger MA, Rintelen F, Stocker H, Wasserman JD, V�gh M, Radimerski T, Greenberg ME, Hafen E
The Drosophila forkhead transcription factor FOXO mediates the reduction in cell number associated with reduced insulin signaling.
J Biol. 2003;2(3):20.
BACKGROUND: Forkhead transcription factors belonging to the FOXO subfamily are negatively regulated by protein kinase B (PKB) in response to signaling by insulin and insulin-like growth factor in Caenorhabditis elegans and mammals. In Drosophila, the insulin-signaling pathway regulates the size of cells, organs, and the entire body in response to nutrient availability, by controlling both cell size and cell number. In this study, we present a genetic characterization of dFOXO, the only Drosophila FOXO ortholog. RESULTS: Ectopic expression of dFOXO and human FOXO3a induced organ-size reduction and cell death in a manner dependent on phosphoinositide (PI) 3-kinase and nutrient levels. Surprisingly, flies homozygous for dFOXO null alleles are viable and of normal size. They are, however, more sensitive to oxidative stress. Furthermore, dFOXO function is required for growth inhibition associated with reduced insulin signaling. Loss of dFOXO suppresses the reduction in cell number but not the cell-size reduction elicited by mutations in the insulin-signaling pathway. By microarray analysis and subsequent genetic validation, we have identified d4E-BP, which encodes a translation inhibitor, as a relevant dFOXO target gene. CONCLUSION: Our results show that dFOXO is a crucial mediator of insulin signaling in Drosophila, mediating the reduction in cell number in insulin-signaling mutants. We propose that in response to cellular stresses, such as nutrient deprivation or increased levels of reactive oxygen species, dFOXO is activated and inhibits growth through the action of target genes such as d4E-BP. [Abstract/Link to Full Text]

Moore P
Stress, sex and evolution.
J Biol. 2003;2(2):10. [Abstract/Link to Full Text]

Elena SF, de Visser JA
Environmental stress and the effects of mutation.
J Biol. 2003;2(2):12.
Mutations are the ultimate fuel for evolution, but most mutations have a negative effect on fitness. It has been widely accepted that these deleterious fitness effects are, on average, magnified in stressful environments. Recent results suggest that the effects of deleterious mutations can, instead, sometimes be ameliorated in stressful environments. [Abstract/Link to Full Text]

Weitzman JB
Tracking evolution's footprints in the genome.
J Biol. 2003;2(2):9. [Abstract/Link to Full Text]

Zhang Z, Gerstein M
Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements.
J Biol. 2003;2(2):11.
Phylogenetic footprinting is an approach to finding functionally important sequences in the genome that relies on detecting their high degrees of conservation across different species. A new study shows how much it improves the prediction of gene-regulatory elements in the human genome. [Abstract/Link to Full Text]

Kishony R, Leibler S
Environmental stresses can alleviate the average deleterious effect of mutations.
J Biol. 2003;2(2):14.
BACKGROUND: Fundamental questions in evolutionary genetics, including the possible advantage of sexual reproduction, depend critically on the effects of deleterious mutations on fitness. Limited existing experimental evidence suggests that, on average, such effects tend to be aggravated under environmental stresses, consistent with the perception that stress diminishes the organism's ability to tolerate deleterious mutations. Here, we ask whether there are also stresses with the opposite influence, under which the organism becomes more tolerant to mutations. RESULTS: We developed a technique, based on bioluminescence, which allows accurate automated measurements of bacterial growth rates at very low cell densities. Using this system, we measured growth rates of Escherichia coli mutants under a diverse set of environmental stresses. In contrast to the perception that stress always reduces the organism's ability to tolerate mutations, our measurements identified stresses that do the opposite - that is, despite decreasing wild-type growth, they alleviate, on average, the effect of deleterious mutations. CONCLUSIONS: Our results show a qualitative difference between various environmental stresses ranging from alleviation to aggravation of the average effect of mutations. We further show how the existence of stresses that are biased towards alleviation of the effects of mutations may imply the existence of average epistatic interactions between mutations. The results thus offer a connection between the two main factors controlling the effects of deleterious mutations: environmental conditions and epistatic interactions. [Abstract/Link to Full Text]

Lenhard B, Sandelin A, Mendoza L, Engstr�m P, Jareborg N, Wasserman WW
Identification of conserved regulatory elements by comparative genome analysis.
J Biol. 2003;2(2):13.
BACKGROUND: For genes that have been successfully delineated within the human genome sequence, most regulatory sequences remain to be elucidated. The annotation and interpretation process requires additional data resources and significant improvements in computational methods for the detection of regulatory regions. One approach of growing popularity is based on the preferential conservation of functional sequences over the course of evolution by selective pressure, termed 'phylogenetic footprinting'. Mutations are more likely to be disruptive if they appear in functional sites, resulting in a measurable difference in evolution rates between functional and non-functional genomic segments. RESULTS: We have devised a flexible suite of methods for the identification and visualization of conserved transcription-factor-binding sites. The system reports those putative transcription-factor-binding sites that are both situated in conserved regions and located as pairs of sites in equivalent positions in alignments between two orthologous sequences. An underlying collection of metazoan transcription-factor-binding profiles was assembled to facilitate the study. This approach results in a significant improvement in the detection of transcription-factor-binding sites because of an increased signal-to-noise ratio, as demonstrated with two sets of promoter sequences. The method is implemented as a graphical web application, ConSite, which is at the disposal of the scientific community at http://www.phylofoot.org/. CONCLUSIONS: Phylogenetic footprinting dramatically improves the predictive selectivity of bioinformatic approaches to the analysis of promoter sequences. ConSite delivers unparalleled performance using a novel database of high-quality binding models for metazoan transcription factors. With a dynamic interface, this bioinformatics tool provides broad access to promoter analysis with phylogenetic footprinting. [Abstract/Link to Full Text]

Conlon I, Raff M
Differences in the way a mammalian cell and yeast cells coordinate cell growth and cell-cycle progression.
J Biol. 2003;2(1):7.
BACKGROUND: It is widely believed that cell-size checkpoints help to coordinate cell growth and cell-cycle progression, so that proliferating eukaryotic cells maintain their size. There is strong evidence for such size checkpoints in yeasts, which maintain a constant cell-size distribution as they proliferate, even though large yeast cells grow faster than small yeast cells. Moreover, when yeast cells are shifted to better or worse nutrient conditions, they alter their size threshold within one cell cycle. Populations of mammalian cells can also maintain a constant size distribution as they proliferate, but it is not known whether this depends on cell-size checkpoints. RESULTS: We show that proliferating rat Schwann cells do not require a cell-size checkpoint to maintain a constant cell-size distribution, as, unlike yeasts, large and small Schwann cells grow at the same rate, which depends on the concentration of extracellular growth factors. In addition, when shifted from serum-free to serum-containing medium, Schwann cells take many divisions to increase their size to that appropriate to the new condition, suggesting that they do not have cell-size checkpoints similar to those in yeasts. CONCLUSIONS: Proliferating Schwann cells and yeast cells seem to use different mechanisms to coordinate their growth with cell-cycle progression. Whereas yeast cells use cell-size checkpoints, Schwann cells apparently do not. It seems likely that many mammalian cells resemble Schwann cells in this respect. [Abstract/Link to Full Text]

Lang MJ, Fordyce PM, Block SM
Combined optical trapping and single-molecule fluorescence.
J Biol. 2003;2(1):6.
BACKGROUND: Two of the mainstay techniques in single-molecule research are optical trapping and single-molecule fluorescence. Previous attempts to combine these techniques in a single experiment - and on a single macromolecule of interest - have met with little success, because the light intensity within an optical trap is more than ten orders of magnitude greater than the light emitted by a single fluorophore. Instead, the two techniques have been employed sequentially, or spatially separated by distances of several micrometers within the sample, imposing experimental restrictions that limit the utility of the combined method. Here, we report the development of an instrument capable of true, simultaneous, spatially coincident optical trapping and single-molecule fluorescence. RESULTS: We demonstrate the capability of the apparatus by studying force-induced strand separation of a rhodamine-labeled, 15 base-pair segment of double-stranded DNA, with force applied perpendicular to the axis of the DNA molecule. As expected, we observed abrupt mechanical transitions corresponding to the unzipping of DNA at a critical force. Transitions occurred concomitant with changes in the fluorescence of dyes attached at the duplex ends, which became unquenched upon strand separation. CONCLUSIONS: Through careful optical design, the use of high-performance spectral notch filters, a judicious choice of fluorophores, and the rapid acquisition of data gained by computer-automating the experiment, it is possible to perform combined optical trapping and single-molecule fluorescence. This opens the door to many types of experiment that employ optical traps to supply controlled external loads while fluorescent molecules report concurrent information about macromolecular structure. [Abstract/Link to Full Text]

Grewal SS, Edgar BA
Controlling cell division in yeast and animals: does size matter?
J Biol. 2003;2(1):5.
In yeast, cell-size checkpoints coordinate cellular growth with cell-cycle progression. Now, evidence has been provided that such checkpoints probably do not exist in mammalian cells. These findings highlight an important difference between how yeast and animal cells proliferate in response to extracellular cues. [Abstract/Link to Full Text]

Wallace MI, Molloy JE, Trentham DR
Combined single-molecule force and fluorescence measurements for biology.
J Biol. 2003;2(1):4.
Recent advances in single-molecule techniques allow the application of force to an individual biomolecule whilst simultaneously monitoring its response using fluorescent probes. The effects of applied mechanical load on single-enzyme turnovers, biomolecular interactions and conformational changes can now be studied with nanometer precision and millisecond time resolution. [Abstract/Link to Full Text]

Weitzman JB
Growing without a size checkpoint.
J Biol. 2003;2(1):3. [Abstract/Link to Full Text]

Weitzman JB
A marriage of techniques.
J Biol. 2003;2(1):2. [Abstract/Link to Full Text]

Frank-Kamenetsky M, Zhang XM, Bottega S, Guicherit O, Wichterle H, Dudek H, Bumcrot D, Wang FY, Jones S, Shulok J, Rubin LL, Porter JA
Small-molecule modulators of Hedgehog signaling: identification and characterization of Smoothened agonists and antagonists.
J Biol. 2002 Nov 6;1(2):10.
BACKGROUND: The Hedgehog (Hh) signaling pathway is vital to animal development as it mediates the differentiation of multiple cell types during embryogenesis. In adults, Hh signaling can be activated to facilitate tissue maintenance and repair. Moreover, stimulation of the Hh pathway has shown therapeutic efficacy in models of neuropathy. The underlying mechanisms of Hh signal transduction remain obscure, however: little is known about the communication between the pathway suppressor Patched (Ptc), a multipass transmembrane protein that directly binds Hh, and the pathway activator Smoothened (Smo), a protein that is related to G-protein-coupled receptors and is capable of constitutive activation in the absence of Ptc. RESULTS: We have identified and characterized a synthetic non-peptidyl small molecule, Hh-Ag, that acts as an agonist of the Hh pathway. This Hh agonist promotes cell-type-specific proliferation and concentration-dependent differentiation in vitro, while in utero it rescues aspects of the Hh-signaling defect in Sonic hedgehog-null, but not Smo-null, mouse embryos. Biochemical studies with Hh-Ag, the Hh-signaling antagonist cyclopamine, and a novel Hh-signaling inhibitor Cur61414, reveal that the action of all these compounds is independent of Hh-protein ligand and of the Hh receptor Ptc, as each binds directly to Smo. CONCLUSIONS: Smo can have its activity modulated directly by synthetic small molecules. These studies raise the possibility that Hh signaling may be regulated by endogenous small molecules in vivo and provide potent compounds with which to test the therapeutic value of activating the Hh-signaling pathway in the treatment of traumatic and chronic degenerative conditions. [Abstract/Link to Full Text]

Weitzman JB
Agonizing hedgehog.
J Biol. 2002 Nov 6;1(2):7. [Abstract/Link to Full Text]

King RW
Roughing up Smoothened: chemical modulators of hedgehog signaling.
J Biol. 2002 Nov 6;1(2):8.
Small-molecule antagonists of Hedgehog-pathway signaling, such as cyclopamine, have been known for some time. Now, small-molecule agonists of the Hedgehog pathway have also been identified. The finding that both antagonists and agonists target the protein Smoothened supports the emerging hypothesis that Smoothened may be regulated by endogenous small molecules. [Abstract/Link to Full Text]

Stecca B, Ruiz i Altaba A
The therapeutic potential of modulators of the Hedgehog-Gli signaling pathway.
J Biol. 2002 Nov 6;1(2):9.
The discovery of small molecules that act as agonists and antagonists of the Hedgehog-Gli signaling pathway, which plays important roles in the embryo and adult, opens a new avenue for the treatment of diseases caused by aberrant suppression or activation of this complex pathway. [Abstract/Link to Full Text]

Spellman PT, Rubin GM
Evidence for large domains of similarly expressed genes in the Drosophila genome.
J Biol. 2002;1(1):5.
BACKGROUND: Transcriptional regulation in eukaryotes generally operates at the level of individual genes. Regulation of sets of adjacent genes by mechanisms operating at the level of chromosomal domains has been demonstrated in a number of cases, but the fraction of genes in the genome subject to regulation at this level is unknown. RESULTS: Drosophila gene-expression profiles that were determined from over 80 experimental conditions using high-density oligonucleotide microarrays were searched for groups of adjacent genes that show similar expression profiles. We found about 200 groups of adjacent and similarly expressed genes, each having between 10 and 30 members; together these groups account for over 20% of assayed genes. Each group covers between 20 and 200 kilobase pairs of genomic sequence, with a mean group size of about 100 kilobase pairs. Groups do not appear to show any correlation with polytene banding patterns or other known chromosomal structures, nor were genes within groups functionally related to one another. CONCLUSIONS: Groups of adjacent and co-regulated genes that are not otherwise functionally related in any obvious way can be identified by expression profiling in Drosophila. The mechanism underlying this phenomenon is not yet known. [Abstract/Link to Full Text]

Weitzman JB
Transcriptional territories in the genome.
J Biol. 2002;1(1):2. [Abstract/Link to Full Text]

Suber P
Open access to the scientific journal literature.
J Biol. 2002;1(1):3.
None of the advantages of traditional scientific journals need be sacrificed in order to provide free online access to scientific journal articles. Objections that open access to scientific journal literature requires the sacrifice of peer-review, revenue, copyright protection, or other strengths of traditional journals, are based on misunderstandings. [Abstract/Link to Full Text]

Oliver B, Parisi M, Clark D
Gene expression neighborhoods.
J Biol. 2002;1(1):4.
The finding that neighboring eukaryotic genes are often expressed in similar patterns suggests the involvement of chromatin domains in the control of genes within a genomic neighborhood. [Abstract/Link to Full Text]

Recent Articles in The Journal of Experimental Biology

Strange K
Revisiting the Krogh Principle in the post-genome era: caenorhabditis elegans as a model system for integrative physiology research.
J Exp Biol. 2007 May;210(Pt 9):1622-31.
Molecular biology drove a powerful reductionist or ;molecule-centric' approach to biological research in the last half of the 20th century. Reductionism is the attempt to explain complex phenomena by defining the functional properties of the individual components that comprise multi-component systems. Systems biology has emerged in the post-genome era as the successor to reductionism. In my opinion, systems biology and physiology are synonymous. Both disciplines seek to understand multi-component processes or 'systems' and the underlying pathways of information flow from an organism's genes up through increasingly complex levels of organization. The physiologist and Nobel laureate August Krogh believed that there is an ideal organism in which almost every physiological problem could be studied most readily (the 'Krogh Principle'). If an investigator's goal were to define a physiological process from the level of genes to the whole animal, the optimal model organism for him/her to utilize would be one that is genetically and molecularly tractable. In other words, an organism in which forward and reverse genetic analyses could be carried out readily, rapidly and economically. Non-mammalian model organisms such as Escherichia coli, Saccharomyces, Caenorhabditis elegans, Drosophila, zebrafish and the plant Arabidopsis are cornerstones of systems biology research. The nematode C. elegans provides a particularly striking example of the experimental utility of non-mammalian model organisms. The aim of this paper is to illustrate how genetic, functional genomic, molecular and physiological methods can be combined in C. elegans to develop a systems biological understanding of fundamental physiological processes common to all animals. I present examples of the experimental tools available for the study of C. elegans and discuss how we have used them to gain new insights into osmotic stress signaling in animal cells. [Abstract/Link to Full Text]

Crawford DL, Oleksiak MF
The biological importance of measuring individual variation.
J Exp Biol. 2007 May;210(Pt 9):1613-21.
Functional genomics research using Fundulus heteroclitus has focused on variation among individuals because of the evolutionary importance and value of Fundulus in explaining the human condition (why individual humans are different and are affected differently by stress, disease and drugs). Among different populations and species of Fundulus, there are evolutionarily adaptive differences in gene expression. This natural variation in gene expression seems to affect cardiac metabolism because up to 81% of the variation in glucose utilization observed in isolated heart ventricles is related to specific patterns of gene expression. The surprising result from this research is that among different groups of individuals, the expression of mRNA from different metabolic pathways explains substrate-specific metabolism. For example, variation in oxidative phosphorylation mRNAs explains glucose metabolism for one group of individuals but expression of glucose metabolism genes explains this metabolism in a different group of individuals. This variation among individuals has important implications for studies using inbred strains: conclusions based on one individual or one strain will not necessarily reflect a generalized conclusion for a population or species. Finally, there are surprisingly strong positive and negative correlations among metabolic genes, both within and between pathways. These data suggest that measures of mRNA expression are meaningful, yet there is a complexity in how gene expression is related to physiological processes. [Abstract/Link to Full Text]

Kim SK
Common aging pathways in worms, flies, mice and humans.
J Exp Biol. 2007 May;210(Pt 9):1607-12.
Development of functional genomics tools has made it possible to define the aging process by performing genome-wide scans for transcriptional differences between the young and the old. Global screens for age regulation have been performed for worms and flies, as well as many tissues in mice and humans. Recent work has begun to analyze the similarities and differences in transcriptional changes in aging among different species. Most age-related expression changes are specific for a given species, but genes in one pathway (the electron transport chain pathway) show common age regulation in species from worms to humans. Evolutionary theories of aging provide a basis to understand how age regulation of a genetic pathway might be preserved between distantly related species. [Abstract/Link to Full Text]

Buckley BA
Comparative environmental genomics in non-model species: using heterologous hybridization to DNA-based microarrays.
J Exp Biol. 2007 May;210(Pt 9):1602-6.
The emerging field of comparative environmental genomics involves the cross-species comparison of broad-scale patterns of gene expression. Often, the goal is to elucidate the evolutionary basis or ecological implications of genomic responses to environmental stimuli. DNA-based microarrays represent powerful means with which to investigate gene expression, and the application of genomic tools to studies on non-model species is becoming increasingly feasible. The use of a microarray generated from one species to probe gene expression in another, a method termed 'heterologous hybridization', eliminates the need to fabricate novel microarray platforms for every new species of interest. In this review, recent advances in heterologous hybridization are reviewed, and the technical caveats of this approach are discussed. [Abstract/Link to Full Text]

K�ltz D, Fiol D, Valkova N, Gomez-Jimenez S, Chan SY, Lee J
Functional genomics and proteomics of the cellular osmotic stress response in 'non-model' organisms.
J Exp Biol. 2007 May;210(Pt 9):1593-601.
All organisms are adapted to well-defined extracellular salinity ranges. Osmoregulatory mechanisms spanning all levels of biological organization, from molecules to behavior, are central to salinity adaptation. Functional genomics and proteomics approaches represent powerful tools for gaining insight into the molecular basis of salinity adaptation and euryhalinity in animals. In this review, we discuss our experience in applying such tools to so-called 'non-model' species, including euryhaline animals that are well-suited for studies of salinity adaptation. Suppression subtractive hybridization, RACE-PCR and mass spectrometry-driven proteomics can be used to identify genes and proteins involved in salinity adaptation or other environmental stress responses in tilapia, sharks and sponges. For protein identification in non-model species, algorithms based on sequence homology searches such as MSBLASTP2 are most powerful. Subsequent gene ontology and pathway analysis can then utilize sets of identified genes and proteins for modeling molecular mechanisms of environmental adaptation. Current limitations for proteomics in non-model species can be overcome by improving sequence coverage, N- and C-terminal sequencing and analysis of intact proteins. Dependence on information about biochemical pathways and gene ontology databases for model species represents a more severe barrier for work with non-model species. To minimize such dependence, focusing on a single biological process (rather than attempting to describe the system as a whole) is key when applying 'omics' approaches to non-model organisms. [Abstract/Link to Full Text]

Gracey AY
Interpreting physiological responses to environmental change through gene expression profiling.
J Exp Biol. 2007 May;210(Pt 9):1584-92.
Identification of differentially expressed genes in response to environmental change offers insights into the roles of the transcriptome in the regulation of physiological responses. A variety of methods are now available to implement large-scale gene expression screens, and each method has specific advantages and disadvantages. Construction of custom cDNA microarrays remains the most popular route to implement expression screens in the non-model organisms favored by comparative physiologists, and we highlight some factors that should be considered when embarking along this path. Using a carp cDNA microarray, we have undertaken a broad, system-wide gene expression screen to investigate the physiological mechanisms underlying cold and hypoxia acclimation. This dataset provides a starting point from which to explore a range of specific mechanistic hypotheses at all levels of organization, from individual biochemical pathways to the level of the whole organism. We demonstrate the utility of two data analysis methods, Gene Ontology profiling and rank-based statistical methods, to summarize the probable physiological function of acclimation-induced gene expression changes, and to prioritize specific genes as candidates for further study. [Abstract/Link to Full Text]

Smith NP, Crampin EJ, Niederer SA, Bassingthwaighte JB, Beard DA
Computational biology of cardiac myocytes: proposed standards for the physiome.
J Exp Biol. 2007 May;210(Pt 9):1576-83.
Predicting information about human physiology and pathophysiology from genomic data is a compelling, but unfulfilled goal of post-genomic biology. This is the aim of the so-called Physiome Project and is, undeniably, an ambitious goal. Yet if we can exploit even a small proportion of the rich and varied experimental data currently available, significant insights into clinically important aspects of human physiology will follow. To achieve this requires the integration of data from disparate sources into a common framework. Extrapolation of available data across species, laboratory techniques and conditions requires a quantitative approach. Mathematical models allow us to integrate molecular information into cellular, tissue and organ-level, and ultimately clinically relevant scales. In this paper we argue that biophysically detailed computational modelling provides the essential tool for this process and, furthermore, that an appropriate framework for annotating, databasing and critiquing these models will be essential for the development of integrative computational biology. [Abstract/Link to Full Text]

Wittkopp PJ
Variable gene expression in eukaryotes: a network perspective.
J Exp Biol. 2007 May;210(Pt 9):1567-75.
Changes in gene expression underlie phenotypic plasticity, variation within species, and phenotypic divergence between species. These expression differences arise from modulation of regulatory networks. To understand the source of expression differences, networks of interactions among genes and gene products that orchestrate gene expression must be considered. Here I review the basic structure of eukaryotic regulatory networks and discuss selected case studies that provide insight into how these networks are altered to create expression differences within and between species. [Abstract/Link to Full Text]

Lehner B
Modelling genotype-phenotype relationships and human disease with genetic interaction networks.
J Exp Biol. 2007 May;210(Pt 9):1559-66.
Probably all heritable traits, including disease susceptibility, are affected by interactions between mutations in multiple genes. We understand little, however, about how genes interact to produce phenotypes, and there is little power to detect interactions between genes in human population studies. An alternative approach towards understanding how mutations combine to produce phenotypes is to construct systematic genetic interaction networks in model organisms. Here I describe the methods that are being used to map genetic interactions in yeast and C. elegans, and the insights that these networks provide for human disease. I also discuss the mechanistic interpretation of genetic interaction networks, how genetic interactions can be used to understand gene function, and methods that have been developed to predict genetic interactions on a genome-wide scale. [Abstract/Link to Full Text]

Almaas E
Biological impacts and context of network theory.
J Exp Biol. 2007 May;210(Pt 9):1548-58.
Many complex systems can be represented and analyzed as networks, and examples that have benefited from this approach span the natural sciences. For instance, we now know that systems as disparate as the World Wide Web, the Internet, scientific collaborations, food webs, protein interactions and metabolism all have common features in their organization, the most salient of which are their scale-free connectivity distributions and their small-world behavior. The recent availability of large-scale datasets that span the proteome or metabolome of an organism have made it possible to elucidate some of the organizational principles and rules that govern their function, robustness and evolution. We expect that combining the currently separate layers of information from gene regulatory networks, signal transduction networks, protein interaction networks and metabolic networks will dramatically enhance our understanding of cellular function and dynamics. [Abstract/Link to Full Text]

Mattick JS
A new paradigm for developmental biology.
J Exp Biol. 2007 May;210(Pt 9):1526-47.
It is usually thought that the development of complex organisms is controlled by protein regulatory factors and morphogenetic signals exchanged between cells and differentiating tissues during ontogeny. However, it is now evident that the majority of all animal genomes is transcribed, apparently in a developmentally regulated manner, suggesting that these genomes largely encode RNA machines and that there may be a vast hidden layer of RNA regulatory transactions in the background. I propose that the epigenetic trajectories of differentiation and development are primarily programmed by feed-forward RNA regulatory networks and that most of the information required for multicellular development is embedded in these networks, with cell-cell signalling required to provide important positional information and to correct stochastic errors in the endogenous RNA-directed program. [Abstract/Link to Full Text]

Hall N
Advanced sequencing technologies and their wider impact in microbiology.
J Exp Biol. 2007 May;210(Pt 9):1518-25.
In the past 10 years, microbiology has undergone a revolution that has been driven by access to cheap high-throughput DNA sequencing. It was not long ago that the cloning and sequencing of a target gene could take months or years, whereas now this entire process has been replaced by a 10 min Internet search of a public genome database. There has been no single innovation that has initiated this rapid technological change; in fact, the core chemistry of DNA sequencing is the same as it was 30 years ago. Instead, progress has been driven by large sequencing centers that have incrementally industrialized the Sanger sequencing method. A side effect of this industrialization is that large-scale sequencing has moved out of small research labs, and the vast majority of sequence data is now generated by large genome centers. Recently, there have been advances in technology that will enable high-throughput genome sequencing to be established in research labs using bench-top instrumentation. These new technologies are already being used to explore the vast microbial diversity in the natural environment and the untapped genetic variation that can occur in bacterial species. It is expected that these powerful new methods will open up new questions to genomic investigation and will also allow high-throughput sequencing to be more than just a discovery exercise but also a routine assay for hypothesis testing. While this review will concentrate on microorganisms, many of the important arguments about the need to measure and understand variation at the species, population and ecosystem level will hold true for many other biological systems. [Abstract/Link to Full Text]

Quackenbush J
Extracting biology from high-dimensional biological data.
J Exp Biol. 2007 May;210(Pt 9):1507-17.
The promise of the genome project was that a complete sequence would provide us with information that would transform biology and medicine. But the 'parts list' that has emerged from the genome project is far from the 'wiring diagram' and 'circuit logic' we need to understand the link between genotype, environment and phenotype. While genomic technologies such as DNA microarrays, proteomics and metabolomics have given us new tools and new sources of data to address these problems, a number of crucial elements remain to be addressed before we can begin to close the loop and develop a predictive quantitative biology that is the stated goal of so much of current biological research, including systems biology. Our approach to this problem has largely been one of integration, bringing together a vast wealth of information to better interpret the experimental data we are generating in genomic assays and creating publicly available databases and software tools to facilitate the work of others. Recently, we have used a similar approach to trying to understand the biological networks that underlie the phenotypic responses we observe and starting us on the road to developing a predictive biology. [Abstract/Link to Full Text]

Carninci P
Constructing the landscape of the mammalian transcriptome.
J Exp Biol. 2007 May;210(Pt 9):1497-506.
The principal route to understanding the biological significance of the genome sequence comes from discovery and characterization of that portion of the genome that is transcribed into RNA products. We now know that this ;transcriptome' is unexpectedly complex and its precise definition in any one species requires multiple technical approaches and an ability to work on a very large scale. A key step is the development of technologies able to capture snapshots of the complexity of the various kinds of RNA generated by the genome. As the human, mouse and other model genome sequencing projects approach completion, considerable effort has been focused on identifying and annotating the protein-coding genes as the principal output of the genome. In pursuing this aim, several key technologies have been developed to generate large numbers and highly diverse sets of full-length cDNAs and their variants. However, the search has identified another hidden transcriptional universe comprising a wide variety of non-protein coding RNA transcripts. Despite initial scepticism, various experiments and complementary technologies have demonstrated that these RNAs are dynamically transcribed and a subset of them can act as sense-antisense RNAs, which influence the transcriptional output of the genome. Recent experimental evidence suggests that the list of non-protein coding RNAs is still largely incomplete and that transcription is substantially more complex even than currently thought. [Abstract/Link to Full Text]

Glossary of terms.
J Exp Biol. 2007 May 1;210(Pt 9):1492-6. [Abstract/Link to Full Text]

Cossins A, Somero G
Guest editors' introduction.
J Exp Biol. 2007 May;210(Pt 9):1491. [Abstract/Link to Full Text]

Hoppeler H
Editor-in-Chief's introduction.
J Exp Biol. 2007 May 1;210(Pt 9):1490. [Abstract/Link to Full Text]

Sun C, Fantner GE, Adams J, Hansma PK, Waite JH
The role of calcium and magnesium in the concrete tubes of the sandcastle worm.
J Exp Biol. 2007 Apr;210(Pt 8):1481-8.
Sandcastle worms Phragmatopoma californica build mound-like reefs by sticking together large numbers of sand grains with cement secreted from the building organ. The cement consists of protein plus substantial amounts of calcium and magnesium, which are not invested in any mineral form. This study examined the effect of calcium and magnesium depletion on the structural and mechanical properties of the cement. Divalent ion removal by chelating with EDTA led to a partial collapse of cement architecture and cement dislodgement from silica surfaces. Mechanical properties examined were sand grain pull-out force, tube resistance to compression and cement adhesive force. EDTA treatment reduced sand grain pull-out forces by 60% and tube compressive strength by 50% relative to controls. EDTA lowered both the maximal adhesive force and energy dissipation of cement by up to an order of magnitude. The adhesiveness of calcium- and magnesium-depleted cement could not be restored by re-exposure to the ions. The results suggest that divalent ions play a complex and multifunctional role in maintaining the structure and stickiness of Phragmatopoma cement. [Abstract/Link to Full Text]

Davis JR, DeNardo DF
The urinary bladder as a physiological reservoir that moderates dehydration in a large desert lizard, the Gila monster Heloderma suspectum.
J Exp Biol. 2007 Apr;210(Pt 8):1472-80.
Animals inhabiting xeric environments use a variety of behavioral and physiological strategies to balance water budgets. We studied the potential contribution of the urinary bladder to osmoregulation in a large desert lizard, the Gila monster Heloderma suspectum. Here we present results of a series of in vivo laboratory experiments which tested the hypothesis that the Gila monster urinary bladder serves as a physiological reservoir, as in amphibians and chelonians, providing water that buffers increases in plasma osmolality when food and water are unavailable. Adult Gila monsters absorbed water from the urinary bladder into circulation and absorption of water from the urinary bladder and drinking water provided similar osmoregulatory benefits within 24 h, although drinking water provided a more immediate osmotic benefit. During food and water deprivation, plasma osmolality increased 2.5 times faster in lizards with an empty urinary bladder compared with those with a full bladder. During rehydration, stereotyped binge drinking behavior increased body mass nearly 22%, which resulted in a 24% reduction in plasma osmolality and a substantial increase in bladder water within 24 h. These results support our hypothesis and demonstrate for the first time in an adult lizard that the urinary bladder can function as a long-term physiological water reservoir. This trait can provide a critical benefit to osmoregulation during the 2- to 3-month summer dry season characteristic of the deserts that Gila monsters inhabit. [Abstract/Link to Full Text]

Hille C, Walz B
A vacuolar-type H+-ATPase and a Na+/H+ exchanger contribute to intracellular pH regulation in cockroach salivary ducts.
J Exp Biol. 2007 Apr;210(Pt 8):1463-71.
Cells of the dopaminergically innervated salivary ducts in the cockroach Periplaneta americana have a vacuolar-type H(+)-ATPase (V-ATPase) of unknown function in their apical membrane. We have studied whether dopamine affects intracellular pH (pH(i)) in duct cells and whether and to what extent the apical V-ATPase contributes to pH(i) regulation. pH(i) measurements with double-barrelled pH-sensitive microelectrodes and the fluorescent dye BCECF have revealed: (1) the steady-state pH(i) is 7.3+/-0.1; (2) dopamine induces a dose-dependent acidification up to pH 6.9+/-0.1 at 1 micromol l(-1) dopamine, EC(50) at 30 nmol l(-1) dopamine; (3) V-ATPase inhibition with concanamycin A or Na(+)-free physiological saline (PS) does not affect the steady-state pH(i); (4) concanamycin A, Na(+) -free PS and Na(+)/H(+) exchange inhibition with 5-(N-ethyl-N-isopropyl)-amiloride (EIPA) each reduce the rate of pH(i) recovery from a dopamine-induced acidification or an acidification induced by an NH(4)Cl pulse; (5) pH(i) recovery after NH(4)Cl-induced acidification is almost completely blocked by concanamycin A in Na(+)-free PS or by concanamycin A applied together with EIPA; (6) pH(i) recovery after dopamine-induced acidification is also completely blocked by concanamycin A in Na(+)-free PS but only partially blocked by concanamycin A applied together with EIPA. We therefore conclude that the apical V-ATPase and a basolateral Na(+)/H(+) exchange play a minor role in steady-state pH(i) regulation but contribute both to H(+) extrusion after an acute dopamine- or NH(4)Cl-induced acid load. [Abstract/Link to Full Text]

Liu-Snyder P, Logan MP, Shi R, Smith DT, Borgens RB
Neuroprotection from secondary injury by polyethylene glycol requires its internalization.
J Exp Biol. 2007 Apr;210(Pt 8):1455-62.
Polyethylene glycol (PEG) is well known to both fuse and repair cell membranes. This capability has been exploited for such diverse usages as the construction of hybridomas and as a reparative agent following neurotrauma. The latter development has proceeded through preclinical testing in cases of naturally induced paraplegia in dogs. The mechanisms of action of polymer-mediated neurorepair/neuroprotection are still under investigation. It is likely that the unique interaction of hydrophilic polymers with the mechanical properties of cell membranes in concert with an ability to interfere with mechanisms of secondary injury such as the production of highly reactive oxygen species (ROS or ;free radicals') is the basis for neuroprotection by polymers. Here we provide further evidence that the ability of PEG to reduce or limit secondary injury and/or lipid peroxidation (LPO) of membranes requires entry of PEG into the cytosol, further suggesting a physical interaction with the membranes of organelles such as mitochondria as the initial event leading to neurorepair/neuroprotection. We have evaluated this relationship in vitro using acrolein, a potent endogenous toxin that is a product of LPO. Acrolein can pass through cell membranes with ease, inducing progressive LPO in ;bystander' cells, and the production of even more acrolein by inducing its own production. Immediate application of PEG (10 mmol l(-1), 2000 Da) to poisoned neurons in vitro was unable to rescue them from necrosis and death. Furthermore, three-dimensional confocal microscopy of fluorescently decorated PEG shows that it does not enter these cells for up to 2 h after application. By this time the mechanisms of necrosis are likely irreversible. Additionally, severe oxygen and or glucose deprivation of spinal cord white matter in vitro also initiates LPO. Addition of potent free radical scavengers such as ascorbic acid or superoxide dismutase (SOD) is able to interfere with this process, but PEG is not. Taken together, these data are consistent with the hypothesis that PEG is able to rescue mechanically damaged cells, based on a restructuring of the damaged plasmalemma. Furthermore, in compromised cells with an intact cell membrane, PEG must first gain access to the cytosol where this same capability may be useful in restoring the integrity of cellular organelles such as mitochondria, though the intracellular concentration of the polymer must be significant relative to the concentration of toxins produced by LPO in order to rescue the cell. [Abstract/Link to Full Text]

Fleming PA, Bateman PW
Just drop it and run: the effect of limb autotomy on running distance and locomotion energetics of field crickets (Gryllus bimaculatus).
J Exp Biol. 2007 Apr;210(Pt 8):1446-54.
This is the first study to examine the direct metabolic costs of autotomy, the voluntary shedding of an appendage as an escape mechanism, in invertebrates. We investigated the effects of limb autotomy upon endurance and metabolic cost of locomotion in the field cricket Gryllus bimaculatus. Compared with control (intact) crickets, animals that had autotomised a single hindlimb were slower, stopped more often, moved a shorter distance and expended more energy doing so. Both the cost of locomotion (COT) and minimal cost of locomotion (MCOT) were significantly higher for autotomised animals. We compare these data with locomotion energetics of 36 other invertebrate species, and discuss the results in terms of the biomechanics of walking in crickets. [Abstract/Link to Full Text]

Ciuhandu CS, Wright PA, Goldberg JI, Stevens ED
Parameters influencing the dissolved oxygen in the boundary layer of rainbow trout (Oncorhynchus mykiss) embryos and larvae.
J Exp Biol. 2007 Apr;210(Pt 8):1435-45.
We investigated the influence of oxygen demand (developmental stage) and supply (hypoxia, water flow rate, the chorion and body movements) on the oxygen concentration within the boundary layer next to the chorion of embryos or skin of larvae of rainbow trout (Oncorhynchus mykiss). Oxygen microelectrodes were used to measure dissolved oxygen (DO) within the boundary layer of trout embryos and larvae. As the embryos and larvae developed, the DO gradient and the thickness of the boundary layer increased. The DO concentration within the boundary layer next to the chorion or skin surface decreased as the DO concentration in the free-stream water decreased. A decrease in water flow rate increased the magnitude of the gradient and thickness of the boundary layer. In normoxia, the DO in the perivitelline fluid inside the chorion was 16+/-3.0% saturation at 31 days post fertilization, indicating that the chorion was a significant barrier to oxygen diffusion. The number of body movements did not change when embryos were exposed to hypoxia before hatching, but after hatching, hypoxia resulted in a decrease in body movements of the larvae. Taken together, our data indicate that the oxygen boundary layer around trout embryos and larvae depends on both the oxygen demand and supply. The factors that significantly impacted boundary layer oxygen were developmental stage, free-stream oxygen levels, water flow rate, and the presence of the chorion. [Abstract/Link to Full Text]

Meunier N, Belgacem YH, Martin JR
Regulation of feeding behaviour and locomotor activity by takeout in Drosophila.
J Exp Biol. 2007 Apr;210(Pt 8):1424-34.
The hormonal regulation of feeding behaviour is well known in vertebrates, whereas it remains poorly understood in insects. Here, we report that the takeout gene is an essential component of nutritional homeostasis in Drosophila. takeout encodes a putative juvenile hormone (JH) binding protein and has been described as a link between circadian rhythm and feeding behaviour. However, the physiological role of takeout and its putative link to JH remain unknown. In this study, we show that takeout (to(1)) flies failed to adapt their food intake according to food availability and that most defects could be genetically rescued. When food is abundant, to(1) are hyperphagic, yielding to hypertrophy of the fat body. When food reappears after a starvation period, to(1) flies do not increase their food intake as much as wild-type flies. This defect in food intake regulation is partly based on the action of Takeout on taste neurons, because the sensitivity of to(1) gustatory neurons to sugars does not increase after starvation, as in wild-type neurons. This lack of regulation is also evident at the locomotor activity, which normally increases during starvation, a behaviour related to food foraging. In addition, to(1) flies lack sexual dimorphism of locomotor activity, which has previously been linked to the JH circulating level. Moreover, application of the JH analog methoprene rescues the phenotype. These results suggest that takeout plays a central role as a feeding regulator and may act by modulating the circulating JH level. [Abstract/Link to Full Text]

Paskins KE, Bowyer A, Megill WM, Scheibe JS
Take-off and landing forces and the evolution of controlled gliding in northern flying squirrels Glaucomys sabrinus.
J Exp Biol. 2007 Apr;210(Pt 8):1413-23.
Flying squirrels are well known for their ability to glide between trees at the top of a forest canopy. We present experimental performance and behavioural evidence that flight in flying squirrels may have evolved out of a need to control landing forces. Northern flying squirrels were filmed jumping from a horizontal branch to a much larger vertical pole. These were both slightly compliant (less than 1.9 mm N(-1)), and instrumented using strain gauges so that forces could be measured. Take-off and landing forces were both positively correlated with horizontal range between 0.5 and 2.5 m (r=0.355 and r=0.811, respectively, P<0.05), but not significantly different to each other at each range tested. Take-off forces ranged from 1 to 10 bodyweights, and landing forces were between 3 and 10 bodyweights. Glide angles increased rapidly with horizontal range, approaching 45 degrees at 3 m, above which they gradually decreased, suggesting that northern flying squirrels are optimised for long distance travel. We show that northern flying squirrels initiate full gliding posture at ranges of less than 1 m, without landing any higher than an equivalent ballistic projectile. However, this gliding posture enables them to pitch upwards, potentially stalling the wing, and spreads the landing reaction force over all four extended limbs. At steeper approach angles of close to 45 degrees , flying squirrels were unable to pitch up sufficiently and landed forelimbs first, consequently sustaining higher impact forces. We investigate four hypotheses to explain the origin of flight in these animals and conclude that the need to reduce landing impact forces was most likely to have stimulated the development of aerial control in flying squirrels. [Abstract/Link to Full Text]

Thompson RN, McMillon R, Napier A, Wekesa KS
Pregnancy block by MHC class I peptides is mediated via the production of inositol 1,4,5-trisphosphate in the mouse vomeronasal organ.
J Exp Biol. 2007 Apr;210(Pt 8):1406-12.
The vomeronasal organ (VNO) has evolved to link an animal's behavior to its environment in a highly species-specific fashion. In mice, it is thought to be the primary sensory system responsible for the detection of pheromones. Pheromones regulate a variety of responses including mate recognition in the context of selective pregnancy failure. MHC (major histocompatibility complex) class I peptides have been identified as compounds that elicit the pregnancy block effect via the VNO. However, the transduction cascade of these molecules is unknown and it is not known if the production of these compounds are androgen dependent. By using male urine and MHC peptides, we show that female mice treated with MHC peptides (in urine or PBS) and urine from castrated males or juvenile mice of different haplotypes respond to the Bruce Effect paradigm in a manner equivalent to female mice exposed to whole urine. In addition to providing new evidence that urine from castrated or juvenile males and MHC peptides can induce pregnancy block, we show correlation of the effect with an increase in inositol 1,4,5-trisphosphate. [Abstract/Link to Full Text]

Goyret J, Markwell PM, Raguso RA
The effect of decoupling olfactory and visual stimuli on the foraging behavior of Manduca sexta.
J Exp Biol. 2007 Apr;210(Pt 8):1398-405.
Within an appetitive context, Manduca sexta, a nectivorous nocturnal hawkmoth, can be attracted by a range of stimuli including floral volatiles and visual display, carbon dioxide and water vapor. Several studies on this and other flower-visiting insects have shown how olfactory and visual stimulation play (or do not play) a role in attraction and feeding. Nevertheless, these studies have consistently manipulated stimuli in a 'presence-absence' manner. Here, we experimentally decoupled the presentation of both stimuli spatially and temporally in a wind tunnel, rather than entirely eliminating either one, and found that the decision-making process based on these stimuli is more flexible and complex than previously asserted. Manduca sexta was most responsive when both cues were present and emanated from the same source. When stimuli were spatially separated, responsiveness levels were comparable to those elicited by a single stimulus. However, transient olfactory stimulation either before or after visually guided approach (temporal decoupling) enhanced responsiveness to an odorless visual target. Additionally, searching times were increased by either a transient olfactory stimulation before take-off or by having the flower model spatially separated from the odor source tracked by the moths. Finally, in a dual-choice experiment, moths showed a strong bias for the visual display over the odor plume, suggesting the former to be the ultimate indicator of a nectar source. Our manipulation of floral cues shows that the feeding behavior of M. sexta, and probably of other nectivorous insects, is based not only on the sensory stimulation per se but also on the temporal and spatial pattern in which these stimuli are perceived. [Abstract/Link to Full Text]

Portugal SJ, Green JA, Butler PJ
Annual changes in body mass and resting metabolism in captive barnacle geese (Branta leucopsis): the importance of wing moult.
J Exp Biol. 2007 Apr;210(Pt 8):1391-7.
Many different physiological changes have been observed in wild waterfowl during the flightless stage of wing moult, including a loss of body mass. We aimed to determine whether captive barnacle geese (Branta leucopsis) would show the characteristic decrease in body mass during their wing moult, even though they had unlimited and unrestricted access to food. Fourteen captive geese were weighed at 1-2-week intervals for two complete years. During the flightless period of the moult, body mass decreased by approximately 25% from the pre-moult value. To understand the basis of this change, the rate of oxygen consumption was measured during daytime and nighttime at six points in the second year, and at three points (before, during and after wing moult) behavioural observations were made. Measurements of the rate of oxygen consumption showed an 80% increase above that of the nonmoulting periods of the year. We propose that metabolism was increased during moult because of the cost of feather synthesis. Although food was available, the captive birds chose not to forage and instead increased the proportion of time spent resting. It is likely that this behaviour in response to wing moult is a strategy to avoid predation in the wild. Thus, the innate nature of this behaviour has potential survival value for wild birds of this species. We conclude that the increase in metabolism led to the use of endogenous energy reserves because the birds reduced rather than increased their food intake rates, and as a result, the barnacle geese lost body mass during wing moult. [Abstract/Link to Full Text]

Jindrich DL, Smith NC, Jespers K, Wilson AM
Mechanics of cutting maneuvers by ostriches (Struthio camelus).
J Exp Biol. 2007 Apr;210(Pt 8):1378-90.
We studied the strategies used by cursorial bipeds (ostriches) to maneuver during running. Eight ostriches were induced to run along a trackway and execute turns. Ground reaction forces and three-dimensional kinematics of the body and leg joints were simultaneously recorded, allowing calculation of joint angles and quasi-static net joint torques. Sidesteps, where the leg on the outside of the turn changes the movement direction, and crossovers using the inside leg, occurred with nearly equal frequency. Ostriches executed maneuvers using a simple control strategy that required minimal changes to leg kinematics or net torque production at individual joints. Although ostriches did use acceleration or braking forces to control body rotation, their morphology allowed for both crossovers and sidesteps to be accomplished with minimal net acceleratory/braking force production. Moreover, body roll and ab/adduction of the leg shifted the foot position away from the turn direction, reducing the acceleratory/braking forces required to prevent under- or over-rotation and aligning the leg with the ground reaction force. [Abstract/Link to Full Text]

Lehmann FO, Pick S
The aerodynamic benefit of wing-wing interaction depends on stroke trajectory in flapping insect wings.
J Exp Biol. 2007 Apr;210(Pt 8):1362-77.
Flying insects may enhance their flight force production by contralateral wing interaction during dorsal stroke reversal ('clap-and-fling'). In this study, we explored the forces and moments due to clap-and-fling at various wing tip trajectories, employing a dynamically scaled electromechanical flapping device. The 17 tested bio-inspired kinematic patterns were identical in stroke amplitude, stroke frequency and angle of attack with respect to the horizontal stroke plane but varied in heaving motion. Clap-and-fling induced vertical force augmentation significantly decreased with increasing vertical force production averaged over the entire stroke cycle, whereas total force augmentation was independent from changes in force produced by a single wing. Vertical force augmentation was also largely independent of forces produced due to wing rotation at the stroke reversals, the sum of rotational circulation and wake capture force. We obtained maximum (17.4%) and minimum (1.4%) vertical force augmentation in two types of figure-eight stroke kinematics whereby rate and direction of heaving motion during fling may explain 58% of the variance in vertical force augmentation. This finding suggests that vertical wing motion distinctly alters the flow regime at the beginning of the downstroke. Using an analytical model, we determined pitching moments acting on an imaginary body of the flapping device from the measured time course of forces, the changes in length of the force vector's moment arm, the position of the centre of mass and body angle. The data show that pitching moments are largely independent from mean vertical force; however, clap-and-fling reinforces mean pitching moments by approximately 21%, compared to the moments produced by a single flapping wing. Pitching moments due to clap-and-fling significantly increase with increasing vertical force augmentation and produce nose-down moments in most of the tested patterns. The analytical model, however, shows that algebraic sign and magnitude of these moments may vary distinctly depending on both body angle and the distance between the wing hinge and the animal's centre of mass. Altogether, the data suggest that the benefit of clap-and-fling wing beat for vertical force enhancement and pitch balance may change with changing heaving motion and thus wing tip trajectory during manoeuvring flight. We hypothesize that these dependencies may have shaped the evolution of wing kinematics in insects that are limited by aerodynamic lift rather than by mechanical power of their flight musculature. [Abstract/Link to Full Text]

Recent Articles in Biological Procedures Online

Sirchia R, Ciacciofera V, Luparello C
Tumor cell-collagen interactions: Identification and semi-quantitative evaluation of selectively-expressed genes by combination of differential display- and multiplex-PCR.
Biol Proced Online. 2003;5222-227.
It is widely acknowledged that the presence of extracellular matrix components as substrates can drastically modulate the phenotype and gene expression of cultured cells, including tumor cells. A number of published reports indicated that substrates made from two peculiar collagen species, i.e. type V and OF/LB, which are abnormally deposited in the stroma of primary ductal infiltrating carcinoma (d.i.c.) of the breast "in vivo," were able to exert marked and opposite effects on "in vitro" viability, growth and invasiveness of the 8701-BC cell line, isolated from d.i.c.-affected breast epithelium. To complement such functional data on the effect of cell-collagen interactions with information at molecular level, we have utilized a combination of differential display- and semi-quantitative multiplex-PCR techniques with the aim of detecting variations in the expression levels of selected genes by cells maintained in either culture condition. Here we report some prototypical data on the identification and semi-quantitation of three of the differentially-amplified PCR products found, i.e. HSP2A and MSF-B which are up-regulated in cells grown onto OF/LB collagen substrate, and SRCAP which is prominently down-regulated in the presence of type V collagen substrate. This protocol represents a powerful tool for evaluating changes in the levels and patterns of gene expression which can be theoretically adapted to any experimental model system. [Abstract/Link to Full Text]

Yung RL, Ray D, Mo RR, Chen J
T Cell Integrin Overexpression as a Model of Murine Autoimmunity.
Biol Proced Online. 2003;5211-221.
Integrin adhesion molecules have important adhesion and signaling functions. They also play a central role in the pathogenesis of many autoimmune diseases. Over the past few years we have described a T cell adoptive transfer model to investigate the role of T cell integrin adhesion molecules in the development of autoimmunity. This report summarizes the methods we used in establishing this murine model. By treating murine CD4+ T cells with DNA hypomethylating agents and by transfection we were able to test the in vitro effects of integrin overexpression on T cell autoreactive proliferation, cytotoxicity, adhesion and trafficking. Furthermore, we showed that the ability to induce in vivo autoimmunity may be unique to the integrin lymphocyte function associated antigen-1 (LFA-1). [Abstract/Link to Full Text]

Azam M, Raz T, Nardi V, Opitz SL, Daley GQ
A screen to identify drug resistant variants to target-directed anti-cancer agents.
Biol Proced Online. 2003;5204-210.
The discovery of oncogenes and signal transduction pathways important for mitogenesis has triggered the development of target-specific small molecule anti-cancer compounds. As exemplified by imatinib (Gleevec), a specific inhibitor of the Chronic Myeloid Leukemia (CML)-associated Bcr-Abl kinase, these agents promise impressive activity in clinical trials, with low levels of clinical toxicity. However, such therapy is susceptible to the emergence of drug resistance due to amino acid substitutions in the target protein. Defining the spectrum of such mutations is important for patient monitoring and the design of next-generation inhibitors. Using imatinib and BCR/ABL as a paradigm for a drug-target pair, we recently reported a retroviral vector-based screening strategy to identify the spectrum of resistance-conferring mutations. Here we provide a detailed methodology for the screen, which can be generally applied to any drug-target pair. [Abstract/Link to Full Text]

Obermaier B, Dauer M, Herten J, Schad K, Endres S, Eigler A
Development of a new protocol for 2-day generation of mature dendritic cells from human monocytes.
Biol Proced Online. 2003;5197-203.
We developed a new 2-day protocol for the generation of dendritic cells (DCs) from human monocytes in vitro. First, we demonstrated that 24 hours of culture with GM-CSF and IL-4 are sufficient to generate immature DCs capable of antigen uptake. We then compared two different strategies for DC maturation: proinflammatory mediators were either added together with GM-CSF and IL-4 from the beginning of cell culture or added after 24 hours of differentiation with GM-CSF and IL-4. After 48 hours of total culture period, expression of activation markers was more pronounced in cells generated by the 2-step differentiation and activation method. Our new protocol for 2-day DC differentiation reduces labor, cost and time and also reliably renders high numbers of mature and viable DCs. [Abstract/Link to Full Text]

Kim W, Surette MG
Swarming populations of Salmonella represent a unique physiological state coupled to multiple mechanisms of antibiotic resistance.
Biol Proced Online. 2003;5189-196.
Salmonella enterica serovar Typhimurium is capable of swarming over semi-solid surfaces. Although its swarming behavior shares many readily observable similarities with other swarming bacteria, the phenomenon remains somewhat of an enigma in this bacterium since some attributes skew away from the better characterized systems. Swarming is quite distinct from the classic swimming motility, as there is a prerequisite for cells to first undergo a morphological transformation into swarmer cells. In some organisms, swarming is controlled by quorum sensing, and in others, swarming has been shown to be coupled to increased expression of important virulence factors. Swarming in serovar Typhimurium is coupled to elevated resistance to a wide variety of structurally and functionally distinct classes of antimicrobial compounds. As serovar Typhimurium differentiates into swarm cells, the pmrHFIJKLM operon is up-regulated, resulting in a more positively charged LPS core. Furthermore, as swarm cells begin to de-differentiate, the pmr operon expression is down-regulated, rapidly reaching the levels observed in swim cells. This is one potential mechanism which confers swarm cells increased resistance to antibiotics such as the cationic antimicrobial peptides. However, additional mechanisms are likely associated with the cells in the swarm state that confer elevated resistance to such a broad spectrum of antimicrobial agents. [Abstract/Link to Full Text]

Mahajan SD, Aalinkeel R, Schwartz SA, Chawda RP, Nair MP
Effector cell mediated cytotoxicity measured by intracellular Granzyme B release in HIV infected subjects.
Biol Proced Online. 2003;5182-188.
CD8+ cytotoxic T lymphocyte (CTL) activity is currently believed to be one of the key immunologic mechanisms responsible for the prevention or attenuation of HIV-1 infection. The induction of CD8+ T cell activation may also result in the production of soluble or non-classical lytic factors that are associated with protection from infection or slower disease progression. Traditionally, CD8+ CTL responses have been measured by the classic chromium release assay, monitoring the ability of T cells (Effector cells) to lyse radiolabelled HLA - matched "target cells" that express the appropriate antigen-MHC complex. This method is not only labor intensive, semi quantitative assay at best, but also needs fresh, non-cryopreserved cells. Recently, cytokine specific ELISPOT assays or tetrameric MHC-I/ peptide complexes have utilized to directly quantitate circulating CD8+ effector cells, and these assays are more sensitive, quantitative and reproducible than the traditional CTL lysis assay and can also be performed on cryopreserved cells. Although these are reproducible assays for the assessment of soluble antiviral activity secreted by activated T cell populations they can be extremely expensive to perform. We have used FACS Analysis to measure Granzyme B release as a function of cell mediated cytotoxicity. This method helps quantitate the CTL activity and also identifies the phenotype of the cells elucidating this immune response. The method described not only monitors immunological response but also is also simple to perform, precise and extremely time efficient and is ideal for screening a large number of samples. [Abstract/Link to Full Text]

Zhang X, Oglesbee M
Use of surface plasmon resonance for the measurement of low affinity binding interactions between HSP72 and measles virus nucleocapsid protein.
Biol Proced Online. 2003;5170-181.
The 72 kDa heat shock protein (HSP72) is a molecular chaperone that binds native protein with low affinity. These interactions can alter function of the substrate, a property known as HSP-mediated activity control. In the present work, BIAcore instrumentation was used to monitor binding reactions between HSP72 and naturally occurring sequence variants of the measles virus (MV) nucleocapsid protein (N), a structural protein regulating transcription/replication of the viral genome. Binding reactions employed synthetic peptides mimicking a putative HSP72 binding motif of N. Sequences were identified that bound HSP72 with affinities comparable to well-characterized activity control reactions. These sequences, but not those binding with lesser affinity, supported HSP72 activity control of MV transcription/replication. BIAcore instrumentation thus provides an effective way to measure biologically relevant low affinity interactions with structural variants of viral proteins. [Abstract/Link to Full Text]

Harkness TA, Arnason TG, Legrand C, Lone A
Methods designed for the identification and characterization of in vitro and in vivo chromatin assembly mutants in Saccharomyces cerevisiae.
Biol Proced Online. 2003;5162-169.
Assembly of DNA into chromatin allows for the formation of a barrier that protects naked DNA from protein and chemical agents geared to degrade or metabolize DNA. Chromatin assembly occurs whenever a length of DNA becomes exposed to the cellular elements, whether during DNA synthesis or repair. This report describes tools to study chromatin assembly in the model system Saccharomyces cerevisiae. Modifications to an in vitro chromatin assembly assay are described that allowed a brute force screen of temperature sensitive (ts) yeast strains in order to identify chromatin assembly defective extracts. This screen yielded mutations in genes encoding two ubiquitin protein ligases (E3s): RSP5, and a subunit of the Anaphase Promoting Complex (APC), APC5. Additional modifications are described that allow for a rapid analysis and an in vivo characterization of yeast chromatin assembly mutants, as well as any other mutant of interest. Our analysis suggests that the in vitro and invivo chromatin assembly assays are responsive to different cellular signals, including cell cycle cues that involve different molecular networks. [Abstract/Link to Full Text]

Underkoffler LA, Collins JN, Choi JD, Oakey RJ
An Application of Molecular Genotyping in Mice.
Biol Proced Online. 2003;5116-122.
Microsatellite markers are simple sequence repeats within the mammalian genome that can be used for identifying disease loci, mapping genes of interest as well as studying segregation patterns related to meiotic nondisjunction. Different strains of mice have variable CA repeat lengths and PCR based methods can be used to identify them, thus allowing for specific genotypes to be assigned. Molecular genotyping offers such identification at any developmental stage, which allows for a broad range of anomalies to be studied. We studied chromosomal segregation in relation to nondisjunction in early-gestation mouse embryos using molecular genotyping. Information on the parental origin as well as the number of chromosomes a given progeny carried was obtained in our analysis. [Abstract/Link to Full Text]

Jacobsson K, Rosander A, Bjerketorp J, Frykberg L
Shotgun Phage Display - Selection for Bacterial Receptins or other Exported Proteins.
Biol Proced Online. 2003;5123-135.
Shotgun phage display cloning involves construction of libraries from randomly fragmented bacterial chromosomal DNA, cloned genes, or eukaryotic cDNAs, into a phagemid vector. The library obtained consists of phages expressing polypeptides corresponding to all genes encoded by the organism, or overlapping peptides derived from the cloned gene. From such a library, polypeptides with affinity for another molecule can be isolated by affinity selection, panning. The technique can be used to identify bacterial receptins and identification of their minimal binding domain, and but also to identify epitopes recognised by antibodies. In addition, after modification of the phagemid vector, the technique has also been used to identify bacterial extracytoplasmic proteins. [Abstract/Link to Full Text]

Maiato H, Sunkel CE, Earnshaw WC
Dissecting mitosis by RNAi in Drosophila tissue culture cells.
Biol Proced Online. 2003;5153-161.
Here we describe a detailed methodology to study the function of genes whose products function during mitosis by dsRNA-mediated interference (RNAi) in cultured cells of Drosophila melanogaster. This procedure is particularly useful for the analysis of genes for which genetic mutations are not available or for the dissection of complicated phenotypes derived from the analysis of such mutants. With the advent of whole genome sequencing it is expected that RNAi-based screenings will be one method of choice for the identification and study of novel genes involved in particular cellular processes. In this paper we focused particularly on the procedures for the proper phenotypic analysis of cells after RNAi-mediated depletion of proteins required for mitosis, the process by which the genetic information is segregated equally between daughter cells. We use RNAi of the microtubule-associated protein MAST/Orbit as an example for the usefulness of the technique. [Abstract/Link to Full Text]

Malloff C, Dullaghan E, Li A, Stokes R, Fernandez R, Lam W
Two-dimensional DNA displays for comparisons of bacterial genomes.
Biol Proced Online. 2003;5143-152.
We have developed two whole genome-scanning techniques to aid in the discovery of polymorphisms as well as horizontally acquired genes in prokaryotic organisms. First, two-dimensional bacterial genomic display (2DBGD) was developed using restriction enzyme fragmentation to separate genomic DNA based on size, and then employing denaturing gradient gel electrophoresis (DGGE) in the second dimension to exploit differences in sequence composition. This technique was used to generate high-resolution displays that enable the direct comparison of > 800 genomic fragments simultaneously and can be adapted for the high-throughput comparison of bacterial genomes. 2DBGDs are capable of detecting acquired and altered DNA, however, only in very closely related strains. If used to compare more distantly related strains (e.g. different species within a genus) numerous small changes (i.e. small deletions and point mutations) unrelated to the interesting phenotype, would encumber the comparison of 2DBGDs. For this reason a second method, bacterial comparative genomic hybridization (BCGH), was developed to directly compare bacterial genomes to identify gain or loss of genomic DNA. BCGH relies on performing 2DBGD on a pooled sample of genomic DNA from 2 strains to be compared and subsequently hybridizing the resulting 2DBGD blot separately with DNA from each individual strain. Unique spots (hybridization signals) represent foreign DNA. The identification of novel DNA is easily achieved by excising the DNA from a dried gel followed by subsequent cloning and sequencing. 2DBGD and BCGH thus represent novel high resolution genome scanning techniques for directly identifying altered and/or acquired DNA. [Abstract/Link to Full Text]

R�thel TR, Leikert J AM, Dirsch VM
Application of 4,5-diaminofluorescein to reliably measure nitric oxide released from endothelial cells in vitro.
Biol Proced Online. 2003;5136-142.
Here we describe in more depth the previously published application of the fluorescent probe 4,5-diaminofluorescein (DAF-2) in order to reliably measure low levels of nitric oxide (NO) as released from human endothelial cells in vitro. The used approach is based on the following considerations a) use low concentrations of DAF-2 (0.1 micro M) in order to reduce the contribution of DAF-2 auto-fluorescence to the measured total fluorescence, and b) subtract the DAF-2 auto-fluorescence from the measured total fluorescence. The advantage of this method is the reliable quantification of NO in a biological system in the nanomolar range once thoroughly validated. Here we focus in addition to the previous publication (Leikert et al., FEBS Lett 2001, 506:131-134) on aspects of validation procedures as well as limitations and pitfalls of this method. [Abstract/Link to Full Text]

Uribe S, Sampedro JG
Measuring Solution Viscosity and its Effect on Enzyme Activity.
Biol Proced Online. 2003;5108-115.
In proteins, some processes require conformational changes involving structural domain diffusion. Among these processes are protein folding, unfolding and enzyme catalysis. During catalysis some enzymes undergo large conformational changes as they progress through the catalytic cycle. According to Kramers theory, solvent viscosity results in friction against proteins in solution, and this should result in decreased motion, inhibiting catalysis in motile enzymes. Solution viscosity was increased by adding increasing concentrations of glycerol, sucrose and trehalose, resulting in a decrease in the reaction rate of the H(+)-ATPase from the plasma membrane of Kluyveromyces lactis. A direct correlation was found between viscosity (eta) and the inhibition of the maximum rate of catalysis (V(max)). The protocol used to measure viscosity by means of a falling ball type viscometer is described, together with the determination of enzyme kinetics and the application of Kramers' equation to evaluate the effect of viscosity on the rate of ATP hydrolysis by the H(+)-ATPase. [Abstract/Link to Full Text]

Breierova E
Yeast Exoglycoproteins Produced Under NaCl-Stress Conditions as Efficient Cryoprotective Agents.
Biol Proced Online. 1998 May 14;110-16.
Six extracellular yeast glycoproteins were prepared from three yeast species in osmotic equilibrium and unequilibrium environments and used as non-penetrating cryoadditives. Glycoproteins secreted by the strain Dipodascus australiensis into growth medium containing NaCl (8% w/v) were found to be the most effective cryoadditives. It was possible to use these glycoproteins alone (without DMSO as penetrating agent) for the cryoprotection of the studied yeasts. [Abstract/Link to Full Text]

Duclohier H, Helluin O, Lea E, Mackie AR, Ladha S
Coupling Optical and Electrical Measurements in Artificial Membranes: Lateral Diffusion of Lipids and Channel Forming Peptides in Planar Bilayers.
Biol Proced Online. 1998 May 14;181-91.
Planar lipid bilayers (PLB) were prepared by the Montal-Mueller technique in a FRAP system designed to simultaneously measure conductivity across, and lateral diffusion of, the bilayer. In the first stage of the project the FRAP system was used to characterise the lateral dynamics of bilayer lipids with regards to phospholipid composition (headgroup, chain unsaturation etc.), presence of cholesterol and the effect of divalent cations on negatively-charged bilayers. In the second stage of the project, lateral diffusion of two fluorescently-labelled voltage-dependent pore-forming peptides (alamethicin and S4s from Shaker K(+) channel) was determined at rest and in the conducting state. This study demonstrates the feasibility of such experiments with PLBs, amenable to physical constraints, and thus offers new opportunities for systematic studies of structure-function relationships in membrane-associating molecules. [Abstract/Link to Full Text]

Lee JI, Woo SK, Kim KI, Park KC, Baek SH, Yoo YJ, Chung CH
A Method for Assaying Deubiquitinating Enzymes.
Biol Proced Online. 1998 Jul 20;192-99.
A general method for the assay of deubiquitinating enzymes was described in detail using (125)I-labeled ubiquitin-fused alphaNH-MHISPPEPESEEEEEHYC (referred to as Ub-PESTc) as a substrate. Since the tyrosine residue in the PESTc portion of the fusion protein was almost exclusively radioiodinated under a mild labeling condition, such as using IODO-BEADS, the enzymes could be assayed directly by simple measurement of the radioactivity released into acid soluble products. Using this assay protocol, we could purify six deubiquitinating enzymes from chick skeletal muscle and yeast and compare their specific activities. Since the extracts of E. coli showed little or no activity against the substrate, the assay protocol should be useful for identification and purification of eukaryotic deubiquitinating enzymes cloned and expressed in the cells. [Abstract/Link to Full Text]

Mar�n D, P�rez P, Teijeiro C, Palecek E
Methods for direct determination of mitomycin C in aqueous solutions and in urine.
Biol Proced Online. 1998 Sep 17;1100-106.
Stripping voltammetry (SV) is used to quantitatively determine concentrations of the anti-neoplastic drug mitomycin C (MMC) alone and in mixtures with 5-fluorouracil and cisplatin, both of which are used in combined chemotherapy with MMC. If the accumulation is performed at the potentials of MMC reduction (-0.35 V vs. SCE), reduced MMC is strongly adsorbed at the electrode. It is possible to prepare a MMC-modified electrode, which, after a washing step, is transferred to the background electrolyte to determine MMC by voltammetry. This procedure, which is termed transfer stripping voltammetry (TSV), helps to eliminate interferences and can be applied for a direct determination of MMC alone or in mixtures with other drugs in urine. [Abstract/Link to Full Text]

Ramalho-Santos J, Pedroso De Lima MC
Role of a Transbilayer pH Gradient in the Membrane Fusion Activity of the Influenza Virus Hemagglutinin: Use of the R18 Assay to Monitor Membrane Merging.
Biol Proced Online. 1999 Mar 16;1107-113.
It had been suggested that influenza virus-mediated membrane fusion might be dependent on a pH gradient across a target membrane. We have designed experiments in which this issue could be addressed. Two populations of liposomes were prepared, both simulating the plasma membrane of target cells, but with the pH of the internal aqueous medium buffered either at pH 7.4 (physiological cytosol pH) or at pH 5.0 (endosomal pH at which influenza virus displays maximal fusion activity). By monitoring fusion using the R18 assay, we found that the internal pH of the target liposomes did not influence membrane merging as mediated by the influenza virus hemagglutinin, thus demonstrating that a transmembrane pH gradient is not required in this fusion process. [Abstract/Link to Full Text]

Sklodowaka A, Wozniak M, Matlakowska R
The method of contact angle measurements and estimation of work of adhesion in bioleaching of metals.
Biol Proced Online. 1999 Apr 29;1114-121.
In this paper, we present our method for the measurement of contact angles on the surface of minerals during the bioleaching process because the standard deviation obtained in our measurements achieved unexpectedly low error. Construction of a goniometer connected with a specially prepared computer program allowed us to repeat measurements several times over a short time course, yielding excellent results.After defining points on the outline of the image of a drop and its baseline as well of the first approximation of the outline of the drop, an iterative process is initiated that is aimed at fitting the model of the drop and baseline. In turn, after defining the medium for which measurements were made, the work of adhesion is determined according to Young-Dupr� equation. Calculations were made with the use of two methods named the L-M and L-Q methods. [Abstract/Link to Full Text]

Lee LE, Misser E
Science through the Internet: Researching, Evaluating and Citing Websites.
Biol Proced Online. 1999 Jan 8;1S100-S106.
This article attempts to convey the joys and frustrations of skimming the Internet trying to find relevant information concerning an academic's work as a scientist, a student or an instructor. A brief overview of the Internet and the "do's and don'ts" for the neophyte as well for the more seasoned "navigator" are given. Some guidelines of "what works and what does not" and "what is out there" are provided for the scientist with specific emphasis for biologists, as well as for all others having an interest in science but with little interest in spending countless hours "surfing the net". An extensive but not exhaustive list of related websites is provided. [Abstract/Link to Full Text]

Bonora GM, Zaramella S, Veronese FM
Synthesis by High-Efficiency Liquid-Phase (HELP) Method of Oligonucleotides Conjugated with High-Molecular Weight Polyethylene Glycols (PEGs).
Biol Proced Online. 1998 May 14;159-69.
The chemical modification of synthetic oligonucleotides has recently been investigated to improve their pharmacological utilization. In addition to chemical alterations of the backbone and of the heterocyclic bases, their conjugation with amphiphylic moieties, such as the polyethylene glycol has been proposed. The large scale production of these molecules as demanded for commercial purposes is hampered by the heterogeneity of the solid-phase processes and by the low reactivity of high-molecular weight PEGs in solution. A new synthetic procedure based on the recently developed liquid-phase method (HELP), has been set up to overcome these limitations. [Abstract/Link to Full Text]

Deng HW
Inferring Deleterious-Mutation Parameters in Natural Daphnia Populations.
Biol Proced Online. 1998 May 14;11-9.
Deng and Lynch (1, 2) proposed to characterize deleterious genomic mutations from changes in the mean and genetic variance of fitness traits upon selfing in outcrossing populations. Such observations can be readily acquired in cyclical parthenogens. Selfing and life-table experiments were performed for two such Daphnia populations. A significant inbreeding depression and an increase of genetic variance for all traits analyzed were observed. Deng and Lynch's (2) procedures were employed to estimate the genomic mutation rate (U), mean dominance coefficient (), mean selection coefficient (), and scaled genomic mutational variance (). On average, and (^ indicates an estimate) are 0.84, 0.30, 0.14 and 4.6E-4 respectively. For the true values, the and are lower bounds, and and upper bounds. [Abstract/Link to Full Text]

Becerra M, Cerd�n E, Gonz�lez Siso MI
Dealing with different methods for Kluyveromyces lactis beta-galactosidase purification.
Biol Proced Online. 1998 May 14;148-58.
Several micro-scale chromatography-based procedures for purification of the beta-galactosidase from the yeast Kluyveromyces lactis were assayed. Purified enzyme was suitable to be used as antigen to induce polyclonal antibodies production. Specific staining of non-denaturing PAGE gels with chromogenic substrates allowed the determination of the number of subunits forming the native enzyme. [Abstract/Link to Full Text]

Burns B, Mendz G, Hazell S
Methods for the Measurement of a Bacterial Enzyme Activity in Cell Lysates and Extracts.
Biol Proced Online. 1998 May 14;117-26.
The kinetic characteristics and regulation of aspartate carbamoyltransferase activity were studied in lysates and cell extracts of Helicobacter pylori by three diffirent methods. Nuclear magnetic resonance spectroscopy, radioactive tracer analysis, and spectrophotometry were employed in conjunction to identify the properties of the enzyme activity and to validate the results obtained with each assay. NMR spectroscopy was the most direct method to provide proof of ACTase activity; radioactive tracer analysis was the most sensitive technique and a microtitre-based colorimetric assay was the most cost-and time-efficient for large scale analyses. Freeze-thawing was adopted as the preferred method for cell lysis in studying enzyme activity in situ. This study showed the benefits of employing several different complementary methods to investigate bacterial enzyme activity. [Abstract/Link to Full Text]

Yeates C, Gillings MR, Davison AD, Altavilla N, Veal DA
Methods for microbial DNA extraction from soil for PCR amplification.
Biol Proced Online. 1998 May 14;140-47.
Amplification of DNA from soil is often inhibited by co-purified contaminants. A rapid, inexpensive, large-scale DNA extraction method involving minimal purification has been developed that is applicable to various soil types (1). DNA is also suitable for PCR amplification using various DNA targets. DNA was extracted from 100g of soil using direct lysis with glass beads and SDS followed by potassium acetate precipitation, polyethylene glycol precipitation, phenol extraction and isopropanol precipitation. This method was compared to other DNA extraction methods with regard to DNA purity and size. [Abstract/Link to Full Text]

Konno R
Methods for the Detection of D-Amino-Acid Oxidase.
Biol Proced Online. 1998 May 14;127-31.
Four methods (an enzyme activity assay, western blotting, RT-PCR, and northern hybridization) to detect the enzyme D-amino-acid oxidase are described. [Abstract/Link to Full Text]

Mizuma T, Awazu S
The Metabolic Inhibition Model Which Predicts the Intestinal Absorbability and Metabolizability of Drug: Theory and Experiment.
Biol Proced Online. 1998 May 14;132-39.
The intestinal absorption of analgesic peptides (leucine enkephalin and kyotorphin) and modified peptides in rat were studied. Although these peptides were not absorbed, the absorbability (absorption clearance) of these peptides were increased in the presence of peptidase inhibitors. In order to kinetically analyze these phenomena, we proposed the metabolic inhibition model, which incorporated the metabolic clearance (metabolizability) with the absorption clearance. Metabolic activity was determined with intestinal homogenates. The higher the metabolic clearance was, the lower was the absorption clearance. The relationships between the absorption clearance and the metabolic clearance of the experimental data as well as of the theoretical values were hyperbolic. This model predicted the maximum absorption clearances of cellobiose-coupled leucine enkephalin (0.654 &mgr;l/min/cm) and kyotorphin (0.247 &mgr;l/min/cm). Details of the experimental methods are described. [Abstract/Link to Full Text]

Geisler M
Expression of a prokaryotic P-type ATPase in E. coli Plasma Membranes and Purification by Ni2+-affinity chromatography.
Biol Proced Online. 1998 May 14;170-80.
In order to characterize the P-type ATPase from Synechocystis 6803 [Geisler (1993) et al. J. Mol. Biol. 234, 1284] and to facilitate its purification, we expressed an N-terminal 6xHis-tagged version of the ATPase in an ATPase deficient E. coli strain. The expressed ATPase was immunodetected as a dominant band of about 97 kDa localized to the E. coli plasma membranes representing about 20-25% of the membrane protein. The purification of the Synecho-cystis 6xHis-ATPase by single-step Ni-affinity chromatography under native and denaturating conditions is described. ATPase activity and the formation of phosphointermediates verify the full function of the enzyme: the ATPase is inhibited by vanadate (IC(50)= 119 &mgr;M) and the formation of phosphorylated enzyme intermediates shown by acidic PAGE depends on calcium, indicating that the Synechocystis P-ATPase functions as a calcium pump. [Abstract/Link to Full Text]

Van Criekinge W, Beyaert R
Yeast Two-Hybrid: State of the Art.
Biol Proced Online. 1999 Oct 4;21-38.
Genome projects are approaching completion and are saturating sequence databases. This paper discusses the role of the two-hybrid system as a generator of hypotheses. Apart from this rather exhaustive, financially and labour intensive procedure, more refined functional studies can be undertaken. Indeed, by making hybrids of two-hybrid systems, customised approaches can be developed in order to attack specific function-related problems. For example, one could set-up a "differential" screen by combining a forward and a reverse approach in a three-hybrid set-up. Another very interesting project is the use of peptide libraries in two-hybrid approaches. This could enable the identification of peptides with very high specificity comparable to "real" antibodies. With the technology available, the only limitation is imagination. [Abstract/Link to Full Text]

Recent Articles in BMC Developmental Biology

Hadzhiev Y, Lele Z, Schindler S, Wilson SW, Ahlberg P, Str�hle U, M�ller F
Hedgehog signaling patterns the outgrowth of unpaired skeletal appendages in zebrafish.
BMC Dev Biol. 2007;775.
BACKGROUND: Little is known about the control of the development of vertebrate unpaired appendages such as the caudal fin, one of the key morphological specializations of fishes. Recent analysis of lamprey and dogshark median fins suggests the co-option of some molecular mechanisms between paired and median in Chondrichthyes. However, the extent to which the molecular mechanisms patterning paired and median fins are shared remains unknown. RESULTS: Here we provide molecular description of the initial ontogeny of the median fins in zebrafish and present several independent lines of evidence that Sonic hedgehog signaling emanating from the embryonic midline is essential for establishment and outgrowth of the caudal fin primordium. However, gene expression analysis shows that the primordium of the adult caudal fin does not harbor a Sonic hedgehog-expressing domain equivalent to the Shh secreting zone of polarizing activity (ZPA) of paired appendages. CONCLUSION: Our results suggest that Hedgehog proteins can regulate skeletal appendage outgrowth independent of a ZPA and demonstrates an unexpected mechanism for mediating Shh signals in a median fin primordium. The median fins evolved before paired fins in early craniates, thus the patterning of the median fins may be an ancestral mechanism that controls the outgrowth of skeletogenic appendages in vertebrates. [Abstract/Link to Full Text]

Maier D, Nagel AC, Gloc H, Hausser A, Kugler SJ, Wech I, Preiss A
Protein kinase D regulates several aspects of development in Drosophila melanogaster.
BMC Dev Biol. 2007;774.
BACKGROUND: Protein Kinase D (PKD) is an effector of diacylglycerol-regulated signaling pathways. Three isoforms are known in mammals that have been linked to diverse cellular functions including regulation of cell proliferation, differentiation, motility and secretory transport from the trans-Golgi network to the plasma membrane. In Drosophila, there is a single PKD orthologue, whose broad expression implicates a more general role in development. RESULTS: We have employed tissue specific overexpression of various PKD variants as well as tissue specific RNAi, in order to investigate the function of the PKD gene in Drosophila. Apart from a wild type (WT), a kinase dead (kd) and constitutively active (SE) Drosophila PKD variant, we also analyzed two human isoforms hPKD2 and hPKD3 for their capacity to substitute PKD activity in the fly. Overexpression of either WT or kd-PKD variants affected primarily wing vein development. However, overexpression of SE-PKD and PKD RNAi was deleterious. We observed tissue loss, wing defects and degeneration of the retina. The latter phenotype conforms to a role of PKD in the regulation of cytoskeletal dynamics. Strongest phenotypes were larval to pupal lethality. RNAi induced phenotypes could be rescued by a concurrent overexpression of Drosophila wild type PKD or either human isoform hPKD2 and hPKD3. CONCLUSION: Our data confirm the hypothesis that Drosophila PKD is a multifunctional kinase involved in diverse processes such as regulation of the cytoskeleton, cell proliferation and death as well as differentiation of various fly tissues. [Abstract/Link to Full Text]

Dong DJ, He HJ, Chai LQ, Jiang XJ, Wang JX, Zhao XF
Identification of genes differentially expressed during larval molting and metamorphosis of Helicoverpa armigera.
BMC Dev Biol. 2007;773.
BACKGROUND: Larval molting and metamorphosis are important physiological processes in the life cycle of the holometabolous insect. We used suppression subtractive hybridization (SSH) to identify genes differentially expressed during larval molting and metamorphosis. RESULTS: We performed SSH between tissues from a variety of developmental stages, including molting 5th and feeding 6th instar larvae, metamorphically committed and feeding 5th instar larvae, and feeding 5th instar and metamorphically committed larvae. One hundred expressed sequence tags (ESTs) were identified and included 73 putative genes with similarity to known genes, and 27 unknown ESTs. SSH results were further characterized by dot blot, Northern blot, and RT-PCR. The expression levels of eleven genes were found to change during larval molting or metamorphosis, suggesting a functional role during these processes. CONCLUSION: These results provide a new set of genes expressed specifically during larval molt or metamorphosis that are candidates for further studies into the regulatory mechanisms of those stage-specific genes during larval molt and metamorphosis. [Abstract/Link to Full Text]

Jedrusik A, Ajduk A, Pomorski P, Maleszewski M
Mouse oocytes fertilised by ICSI during in vitro maturation retain the ability to be activated after refertilisation in metaphase II and can generate Ca2+ oscillations.
BMC Dev Biol. 2007;772.
BACKGROUND: At fertilisation, mammalian oocytes are activated by oscillations of intracellular Ca2+ ([Ca2+]i). Phospholipase Czeta, which is introduced by fertilising spermatozoon, triggers [Ca2+]i oscillations through the generation of inositol 1,4,5-triphosphate (IP3), which causes Ca2+ release by binding to IP3 receptors located on the endoplasmic reticulum (ER) of the oocyte. Ability to respond to this activating stimulus develops during meiotic maturation of the oocyte. Here we examine how the development of this ability is perturbed when a single spermatozoon is introduced into the oocyte prematurely, i.e. during oocyte maturation. RESULTS: Mouse oocytes during maturation in vitro were fertilised by ICSI (intracytoplasmic sperm injection) 1 - 4 h after germinal vesicle break-down (GVBD) and were subsequently cultured until they reached metaphase II (MII) stage. At MII stage they were fertilised in vitro for the second time (refertilisation). We observed that refertilised oocytes underwent activation with similar frequency as control oocytes, which also went through maturation in vitro, but were fertilised only once at MII stage (87% and 93%, respectively). Refertilised MII oocytes were able to develop [Ca2+]i oscillations in response to penetration by spermatozoa. We found however, that they generated a lower number of transients than control oocytes. We also showed that the oocytes, which were fertilised during maturation had a similar level of MPF activity as control oocytes, which were not subjected to ICSI during maturation, but had reduced level of IP3 receptors. CONCLUSION: Mouse oocytes, which were experimentally fertilised during maturation retain the ability to generate repetitive [Ca2+]i transients, and to be activated after completion of maturation. [Abstract/Link to Full Text]

Campinho MA, Silva N, Nowell MA, Llewellyn L, Sweeney GE, Power DM
Troponin T isoform expression is modulated during Atlantic halibut metamorphosis.
BMC Dev Biol. 2007;771.
BACKGROUND: Flatfish metamorphosis is a thyroid hormone (TH) driven process which leads to a dramatic change from a symmetrical larva to an asymmetrical juvenile. The effect of THs on muscle and in particular muscle sarcomer protein genes is largely unexplored in fish. The change in Troponin T (TnT), a pivotal protein in the assembly of skeletal muscles sarcomeres and a modulator of calcium driven muscle contraction, during flatfish metamophosis is studied. RESULTS: In the present study five cDNAs for halibut TnT genes were cloned; three were splice variants arising from a single fast TnT (fTnT) gene; a fourth encoded a novel teleost specific fTnT-like cDNA (AfTnT) expressed exclusively in slow muscle and the fifth encoded the teleost specific sTnT2. THs modified the expression of halibut fTnT isoforms which changed from predominantly basic to acidic isoforms during natural and T4 induced metamorphosis. In contrast, expression of red muscle specific genes, AfTnT and sTnT2, did not change during natural metamorphosis or after T4 treatment. Prior to and after metamorphosis no change in the dorso-ventral symmetry or temporal-spatial expression pattern of TnT genes and muscle fibre organization occurred in halibut musculature. CONCLUSION: Muscle organisation in halibut remains symmetrical even after metamorphosis suggesting TH driven changes are associated with molecular adaptations. We hypothesize that species specific differences in TnT gene expression in teleosts underlies different larval muscle developmental programs which better adapts them to the specific ecological constraints. [Abstract/Link to Full Text]

Barchuk AR, Cristino AS, Kucharski R, Costa LF, Sim�es ZL, Maleszka R
Molecular determinants of caste differentiation in the highly eusocial honeybee Apis mellifera.
BMC Dev Biol. 2007;770.
BACKGROUND: In honeybees, differential feeding of female larvae promotes the occurrence of two different phenotypes, a queen and a worker, from identical genotypes, through incremental alterations, which affect general growth, and character state alterations that result in the presence or absence of specific structures. Although previous studies revealed a link between incremental alterations and differential expression of physiometabolic genes, the molecular changes accompanying character state alterations remain unknown. RESULTS: By using cDNA microarray analyses of >6,000 Apis mellifera ESTs, we found 240 differentially expressed genes (DEGs) between developing queens and workers. Many genes recorded as up-regulated in prospective workers appear to be unique to A. mellifera, suggesting that the workers' developmental pathway involves the participation of novel genes. Workers up-regulate more developmental genes than queens, whereas queens up-regulate a greater proportion of physiometabolic genes, including genes coding for metabolic enzymes and genes whose products are known to regulate the rate of mass-transforming processes and the general growth of the organism (e.g., tor). Many DEGs are likely to be involved in processes favoring the development of caste-biased structures, like brain, legs and ovaries, as well as genes that code for cytoskeleton constituents. Treatment of developing worker larvae with juvenile hormone (JH) revealed 52 JH responsive genes, specifically during the critical period of caste development. Using Gibbs sampling and Expectation Maximization algorithms, we discovered eight overrepresented cis-elements from four gene groups. Graph theory and complex networks concepts were adopted to attain powerful graphical representations of the interrelation between cis-elements and genes and objectively quantify the degree of relationship between these entities. CONCLUSION: We suggest that clusters of functionally related DEGs are co-regulated during caste development in honeybees. This network of interactions is activated by nutrition-driven stimuli in early larval stages. Our data are consistent with the hypothesis that JH is a key component of the developmental determination of queen-like characters. Finally, we propose a conceptual model of caste differentiation in A. mellifera based on gene-regulatory networks. [Abstract/Link to Full Text]

Gordon J, Xiao S, Hughes B, Su DM, Navarre SP, Condie BG, Manley NR
Specific expression of lacZ and cre recombinase in fetal thymic epithelial cells by multiplex gene targeting at the Foxn1 locus.
BMC Dev Biol. 2007;769.
BACKGROUND: Thymic epithelial cells (TECs) promote thymocyte maturation and are required for the early stages of thymocyte development and for positive selection. However, investigation of the mechanisms by which TECs perform these functions has been inhibited by the lack of genetic tools. Since the Foxn1 gene is expressed in all presumptive TECs from the early stages of thymus organogenesis and broadly in the adult thymus, it is an ideal locus for driving gene expression in differentiating and mature TECs. RESULTS: We generated two knock-in alleles of Foxn1 by inserting IRES-Cre or IRES-lacZ cassettes into the 3' UTR of the Foxn1 locus. We simultaneously electroporated the two targeting vectors to generate the two independent alleles in the same experiment, demonstrating the feasibility of multiplex gene targeting at this locus. Our analysis shows that the knockin alleles drive expression of Cre or lacZ in all TECs in the fetal thymus. Furthermore, the knockin alleles express Cre or lacZ in a Foxn1-like pattern without disrupting Foxn1 function as determined by phenotype analysis of Foxn1 knockin/Foxn1 null compound heterozygotes. CONCLUSION: These data show that multiplex gene targeting into the 3' UTR of the Foxn1 locus is an efficient method to express any gene of interest in TECs from the earliest stage of thymus organogenesis. The resulting alleles will make possible new molecular and genetic studies of TEC differentiation and function. We also discuss evidence indicating that gene targeting into the 3' UTR is a technique that may be broadly applicable for the generation of genetically neutral driver strains. [Abstract/Link to Full Text]

Teppner I, Becker S, de Angelis MH, Gossler A, Beckers J
Compartmentalised expression of Delta-like 1 in epithelial somites is required for the formation of intervertebral joints.
BMC Dev Biol. 2007;768.
BACKGROUND: Expression of the mouse Delta-like 1 (Dll1) gene in the presomitic mesoderm and in the caudal halves of somites of the developing embryo is required for the formation of epithelial somites and for the maintenance of caudal somite identity, respectively. The rostro-caudal polarity of somites is initiated early on within the presomitic mesoderm in nascent somites. Here we have investigated the requirement of restricted Dll1 expression in caudal somite compartments for the maintenance of rostro-caudal somite polarity and the morphogenesis of the axial skeleton. We did this by overexpressing a functional copy of the Dll1 gene throughout the paraxial mesoderm, in particular in anterior somite compartments, during somitogenesis in transgenic mice. RESULTS: Epithelial somites were generated normally and appeared histologically normal in embryos of two independent Dll1 over-expressing transgenic lines. Gene expression analyses of rostro-caudal marker genes suggested that over-expression of Dll1 without restriction to caudal compartments was not sufficient to confer caudal identity to rostral somite halves in transgenic embryos. Nevertheless, Dll1 over-expression caused dysmorphologies of the axial skeleton, in particular, in morphological structures that derive from the articular joint forming compartment of vertebrae. Accordingly, transgenic animals exhibited missing or reduced intervertebral discs, rostral and caudal articular processes as well as costal heads of ribs. In addition, the midline of the vertebral column did not develop normally. Transgenic mice had open neural arches and split vertebral bodies with ectopic pseudo-growth plates. Endochondral bone formation and ossification in the developing vertebrae were delayed. CONCLUSION: The mice overexpressing Dll1 exhibit skeletal dysmorphologies that are also evident in several mutant mice with defects in somite compartmentalisation. The Dll1 transgenic mice demonstrate that vertebral dysmorphologies such as bony fusions of vertebrae and midline vertebral defects can occur without apparent changes in somitic rostro-caudal marker gene expression. Also, we demonstrate that the over-expression of the Dll1 gene in rostral epithelial somites is not sufficient to confer caudal identity to rostral compartments. Our data suggest that the restricted Dll1 expression in caudal epithelial somites may be particularly required for the proper development of the intervertebral joint forming compartment. [Abstract/Link to Full Text]

Joshi S, Davies H, Sims LP, Levy SE, Dean J
Ovarian gene expression in the absence of FIGLA, an oocyte-specific transcription factor.
BMC Dev Biol. 2007;767.
BACKGROUND: Ovarian folliculogenesis in mammals is a complex process involving interactions between germ and somatic cells. Carefully orchestrated expression of transcription factors, cell adhesion molecules and growth factors are required for success. We have identified a germ-cell specific, basic helix-loop-helix transcription factor, FIGLA (Factor In the GermLine, Alpha) and demonstrated its involvement in two independent developmental processes: formation of the primordial follicle and coordinate expression of zona pellucida genes. RESULTS: Taking advantage of Figla null mouse lines, we have used a combined approach of microarray and Serial Analysis of Gene Expression (SAGE) to identify potential downstream target genes. Using high stringent cutoffs, we find that FIGLA functions as a key regulatory molecule in coordinating expression of the NALP family of genes, genes of known oocyte-specific expression and a set of functionally un-annotated genes. FIGLA also inhibits expression of male germ cell specific genes that might otherwise disrupt normal oogenesis. CONCLUSION: These data implicate FIGLA as a central regulator of oocyte-specific genes that play roles in folliculogenesis, fertilization and early development. [Abstract/Link to Full Text]

Te Pas MF, Hulsegge I, Coster A, Pool MH, Heuven HH, Janss LL
Biochemical pathways analysis of microarray results: regulation of myogenesis in pigs.
BMC Dev Biol. 2007;766.
BACKGROUND: Combining microarray results and biological pathway information will add insight into biological processes. Pathway information is widely available in databases through the internet.Mammalian muscle formation has been previously studied using microarray technology in pigs because these animals are an interesting animal model for muscle formation due to selection for increased muscle mass. Results indicated regulation of the expression of genes involved in proliferation and differentiation of myoblasts, and energy metabolism. The aim of the present study was to analyse microarrays studying myogenesis in pigs. It was necessary to develop methods to search biochemical pathways databases. RESULTS: PERL scripts were developed that used the names of the genes on the microarray to search databases. Synonyms of gene names were added to the list by searching the Gene Ontology database. The KEGG database was searched for pathway information using this updated gene list. The KEGG database returned 88 pathways. Most genes were found in a single pathway, but others were found in up to seven pathways. Combining the pathways and the microarray information 21 pathways showed sufficient information content for further analysis. These pathways were related to regulation of several steps in myogenesis and energy metabolism. Pathways regulating myoblast proliferation and muscle fibre formation were described. Furthermore, two networks of pathways describing the formation of the myoblast cytoskeleton and regulation of the energy metabolism during myogenesis were presented. CONCLUSION: Combining microarray results and pathways information available through the internet provide biological insight in how the process of porcine myogenesis is regulated. [Abstract/Link to Full Text]

Merrick D, Ting T, Stadler LK, Smith J
A role for Insulin-like growth factor 2 in specification of the fast skeletal muscle fibre.
BMC Dev Biol. 2007;765.
BACKGROUND: Fibre type specification is a poorly understood process beginning in embryogenesis in which skeletal muscle myotubes switch myosin-type to establish fast, slow and mixed fibre muscle groups with distinct function. Growth factors are required to establish slow fibres; it is unknown how fast twitch fibres are specified. Igf-2 is an embryonically expressed growth factor with established in vitro roles in skeletal muscle. Its localisation and role in embryonic muscle differentiation had not been established. RESULTS: Between E11.5 and E15.5 fast Myosin (FMyHC) localises to secondary myotubes evenly distributed throughout the embryonic musculature and gradually increasing in number so that by E15.5 around half contain FMyHC. The Igf-2 pattern closely correlates with FMyHC from E13.5 and peaks at E15.5 when over 90% of FMyHC+ myotubes also contain Igf-2. Igf-2 lags FMyHC and it is absent from muscle myotubes until E13.5. Igf-2 strongly down-regulates by E17.5. A striking feature of the FMyHC pattern is its increased heterogeneity and attenuation in many fibres from E15.5 to day one after birth (P1). Transgenic mice (MIG) which express Igf-2 in all of their myotubes, have increased FMyHC staining, a higher proportion of FMyHC+ myotubes and loose their FMyHC staining heterogeneity. In Igf-2 deficient mice (MatDi) FMyHC+ myotubes are reduced to 60% of WT by E15.5. In vitro, MIG induces a 50% excess of FMyHC+ and a 30% reduction of SMHyC+ myotubes in C2 cells which can be reversed by Igf-2-targeted ShRNA resulting in 50% reduction of FMyHC. Total number of myotubes was not affected. CONCLUSION: In WT embryos the appearance of Igf-2 in embryonic myotubes lags FMyHC, but by E15.5 around 45% of secondary myotubes contain both proteins. Forced expression of Igf-2 into all myotubes causes an excess, and absence of Igf-2 suppresses, the FMyHC+ myotube component in both embryonic muscle and differentiated myoblasts. Igf-2 is thus required, not for initiating secondary myotube differentiation, but for establishing the correct proportion of FMyHC+ myotubes during fibre type specification (E15.5-P1). Since specific loss of FMyHC fibres is associated with many skeletal muscle pathologies these data have important medical implications. [Abstract/Link to Full Text]

Goossens K, Van Soom A, Van Poucke M, Vandaele L, Vandesompele J, Van Zeveren A, Peelman LJ
Identification and expression analysis of genes associated with bovine blastocyst formation.
BMC Dev Biol. 2007;764.
BACKGROUND: Normal preimplantation embryo development encompasses a series of events including first cleavage division, activation of the embryonic genome, compaction and blastocyst formation.First lineage differentiation starts at the blastocyst stage with the formation of the trophectoderm and the inner cell mass. The main objective of this study was the detection, identification and expression analysis of genes associated with blastocyst formation in order to help us better understand this process. This information could lead to improvements of in vitro embryo production procedures. RESULTS: A subtractive cDNA library was constructed enriched for transcripts preferentially expressed at the blastocyst stage compared to the 2-cell and 8-cell stage. Sequence information was obtained for 65 randomly selected clones. The RNA expression levels of 12 candidate genes were determined throughout 3 stages of preimplantation embryo development (2-cell, 8-cell and blastocyst) and compared with the RNA expression levels of in vivo "golden standard" embryos using real-time PCR. The RNA expression profiles of 9 (75%) transcripts (KRT18, FN1, MYL6, ATP1B3, FTH1, HINT1, SLC25A5, ATP6V0B, RPL10) were in agreement with the subtractive cDNA cloning approach, whereas for the remaining 3 (25%) (ACTN1, COPE, EEF1A1) the RNA expression level was equal or even higher at the earlier developmental stages compared to the blastocyst stage. Moreover, significant differences in RNA expression levels were observed between in vitro and in vivo produced embryos. By immunofluorescent labelling, the protein expression of KRT18, FN1 and MYL6 was determined throughout bovine preimplantation embryo development and showed the same pattern as the RNA expression analyses. CONCLUSION: By subtractive cDNA cloning, candidate genes involved in blastocyst formation were identified. For several candidate genes, important differences in gene expression were observed between in vivo and in vitro produced embryos, reflecting the influence of the in vitro culture system on the embryonic gene expression. Both RNA and protein expression analysis demonstrated that KRT18, FN1 and MYL6 are differentially expressed during preimplantation embryo development and those genes can be considered as markers for bovine blastocyst formation. [Abstract/Link to Full Text]

Ahnfelt-R�nne J, Hald J, B�dker A, Yassin H, Serup P, Hecksher-S�rensen J
Preservation of proliferating pancreatic progenitor cells by Delta-Notch signaling in the embryonic chicken pancreas.
BMC Dev Biol. 2007;763.
BACKGROUND: Genetic studies have shown that formation of pancreatic endocrine cells in mice is dependent on the cell autonomous action of the bHLH transcription factor Neurogenin3 and that the extent and timing of endocrine differentiation is controlled by Notch signaling. To further understand the mechanism by which Notch exerts this function, we have investigated pancreatic endocrine development in chicken embryos. RESULTS: In situ hybridization showed that expression of Notch signaling components and pro-endocrine bHLH factors is conserved to a large degree between chicken and mouse. Cell autonomous inhibition of Notch signal reception results in significantly increased endocrine differentiation demonstrating that these early progenitors are prevented from differentiating by ongoing Notch signaling. Conversely, activated Notch1 induces Hes5-1 expression and prevents endocrine development. Notably, activated Notch also prevents Ngn3-mediated induction of a number of downstream targets including NeuroD, Hes6-1, and MyT1 suggesting that Notch may act to inhibit both Ngn3 gene expression and protein function. Activated Notch1 could also block endocrine development and gene expression induced by NeuroD. Nevertheless, Ngn3- and NeuroD-induced delamination of endodermal cells was insensitive to activated Notch under these conditions. Finally, we show that Myt1 can partially overcome the repressive effect of activated Notch on endocrine gene expression. CONCLUSION: We conclude that pancreatic endocrine development in the chicken relies on a conserved bHLH cascade under inhibitory control of Notch signaling. This lays the ground for further studies that take advantage of the ease at which chicken embryos can be manipulated. Our results also demonstrate that Notch can repress Ngn3 and NeuroD protein function and stimulate progenitor proliferation. To determine whether Notch in fact does act in Ngn3-expressing cells in vivo will require further studies relying on conditional mutagenesis. Lastly, our results demonstrate that expression of differentiation markers can be uncoupled from the process of delamination of differentiating cells from the epithelium. [Abstract/Link to Full Text]

Molina GA, Watkins SC, Tsang M
Generation of FGF reporter transgenic zebrafish and their utility in chemical screens.
BMC Dev Biol. 2007;762.
BACKGROUND: Fibroblast Growth Factors (FGFs) represent a large family of secreted proteins that are required for proper development and physiological processes. Mutations in mouse and zebrafish FGFs result in abnormal embryogenesis and lethality. A key to understanding the precise role for these factors is to determine their spatial and temporal activity during embryogenesis. RESULTS: Expression of Dual Specificity Phosphatase 6 (dusp6, also known as Mkp3) is controlled by FGF signalling throughout development. The Dusp6 promoter was isolated from zebrafish and used to drive expression of destabilized green fluorescent protein (d2EGFP) in transgenic embryos (Tg(Dusp6:d2EGFP)). Expression of d2EGFP is initiated as early as 4 hours post-fertilization (hpf) within the future dorsal region of the embryo, where fgf3 and fgf8 are initially expressed. At later stages, d2EGFP is detected within structures that correlate with the expression of Fgf ligands and their receptors. This includes the mid-hindbrain boundary (MHB), pharyngeal endoderm, otic vesicle, hindbrain, and Kupffer's vesicle. The expression of d2EGFP is under the control of FGF signalling as treatment with FGF Receptor (FGFR) inhibitors results in the suppression of d2EGFP expression. In a pilot screen of commercially available small molecules we have evaluated the effectiveness of the transgenic lines to identify specific FGF inhibitors within the class of indolinones. These compounds were counter screened with the transgenic line Tg(Fli1:EGFP)y1, that serves as an indirect read-out for Vascular Endothelial Growth Factor (VEGF) signalling in order to determine the specificity between related receptor tyrosine kinases (RTKs). From these assays it is possible to determine the specificity of these indolinones towards specific RTK signalling pathways. This has enabled the identification of compounds that can block specifically the VEGFR or the FGFR signalling pathway. CONCLUSION: The generation of transgenic reporter zebrafish lines has allowed direct visualization of FGF signalling within the developing embryo. These FGF reporter transgenic lines provide a tool to screen for specific compounds that can distinguish between two conserved members of the RTK family. [Abstract/Link to Full Text]

Ax�ng C, Rauthan M, Hall DH, Pilon M
The twisted pharynx phenotype in C. elegans.
BMC Dev Biol. 2007;761.
BACKGROUND: The pharynx of C. elegans is an epithelial tube whose development has been compared to that of the embryonic heart and the kidney and hence serves as an interesting model for organ development. Several C. elegans mutants have been reported to exhibit a twisted pharynx phenotype but no careful studies have been made to directly address this phenomenon. In this study, the twisting mutants dig-1, mig-4, mnm-4 and unc-61 are examined in detail and the nature of the twist is investigated. RESULTS: We find that the twisting phenotype worsens throughout larval development, that in most mutants the pharynx retains its twist when dissected away from the worm body, and that double mutants between mnm-4 and mutants with thickened pharyngeal domains (pha-2 and sma-1) have less twisting in these regions. We also describe the ultrastructure of pharyngeal tendinous organs that connect the pharyngeal basal lamina to that of the body wall, and show that these are pulled into a spiral orientation by twisted pharynges. Within twisted pharynges, actin filaments also show twisting and are longer than in controls. In a mini screen of adhesionmolecule mutants, we also identified one more twisting pharynx mutant, sax-7. CONCLUSION: Defects in pharyngeal cytoskeleton length or its anchor points to the extracellular matrix are proposed as the actual source of the twisting force. The twisted pharynx is a useful and easy-to-score phenotype for genes required in extracellular adhesion or organ attachment, and perhaps forgenes required for cytoskeleton regulation. [Abstract/Link to Full Text]

Lee BR, Kim H, Park TS, Moon S, Cho S, Park T, Lim JM, Han JY
A set of stage-specific gene transcripts identified in EK stage X and HH stage 3 chick embryos.
BMC Dev Biol. 2007;760.
BACKGROUND: The embryonic developmental process in avian species is quite different from that in mammals. The first cleavage begins 4 h after fertilization, but the first differentiation does not occur until laying of the egg (Eyal-Giladi and Kochav (EK) stage X). After 12 to 13 h of incubation (Hamburger and Hamilton (HH) stage 3), the three germ layers form and germ cell segregation in the early chick embryo are completed. Thus, to identify genes associated with early embryonic development, we compared transcript expression patterns between undifferentiated (stage X) and differentiated (HH stage 3) embryos. RESULTS: Microarray analysis primarily showed 40 genes indicating the significant changes in expression levels between stage X and HH stage 3, and 80% of the genes (32/40) were differentially expressed with more than a twofold change. Among those, 72% (23/32) were relatively up-regulated at stage X compared to HH stage 3, while 28% (9/32) were relatively up-regulated at HH stage 3 compared to stage X. Verification and gene expression profiling of these GeneChip expression data were performed using quantitative RT-PCR for 32 genes at developmental four points; stage X (0 h), HH stage 3 (12 h), HH stage 6 (24 h), and HH stage 9 (30 h). Additionally, we further analyzed four genes with less than twofold expression increase at HH stage 3. As a result, we identified a set of stage-specific genes during the early chick embryo development; 21 genes were relatively up-regulated in the stage X embryo and 12 genes were relatively up-regulated in the HH stage 3 embryo based on both results of microarray and quantitative RT-PCR. CONCLUSION: We identified a set of genes with stage-specific expression from microarray Genechip and quantitative RT-PCR. Discovering stage-specific genes will aid in uncovering the molecular mechanisms involved the formation of the three germ layers and germ cell segregation in the early chick embryos. [Abstract/Link to Full Text]

Huang JK, Dorey K, Ishibashi S, Amaya E
BDNF promotes target innervation of Xenopus mandibular trigeminal axons in vivo.
BMC Dev Biol. 2007;759.
BACKGROUND: Trigeminal nerves consist of ophthalmic, maxillary, and mandibular branches that project to distinct regions of the facial epidermis. In Xenopus embryos, the mandibular branch of the trigeminal nerve extends toward and innervates the cement gland in the anterior facial epithelium. The cement gland has previously been proposed to provide a short-range chemoattractive signal to promote target innervation by mandibular trigeminal axons. Brain derived neurotrophic factor, BDNF is known to stimulate axon outgrowth and branching. The goal of this study is to determine whether BDNF functions as the proposed target recognition signal in the Xenopus cement gland. RESULTS: We found that the cement gland is enriched in BDNF mRNA transcripts compared to the other neurotrophins NT3 and NT4 during mandibular trigeminal nerve innervation. BDNF knockdown in Xenopus embryos or specifically in cement glands resulted in the failure of mandibular trigeminal axons to arborise or grow into the cement gland. BDNF expressed ectodermal grafts, when positioned in place of the cement gland, promoted local trigeminal axon arborisation in vivo. CONCLUSION: BDNF is necessary locally to promote end stage target innervation of trigeminal axons in vivo, suggesting that BDNF functions as a short-range signal that stimulates mandibular trigeminal axon arborisation and growth into the cement gland. [Abstract/Link to Full Text]

Kuijk EW, du Puy L, van Tol HT, Haagsman HP, Colenbrander B, Roelen BA
Validation of reference genes for quantitative RT-PCR studies in porcine oocytes and preimplantation embryos.
BMC Dev Biol. 2007;758.
BACKGROUND: In the developing embryo, total RNA abundance fluctuates caused by functional RNA degradation and zygotic genome activation. These variations in the transcriptome in early development complicate the choice of good reference genes for gene expression studies by quantitative real time polymerase chain reaction. RESULTS: In order to identify stably expressed genes for normalisation of quantitative data, within early stages of development, transcription levels were examined of 7 frequently used reference genes (B2M, BACT, GAPDH, H2A, PGK1, SI8, and UBC) at different stages of early porcine embryonic development (germinal vesicle, metaphase-2, 2-cell, 4-cell, early blastocyst, expanded blastocyst). Analysis of transcription profiling by geNorm software revealed that GAPDH, PGK1, S18, and UBC showed high stability in early porcine embryonic development, while transcription levels of B2M, BACT, and H2A were highly regulated. CONCLUSION: Good reference genes that reflect total RNA content were identified in early embryonic development from oocyte to blastocyst. A selection of either GAPDH or PGK1, together with ribosomal protein S18 (S18), and UBC is proposed as reference genes, but the use of B2M, BACT, or H2A is discouraged. [Abstract/Link to Full Text]

Li C, Li X, Chen W, Yu S, Chen J, Wang H, Ruan D
The different roles of cyclinD1-CDK4 in STP and mGluR-LTD during the postnatal development in mice hippocampus area CA1.
BMC Dev Biol. 2007;757.
BACKGROUND: Cell-cycle-related proteins, such as cyclins or cyclin-dependent kinases, may have functions beyond that of cell cycle regulation. The expression and translocation of cyclinD1-CDK4 in post-mitotic neurons indicate that they may have supplementary functions in differentiated neurons that might be associated with neuronal plasticity. RESULTS: In the present study, our findings showed that the expression of CDK4 was localized mostly in nuclei and cytoplasm of pyramidal cells of CA1 at postnatal day 10 (P10); whereas at P28 staining of CDK4 could be detected predominantly in the cytoplasm but not nuclei. Basal synaptic transmission was normal in the presence of CDK4 inhibitor. Short-term synaptic plasticity (STP) was impaired in CDK4 inhibitor pre-treated slices both from neonatal (P8-15) and adolescent (P21-35) animals; however there was no significant change in paired-pulse facilitation (PPF) in slices pre-incubated with the CDK4 inhibitor from adolescent animals. By the treatment of CDK4 inhibitor, the induction or the maintenance of Long-term potentiation (LTP) in response to a strong tetanus and NMDA receptor-dependent long-term depression (LTD) were normal in hippocampus. However, long-term depression (LTD) induced either by group I metabotropic glutamate receptors (mGluRs) agonist or by paired-pulse low-frequency stimulation (PP-LFS) was impaired in CDK4 inhibitor pretreated slices both from neonatal and adolescent animals. But the effects of the CDK4 inhibitor at slices from adolescent animals were not as robust as at slices from neonatal animals. CONCLUSION: Our results indicated that the activation of cyclinD1-CDK4 is required for short-term synaptic plasticity and mGluR-dependent LTD, and suggested that this cyclin-dependent kinase may have different roles during the postnatal development in mice hippocampus area CA1. [Abstract/Link to Full Text]

Lin G, Chen Y, Slack JM
Regeneration of neural crest derivatives in the Xenopus tadpole tail.
BMC Dev Biol. 2007;756.
BACKGROUND: After amputation of the Xenopus tadpole tail, a functionally competent new tail is regenerated. It contains spinal cord, notochord and muscle, each of which has previously been shown to derive from the corresponding tissue in the stump. The regeneration of the neural crest derivatives has not previously been examined and is described in this paper. RESULTS: Labelling of the spinal cord by electroporation, or by orthotopic grafting of transgenic tissue expressing GFP, shows that no cells emigrate from the spinal cord in the course of regeneration.There is very limited regeneration of the spinal ganglia, but new neurons as well as fibre tracts do appear in the regenerated spinal cord and the regenerated tail also contains abundant peripheral innervation.The regenerated tail contains a normal density of melanophores. Cell labelling experiments show that melanophores do not arise from the spinal cord during regeneration, nor from the mesenchymal tissues of the skin, but they do arise by activation and proliferation of pre-existing melanophore precursors. If tails are prepared lacking melanophores, then the regenerates also lack them. CONCLUSION: On regeneration there is no induction of a new neural crest similar to that seen in embryonic development. However there is some regeneration of neural crest derivatives. Abundant melanophores are regenerated from unpigmented precursors, and, although spinal ganglia are not regenerated, sufficient sensory systems are produced to enable essential functions to continue. [Abstract/Link to Full Text]

Fazzari P, Penachioni J, Gianola S, Rossi F, Eickholt BJ, Maina F, Alexopoulou L, Sottile A, Comoglio PM, Flavell RA, Tamagnone L
Plexin-B1 plays a redundant role during mouse development and in tumour angiogenesis.
BMC Dev Biol. 2007;755.
BACKGROUND: Plexins are a large family of transmembrane receptors for the Semaphorins, known for their role in the assembly of neural circuitry. More recently, Plexins have been implicated in diverse biological functions, including vascular growth, epithelial tissue morphogenesis and tumour development. In particular, PlexinB1, the receptor for Sema4D, has been suggested to play a role in neural development and in tumour angiogenesis, based on in vitro studies. However, the tissue distribution of PlexinB1 has not been extensively studied and the functional relevance of this receptor in vivo still awaits experimental testing. In order to shed light on PlexinB1 function in vivo, we therefore undertook the genomic targeting of the mouse gene to obtain loss of function mutants. RESULTS: This study shows that PlexinB1 receptor and its putative ligand, Sema4D, have a selective distribution in nervous and epithelial tissues during development and in the adult. PlexinB1 and Sema4D show largely complementary cell distribution in tissues, consistent with the idea that PlexinB1 acts as the receptor for Sema4D in vivo. Interestingly, PlexinB1 is also expressed in certain tissues in the absence of Sema4D, suggesting Sema4D independent activities. High expression of PlexinB1 was found in lung, kidney, liver and cerebellum.Mutant mice lacking expression of semaphorin receptor PlexinB1 are viable and fertile. Although the axon collapsing activity of Sema4D is impaired in PlexinB1 deficient neurons, we could not detect major defects in development, or in adult histology and basic functional parameters of tissues expressing PlexinB1. Moreover, in the absence of PlexinB1 the angiogenic response induced by orthotopically implanted tumours was not affected, suggesting that the expression of this semaphorin receptor in endothelial cells is redundant. CONCLUSION: Our expression analysis suggests a multifaceted role of PlexinB1 during mouse development and tissue homeostasis in the adult. Nonetheless, the genetic deletion of PlexinB1 does not result in major developmental defects or clear functional abnormalities. We infer that PlexinB1 plays a redundant role in mouse development and it is not strictly required for tumour induced angiogenesis. [Abstract/Link to Full Text]

Chong SW, Nguyet LM, Jiang YJ, Korzh V
The chemokine Sdf-1 and its receptor Cxcr4 are required for formation of muscle in zebrafish.
BMC Dev Biol. 2007;754.
BACKGROUND: During development cell migration takes place prior to differentiation of many cell types. The chemokine receptor Cxcr4 and its ligand Sdf1 are implicated in migration of several cell lineages, including appendicular muscles. RESULTS: We dissected the role of sdf1-cxcr4 during skeletal myogenesis. We demonstrated that the receptor cxcr4a is expressed in the medial-anterior part of somites, suggesting that chemokine signaling plays a role in this region of the somite. Previous reports emphasized co-operation of Sdf1a and Cxcr4b. We found that during early myogenesis Sdf1a co-operates with the second Cxcr4 of zebrafish - Cxcr4a resulting in the commitment of myoblast to form fast muscle. Disrupting this chemokine signal caused a reduction in myoD and myf5 expression and fast fiber formation. In addition, we showed that a dimerization partner of MyoD and Myf5, E12, positively regulates transcription of cxcr4a and sdf1a in contrast to that of Sonic hedgehog, which inhibited these genes through induction of expression of id2. CONCLUSION: We revealed a regulatory feedback mechanism between cxcr4a-sdf1a and genes encoding myogenic regulatory factors, which is involved in differentiation of fast myofibers. This demonstrated a role of chemokine signaling during development of skeletal muscles. [Abstract/Link to Full Text]

Andrews SC, Wood MD, Tunster SJ, Barton SC, Surani MA, John RM
Cdkn1c (p57Kip2) is the major regulator of embryonic growth within its imprinted domain on mouse distal chromosome 7.
BMC Dev Biol. 2007;753.
BACKGROUND: Cdkn1c encodes an embryonic cyclin-dependant kinase inhibitor that acts to negatively regulate cell proliferation and, in some tissues, to actively direct differentiation. This gene, which is an imprinted gene expressed only from the maternal allele, lies within a complex region on mouse distal chromosome 7, called the IC2 domain, which contains several other imprinted genes. Studies on mouse embryos suggest a key role for genomic imprinting in regulating embryonic growth and this has led to the proposal that imprinting evolved as a consequence of the mismatched contribution of parental resources in mammals. RESULTS: In this study, we characterised the phenotype of mice carrying different copy number integrations of a bacterial artificial chromosome spanning Cdkn1c. Excess Cdkn1c resulted in embryonic growth retardation that was dosage-dependent and also responsive to the genetic background. Two-fold expression of Cdkn1c in a subset of tissues caused a 10-30% reduction in embryonic weight, embryonic lethality and was associated with a reduction in the expression of the potent, non-imprinted embryonic growth factor, Igf1. Conversely, loss of expression of Cdkn1c resulted in embryos that were 11% heavier with a two-fold increase in Igf1. CONCLUSION: We have shown that embryonic growth in mice is exquisitely sensitive to the precise dosage of Cdkn1c. Cdkn1c is a maternally expressed gene and our findings support the prediction of the parental conflict hypothesis that that the paternal genome silences genes that have an inhibitory role in embryonic growth. Within the IC2 imprinted domain, Cdkn1c encodes the major regulator of embryonic growth and we propose that Cdkn1c was the focal point of the selective pressure for imprinting of this domain. [Abstract/Link to Full Text]

Clark IB, Jarman AP, Finnegan DJ
Live imaging of Drosophila gonad formation reveals roles for Six4 in regulating germline and somatic cell migration.
BMC Dev Biol. 2007;752.
BACKGROUND: Movement of cells, either as amoeboid individuals or in organised groups, is a key feature of organ formation. Both modes of migration occur during Drosophila embryonic gonad development, which therefore provides a paradigm for understanding the contribution of these processes to organ morphogenesis. Gonads of Drosophila are formed from three distinct cell types: primordial germ cells (PGCs), somatic gonadal precursors (SGPs), and in males, male-specific somatic gonadal precursors (msSGPs). These originate in distinct locations and migrate to associate in two intermingled clusters which then compact to form the spherical primitive gonads. PGC movements are well studied, but much less is known of the migratory events and other interactions undergone by their somatic partners. These appear to move in organised groups like, for example, lateral line cells in zebra fish or Drosophila ovarian border cells. RESULTS: We have used time-lapse fluorescence imaging to characterise gonadal cell behaviour in wild type and mutant embryos. We show that the homeodomain transcription factor Six4 is required for the migration of the PGCs and the msSGPs towards the SGPs. We have identified a likely cause of this in the case of PGCs as we have found that Six4 is required for expression of Hmgcr which codes for HMGCoA reductase and is necessary for attraction of PGCs by SGPs. Six4 affects msSGP migration by a different pathway as these move normally in Hmgcr mutant embryos. Additionally, embryos lacking fully functional Six4 show a novel phenotype in which the SGPs, which originate in distinct clusters, fail to coalesce to form unified gonads. CONCLUSION: Our work establishes the Drosophila gonad as a model system for the analysis of coordinated cell migrations and morphogenesis using live imaging and demonstrates that Six4 is a key regulator of somatic cell function during gonadogenesis. Our data suggest that the initial association of SGP clusters is under distinct control from the movements that drive gonad compaction. [Abstract/Link to Full Text]

Yu SS, Wang M, Li XM, Chen WH, Chen JT, Wang HL, Ruan DY
Influences of different developmental periods of taurine supplements on synaptic plasticity in hippocampal CA1 area of rats following prenatal and perinatal lead exposure.
BMC Dev Biol. 2007;751.
BACKGROUND: Previous study has demonstrated that dietary taurine supplement protected rats from impairments of synaptic plasticity induced by postnatal lead exposure. However, little is known about the role of taurine in the presence of prenatal and perinatal lead exposure. We investigated the possible effect of taurine supplement on prenatal and perinatal lead-induced synaptic plasticity deficit and determined developmental periods critical for the effect of taurine. RESULTS: In the present study, taurine was administrated to prenatal and perinatal lead-exposed rats in different developmental periods: from prenatal to weaning (Lead+PW-Tau), from weaning to life (Lead+WL-Tau), and from prenatal to life (Lead+PL-Tau). We examined the input-output (I/O) function, paired-pulse facilitation (PPF) and the long-term potentiation (LTP) of field excitatory postsynaptic potential (fEPSP) in the hippocampal CA1 area of rats on postnatal days 18-25 (P18-25) or days 60-75 (P60-75). We found that (1) on P18-25, taurine had no evident effect on I/O functions and PPF ratios of lead-exposed rats but caused a 12.0% increase in the LTP amplitudes of these animals; (2) on P60-75, taurine significantly elevated lead depressed I/O functions and PPF ratios in Lead+PW-Tau and Lead+PL-Tau rats, but failed in Lead+WL-Tau rats. The amplitudes of LTP of lead-exposed rats were all significantly increased by additional taurine supplement in any developmental period compared with untreated rats. Thus, taurine appeared to have the most effect during the prenatal and lactation periods and its effects on younger rats would not be manifest until the adult life; and (3) the level of lead deposition in hippocampus was evidently reduced by additional treatment of taurine in lead-exposed rats, compared with untreated rats. CONCLUSION: Taurine supplement can protect the adult rats from synaptic plasticity deficits following prenatal and perinatal lead exposure, and the protective effects are critical for the prenatal and lactation periods of lead-exposed rats. [Abstract/Link to Full Text]

Ma ACh, Lin R, Chan PK, Leung JC, Chan LY, Meng A, Verfaillie CM, Liang R, Leung AY
The role of survivin in angiogenesis during zebrafish embryonic development.
BMC Dev Biol. 2007;750.
BACKGROUND: Survivin is the smallest member of the inhibitor of apoptosis (IAP) gene family. Recently, the zebrafish survivin-1 gene has been cloned, showing remarkable sequence identity and similarity over the BIR domain compared with human and mouse survivin gene. Here we investigated the role of survivin in angiogenesis during zebrafish development. Morpholinos (MOs) targeting the 5' untranslated region (UTR) (SurUTR) and sequences flanking the initiation codon (SurATG) of zebrafish survivin-1 gene were injected into embryos at 1-4 cell stage. Vasculature was examined by microangiography and GFP expression in Tg(fli1:EGFP)y1 embryos. RESULTS: In embryos co-injected with SurUTR and SurATG-MOs, vasculogenesis was intact but angiogenesis was markedly perturbed, especially in the inter-segmental vessels (ISV) and dorsal longitudinal anastomotic vessels (DLAV) of the trunk, the inner optic circle and optic veins of developing eyes and the sub-intestinal vessels. Apoptosis was increased, as shown by TUNEL staining and increase in caspase-3 activity. Efficacy of SurUTR and SurATG-MOs was demonstrated by translation inhibition of co-injected 5'UTR survivin:GFP plasmids. The phenotypes could be recapitulated by splice-site MO targeting the exon2-intron junction of survivin gene and rescued by survivin mRNA. Injection of human vascular endothelial growth factor (VEGF) protein induced ectopic angiogenesis and increased survivin expression, whereas treatment with a VEGF receptor inhibitor markedly reduced angiogenesis and suppressed survivin expression. CONCLUSION: Survivin is involved in angiogenesis during zebrafish development and may be under VEGF regulation. [Abstract/Link to Full Text]

Popichenko D, Sellin J, Bartkuhn M, Paululat A
Hand is a direct target of the forkhead transcription factor Biniou during Drosophila visceral mesoderm differentiation.
BMC Dev Biol. 2007;749.
BACKGROUND: The visceral trunk mesoderm in Drosophila melanogaster develops under inductive signals from the ectoderm. This leads to the activation of the key regulators Tinman, Bagpipe and Biniou that are crucial for specification of the circular visceral muscles. How further differentiation is regulated is widely unknown, therefore it seems to be essential to identify downstream target genes of the early key regulators. In our report we focus on the analysis of the transcriptional control of the highly conserved transcription factor Hand in circular visceral muscle cells, providing evidence that the hand gene is a direct target of Biniou. RESULTS: Herein we describe the identification of a regulatory region in the hand gene essential and sufficient for the expression in the visceral mesoderm during embryogenesis. We found that hand expression in the circular visceral mesoderm is abolished in embryos mutant for the FoxF domain containing transcription factor Biniou. Furthermore we demonstrate that Biniou regulates hand expression by direct binding to a 300 bp sequence element, located within the 3rd intron of the hand gene. This regulatory element is highly conserved in different Drosophila species. In addition, we provide evidence that Hand is dispensable for the initial differentiation of the embryonic visceral mesoderm. CONCLUSION: In the present report we show that cross species sequence comparison of non-coding sequences between orthologous genes is a powerful tool to identify conserved regulatory elements. Combining functional dissection experiments in vivo and protein/DNA binding studies we identified hand as a direct target of Biniou in the circular visceral muscles. [Abstract/Link to Full Text]

Williams EO, Xiao Y, Sickles HM, Shafer P, Yona G, Yang JY, Lin DM
Novel subdomains of the mouse olfactory bulb defined by molecular heterogeneity in the nascent external plexiform and glomerular layers.
BMC Dev Biol. 2007;748.
BACKGROUND: In the mouse olfactory system, the role of the olfactory bulb in guiding olfactory sensory neuron (OSN) axons to their targets is poorly understood. What cell types within the bulb are necessary for targeting is unknown. What genes are important for this process is also unknown. Although projection neurons are not required, other cell-types within the external plexiform and glomerular layers also form synapses with OSNs. We hypothesized that these cells are important for targeting, and express spatially differentially expressed guidance cues that act to guide OSN axons within the bulb. RESULTS: We used laser microdissection and microarray analysis to find genes that are differentially expressed along the dorsal-ventral, medial-lateral, and anterior-posterior axes of the bulb. The expression patterns of these genes divide the bulb into previously unrecognized subdomains. Interestingly, some genes are expressed in both the medial and lateral bulb, showing for the first time the existence of symmetric expression along this axis. We use a regeneration paradigm to show that several of these genes are altered in expression in response to deafferentation, consistent with the interpretation that they are expressed in cells that interact with OSNs. CONCLUSION: We demonstrate that the nascent external plexiform and glomerular layers of the bulb can be divided into multiple domains based on the expression of these genes, several of which are known to function in axon guidance, synaptogenesis, and angiogenesis. These genes represent candidate guidance cues that may act to guide OSN axons within the bulb during targeting. [Abstract/Link to Full Text]

Saka Y, Smith JC
A mechanism for the sharp transition of morphogen gradient interpretation in Xenopus.
BMC Dev Biol. 2007;747.
BACKGROUND: One way in which positional information is established during embryonic development is through the graded distribution of diffusible morphogens. Unfortunately, little is known about how cells interpret different concentrations of morphogen to activate different genes or how thresholds are generated in a morphogen gradient. RESULTS: Here we show that the concentration-dependent induction of the T-box transcription factor Brachyury (Xbra) and the homeobox-containing gene Goosecoid (Gsc) by activin in Xenopus can be explained by the dynamics of a simple network consisting of three elements with a mutual negative feedback motif that can function to convert a graded signal (activin) into a binary output (Xbra on and Gsc off, or vice versa). Importantly, such a system can display sharp thresholds. Consistent with the predictions of our model, Xenopus ectodermal cells display a binary response at the single cell level after treatment with activin. CONCLUSION: This kind of simple network with mutual negative feedback might provide a general mechanism for selective gene activation in response to different levels of a single external signal. It provides a mechanism by which a sharp boundary might be created between domains of different cell types in response to a morphogen gradient. [Abstract/Link to Full Text]

Greber B, Lehrach H, Adjaye J
Silencing of core transcription factors in human EC cells highlights the importance of autocrine FGF signaling for self-renewal.
BMC Dev Biol. 2007;746.
BACKGROUND: Despite their distinct origins, human embryonic stem (hES) and embryonic carcinoma (hEC) cells share a number of similarities such as surface antigen expression, growth characteristics, the ability to either self-renew or differentiate, and control of the undifferentiated state by the same core transcription factors. To obtain further insights into the regulation of self-renewal, we have silenced hES/hEC cell-specific genes in NCCIT hEC cells and analysed the downstream effects by means of microarrays. RESULTS: RNAi-mediated silencing of OCT4 and SOX2 induced differentiation with mesodermal characteristics. Markers of trophoblast induction were only transiently up-regulated in the OCT4 knock-down. Independent knock-downs of NANOG produced a proliferation rather than a differentiation phenotype, which may be due to high NANOG expression levels in the cell line used. Published ChIP-chip data from hES cells were used to identify putative direct targets. RNAi-mediated differentiation was accompanied by direct down-regulation of known hES/hEC cell markers. This included all three core transcription factors in the case of the OCT4 and SOX2 knock-downs, confirming previous findings of reciprocal activation in ES cells. Furthermore, large numbers of histone genes as well as epigenetic regulators were differentially expressed, pointing at chromatin remodeling as an additional regulatory level in the differentiation process. Moreover, loss of self-renewal was accompanied by the down-regulation of genes involved in FGF signaling. FGF receptor inhibition for short and prolonged periods of time revealed that the ERK/MAPK cascade is activated by endogenously expressed fibroblast growth factors and that FGF signaling is cruicial for maintaining the undifferentiated state of hEC cells, like in hES cells. CONCLUSION: Control of self-renewal appears to be very similar in hEC and hES cells. This is supported by large numbers of common transcription factor targets and the requirement for autocrine FGF signaling. [Abstract/Link to Full Text]

Recent Articles in BMC Evolutionary Biology

Bininda-Emonds OR, Jeffery JE, Sanchez-Villagra MR, Hanken J, Colbert MW, Pieau C, Selwood L, Ten Cate CJ, Raynaud A, Osabutey CK, Richardson MK
Forelimb-hindlimb developmental timing differences across tetrapod phylogeny.
BMC Evol Biol. 2007 Oct 1;7(1):182.
ABSTRACT: BACKGROUND: Tetrapods exhibit great diversity in limb structures among species and also between forelimbs and hindlimbs within species, diversity which frequently correlates with locomotor modes and life history. We aim to examine the potential relation of changes in developmental timing (heterochrony) to the origin of limb morphological diversity in an explicit comparative and quantitative framework. In particular, we studied the relative time sequence of development of the forelimbs versus the hindlimbs in 138 embryos of 14 tetrapod species spanning a diverse taxonomic, ecomorphological and life-history breadth. Whole-mounts and histological sections were used to code the appearance of 10 developmental events comprising landmarks of development from the early bud stage to late chondrogenesis in the forelimb and the corresponding serial homologues in the hindlimb. RESULTS: An overall pattern of change across tetrapod phylogeny can be discerned, and it appears to be relatively clade-specific. In the primitive condition, as seen in Chondrichthyes and Osteichthyes, the forelimb or pectoral fin develops earlier than the hindlimb or pelvic fin. This pattern is either retained or re-evolved in eulipotyphlan insectivores and taken to its extreme in marsupials. Although exceptions are known, the two anurans we examined reversed the pattern and displayed a significant advance in hindlimb development compared to forelimbs. All other species examined, including a bat with its greatly enlarged forelimbs modified as wings in the adult, showed near synchrony in the development of the forelimbs and hindlimbs. CONCLUSION: Major heterochronic changes in early limb development and chondrogenesis were absent within major clades except Lissamphibia, and their presence across vertebrate phylogeny are not easily correlated with adaptive phenomena related to morphological differences in the adult fore- and hindlimbs. The apparently conservative nature of this trait means that changes in chondrogenetic patterns may serve as useful phylogenetic characters at higher taxonomic levels in tetrapods. Our results highlight the more important role generally played by allometric heterochrony in this instance to shape adult morphology. [Abstract/Link to Full Text]

Tamames J, Gil R, Latorre A, Pereto J, Silva FJ, Moya A
The frontier between cell and organelle: genome analysis of Candidatus Carsonella ruddii.
BMC Evol Biol. 2007 Oct 1;7(1):181.
ABSTRACT: BACKGROUND: Bacterial symbioses are widespread among insects. The early establishment of such symbiotic associations has probably been one of the key factors for the evolutionary success of insects, since it may have allowed access to novel ecological niches and to new, imbalanced food resources, such as plant sap or blood. Several genomes of bacterial endosymbionts of different insect species have been recently sequenced, and their biology has been extensively studied. Recently, the complete genome sequence of Candidatus Carsonella ruddii, considered the primary endosymbiont of the psyllid Pachpsylla venusta, has been published. This genome consists of a circular chromosome of 159,662 bp and has been proposed as the smallest bacterial endosymbiont genome known to date. RESULTS: The detailed analysis of the gene content of C. ruddii shows that the extensive degradation of the genome is not compatible with its consideration as a living organism and, therefore, as an endosymbiont. The ability to perform most essential functions for a cell to be considered alive is heavily impaired by the lack of genes involved in DNA replication, transcription and translation. Furthermore, the shortening of genes causes, in some cases, the loss of essential domains and functional residues needed to fulfill such vital functions. In addition, at least half of the pathways towards the biosynthesis of essential amino acids, its proposed symbiotic function, are completely or partially lost. CONCLUSIONS: We propose that this strain of C. ruddii can be viewed as a further step towards the degeneration of the former primary endosymbiont and its transformation in a subcellular new entity between living cells and organelles. Although the transition of genes from C. ruddii to the host nucleus has been proposed, the amount of genes that should have been transferred to the germinal line of the insect would be so big that it would be more plausible to consider the implication of the mitochondrial machinery encoded in the insect nucleus. Furthermore, since most genes for the biosynthesis of essential amino acids have also been lost, the host must depend on another yet unidentified symbiont to complement its deficient diet. [Abstract/Link to Full Text]

Villiard E, Brinkmann H, Moiseeva O, Mallette FA, Ferbeyre G, Roy S
Urodele p53 tolerates amino acid changes found in p53 variants linked to human cancer.
BMC Evol Biol. 2007;7180.
BACKGROUND: Urodele amphibians like the axolotl are unique among vertebrates in their ability to regenerate and their resistance to develop cancers. It is unknown whether these traits are linked at the molecular level. RESULTS: Blocking p53 signaling in axolotls using the p53 inhibitor, pifithrin-alpha, inhibited limb regeneration and the expression of p53 target genes such as Mdm2 and Gadd45, suggesting a link between tumor suppression and regeneration. To understand this relationship we cloned the p53 gene from axolotl. When comparing its sequence with p53 from other organisms, and more specifically human we observed multiple amino acids changes found in human tumors. Phylogenetic analysis of p53 protein sequences from various species is in general agreement with standard vertebrate phylogeny; however, both mice-like rodents and teleost fishes are fast evolving. This leads to long branch attraction resulting in an artefactual basal emergence of these groups in the phylogenetic tree. It is tempting to assume a correlation between certain life style traits (e.g. lifespan) and the evolutionary rate of the corresponding p53 sequences. Functional assays of the axolotl p53 in human or axolotl cells using p53 promoter reporters demonstrated a temperature sensitivity (ts), which was further confirmed by performing colony assays at 37 degrees C. In addition, axolotl p53 was capable of efficient transactivation at the Hmd2 promoter but has moderate activity at the p21 promoter. Endogenous axolotl p53 was activated following UV irradiation (100 j/m2) or treatment with an alkylating agent as measured using serine 15 phosphorylation and the expression of the endogenous p53 target Gadd45. CONCLUSION: Urodele p53 may play a role in regeneration and has evolved to contain multiple amino acid changes predicted to render the human protein defective in tumor suppression. Some of these mutations were probably selected to maintain p53 activity at low temperature. However, other significant changes in the axolotl proteins may play more subtle roles on p53 functions, including DNA binding and promoter specificity and could represent useful adaptations to ensure p53 activity and tumor suppression in animals able to regenerate or subject to large variations in oxygen levels or temperature. [Abstract/Link to Full Text]

Chen FC, Chuang TJ
Different alternative splicing patterns are subject to opposite selection pressure for protein reading frame preservation.
BMC Evol Biol. 2007;7179.
BACKGROUND: Alternative splicing (AS) has been regarded capable of altering selection pressure on protein subsequences. Particularly, the frequency of reading frame preservation (FRFP), as a measure of selection pressure, has been reported to be higher in alternatively spliced exons (ASEs) than in constitutively spliced exons (CSEs). However, recently it has been reported that different ASE types - simple and complex ASEs - may be subject to opposite selection forces. Therefore, it is necessary to re-evaluate the evolutionary effects of such splicing patterns on frame preservation. RESULTS: Here we show that simple and complex ASEs, respectively, have higher and lower FRFPs than CSEs. Since complex ASEs may alter the ends of their flanking exons, the selection pressure on frame preservation is likely relaxed in this ASE type. Furthermore, conservation of the ASE/CSE splicing pattern increases the FRFPs of simple ASEs but decreases those of complex ASEs. Contrary to the well-recognized concept of strong selection pressure on conserved ASEs for protein reading frame preservation, our results show that conserved complex ASEs are relaxed from such pressure and the frame-disrupting effect caused by the insertion of complex ASEs can be offset by compensatory changes in their flanking exons. CONCLUSION: In this study, we find that simple and complex ASEs undergo opposite selection pressure for protein reading frame preservation, with CSEs in-between. Simple ASEs have much higher FRFPs than complex ones. We further find that the FRFPs of complex ASEs coupled with flanking exons are close to those of simple ASEs, indicating that neighboring exons of an ASE may evolve in a coordinated way to avoid protein dysfunction. Therefore, we suggest that evolutionary analyses of AS should take into consideration the effects of different splicing patterns and the joint effects of multiple AS events. [Abstract/Link to Full Text]

Kawahara T, Lambeth JD
Molecular evolution of Phox-related regulatory subunits for NADPH oxidase enzymes.
BMC Evol Biol. 2007;7178.
BACKGROUND: The reactive oxygen-generating NADPH oxidases (Noxes) function in a variety of biological roles, and can be broadly classified into those that are regulated by subunit interactions and those that are regulated by calcium. The prototypical subunit-regulated Nox, Nox2, is the membrane-associated catalytic subunit of the phagocyte NADPH-oxidase. Nox2 forms a heterodimer with the integral membrane protein, p22phox, and this heterodimer binds to the regulatory subunits p47phox, p67phox, p40phox and the small GTPase Rac, triggering superoxide generation. Nox-organizer protein 1 (NOXO1) and Nox-activator 1 (NOXA1), respective homologs of p47phox and p67phox, together with p22phox and Rac, activate Nox1, a non-phagocytic homolog of Nox2. NOXO1 and p22phox also regulate Nox3, whereas Nox4 requires only p22phox. In this study, we have assembled and analyzed amino acid sequences of Nox regulatory subunit orthologs from vertebrates, a urochordate, an echinoderm, a mollusc, a cnidarian, a choanoflagellate, fungi and a slime mold amoeba to investigate the evolutionary history of these subunits. RESULTS: Ancestral p47phox, p67phox, and p22phox genes are broadly seen in the metazoa, except for the ecdysozoans. The choanoflagellate Monosiga brevicollis, the unicellular organism that is the closest relatives of multicellular animals, encodes early prototypes of p22phox, p47phox as well as the earliest known Nox2-like ancestor of the Nox1-3 subfamily. p67phox- and p47phox-like genes are seen in the sea urchin Strongylocentrotus purpuratus and the limpet Lottia gigantea that also possess Nox2-like co-orthologs of vertebrate Nox1-3. Duplication of primordial p47phox and p67phox genes occurred in vertebrates, with the duplicated branches evolving into NOXO1 and NOXA1. Analysis of characteristic domains of regulatory subunits suggests a novel view of the evolution of Nox: in fish, p40phox participated in regulating both Nox1 and Nox2, but after the appearance of mammals, Nox1 (but not Nox2) became independent of p40phox. In the fish Oryzias latipes, a NOXO1 ortholog retains an autoinhibitory region that is characteristic of mammalian p47phox, and this was subsequently lost from NOXO1 in later vertebrates. Detailed amino acid sequence comparisons identified both putative key residues conserved in characteristic domains and previously unidentified conserved regions. Also, candidate organizer/activator proteins in fungi and amoeba are identified and hypothetical activation models are suggested. CONCLUSION: This is the first report to provide the comprehensive view of the molecular evolution of regulatory subunits for Nox enzymes. This approach provides clues for understanding the evolution of biochemical and physiological functions for regulatory-subunit-dependent Nox enzymes. [Abstract/Link to Full Text]

K�ser M, Rondini S, Naegeli M, Stinear T, Portaels F, Certa U, Pluschke G
Evolution of two distinct phylogenetic lineages of the emerging human pathogen Mycobacterium ulcerans.
BMC Evol Biol. 2007;7177.
BACKGROUND: Comparative genomics has greatly improved our understanding of the evolution of pathogenic mycobacteria such as Mycobacterium tuberculosis. Here we have used data from a genome microarray analysis to explore insertion-deletion (InDel) polymorphism among a diverse strain collection of Mycobacterium ulcerans, the causative agent of the devastating skin disease, Buruli ulcer. Detailed analysis of large sequence polymorphisms in twelve regions of difference (RDs), comprising irreversible genetic markers, enabled us to refine the phylogenetic succession within M. ulcerans, to define features of a hypothetical M. ulcerans most recent common ancestor and to confirm its origin from Mycobacterium marinum. RESULTS: M. ulcerans has evolved into five InDel haplotypes that separate into two distinct lineages: (i) the "classical" lineage including the most pathogenic genotypes - those that come from Africa, Australia and South East Asia; and (ii) an "ancestral" M. ulcerans lineage comprising strains from Asia (China/Japan), South America and Mexico. The ancestral lineage is genetically closer to the progenitor M. marinum in both RD composition and DNA sequence identity, whereas the classical lineage has undergone major genomic rearrangements. CONCLUSION: Results of the InDel analysis are in complete accord with recent multi-locus sequence analysis and indicate that M. ulcerans has passed through at least two major evolutionary bottlenecks since divergence from M. marinum. The classical lineage shows more pronounced reductive evolution than the ancestral lineage, suggesting that there may be differences in the ecology between the two lineages. These findings improve the understanding of the adaptive evolution and virulence of M. ulcerans and pathogenic mycobacteria in general and will facilitate the development of new tools for improved diagnostics and molecular epidemiology. [Abstract/Link to Full Text]

Fink S, Excoffier L, Heckel G
High variability and non-neutral evolution of the mammalian avpr1a gene.
BMC Evol Biol. 2007;7176.
BACKGROUND: The arginine-vasopressin 1a receptor has been identified as a key determinant for social behaviour in Microtus voles, humans and other mammals. Nevertheless, the genetic bases of complex phenotypic traits like differences in social and mating behaviour among species and individuals remain largely unknown. Contrary to previous studies focusing on differences in the promotor region of the gene, we investigate here the level of functional variation in the coding region (exon 1) of this locus. RESULTS: We detected high sequence diversity between higher mammalian taxa as well as between species of the genus Microtus. This includes length variation and radical amino acid changes, as well as the presence of distinct protein variants within individuals. Additionally, negative selection prevails on most parts of the first exon of the arginine-vasopressin receptor 1a (avpr1a) gene but it contains regions with higher rates of change that harbour positively selected sites. Synonymous and non-synonymous substitution rates in the avpr1a gene are not exceptional compared to other genes, but they exceed those found in related hormone receptors with similar functions. DISCUSSION: These results stress the importance of considering variation in the coding sequence of avpr1a in regards to associations with life history traits (e.g. social behaviour, mating system, habitat requirements) of voles, other mammals and humans in particular. [Abstract/Link to Full Text]

Pahari S, Bickford D, Fry BG, Kini RM
Expression pattern of three-finger toxin and phospholipase A2 genes in the venom glands of two sea snakes, Lapemis curtus and Acalyptophis peronii: comparison of evolution of these toxins in land snakes, sea kraits and sea snakes.
BMC Evol Biol. 2007 Sep 27;7(1):175.
ABSTRACT: BACKGROUND: Snake venom composition varies widely both among closely related species and within the same species, based on ecological variables. In terrestrial snakes, such variation has been proposed to be due to snakes' diet. Land snakes target various prey species including insects (arthropods), lizards (reptiles), frogs and toads (amphibians), birds (aves), and rodents (mammals), whereas sea snakes target a single vertebrate class (fishes) and often specialize on specific types of fish. It is therefore interesting to examine the evolution of toxins in sea snake venoms compared to that of land snakes. RESULTS: Here we describe the expression of toxin genes in the venom glands of two sea snakes, Lapemis curtus (Spine-bellied Sea Snake) and Acalyptophis peronii (Horned Sea Snake), two members of a large adaptive radiation which occupy very different ecological niches. We constructed cDNA libraries from their venom glands and sequenced 214 and 192 clones, respectively. Our data show that despite their explosive evolutionary radiation, there is very little variability in the three-finger toxin (3FTx) as well as the phospholipase A2 (PLA2) enzymes, the two main constituents of Lapemis curtus and Acalyptophis peronii venom. To understand the evolutionary trends among land snakes, sea snakes and sea kraits, pairwise genetic distances (intraspecific and interspecific) of 3FTx and PLA2 sequences were calculated. Results show that these proteins appear to be highly conserved in sea snakes in contrast to land snakes or sea kraits, despite their extremely divergent and adaptive ecological radiation. CONCLUSION: Based on these results, we suggest that streamlining in habitat and diet in sea snakes has possibly kept their toxin genes conserved, suggesting the idea that prey composition and diet breadth may contribute to the diversity and evolution of venom components. [Abstract/Link to Full Text]

Patron NJ, Waller RF, Cozijnsen AJ, Straney DC, Gardiner DM, Nierman WC, Howlett BJ
Origin and distribution of epipolythiodioxopiperazine (ETP) gene clusters in filamentous ascomycetes.
BMC Evol Biol. 2007;7174.
BACKGROUND: Genes responsible for biosynthesis of fungal secondary metabolites are usually tightly clustered in the genome and co-regulated with metabolite production. Epipolythiodioxopiperazines (ETPs) are a class of secondary metabolite toxins produced by disparate ascomycete fungi and implicated in several animal and plant diseases. Gene clusters responsible for their production have previously been defined in only two fungi. Fungal genome sequence data have been surveyed for the presence of putative ETP clusters and cluster data have been generated from several fungal taxa where genome sequences are not available. Phylogenetic analysis of cluster genes has been used to investigate the assembly and heredity of these gene clusters. RESULTS: Putative ETP gene clusters are present in 14 ascomycete taxa, but absent in numerous other ascomycetes examined. These clusters are discontinuously distributed in ascomycete lineages. Gene content is not absolutely fixed, however, common genes are identified and phylogenies of six of these are separately inferred. In each phylogeny almost all cluster genes form monophyletic clades with non-cluster fungal paralogues being the nearest outgroups. This relatedness of cluster genes suggests that a progenitor ETP gene cluster assembled within an ancestral taxon. Within each of the cluster clades, the cluster genes group together in consistent subclades, however, these relationships do not always reflect the phylogeny of ascomycetes. Micro-synteny of several of the genes within the clusters provides further support for these subclades. CONCLUSION: ETP gene clusters appear to have a single origin and have been inherited relatively intact rather than assembling independently in the different ascomycete lineages. This progenitor cluster has given rise to a small number of distinct phylogenetic classes of clusters that are represented in a discontinuous pattern throughout ascomycetes. The disjunct heredity of these clusters is discussed with consideration to multiple instances of independent cluster loss and lateral transfer of gene clusters between lineages. [Abstract/Link to Full Text]

Nosenko T, Bhattacharya D
Horizontal gene transfer in chromalveolates.
BMC Evol Biol. 2007;7173.
BACKGROUND: Horizontal gene transfer (HGT), the non-genealogical transfer of genetic material between different organisms, is considered a potentially important mechanism of genome evolution in eukaryotes. Using phylogenomic analyses of expressed sequence tag (EST) data generated from a clonal cell line of a free living dinoflagellate alga Karenia brevis, we investigated the impact of HGT on genome evolution in unicellular chromalveolate protists. RESULTS: We identified 16 proteins that have originated in chromalveolates through ancient HGTs before the divergence of the genera Karenia and Karlodinium and one protein that was derived through a more recent HGT. Detailed analysis of the phylogeny and distribution of identified proteins demonstrates that eight have resulted from independent HGTs in several eukaryotic lineages. CONCLUSION: Recurring intra- and interdomain gene exchange provides an important source of genetic novelty not only in parasitic taxa as previously demonstrated but as we show here, also in free-living protists. Investigating the tempo and mode of evolution of horizontally transferred genes in protists will therefore advance our understanding of mechanisms of adaptation in eukaryotes. [Abstract/Link to Full Text]

Imanian B, Keeling PJ
The dinoflagellates Durinskia baltica and Kryptoperidinium foliaceum retain functionally overlapping mitochondria from two evolutionarily distinct lineages.
BMC Evol Biol. 2007;7172.
BACKGROUND: The dinoflagellates Durinskia baltica and Kryptoperidinium foliaceum are distinguished by the presence of a tertiary plastid derived from a diatom endosymbiont. The diatom is fully integrated with the host cell cycle and is so altered in structure as to be difficult to recognize it as a diatom, and yet it retains a number of features normally lost in tertiary and secondary endosymbionts, most notably mitochondria. The dinoflagellate host is also reported to retain mitochondrion-like structures, making these cells unique in retaining two evolutionarily distinct mitochondria. This redundancy raises the question of whether the organelles share any functions in common or have distributed functions between them. RESULTS: We show that both host and endosymbiont mitochondrial genomes encode genes for electron transport proteins. We have characterized cytochrome c oxidase 1 (cox1), cytochrome oxidase 2 (cox2), cytochrome oxidase 3 (cox3), cytochrome b (cob), and large subunit of ribosomal RNA (LSUrRNA) of endosymbiont mitochondrial ancestry, and cox1 and cob of host mitochondrial ancestry. We show that all genes are transcribed and that those ascribed to the host mitochondrial genome are extensively edited at the RNA level, as expected for a dinoflagellate mitochondrion-encoded gene. We also found evidence for extensive recombination in the host mitochondrial genes and that recombination products are also transcribed, as expected for a dinoflagellate. CONCLUSION: Durinskia baltica and K. foliaceum retain two mitochondria from evolutionarily distinct lineages, and the functions of these organelles are at least partially overlapping, since both express genes for proteins in electron transport. [Abstract/Link to Full Text]

Ellis PJ, Ferguson L, Clemente EJ, Affara NA
Bidirectional transcription of a novel chimeric gene mapping to mouse chromosome Yq.
BMC Evol Biol. 2007 Sep 24;7(1):171.
ABSTRACT: BACKGROUND: The male-specific region of the mouse Y chromosome long arm (MSYq) contains three known highly multi-copy X-Y homologous gene families, Ssty1/2, Sly and Asty. Deletions on MSYq lead to teratozoospermia and subfertility or infertility, with a sex ratio skew in the offspring of subfertile MSYqdel males RESULTS: We report the highly unusual genomic structure of a novel MSYq locus, Orly, and a diverse set of spermatid-specific transcripts arising from copies of this locus. Orly is composed of partial copies of Ssty1, Asty and Sly arranged in sequence. The Ssty1- and Sly-derived segments are in antisense orientation relative to each other, leading to bi-directional transcription of Orly. Genome search and phylogenetic tree analysis is used to determine the order of events in mouse Yq evolution. We find that Orly is the most recent gene to arise on Yq, and that subsequently there was massive expansion in copy number of all Yq-linked genes. CONCLUSIONS: Orly has an unprecedented chimeric structure, and generates both "forward" (Orly) and "reverse" (Orlyos) transcripts arising from the promoters at each end of the locus. The region of overlap of known Orly and Orlyos transcripts is homologous to Sly intron 2. We propose that Orly may be involved in an intragenomic conflict between mouse X and Y chromosomes, and that this process underlies the massive expansion in copy number of the genes on MSYq and their X homologues. [Abstract/Link to Full Text]

Mart�nez-Cruz B, Godoy JA
Genetic evidence for a recent divergence and subsequent gene flow between Spanish and Eastern imperial eagles.
BMC Evol Biol. 2007;7170.
BACKGROUND: Dating of population divergence is critical in understanding speciation and in evaluating the evolutionary significance of genetic lineages, upon which identification of conservation and management units should be based. In this study we used a multilocus approach and the Isolation-Migration model based on coalescence theory to estimate the time of divergence of the Spanish and Eastern imperial eagle sister species. This model enables estimation of population sizes at split, and inference of gene flow after divergence. RESULTS: Our results indicate that divergence may have occurred during the Holocene or the late Pleistocene, much more recently than previously suspected. They also suggest a large population reduction at split, with an estimated effective population size several times smaller for the western population than for the eastern population. Asymmetrical gene flow after divergence, from the Eastern imperial eagle to the Spanish imperial eagle, was detected for the nuclear genome but not the mitochondrial genome. Male-mediated gene flow after divergence may explain this result, and the previously reported lower mitochondrial diversity but similar nuclear diversity in Spanish imperial eagles compared to the Eastern species. CONCLUSION: Spanish and Eastern imperial eagles split from a common ancestor much more recently than previously thought, and asymmetrical gene flow occurred after divergence. Revision of the phylogenetic proximity of both species is warranted, with implications for conservation. [Abstract/Link to Full Text]

Parter M, Kashtan N, Alon U
Environmental variability and modularity of bacterial metabolic networks.
BMC Evol Biol. 2007 Sep 23;7(1):169.
ABSTRACT: BACKGROUND: Biological systems are often modular: they can be decomposed into nearly-independent structural units that perform specific functions. The evolutionary origin of modularity is a subject of much current interest. Recent theory suggests that modularity can be enhanced when the environment changes over time. However, this theory has not yet been tested using biological data. RESULTS: To address this, we studied the relation between environmental variability and modularity in a natural and well-studied system, the metabolic networks of bacteria. We classified 117 bacterial species according to the degree of variability in their natural habitat. We find that metabolic networks of organisms in variable environments are significantly more modular than networks of organisms that evolved under more constant conditions. CONCLUSIONS: This study supports the view that variability in the natural habitat of an organism promotes modularity in its metabolic network and perhaps in other biological systems. [Abstract/Link to Full Text]

Vallender EJ, Lahn BT
Uncovering the mutation-fixation correlation in short lineages.
BMC Evol Biol. 2007;7168.
BACKGROUND: We recently reported a highly unexpected positive correlation between the fixation probability of nonsynonymous mutations (estimated by omega) and neutral mutation rate (estimated by Ks) in mammalian lineages. However, this positive correlation was observed for lineages with relatively long divergence time such as the human-mouse lineage, and was not found for very short lineages such as the human-chimpanzee lineage. It was previously unclear how to interpret this discrepancy. It may indicate that the positive correlation between omega and Ks in long lineages is a false finding. Alternatively, it may reflect a biologically meaningful difference between various lineages. Finally, the lack of positive correlation in short lineages may be the result of methodological artifacts. RESULTS: Here we show that a strong positive correlation can indeed be seen in short lineages when a method was introduced to correct for the inherently high levels of stochastic noise in the use of Ks as an estimator of neutral mutation rate. Thus, the previously noted lack of positive correlation between omega and Ks in short lineages is due to stochastic noise in Ks that makes it a far less reliable estimator of neutral mutation rate in short lineages as compared to long lineages. CONCLUSION: A positive correlation between omega and Ks can be observed in all mammalian lineages for which large amounts of sequence data are available, including very short lineages. It confirms the authenticity of this highly unexpected correlation, and argues that the correction likely applies broadly across all mammals and perhaps even non-mammalian species. [Abstract/Link to Full Text]

Osorio DS, Antunes A, Ramos MJ
Structural and functional implications of positive selection at the primate angiogenin gene.
BMC Evol Biol. 2007 Sep 20;7(1):167.
ABSTRACT: BACKGROUND: Angiogenesis, the formation of new blood vessels, is a primordial process in development and its dysregulation has a central role in the pathogenesis of many diseases. Angiogenin (ANG), a peculiar member of the RNase A superfamily, is a potent inducer of angiogenesis involved in many different types of cancer, amyotrophic lateral sclerosis and also with a possible role in the innate immune defense. The evolutionary path of this family has been a highly dynamic one, where positive selection has played a strong role. In this work we used a combined gene and protein level approach to determine the main sites under diversifying selection on the primate ANG gene and analyze its structural and functional implications. RESULTS: We obtained evidence for positive selection in the primate ANG gene. Site specific analysis pointed out 15 sites under positive selection, most of which also exhibited drastic changes in amino acid properties. The mapping of these sites in the ANG 3D-structure described five clusters, four of which were located in functional regions: two in the active site region, one in the nucleolar location signal and one in the cell-binding site. Eight of the 15 sites under selection in the primate ANG gene were highly or moderately conserved in the RNase A family, suggesting a directed event and not a simple consequence of local structural or functional permissiveness. Moreover, 11 sites were exposed to the surface of the protein indicating that they may influence the interactions performed by ANG. CONCLUSIONS: Using a maximum likelihood gene level analysis we identified 15 sites under positive selection in the primate ANG genes, that were further corroborated through a protein level analysis of radical changes in amino acid properties. These sites mapped onto the main functional regions of the ANG protein. The fact that evidence for positive selection is present in all ANG regions required for angiogenesis may be a good indication that angiogenesis is the process under selection. However, other possibilities to be considered arise from the possible involvement of ANG in innate immunity and the potential influence or co-evolution with its interacting proteins and ligands. [Abstract/Link to Full Text]

Baisse B, Galisson F, Giraud S, Schapira M, Spertini O
Evolutionary conservation of P-selectin glycoprotein ligand-1 primary structure and function.
BMC Evol Biol. 2007 Sep 14;7(1):166.
ABSTRACT: BACKGROUND: P-selectin glycoprotein ligand-1 (PSGL-1) plays a critical role in recruiting leukocytes in inflammatory lesions by mediating leukocyte rolling on selectins. Core-2 O-glycosylation of a N-terminal threonine and sulfation of at least one tyrosine residue of PSGL-1 are required for L- and P-selectin binding. Little information is available on the intra- and inter-species evolution of PSGL-1 primary structure. In addition, the evolutionary conservation of selectin binding site on PSGL-1 has not been previously examined in detail. Therefore, we performed multiple sequence alignment of PSGL-1 amino acid sequences of 14 mammals (human, chimpanzee, rhesus monkey, bovine, pig, rat, tree-shrew, bushbaby, mouse, bat, horse, cat, sheep and dog) and examined mammalian PSGL-1 interactions with human selectins. RESULTS: A signal peptide was predicted in each sequence and a propeptide cleavage site was found in 9/14 species. PSGL-1 N-terminus is poorly conserved. However, each species exhibits at least one tyrosine sulfation site and, except in horse and dog, a T[D/E]PP[D/E] motif associated to the core-2 O-glycosylation of a N-terminal threonine. A mucin-like domain of 250-280 amino acids long was disclosed in all studied species. It lies between the conserved N-terminal O-glycosylated threonine (Thr-57 in human) and the transmembrane domain, and contains a central region exhibiting a variable number of decameric repeats (DR). Interspecies and intraspecies polymorphisms were observed. Transmembrane and cytoplasmic domain sequences are well conserved. The moesin binding residues that serve as adaptor between PSGL-1 and Syk, and are involved in regulating PSGL-1-dependent rolling on P-selectin are perfectly conserved in all analyzed mammalian sequences. Despite a poor conservation of PSGL-1 N-terminal sequence, CHO cells co-expressing human glycosyltransferases and human, bovine, pig or rat PSGL-1 efficiently rolled on human L- or P-selectin. By contrast, pig or rat neutrophils were much less efficiently recruited than human or bovine neutrophils on human selectins. Horse PSGL-1, glycosylated by human or equine glycosyltransferases, did not interact with human P-selectin. In all five species, tyrosine sulfation of PSGL-1 was required for selectin binding. CONCLUSIONS: These observations show that PSGL-1 amino acid sequence of the transmembrane and cytoplasmic domains are well conserved and that, despite a poor conservation of PSGL-1 N-terminus, L- and P-selectin binding sites are evolutionary conserved. Functional assays reveal a critical role for post-translational modifications in regulating mammalian PSGL-1 interactions with selectins. [Abstract/Link to Full Text]

Hulva P, Horacek I, Benda P
Molecules, morphometrics and new fossils provide an integrated view of the evolutionary history of Rhinopomatidae (Mammalia: Chiroptera).
BMC Evol Biol. 2007 Sep 14;7(1):165.
ABSTRACT: BACKGROUND: The Rhinopomatidae, traditionally considered to be one of the most ancient chiropteran clades, remains one of the least known groups of Rhinolophoidea. No relevant fossil record is available for this family. Whereas there have been extensive radiations in related families Rhinolophidae and Hipposideridae, there are only a few species in the Rhinopomatidae and their phylogenetic relationship and status are not fully understood. RESULTS: Here we present (a) a phylogenetic analysis based on a partial cytochrome b sequence, (b) new fossils from the Upper Miocene site Elaiochoria 2 (Chalkidiki, Greece), which represents the first appearance datum of the family based on the fossil record, and (c) discussion of the phylogeographic patterns in both molecular and morphological traits. We found deep divergences in the Rhinopoma hardwickii lineage, suggesting that the allopatric populations in (i) Iran and (ii) North Africa and the Middle East should have separate species status. The latter species (R. cystops) exhibits a shallow pattern of isolation by distance (separating the Middle East and the African populations) that contrasts with the pattern of geographic variation in the morphometrical traits. A deep genetic gap was also found in Rhinopoma muscatellum (Iran vs. Yemen). We found only minute genetic distance between R. microphyllum from the Levant and India, which fails to support the sub/species distinctness of the Indian form (R. microphyllum kinneari). CONCLUSION: The mtDNA survey provided phylogenetic tree of the family Rhinopomatidae for the first time and revealed an unexpected diversification of the group both within R. hardwickii and R. muscatellum morphospecies. The paleobiogeographic scenario compiled in respect to molecular clock data suggests that the family originated in the region south of the Eocene Western Tethyan seaway or in India, and extended its range during the Early Miocene. The fossil record suggests a Miocene spread into the Mediterranean region, followed by a post-Miocene retreat. Morphological analysis compared with genetic data indicates considerable phenotypic plasticity in this group. [Abstract/Link to Full Text]

Gu�rette D, Khan PA, Savard PE, Vincent M
Molecular evolution of type VI intermediate filament proteins.
BMC Evol Biol. 2007;7164.
BACKGROUND: Tanabin, transitin and nestin are type VI intermediate filament (IF) proteins that are developmentally regulated in frogs, birds and mammals, respectively. Tanabin is expressed in the growth cones of embryonic vertebrate neurons, whereas transitin and nestin are found in myogenic and neurogenic cells. Another type VI IF protein, synemin, is expressed in undifferentiated and mature muscle cells of birds and mammals. In addition to an IF-typical alpha-helical core domain, type VI IF proteins are characterized by a long C-terminal tail often containing distinct repeated motifs. The molecular evolution of type VI IF proteins remains poorly studied. RESULTS: To examine the evolutionary history of type VI IF proteins, sequence comparisons, BLAST searches, synteny studies and phylogenic analyses were performed. This study provides new evidence that tanabin, transitin and nestin are indeed orthologous type VI IF proteins. It demonstrates that tanabin, transitin and nestin genes share intron positions and sequence identities, have a similar chromosomal context and display closely related positions in phylogenic analyses. Despite this homology, fast evolution rates of their C-terminal extremity have caused the appearance of repeated motifs with distinct biological activities. In particular, our in silico and in vitro analyses of their tail domain have shown that (avian) transitin, but not (mammalian) nestin, contains a repeat domain displaying nucleotide hydrolysis activity. CONCLUSION: These analyses of the evolutionary history of the IF proteins fit with a model in which type VI IFs form a branch distinct from NF proteins and are composed of two major proteins: synemin and nestin orthologs. Rapid evolution of the C-terminal extremity of nestin orthologs could be responsible for their divergent functions. [Abstract/Link to Full Text]

Ceresini PC, Shew HD, James TY, Vilgalys RJ, Cubeta MA
Phylogeography of the Solanaceae-infecting Basidiomycota fungus Rhizoctonia solani AG-3 based on sequence analysis of two nuclear DNA loci.
BMC Evol Biol. 2007;7163.
BACKGROUND: The soil fungus Rhizoctonia solani anastomosis group 3 (AG-3) is an important pathogen of cultivated plants in the family Solanaceae. Isolates of R. solani AG-3 are taxonomically related based on the composition of cellular fatty acids, phylogenetic analysis of nuclear ribosomal DNA (rDNA) and beta-tubulin gene sequences, and somatic hyphal interactions. Despite the close genetic relationship among isolates of R. solani AG-3, field populations from potato and tobacco exhibit comparative differences in their disease biology, dispersal ecology, host specialization, genetic diversity and population structure. However, little information is available on how field populations of R. solani AG-3 on potato and tobacco are shaped by population genetic processes. In this study, two field populations of R. solani AG-3 from potato in North Carolina (NC) and the Northern USA; and two field populations from tobacco in NC and Southern Brazil were examined using sequence analysis of two cloned regions of nuclear DNA (pP42F and pP89). RESULTS: Populations of R. solani AG-3 from potato were genetically diverse with a high frequency of heterozygosity, while limited or no genetic diversity was observed within the highly homozygous tobacco populations from NC and Brazil. Except for one isolate (TBR24), all NC and Brazilian isolates from tobacco shared the same alleles. No alleles were shared between potato and tobacco populations of R. solani AG-3, indicating no gene flow between them. To infer historical events that influenced current geographical patterns observed for populations of R. solani AG-3 from potato, we performed an analysis of molecular variance (AMOVA) and a nested clade analysis (NCA). Population differentiation was detected for locus pP89 (Phi ST = 0.257, significant at P < 0.05) but not for locus pP42F (Phi ST = 0.034, not significant). Results based on NCA of the pP89 locus suggest that historical restricted gene flow is a plausible explanation for the geographical association of clades. Coalescent-based simulations of genealogical relationships between populations of R. solani AG-3 from potato and tobacco were used to estimate the amount and directionality of historical migration patterns in time, and the ages of mutations of populations. Low rates of historical movement of genes were observed between the potato and tobacco populations of R. solani AG-3. CONCLUSION: The two sisters populations of the basidiomycete fungus R. solani AG-3 from potato and tobacco represent two genetically distinct and historically divergent lineages that have probably evolved within the range of their particular related Solanaceae hosts as sympatric species. [Abstract/Link to Full Text]

Bass D, Richards TA, Matthai L, Marsh V, Cavalier-Smith T
DNA evidence for global dispersal and probable endemicity of protozoa.
BMC Evol Biol. 2007 Sep 13;7(1):162.
ABSTRACT: BACKGROUND: It is much debated whether microbes are easily dispersed globally or whether they, like many macro-organisms, have historical biogeographies. The ubiquitous dispersal hypothesis states that microbes are so numerous and so easily dispersed worldwide that all should be globally distributed and found wherever growing conditions suit them. This has been broadly upheld for protists (microbial eukaryotes) by most morphological and some molecular analyses. However, morphology and most previously used evolutionary markers evolve too slowly to test this important hypothesis adequately. RESULTS: Here we use a fast-evolving marker (ITS1 rDNA) to map global diversity and distribution of three different clades of cercomonad Protozoa (Eocercomonas and Paracercomonas: phylum Cercozoa) by sequencing multiple environmental gene libraries constructed from 47-80 globally-dispersed samples per group. Even with this enhanced resolution, identical ITS sequences (ITS-types) were retrieved from widely separated sites and on all continents for several genotypes, implying relatively rapid global dispersal. Some identical ITS-types were even recovered from both marine and non-marine samples, habitats that generally harbour significantly different protist communities. Conversely, other ITS-types had either patchy or restricted distributions. CONCLUSION: Our results strongly suggest that geographic dispersal in macro-organisms and microbes is not fundamentally different: some taxa show restricted and/or patchy distributions while others are clearly cosmopolitan. These results are concordant with the 'moderate endemicity model' of microbial biogeography. Rare or continentally endemic microbes may be ecologically significant and potentially of conservational concern. We also demonstrate that strains with identical 18S but different ITS1 rDNA sequences can differ significantly in terms of morphological and important physiological characteristics, providing strong additional support for global protist biodiversity being significantly higher than previously thought. [Abstract/Link to Full Text]

Zierold T, Hanfling B, G�mez A
Recent evolution of alternative reproductive modes in the 'living fossil' Triops cancriformis.
BMC Evol Biol. 2007;7161.
BACKGROUND: The Notostraca is a small but ancient crustacean order with a contrasting combination of a conservative morphology and a wide range of reproductive modes. The tadpole shrimp Triops cancriformis, includes bisexual - the putatively ancestral state -, androdioecious and hermaphrodite populations. As hermaphroditism and androdioecy confer a colonisation advantage, we expect the postglacial colonisation of northern Europe to have been effected by lineages with such reproductive modes. Therefore, N European populations should be composed of closely related lineages reflecting a recent range expansion. In contrast, glacial refugia in the south should contain bisexual populations with high haplotype diversity and more population structuring. To test these hypotheses, we analysed the geographic distribution of reproductive modes based on new and published sex ratio data. In addition, we investigated the European phylogeography of T. cancriformis by sequencing over a 1000 bp of mitochondrial DNA (mtDNA) in individuals from a large sample of populations of the three recognised subspecies. RESULTS: Bisexual populations were only found in the Iberian Peninsula, with the rest of European populations showing low male proportions or no males. Androdioecious populations were found in Central and Eastern Europe. Regarding mtDNA diversity, Spanish and Moroccan populations of T. c. mauritanicus were highly divergent, and showed strong population structure. In contrast, Triops c. cancriformis and T. c. simplex formed a single mtDNA lineage with low haplotype diversity. This diversity was structured into two phylogenetic clades (A, B), coexisting in E Germany. Basal haplotypes of both lineages were found in the Iberian Peninsula. Most of the populations in clade A and B are either hermaphroditic or androdioecious, with the only bisexual population in these clades found in the Iberian Peninsula. The genetic divergence between these two clades suggests a split in the Late Pleistocene and their geographic distribution reflects a complex evolutionary history of European Triops populations, with possibly two episodes of range expansions - one of them by clade A - involving androdioecious and hermaphroditic populations. CONCLUSION: As we predicted, N European populations of T. cancriformis are closely related, with few widely distributed haplotypes and indications of a recent range expansion involving hermaphroditic/androdioecious lineages. A possible second range expansion or long distance colonisation may have created the secondary contact zone between T. c. cancriformis/simplex clades A and B. The large haplotype diversity and strong genetic subdivision in the Iberian Peninsula, which is known to contain only bisexual populations, strongly suggest that this area was a Pleistocene refugium for T. cancriformis, although the occurrence of additional eastern refugia cannot be ruled out. Our data support the status of T. c. mauritanicus as a separate species and the colonisation of N Africa from the Iberian Peninsula. We suggest that hermaphroditism/androdioecy has evolved recently in T. cancriformis and has facilitated the postglacial colonisation of northern Europe. [Abstract/Link to Full Text]

Ricci C, Caprioli M, Fontaneto D
Stress and fitness in parthenogens: is dormancy a key feature for bdelloid rotifers?
BMC Evol Biol. 2007;7 Suppl 2S9.
BACKGROUND: Bdelloid rotifers are the most common and abundant group of animals that reproduce by ameiotic parthenogenesis, only. They are common in temporally ephemeral habitats, and it is unclear if they dwell in unstable habitats because are excluded from better conditions by stronger competitors, or because they need unstable conditions for their success. We tested the hypothesis that bdelloids 'require' stressful conditions for their persistence by comparing fitness-related traits of stressed (desiccated, D) and unstressed (hydrated, H) lines of two species, Adineta ricciae and Macrotrachela quadricornifera. RESULTS: For both bdelloid species, fecundity was significantly lower in H than in parallel D line. Fitness components decreased with time progressively in the H line but not in the D line. Recovery rates of D lines were recorded after every desiccation and did not reveal any trend in time, suggesting that no selection was operating. CONCLUSION: Stress in the form of reiterated desiccations seemed to help both bdelloid species to keep fitness stable; in contrast under stable conditions, like permanent hydration, these bdelloid species had poorer performances. Bdelloids, although aquatic animals, are not only efficient in tolerating desiccation, but seem somehow dependent on anhydrobiosis, a circumstance that might represent a key event in their life cycle. If this is true, life in unpredictable habitats should not be seen as the result of competitive exclusion from 'easier' habitats, but a requirement for long-term survival of these parthenogenetic animals. [Abstract/Link to Full Text]

Carapelli A, Li� P, Nardi F, van der Wath E, Frati F
Phylogenetic analysis of mitochondrial protein coding genes confirms the reciprocal paraphyly of Hexapoda and Crustacea.
BMC Evol Biol. 2007;7 Suppl 2S8.
BACKGROUND: The phylogeny of Arthropoda is still a matter of harsh debate among systematists, and significant disagreement exists between morphological and molecular studies. In particular, while the taxon joining hexapods and crustaceans (the Pancrustacea) is now widely accepted among zoologists, the relationships among its basal lineages, and particularly the supposed reciprocal paraphyly of Crustacea and Hexapoda, continues to represent a challenge. Several genes, as well as different molecular markers, have been used to tackle this problem in molecular phylogenetic studies, with the mitochondrial DNA being one of the molecules of choice. In this study, we have assembled the largest data set available so far for Pancrustacea, consisting of 100 complete (or almost complete) sequences of mitochondrial genomes. After removal of unalignable sequence regions and highly rearranged genomes, we used nucleotide and inferred amino acid sequences of the 13 protein coding genes to reconstruct the phylogenetic relationships among major lineages of Pancrustacea. The analysis was performed with Bayesian inference, and for the amino acid sequences a new, Pancrustacea-specific, matrix of amino acid replacement was developed and used in this study. RESULTS: Two largely congruent trees were obtained from the analysis of nucleotide and amino acid datasets. In particular, the best tree obtained based on the new matrix of amino acid replacement (MtPan) was preferred over those obtained using previously available matrices (MtArt and MtRev) because of its higher likelihood score. The most remarkable result is the reciprocal paraphyly of Hexapoda and Crustacea, with some lineages of crustaceans (namely the Malacostraca, Cephalocarida and, possibly, the Branchiopoda) being more closely related to the Insecta s.s. (Ectognatha) than two orders of basal hexapods, Collembola and Diplura. Our results confirm that the mitochondrial genome, unlike analyses based on morphological data or nuclear genes, consistently supports the non monophyly of Hexapoda. CONCLUSION: The finding of the reciprocal paraphyly of Hexapoda and Crustacea suggests an evolutionary scenario in which the acquisition of the hexapod condition may have occurred several times independently in lineages descending from different crustacean-like ancestors, possibly as a consequence of the process of terrestrialization. If this hypothesis was confirmed, we should therefore re-think our interpretation of the evolution of the Arthropoda, where terrestrialization may have led to the acquisition of similar anatomical features by convergence. At the same time, the disagreement between reconstructions based on morphological, nuclear and mitochondrial data sets seems to remain, despite the use of larger data sets and more powerful analytical methods. [Abstract/Link to Full Text]

Passamonti M
An unusual case of gender-associated mitochondrial DNA heteroplasmy: the mytilid Musculista senhousia (Mollusca Bivalvia).
BMC Evol Biol. 2007;7 Suppl 2S7.
BACKGROUND: Doubly Uniparental Inheritance (DUI) represents the most outstanding exception to matrilinear inheritance of mitochondrial DNA (mtDNA), typical of Metazoa. In a few bivalve mollusks, two sex-linked mtDNAs (the so-called M and F) are inherited in a peculiar way: both daughters and sons receive their F from the mother, whereas sons inherit M from the father (males do not transmit F to their progeny). This realizes a double mechanism of transmission, in which M and F mtDNAs are inherited uniparentally.DUI systems represent a unique experimental model for testing the evolutionary mechanisms that apply to mitochondrial genomes and their transmission patterns as well as to mtDNA recombination. RESULTS: A new case of DUI is described in Musculista senhousia (Mollusca: Bivalvia: Mytilidae). Its heteroplasmy pattern is in line with standard DUI. Sequence variability analysis evidenced two main results: F haplotypes sequence variability is higher than that of M haplotypes, and F mitochondrial haplotypes experience a higher mutation rate in males' somatic tissues than in females' ones. Phylogenetic analysis revealed also that M. senhousia M and F haplotypes cluster separately from that of the other mytilids. CONCLUSION: Sequence variability analysis evidenced some unexpected traits. The inverted variability pattern (the F being more variable than M) was new and it challenges most of the rationales proposed to account for sex-linked mtDNA evolution. We tentatively related this to the history of the Northern Adriatic populations analyzed. Moreover, F sequences evidenced a higher mutation level in male's soma, this variability being produced de novo each generation. This suggests that mechanisms evolved to protect mtDNA in females (f.i. antioxidant gene complexes) might be under relaxed selection in males. Phylogenetic analysis of sex-linked haplotypes confirmed that they have switched their roles during the evolutionary history of mytilids, at variance to what has been observed in unionids. Consequently, reciprocal monophyly of M and F lineages got easily lost because of role-reversals and consequent losses of M lineages, as already observed in Mytilus. [Abstract/Link to Full Text]

Paffetti D, Vettori C, Caramelli D, Vernesi C, Lari M, Paganelli A, Paule L, Giannini R
Unexpected presence of Fagus orientalis complex in Italy as inferred from 45,000-year-old DNA pollen samples from Venice lagoon.
BMC Evol Biol. 2007;7 Suppl 2S6.
BACKGROUND: Phylogeographic analyses on the Western Euroasiatic Fagus taxa (F. orientalis, F. sylvatica, F. taurica and F. moesiaca) is available, however, the subdivision of Fagus spp. is unresolved and there is no consensus on the phylogeny and on the identification (both with morphological than molecular markers) of Fagus Eurasiatic taxa. For the first time molecular analyses of ancient pollen, dated at least 45,000 years ago, were used in combination with the phylogeny analysis on current species, to identify the Fagus spp. present during the Last Interglacial period in Italy. In this work we aim at testing if the trnL-trnF chloroplast DNA (cpDNA) region, that has been previously proved efficient in discriminating different Quercus taxa, can be employed in distinguishing the Fagus species and in identifying the ancient pollen. RESULTS: 86 populations from 4 Western Euroasistic taxa were sampled, and sequenced for the trnL-trnF region to verify the efficiency of this cpDNA region in identifying the Fagus spp.. Furthermore, Fagus crenata (2 populations), Fagus grandifolia (2 populations), Fagus japonica, Fagus hayatae, Quercus species and Castanea species were analysed to better resolve the phylogenetic inference. Our results show that this cpDNA region harbour some informative sites that allow to infer relationships among the species within the Fagaceae family. In particular, few specific and fixed mutations were able to discriminate and identify all the different Fagus species. Considering a short fragment of 176 base pairs within the trnL intron, 2 transversions were found able in distinguishing the F. orientalis complex taxa (F. orientalis, F. taurica and F. moesiaca) from the remaining Fagus spp. (F. sylvatica, F. japonica, F. hayataea, F. crenata and F. grandifolia). This permits to analyse this fragment also in ancient samples, where DNA is usually highly degraded. The sequences data indicate that the DNA recovered from ancient pollen belongs to the F. orientalis complex since it displays the informative sites characteristic of this complex. CONCLUSION: The ancient DNA sequences demonstrate for the first time that, in contrast to current knowledge based on palynological and macrofossil data, the F. orientalis complex was already present during the Tyrrhenian period in what is now the Venice lagoon (Italy). This is a new and important insight considering that nowadays West Europe is not the natural area of Fagus orientalis complex, and up to now nobody has hypothesized the presence during the Last Interglacial period of F. orientalis complex in Italy. [Abstract/Link to Full Text]

Sguanci L, Bagnoli F, Li� P
Modeling HIV quasispecies evolutionary dynamics.
BMC Evol Biol. 2007;7 Suppl 2S5.
BACKGROUND: During the HIV infection several quasispecies of the virus arise, which are able to use different coreceptors, in particular the CCR5 and CXCR4 coreceptors (R5 and X4 phenotypes, respectively). The switch in coreceptor usage has been correlated with a faster progression of the disease to the AIDS phase. As several pharmaceutical companies are starting large phase III trials for R5 and X4 drugs, models are needed to predict the co-evolutionary and competitive dynamics of virus strains. RESULTS: We present a model of HIV early infection which describes the dynamics of R5 quasispecies and a model of HIV late infection which describes the R5 to X4 switch. We report the following findings: after superinfection (multiple infections at different times) or coinfection (simultaneous infection by different strains), quasispecies dynamics has time scales of several months and becomes even slower at low number of CD4+ T cells. Phylogenetic inference of chemokine receptors suggests that viral mutational pathway may generate a large variety of R5 variants able to interact with chemokine receptors different from CXCR4. The decrease of CD4+ T cells, during AIDS late stage, can be described taking into account the X4-related Tumor Necrosis Factor dynamics. CONCLUSION: The results of this study bridge the gap between the within-patient and the inter-patients (i.e. world-wide) evolutionary processes during HIV infection and may represent a framework relevant for modeling vaccination and therapy. [Abstract/Link to Full Text]

Fani R, Brilli M, Fondi M, Li� P
The role of gene fusions in the evolution of metabolic pathways: the histidine biosynthesis case.
BMC Evol Biol. 2007;7 Suppl 2S4.
BACKGROUND: Histidine biosynthesis is one of the best characterized anabolic pathways. There is a large body of genetic and biochemical information available, including operon structure, gene expression, and increasingly larger sequence databases. For over forty years this pathway has been the subject of extensive studies, mainly in Escherichia coli and Salmonella enterica, in both of which details of histidine biosynthesis appear to be identical. In these two enterobacteria the pathway is unbranched, includes a number of unusual reactions, and consists of nine intermediates; his genes are arranged in a compact operon (hisGDC [NB]HAF [IE]), with three of them (hisNB, hisD and hisIE) coding for bifunctional enzymes. We performed a detailed analysis of his gene fusions in available genomes to understand the role of gene fusions in shaping this pathway. RESULTS: The analysis of HisA structures revealed that several gene elongation events are at the root of this protein family: internal duplication have been identified by structural superposition of the modules composing the TIM-barrel protein. Several his gene fusions happened in distinct taxonomic lineages; hisNB originated within gamma-proteobacteria and after its appearance it was transferred to Campylobacter species (epsilon-proteobacteria) and to some Bacteria belonging to the CFB group. The transfer involved the entire his operon. The hisIE gene fusion was found in several taxonomic lineages and our results suggest that it probably happened several times in distinct lineages. Gene fusions involving hisIE and hisD genes (HIS4) and hisH and hisF genes (HIS7) took place in the Eukarya domain; the latter has been transferred to some delta-proteobacteria. CONCLUSION: Gene duplication is the most widely known mechanism responsible for the origin and evolution of metabolic pathways; however, several other mechanisms might concur in the process of pathway assembly and gene fusion appeared to be one of the most important and common. [Abstract/Link to Full Text]

Fondi M, Brilli M, Emiliani G, Paffetti D, Fani R
The primordial metabolism: an ancestral interconnection between leucine, arginine, and lysine biosynthesis.
BMC Evol Biol. 2007;7 Suppl 2S3.
BACKGROUND: It is generally assumed that primordial cells had small genomes with simple genes coding for enzymes able to react with a wide range of chemically related substrates, interconnecting different metabolic routes. New genes coding for enzymes with a narrowed substrate specificity arose by paralogous duplication(s) of ancestral ones and evolutionary divergence. In this way new metabolic pathways were built up by primordial cells. Useful hints to disclose the origin and evolution of ancestral metabolic routes and their interconnections can be obtained by comparing sequences of enzymes involved in the same or different metabolic routes. From this viewpoint, the lysine, arginine, and leucine biosynthetic routes represent very interesting study-models. Some of the lys, arg and leu genes are paralogs; this led to the suggestion that their ancestor genes might interconnect the three pathways. The aim of this work was to trace the evolutionary pathway leading to the appearance of the extant biosynthetic routes and to try to disclose the interrelationships existing between them and other pathways in the early stages of cellular evolution. RESULTS: The comparative analysis of the genes involved in the biosynthesis of lysine, leucine, and arginine, their phylogenetic distribution and analysis revealed that the extant metabolic "grids" and their interrelationships might be the outcome of a cascade of duplication of ancestral genes that, according to the patchwork hypothesis, coded for unspecific enzymes able to react with a wide range of substrates. These genes belonged to a single common pathway in which the three biosynthetic routes were highly interconnected between them and also to methionine, threonine, and cell wall biosynthesis. A possible evolutionary model leading to the extant metabolic scenarios was also depicted. CONCLUSION: The whole body of data obtained in this work suggests that primordial cells synthesized leucine, lysine, and arginine through a single common metabolic pathway, whose genes underwent a set of duplication events, most of which can have predated the appearance of the last common universal ancestor of the three cell domains (Archaea, Bacteria, and Eucaryotes). The model proposes a relative timing for the appearance of the three routes and also suggests a possible evolutionary pathway for the assembly of bacterial cell-wall. [Abstract/Link to Full Text]

Biondi E, Branciamore S, Maurel MC, Gallori E
Montmorillonite protection of an UV-irradiated hairpin ribozyme: evolution of the RNA world in a mineral environment.
BMC Evol Biol. 2007;7 Suppl 2S2.
BACKGROUND: The hypothesis of an RNA-based origin of life, known as the "RNA world", is strongly affected by the hostile environmental conditions probably present in the early Earth. In particular, strong UV and X-ray radiations could have been a major obstacle to the formation and evolution of the first biomolecules. In 1951, J. D. Bernal first proposed that clay minerals could have served as the sites of accumulation and protection from degradation of the first biopolymers, providing the right physical setting for the evolution of more complex systems. Numerous subsequent experimental studies have reinforced this hypothesis. RESULTS: The ability of the possibly widespread prebiotic, clay mineral montmorillonite to protect the catalytic RNA molecule ADHR1 (Adenine Dependent Hairpin Ribozyme 1) from UV-induced damages was experimentally checked. In particular, the self-cleavage reaction of the ribozyme was evaluated after UV-irradiation of the molecule in the absence or presence of clay particles. Results obtained showed a three-fold retention of the self-cleavage activity of the montmorillonite-protected molecule, with respect to the same reaction performed by the ribozyme irradiated in the absence of the clay. CONCLUSION: These results provide a suggestion with which RNA, or RNA-like molecules, could have overcame the problem of protection from UV irradiation in the RNA world era, and suggest that a clay-rich environment could have favoured not only the formation of first genetic molecules, but also their evolution towards increasingly complex molecular organization. [Abstract/Link to Full Text]

Recent Articles in BMC Structural Biology

Casares S, Ab E, Eshuis H, Lopez-Mayorga O, van Nuland NA, Conejero-Lara F
The high-resolution NMR structure of the R21A Spc-SH3:P41 complex: understanding the determinants of binding affinity by comparison with Abl-SH3.
BMC Struct Biol. 2007;722.
BACKGROUND: SH3 domains are small protein modules of 60-85 amino acids that bind to short proline-rich sequences with moderate-to-low affinity and specificity. Interactions with SH3 domains play a crucial role in regulation of many cellular processes (some are related to cancer and AIDS) and have thus been interesting targets in drug design. The decapeptide APSYSPPPPP (p41) binds with relatively high affinity to the SH3 domain of the Abl tyrosine kinase (Abl-SH3), while it has a 100 times lower affinity for the alpha-spectrin SH3 domain (Spc-SH3). RESULTS: Here we present the high-resolution structure of the complex between the R21A mutant of Spc-SH3 and p41 derived from NMR data. Thermodynamic parameters of binding of p41 to both WT and R21A Spc-SH3 were measured by a combination of isothermal titration and differential scanning calorimetry. Mutation of arginine 21 to alanine in Spc-SH3 increases 3- to 4-fold the binding affinity for p41 due to elimination at the binding-site interface of the steric clash produced by the longer arginine side chain. Amide hydrogen-deuterium experiments on the free and p41-bound R21A Spc-SH3 domain indicate that binding elicits a strong reduction in the conformational flexibility of the domain. Despite the great differences in the thermodynamic magnitudes of binding, the structure of the R21A Spc-SH3:P41 complex is remarkably similar to that of the Abl-SH3:P41 complex, with only few differences in protein-ligand contacts at the specificity pocket. Using empirical methods for the prediction of binding energetics based on solvent-accessible surface area calculations, the differences in experimental energetics of binding between the two complexes could not be properly explained only on the basis of the structural differences observed between the complexes. We suggest that the experimental differences in binding energetics can be at least partially ascribed to the absence in the R21A Spc-SH3:P41 complex of several buried water molecules, which have been proposed previously to contribute largely to the highly negative enthalpy and entropy of binding in the Abl-SH3:P41 complex. CONCLUSION: Based on a deep structural and thermodynamic analysis of a low and high affinity complex of two different SH3 domains with the same ligand p41, we underline the importance of taking into account in any effective strategy of rational design of ligands, factors different from the direct protein-ligand interactions, such as the mediation of interactions by water molecules or the existence of cooperative conformational effects induced by binding. [Abstract/Link to Full Text]

Jang H, Ma B, Nussinov R
Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect.
BMC Struct Biol. 2007;721.
BACKGROUND: Protegrin-1 (PG-1) is known as a potent antibiotic peptide; it prevents infection via an attack on the membrane surface of invading microorganisms. In the membrane, the peptide forms a pore/channel through oligomerization of multiple subunits. Recent experimental and computational studies have increasingly unraveled the molecular-level mechanisms underlying the interactions of the PG-1 beta-sheet motifs with the membrane. The PG-1 dimer is important for the formation of oligomers, ordered aggregates, and for membrane damaging effects. Yet, experimentally, different dimeric behavior has been observed depending on the environment: antiparallel in the micelle environment, and parallel in the POPC bilayer. The experimental structure of the PG-1 dimer is currently unavailable. RESULTS: Although the beta-sheet structures of the PG-1 dimer are less stable in the bulk water environment, the dimer interface is retained by two intermolecular hydrogen bonds. The formation of the dimer in the water environment implies that the pathway of the dimer invasion into the membrane can originate from the bulk region. In the initial contact with the membrane, both the antiparallel and parallel beta-sheet conformations of the PG-1 dimer are well preserved at the amphipathic interface of the lipid bilayer. These beta-sheet structures illustrate the conformations of PG-1 dimer in the early stage of the membrane attack. Here we observed that the activity of PG-1 beta-sheets on the bilayer surface is strongly correlated with the dimer conformation. Our long-term goal is to provide a detailed mechanism of the membrane-disrupting effects by PG-1 beta-sheets which are able to attack the membrane and eventually assemble into the ordered aggregates. CONCLUSION: In order to understand the dimeric effects leading to membrane damage, extensive molecular dynamics (MD) simulations were performed for the beta-sheets of the PG-1 dimer in explicit water, salt, and lipid bilayers composed of POPC lipids. Here, we studied PG-1 dimers when organized into a beta-sheet motif with antiparallel and parallel beta-sheet arrangements in an NCCN packing mode. We focus on the conformations of PG-1 dimers in the lipid bilayer, and on the correlation between the conformations and the membrane disruption effects by PG-1 dimers. We investigate equilibrium structures of the PG-1 dimers in different environments in the early stage of the dimer invasion. The dimer interface of the antiparallel beta-sheets is more stable than the parallel beta-sheets, similar to the experimental observation in micelle environments. However, we only observe membrane disruption effects by the parallel beta-sheets of the PG-1 dimer. This indicates that the parallel beta-sheets interact with the lipids with the beta-sheet plane lying obliquely to the bilayer surface, increasing the surface pressure in the initial insertion into the lipid bilayer. Recent experimental observation verified that parallel PG-1 dimer is biologically more active to insert into the POPC lipid bilayer. [Abstract/Link to Full Text]

Sgraja T, Smith TK, Hunter WN
Structure, substrate recognition and reactivity of Leishmania major mevalonate kinase.
BMC Struct Biol. 2007;720.
BACKGROUND: Isoprenoid precursor synthesis via the mevalonate route in humans and pathogenic trypanosomatids is an important metabolic pathway. There is however, only limited information available on the structure and reactivity of the component enzymes in trypanosomatids. Since isoprenoid biosynthesis is essential for trypanosomatid viability and may provide new targets for therapeutic intervention it is important to characterize the pathway components. RESULTS: Putative mevalonate kinase encoding genes from Leishmania major (LmMK) and Trypanosoma brucei (TbMK) have been cloned, over-expressed in and proteins isolated from procyclic-form T. brucei. A highly sensitive radioactive assay was developed and shows ATP-dependent phosphorylation of mevalonate. Apo and (R)-mevalonate bound crystal structures of LmMK, from a bacterial expression system, have been determined to high resolution providing, for the first time, information concerning binding of mevalonate to an MK. The mevalonate binds in a deep cavity lined by highly conserved residues. His25 is key for binding and for discrimination of (R)- over (S)-mevalonate, with the main chain amide interacting with the C3 hydroxyl group of (R)-mevalonate, and the side chain contributing, together with Val202 and Thr283, to the construction of a hydrophobic binding site for the C3 methyl substituent. The C5 hydroxyl, where phosphorylation occurs, points towards catalytic residues, Lys18 and Asp155. The activity of LmMK was significantly reduced compared to MK from other species and we were unable to obtain ATP-binding data. Comparisons with the rat MK:ATP complex were used to investigate how this substrate might bind. In LmMK, helix alpha2 and the preceding polypeptide adopt a conformation, not seen in related kinase structures, impeding access to the nucleotide triphosphate binding site suggesting that a conformational rearrangement is required to allow ATP binding. CONCLUSION: Our new structural information, consistent with data on homologous enzymes allows a detailed description of how mevalonate is recognized and positioned for catalysis in MK. The mevalonate-binding site is highly conserved yet the ATP-binding site is structurally distinct in LmMK. We are unable to provide a definitive explanation for the low activity of recombinant protein isolated from a bacterial expression system compared to material isolated from procyclic-form Trypanosoma brucei. [Abstract/Link to Full Text]

Rakhmanov SV, Makeev VJ
Atomic hydration potentials using a Monte Carlo Reference State (MCRS) for protein solvation modeling.
BMC Struct Biol. 2007;719.
BACKGROUND: Accurate description of protein interaction with aqueous solvent is crucial for modeling of protein folding, protein-protein interaction, and drug design. Efforts to build a working description of solvation, both by continuous models and by molecular dynamics, yield controversial results. Specifically constructed knowledge-based potentials appear to be promising for accounting for the solvation at the molecular level, yet have not been used for this purpose. RESULTS: We developed original knowledge-based potentials to study protein hydration at the level of atom contacts. The potentials were obtained using a new Monte Carlo reference state (MCRS), which simulates the expected probability density of atom-atom contacts via exhaustive sampling of structure space with random probes. Using the MCRS allowed us to calculate the expected atom contact densities with high resolution over a broad distance range including very short distances. Knowledge-based potentials for hydration of protein atoms of different types were obtained based on frequencies of their contacts at different distances with protein-bound water molecules, in a non-redundant training data base of 1776 proteins with known 3D structures. Protein hydration sites were predicted in a test set of 12 proteins with experimentally determined water locations. The MCRS greatly improves prediction of water locations over existing methods. In addition, the contribution of the energy of macromolecular solvation into total folding free energy was estimated, and tested in fold recognition experiments. The correct folds were preferred over all the misfolded decoys for the majority of proteins from the improved Rosetta decoy set based on the structure hydration energy alone. CONCLUSION: MCRS atomic hydration potentials provide a detailed distance-dependent description of hydropathies of individual protein atoms. This allows placement of water molecules on the surface of proteins and in protein interfaces with much higher precision. The potentials provide a means to estimate the total solvation energy for a protein structure, in many cases achieving a successful fold recognition. Possible applications of atomic hydration potentials to structure verification, protein folding and stability, and protein-protein interactions are discussed. [Abstract/Link to Full Text]

Greaves RB, Warwicker J
Mechanisms for stabilisation and the maintenance of solubility in proteins from thermophiles.
BMC Struct Biol. 2007;718.
BACKGROUND: The database of protein structures contains representatives from organisms with a range of growth temperatures. Various properties have been studied in a search for the molecular basis of protein adaptation to higher growth temperature. Charged groups have emerged as key distinguishing factors for proteins from thermophiles and mesophiles. RESULTS: A dataset of 291 thermophile-derived protein structures is compared with mesophile proteins. Calculations of electrostatic interactions support the importance of charges, but indicate that increases in charge contribution to folded state stabilisation do not generally correlate with the numbers of charged groups. Relative propensities of charged groups vary, such as the substitution of glutamic for aspartic acid sidechains. Calculations suggest an energetic basis, with less dehydration for longer sidechains. Most other properties studied show weak or insignificant separation of proteins from moderate thermophiles or hyperthermophiles and mesophiles, including an estimate of the difference in sidechain rotameric entropy upon protein folding. An exception is increased burial of alanine and proline residues and decreased burial of phenylalanine, methionine, tyrosine and tryptophan in hyperthermophile proteins compared to those from mesophiles. CONCLUSION: Since an increase in the number of charged groups for hyperthermophile proteins is separable from charged group contribution to folded state stability, we hypothesise that charged group propensity is important in the context of protein solubility and the prevention of aggregation. Accordingly we find some separation between mesophile and hyperthermophile proteins when looking at the largest surface patch that does not contain a charged sidechain. With regard to our observation that aromatic sidechains are less buried in hyperthermophile proteins, further analysis indicates that the placement of some of these groups may facilitate the reduction of folding fluctuations in proteins of the higher growth temperature organisms. [Abstract/Link to Full Text]

Alva V, Ammelburg M, S�ding J, Lupas AN
On the origin of the histone fold.
BMC Struct Biol. 2007;717.
BACKGROUND: Histones organize the genomic DNA of eukaryotes into chromatin. The four core histone subunits consist of two consecutive helix-strand-helix motifs and are interleaved into heterodimers with a unique fold. We have searched for the evolutionary origin of this fold using sequence and structure comparisons, based on the hypothesis that folded proteins evolved by combination of an ancestral set of peptides, the antecedent domain segments. RESULTS: Our results suggest that an antecedent domain segment, corresponding to one helix-strand-helix motif, gave rise divergently to the N-terminal substrate recognition domain of Clp/Hsp100 proteins and to the helical part of the extended ATPase domain found in AAA+ proteins. The histone fold arose subsequently from the latter through a 3D domain-swapping event. To our knowledge, this is the first example of a genetically fixed 3D domain swap that led to the emergence of a protein family with novel properties, establishing domain swapping as a mechanism for protein evolution. CONCLUSION: The helix-strand-helix motif common to these three folds provides support for our theory of an 'ancient peptide world' by demonstrating how an ancestral fragment can give rise to 3 different folds. [Abstract/Link to Full Text]

Li L, Gao HW, Ren JR, Chen L, Li YC, Zhao JF, Zhao HP, Yuan Y
Binding of Sudan II and IV to lecithin liposomes and E. coli membranes: insights into the toxicity of hydrophobic azo dyes.
BMC Struct Biol. 2007;716.
BACKGROUND: Sudan red compounds are hydrophobic azo dyes, still used as food additives in some countries. However, they have been shown to be unsafe, causing tumors in the liver and urinary bladder in rats. They have been classified as category 3 human carcinogens by the International Agency for Research on Cancer. A number of hypotheses that could explain the mechanism of carcinogenesis have been proposed for dyes similar to the Sudan red compounds. Traditionally, investigations of the membrane toxicity of organic substances have focused on hydrocarbons, e.g. polycyclic aromatic hydrocarbons (PAHs), and DDT. In contrast to hydrocarbons, Sudan red compounds contain azo and hydroxy groups, which can form hydrogen bonds with the polar head groups of membrane phospholipids. Thus, entry may be impeded. They could have different toxicities from other lipophilic hydrocarbons. The available data show that because these compounds are lipophilic, interactions with hydrophobic parts of the cell are important for their toxicity. Lipophilic compounds accumulate in the membrane, causing expansion of the membrane surface area, inhibition of primary ion pumps and increased proton permeability. RESULTS: This work investigated the interactions of the amphiphilic compounds Sudan II and IV with lecithin liposomes and live Escherichia coli (E. coli). Sudan II and IV binding to lecithin liposomes and live E. coli corresponds to the Langmuir adsorption isotherm. In the Sudan red compounds--lecithin liposome solutions, the binding ratio of Sudan II to lecithin is 1/31 and that of Sudan IV to 1/314. The binding constant of the Sudan II-lecithin complex is 1.75 x 104 and that of the Sudan IV-lecithin complex 2.92 x 105. Besides, the influences of pH, electrolyte and temperature were investigated and analyzed quantitatively. In the Sudan red compounds--E.coli mixture, the binding ratios of Sudan II and Sudan IV to E.coli membrane phospholipid are 1/29 and 1/114. The binding constants of the Sudan II--and Sudan IV- E.coli membrane phospholipid complexes are 1.86 x 104 and 6.02 x 104. Over 60% of Sudan II and 75% of Sudan IV penetrated into E.coli, in which 90% of them remained in the E.coli membrane. CONCLUSION: Experiments of Sudan II and IV binding to lecithin liposomes and live E. coli indicates that amphiphilic compounds may be sequestered in the lecithin liposomes and membrane phospholipid bilayer according to the Langmuir adsorption law. Penetration into the cytosol was impeded and inhibited for Sudan red compounds. It is possible for such compounds themselves (excluding their metabolites and by-products)not result directly in terminal toxicity. Therefore, membrane toxicity could be manifested as membrane blocking and membrane expansion. The method established here may be useful for evaluating the interaction of toxins with membranes. [Abstract/Link to Full Text]

Fogolari F, Pieri L, Dovier A, Bortolussi L, Giugliarelli G, Corazza A, Esposito G, Viglino P
Scoring predictive models using a reduced representation of proteins: model and energy definition.
BMC Struct Biol. 2007;715.
BACKGROUND: Reduced representations of proteins have been playing a keyrole in the study of protein folding. Many such models are available, with different representation detail. Although the usefulness of many such models for structural bioinformatics applications has been demonstrated in recent years, there are few intermediate resolution models endowed with an energy model capable, for instance, of detecting native or native-like structures among decoy sets. The aim of the present work is to provide a discrete empirical potential for a reduced protein model termed here PC2CA, because it employs a PseudoCovalent structure with only 2 Centers of interactions per Amino acid, suitable for protein model quality assessment. RESULTS: All protein structures in the set top500H have been converted in reduced form. The distribution of pseudobonds, pseudoangle, pseudodihedrals and distances between centers of interactions have been converted into potentials of mean force. A suitable reference distribution has been defined for non-bonded interactions which takes into account excluded volume effects and protein finite size. The correlation between adjacent main chain pseudodihedrals has been converted in an additional energetic term which is able to account for cooperative effects in secondary structure elements. Local energy surface exploration is performed in order to increase the robustness of the energy function. CONCLUSION: The model and the energy definition proposed have been tested on all the multiple decoys' sets in the Decoys'R'us database. The energetic model is able to recognize, for almost all sets, native-like structures (RMSD less than 2.0 A). These results and those obtained in the blind CASP7 quality assessment experiment suggest that the model compares well with scoring potentials with finer granularity and could be useful for fast exploration of conformational space. Parameters are available at the url: http://www.dstb.uniud.it/~ffogolari/download/. [Abstract/Link to Full Text]

Guvench O, Qu CK, MacKerell AD
Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft.
BMC Struct Biol. 2007;714.
BACKGROUND: The N-terminal SH2 domain (N-SH2) of the non-receptor tyrosine phosphatase SHP-2 is involved both in localization of SHP-2 by recognition of phosphotyrosine (pY) peptides and self-inhibition of SHP-2 phosphatase activity through the formation of a protein-protein interface with the phosphatase domain. Mutations that disrupt this interface break the coupling between pY-peptide binding cleft conformation and self-inhibition, thereby increasing both SHP-2 phosphatase activity and pY-peptide binding affinity, and are associated with the congenital condition Noonan syndrome and various pediatric leukemias. To better characterize the molecular process involved in N-SH2 pY-dependent binding, we have applied explicit-solvent molecular dynamics simulations to study the closed-to-open transition of the N-SH2 pY-peptide binding cleft. RESULTS: The existence of stable conformations in the left-handed helical and the extended regions of Tyr66 phi/psi space prevent rapid interconversion of the backbone and create a conformational switch such that Tyr66 in a left-handed helical backbone conformation results in an open cleft and in an extended backbone conformation results in a closed cleft. The stable conformations arise from deep, well-localized free-energy minima in the left-handed helical and extended regions of the Tyr66 phi/psi map. Changing the Tyr66 backbone conformation from extended to left-handed helical induces a closed-to-open transition in the cleft, and the reverse change in backbone conformation induces the reverse, open-to-closed transition. In the open-cleft state, weak solvent-exposed interactions involving the sidechains of Tyr66, Asp40, Lys55, and Gln57 serve to anchor the Tyr66 sidechain to the surface of the protein and away from the binding cleft entrance, thereby facilitating pY-peptide access to the binding cleft. CONCLUSION: The simulations point to a regulatory role for Tyr66 and surrounding residues in SHP-2 function: mutations at Tyr66, Asp40, Lys55, and/or Gln57 are predicted to break the switching mechanism and negatively impact pY-peptide binding. This in turn would interfere with cellular localization and the coupled SHP-2 phosphatase activity. The structurally well-defined binding cleft conformations resulting from the switch-like transition suggest the possibility of applying structure-based methods to develop inhibitors of N-SH2 pY-peptide binding to serve as research tools for signal transduction and precursors to therapeutics for SHP-2-related diseases. [Abstract/Link to Full Text]

Gore SP, Karmali AM, Blundell TL
Rappertk: a versatile engine for discrete restraint-based conformational sampling of macromolecules.
BMC Struct Biol. 2007;713.
BACKGROUND: Macromolecular structures are modeled by conformational optimization within experimental and knowledge-based restraints. Discrete restraint-based sampling generates high-quality structures within these restraints and facilitates further refinement in a continuous all-atom energy landscape. This approach has been used successfully for protein loop modeling, comparative modeling and electron density fitting in X-ray crystallography. RESULTS: Here we present a software toolkit (Rappertk) which generalizes discrete restraint-based sampling for use in structural biology. Modular design and multi-layered architecture enables Rappertk to sample conformations of any macromolecule at many levels of detail and within a variety of experimental restraints. Performance against a Calpha-tracing benchmark shows that the efficiency has not suffered despite the overhead required by this flexibility. We demonstrate the toolkit's capabilities by building high-quality beta-sheets and by introducing restraint-driven sampling. RNA sampling is demonstrated by rebuilding a protein-RNA interface. Ability to construct arbitrary ligands is used in sampling protein-ligand interfaces within electron density. Finally, secondary structure and shape information derived from EM are combined to generate multiple conformations of a protein consistent with the observed density. CONCLUSION: Through its modular design and ease of use, Rappertk enables exploration of a wide variety of interesting avenues in structural biology. This toolkit, with illustrative examples, is freely available to academic users from http://www-cryst.bioc.cam.ac.uk/~swanand/mysite/rtk/index.html. [Abstract/Link to Full Text]

Verma A, Wenzel W
Protein structure prediction by all-atom free-energy refinement.
BMC Struct Biol. 2007;712.
BACKGROUND: The reliable prediction of protein tertiary structure from the amino acid sequence remains challenging even for small proteins. We have developed an all-atom free-energy protein forcefield (PFF01) that we could use to fold several small proteins from completely extended conformations. Because the computational cost of de-novo folding studies rises steeply with system size, this approach is unsuitable for structure prediction purposes. We therefore investigate here a low-cost free-energy relaxation protocol for protein structure prediction that combines heuristic methods for model generation with all-atom free-energy relaxation in PFF01. RESULTS: We use PFF01 to rank and cluster the conformations for 32 proteins generated by ROSETTA. For 22/10 high-quality/low quality decoy sets we select near-native conformations with an average Calpha root mean square deviation of 3.03 A/6.04 A. The protocol incorporates an inherent reliability indicator that succeeds for 78% of the decoy sets. In over 90% of these cases near-native conformations are selected from the decoy set. This success rate is rationalized by the quality of the decoys and the selectivity of the PFF01 forcefield, which ranks near-native conformations an average 3.06 standard deviations below that of the relaxed decoys (Z-score). CONCLUSION: All-atom free-energy relaxation with PFF01 emerges as a powerful low-cost approach toward generic de-novo protein structure prediction. The approach can be applied to large all-atom decoy sets of any origin and requires no preexisting structural information to identify the native conformation. The study provides evidence that a large class of proteins may be foldable by PFF01. [Abstract/Link to Full Text]

Gonin S, Arnoux P, Pierru B, Lavergne J, Alonso B, Sabaty M, Pignol D
Crystal structures of an Extracytoplasmic Solute Receptor from a TRAP transporter in its open and closed forms reveal a helix-swapped dimer requiring a cation for alpha-keto acid binding.
BMC Struct Biol. 2007;711.
BACKGROUND: The import of solutes into the bacterial cytoplasm involves several types of membrane transporters, which may be driven by ATP hydrolysis (ABC transporters) or by an ion or H+ electrochemical membrane potential, as in the tripartite ATP-independent periplasmic system (TRAP). In both the ABC and TRAP systems, a specific periplasmic protein from the ESR family (Extracytoplasmic Solute Receptors) is often involved for the recruitment of the solute and its presentation to the membrane complex. In Rhodobacter sphaeroides, TakP (previously named SmoM) is an ESR from a TRAP transporter and binds alpha-keto acids in vitro. RESULTS: We describe the high-resolution crystal structures of TakP in its unliganded form and as a complex with sodium-pyruvate. The results show a limited "Venus flytrap" conformational change induced by substrate binding. In the liganded structure, a cation (most probably a sodium ion) is present and plays a key role in the association of the pyruvate to the protein. The structure of the binding pocket gives a rationale for the relative affinities of various ligands that were tested from a fluorescence assay. The protein appears to be dimeric in solution and in the crystals, with a helix-swapping structure largely participating in the dimer formation. A 30 A-long water channel buried at the dimer interface connects the two ligand binding cavities of the dimer. CONCLUSION: The concerted recruitment by TakP of the substrate group with a cation could represent a first step in the coupled transport of both partners, providing the driving force for solute import. Furthermore, the unexpected dimeric structure of TakP suggests a molecular mechanism of solute uptake by the dimeric ESR via a channel that connects the binding sites of the two monomers. [Abstract/Link to Full Text]

Ferraro DJ, Brown EN, Yu CL, Parales RE, Gibson DT, Ramaswamy S
Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1.
BMC Struct Biol. 2007;710.
BACKGROUND: The initial step involved in oxidative hydroxylation of monoaromatic and polyaromatic compounds by the microorganism Sphingobium yanoikuyae strain B1 (B1), previously known as Sphingomonas yanoikuyae strain B1 and Beijerinckia sp. strain B1, is performed by a set of multiple terminal Rieske non-heme iron oxygenases. These enzymes share a single electron donor system consisting of a reductase and a ferredoxin (BPDO-FB1). One of the terminal Rieske oxygenases, biphenyl 2,3-dioxygenase (BPDO-OB1), is responsible for B1's ability to dihydroxylate large aromatic compounds, such as chrysene and benzo[a]pyrene. RESULTS: In this study, crystal structures of BPDO-OB1 in both native and biphenyl bound forms are described. Sequence and structural comparisons to other Rieske oxygenases show this enzyme to be most similar, with 43.5 % sequence identity, to naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4. While structurally similar to naphthalene 1,2-dioxygenase, the active site entrance is significantly larger than the entrance for naphthalene 1,2-dioxygenase. Differences in active site residues also allow the binding of large aromatic substrates. There are no major structural changes observed upon binding of the substrate. BPDO-FB1 has large sequence identity to other bacterial Rieske ferredoxins whose structures are known and demonstrates a high structural homology; however, differences in side chain composition and conformation around the Rieske cluster binding site are noted. CONCLUSION: This is the first structure of a Rieske oxygenase that oxidizes substrates with five aromatic rings to be reported. This ability to catalyze the oxidation of larger substrates is a result of both a larger entrance to the active site as well as the ability of the active site to accommodate larger substrates. While the biphenyl ferredoxin is structurally similar to other Rieske ferredoxins, there are distinct changes in the amino acids near the iron-sulfur cluster. Because this ferredoxin is used by multiple oxygenases present in the B1 organism, this ferredoxin-oxygenase system provides the structural platform to dissect the balance between promiscuity and selectivity in protein-protein electron transport systems. [Abstract/Link to Full Text]

Costantini S, Facchiano AM, Colonna G
Evaluation of the structural quality of modeled proteins by using globularity criteria.
BMC Struct Biol. 2007;79.
BACKGROUND: The knowledge of the three-dimensional structure of globular proteins is fundamental for a detailed investigation of their functional properties. Experimental methods are too slow for structure investigation on a large scale, while computational prediction methods offer alternatives that are continuously being improved. The international Comparative Assessment of Structure Prediction (CASP), an "a posteriori" evaluation of the quality of theoretical models when the experimental structure becomes available, demonstrates that predictions can be successful as well as unsuccessful, and this suggests the necessity for evaluations able to discard "a priori" the wrong models. RESULTS: We analyzed different structural properties of globular proteins for experimentally solved proteins belonging to the four different structural classes: "mainly alpha", "mainly beta", "alpha/beta" and "alpha+beta". The properties were found to be linearly correlated to protein molecular weight, but with some differences among the four classes. These results were applied to develop an evaluation test of theoretical models based on the expected globular properties of proteins. To verify the success of our test, we applied it to several protein models submitted to the sixth edition of CASP. The best theoretical models, as judged by CASP assessors, were in agreement with the expected properties, while most of the low-quality models had not passed our evaluations. CONCLUSION: This study supports the need for careful checks to avoid the diffusion of incorrect structural models. Our test allows the evaluation of models in the absence of experimental reference structures, thereby preventing the diffusion of incorrect structural models and the formulation of incorrect functional hypotheses. It can be used to check the globularity of predicted models, and to supplement other methods already used to evaluate their quality. [Abstract/Link to Full Text]

Hyt�nen VP, M��tt� JA, Niskanen EA, Huuskonen J, Helttunen KJ, Halling KK, Nordlund HR, Rissanen K, Johnson MS, Salminen TA, Kulomaa MS, Laitinen OH, Airenne TT
Structure and characterization of a novel chicken biotin-binding protein A (BBP-A).
BMC Struct Biol. 2007;78.
BACKGROUND: The chicken genome contains a BBP-A gene showing similar characteristics to avidin family genes. In a previous study we reported that the BBP-A gene may encode a biotin-binding protein due to the high sequence similarity with chicken avidin, especially at regions encoding residues known to be located at the ligand-binding site of avidin. RESULTS: Here, we expand the repertoire of known macromolecular biotin binders by reporting a novel biotin-binding protein A (BBP-A) from chicken. The BBP-A recombinant protein was expressed using two different expression systems and purified with affinity chromatography, biochemically characterized and two X-ray structures were solved - in complex with D-biotin (BTN) and in complex with D-biotin D-sulfoxide (BSO). The BBP-A protein binds free biotin with high, "streptavidin-like" affinity (Kd ~ 10-13 M), which is about 50 times lower than that of chicken avidin. Surprisingly, the affinity of BBP-A for BSO is even higher than the affinity for BTN. Furthermore, the solved structures of the BBP-A--BTN and BBP-A--BSO complexes, which share the fold with the members of the avidin and lipocalin protein families, are extremely similar to each other. CONCLUSION: BBP-A is an avidin-like protein having a beta-barrel fold and high affinity towards BTN. However, BBP-A differs from the other known members of the avidin protein family in thermal stability and immunological properties. BBP-A also has a unique ligand-binding property, the ability to bind BTN and BSO at comparable affinities. BBP-A may have use as a novel material in, e.g. modern bio(nano)technological applications. [Abstract/Link to Full Text]

Wang Y, Schlick T
Distinct energetics and closing pathways for DNA polymerase beta with 8-oxoG template and different incoming nucleotides.
BMC Struct Biol. 2007;77.
BACKGROUND: 8-Oxoguanine (8-oxoG) is a common oxidative lesion frequently encountered by DNA polymerases such as the repair enzyme DNA polymerase beta (pol beta). To interpret in atomic and energetic detail how pol beta processes 8-oxoG, we apply transition path sampling to delineate closing pathways of pol beta 8-oxoG complexes with dCTP and dATP incoming nucleotides and compare the results to those of the nonlesioned G:dCTP and G:dATPanalogues. RESULTS: Our analyses show that the closing pathways of the 8-oxoG complexes are different from one another and from the nonlesioned analogues in terms of the individual transition states along each pathway, associated energies, and the stability of each pathway's closed state relative to the corresponding open state. In particular, the closed-to-open state stability difference in each system establishes a hierarchy of stability (from high to low) as G:C > 8-oxoG:C > 8-oxoG:A > G:A, corresponding to -3, -2, 2, 9 kBT, respectively. This hierarchy of closed state stability parallels the experimentally observed processing efficiencies for the four pairs. Network models based on the calculated rate constants in each pathway indicate that the closed species are more populated than the open species for 8-oxoG:dCTP, whereas the opposite is true for 8-oxoG:dATP. CONCLUSION: These results suggest that the lower insertion efficiency (larger Km) for dATP compared to dCTP opposite 8-oxoG is caused by a less stable closed-form of pol beta, destabilized by unfavorable interactions between Tyr271 and the mispair. This stability of the closed vs. open form can also explain the higher insertion efficiency for 8-oxoG:dATP compared to the nonlesioned G:dATP pair, which also has a higher overall conformational barrier. Our study offers atomic details of the complexes at different states, in addition to helping interpret the different insertion efficiencies of dATP and dCTP opposite 8-oxoG and G. [Abstract/Link to Full Text]

Weber D, Kotzsch A, Nickel J, Harth S, Seher A, Mueller U, Sebald W, Mueller TD
A silent H-bond can be mutationally activated for high-affinity interaction of BMP-2 and activin type IIB receptor.
BMC Struct Biol. 2007;76.
BACKGROUND: Bone morphogenetic proteins (BMPs) are key regulators in the embryonic development and postnatal tissue homeostasis in all animals. Loss of function or dysregulation of BMPs results in severe diseases or even lethality. Like transforming growth factors beta (TGF-betas), activins, growth and differentiation factors (GDFs) and other members of the TGF-beta superfamily, BMPs signal by assembling two types of serine/threonine-kinase receptor chains to form a hetero-oligomeric ligand-receptor complex. BMP ligand receptor interaction is highly promiscuous, i.e. BMPs bind more than one receptor of each subtype, and a receptor bind various ligands. The activin type II receptors are of particular interest, since they bind a large number of diverse ligands. In addition they act as high-affinity receptors for activins but are also low-affinity receptors for BMPs. ActR-II and ActR-IIB therefore represent an interesting example how affinity and specificity might be generated in a promiscuous background. RESULTS: Here we present the high-resolution structures of the ternary complexes of wildtype and a variant BMP-2 bound to its high-affinity type I receptor BMPR-IA and its low-affinity type II receptor ActR-IIB and compare them with the known structures of binary and ternary ligand-receptor complexes of BMP-2. In contrast to activin or TGF-beta3 no changes in the dimer architecture of the BMP-2 ligand occur upon complex formation. Functional analysis of the ActR-IIB binding epitope shows that hydrophobic interactions dominate in low-affinity binding of BMPs; polar interactions contribute only little to binding affinity. However, a conserved H-bond in the center of the type II ligand-receptor interface, which does not contribute to binding in the BMP-2 - ActR-IIB interaction can be mutationally activated resulting in a BMP-2 variant with high-affinity for ActR-IIB. Further mutagenesis studies were performed to elucidate the binding mechanism allowing us to construct BMP-2 variants with defined type II receptor binding properties. CONCLUSION: Binding specificity of BMP-2 for its three type II receptors BMPR-II, Act-RII and ActR-IIB is encoded on single amino acid level. Exchange of only one or two residues results in BMP-2 variants with a dramatically altered type II receptor specificity profile, possibly allowing construction of BMP-2 variants that address a single type II receptor. The structure-/function studies presented here revealed a new mechanism, in which the energy contribution of a conserved H-bond is modulated by surrounding intramolecular interactions to achieve a switch between low- and high-affinity binding. [Abstract/Link to Full Text]

Bruhova I, Zhorov BS
Monte Carlo-energy minimization of correolide in the Kv1.3 channel: possible role of potassium ion in ligand-receptor interactions.
BMC Struct Biol. 2007;75.
BACKGROUND: Correolide, a nortriterpene isolated from the Costa Rican tree Spachea correa, is a novel immunosuppressant, which blocks Kv1.3 channels in human T lymphocytes. Earlier mutational studies suggest that correolide binds in the channel pore. Correolide has several nucleophilic groups, but the pore-lining helices in Kv1.3 are predominantly hydrophobic raising questions about the nature of correolide-channel interactions. RESULTS: We employed the method of Monte Carlo (MC) with energy minimization to search for optimal complexes of correolide in Kv1.2-based models of the open Kv1.3 with potassium binding sites 2/4 or 1/3/5 loaded with K+ ions. The energy was MC-minimized from many randomly generated starting positions and orientations of the ligand. In all the predicted low-energy complexes, oxygen atoms of correolide chelate a K+ ion. Correolide-sensing residues known from mutational analysis along with the ligand-bound K+ ion provide major contributions to the ligand-binding energy. Deficiency of K+ ions in the selectivity filter of C-type inactivated Kv1.3 would stabilize K+-bound correolide in the inner pore. CONCLUSION: Our study explains the paradox that cationic and nucleophilic ligands bind to the same region in the inner pore of K+ channels and suggests that a K+ ion is an important determinant of the correolide receptor and possibly receptors of other nucleophilic blockers of the inner pore of K+ channels. [Abstract/Link to Full Text]

Spyrakis F, Cozzini P, Bertoli C, Marabotti A, Kellogg GE, Mozzarelli A
Energetics of the protein-DNA-water interaction.
BMC Struct Biol. 2007;74.
BACKGROUND: To understand the energetics of the interaction between protein and DNA we analyzed 39 crystallographically characterized complexes with the HINT (Hydropathic INTeractions) computational model. HINT is an empirical free energy force field based on solvent partitioning of small molecules between water and 1-octanol. Our previous studies on protein-ligand complexes demonstrated that free energy predictions were significantly improved by taking into account the energetic contribution of water molecules that form at least one hydrogen bond with each interacting species. RESULTS: An initial correlation between the calculated HINT scores and the experimentally determined binding free energies in the protein-DNA system exhibited a relatively poor r2 of 0.21 and standard error of +/- 1.71 kcal mol-1. However, the inclusion of 261 waters that bridge protein and DNA improved the HINT score-free energy correlation to an r2 of 0.56 and standard error of +/- 1.28 kcal mol-1. Analysis of the water role and energy contributions indicate that 46% of the bridging waters act as linkers between amino acids and nucleotide bases at the protein-DNA interface, while the remaining 54% are largely involved in screening unfavorable electrostatic contacts. CONCLUSION: This study quantifies the key energetic role of bridging waters in protein-DNA associations. In addition, the relevant role of hydrophobic interactions and entropy in driving protein-DNA association is indicated by analyses of interaction character showing that, together, the favorable polar and unfavorable polar/hydrophobic-polar interactions (i.e., desolvation) mostly cancel. [Abstract/Link to Full Text]

Sitbon E, Pietrokovski S
Occurrence of protein structure elements in conserved sequence regions.
BMC Struct Biol. 2007;73.
BACKGROUND: Conserved protein sequence regions are extremely useful for identifying and studying functionally and structurally important regions. By means of an integrated analysis of large-scale protein structure and sequence data, structural features of conserved protein sequence regions were identified. RESULTS: Helices and turns were found to be underrepresented in conserved regions, while strands were found to be overrepresented. Similar numbers of loops were found in conserved and random regions. CONCLUSION: These results can be understood in light of the structural constraints on different secondary structure elements, and their role in protein structural stabilization and topology. Strands can tolerate fewer sequence changes and nonetheless keep their specific shape and function. They thus tend to be more conserved than helices, which can keep their shape and function with more changes. Loop behavior can be explained by the presence of both constrained and freely changing loops in proteins. Our detailed statistical analysis of diverse proteins links protein evolution to the biophysics of protein thermodynamic stability and folding. The basic structural features of conserved sequence regions are also important determinants of protein structure motifs and their function. [Abstract/Link to Full Text]

Eudes R, Le Tuan K, Delettr� J, Mornon JP, Callebaut I
A generalized analysis of hydrophobic and loop clusters within globular protein sequences.
BMC Struct Biol. 2007;72.
BACKGROUND: Hydrophobic Cluster Analysis (HCA) is an efficient way to compare highly divergent sequences through the implicit secondary structure information directly derived from hydrophobic clusters. However, its efficiency and application are currently limited by the need of user expertise. In order to help the analysis of HCA plots, we report here the structural preferences of hydrophobic cluster species, which are frequently encountered in globular domains of proteins. These species are characterized only by their hydrophobic/non-hydrophobic dichotomy. This analysis has been extended to loop-forming clusters, using an appropriate loop alphabet. RESULTS: The structural behavior of hydrophobic cluster species, which are typical of protein globular domains, was investigated within banks of experimental structures, considered at different levels of sequence redundancy. The 294 more frequent hydrophobic cluster species were analyzed with regard to their association with the different secondary structures (frequencies of association with secondary structures and secondary structure propensities). Hydrophobic cluster species are predominantly associated with regular secondary structures, and a large part (60 %) reveals preferences for alpha-helices or beta-strands. Moreover, the analysis of the hydrophobic cluster amino acid composition generally allows for finer prediction of the regular secondary structure associated with the considered cluster within a cluster species. We also investigated the behavior of loop forming clusters, using a "PGDNS" alphabet. These loop clusters do not overlap with hydrophobic clusters and are highly associated with coils. Finally, the structural information contained in the hydrophobic structural words, as deduced from experimental structures, was compared to the PSI-PRED predictions, revealing that beta-strands and especially alpha-helices are generally over-predicted within the limits of typical beta and alpha hydrophobic clusters. CONCLUSION: The dictionary of hydrophobic clusters described here can help the HCA user to interpret and compare the HCA plots of globular protein sequences, as well as provides an original fundamental insight into the structural bricks of protein folds. Moreover, the novel loop cluster analysis brings additional information for secondary structure prediction on the whole sequence through a generalized cluster analysis (GCA), and not only on regular secondary structures. Such information lays the foundations for developing a new and original tool for secondary structure prediction. [Abstract/Link to Full Text]

Malik A, Ahmad S
Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network.
BMC Struct Biol. 2007;71.
BACKGROUND: Protein-Carbohydrate interactions are crucial in many biological processes with implications to drug targeting and gene expression. Nature of protein-carbohydrate interactions may be studied at individual residue level by analyzing local sequence and structure environments in binding regions in comparison to non-binding regions, which provide an inherent control for such analyses. With an ultimate aim of predicting binding sites from sequence and structure, overall statistics of binding regions needs to be compiled. Sequence-based predictions of binding sites have been successfully applied to DNA-binding proteins in our earlier works. We aim to apply similar analysis to carbohydrate binding proteins. However, due to a relatively much smaller region of proteins taking part in such interactions, the methodology and results are significantly different. A comparison of protein-carbohydrate complexes has also been made with other protein-ligand complexes. RESULTS: We have compiled statistics of amino acid compositions in binding versus non-binding regions- general as well as in each different secondary structure conformation. Binding propensities of each of the 20 residue types and their structure features such as solvent accessibility, packing density and secondary structure have been calculated to assess their predisposition to carbohydrate interactions. Finally, evolutionary profiles of amino acid sequences have been used to predict binding sites using a neural network. Another set of neural networks was trained using information from single sequences and the prediction performance from the evolutionary profiles and single sequences were compared. Best of the neural network based prediction could achieve an 87% sensitivity of prediction at 23% specificity for all carbohydrate-binding sites, using evolutionary information. Single sequences gave 68% sensitivity and 55% specificity for the same data set. Sensitivity and specificity for a limited galactose binding data set were obtained as 63% and 79% respectively for evolutionary information and 62% and 68% sensitivity and specificity for single sequences. Propensity and other sequence and structural features of carbohydrate binding sites have also been compared with our similar extensive studies on DNA-binding proteins and also with protein-ligand complexes. CONCLUSION: Carbohydrates typically show a preference to bind aromatic residues and most prominently tryptophan. Higher exposed surface area of binding sites indicates a role of hydrophobic interactions. Neural networks give a moderate success of prediction, which is expected to improve when structures of more protein-carbohydrate complexes become available in future. [Abstract/Link to Full Text]

Saikatendu KS, Zhang X, Kinch L, Leybourne M, Grishin NV, Zhang H
Structure of a conserved hypothetical protein SA1388 from S. aureus reveals a capped hexameric toroid with two PII domain lids and a dinuclear metal center.
BMC Struct Biol. 2006;627.
BACKGROUND: The protein encoded by the SA1388 gene from Staphylococcus aureus was chosen for structure determination to elucidate its domain organization and confirm our earlier remote homology based prediction that it housed a nitrogen regulatory PII protein-like domain. SA1388 was predicted to contain a central PII-like domain and two flanking regions, which together belong to the NIF3-like protein family. Proteins like SA1388 remain a poorly studied group and their structural characterization could guide future investigations aimed at understanding their function. RESULTS: The structure of SA1388 has been solved to 2.0A resolution by single wavelength anomalous dispersion phasing method using selenium anomalous signals. It reveals a canonical NIF3-like fold containing two domains with a PII-like domain inserted in the middle of the polypeptide. The N and C terminal halves of the NIF3-like domains are involved in dimerization, while the PII domain forms trimeric contacts with symmetry related monomers. Overall, the NIF3-like domains of SA1388 are organized as a hexameric toroid similar to its homologs, E. coli ybgI and the hypothetical protein SP1609 from Streptococcus pneumoniae. The openings on either side of the toroid are partially covered by trimeric "lids" formed by the PII domains. The junction of the two NIF3 domains has two zinc ions bound at what appears to be a histidine rich active site. A well-defined electron density corresponding to an endogenously bound ligand of unknown identity is observed in close proximity to the metal site. CONCLUSION: SA1388 is the third member of the NIF3-like family of proteins to be structurally characterized, the other two also being hypothetical proteins of unknown function. The structure of SA1388 confirms our earlier prediction that the inserted domain that separates the two NIF3 domains adopts a PII-like fold and reveals an overall capped toroidal arrangement for the protein hexamer. The six PII-like domains form two trimeric "lids" that cap the central cavity of the toroid on either side and provide only small openings to allow regulated entry of small molecules into the occluded chamber. The presence of the electron density of the bound ligand may provide important clues on the likely function of NIF3-like proteins. [Abstract/Link to Full Text]

Antczak AJ, Tsubota T, Kaufman PD, Berger JM
Structure of the yeast histone H3-ASF1 interaction: implications for chaperone mechanism, species-specific interactions, and epigenetics.
BMC Struct Biol. 2006;626.
BACKGROUND: The histone H3/H4 chaperone Asf1 (anti-silencing function 1) is required for the establishment and maintenance of proper chromatin structure, as well as for genome stability in eukaryotes. Asf1 participates in both DNA replication-coupled (RC) and replication-independent (RI) histone deposition reactions in vitro and interacts with complexes responsible for both pathways in vivo. Asf1 is known to directly bind histone H3, however, high-resolution structural information about the geometry of this interaction was previously unknown. RESULTS: Here we report the structure of a histone/histone chaperone interaction. We have solved the 2.2 A crystal structure of the conserved N-terminal immunoglobulin fold domain of yeast Asf1 (residues 2-155) bound to the C-terminal helix of yeast histone H3 (residues 121-134). The structure defines a histone-binding patch on Asf1 consisting of both conserved and yeast-specific residues; mutation of these residues abrogates H3/H4 binding affinity. The geometry of the interaction indicates that Asf1 binds to histones H3/H4 in a manner that likely blocks sterically the H3/H3 interface of the nucleosomal four-helix bundle. CONCLUSION: These data clarify how Asf1 regulates histone stoichiometry to modulate epigenetic inheritance. The structure further suggests a physical model in which Asf1 contributes to interpretation of a "histone H3 barcode" for sorting H3 isoforms into different deposition pathways. [Abstract/Link to Full Text]

Martin J, Gibrat JF, Rodolphe F
Analysis of an optimal hidden Markov model for secondary structure prediction.
BMC Struct Biol. 2006;625.
BACKGROUND: Secondary structure prediction is a useful first step toward 3D structure prediction. A number of successful secondary structure prediction methods use neural networks, but unfortunately, neural networks are not intuitively interpretable. On the contrary, hidden Markov models are graphical interpretable models. Moreover, they have been successfully used in many bioinformatic applications. Because they offer a strong statistical background and allow model interpretation, we propose a method based on hidden Markov models. RESULTS: Our HMM is designed without prior knowledge. It is chosen within a collection of models of increasing size, using statistical and accuracy criteria. The resulting model has 36 hidden states: 15 that model alpha-helices, 12 that model coil and 9 that model beta-strands. Connections between hidden states and state emission probabilities reflect the organization of protein structures into secondary structure segments. We start by analyzing the model features and see how it offers a new vision of local structures. We then use it for secondary structure prediction. Our model appears to be very efficient on single sequences, with a Q3 score of 68.8%, more than one point above PSIPRED prediction on single sequences. A straightforward extension of the method allows the use of multiple sequence alignments, rising the Q3 score to 75.5%. CONCLUSION: The hidden Markov model presented here achieves valuable prediction results using only a limited number of parameters. It provides an interpretable framework for protein secondary structure architecture. Furthermore, it can be used as a tool for generating protein sequences with a given secondary structure content. [Abstract/Link to Full Text]

Saha RP, Chakrabarti P
Molecular modeling and characterization of Vibrio cholerae transcription regulator HlyU.
BMC Struct Biol. 2006;624.
BACKGROUND: The SmtB/ArsR family of prokaryotic metal-regulatory transcriptional repressors represses the expression of operons linked to stress-inducing concentrations of heavy metal ions, while derepression results from direct binding of metal ions by these 'metal-sensor' proteins. The HlyU protein from Vibrio cholerae is the positive regulator of haemolysin gene, it also plays important role in the regulation of expression of the virulence genes. Despite the understanding of biochemical properties, its structure and relationship to other protein families remain unknown. RESULTS: We find that HlyU exhibits structural features common to the SmtB/ArsR family of transcriptional repressors. Analysis of the modeled structure of HlyU reveals that it does not have the key metal-sensing residues which are unique to the SmtB/ArsR family of repressors, yet the tertiary structure is very similar to the family members. HlyU is the only member that has a positive control on transcription, while all the other members in the family are repressors. An evolutionary analysis with other SmtB/ArsR family members suggests that during evolution HlyU probably occurred by gene duplication and mutational events that led to the emergence of this protein from ancestral transcriptional repressor by the loss of the metal-binding sites. CONCLUSION: The study indicates that the same protein family can contain both the positive regulator of transcription and repressors--the exact function being controlled by the absence or the presence of metal-binding sites. [Abstract/Link to Full Text]

Wahab HA, Ahmad Khairudin NB, Samian MR, Najimudin N
Sequence analysis and structure prediction of type II Pseudomonas sp. USM 4-55 PHA synthase and an insight into its catalytic mechanism.
BMC Struct Biol. 2006;623.
BACKGROUND: Polyhydroxyalkanoates (PHA), are biodegradable polyesters derived from many microorganisms such as the pseudomonads. These polyesters are in great demand especially in the packaging industries, the medical line as well as the paint industries. The enzyme responsible in catalyzing the formation of PHA is PHA synthase. Due to the limited structural information, its functional properties including catalysis are lacking. Therefore, this study seeks to investigate the structural properties as well as its catalytic mechanism by predicting the three-dimensional (3D) model of the Type II Pseudomonas sp. USM 4-55 PHA synthase 1 (PhaC1P.sp USM 4-55). RESULTS: Sequence analysis demonstrated that PhaC1P.sp USM 4-55 lacked similarity with all known structures in databases. PSI-BLAST and HMM Superfamily analyses demonstrated that this enzyme belongs to the alpha/beta hydrolase fold family. Threading approach revealed that the most suitable template to use was the human gastric lipase (PDB ID: 1HLG). The superimposition of the predicted PhaC1P.sp USM 4-55 model with 1HLG covering 86.2% of the backbone atoms showed an RMSD of 1.15 A. The catalytic residues comprising of Cys296, Asp451 and His479 were found to be conserved and located adjacent to each other. In addition to this, an extension to the catalytic mechanism was also proposed whereby two tetrahedral intermediates were believed to form during the PHA biosynthesis. These transition state intermediates were further postulated to be stabilized by the formation of oxyanion holes. Based on the sequence analysis and the deduced model, Ser297 was postulated to contribute to the formation of the oxyanion hole. CONCLUSION: The 3D model of the core region of PhaC1P.sp USM 4-55 from residue 267 to residue 484 was developed using computational techniques and the locations of the catalytic residues were identified. Results from this study for the first time highlighted Ser297 potentially playing an important role in the enzyme's catalytic mechanism. [Abstract/Link to Full Text]

El Omari K, Solaroli N, Karlsson A, Balzarini J, Stammers DK
Structure of vaccinia virus thymidine kinase in complex with dTTP: insights for drug design.
BMC Struct Biol. 2006;622.
BACKGROUND: Development of countermeasures to bioterrorist threats such as those posed by the smallpox virus (variola), include vaccination and drug development. Selective activation of nucleoside analogues by virus-encoded thymidine (dThd) kinases (TK) represents one of the most successful strategies for antiviral chemotherapy as demonstrated for anti-herpes drugs. Vaccinia virus TK is a close orthologue of variola TK but also shares a relatively high sequence identity to human type 2 TK (hTK), thus achieving drug selectivity relative to the host enzyme is challenging. RESULTS: In order to identify any differences compared to hTK that may be exploitable in drug design, we have determined the crystal structure of VVTK, in complex with thymidine 5'-triphosphate (dTTP). Although most of the active site residues are conserved between hTK and VVTK, we observe a difference in conformation of residues Asp-43 and Arg-45. The equivalent residues in hTK hydrogen bond to dTTP, whereas in subunit D of VVTK, Asp-43 and Arg-45 adopt a different conformation preventing interaction with this nucleotide. Asp-43 and Arg-45 are present in a flexible loop, which is disordered in subunits A, B and C. The observed difference in conformation and flexibility may also explain the ability of VVTK to phosphorylate (South)-methanocarbathymine whereas, in contrast, no substrate activity with hTK is reported for this compound. CONCLUSION: The difference in conformation for Asp-43 and Arg-45 could thus be used in drug design to generate VVTK/Variola TK-selective nucleoside analogue substrates and/or inhibitors that have lower affinity for hTK. [Abstract/Link to Full Text]

Ashley RH, Harroun TA, Hauss T, Breen KC, Bradshaw JP
Autoinsertion of soluble oligomers of Alzheimer's Abeta(1-42) peptide into cholesterol-containing membranes is accompanied by relocation of the sterol towards the bilayer surface.
BMC Struct Biol. 2006;621.
BACKGROUND: Soluble Alzheimer's Abeta oligomers autoinsert into neuronal cell membranes, contributing to the pathology of Alzheimer's Disease (AD), and elevated serum cholesterol is a risk factor for AD, but the reason is unknown. We investigated potential connections between these two observations at the membrane level by testing the hypothesis that Abeta(1-42) relocates membrane cholesterol. RESULTS: Oligomers of Abeta(1-42), but not the monomeric peptide, inserted into cholesterol-containing phosphatidylcholine monolayers with an anomalously low molecular insertion area, suggesting concurrent lipid rearrangement. Membrane neutron diffraction, including isomorphous replacement of specific lipid hydrogens with highly-scattering deuterium, showed that Abeta(1-42) insertion was accompanied by outward displacement of membrane cholesterol, towards the polar surfaces of the bilayer. Changes in the generalised polarisation of laurdan confirmed that the structural changes were associated with a functional alteration in membrane lipid order. CONCLUSION: Cholesterol is known to regulate membrane lipid order, and this can affect a wide range of membrane mechanisms, including intercellular signalling. Previously unrecognised Abeta-dependent rearrangement of the membrane sterol could have an important role in AD. [Abstract/Link to Full Text]

Boucher IW, Brzozowski AM, Brannigan JA, Schnick C, Smith DJ, Kyes SA, Wilkinson AJ
The crystal structure of superoxide dismutase from Plasmodium falciparum.
BMC Struct Biol. 2006;620.
BACKGROUND: Superoxide dismutases (SODs) are important enzymes in defence against oxidative stress. In Plasmodium falciparum, they may be expected to have special significance since part of the parasite life cycle is spent in red blood cells where the formation of reactive oxygen species is likely to be promoted by the products of haemoglobin breakdown. Thus, inhibitors of P. falciparum SODs have potential as anti-malarial compounds. As a step towards their development we have determined the crystal structure of the parasite's cytosolic iron superoxide dismutase. RESULTS: The cytosolic iron superoxide dismutase from P. falciparum (PfFeSOD) has been overexpressed in E. coli in a catalytically active form. Its crystal structure has been solved by molecular replacement and refined against data extending to 2.5 A resolution. The structure reveals a two-domain organisation and an iron centre in which the metal is coordinated by three histidines, an aspartate and a solvent molecule. Consistent with ultracentrifugation analysis the enzyme is a dimer in which a hydrogen bonding lattice links the two active centres. CONCLUSION: The tertiary structure of PfFeSOD is very similar to those of a number of other iron-and manganese-dependent superoxide dismutases, moreover the active site residues are conserved suggesting a common mechanism of action. Comparison of the dimer interfaces of PfFeSOD with the human manganese-dependent superoxide dismutase reveals a number of differences, which may underpin the design of parasite-selective superoxide dismutase inhibitors. [Abstract/Link to Full Text]