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Recent Articles in Journal of Biology

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

Kinoshita M, Pfeiffer K, Homberg U
Spectral properties of identified polarized-light sensitive interneurons in the brain of the desert locust Schistocerca gregaria.
J Exp Biol. 2007 Apr;210(Pt 8):1350-61.
Many migrating animals employ a celestial compass mechanism for spatial navigation. Behavioral experiments in bees and ants have shown that sun compass navigation may rely on the spectral gradient in the sky as well as on the pattern of sky polarization. While polarized-light sensitive interneurons (POL neurons) have been identified in the brain of several insect species, there are at present no data on the neural basis of coding the spectral gradient of the sky. In the present study we have analyzed the chromatic properties of two identified POL neurons in the brain of the desert locust. Both neurons, termed TuTu1 and LoTu1, arborize in the anterior optic tubercle and respond to unpolarized light as well as to polarized light. We show here that the polarized-light response of both types of neuron relies on blue-sensitive photoreceptors. Responses to unpolarized light depended on stimulus position and wavelength. Dorsal unpolarized blue light inhibited the neurons, while stimulation from the ipsilateral side resulted in opponent responses to UV light and green light. While LoTu1 was inhibited by UV light and was excited by green light, one subtype of TuTu1 was excited by UV and inhibited by green light. In LoTu1 the sensitivity to polarized light was at least 2 log units higher than the response to unpolarized light stimuli. Taken together, the spatial and chromatic properties of the neurons may be suited to signal azimuthal directions based on a combination of the spectral gradient and the polarization pattern of the sky. [Abstract/Link to Full Text]

Wood CM, Kajimura M, Bucking C, Walsh PJ
Osmoregulation, ionoregulation and acid-base regulation by the gastrointestinal tract after feeding in the elasmobranch (Squalus acanthias).
J Exp Biol. 2007 Apr;210(Pt 8):1335-49.
In order to study the physiological consequences of voluntary feeding in the gastrointestinal tract of a ureotelic marine elasmobranch, dogfish (fasted for 96 h) were sampled at various times up to 360 h after consuming a 5-6% ration of teleost fish (hake) under natural feeding conditions. Digestion and absorption were completed between 120 and 360 h post-feeding. The tissue masses of different segments of the gastrointestinal tract increased and decreased markedly as the chyme moved through, mainly because of fluid engorgement rather than hyperplasia. In fasted dogfish, the cardiac and pyloric stomachs contained only small volumes of highly acidic fluid (pH 1.77+/-1.12, 2.05+/-0.08) similar in composition to seawater. Feeding resulted in gastric pHs of 3.20+/-0.31 and 3.95+/-0.40 at 6 h, followed by slow declines through 60 h. An alkaline tide in the blood also occurred at 6 h. In the face of large changing masses of highly acidic chyme in the stomachs, the pH (6.50+/-0.10), ionic composition and volume of chyme in the intestine (spiral valve) were precisely regulated from 6 to 60 h post-feeding at very different values from those in the stomachs, and intestinal HCO3(-) remained low (5.12+/-0.83 mmol l(-1)). The colon was usually empty and its pH constant at 7.20+/-0.16 at all times. Despite the ingestion of strongly hypo-osmotic teleost tissue, the osmolality of the chyme remained in equilibrium with that of the blood plasma in all segments at all times after feeding. Much of the osmotic equilibration was because of the secretion of urea into the chyme, particularly in the intestine. After feeding, gastric fluid concentrations of Na(+) and Mg(2+) declined, K(+) and Ca(2+) increased, whereas Cl(-) exhibited little change, indicating that additional drinking of seawater was minimal. Na(+), K(+), water and especially Cl(-) were absorbed in the intestine, whereas Mg(2+) and Ca(2+) were largely excluded. Our results illustrate the complex integration of digestive and ionoregulatory function in the elasmobranch digestive tract, and marked differences from the teleost pattern. [Abstract/Link to Full Text]

Salvante KG, Walzem RL, Williams TD
What comes first, the zebra finch or the egg: temperature-dependent reproductive, physiological and behavioural plasticity in egg-laying zebra finches.
J Exp Biol. 2007 Apr;210(Pt 8):1325-34.
Avian reproduction is generally timed to synchronize chick-rearing with periods of increased food abundance. Consequently, the energetically demanding period of egg production may coincide with periods of lower food availability, fluctuating temperature and more unstable weather. Little is known about the physiological mechanisms underlying temperature-induced variation in egg production. We therefore examined the influence of low ambient temperature (7 degrees C vs 21 degrees C) on reproductive output (e.g. egg mass, clutch size, laying interval, laying rate), daily food consumption and lipid variables in zebra finches Taeniopygia guttata. When faced with egg production at 7 degrees C, laying zebra finches increased energy intake by 12.67 kJ day(-1), and were thus able to maintain body condition (e.g. body mass, fat and muscle score) and circulating triacylglyceride at levels comparable to those at 21 degrees C. However, when producing eggs at 7 degrees C, females took longer to initiate egg laying (6.5 vs 6.1 days at 21 degrees C), and ultimately laid fewer eggs (5.5 vs 6.0 eggs) at a slower rate (0.90 eggs day(-1) vs 0.95 eggs day(-1)). These temperature-related declines in reproductive output were accompanied by decreases in modal (from 36.6 at 21 degrees C to 24.3 nm at 7 degrees C) and median very low density lipoprotein (VLDL) particle diameter (from 29.6 to 26.4 nm) and in the proportion of VLDL particles that were capable of passing through the pores in the ovary to access the developing ovarian follicles (i.e. particles with diameters between 25 and 44 nm; from 45.90% to 32.55%). However, variation in reproductive output was not related to any static concentration or structural measure of VLDL. Therefore, other temperature-dependent mechanisms must be involved in the physiological processes that regulate reproductive output of passerine birds at low ambient temperatures. [Abstract/Link to Full Text]

Song CK, Johnstone LM, Schmidt M, Derby CD, Edwards DH
Social domination increases neuronal survival in the brain of juvenile crayfish Procambarus clarkii.
J Exp Biol. 2007 Apr;210(Pt 8):1311-24.
Olfactory cues are among the sensory inputs that crayfish use in establishing dominance hierarchies. Throughout their lives, new neurons are continuously added into brain cell clusters 9 and 10, which contain somata of olfactory local and projection interneurons, respectively. Using markers for DNA synthesis (bromodeoxyuridine) and mitosis (phospho-histone-3), we tested juvenile crayfish (Procambarus clarkii) to examine effects of pairwise social experience on proliferation and survival of cells in these brain regions. Proliferating and mitotic cells appeared within restricted neurogenic areas in both clusters and in ;tails' extending from them. These tails, embedded in tubulin-positive strands, are linked by a patch of cells. Neither cell proliferation nor mitotic activity was affected by social dominance. Cell survival of neuronal precursors was affected by dominance: compared to dominants, subordinates had fewer newborn cells surviving in cluster 9 after 14 days of social experience. Social experience also affected body growth rate, but the effect of social experience on neurogenesis remained when differences in body growth rate were statistically controlled. We conclude that social domination enhances survival of new olfactory interneuronal precursors compared to social subordination but not compared to social isolation. [Abstract/Link to Full Text]

Hyodo S, Bell JD, Healy JM, Kaneko T, Hasegawa S, Takei Y, Donald JA, Toop T
Osmoregulation in elephant fish Callorhinchus milii (Holocephali), with special reference to the rectal gland.
J Exp Biol. 2007 Apr;210(Pt 8):1303-10.
Osmoregulatory mechanisms in holocephalan fishes are poorly understood except that these fish are known to conduct urea-based osmoregulation as in elasmobranchs. We, therefore, examined changes in plasma parameters of elephant fish Callorhinchus milii, after gradual transfer to concentrated (120%) or diluted (80%) seawater (SW). In control fish, plasma Na and urea concentrations were about 300 mmol l(-1) and 450 mmol l(-1), respectively. These values were equivalent to those of sharks and rays, but the plasma urea concentration of elephant fish was considerably higher than that reported for chimaeras, another holocephalan. After transfer to 120% SW, plasma osmolality, urea and ion concentrations were increased, whereas transfer to 80% SW resulted in a fall in these parameters. The rises in ion concentrations were notable after transfer to 120% SW, whereas urea concentration decreased predominantly following transfer to 80% SW. In elephant fish, we could not find a discrete rectal gland. Instead, approximately 10 tubular structures were located in the wall of post-valvular intestine. Each tubular structure was composed of a putative salt-secreting component consisting of a single-layered columnar epithelium, which was stained with an anti-Na(+),K(+)-ATPase serum. Furthermore, Na(+),K(+)-ATPase activity in the tubular structures was significantly increased after acute transfer of fish to concentrated SW (115%). These results suggest that the tubular structures are a rectal gland equivalent, functioning as a salt-secreting organ. Since the rectal gland of elephant fish is well developed compared to that of Southern chimaera, the salt-secreting ability may be higher in elephant fish than chimaeras, which may account for the lower plasma NaCl concentration in elephant fish compared to other chimaeras. Since elephant fish have also attracted attention from a viewpoint of genome science, the availability of fish for physiological studies will make this species an excellent model in holocephalan fish group. [Abstract/Link to Full Text]

Greenlee KJ, Nebeker C, Harrison JF
Body size-independent safety margins for gas exchange across grasshopper species.
J Exp Biol. 2007 Apr;210(Pt 7):1288-96.
Why is maximal insect body size relatively small compared to that of vertebrates? Possibly insect body size is limited by the capacity of the tracheal respiratory system to delivery oxygen down longer and longer tracheae to the tissues. If so, one possible outcome would be that larger insect species would have a smaller safety margin for oxygen delivery (higher critical P(O2), P(c)). We tested this idea by exposing inactive adult grasshoppers of a range of species and body sizes (0.07-6.4 g) to progressively lower oxygen atmospheres and measuring their ventilation frequency and their ability to maintain metabolic rate (indexed by CO(2) emission rate). We analyzed effects of body size on these parameters by simple linear regressions, as well as methods to control for phylogenetic relatedness among species. We found interspecific variation in P(c), but P(c) did not significantly correlate with body mass (average P(c) across all species = 4 kPa). Maximal tracheal system conductance scaled approximately with mass(0.7), and estimated ventilation in hypoxia (ventilatory frequency x tidal volume) scaled directly with mass, suggesting that convection is the major mechanism of gas exchange in all these species. These comparative data strengthen the growing body of evidence that body size does not affect the safety margin for oxygen delivery in insects. [Abstract/Link to Full Text]

Browne CL, Swan JB, Rankin EE, Calvert H, Griffiths S, Tytell M
Extracellular heat shock protein 70 has novel functional effects on sea urchin eggs and coelomocytes.
J Exp Biol. 2007 Apr;210(Pt 7):1275-87.
Numerous reports document that the 70 kDa heat shock proteins are not only intracellular proteins but are also present in blood and other extracellular compartments. How they affect cell function from the extracellular space remains unclear. Using two well-characterized cell types from the sea urchin, we show that extracellular mixtures of the constitutive and inducible forms of the 70 kDa heat shock proteins (Hsc70 and Hsp70, respectively) have dramatic effects on initiation of cell division in fertilized eggs and on the clotting reaction of hypotonically stressed coelomocytes. In suspensions of fertilized eggs to which Hsc70 or a 2:3 mixture of Hsc and Hsp70 was added, progression to the first mitotic division was accelerated. Evidence is provided that the extracellular Hsc70 passes into the egg cells in an unconventional manner, being distributed through the cytoplasm, and that it may alter the intracellular signaling cascade initiated by sperm penetration. In coelomocytes that were stimulated by hypotonic shock to mimic injury, the spreading reaction of the clotting response was significantly inhibited when either Hsp70 or Hsc70 was in the medium. These results suggest that the presence of Hsc and/or Hsp70 in the extracellular fluid may promote mitosis of dividing cells and suppress the reactivity of immune system cells. [Abstract/Link to Full Text]

Helinski ME, Hood-Nowotny R, Mayr L, Knols BG
Stable isotope-mass spectrometric determination of semen transfer in malaria mosquitoes.
J Exp Biol. 2007 Apr;210(Pt 7):1266-74.
The potential use of stable isotopes to study mosquito mating was investigated by tracing the fate of labelled semen into spermathecae. [(13)C]glucose was incorporated in the diet of the malaria mosquito Anopheles arabiensis. Treatments included labelling of either the larval water or adult sugar water, or a combination of both. After mating, ;spiked' spermathecae were analysed for isotope ratios using mass spectrometry. Results demonstrated that spermathecae positive for semen could successfully be distinguished from empty ones or controls (i.e. filled with unlabelled semen) using the raw delta(13)C values. Labelling during larval development and combined labelling of larvae and adults resulted in detectable values. The label persisted in spermathecae for up to 7 days after mating, and unlabelled sugar feeding of males labelled in the larval stage did not result in a detectable turnover of the semen label. There were no detrimental effects of the addition of labelled glucose on larval development and survival, adult size, male longevity and mating performance. We have proved that it is possible to label male mosquitoes and detect the semen label in females after insemination. This method offers great potential to study mating in mosquitoes and other insects and could prove useful in genetic control studies of medical or agricultural pest insects, with male mating success in the field as a critical verifiable indicator for a positive outcome of the intervention. [Abstract/Link to Full Text]

McGowan CP, Baudinette RV, Biewener AA
Modulation of proximal muscle function during level versus incline hopping in tammar wallabies (Macropus eugenii).
J Exp Biol. 2007 Apr;210(Pt 7):1255-65.
We examined the functional role of two major proximal leg extensor muscles of tammar wallabies during level and inclined hopping (12 degrees, 21.3% grade). Previous in vivo studies of hopping wallabies have revealed that, unlike certain avian bipeds, distal hindlimb muscles do not alter their force-length behavior to contribute positive work during incline hopping. This suggests that proximal muscles produce the increased mechanical work associated with moving up an incline. Based on relative size and architectural anatomy, we hypothesized that the biceps femoris (BF), primarily a hip extensor, and the vastus lateralis (VL), the main knee extensor, would exhibit changes in muscle strain and activation patterns consistent with increased work production during incline versus level hopping. Our results clearly support this hypothesis. The BF experienced similar activation patterns during level and incline hopping but net fascicle shortening increased (-0.5% for level hopping versus -4.2% for incline hopping) during stance when the muscle likely generated force. Unlike the BF, the VL experienced active net lengthening during stance, indicating that it absorbs energy during both level and incline hopping. However, during incline hopping, net lengthening was reduced (8.3% for level hopping versus 3.9% for incline hopping), suggesting that the amount of energy absorbed by the VL was reduced. Consequently, the changes in contractile behavior of these two muscles are consistent with a net production of work by the whole limb. A subsidiary aim of our study was to explore possible regional variation within the VL. Although there was slightly higher fascicle strain in the proximal VL compared with the distal VL, regional differences in strain were not significant, suggesting that the overall pattern of in vivo strain is fairly uniform throughout the muscle. Estimates of muscle work based on inverse dynamics calculations support the conclusion that both the BF and VL contribute to the additional work required for incline hopping. However, on a muscle mass-specific basis, these two muscles appear to contribute less than their share. This indicates that other hindlimb muscles, or possibly trunk and back muscles, must contribute substantial work during incline hopping. [Abstract/Link to Full Text]

Qadri SA, Camacho J, Wang H, Taylor JR, Grosell M, Worden MK
Temperature and acid-base balance in the American lobster Homarus americanus.
J Exp Biol. 2007 Apr;210(Pt 7):1245-54.
Lobsters (Homarus americanus) in the wild inhabit ocean waters where temperature can vary over a broad range (0-25 degrees C). To examine how environmental thermal variability might affect lobster physiology, we examine the effects of temperature and thermal change on the acid-base status of the lobster hemolymph. Total CO(2), pH, P(CO)2 and HCO(-)(3) were measured in hemolymph sampled from lobsters acclimated to temperature in the laboratory as well as from lobsters acclimated to seasonal temperatures in the wild. Our results demonstrate that the change in hemolymph pH as a function of temperature follows the rule of constant relative alkalinity in lobsters acclimated to temperature over a period of weeks. However, thermal change can alter lobster acid-base status over a time course of minutes. Acute increases in temperature trigger a respiratory compensated metabolic acidosis of the hemolymph. Both the strength and frequency of the lobster heartbeat in vitro are modulated by changes in pH within the physiological range measured in vivo. These observations suggest that changes in acid-base status triggered by thermal variations in the environment might modulate lobster cardiac performance in vivo. [Abstract/Link to Full Text]

Costantini D, Fanfani A, Dell'Omo G
Carotenoid availability does not limit the capability of nestling kestrels (Falco tinnunculus) to cope with oxidative stress.
J Exp Biol. 2007 Apr;210(Pt 7):1238-44.
It is recognized that carotenoids are useful anti-oxidants in embryo and hatchling avian models. However, recent evidence suggests that the anti-oxidant role of carotenoids in nestling or adult birds may not be as important as previously thought. The aim of the present work was to investigate if supplemental carotenoids decreased the level of oxidative damage (by reactive oxygen metabolites, ROMs) and increased the serum anti-oxidant capacity (OXY) in nestling Eurasian kestrels Falco tinnunculus. Circulating carotenoids in supplemented nestlings increased about 1.5-fold compared to the control and pre-treatment levels at the end of the supplementation period. There was no effect on ROMs, OXY or the level of oxidative stress (ratio between ROMs and OXY), however, or on body mass or body condition of nestlings. ROMs and OXY decreased with age, but this pattern varied across the nests. Our results show that (i) in general, younger nestlings actually have to cope with a high free radical production, and (ii) the ability of wild nestling kestrels to cope with oxidative stress is not affected by carotenoid availability. [Abstract/Link to Full Text]

Sugai R, Azami S, Shiga H, Watanabe T, Sadamoto H, Kobayashi S, Hatakeyama D, Fujito Y, Lukowiak K, Ito E
One-trial conditioned taste aversion in Lymnaea: good and poor performers in long-term memory acquisition.
J Exp Biol. 2007 Apr;210(Pt 7):1225-37.
In the majority of studies designed to elucidate the causal mechanisms of memory formation, certain members of the experimental cohort, even though subjected to exactly the same conditioning procedures, remember significantly better than others, whereas others show little or no long-term memory (LTM) formation. To begin to address the question of why this phenomenon occurs and thereby help clarify the causal mechanism of LTM formation, we used a conditioned taste aversion (CTA) procedure on individuals of the pond snail Lymnaea stagnalis and analyzed their subsequent behavior. Using sucrose as an appetitive stimulus and KCl as an aversive stimulus, we obtained a constant ratio of ;poor' to ;good' performers for CTA-LTM. We found that approximately 40% of trained snails possessed LTM following a one-trial conditioning procedure. When we examined the time-window necessary for the memory consolidation, we found that if we cooled snails to 4 degrees C for 30 min within 10 min after the one-trial conditioning, LTM was blocked. However, with delayed cooling (i.e. longer than 10 min), LTM was present. We could further interfere with LTM formation by inducing inhibitory learning (i.e. backward conditioning) after the one-trial conditioning. Finally, we examined whether we could motivate snails to acquire LTM by depriving them of food for 5 days before the one-trial conditioning. Food-deprived snails, however, failed to exhibit LTM following the one-trial conditioning. These results will help us begin to clarify why some individuals are better at learning and forming memory for specific tasks at the neuronal level. [Abstract/Link to Full Text]

Farrell AP, Axelsson M, Altimiras J, Sandblom E, Claireaux G
Maximum cardiac performance and adrenergic sensitivity of the sea bass Dicentrarchus labrax at high temperatures.
J Exp Biol. 2007 Apr;210(Pt 7):1216-24.
We examined maximum cardiac performance of sea bass Dicentrarchus labrax acclimated to 18 degrees C and 22 degrees C, temperatures near the optimum for growth of this species. Our aim was to study whether cardiac performance, especially the effect of adrenergic stimulation, differed when compared to salmonids. Sea bass and salmonids are both athletic swimmers but their cardiac anatomy differs markedly. The sea bass ventricle does not receive any oxygenated blood via a coronary circulation while salmonids have a well-developed arterial supply of oxygen to the compact layer of the ventricle. Using in situ perfused heart preparations, maximum cardiac performance of 18 degrees C-acclimated sea bass (i.e. cardiac output = 90.8+/- 6.6 ml min(-1) kg(-1) and power output = 11.41+/-0.83 mW g(-1)) was found to be comparable to that previously reported for rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta at similar temperatures and with tonic adrenergic (5 nmol l(-1) adrenaline) stimulation. For 22 degrees C-acclimated sea bass, heart rate was significantly higher, but maximum stroke volume was reduced by 22% (1.05+/-0.05 ml kg(-1)) compared with 18 degrees C (1.38+/- 0.11 ml kg(-1)). As a result, maximum cardiac output (99.4+/-3.9 ml min(-1) kg(-1)) was not significantly different at 22 degrees C. Instead, maximum power output was 27% higher at 22 degrees C (14.95+/-0.96 mW g(-1)) compared with 18 degrees C, primarily because of the smaller relative ventricular mass in 22 degrees C-acclimated sea bass. Compared with tonic adrenergic stimulation with 5 nmol l(-1) adrenaline, maximum adrenergic stimulation of the sea bass heart produced only modest stimulatory effects at both temperatures (12-13% and 14-15% increases in maximum cardiac output and power output, respectively, with no chronotropic effect). Adrenergic stimulation also increased the cardiac sensitivity to filling pressure, with the maximum left-shift in the Starling curve being produced by 50-100 nmol l(-1) adrenaline at 18 degrees C and 10-50 nmol l(-1) adrenaline at 22 degrees C. We show that the sea bass, which lacks a coronary arterial oxygen supply to the ventricle, has a powerful heart. Its maximum performance is comparable to a salmonid heart, as is the modest stimulatory effect of adrenaline at high temperature. [Abstract/Link to Full Text]

Larson SG, Stern JT
Humeral retractor EMG during quadrupedal walking in primates.
J Exp Biol. 2007 Apr;210(Pt 7):1204-15.
The mammalian humeral retractors latissimus dorsi, teres major and caudal parts of the pectoral muscles are commonly thought to contribute to forward impulse during quadrupedal locomotion by pulling the body over the supporting forelimb. While most electromyographic studies on recruitment patterns for these muscles tend to support this functional interpretation, data on muscle use in chimpanzees and vervet monkeys have suggested that the humeral retractors of nonhuman primates are largely inactive during the support phase of quadrupedal locomotion. In the chimpanzee and vervet monkey, in contrast to what has been documented for other mammals, the contributions of latissimus dorsi, caudal pectoralis major, and teres major during quadrupedal locomotion are restricted to slowing down the swinging forelimb in preparation for hand touchdown and/or retracting the humerus to help lift the hand off the substrate at the initiation of swing phase. Based on these results, it has been proposed that unique patterns of shoulder muscle recruitment are among a set of characteristics that distinguish the form of quadrupedalism displayed by nonhuman primates from that of other nonprimate mammals. However, two primate taxa is a limited sample upon which to base such far-reaching conclusions. Here we report on the activity patterns for the humeral retractors during quadrupedal walking in an additional eight species of nonhuman primates. There is some variability in the activity patterns for latissimus dorsi, caudal pectoralis major and teres major, both between and within species, but in general the results confirm that the humeral retractors of primate quadrupeds do not contribute to forward impulse by pulling the body over the supporting forelimb. [Abstract/Link to Full Text]

Donley JM, Shadwick RE, Sepulveda CA, Syme DA
Thermal dependence of contractile properties of the aerobic locomotor muscle in the leopard shark and shortfin mako shark.
J Exp Biol. 2007 Apr;210(Pt 7):1194-203.
The work loop technique was used to examine contractile properties of the red aerobic locomotor muscle (RM) in the ectothermic leopard shark Triakis semifasciata and endothermic shortfin mako shark Isurus oxyrinchus. The effects of axial position and temperature on the twitch kinetics, and the stimulus duration and phase producing maximum net positive work and power output were investigated. Contractile performance was measured over the temperature range of 15 to 25 degrees C for Triakis and 15 to 28 degrees C for Isurus at cycle frequencies (analogous to tailbeat frequencies) ranging from 0.25 to 3 Hz using muscle bundles isolated from anterior (0.4 L where L is total body length) and posterior (0.6-0.65 L) axial positions. Pairwise comparisons of twitch times for anterior and posterior muscle samples indicated that there were no significant differences related to body position, except in mako sharks at unphysiologically cool temperatures (<20 degrees C). We found no significant differences in optimal stimulus duration, phase, net work or power output between anterior and posterior bundles in each species. With increasing cycle frequency the stimulus duration yielding maximum power decreased while optimal phase occurred earlier. The cycle frequency at which peak power was generated in leopard shark RM was only affected slightly by temperature, increasing from about 0.6 to 1.0 Hz between 15 and 25 degrees C. In contrast, mako RM showed a much more dramatic temperature sensitivity, with the peak power frequency rising from <0.25 to 2.25 Hz between 15 and 28 degrees C. These data support the hypothesis that the contractile properties of RM are functionally similar along the body in both species. In addition, our data identify a significant difference in the effect of temperature on net work and power output between these two shark species; at 15 degrees C muscle from the ectothermic leopard shark performs relatively well in comparison with mako, while at higher temperatures, which reflect those normally experienced by the mako, the optimal cycle frequency for power is nearly double that of the leopard shark, suggesting that the mako may be able to maintain greater aerobic swimming speeds. [Abstract/Link to Full Text]

Van Wassenbergh S, Herrel A, James RS, Aerts P
Scaling of contractile properties of catfish feeding muscles.
J Exp Biol. 2007 Apr;210(Pt 7):1183-93.
Biomechanical models are intrinsically limited in explaining the ontogenetic scaling relationships for prey capture kinematics in aquatic vertebrates because no data are available on the scaling of intrinsic contractile properties of the muscles that power feeding. However, functional insight into scaling relationships is fundamental to our understanding of the ecology, performance and evolution of animals. In this study, in vitro contractile properties of three feeding muscles were determined for a series of different sizes of African air-breathing catfishes (Clarias gariepinus). These muscles were the mouth closer musculus adductor mandibulae A2A3', the mouth opener m. protractor hyoidei and the hypaxial muscles responsible for pectoral girdle retraction. Tetanus and twitch activation rise times increased significantly with size, while latency time was size independent. In accordance with the decrease in feeding velocity with increasing size, the cycle frequency for maximal power output of the protractor hyoidei and the adductor mandibulae showed a negative scaling relationship. Theoretical modelling predicts a scaling relationship for in vivo muscle function during which these muscles always produced at least 80% of their maximal in vitro power. These findings suggest that the contractile properties of these feeding muscles are fine-tuned to the changes in biomechanical constraints of movement of the feeding apparatus during ontogeny. However, each muscle appears to have a unique set of contractile properties. The hypaxials, the most important muscle for powering suction feeding in clariid catfish, differed from the other muscles by generating higher maximal stress and mass-specific power output with increased size, whilst the optimum cycle frequency for maximal power output only decreased significantly with size in the larger adults (cranial lengths greater than 60 mm). [Abstract/Link to Full Text]

Martell DJ, Kieffer JD
Persistent effects of incubation temperature on muscle development in larval haddock (Melanogrammus aeglefinus L.).
J Exp Biol. 2007 Apr;210(Pt 7):1170-82.
Muscle development and growth were investigated in haddock larvae (Melanogrammus aeglefinus L.) incubated under controlled temperatures (4, 6, 8 degrees C) and reared post-hatch through yolk-dependent and exogenous-feeding stages in a 6 degrees C post-hatch environment. Changes in cell number and size in superficial and deep myotomes within the epaxial muscle were investigated for 28 days following hatch. Distinct and significant differences in muscle cellularity following separate developmental strategies were observed in superficial and deep myotomes. The number of superficial myofibres increased with time and, although not in a manner proportional to temperature during the first 21 days post hatch (d.p.h.), there was observed a trend during the final 7 days of greater mean cell size that was strongly associated with increased temperature. In addition, there was an apparent correspondence between increased temperature and increased size between 21 and 28 d.p.h. Among all temperature groups the superficial myotome not only demonstrated a consistent unimodal myofibre-size distribution but one that increased in range proportional to temperature. In the deep muscle, myotomes from higher incubation temperatures had a broader range of fibre sizes and greater numbers of myofibres. The onset of a proliferative event, characterized by a significant recruitment of new smaller myofibres and a bimodal distribution of cell sizes, was directly proportional to incubation temperature such that it occurred at 14 d.p.h. at 8 degrees C but not until 28 d.p.h. at 4 degrees C. The magnitude of that recruitment was also directly proportional to temperature. Following hatch, those embryos from the greatest temperature groups had the largest mean deep muscle size but, as a result of the proliferative event, had the smallest-sized cells 28 days later. The muscle developmental and growth strategy as indicated by sequential changes in cellularity and cell-size distributions between myotomes in response to temperature are also discussed in light of whole animal growth and development. [Abstract/Link to Full Text]

Vaillancourt E, Weber JM
Lipid mobilization of long-distance migrant birds in vivo: the high lipolytic rate of ruff sandpipers is not stimulated during shivering.
J Exp Biol. 2007 Apr;210(Pt 7):1161-9.
For long migrations, birds must rely on high flux capacities at all steps of lipid metabolism, from the mobilization of adipose reserves to fatty acid oxidation in flight muscle mitochondria. Substrate kinetics and indirect calorimetry were used to investigate key parameters of lipid metabolism in a highly aerobic shorebird: the ruff sandpiper Philomachus pugnax. In this study, we have quantified the effects of cold exposure because such measurements are presently impossible during flight. Lipolytic rate was monitored by continuous infusion of 2-[(3)H]-glycerol and lipid oxidation by respirometry. Plasma lipid concentrations (non-esterified fatty acids, neutral lipids and phospholipids) and their fatty acid composition were also measured to assess whether cold exposure causes selective metabolism of specific lipids. Results show that shivering leads to a 47% increase in metabolic rate (44.4+/-3.8 ml O(2)kg(-1) min(-1) to 65.2+/-8.1 ml O(2) kg(-1) min(-1)), almost solely by stimulating lipid oxidation (33.3+/- 3.3 ml O(2) kg(-1) min(-1) to 48.2+/-6.8 ml O(2) kg(-1) min(-1)) because carbohydrate oxidation remains close to 11.5+/- 0.5 ml O(2) kg(-1) min(-1). Sandpipers support an unusually high lipolytic rate of 55-60 micromol glycerol kg(-1) min(-1). Its stimulation above thermoneutral rates is unnecessary during shivering when the birds are still able to re-esterify 50% of released fatty acids. No changes in plasma lipid composition were observed, suggesting that cold exposure does not lead to selective metabolism of particular fatty acids. This study provides the first measurements of lipolytic rate in migrant birds and shows that their capacity for lipid mobilization reaches the highest values measured to date in vertebrates. Extending the limits of conventional lipid metabolism has clearly been necessary to achieve long-distance migrations. [Abstract/Link to Full Text]

Jayne BC, Riley MA
Scaling of the axial morphology and gap-bridging ability of the brown tree snake, Boiga irregularis.
J Exp Biol. 2007 Apr;210(Pt 7):1148-60.
Networks of branches in arboreal environments create many functional challenges for animals, including traversing gaps between perches. Many snakes are arboreal and their elongate bodies are theoretically well suited for bridging gaps. However, only two studies have previously investigated gap bridging in snakes, and the effects of size are poorly understood. Thus, we videotaped and quantified maximal gap-bridging ability in a highly arboreal species of snake (Boiga irregularis), for which we were able to obtain a large range in snout-vent length (SVL=43-188 cm) and mass (10-1391 g). We expected smaller snakes to bridge relatively larger gaps than larger individuals because of their proportionately higher ratio of muscle cross-sectional area to mass. The maximal length of the gaps spanned by B. irregularis had negative allometry, indicating that smaller snakes could span a greater proportion of their length than larger snakes. The greatest relative gap distance spanned (64% SVL) was by the smallest individual. The majority of snakes (85%) simply crawled slowly to cross a gap. Most of the suspended portion of the body and the path traveled by the head were below the perch that supported the posterior body, which may decrease the tendency of the snake to roll. Some (15%) of the snakes used another behavior in which the neck inclined as much as 45 degrees and then rapidly lunged towards the anterior perch, and this enabled them to cross larger gaps than those using the crawling behavior. Perhaps the launching behavior of the gliding tree snakes (Chrysopelea sp.) evolved from an ancestral behavior of lunging to bridge gaps analogous to that of the brown tree snakes. An estimate of the muscle strain required to prevent the body of the snake from buckling suggests that, despite being light-bodied, brown tree snakes bridging a gap may be at the limit of the physiological capacity of their epaxial muscles. [Abstract/Link to Full Text]

Barbosa A, M�thger LM, Chubb C, Florio C, Chiao CC, Hanlon RT
Disruptive coloration in cuttlefish: a visual perception mechanism that regulates ontogenetic adjustment of skin patterning.
J Exp Biol. 2007 Apr;210(Pt 7):1139-47.
Among the changeable camouflage patterns of cuttlefish, disruptive patterning is shown in response to certain features of light objects in the visual background. However, whether animals show disruptive patterns is dependent not only on object size but also on their body size. Here, we tested whether cuttlefish (Sepia officinalis) are able to match their disruptive body patterning with increasing size of background objects as they grow from hatchling to adult size (0.7 to 19.6 cm mantle length; factor of 28). Specifically, do cuttlefish have a single ;visual sampling rule' that scales accurately during ontogeny? For each of seven size classes of cuttlefish, we created black and white checkerboards whose check sizes corresponded to 4, 12, 40, 120, 400 and 1200% of the area of the cuttlefish's White square, which is a neurophysiologically controlled component of the skin. Disruptive body patterns were evoked when, regardless of animal size, the check size measured either 40 or 120% of the area of the cuttlefish's White square, thus demonstrating a remarkable ontogenetic conformity to a single visual sampling rule. Cuttlefish have no known visual feedback loop with which to adjust their skin patterns. Since the area of a cuttlefish's White square skin component is a function of body size, our results indicate that cuttlefish are solving a visual scaling problem of camouflage presumably without visual confirmation of the size of their own skin component. [Abstract/Link to Full Text]

Gagliardo A, Ioal� P, Savini M, Lipp HP, Dell'Omo G
Finding home: the final step of the pigeons' homing process studied with a GPS data logger.
J Exp Biol. 2007 Apr;210(Pt 7):1132-8.
Experiments have shown that homing pigeons are able to develop navigational abilities even if reared and kept confined in an aviary, provided that they are exposed to natural winds. These and other experiments performed on inexperienced birds have shown that previous homing experiences are not necessary to determine the direction of displacement. While the cues used in the map process for orienting at the release site have been extensively investigated, the final step of the homing process has received little attention by researchers. Although there is general agreement on the relevance of visual cues in navigation within the home area, there is a lack of clear evidence. In order to investigate the final step of the homing process, we released pigeons raised under confined conditions and others that had been allowed to fly freely around the loft and compared their flight paths recorded with a Global-Positioning-System logger. Our data show that a limited view of the home area impairs the pigeons' ability to relocate the loft at their first homing flight, suggesting that the final step of the homing process is mediated via recognition of familiar visual landmarks in the home area. [Abstract/Link to Full Text]

Hasselquist D, Lindstr�m A, Jenni-Eiermann S, Koolhaas A, Piersma T
Long flights do not influence immune responses of a long-distance migrant bird: a wind-tunnel experiment.
J Exp Biol. 2007 Apr;210(Pt 7):1123-31.
Heavy physical work can result in physiological stress and suppressed immune function. Accordingly, long-distance migrant birds that fly for thousands of km within days can be expected to show immunosuppression, and hence be more vulnerable to infections en route. The red knot Calidris canutus Linnaeus is a long-distance migrant shorebird. We flew red knots the equivalent of 1500 km over 6 days in a wind tunnel. The humoral and cell-mediated immune responses of the flyers were compared to those of non-flying controls. Humoral immunity was measured as antibody production against injected diphtheria and tetanus antigens, and cell-mediated response as phytohemagglutinin-induced wing-web swelling. Blood corticosterone levels, which may modulate immune function, were measured in parallel. The long flights had no detectable effects on humoral or cell-mediated immune responses, or on corticosterone levels. Thus, flight performance per se may not be particularly stressful or immunosuppressive in red knots. Some birds assigned as flyers refused to fly for extended periods. Before flights started, these non-flyers had significantly lower antibody responses against tetanus than the birds that carried out the full flight program. This suggests that only birds in good physical condition may be willing to take on heavy exercise. We conclude that these long-distance migrants appear well adapted to the work load induced by long flights, enabling them to cope with long flight distances without increased stress levels and suppression of immunity. Whether this also applies in the wild, where the migrating birds may face adverse weather and food conditions, remains to be investigated. [Abstract/Link to Full Text]

Nachtigall PE, Supin AY, Amundin M, R�ken B, M�ller T, Mooney TA, Taylor KA, Yuen M
Polar bear Ursus maritimus hearing measured with auditory evoked potentials.
J Exp Biol. 2007 Apr;210(Pt 7):1116-22.
While there has been recent concern about the effects of sound on marine mammals, including polar bears, there are no data available measuring the hearing of any bear. The in-air hearing of three polar bears was measured using evoked auditory potentials obtained while tone pips were played to three individually anaesthetized bears at the Kolm�rden Djurpark. Hearing was tested in half-octave steps from 1 to 22.5 kHz. Measurements were not obtainable at 1 kHz and best sensitivity was found in the range from 11.2-22.5 kHz. Considering the tone pips were short and background noise measurements were available, absolute measurements were estimated based on an assumed mammalian integration time of 300 ms. These data show sensitive hearing in the polar bear over a wide frequency range and should cause those concerned with the introduction of anthropogenic noise into the polar bear's environment to operate with caution. [Abstract/Link to Full Text]

Ong KJ, Stevens ED, Wright PA
Gill morphology of the mangrove killifish (Kryptolebias marmoratus) is plastic and changes in response to terrestrial air exposure.
J Exp Biol. 2007 Apr;210(Pt 7):1109-15.
Amphibious mangrove killifish, Kryptolebias marmoratus (formerly Rivulus marmoratus), are frequently exposed to aerial conditions in their natural environment. We tested the hypothesis that gill structure is plastic and that metabolic rate is maintained in response to air exposure. During air exposure, when gills are no longer functional, we predicted that gill surface area would decrease. In the first experiment, K. marmoratus were exposed to either water (control) or air for 1 h, 1 day, 1 week, or 1 week followed by a return to water for 1 week (recovery). Scanning electron micrographs (SEM) and light micrographs of gill sections were taken, and morphometric analyses of lamellar width, lamellar length and interlamellar cell mass (ILCM) height were performed. Following 1 week of air exposure, SEM indicated that there was a decrease in lamellar surface area. Morphometric analysis of light micrographs revealed that there were significant changes in the height of the ILCM, but there were no significant differences in lamellae width and length between any of the treatments. Following 1 week of recovery in water, the ILCM regressed and gill lamellae were similar to control fish, indicating that the morphological changes were reversible. In the second experiment, V(CO(2)) was measured in fish continuously over a 5-day period in air and compared with previous measurements of oxygen uptake (V(O(2))) in water. V(CO(2)) varied between 6 and 10 micromol g(-1) h(-1) and was significantly higher on days 3, 4 and 5 relative to days 1 and 2. In contrast to V(O(2)) in water, V(CO(2)) in air showed no diurnal rhythm over a 24 h period. These findings indicate that K. marmoratus remodel their gill structures in response to air exposure and that these changes are completely reversible. Furthermore, over a similar time frame, changes in V(CO(2)) indicate that metabolic rate is maintained at a rate comparable to that of fish in water, underlying the remarkable ability of K. marmoratus to thrive in both aquatic and terrestrial habitats. [Abstract/Link to Full Text]

Guschlbauer C, Scharstein H, B�schges A
The extensor tibiae muscle of the stick insect: biomechanical properties of an insect walking leg muscle.
J Exp Biol. 2007 Mar;210(Pt 6):1092-108.
We investigated the properties of the extensor tibiae muscle of the stick insect (Carausius morosus) middle leg. Muscle geometry of the middle leg was compared to that of the front and hind legs and to the flexor tibiae, respectively. The mean length of the extensor tibiae fibres is 1.41+/-0.23 mm and flexor fibres are 2.11+/-0.30 mm long. The change of fibre length with joint angle was measured and closely follows a cosine function. Its amplitude gives effective moment arm lengths of 0.28+/-0.02 mm for the extensor and 0.56+/-0.04 mm for the flexor. Resting extensor tibiae muscle passive tonic force increased from 2 to 5 mN in the maximum femur-tibia (FT)-joint working range when stretched by ramps. Active muscle properties were measured with simultaneous activation (up to 200 pulses s(-1)) of all three motoneurons innervating the extensor tibiae, because this reflects most closely physiological muscle activation during leg swing. The force-length relationship corresponds closely to the typical characteristic according to the sliding filament hypothesis: it has a plateau at medium fibre lengths, declines nearly linearly in force at both longer and shorter fibre lengths, and the muscle's working range lies in the short to medium fibre length range. Maximum contraction velocity showed a similar relationship. The force-velocity relationship was the traditional Hill curve hyperbola, but deviated from the hyperbolic shape in the region of maximum contraction force close to the isometric contraction. Step-like changes in muscle length induced by loaded release experiments characterised the non-linear series elasticity as a quadratic spring. [Abstract/Link to Full Text]

Holmberg A, Olsson C, Hennig GW
TTX-sensitive and TTX-insensitive control of spontaneous gut motility in the developing zebrafish (Danio rerio) larvae.
J Exp Biol. 2007 Mar;210(Pt 6):1084-91.
Spontaneous regular gut motility in zebrafish begins around 4 days post fertilisation (d.p.f.) and is modulated by release of acetylcholine and nitric oxide. The role of intrinsic or extrinsic innervation for initiating and propagating the spontaneous contractions, however, is not well understood. By creating spatiotemporal maps, we could examine spontaneous motility patterns in zebrafish larvae in vivo at 4 and 7 d.p.f. in more detail. Tetrodotoxin (TTX) was added to elucidate the importance of nervous control. Anterograde and retrograde contraction waves originated in the same region, just posterior to the intestinal bulb. This area correlates well with the distribution of Hu (human neuronal protein C/D)-immunoreactive nerve cell bodies. Whereas numerous immunoreactive nerve cells were present in the mid and distal intestine at both 4 and 7 d.p.f., fewer cells were seen anterior to the origin of contractions. The overall frequency of contractions (1.16+/-0.15 cycles min(-1), N=14 at 4 d.p.f.; 1.05+/-0.09 cycles min(-1), N=13 at 7 d.p.f.) and the interval between individual anterograde contraction waves (54.8+/-7.9 s at 4 d.p.f., N=14; 56.9+/-4.4 s, N=13 at 7 d.p.f.) did not differ between the two stages but the properties of the contractions were altered. The distance travelled by each wave increased from 591.0+/-43.8 microm at 4 d.p.f. (N=14) to 719.9+/-33.2 microm at 7 d.p.f. (N=13). By contrast, the velocity decreased from 4 d.p.f. (49.5+/-5.5 microm s(-1), N=12) to 7 d.p.f. (27.8+/-3.6 microm s(-1), N=13). At 4 d.p.f., TTX did not affect any of the parameters whereas at 7 d.p.f. anterograde frequency (control 1.07+/-0.12 cycles min(-1), N=8; TTX 0.55+/-0.13 cycles min(-1), N=8) and distance travelled (control 685.1+/-45.9 microm, N=8; TTX 318.7+/-88.7 microm, N=6) were decreased. In conclusion, enteric or extrinsic innervation does not seem to be necessary to initiate spontaneous contractions of the gut in zebrafish larvae. However, later in development, nerves have an increasingly important role as modulators of intestinal activity. [Abstract/Link to Full Text]

Bundle MW, Hansen KS, Dial KP
Does the metabolic rate-flight speed relationship vary among geometrically similar birds of different mass?
J Exp Biol. 2007 Mar;210(Pt 6):1075-83.
Based on aerodynamic considerations, the energy use-flight speed relationship of all airborne animals and aircraft should be U-shaped. However, measures of the metabolic rate-flight speed relationship in birds have been available since Tucker's pioneering experiments with budgerigars nearly forty years ago, but this classic work remains the only study to have found a clearly U-shaped metabolic power curve. The available data suggests that the energetic requirements for flight within this species are unique, yet the metabolic power curve of the budgerigar is widely considered representative of birds in general. Given these conflicting results and the observation that the budgerigar's mass is less than 50% of the next smallest species to have been studied, we asked whether large and small birds have metabolic power curves of different shapes. To address this question we measured the rates of oxygen uptake and wingbeat kinematics in budgerigars and cockatiels flying within a variable-speed wind tunnel. These species are close phylogenetic relatives, have similar flight styles, wingbeat kinematics, and are geometrically similar but have body masses that differ by a factor of two. In contrast to our expectations, we found the metabolic rate-flight speed relationship of both species to be acutely U-shaped. We also found that neither budgerigars nor cockatiels used their normal intermittent flight style while wearing a respirometric mask. We conclude that species size differences alone do not explain the previously unique metabolic power curve of the budgerigar; however, due to the absence of comparable data we cannot evaluate whether the mask-related kinematic response we document influences the metabolic rate-flight speed relationship of these parrots, or whether the energetics of flight differ between this and other avian clades. [Abstract/Link to Full Text]

Salvante KG, Lin G, Walzem RL, Williams TD
Characterization of very-low density lipoprotein particle diameter dynamics in relation to egg production in a passerine bird.
J Exp Biol. 2007 Mar;210(Pt 6):1064-74.
During avian egg production, oestrogen mediates marked increases in hepatic lipid production and changes in the diameter of assembled very-low density lipoprotein (VLDL). A nearly complete shift from generic VLDL ( approximately 70 nm in diameter), which transports lipids to peripheral tissues, to yolk-targeted VLDL (VLDLy) ( approximately 30 nm), which supplies the yolk with energy-rich lipid, has been observed in the plasma of laying domestic fowl. We validated an established dynamic laser scattering technique for a passerine songbird Taeniopygia guttata, the zebra finch, to characterize the dynamics of VLDL particle diameter distribution in relation to egg production. We predicted that non-gallinaceous avian species that have not been selected for maximum egg production would exhibit less dramatic shifts in lipid metabolism during egg production. As predicted, there was considerable overlap between the VLDL particle diameter distributions of laying and non-laying zebra finches. But unexpectedly, non-laying zebra finches had VLDL diameter distributions that peaked at small particles and had relatively few large VLDL particles. As a result, laying zebra finches, in comparison, had diameter distributions that were shifted towards larger VLDL particles. Nevertheless, laying zebra finches, like laying chickens, had larger proportions of particles within proposed VLDLy particle diameter ranges than non-laying zebra finches (e.g. sVLDLy: 50% vs 37%). Furthermore, zebra finches and chickens had similar modal (29.7 nm in both species) and median (32.7 nm vs 29.6 nm) VLDL particle diameters during egg production. Therefore, although zebra finches and chickens exhibited opposing directional shifts in VLDL particle diameter distribution during egg production, the modifications to VLDL particle structure in both species resulted in the realization of a common goal, i.e. to produce and maintain a large proportion of small VLDL particles of specific diameters that are capable of being incorporated into newly forming egg yolks. [Abstract/Link to Full Text]

Ross CF, Dharia R, Herring SW, Hylander WL, Liu ZJ, Rafferty KL, Ravosa MJ, Williams SH
Modulation of mandibular loading and bite force in mammals during mastication.
J Exp Biol. 2007 Mar;210(Pt 6):1046-63.
Modulation of force during mammalian mastication provides insight into force modulation in rhythmic, cyclic behaviors. This study uses in vivo bone strain data from the mandibular corpus to test two hypotheses regarding bite force modulation during rhythmic mastication in mammals: (1) that bite force is modulated by varying the duration of force production, or (2) that bite force is modulated by varying the rate at which force is produced. The data sample consists of rosette strain data from 40 experiments on 11 species of mammals, including six primate genera and four nonprimate species: goats, pigs, horses and alpacas. Bivariate correlation and multiple regression methods are used to assess relationships between maximum (epsilon(1)) and minimum (epsilon(2)) principal strain magnitudes and the following variables: loading time and mean loading rate from 5% of peak to peak strain, unloading time and mean unloading rate from peak to 5% of peak strain, chew cycle duration, and chew duty factor. Bivariate correlations reveal that in the majority of experiments strain magnitudes are significantly (P<0.001) correlated with strain loading and unloading rates and not with strain loading and unloading times. In those cases when strain magnitudes are also correlated with loading times, strain magnitudes are more highly correlated with loading rate than loading time. Multiple regression analyses reveal that variation in strain magnitude is best explained by variation in loading rate. Loading time and related temporal variables (such as overall chew cycle time and chew duty factor) do not explain significant amounts of additional variance. Few and only weak correlations were found between strain magnitude and chew cycle time and chew duty factor. These data suggest that bite force modulation during rhythmic mastication in mammals is mainly achieved by modulating the rate at which force is generated within a chew cycle, and less so by varying temporal parameters. Rate modulation rather than time modulation may allow rhythmic mastication to proceed at a relatively constant frequency, simplifying motor control computation. [Abstract/Link to Full Text]

Ebner HL, Blatzer M, Nawaz M, Krumschnabel G
Activation and nuclear translocation of ERK in response to ligand-dependent and -independent stimuli in liver and gill cells from rainbow trout.
J Exp Biol. 2007 Mar;210(Pt 6):1036-45.
The mitogen-activated protein kinase ERK is an important signalling molecule involved in the control of cell proliferation, differentiation and cell death, targeting molecules at the cell membrane, in the cytosol, and in the nucleus. This study investigated the activation pattern and subcellular distribution of ERK in liver and gill cells of rainbow trout upon hypo-osmotic shock, addition of epidermal growth factor (EGF) and copper treatment. It further set out to characterize the hypothetical role of nuclear-export signal (NES)-dependent relocation of ERK after nuclear entry and the potential involvement of the ERK activator MEK. Although, in primary hepatocytes, ERK was activated in all conditions in a stimulus-specific manner, it did not accumulate in the nucleus, irrespective of the absence or presence of the inhibitor of NES-dependent export leptomycin B (LB). Similarly, in trout hepatoma cells, where pERK levels increased upon osmotic and mitotic stimulation, but not after toxic insult, no significant nuclear translocation was observed. In a gill cell line, levels of pERK increased after osmotic and mitotic stimulation and showed a decrease during incubation with a toxicant. Again, none of these conditions triggered nuclear accumulation of pERK in the gill cells in the absence of LB, but in contrast to the observation in liver cells, both osmotic and mitotic stimulation caused nuclear accumulation in the presence of the inhibitor. The ERK activator MEK, which possesses a NES-sequence, was apparently not involved in nuclear export, as it did not seem to enter the nucleus. Altogether, ERK is activated in trout cells in a stimulus- and cell type-specific manner, and our data suggest that it acutely acts primarily on cytoplasmic or membrane-situated targets in liver cells, whereas it presumably triggers rapid transcriptional activities in gill cells. [Abstract/Link to Full Text]

Recent Articles in Biological Procedures Online

Conrad CC, Talent JM, Malakowsky CA, Gracy RW
Post-Electrophoretic Identification of Oxidized Proteins.
Biol Proced Online. 2000 Mar 23;239-45.
The oxidative modification of proteins has been shown to play a major role in a number of human diseases. However, the ability to identify specific proteins that are most susceptible to oxidative modifications is difficult. Separation of proteins using polyacrylamide gel electrophoresis (PAGE) offers the analytical potential for the recovery, amino acid sequencing, and identification of thousands of individual proteins from cells and tissues. We have developed a method to allow underivatized proteins to be electroblotted onto PVDF membranes before derivatization and staining. Since both the protein and oxidation proteins are quantifiable, the specific oxidation index of each protein can be determined. The optimal sequence and conditions for the staining process are (a) electrophoresis, (b) electroblotting onto PVDF membranes, (c) derivatization of carbonyls with 2,4-DNP, (d) immunostaining with anti DNP antibody, and (e) protein staining with colloidal gold. [Abstract/Link to Full Text]

Zheng W, Izaki J, Furusawa S, Yoshimura Y
A sensitive non-radioactive in situ hybridization method for the detection of chicken IgG gamma-chain mRNA: a technique suitable for detecting of variety of mRNAs in tissue sections.
Biol Proced Online. 2001 May 14;31-7.
We established a sensitive non-radioactive in situ hybridization (ISH) method for the detection of chicken IgG gamma-chain mRNA in paraffin sections. RNA probes were transcribed in vitro from cloned chicken IgG CH1 nucleotide sequences with SP6/T7 RNA polymerases in the presence of DIG-UTP. These probes were used for hybridization and were immunodetected using anti-DIG antibodies conjugated to horseradish peroxidase. The immunoreactive products were visualized with DAB-H(2)O(2). IgG gamma-chain mRNA-expressing cells were localized in both the spleen and oviductal tissues. This method demonstrated an excellent sensitivity since the ISH signal was clear and the background was negligible. We found that in the spleen IgG gamma-chain mRNA-expressing cells were present mainly in the red pulp, whereas in the oviduct they appeared mainly in the mucosal stroma and not in the mucosal epithelium. [Abstract/Link to Full Text]

Vannier-Santos MA, Lins U
Cytochemical techniques and energy-filtering transmission electron microscopy applied to the study of parasitic protozoa.
Biol Proced Online. 2001 Aug 4;38-18.
The study of parasitic protozoa plays a major role in cell biology, biochemistry and molecular biology. Numerous cytochemical techniques have been developed in order to unequivocally identify the nature of subcellular compartments. Enzyme and immuno-cytochemistry allow the detection of, respectively, enzymatic activity products and antigens in particular sites within the cell. Energy-filtering transmission electron microscopy permits the detection of specific elements within such compartments. These approaches are particularly useful for studies employing antimicrobial agents where cellular compartments may be destroyed or remarkably altered and thus hardly identified by standard methods of observation. In this regard cytochemical and spectroscopic techniques provide valuable data allowing the determination of the mechanisms of action of such compounds. [Abstract/Link to Full Text]

Marone M, Mozzetti S, De Ritis D, Pierelli L, Scambia G
Semiquantitative RT-PCR analysis to assess the expression levels of multiple transcripts from the same sample.
Biol Proced Online. 2001 Nov 16;319-25.
We describe a semiquantitative RT-PCR protocol optimized in our laboratory to extract RNA from as little as 10,000 cells and to measure the expression levels of several target mRNAs from each sample. This procedure was optimized on the human erythroleukemia cell line TF-1 but was successfully used on primary cells and on different cell lines. We describe the detailed procedure for the analysis of Bcl-2 levels. Aldolase A was used as an internal control to normalize for sample to sample variations in total RNA amounts and for reaction efficiency. As for all quantitative techniques, great care must be taken in all optimization steps: the necessary controls to ensure a rough quantitative (semi-quantitative) analysis are described here, together with an example from a study on the effects of TGF-beta1 in TF-1 cells. [Abstract/Link to Full Text]

Abou-Haila A, Tulsiani DR
Acid Glycohydrolases in Rat Spermatocytes, Spermatids and Spermatozoa: Enzyme Activities, Biosynthesis and Immunolocalization.
Biol Proced Online. 2001 Dec 3;335-42.
Mammalian sperm acrosome contains several glycohydrolases thought to aid in the dispersion and digestion of vestments surrounding the egg. In this study, we have used multiple approaches to examine the origin of acrosome-associated glycohdyrdolases. Mixed spermatogenic cells, prepared from rat testis, were separated by unit gravity sedimentation. The purified germ cells (spermatocytes [SP], round spermatids [RS], and elongated/condensed spermatids [E/CS]) contained several glycohydrolase activities. Metabolic labeling in the cell culture, immunoprecipitation, and autoradiographic approaches revealed that beta-D-galactosidase was synthesized in SP and RS in 88/90 kDa forms which undergo processing in a cell-specific manner. Immunohistochemical approaches demonstrated that the enzyme was localized in Golgi membranes/vesicles, and lysosome-like structures in SP and RS, and forming/formed acrosome of E/CS. [Abstract/Link to Full Text]

Ren J, Wold LE
Measurement of Cardiac Mechanical Function in Isolated Ventricular Myocytes from Rats and Mice by Computerized Video-Based Imaging.
Biol Proced Online. 2001 Dec 11;343-53.
Isolated adult cardiac ventricular myocytes have been a useful model for cardiovascular research for more than 20 years. With the recent advances in cellular physiology and transgenic techniques, direct measurement of isolated ventricular myocyte mechanics is becoming an increasingly important technique in cardiac physiology that provides fundamental information on excitation-contraction coupling of the heart, either in drug intervention or pathological states. The goal of this article is to describe the isolation of ventricular myocytes from both rats and mice, and the use of real-time beat-to-beat simultaneous recording of both myocyte contraction and intracellular Ca(2+) transient. [Abstract/Link to Full Text]

Franks DJ, Mroske C, Laneuville O
A fluorescence microscopy method for quantifying levels of prostaglandin endoperoxide H synthase-1 and CD-41 in MEG-01 cells.
Biol Proced Online. 2001 Dec 12;354-63.
In platelets, PGHS-1-dependant formation of thromboxane A(2) is an important modulator of platelet function and a target for pharmacological inhibition of platelet function by aspirin. Since platelets are a-nucleated cells, we have used the immortalized human megakaryoblastic cell line MEG-01 which can be induced to differentiate into platelet-like structures upon addition of TPA as a model system to study PGHS-1 gene expression. Using a specific antibody to PGHS-1 we have developed a technique utilizing immunofluorescence microscopy and analysis of multiple digital images to monitor PGHS-1 protein levels as MEG-01 cells were induced to differentiate by a single addition of TPA (1.6 x 10(-8) M) over a period of 8 days. The method represents a rapid and economical alternative to flow cytometry. Using this technique we observed that TPA induced adherence of MEG-01 cells, and only the non-adherent TPA-stimulated cells demonstrated compromised viability. The differentiation of MEG-01 cells was evaluated by the expression of the platelet-specific cell surface antigen, CD-41. The latter was expressed in MEG-01 cells at the later stages of differentiation. We demonstrated a good correlation between PGHS-1 levels and the overall level of cellular differentiation of MEG-01 cells. Furthermore, PGHS-1 protein level, which shows a consistent increase over the entire course of differentiation, can be used as an additional and better index by which to monitor megakaryocyte differentiation. [Abstract/Link to Full Text]

Baliga NS
Promoter analysis by saturation mutagenesis.
Biol Proced Online. 2001 Dec 22;364-69.
Gene expression and regulation are mediated by DNA sequences, in most instances, directly upstream to the coding sequences by recruiting transcription factors, regulators, and a RNA polymerase in a spatially defined fashion. Few nucleotides within a promoter make contact with the bound proteins. The minimal set of nucleotides that can recruit a protein factor is called a cis-acting element. This article addresses a powerful mutagenesis strategy that can be employed to define cis-acting elements at a molecular level. Technical details including primer design, saturation mutagenesis, construction of promoter libraries, phenotypic analysis, data analysis, and interpretation are discussed. [Abstract/Link to Full Text]

Schultheiss G, Lan Kocks S, Diener M
Methods for the study of ionic currents and Ca2+-signals in isolated colonic crypts.
Biol Proced Online. 2002 Apr 8;370-78.
Isolated epithelial cells from intestinal mucosae are a suitable object for the study of the regulation of ion transport in the gut. This regulation possesses a great importance for human and veterinary medicine, as diarrheal diseases, which often are caused by an inadequate activation of intestinal anion secretion, are one of the major lethal diseases of children or young animals. The aim of this paper is to describe a method for the isolation of intact colonic crypts, e.g. for the subsequent investigation of the regulation of anion secretion by the intracellular second messenger, Ca(2+) using electrophysiological and imaging techniques. [Abstract/Link to Full Text]

Mima K, Donai H, Yamauchi T
Investigation of Neuronal Cell Type-Specific Gene Expression of Ca2+/Calmodulin-dependent Protein Kinase II.
Biol Proced Online. 2002 Apr 12;379-90.
The promoter activity of the rat Ca(2+)/calmodulin-dependent protein kinase II gene was analyzed using the luciferase reporter gene in neuronal and non-neuronal cell lines. Neuronal cell type-specific promoter activity was found in the 5'-flanking region of alpha and beta isoform genes of the kinase. Silencer elements were also found further upstream of promoter regions. A brain-specific protein bound to the DNA sequence of the 5'-flanking region of the gene was found by gel mobility shift analysis in the nuclear extract of the rat brain, including the cerebellum, forebrain, and brainstem, but not in that of non-neuronal tissues, including liver, kidney and spleen. The luciferase expression system and gel shift analysis can be used as an additional and better index by which to monitor gene expression in most cell types. [Abstract/Link to Full Text]

Xin KQ, Sasaki S, Kojima Y, Jounai N, Kumamoto Y, Hashimoto K, Shinoda K, Hamajima K, Okuda K
Detection of Progeny Immune Responses after Intravenous Administration of DNA Vaccine to Pregnant Mice.
Biol Proced Online. 2002 Apr 23;391-101.
A number of factors influence the development of tolerance, including the nature, concentration and mode of antigen presentation to the immune system, as well as the age of the host. The studies were conducted to determine whether immunizing pregnant mice with liposome-encapsulated DNA vaccines had an effect on the immune status of their offspring. Two different plasmids (encoding antigens from HIV-1 and influenza virus) were administered intravenously to pregnant mice. At 9.5 days post conception with cationic liposomes, injected plasmid was present in the tissues of the fetus, consistent with trans-placental transfer. When the offspring of vaccinated dams were immunized with DNA vaccine, they mounted stronger antigen-specific immune responses than controls and were protected against challenge by homologous influenza virus after vaccination. Moreover, such immune responses were strong in the offspring of mothers injected with DNA plasmid 9.5 days after coitus. These results suggest that DNA vaccinated mothers confer the antigen-specific immunity to their progeny. Here we describe the methods in detail as they relate to our previously published work. [Abstract/Link to Full Text]

Zhu L, Goldstein B
Use of an Anaerobic Chamber Environment for the Assay of Endogenous Cellular Protein-Tyrosine Phosphatase Activities.
Biol Proced Online. 2002 Jun 11;41-9.
Protein-tyrosine phosphatases (PTPases) have a catalytic cysteine residue whose reduced state is integral to the reaction mechanism. Since exposure to air can artifactually oxidize this highly reactive thiol, PTPase assays have typically used potent reducing agents to reactivate the enzymes present; however, this approach does not allow for the measurement of the endogenous PTPase activity directly isolated from the in vivo cellular environment. Here we provide a method for using an anaerobic chamber to preserve the activity of the total PTPase complement in a tissue lysate or of an immunoprecipitated PTPase homolog to characterize their endogenous activation state. Comparison with a sample treated with biochemical reducing agents allows the determination of the activatable (reducible) fraction of the endogenous PTPase pool. [Abstract/Link to Full Text]

Muench MO, Suskind DL, B�rcena A
Isolation, growth and identification of colony-forming cells with erythroid, myeloid, dendritic cell and NK-cell potential from human fetal liver.
Biol Proced Online. 2002 Jun 11;410-23.
The study of hematopoietic stem cells (HSCs) and the process by which they differentiate into committed progenitors has been hampered by the lack of in vitro clonal assays that can support erythroid, myeloid and lymphoid differentiation. We describe a method for the isolation from human fetal liver of highly purified candidate HSCs and progenitors based on the phenotypes CD38(-)CD34(++) and CD38(+)CD34(++), respectively. We also describe a method for the growth of colony-forming cells (CFCs) from these cell populations, under defined culture conditions, that supports the differentiation of erythroid, CD14/CD15(+) myeloid, CD1a(+) dendritic cell and CD56(+) NK cell lineages. Flow cytometric analyses of individual colonies demonstrate that CFCs with erythroid, myeloid and lymphoid potential are distributed among both the CD38(-) and CD38(+) populations of CD34(++) progenitors. [Abstract/Link to Full Text]

Masson V L, Grignet-Debrus C, Bernt S, Bajou K, Blacher S, Roland G, Chang Y, Fong T, Carmeliet P, Foidart JM, No�l A
Mouse Aortic Ring Assay: A New Approach of the Molecular Genetics of Angiogenesis.
Biol Proced Online. 2002 Oct 28;424-31.
Angiogenesis, a key step in many physiological and pathological processes, involves proteolysis of the extracellular matrix. To study the role of two enzymatic families, serine-proteases and matrix metalloproteases in angiogenesis, we have adapted to the mouse, the aortic ring assay initially developed in the rat. The use of deficient mice allowed us to demonstrate that PAI-1 is essential for angiogenesis while the absence of an MMP, MMP-11, did not affect vessel sprouting. We report here that this model is attractive to elucidate the cellular and molecular mechanisms of angiogenesis, to identify, characterise or screen "pro- or anti-angiogenic agents that could be used for the treatment of angiogenesis-dependent diseases. Approaches include using recombinant proteins, synthetic molecules and adenovirus-mediated gene transfer. [Abstract/Link to Full Text]

Nistri S, Mazzetti L, Failli P, Bani D
High-Yield Method for Isolation and Culture of Endothelial Cells from Rat Coronary Blood Vessels Suitable for Analysis of Intracellular Calcium and Nitric Oxide Biosynthetic Pathways.
Biol Proced Online. 2002 Oct 28;432-37.
We describe here a method for isolating endothelial cells from rat heart blood vessels by means of coronary microperfusion with collagenase. This methods makes it possible to obtain high amounts of endothelial cells in culture which retain the functional properties of their in vivo counterparts, including the ability to uptake fluorescently-labeled acetylated low-density lipoproteins and to respond to vasoactive agents by modulating intracellular calcium and by upregulating intrinsic nitric oxide generation. The main advantages of our technique are: (i) good reproducibility, (ii) accurate sterility that can be maintained throughout the isolation procedure and (iii) high yield of pure endothelial cells, mainly due to microperfusion and temperature-controlled incubation with collagenase which allow an optimal distribution of this enzyme within the coronary vascular bed. [Abstract/Link to Full Text]

Fernandez-Patron C, Zouki C, Whittal RM, Chan JS, Davidge ST, Filep J
Methods for Analysis of Matrix Metalloproteinase Regulation of Neutrophil-Endothelial Cell Adhesion.
Biol Proced Online. 2002 Oct 28;438-48.
Recent evidence indicates novel role for matrix metalloproteinases (MMPs), in particular gelatinase A (MMP-2), in the regulation of vascular biology that are unrelated to their well-known proteolytic breakdown of matrix proteins. We have previously reported that MMP-2 can modulate vascular reactivity by cleavage of the Gly32-Leu33 bound in big endothelin-1 (ET-1) yielding a novel vasoactive peptide ET-1[1-32]. These studies were conducted to investigate whether gelatinolytic MMPs could affect neutrophil-endothelial cell attachment. ET-1[1-32] produced by MMP-2 up-regulated CD11b/CD18 expression on human neutrophils, thereby promoted their adhesion to cultured endothelial cells. ET-1[1-32] evoked release of gelatinase B (MMP-9), which in turn cleaved big ET-1 to yield ET-1[1-32], thus revealing a self-amplifying loop for ET-1[1-32] generation. ET-1[1-32] was rather resistant to cleavage by neutrophil proteases and further metabolism of ET-1[1-32] was not a prerequisite for its biological actions on neutrophils. The neutrophil responses to ET-1[1-32] were mediated via activation of ET(A)receptors through activation of the Ras/Raf-1/MEK/ERK signaling pathway. These results suggest a novel role for gelatinase A and B in the regulation of neutrophil functions and their interactions with endothelial cells. Here we describe the methods in detail as they relate to our previously published work. [Abstract/Link to Full Text]

I, Soramoto S, Suzuki M, Nishigaki K, Nemoto N, Husimi Y
An Efficient Ligation Method in the Making of an in vitro Virus for in vitro Protein Evolution.
Biol Proced Online. 2002 Oct 28;449-54.
The "in vitro virus" is a molecular construct to perform evolutionary protein engineering. The "virion (=viral particle)" (mRNA-peptide fusion), is made by bonding a nascent protein with its coding mRNA via puromycin in a test tube for in vitro translation. In this work, the puromycin-linker was attached to mRNA using the Y-ligation, which was a method of two single-strands ligation at the end of a double-stranded stem to make a stem-loop structure. This reaction gave a yield of about 95%. We compared the Y-ligation with two other ligation reactions and showed that the Y-ligation gave the best productivity. An efficient amplification of the in vitro virus with this "viral genome" was demonstrated. [Abstract/Link to Full Text]

Dunfield LD, Shepherd TG, Nachtigal MW
Primary culture and mRNA analysis of human ovarian cells.
Biol Proced Online. 2002 Oct 28;455-61.
Established cell lines are invaluable for studying cell and molecular biological questions. A variety of human ovarian cancer (OC) cell lines exist, however, most have acquired significant genetic alterations from their cells of origin, including deletion of important cell cycle regulatory genes. In order to analyze signaling events related to cell cycle control in human OC, we have modified existing protocols for isolating and culturing OC cells from patient ascites fluid and normal ovarian surface epithelial (OSE) cells from benign ovarian tissue sections. These cells maintain an epithelial phenotype and can be manipulated experimentally for several passages before cellular senescence. An example using TGFb1 treatment of OC cells to examine signaling and target gene activation is presented. [Abstract/Link to Full Text]

Klotzbucher A, Pascreau G, Prigent C, Arlot-Bonnemains Y
A Method for Analyzing the Ubiquitination and Degradation of Aurora-A.
Biol Proced Online. 2002 Nov 11;462-69.
The cell cycle machinery consists of regulatory proteins that control the progression through the cell cycle ensuring that DNA replication alternates with DNA segregation in mitosis to maintain cell integrity. Some of these key regulators have to be degraded at each cell cycle to prevent cellular dysfunction. Mitotic exit requires the inactivation of cyclin dependent kinase1 (cdk1) and it is the degradation of the cyclin subunit that inactivates the kinase. Cyclin degradation has been well characterized and it was shown that it is ubiquitin proteasome pathway that leads to the elimination of cyclins. By now, many other regulatory proteins were shown to be degraded by the same pathway, among them members of the aurora kinase family, degraded many other regulatory proteins. Aurora kinases are involved in mitotic spindle formation as well as in cytokinesis. The abundance and activity of the kinase is precisely regulated during the cell cycle. To understand how proteolysis regulates transitions through the cell cycle we describe two assays for ubiquitination and degradation of xenopus aurora kinase A using extracts from xenopus eggs or somatic cell lines. [Abstract/Link to Full Text]

Saveliev SV
PCR-based detection of a rare linear DNA in cell culture.
Biol Proced Online. 2002 Nov 11;470-80.
The described method allows for detection of rare linear DNA fragments generated during genomic deletions. The predicted limit of the detection is one DNA molecule per 10(7) or more cells. The method is based on anchor PCR and involves gel separation of the linear DNA fragment and chromosomal DNA before amplification. The detailed chemical structure of the ends of the linear DNA can be defined with the use of additional PCR-based protocols. The method was applied to study the short-lived linear DNA generated during programmed genomic deletions in a ciliate. It can be useful in studies of spontaneous DNA deletions in cell culture or for tracking intracellular modifications at the ends of transfected DNA during gene therapy trials. [Abstract/Link to Full Text]

Bao W, Str�mblad S
Use of an Immobilized Monoclonal Antibody to Examine Integrin alpha5beta1 Signaling Independent of Cell Spreading.
Biol Proced Online. 2002 Nov 11;481-87.
Cell attachment to the extracellular matrix (ECM) engages integrin signaling into the cell, but part of the signaling response also stem from cell spreading (3). To analyze specific integrin signaling-mediated responses independent of cell spreading, we developed a method engaging integrin signaling by use of an immobilized anti-integrin monoclonal antibody (mab) directed against the fibronectin (FN) receptor integrin alpha5beta1. ECV 304 cells were plated onto FN or immobilized mab JBS5 (anti-integrin alpha5beta1) or onto poly-L-lysin (P-L-L), which mediates integrin-independent attachment. Cells attached and spread on FN, while cells on JBS5 or P-L-L attached but did not spread. Importantly, plating onto FN or mab JBS5 gave rise to identical integrin-induced responses, including a down-regulation of the cyclin-dependent kinase (Cdk2) inhibitors p21(CIP1) and p27(KIP1), while attachment to P-L-L did not. We conclude that engagement of the FN-receptor integrin alpha5beta1 induces integrin signaling regulating the Cdk2-inhibitors independent of cell spreading and present a method for how integrin signaling can be analyzed separate from the effects of cell spreading. [Abstract/Link to Full Text]

�Ster B, H�llsberg P
A Sensitive Quantification of HHV-6B by Real-time PCR.
Biol Proced Online. 2002 Dec 9;488-93.
Human herpesvirus (HHV)-6B is a pathogen causing latent infection in virtually all humans. Nevertheless, the interaction of HHV-6B with its host cells is poorly understood. Although HHV-6B is approximately 90% homologous to HHV-6A, it expresses certain B-specific genes. In order to quantify the amount of expressed viral mRNA we have developed a method using real-time PCR on a LightCycler instrument. Here we describe an assay for the detection of the HHV-6B B6 mRNA, but our approach can easily be extended to involve other mRNAs. This method is useful during the study of HHV-6B biology and offers reliable and reproducible, quantitative detection of viral mRNA below the attomol range. [Abstract/Link to Full Text]

B�camel C, Gal�otti N, Poncet J, Jouin P, Dumuis A, Bockaert J, Marin P
A proteomic approach based on peptide affinity chromatography, 2-dimensional electrophoresis and mass spectrometry to identify multiprotein complexes interacting with membrane-bound receptors.
Biol Proced Online. 2002 Dec 9;494-104.
There is accumulating evidence that membrane-bound receptors interact with many intracellular proteins. Multiprotein complexes associated with ionotropic receptors have been extensively characterized, but the identification of proteins interacting with G protein-coupled receptors (GPCRs) has so far only been achieved in a piecemeal fashion, focusing on one or two protein species. We describe a method based on peptide affinity chromatography, two-dimensional electrophoresis, mass spectrometry and immunoblotting to identify the components of multiprotein complexes interacting directly or indirectly with intracellular domains of GPCRs or, more generally, any other membrane-bound receptor. Using this global approach, we have characterized multiprotein complexes that bind to the carboxy-terminal tail of the 5-hydroxytryptamine type 2C receptor and are important for its subcellular localization in CNS cells (B�camel et al., EMBO J., 21(10): 2332, 2002). [Abstract/Link to Full Text]

Mith�fer A, Mazars C
Aequorin-based measurements of intracellular Ca2+-signatures in plant cells.
Biol Proced Online. 2002 Dec 9;4105-118.
Due to the involvement of calcium as a main second messenger in the plant signaling pathway, increasing interest has been focused on the calcium signatures supposed to be involved in the patterning of the specific response associated to a given stimulus. In order to follow these signatures we described here the practical approach to use the non-invasive method based on the aequorin technology. Besides reviewing the advantages and disadvantages of this method we report on results showing the usefulness of aequorin to study the calcium response to biotic (elicitors) and abiotic stimuli (osmotic shocks) in various compartments of plant cells such as cytosol and nucleus. [Abstract/Link to Full Text]

Aberle II NS, Ren J
Experimental Assessment of the Role of Acetaldehyde in Alcoholic Cardiomyopathy.
Biol Proced Online. 2003;51-12.
Alcoholism is one of the major causes of non-ischemic heart damage. The myopathic state of the heart due to alcohol consumption, namely alcoholic cardiomyopathy, is manifested by cardiac hypertrophy, compromised ventricular contractility and cardiac output. Several mechanisms have been postulated for alcoholic cardiomyopathy including oxidative damage, accumulation of triglycerides, altered fatty acid extraction, decreased myofilament Ca(2+ )sensitivity, and impaired protein synthesis. Despite intensive efforts to unveil the mechanism and ultimate toxin responsible for alcohol-induced cardiac toxicity, neither has been clarified thus far. Primary candidates for the specific toxins are ethanol, its first and major metabolic product - acetaldehyde (ACA) and fatty acid ethyl esters. Evidence from our lab suggests that ACA directly impairs cardiac function and promotes lipid peroxidation resulting in oxidative damage. The ACA-induced cardiac contractile depression may be reconciled with inhibitors of Cytochrome P-450 oxidase, xanthine oxidase and lipid peroxidation Unfortunately, the common methods to investigate the toxicity of ACA have been hampered by the fact that direct intake of ACA is toxic and unsuitable for chronic study, which is unable to provide direct evidence of direct cardiac toxicity for ACA. In order to overcome this obstacle associated with the chemical properties of ACA, our laboratory has used the chronic ethanol feeding model in transgenic mice with cardiac over-expression of alcohol dehydrogenase (ADH) and an in vitro ventricular myocyte culture model. The combination of both in vivo and in vitro approaches allows us to evaluate the role of ACA in ethanol-induced cardiac toxicity and certain cellular signaling pathways leading to alcoholic cardiomyopathy. [Abstract/Link to Full Text]

Smith DC, Marsden CJ, Lord JM, Roberts LM
Expression, Purification and Characterization of Ricin vectors used for exogenous antigen delivery into the MHC Class I presentation pathway.
Biol Proced Online. 2003;513-19.
Disarmed versions of the cytotoxin ricin can deliver fused peptides into target cells leading to MHC class I-restricted antigen presentation [Smith et al. J Immunol 2002; 169:99-107]. The ricin delivery vector must contain an attenuated catalytic domain to prevent target cell death, and the fused peptide epitope must remain intact for delivery and functional loading to MHC class I molecules. Expression in E. coli and purification by cation exchange chromatography of the fusion protein is described. Before used for delivery, the activity of the vector must be characterized in vitro, via an N-glycosidase assay, and in vivo, by a cytotoxicity assay. The presence of an intact epitope must be confirmed using mass spectrometry by comparing the actual mass with the predicted mass. [Abstract/Link to Full Text]

Meadus WJ
A semi-quantitative RT-PCR method to measure the in vivo effect of dietary conjugated linoleic acid on porcine muscle PPAR gene expression.
Biol Proced Online. 2003;520-28.
Conjugated linoleic acid (CLA) can activate (in vitro) the nuclear transcription factors known as the peroxisome proliferators activated receptors (PPAR). CLA was fed at 11 g CLA/kg of feed for 45d to castrated male pigs (barrows) to better understand long term effects of PPAR activation in vivo. The barrows fed CLA had lean muscle increased by 3.5% and overall fat reduced by 9.2% but intramuscular fat (IMF %) was increased by 14% (P < 0.05). To measure the effect of long term feeding of CLA on porcine muscle gene expression, a semi-quantitative RT-PCR method was developed using cDNA normalized against the housekeeping genes cyclophilin and beta-actin. This method does not require radioactivity or expensive PCR instruments with real-time fluorescent detection. PPARgamma and the PPAR responsive gene AFABP but not PPARalpha were significantly increased (P < 0.05) in the CLA fed pig's muscle. PPARalpha and PPARgamma were also quantitatively tested for large differences in gene expression by western blot analysis but no significant difference was detected at this level. Although large differences in gene expression of the PPAR transcriptional factors could not be confirmed by western blotting techniques. The increased expression of AFABP gene, which is responsive to PPAR transcriptional factors, confirmed that dietary CLA can induce a detectable increase in basal PPAR transcriptional activity in the live animal. [Abstract/Link to Full Text]

Gunge N, Takata H, Matsuura A, Fukuda K
Progressive Rearrangement of Telomeric Sequences Added to Both the ITR Ends of the Yeast Linear pGKL Plasmid.
Biol Proced Online. 2003;529-42.
Relocation into the nucleus of the yeast cytoplasmic linear plasmids was studied using a monitor plasmid pCLU1. In Saccharomyces cerevisiae, the nuclearly-relocated pCLU1 replicated in a linear form (termed pTLU-type plasmid) which carried the host telomeric repeats TG(1-3) of 300-350 bp at both ends. The telomere sequences mainly consisted of a major motif TGTGTGGGTGTGG which was complementary to part of the RNA template of yeast telomerase and were directly added to the very end of the pCLU1-terminal element ITR (inverted terminal repeat), suggesting that the ITR end played a role as a substrate of telomerase. The telomere sequences varied among isolated pTLU-type plasmids, but the TG(1-3) organization was symmetrically identical on both ends of any one plasmid. During cell growth under non-selective condition, the telomeric repeat sequences were progressively rearranged on one side, but not on the opposite side of pTLU plasmid ends. This indicates that the mode of telomeric DNA replication or repair differed between both ends. Clonal analysis showed that the intense rearrangement of telomeric DNA was closely associated with extreme instability of pTLU plasmids. [Abstract/Link to Full Text]

Bartlett EJ, Cull VS, Mowe EN, Mansfield JP, James CM
Optimization of Naked DNA Delivery for Interferon Subtype Immunotherapy in Cytomegalovirus Infection.
Biol Proced Online. 2003;543-52.
Type I interferon (IFN) gene therapy modulates the immune response leading to inflammatory heart disease following cytomegalovirus (CMV) infection in a murine model of post-viral myocarditis. Efficacy of different immunisation protocols for the IFN constructs was influenced by the dose of DNA, subtype choice, combination use, pre-medication, and timing of DNA administration. Optimal efficacy was found with bupivacaine treatment prior to DNA inoculation of 200mg IFN DNA 14 days prior to virus challenge. Maximal antiviral and antimyocarditic effects were achieved with this vaccination schedule. Furthermore, inoculation of synergistic IFN subtypes demonstrated enhanced efficacy when delivered either alone or with CMV gB DNA vaccination in the CMV model. Thus naked DNA delivery of IFN provides an avenue of immunotherapy for regulating herpesvirus-induced diseases. [Abstract/Link to Full Text]

Nunemaker CS, DeFazio RA, Moenter SM
A targeted extracellular approach for recording long-term firing patterns of excitable cells: a practical guide.
Biol Proced Online. 2003;553-62.
Excitable cells in many endocrine and neuronal systems display rhythms with periodicities on the order of many minutes. To observe firing patterns that represent the output of these rhythms requires a recording technique that can monitor electrophysiological activity for several hours without affecting cell behavior. A targeted extracellular approach (also known as loose-patch) accomplishes this objective. Because low resistance seals (<20 MOmega) do not influence the cell membrane and because the normal intracellular milieu is maintained, this approach is the least invasive method for monitoring the endogenous electrical activity of single cells. In this report, we detail our use of this technique to record the firing patterns of gonadotropin-releasing hormone (GnRH) neurons in brain slices continuously for several hours. [Abstract/Link to Full Text]

Recent Articles in BMC Developmental Biology

Geoffroy CG, Raineteau O
A Cre-lox approach for transient transgene expression in neural precursor cells and long-term tracking of their progeny in vitro and in vivo.
BMC Dev Biol. 2007;745.
BACKGROUND: Neural precursor cells (NPCs) can be isolated from various regions of the postnatal central nervous system (CNS). Manipulation of gene expression in these cells offers a promising strategy to manipulate their fate both in vitro and in vivo. In this study, we developed a technique that allows the transient manipulation of single/multiple gene expression in NPCs in vitro, and the long-term tracking of their progeny both in vitro and in vivo. RESULTS: In order to combine the advantages of transient transfection with the long-term tracking of the transfected cells progeny, we developed a new approach based on the cre-lox technology. We first established a fast and reliable protocol to isolate and culture NPCs as monolayer, from the spinal cord of neonatal transgenic Rosa26-YFP cre-reporter mice. These cells could be reliably transfected with single/multiple plasmids by nucleofection. Nucleofection with mono- or bicistronic plasmids containing the Cre recombinase gene resulted in efficient recombination and the long-term expression of the YFP-reporter gene. The transient cre-expression was non-toxic for the transfected cells and did not alter their intrinsic properties. Finally, we demonstrated that cre-transfected cells could be transplanted into the adult brain, where they maintained YFP expression permitting long-term tracking of their migration and differentiation. CONCLUSION: This approach allows single/multiple genes to be manipulated in NPCs, while at the same time allowing long-term tracking of the transfected cells progeny to be analyzed both in vitro and in vivo. [Abstract/Link to Full Text]

Prabhu Y, M�ller R, Anjard C, Noegel AA
GrlJ, a Dictyostelium GABAB-like receptor with roles in post-aggregation development.
BMC Dev Biol. 2007;744.
BACKGROUND: The G-protein-coupled receptor (GPCR) family represents the largest and most important group of targets for chemotherapeutics. They are extremely versatile receptors that transduce signals as diverse as biogenic amines, purins, odorants, ions and pheromones from the extracellular compartment to the interior via biochemical processes involving GTP-binding proteins. Until recently, the cyclic AMP receptors (cARs) were the only known G protein coupled receptors in Dictyostelium discoideum. The completed genome sequence revealed the presence of several families of GPCRs in Dictyostelium, among them members of the family 3 of GPCRs, the GABAB/glutamate like receptor family, which in higher eukaryotes is involved in neuronal signaling. RESULTS: D. discoideum has seventeen Family 3 members of GPCRs, denoted GrlA through GrlR. Their transcripts are detected throughout development with increased levels during early and late development. We have examined here GrlJ. GFP-tagged GrlJ localises to the plasma-membrane and to internal membranes. Inactivation of the grlJ gene leads to precocious development, and the mutant completes development ~6 hours earlier. Alterations were also noted at the slug stage and in spore formation. grlJ- slugs were longer and broke apart several times on their way to culmination forming smaller but proportionate fruiting bodies. Spores from grlJ- fruiting bodies were malformed and less viable, although the spore differentiation factors were synthesized and sensed normally. Expression of a GFP-tagged full length GrlJ rescued the phenotype. CONCLUSION: Our data suggest that GrlJ acts at several stages of Dictyostelium development and that it is a negative regulator in Dictyostelium development. [Abstract/Link to Full Text]

Su VF, Jones KA, Brodsky M, The I
Quantitative analysis of Hedgehog gradient formation using an inducible expression system.
BMC Dev Biol. 2007;743.
BACKGROUND: The Hedgehog (Hh) family of secreted growth factors are morphogens that act in development to direct growth and patterning. Mutations in human Hh and other Hh pathway components have been linked to human diseases. Analysis of Hh distribution during development indicates that cholesterol modification and receptor mediated endocytosis affect the range of Hh signaling and the cellular localization of Hh. RESULTS: We have used an inducible, cell type-specific expression system to characterize the three-dimensional distribution of newly synthesized, GFP-tagged Hh in the developing Drosophila wing. Following induction of Hh-GFP expression in posterior producing cells, punctate structures containing Hh-GFP were observed in the anterior target cells. The distance of these particles from the expressing cells was quantified to determine the shape of the Hh gradient at different time points following induction. The majority of cholesterol-modified Hh-GFP was found associated with cells near the anterior/posterior (A/P) boundary, which express high levels of Hh target genes. Without cholesterol, the Hh gradient was flatter, with a lower percentage of particles near the source and a greater maximum distance. Inhibition of Dynamin-dependent endocytosis blocked formation of intracellular Hh particles, but did not prevent movement of newly synthesized Hh to the apical or basolateral surfaces of target cells. In the absence of both cholesterol and endocytosis, Hh particles accumulated in the extracellular space. Staining for the Hh receptor Ptc revealed four categories of Hh particles: cytoplasmic with and without Ptc, and cell surface with and without Ptc. Interestingly, mainly cholesterol-modified Hh is detected in the cytoplasmic particles lacking Ptc. CONCLUSION: We have developed a system to quantitatively analyze Hh distribution during gradient formation. We directly demonstrate that inhibition of Dynamin-dependent endocytosis is not required for movement of Hh across target cells, indicating that transcytosis is not required for Hh gradient formation. The localization of Hh in these cells suggests that Hh normally moves across both apical and basolateral regions of the target cells. We also conclude that cholesterol modification is required for formation of a specific subset of Hh particles that are both cytoplasmic and not associated with the receptor Ptc. [Abstract/Link to Full Text]

Hall C, Flores MV, Storm T, Crosier K, Crosier P
The zebrafish lysozyme C promoter drives myeloid-specific expression in transgenic fish.
BMC Dev Biol. 2007;742.
BACKGROUND: How different immune cell compartments contribute to a successful immune response is central to fully understanding the mechanisms behind normal processes such as tissue repair and the pathology of inflammatory diseases. However, the ability to observe and characterize such interactions, in real-time, within a living vertebrate has proved elusive. Recently, the zebrafish has been exploited to model aspects of human disease and to study specific immune cell compartments using fluorescent reporter transgenic lines. A number of blood-specific lines have provided a means to exploit the exquisite optical clarity that this vertebrate system offers and provide a level of insight into dynamic inflammatory processes previously unavailable. RESULTS: We used regulatory regions of the zebrafish lysozyme C (lysC) gene to drive enhanced green fluorescent protein (EGFP) and DsRED2 expression in a manner that completely recapitulated the endogenous expression profile of lysC. Labeled cells were shown by co-expression studies and FACS analysis to represent a subset of macrophages and likely also granulocytes. Functional assays within transgenic larvae proved that these marked cells possess hallmark traits of myelomonocytic cells, including the ability to migrate to inflammatory sources and phagocytose bacteria. CONCLUSION: These reporter lines will have utility in dissecting the genetic determinants of commitment to the myeloid lineage and in further defining how lysozyme-expressing cells participate during inflammation. [Abstract/Link to Full Text]

McGovern M, Yu L, Kosinski M, Greenstein D, Savage-Dunn C
A role for sperm in regulation of egg-laying in the nematode C. elegans.
BMC Dev Biol. 2007;741.
BACKGROUND: In insects and in mammals, male sperm and seminal fluid provide signaling factors that influence various aspects of female physiology and behavior to promote reproductive success and to compete with other males. It is less apparent how important such signaling is in the context of a self-fertile hermaphrodite species. We have addressed this question in the nematode Caenorhabditis elegans, which can reproduce either by hermaphrodite self-fertilization or by male-hermaphrodite mating. RESULTS: We have studied the egg-laying defective mutant, egl-32, and found that the cellular basis of the egl-32 egg-laying phenotype is likely a defect in sperm. First, the time of egl-32 action coincides with the timing of spermatogenesis in the hermaphrodite. Second, egl-32 interacts with genes expressed in sperm. Third, mating experiments have revealed that wild-type sperm can rescue the egg-laying defect of egl-32 mutant animals. Most importantly, introduction of mutant egl-32 sperm into wild-type hermaphrodites or females is sufficient to induce an egg-laying defective phenotype. CONCLUSION: Previous work has revealed that C. elegans sperm release factors that stimulate oocyte maturation and ovulation. Here we describe evidence that sperm also promote egg laying, the release of embryos from the uterus. [Abstract/Link to Full Text]

Davies JA
Developmental biologists' choice of subjects approximates to a power law, with no evidence for the existence of a special group of 'model organisms'.
BMC Dev Biol. 2007;740.
BACKGROUND: This report describes an unexpected aspect of the structure and development of developmental biology research, rather than the development of a specific embryo. Descriptions of modern developmental biology emphasize investigators' concentration on a small number of 'model' organisms and it is assumed that a clear division exists between the attention paid to these 'model' organisms and that paid to other species. This report describes a quantitative analysis of the organisms that were the subjects of studies reported in developmental biology journals published in the years 1965, 1975, 1985, 1995 and 2005, chosen to represent five decades of modern developmental biology. RESULTS: The results demonstrate that the distribution of attention paid to different organisms has a smooth distribution that approximates to a scale-free power law, in which there is no clear discontinuity that divides organisms into 'models' and the rest. This is true for both individual years and for the aggregate of all years' data. In other systems (eg connections in the World Wide Web), such power-law distributions arise from mechanisms of preferential attachment ('the rich get richer'). Detailed analysis of the progress of different organisms over the years under study shows that, while preferential attachment may be part of the mechanism that generates the power law distribution, it is insufficient to explain it. CONCLUSION: The smoothness of the distribution suggests that there is no empirical basis for dividing species under study into 'model' organisms and 'the rest', and that the widely-held view about organism choice in developmental biology is distorted. [Abstract/Link to Full Text]

Pirity MK, Wang WL, Wolf LV, Tamm ER, Schreiber-Agus N, Cvekl A
Rybp, a polycomb complex-associated protein, is required for mouse eye development.
BMC Dev Biol. 2007;739.
BACKGROUND: Rybp (Ring1 and YY1 binding protein) is a zinc finger protein which interacts with the members of the mammalian polycomb complexes. Previously we have shown that Rybp is critical for early embryogenesis and that haploinsufficiency of Rybp in a subset of embryos causes failure of neural tube closure. Here we investigated the requirement for Rybp in ocular development using four in vivo mouse models which resulted in either the ablation or overexpression of Rybp. RESULTS: Our results demonstrate that loss of a single Rybp allele in conventional knockout mice often resulted in retinal coloboma, an incomplete closure of the optic fissure, characterized by perturbed localization of Pax6 but not of Pax2. In addition, about one half of Rybp-/- <-> Rybp+/+ chimeric embryos also developed retinal colobomas and malformed lenses. Tissue-specific transgenic overexpression of Rybp in the lens resulted in abnormal fiber cell differentiation and severe lens opacification with increased levels of AP-2alpha and Sox2, and reduced levels of betaA4-crystallin gene expression. Ubiquitous transgenic overexpression of Rybp in the entire eye caused abnormal retinal folds, corneal neovascularization, and lens opacification. Additional changes included defects in anterior eye development. CONCLUSION: These studies establish Rybp as a novel gene that has been associated with coloboma. Other genes linked to coloboma encode various classes of transcription factors such as BCOR, CBP, Chx10, Pax2, Pax6, Six3, Ski, Vax1 and Vax2. We propose that the multiple functions for Rybp in regulating mouse retinal and lens development are mediated by genetic, epigenetic and physical interactions between these genes and proteins. [Abstract/Link to Full Text]

Ouellet J, Roy R
The lin-35/Rb and RNAi pathways cooperate to regulate a key cell cycle transition in C. elegans.
BMC Dev Biol. 2007;738.
BACKGROUND: The Retinoblastoma gene product (Rb) has been shown to regulate the transcription of key genes involved in cell growth and proliferation. Consistent with this, mutations in Rb are associated with numerous types of cancer making it a critical tumour suppressor gene. Its function is conferred through a large multiprotein complex that exhibits a dual function in both activation and repression of gene targets. In C. elegans, the Rb orthologue lin-35 functions redundantly with other transcriptional regulators to appropriately specify both vulval and pharyngeal cell fates. RESULTS: In C. elegans the intestinal cells must alter their cell cycle from the mitotic cell divisions typical of embryogenesis to karyokinesis and then endoreplication, which facilitates growth during larval development. While screening for genes that affect the ability of the intestinal cells to appropriately make this cell cycle transition during post-embryonic development, we isolated mutants that either compromise this switch and remain mononucleate, or cause these cells to undergo multiple rounds of nuclear division. Among these mutants we identified a novel allele of lin-35/Rb, while we also found that the components of the synMuv B complex, which are involved in vulval specification, are also required to properly regulate the developmentally-controlled cell cycle transition typical of these intestinal cells during larval development. More importantly, our work uncovered a role for certain members of the pathways involved in RNAi in mediating the efficient transition between these cell cycle programs, suggesting that lin-35/Rb cooperates with these RNAi components. Furthermore, our findings suggest that met-2, a methyltransferase as well as hpl-1 and hpl-2, two C. elegans homologues of the heterochromatin protein HP1 are also required for this transition. CONCLUSION: Our findings are consistent with lin-35/Rb, synMuv and RNAi components cooperating, probably through their additive effects on chromatin modification, to appropriately modulate the expression of genes that are required to switch from the karyokinesis cell cycle to endoreplication; a highly specified growth pathway in the intestinal epithelium. The lin-35/Rb repressor complex may be required to initiate this process, while components of the RNAi machinery positively reinforce this repression. [Abstract/Link to Full Text]

Watt AJ, Zhao R, Li J, Duncan SA
Development of the mammalian liver and ventral pancreas is dependent on GATA4.
BMC Dev Biol. 2007;737.
BACKGROUND: In the mouse, the parenchyma of both the liver and ventral pancreas is specified from adjacent domains of the ventral foregut endoderm. GATA4, a zinc finger transcription factor, is strongly expressed in these endodermal domains and molecular analyses have implicated GATA4 in potentiating liver gene expression during the onset of hepatogenesis. We therefore hypothesized that GATA4 has an integral role in controlling the early stages of pancreatic and liver development. RESULTS: To determine whether GATA4 contributes to development of either the pancreas or liver we characterized the formation of pancreatic and hepatic tissues in embryos derived from Gata4-/- ES cells by tetraploid embryo complementation. In the absence of GATA4, development of the liver and ventral pancreas was disrupted. At embryonic day (E) 9.5, the liver bud failed to expand although, contrary to expectations, the hepatic endoderm was able to form a pseudo-stratified epithelial liver bud that expressed hepatic genes. Moreover, as we had shown previously, the embryos lacked septum transversum mesenchyme suggesting that liver defects may be cell non-autonomous. Analyses of pancreatic development revealed a complete absence of the ventral but not the dorsal pancreas in Gata4-/- embryos. Moreover, Gata6-/- embryos displayed a similar, although less dramatic phenotype, suggesting a critical role for multiple GATA factors at the earliest stages of ventral pancreas development. CONCLUSION: This study defines integral roles for GATA factors in controlling early development of the mammalian liver and pancreas. [Abstract/Link to Full Text]

Lucifero D, La Salle S, Bourc'his D, Martel J, Bestor TH, Trasler JM
Coordinate regulation of DNA methyltransferase expression during oogenesis.
BMC Dev Biol. 2007;736.
BACKGROUND: Normal mammalian development requires the action of DNA methyltransferases (DNMTs) for the establishment and maintenance of DNA methylation within repeat elements and imprinted genes. Here we report the expression dynamics of Dnmt3a and Dnmt3b, as well as a regulator of DNA methylation, Dnmt3L, in isolated female germ cells. RESULTS: Our results indicate that these enzymes are coordinately regulated and that their expression peaks during the stage of postnatal oocyte development when maternal methylation imprints are established. We find that Dnmt3a, Dnmt3b, Dnmt3L and Dnmt1o transcript accumulation is related to oocyte diameter. Furthermore, DNMT3L deficient 15 dpp oocytes have aberrantly methylated Snrpn, Peg3 and Igf2r DMRs, but normal IAP and LINE-1 methylation levels, thereby highlighting a male germ cell specific role for DNMT3L in the establishment of DNA methylation at repeat elements. Finally, real-time RT-PCR analysis indicates that the depletion of either DNMT3L or DNMT1o in growing oocytes results in the increased expression of the de novo methyltransferase Dnmt3b, suggesting a potential compensation mechanism by this enzyme for the loss of one of the other DNA methyltransferases. CONCLUSION: Together these results provide a better understanding of the developmental regulation of Dnmt3a, Dnmt3b and Dnmt3L at the time of de novo methylation during oogenesis and demonstrate that the involvement of DNMT3L in retrotransposon silencing is restricted to the male germ line. This in turn suggests the existence of other factors in the oocyte that direct DNA methylation to transposons. [Abstract/Link to Full Text]

Klink VP, Martins VE, Alkharouf NW, Overall CC, MacDonald MH, Matthews BF
A decline in transcript abundance for Heterodera glycines homologs of Caenorhabditis elegans uncoordinated genes accompanies its sedentary parasitic phase.
BMC Dev Biol. 2007;735.
BACKGROUND: Heterodera glycines (soybean cyst nematode [SCN]), the major pathogen of Glycine max (soybean), undergoes muscle degradation (sarcopenia) as it becomes sedentary inside the root. Many genes encoding muscular and neuromuscular components belong to the uncoordinated (unc) family of genes originally identified in Caenorhabditis elegans. Previously, we reported a substantial decrease in transcript abundance for Hg-unc-87, the H. glycines homolog of unc-87 (calponin) during the adult sedentary phase of SCN. These observations implied that changes in the expression of specific muscle genes occurred during sarcopenia. RESULTS: We developed a bioinformatics database that compares expressed sequence tag (est) and genomic data of C. elegans and H. glycines (CeHg database). We identify H. glycines homologs of C. elegans unc genes whose protein products are involved in muscle composition and regulation. RT-PCR reveals the transcript abundance of H. glycines unc homologs at mobile and sedentary stages of its lifecycle. A prominent reduction in transcript abundance occurs in samples from sedentary nematodes for homologs of actin, unc-60B (cofilin), unc-89, unc-15 (paromyosin), unc-27 (troponin I), unc-54 (myosin), and the potassium channel unc-110 (twk-18). Less reduction is observed for the focal adhesion complex gene Hg-unc-97. CONCLUSION: The CeHg bioinformatics database is shown to be useful in identifying homologs of genes whose protein products perform roles in specific aspects of H. glycines muscle biology. Our bioinformatics comparison of C. elegans and H. glycines genomic data and our Hg-unc-87 expression experiments demonstrate that the transcript abundance of specific H. glycines homologs of muscle gene decreases as the nematode becomes sedentary inside the root during its parasitic feeding stages. [Abstract/Link to Full Text]

Kamel R, Garcia S, Lezoualc'h F, Fischmeister R, Muller S, Hoebek J, Eftekhari P
Immunomodulation by maternal autoantibodies of the fetal serotoninergic 5-HT4 receptor and its consequences in early BALB/c mouse embryonic development.
BMC Dev Biol. 2007;734.
BACKGROUND: The presence of functional 5-HT4 receptors in human and its involvement in neonatal lupus erythematosus (NLE) have prompted us to study the receptor expression and role during embryogenesis. Earlier we managed to demonstrate that female BALB/c mice immunized against the second extracellular loop (SEL) of the 5-HT4 receptor gave birth to pups with heart block. To explain this phenomenon we investigated the expression of 5-HT4 receptors during mouse embryogenesis. At the same time we looked whether the consequence of 5-HT4 receptor immunomodulation observed earlier is in relation to receptor expression.We studied the expression of 5-HT4 receptor at the mRNA level and its two isoforms 5-HT4(a) and 5-HT4(d) at the protein level in embryos from BALB/c mice, at 8th, 12th, 18th gestation days (GD) and 1 day post natal (DPN). Simultaneously the receptor activity was inhibited by rising antibodies, in female mice against SEL of the receptor. The mice were mated and embryos were collected at 8th, 12th, 18th GD and 1 DPN. RESULTS: 5-HT4 receptor mRNA increased in brain from 12th GD to 1 DPN. Its expression gradually decreased in heart and disappeared at birth. This was consistent with expression of the receptor isoforms 5-HT4(a) and (d). Abnormalities like decreased number of embryos, growth delay, spina bifida and sinus arrhythmia from 12th GD were documented in pups of mice showing anti-5-HT4 receptor antibodies. CONCLUSION: serotoninergic 5-HT4 receptor plays an important role in mouse foetal development. In BALB/c mice there is a direct relation between the expression of receptor and the deleterious effect of maternal anti-5-HT4 receptor autoantibodies in early embryogenesis. [Abstract/Link to Full Text]

Strathmann FG, Wang X, Mayer-Pr�schel M
Identification of two novel glial-restricted cell populations in the embryonic telencephalon arising from unique origins.
BMC Dev Biol. 2007;733.
BACKGROUND: Considerably less attention has been given to understanding the cellular components of gliogenesis in the telencephalon when compared to neuronogenesis, despite the necessity of normal glial cell formation for neurological function. Early proposals of exclusive ventral oligodendrocyte precursor cell (OPC) generation have been challenged recently with studies revealing the potential of the dorsal telencephalon to also generate oligodendrocytes. The identification of OPCs generated from multiple regions of the developing telencephalon, together with the need of the embryonic telencephalon to provide precursor cells for oligodendrocytes as well as astrocytes in ventral and dorsal areas, raises questions concerning the identity of the precursor cell populations capable of generating macroglial subtypes during multiple developmental windows and in differing locations. RESULTS: We have identified progenitor populations in the ventral and dorsal telencephalon restricted to the generation of astrocytes and oligodendrocytes. We further demonstrate that the dorsal glial progenitor cells can be generated de novo from the dorsal telencephalon and we demonstrate their capacity for in vivo production of both myelin-forming oligodendrocytes and astrocytes upon transplantation. CONCLUSION: Based on our results we offer a unifying model of telencephalic gliogenesis, with the generation of both oligodendrocytes and astrocytes from spatially separate, but functionally similar, glial restricted populations at different developmental times in the dorsal and ventral CNS. [Abstract/Link to Full Text]

Caltharp SA, Pira CU, Mishima N, Youngdale EN, McNeill DS, Liwnicz BH, Oberg KC
NOGO-A induction and localization during chick brain development indicate a role disparate from neurite outgrowth inhibition.
BMC Dev Biol. 2007;732.
BACKGROUND: Nogo-A, a myelin-associated protein, inhibits neurite outgrowth and abates regeneration in the adult vertebrate central nervous system (CNS) and may play a role in maintaining neural pathways once established. However, the presence of Nogo-A during early CNS development is counterintuitive and hints at an additional role for Nogo-A beyond neurite inhibition. RESULTS: We isolated chicken NOGO-A and determined its sequence. A multiple alignment of the amino acid sequence across divergent species, identified five previously undescribed, Nogo-A specific conserved regions that may be relevant for development. NOGO gene transcripts (NOGO-A, NOGO-B and NOGO-C) were differentially expressed in the CNS during development and a second NOGO-A splice variant was identified. We further localized NOGO-A expression during key phases of CNS development by in situ hybridization. CNS-associated NOGO-A was induced coincident with neural plate formation and up-regulated by FGF in the transformation of non-neural ectoderm into neural precursors. NOGO-A expression was diffuse in the neuroectoderm during the early proliferative phase of development, and migration, but localized to large projection neurons of the optic tectum and tectal-associated nuclei during architectural differentiation, lamination and network establishment. CONCLUSION: These data suggest Nogo-A plays a functional role in the determination of neural identity and/or differentiation and also appears to play a later role in the networking of large projection neurons during neurite formation and synaptogenesis. These data indicate that Nogo-A is a multifunctional protein with additional roles during CNS development that are disparate from its later role of neurite outgrowth inhibition in the adult CNS. [Abstract/Link to Full Text]

Pritchett J, Wright C, Zeef L, Nadarajah B
Stromal derived factor-1 exerts differential regulation on distinct cortical cell populations in vitro.
BMC Dev Biol. 2007;731.
BACKGROUND: Stromal derived factor (SDF-1), an alpha chemokine, is a widely known chemoattractant in the immune system. A growing body of evidence now suggests multiple regulatory roles for SDF-1 in the developing nervous system. RESULTS: To investigate the role of SDF-1 signaling in the growth and differentiation of cortical cells, we performed numerous in vitro experiments, including gene chip and quantitative RT-PCR analysis. Using SDF-1 medium and AMD3100, a receptor antagonist, we demonstrate that the chemokine signaling regulates key events during early cortical development. First, SDF-1 signaling maintains cortical progenitors in proliferation, possibly through a mechanism involving connexin 43 mediated intercellular coupling. Second, SDF-1 signaling upregulates the differentiation of cortical GABAergic neurons, independent of sonic signaling pathway. Third, SDF-1 enables the elongation and branching of axons of cortical glutamatergic neurons. Finally, cortical cultures derived from CXCR4-/- mutants show a close parallel to AMD3100 treatment with reduced cell proliferation and differentiation of GABAergic neurons. CONCLUSION: Results from this study show that SDF-1 regulates distinct cortical cell populations in vitro. [Abstract/Link to Full Text]

Ceron J, Rual JF, Chandra A, Dupuy D, Vidal M, van den Heuvel S
Large-scale RNAi screens identify novel genes that interact with the C. elegans retinoblastoma pathway as well as splicing-related components with synMuv B activity.
BMC Dev Biol. 2007;730.
BACKGROUND: The retinoblastoma tumor suppressor (Rb) acts in a conserved pathway that is deregulated in most human cancers. Inactivation of the single Rb-related gene in Caenorhabditis elegans, lin-35, has only limited effects on viability and fertility, yet causes changes in cell-fate and cell-cycle regulation when combined with inactivation of specific other genes. For instance, lin-35 Rb is a synthetic multivulva (synMuv) class B gene, which causes a multivulva phenotype when inactivated simultaneously with a class A or C synMuv gene. RESULTS: We used the ORFeome RNAi library to identify genes that interact with C. elegans lin-35 Rb and identified 57 genes that showed synthetic or enhanced RNAi phenotypes in lin-35 mutants as compared to rrf-3 and eri-1 RNAi hypersensitive mutants. Based on characterizations of a deletion allele, the synthetic lin-35 interactor zfp-2 was found to suppress RNAi and to cooperate with lin-35 Rb in somatic gonad development. Interestingly, ten splicing-related genes were found to function similar to lin-35 Rb, as synMuv B genes that prevent inappropriate vulval induction. Partial inactivation of specific spliceosome components revealed further similarities with lin-35 Rb functions in cell-cycle control, transgene expression and restricted expression of germline granules. CONCLUSION: We identified an extensive series of candidate lin-35 Rb interacting genes and validated zfp-2 as a novel lin-35 synthetic lethal gene. In addition, we observed a novel role for a subset of splicing components in lin-35 Rb-controlled processes. Our data support novel hypotheses about possibilities for anti-cancer therapies and multilevel regulation of gene expression. [Abstract/Link to Full Text]

Gir�s A, Morante J, Gil-Sanz C, Fair�n A, Costell M
Perlecan controls neurogenesis in the developing telencephalon.
BMC Dev Biol. 2007;729.
BACKGROUND: Perlecan is a proteoglycan expressed in the basal lamina of the neuroepithelium during development. Perlecan absence does not impair basal lamina assembly, although in the 55% of the mutants early disruptions of this lamina conducts to exencephaly, impairing brain development. The rest of perlecan-null brains complete its prenatal development, maintain basal lamina continuity interrupted by some isolated ectopias, and are microcephalic. Microcephaly consists of thinner cerebral walls and underdeveloped ganglionic eminences. We have studied the mechanisms that generate brain atrophy in telencephalic areas where basal lamina is intact. RESULTS: Brain atrophy in the absence of perlecan started in the ventral forebrain and extended to lateral and dorsal parts of the cortex in the following stages. First, the subpallial forebrain developed poorly in early perlecan-null embryos, because of a reduced cell proliferation: the number of cells in mitosis decreased since the early stages of development. This reduction resulted in a decreased tangential migration of interneurons to the cerebral cortex. Concomitant with the early hypoplasia observed in the medial ganglionic eminences, Sonic Hedgehog signal decreased in the perlecan-null floor plate basal lamina at E12.5. Second, neurogenesis in the pallial neuroepithelium was affected in perlecan deficient embryos. We found reductions of nearly 50% in the number of cells exiting the cell cycle at E12-E13. The labeling index, which was normal at this age, significantly decreased with advancing corticogenesis. Moreover, nestin+ or PCNA+ progenitors increased since E14.5, reaching up to about 150% of the proportion of PCNA+ cells in the wild-type at E17.5. Thus, labeling index reduction together with increased progenitor population, suggests that atrophy is the result of altered cell cycle progression in the cortical progenitors. Accordingly, less neurons populated the cortical plate and subplate of perlecan-null neocortex, as seen with the neuronal markers beta-tubulin and Tbr1. CONCLUSION: As a component of the basal lamina, perlecan both maintains this structure and controls the response of the neuroepithelium to growth factors. Less mitotic cells in the early medial ganglionic eminences, and impaired cell cycle progression in the late neocortex, suggests insufficient recruitment and signaling by neurogenic morphogens, such as SHH or FGF2. [Abstract/Link to Full Text]

Baye LM, Link BA
The disarrayed mutation results in cell cycle and neurogenesis defects during retinal development in zebrafish.
BMC Dev Biol. 2007;728.
BACKGROUND: The vertebrate retina is derived from proliferative neuroepithelial cells of the optic cup. During retinal development, cell proliferation and the processes of cell cycle exit and neurogenesis are coordinated in neuroepithelial progenitor cells. Previous studies have demonstrated reciprocal influences between the cell cycle and neurogenesis. However the specific mechanisms and exact relationships of cell cycle regulation and neurogenesis in the vertebrate retina remain largely unknown. RESULTS: We have isolated and characterized a zebrafish mutant, disarrayed (drya64), which exhibits retinal defects in cell cycle regulation and neurogenesis. By 42 hours post fertilization, disarrayed mutants show small eyes and a reduced forebrain. Other aspects of development appear normal. Although retinogenesis is delayed, mutant retinal cells eventually differentiate to all major cell types. Examination of the disarrayed mitotic cycle using BrdU and direct imaging techniques revealed that retinal neuroepithelial cells have an extended cell cycle period and reduced rate of cell cycle exit and neurogenesis, despite the fact that neurogenesis initiates at the appropriate time of development. Genetic mosaic analyses indicate that the cell cycle phenotype of disarrayed is cell-non-autonomous. CONCLUSION: The disarrayed mutant shows defects in both cell cycle regulation and neurogenesis and provides insights into the coordinated regulation of these processes during retinal development. [Abstract/Link to Full Text]

Yu H, Li M, Tint GS, Chen J, Xu G, Patel SB
Selective reconstitution of liver cholesterol biosynthesis promotes lung maturation but does not prevent neonatal lethality in Dhcr7 null mice.
BMC Dev Biol. 2007;727.
BACKGROUND: Targeted disruption of the murine 3beta-hydroxysterol-Delta7-reductase gene (Dhcr7), an animal model of Smith-Lemli-Opitz syndrome, leads to loss of cholesterol synthesis and neonatal death that can be partially rescued by transgenic replacement of DHCR7 expression in brain during embryogenesis. To gain further insight into the role of non-brain tissue cholesterol deficiency in the pathophysiology, we tested whether the lethal phenotype could be abrogated by selective transgenic complementation with DHCR7 expression in the liver. RESULTS: We generated mice that carried a liver-specific human DHCR7 transgene whose expression was driven by the human apolipoprotein E (ApoE) promoter and its associated liver-specific enhancer. These mice were then crossed with Dhcr7+/- mutants to generate Dhcr7-/- mice bearing a human DHCR7 transgene. Robust hepatic transgene expression resulted in significant improvement of cholesterol homeostasis with cholesterol concentrations increasing to 80~90 % of normal levels in liver and lung. Significantly, cholesterol deficiency in brain was not altered. Although late gestational lung sacculation defect reported previously was significantly improved, there was no parallel increase in postnatal survival in the transgenic mutant mice. CONCLUSION: The reconstitution of DHCR7 function selectively in liver induced a significant improvement of cholesterol homeostasis in non-brain tissues, but failed to rescue the neonatal lethality of Dhcr7 null mice. These results provided further evidence that CNS defects caused by Dhcr7 null likely play a major role in the lethal pathogenesis of Dhcr7-/- mice, with the peripheral organs contributing the morbidity. [Abstract/Link to Full Text]

Winterhager E, Pielensticker N, Freyer J, Ghanem A, Schrickel JW, Kim JS, Behr R, Gr�mmer R, Maass K, Urschel S, Lewalter T, Tiemann K, Simoni M, Willecke K
Replacement of connexin43 by connexin26 in transgenic mice leads to dysfunctional reproductive organs and slowed ventricular conduction in the heart.
BMC Dev Biol. 2007;726.
BACKGROUND: In order to further distinguish unique from general functions of connexin43, we have generated mice in which the coding region of connexin43 was replaced by that of connexin26. RESULTS: Heterozygous mothers showed impaired mammary gland development responsible for decreased lactation and early postnatal death of the pups which could be partially rescued by wild type foster mothers. Only about 17% of the homozygous connexin43 knock-in connexin26 mice instead of 25% expected according to Mendelian inheritance, were born and only 6% survived to day 21 post partum and longer. Neonatal and adult connexin43 knock-in connexin26 mice exhibited slowed ventricular conduction in their hearts, i.e. similar but delayed electrophysiological abnormalities as connexin43 deficient mice. Furthermore, connexin43 knock-in connexin26 male and female mice were infertile and exhibited hypotrophic gonads. In testes, tubuli seminiferi were developed and spermatogonia as well as some primary spermatocytes were present, but further differentiated stages of spermatogenesis were absent. Ovaries of female connexin43 knock-in connexin26 mice revealed only few follicles and the maturation of follicles was completely impaired. CONCLUSION: The impaired gametogenesis of homozygous males and females can explain their infertility. [Abstract/Link to Full Text]

Albazerchi A, Cinquin O, Stern CD
A new method to transfect the hypoblast of the chick embryo reveals conservation of the regulation of an Otx2 enhancer between mouse and chick extraembryonic endoderm.
BMC Dev Biol. 2007;725.
BACKGROUND: The mouse anterior visceral endoderm (AVE) and the chick hypoblast are thought to have homologous roles in the early stages of neural induction and primitive streak formation. In mouse, many regulatory elements directing gene expression to the AVE have been identified. However, there is no technique to introduce DNA into the chick hypoblast that would enable a comparison of their activity and this has hampered a direct comparison of the regulation of gene expression in the mouse and chick extraembryonic endoderm. RESULTS: Here we describe a new method to introduce DNA into the chick hypoblast, using lipofectamine-mediated transfection. We show that the hypoblast can be easily transfected and that it starts to express a luciferase reporter within 2 hours of transfection. The validity of technique is tested by following the movement and fate of hypoblast cells, which reveals their translocation to the anterior germinal crescent. We then introduce a vector containing GFP driven by the mouse VEcis-Otx2 enhancer (which directs gene expression to the mouse AVE) and we detect activity in the hypoblast. CONCLUSION: The new technique for delivering expression constructs to the chick hypoblast will enable studies on gene activity and regulation to be performed in this tissue, which has proved difficult to transfect by electroporation. Our findings also reveal that regulatory elements that direct gene expression to the mouse AVE are active in chick hypoblast, supporting the idea that these two tissues have homologous functions. [Abstract/Link to Full Text]

Snykers S, Vanhaecke T, De Becker A, Papeleu P, Vinken M, Van Riet I, Rogiers V
Chromatin remodeling agent trichostatin A: a key-factor in the hepatic differentiation of human mesenchymal stem cells derived of adult bone marrow.
BMC Dev Biol. 2007;724.
BACKGROUND: The capability of human mesenchymal stem cells (hMSC) derived of adult bone marrow to undergo in vitro hepatic differentiation was investigated. RESULTS: Exposure of hMSC to a cocktail of hepatogenic factors [(fibroblast growth factor-4 (FGF-4), hepatocyte growth factor (HGF), insulin-transferrin-sodium-selenite (ITS) and dexamethasone)] failed to induce hepatic differentiation. Sequential exposure to these factors (FGF-4, followed by HGF, followed by HGF+ITS+dexamethasone), however, resembling the order of secretion during liver embryogenesis, induced both glycogen-storage and cytokeratin (CK)18 expression. Additional exposure of the cells to trichostatin A (TSA) considerably improved endodermal differentiation, as evidenced by acquisition of an epithelial morphology, chronological expression of hepatic proteins, including hepatocyte-nuclear factor (HNF)-3beta, alpha-fetoprotein (AFP), CK18, albumin (ALB), HNF1alpha, multidrug resistance-associated protein (MRP)2 and CCAAT-enhancer binding protein (C/EBP)alpha, and functional maturation, i.e. upregulated ALB secretion, urea production and inducible cytochrome P450 (CYP)-dependent activity. CONCLUSION: hMSC are able to undergo mesenchymal-to-epithelial transition. TSA is hereby essential to promote differentiation of hMSC towards functional hepatocyte-like cells. [Abstract/Link to Full Text]

Dambly-Chaudi�re C, Cubedo N, Ghysen A
Control of cell migration in the development of the posterior lateral line: antagonistic interactions between the chemokine receptors CXCR4 and CXCR7/RDC1.
BMC Dev Biol. 2007;723.
BACKGROUND: The formation of the posterior lateral line of teleosts depends on the migration of a primordium that originates near the otic vesicle and moves to the tip of the tail. Groups of cells at the trailing edge of the primordium slow down at regular intervals and eventually settle to differentiate as sense organs. The migration of the primordium is driven by the chemokine SDF1 and by its receptor CXCR4, encoded respectively by the genes sdf1a and cxcr4b. cxcr4b is expressed in the migrating cells and is down-regulated in the trailing cells of the primordium. sdf1a is expressed along the path of migration. There is no evidence for a gradient of sdf1a expression, however, and the origin of the directionality of migration is not known. RESULTS: Here we document the expression of a second chemokine receptor gene, cxcr7, in the migrating primordium. We show that cxcr7 is highly expressed in the trailing cells of the primordium but not at all in the leading cells, a pattern that is complementary to that of cxcr4b. Even though cxcr7 is not expressed in the cells that lead primordium migration, its inactivation results in impaired migration. The phenotypes of cxcr4b, cxcr7 double morphant embryos suggest, however, that CXCR7 does not contribute to the migratory capabilities of primordium cells. We also show that, in the absence of cxcr4b, expression of cxcr7 becomes ubiquitous in the stalled primordium. CONCLUSION: Our observations suggest that CXCR7 is required to provide directionality to the migration. We propose that directionality is imposed on the primordium as soon as it comes in contact with the stripe of SDF1, and is maintained throughout migration by a negative interaction between the two receptors. [Abstract/Link to Full Text]

Hagos EG, Dougan ST
Time-dependent patterning of the mesoderm and endoderm by Nodal signals in zebrafish.
BMC Dev Biol. 2007;722.
BACKGROUND: The vertebrate body plan is generated during gastrulation with the formation of the three germ layers. Members of the Nodal-related subclass of the TGF-beta superfamily induce and pattern the mesoderm and endoderm in all vertebrates. In zebrafish, two nodal-related genes, called squint and cyclops, are required in a dosage-dependent manner for the formation of all derivatives of the mesoderm and endoderm. These genes are expressed dynamically during the blastula stages and may have different roles at different times. This question has been difficult to address because conditions that alter the timing of nodal-related gene expression also change Nodal levels. We utilized a pharmacological approach to conditionally inactivate the ALK 4, 5 and 7 receptors during the blastula stages without disturbing earlier signaling activity. This permitted us to directly examine when Nodal signals specify cell types independently of dosage effects. RESULTS: We show that two drugs, SB-431542 and SB-505124, completely block the response to Nodal signals when added to embryos after the mid-blastula transition. By blocking Nodal receptor activity at later stages, we demonstrate that Nodal signaling is required from the mid-to-late blastula period to specify sequentially, the somites, notochord, blood, Kupffer's vesicle, hatching gland, heart, and endoderm. Blocking Nodal signaling at late times prevents specification of cell types derived from the embryo margin, but not those from more animal regions. This suggests a linkage between cell fate and length of exposure to Nodal signals. Confirming this, cells exposed to a uniform Nodal dose adopt progressively more marginal fates with increasing lengths of exposure. Finally, cell fate specification is delayed in squint mutants and accelerated when Nodal levels are elevated. CONCLUSION: We conclude that (1) Nodal signals are most active during the mid-to-late blastula stages, when nodal-related gene expression and the movement of responding cells are at their most dynamic; (2) Nodal signals specify cell fates along the animal-vegetal axis in a time-dependent manner; (3) cells respond to the total cumulative dose of Nodal signals to which they are exposed, as a function of distance from the source and duration of exposure. [Abstract/Link to Full Text]

Smith MK, Wakimoto BT
Complex regulation and multiple developmental functions of misfire, the Drosophila melanogaster ferlin gene.
BMC Dev Biol. 2007;721.
BACKGROUND: Ferlins are membrane proteins with multiple C2 domains and proposed functions in Ca2+ mediated membrane-membrane interactions in animals. Caenorhabditis elegans has two ferlin genes, one of which is required for sperm function. Mammals have several ferlin genes and mutations in the human dysferlin (DYSF) and otoferlin (OTOF) genes result in muscular dystrophy and hearing loss, respectively. Drosophila melanogaster has a single ferlin gene called misfire (mfr). A previous study showed that a mfr mutation caused male sterility because of defects in fertilization. Here we analyze the expression and structure of the mfr gene and the consequences of multiple mutations to better understand the developmental function of ferlins. RESULTS: We show that mfr is expressed in the testis and ovaries of adult flies, has tissue-specific promoters, and expresses alternatively spliced transcripts that are predicted to encode distinct protein isoforms. Studies of 11 male sterile mutations indicate that a predicted Mfr testis isoform with five C2 domains and a transmembrane (TM) domain is required for sperm plasma membrane breakdown (PMBD) and completion of sperm activation during fertilization. We demonstrate that Mfr is not required for localization of Sneaky, another membrane protein necessary for PMBD. The mfr mutations vary in their effects in females, with a subset disrupting egg patterning and causing a maternal effect delay in early embryonic development. Locations of these mutations indicate that a short Mfr protein isoform carries out ferlin activities during oogenesis. CONCLUSION: The mfr gene exhibits complex transcriptional and post-transcriptional regulation and functions in three developmental processes: sperm activation, egg patterning, and early embryogenesis. These functions are in part due to the production of protein isoforms that vary in the number of C2 domains. These findings help establish D. melanogaster as model system for understanding ferlin function and dysfunction in animals, including humans. [Abstract/Link to Full Text]

Soete G, Betist MC, Korswagen HC
Regulation of Caenorhabditis elegans body size and male tail development by the novel gene lon-8.
BMC Dev Biol. 2007;720.
BACKGROUND: In C. elegans and other nematode species, body size is determined by the composition of the extracellular cuticle as well as by the nuclear DNA content of the underlying hypodermis. Mutants that are defective in these processes can exhibit either a short or a long body size phenotype. Several mutations that give a long body size (Lon) phenotype have been characterized and found to be regulated by the DBL-1/TGF-beta pathway, that controls post-embryonic growth and male tail development. RESULTS: Here we characterize a novel gene affecting body size. lon-8 encodes a secreted product of the hypodermis that is highly conserved in Rhabditid nematodes. lon-8 regulates larval elongation as well as male tail development. In both processes, lon-8 appears to function independently of the Sma/Mab pathway. Rather, lon-8 genetically interacts with dpy-11 and dpy-18, which encode cuticle collagen modifying enzymes. CONCLUSION: The novel gene lon-8 encodes a secreted product of the hypodermis that controls body size and male ray morphology in C. elegans. lon-8 genetically interacts with enzymes that affect the composition of the cuticle. [Abstract/Link to Full Text]

Dong Y, Bogdanova A, Habermann B, Zachariae W, Ahringer J
Identification of the C. elegans anaphase promoting complex subunit Cdc26 by phenotypic profiling and functional rescue in yeast.
BMC Dev Biol. 2007;719.
BACKGROUND: RNA interference coupled with videorecording of C. elegans embryos is a powerful method for identifying genes involved in cell division processes. Here we present a functional analysis of the gene B0511.9, previously identified as a candidate cell polarity gene in an RNAi videorecording screen of chromosome I embryonic lethal genes. RESULTS: Whereas weak RNAi inhibition of B0511.9 causes embryonic cell polarity defects, strong inhibition causes embryos to arrest in metaphase of meiosis I. The range of defects induced by RNAi of B0511.9 is strikingly similar to those displayed by mutants of anaphase-promoting complex/cyclosome (APC/C) components. Although similarity searches did not reveal any obvious homologue of B0511.9 in the non-redundant protein database, we found that the N-terminus shares a conserved sequence pattern with the N-terminus of the small budding yeast APC/C subunit Cdc26 and its orthologues from a variety of other organisms. Furthermore, we show that B0511.9 robustly complements the temperature-sensitive growth defect of a yeast cdc26Delta mutant. CONCLUSION: These data demonstrate that B0511.9 encodes the C. elegans APC/C subunit CDC-26. [Abstract/Link to Full Text]

Agoston H, Khan S, James CG, Gillespie JR, Serra R, Stanton LA, Beier F
C-type natriuretic peptide regulates endochondral bone growth through p38 MAP kinase-dependent and -independent pathways.
BMC Dev Biol. 2007;718.
BACKGROUND: C-type natriuretic peptide (CNP) has recently been identified as an important anabolic regulator of endochondral bone growth, but the molecular mechanisms mediating its effects are not completely understood. RESULTS: We demonstrate in a tibia organ culture system that pharmacological inhibition of p38 blocks the anabolic effects of CNP. We further show that CNP stimulates endochondral bone growth largely through expansion of the hypertrophic zone of the growth plate, while delaying mineralization. Both effects are reversed by p38 inhibition. We also performed Affymetrix microarray analyses on micro-dissected tibiae to identify CNP target genes. These studies confirmed that hypertrophic chondrocytes are the main targets of CNP signaling in the growth plate, since many more genes were regulated by CNP in this zone than in the others. While CNP receptors are expressed at similar levels in all three zones, cGMP-dependent kinases I and II, important transducers of CNP signaling, are expressed at much higher levels in hypertrophic cells than in other areas of the tibia, providing a potential explanation for the spatial distribution of CNP effects. In addition, our data show that CNP induces the expression of NPR3, a decoy receptor for natriuretic peptides, suggesting the existence of a feedback loop to limit CNP signaling. Finally, detailed analyses of our microarray data showed that CNP regulates numerous genes involved in BMP signaling and cell adhesion. CONCLUSION: Our data identify novel target genes of CNP and demonstrate that the p38 pathway is a novel, essential mediator of CNP effects on endochondral bone growth, with potential implications for understanding and treatment of numerous skeletal diseases. [Abstract/Link to Full Text]

Hachem S, Laurenson AS, Hugnot JP, Legraverend C
Expression of S100B during embryonic development of the mouse cerebellum.
BMC Dev Biol. 2007;717.
BACKGROUND: In the cerebellum of newborn S100B-EGFP mice, we had previously noted the presence of a large population of S100B-expressing cells, which we assumed to be immature Bergmann glial cells. In the present study, we have drawn on this observation to establish the precise spatio-temporal pattern of S100B gene expression in the embryonic cerebellum. RESULTS: From E12.5 until E17.5, S100B was expressed in the primary radial glial scaffold involved in Purkinje progenitor exit from the ventricular zone and in the Sox9+ glial progenitors derived from it. During the same period coinciding with the primary phase of granule neuron precursor genesis, transient EGFP expression tagged the Pax6+ forerunners of granule precursors born in the cerebellar rhombic lip. CONCLUSION: This study provides the first characterization of S100B-expressing cell types of the embryonic mouse cerebellum in a high-resolution map. The transient activation of the S100B gene distinguishes granule neuron precursors from all other types of precursors so far identified in the rhombic lip, whereas its activation in radial glial precursors is a feature of Bergmann cell gliogenesis. [Abstract/Link to Full Text]

Ushizawa K, Takahashi T, Hosoe M, Kizaki K, Abe Y, Sasada H, Sato E, Hashizume K
Gene expression profiles of novel caprine placental prolactin-related proteins similar to bovine placental prolactin-related proteins.
BMC Dev Biol. 2007;716.
BACKGROUND: This study reports the identification of a full-length cDNA sequence for two novel caprine prolactin-related proteins (cPRP1 and cPRP6), and their localization and quantitative expression in the placenta. Caprine PRPs are compared with known bovine PRPs. We examined their evolution and role in the ruminant placenta. RESULTS: Full-length cPRP1 and cPRP6 cDNA were cloned with a 717- and 720- nucleotide open-reading frame corresponding to proteins of 238 and 239 amino acids. The cPRP1 predicted amino acid sequence shares a 72% homology with bovine PRP1 (bPRP1). The cPRP6 predicted amino acid sequence shares a 74% homology with bovine PRP6 (bPRP6). The two cPRPs as well as bPRPs were detected only in the placentome by RT-PCR. Analysis by in situ hybridization revealed the presence of both cPRPs mRNA in the trophoblast binucleate cells. These mRNA were quantified by real-time RT-PCR analysis of the placentome at 30, 50, 90 and 140 days of pregnancy. Both new cPRP genes were able to translate a mature protein in a mammalian cell-expression system. Western blotting established the molecular sizes of 33 kDa for cPRP1 with FLAG-tag and 45 kDa for cPRP6 with FLAG-tag. The sequence properties and localized expression of cPRP1 and cPRP6 were similar to those of bovine. However, their expression profiles differed from those in bovine placenta. Although this study demonstrated possible roles of PRPs in caprine placenta, PRPs may regulate binucleate-cell functions like those in bovine, but their crucial roles are still unclear. CONCLUSION: We have identified the novel PRPs in caprine placenta. Localization and quantitative expression of caprine PRPs were compared with bovine PRPs. The data indicate that PRP genes in caprine placenta have coordination functions for gestation, as they do in bovine. This is the first study of PRPs function in caprine placenta. [Abstract/Link to Full Text]

Recent Articles in BMC Evolutionary Biology

Guidetti R, Baraldi L, Calzolai C, Pini L, Veronesi P, Pederzoli A
Fantastic animals as an experimental model to teach animal adaptation.
BMC Evol Biol. 2007;7 Suppl 2S13.
BACKGROUND: Science curricula and teachers should emphasize evolution in a manner commensurate with its importance as a unifying concept in science. The concept of adaptation represents a first step to understand the results of natural selection. We settled an experimental project of alternative didactic to improve knowledge of organism adaptation. Students were involved and stimulated in learning processes by creative activities. To set adaptation in a historic frame, fossil records as evidence of past life and evolution were considered. RESULTS: The experimental project is schematized in nine phases: review of previous knowledge; lesson on fossils; lesson on fantastic animals; planning an imaginary world; creation of an imaginary animal; revision of the imaginary animals; adaptations of real animals; adaptations of fossil animals; and public exposition. A rubric to evaluate the student's performances is reported. The project involved professors and students of the University of Modena and Reggio Emilia and of the "G. Marconi" Secondary School of First Degree (Modena, Italy). CONCLUSION: The educational objectives of the project are in line with the National Indications of the Italian Ministry of Public Instruction: knowledge of the characteristics of living beings, the meanings of the term "adaptation", the meaning of fossils, the definition of ecosystem, and the particularity of the different biomes. At the end of the project, students will be able to grasp particular adaptations of real organisms and to deduce information about the environment in which the organism evolved. This project allows students to review previous knowledge and to form their personalities. [Abstract/Link to Full Text]

Besaggio D, Fuselli S, Srikummool M, Kampuansai J, Castr� L, Tyler-Smith C, Seielstad M, Kangwanpong D, Bertorelle G
Genetic variation in Northern Thailand Hill Tribes: origins and relationships with social structure and linguistic differences.
BMC Evol Biol. 2007;7 Suppl 2S12.
BACKGROUND: Ethnic minorities in Northern Thailand, often referred to as Hill Tribes, are considered an ideal model to study the different genetic impact of sex-specific migration rates expected in matrilocal (women remain in their natal villages after the marriage and men move to their wife's village) and patrilocal societies (the opposite is true). Previous studies identified such differences, but little is known about the possible interaction with another cultural factor that may potentially affect genetic diversity, i.e. linguistic differences. In addition, Hill Tribes started to migrate to Thailand in the last centuries from different Northern areas, but the history of these migrations, the level of genetic legacy with their places of origin, and the possible confounding effects related to this migration history in the patterns of genetic diversity, have not been analysed yet. Using both original and published data on the Hill Tribes and several other Asian populations, we focused on all these aspects. RESULTS: Genetic variation within population at mtDNA is lower in matrilocal, compared to patrilocal, tribes. The opposite is true for Y-chromosome microsatellites within the Sino-Tibetan linguistic family, but Hmong-Mien speaking patrilocal groups have a genetic diversity very similar to the matrilocal samples. Population divergence ranges between 5% and 14% at mtDNA sequences, and between 5% and 36% at Y-chromosomes STRs, and follows the sex-specific differences expected in patrilocal and matrilocal tribes. On the average, about 2 men and 14 women, and 4 men and 4 women, are exchanged in patrilocal and matrilocal tribes every generation, respectively. Most of the Hill Tribes in Thailand seem to preserve a genetic legacy with their likely geographic origin, with children adoption probably affecting this pattern in one tribe. CONCLUSION: Overall, the sex specific genetic signature of different postmarital habits of residence in the Hill Tribes is robust. However, specific perturbations related to linguistic differences, population specific traits, and the complex migratory history of these groups, can be identified. Additional studies in different populations are needed, especially to obtain more precise estimates of the migration parameters. [Abstract/Link to Full Text]

Dumas F, Stanyon R, Sineo L, Stone G, Bigoni F
Phylogenomics of species from four genera of New World monkeys by flow sorting and reciprocal chromosome painting.
BMC Evol Biol. 2007;7 Suppl 2S11.
BACKGROUND: The taxonomic and phylogenetic relationships of New World monkeys (Platyrrhini) are difficult to distinguish on the basis of morphology and because diagnostic fossils are rare. Recently, molecular data have led to a radical revision of the traditional taxonomy and phylogeny of these primates. Here we examine new hypotheses of platyrrhine evolutionary relationships by reciprocal chromosome painting after chromosome flow sorting of species belonging to four genera of platyrrhines included in the Cebidae family: Callithrix argentata (silvered-marmoset), Cebuella pygmaea (pygmy marmoset), Callimico goeldii (Goeldi's marmoset) and Saimiri sciureus (squirrel monkey). This is the first report of reciprocal painting in marmosets. RESULTS: The paints made from chromosome flow sorting of the four platyrrhine monkeys provided from 42 to 45 hybridization signals on human metaphases. The reciprocal painting of monkey probes on human chromosomes revealed that 21 breakpoints are common to all four studied species. There are only three additional breakpoints. A breakpoint on human chromosome 13 was found in Callithrix argentata, Cebuella pygmaea and Callimico goeldii, but not in Saimiri sciureus. There are two additional breakpoints on human chromosome 5: one is specific to squirrel monkeys, and the other to Goeldi's marmoset. CONCLUSION: The reciprocal painting results support the molecular genomic assemblage of Cebidae. We demonstrated that the five chromosome associations previously hypothesized to phylogenetically link tamarins and marmosets are homologous and represent derived chromosome rearrangements. Four of these derived homologous associations tightly nest Callimico goeldii with marmosets. One derived association 2/15 may place squirrel monkeys within the Cebidae assemblage. An apparently common breakpoint on chromosome 5q33 found in both Saimiri and Aotus nancymae could be evidence of a phylogenetic link between these species. Comparison with previous reports shows that many syntenic associations found in platyrrhines have the same breakpoints and are homologous, derived rearrangements showing that the New World monkeys are a closely related group of species. Our data support the hypothesis that the ancestral karyotype of the Platyrrhini has a diploid number of 2n = 54 and is almost identical to that found today in capuchin monkeys; congruent with a basal position of the Cebidae among platyrrhine families. [Abstract/Link to Full Text]

Trotta V, Calboli FC, Ziosi M, Cavicchi S
Fitness variation in response to artificial selection for reduced cell area, cell number and wing area in natural populations of Drosophila melanogaster.
BMC Evol Biol. 2007;7 Suppl 2S10.
BACKGROUND: Genetically based body size differences are naturally occurring in populations of Drosophila melanogaster, with bigger flies in the cold. Despite the cosmopolitan nature of body size clines in more than one Drosophila species, the actual selective mechanisms controlling the genetic basis of body size variation are not fully understood. In particular, it is not clear what the selective value of cell size and cell area variation exactly is. In the present work we determined variation in viability, developmental time and larval competitive ability in response to crowding at two temperatures after artificial selection for reduced cell area, cell number and wing area in four different natural populations of D. melanogaster. RESULTS: No correlated effect of selection on viability or developmental time was observed among all selected populations. An increase in competitive ability in one thermal environment (18 degrees C) under high larval crowding was observed as a correlated response to artificial selection for cell size. CONCLUSION: Viability and developmental time are not affected by selection for the cellular component of body size, suggesting that these traits only depend on the contingent genetic makeup of a population. The higher larval competitive ability shown by populations selected for reduced cell area seems to confirm the hypothesis that cell area mediated changes have a relationship with fitness, and might be the preferential way to change body size under specific circumstances. [Abstract/Link to Full Text]

Costanzo G, Saladino R, Crestini C, Ciciriello F, Di Mauro E
Formamide as the main building block in the origin of nucleic acids.
BMC Evol Biol. 2007;7 Suppl 2S1.
The simplest molecules grouping the four most common elements of the universe H,C,O and N (with the exception of the biologically inert He) are isocyanate HNCO and formamide H2NCOH. Reasons for the availability of formamide on prebiotic Earth are presented. We review evidence showing that formamide in the presence of largely available catalysts and by moderate heating yields the complete set of nucleic bases necessary for the formation of nucleic acids. Formamide also favours the formation of acyclonucleosides and the phosphorylation and trans-phosphorylation of nucleosides, thus providing a plausible chemical frame for the passage from a simple one-carbon compound to nucleic polymers. Physico-chemical conditions exist in which formamide favours the stability of the phosphoester bonds in nucleic polymers relative to that of the same bonds in monomers. Starting from a formamide-laden environment subject only to the laws of chemistry, a hypothesis is outlined sketching the passage towards an aqueous world in which Darwinian rules apply. [Abstract/Link to Full Text]

Jackson DJ, W�rheide G, Degnan BM
Dynamic expression of ancient and novel molluscan shell genes during ecological transitions.
BMC Evol Biol. 2007;7160.
BACKGROUND: The Mollusca constitute one of the most morphologically and ecologically diverse metazoan phyla, occupying a wide range of marine, terrestrial and freshwater habitats. The evolutionary success of the molluscs can in part be attributed to the evolvability of the external shell. Typically, the shell first forms during embryonic and larval development, changing dramatically in shape, colour and mineralogical composition as development and maturation proceeds. Major developmental transitions in shell morphology often correlate with ecological transitions (e.g. from a planktonic to benthic existence at metamorphosis). While the genes involved in molluscan biomineralisation are beginning to be identified, there is little understanding of how these are developmentally regulated, or if the same genes are operational at different stages of the mollusc's life. RESULTS: Here we relate the developmental expression of nine genes in the tissue responsible for shell production - the mantle - to ecological transitions that occur during the lifetime of the tropical abalone Haliotis asinina (Vetigastropoda). Four of these genes encode evolutionarily ancient proteins, while four others encode secreted proteins with little or no identity to known proteins. Another gene has been previously described from the mantle of another haliotid vetigastropod. All nine genes display dynamic spatial and temporal expression profiles within the larval shell field and juvenile mantle. CONCLUSION: These expression data reflect the regulatory complexity that underlies molluscan shell construction from larval stages to adulthood, and serves to highlight the different ecological demands placed on each stage. The use of both ancient and novel genes in all stages of shell construction also suggest that a core set of shell-making genes was provided by a shared metazoan ancestor, which has been elaborated upon to produce the range of molluscan shell types we see today. [Abstract/Link to Full Text]

Haugen P, Bhattacharya D, Palmer JD, Turner S, Lewis LA, Pryer KM
Cyanobacterial ribosomal RNA genes with multiple, endonuclease-encoding group I introns.
BMC Evol Biol. 2007;7159.
BACKGROUND: Group I introns are one of the four major classes of introns as defined by their distinct splicing mechanisms. Because they catalyze their own removal from precursor transcripts, group I introns are referred to as autocatalytic introns. Group I introns are common in fungal and protist nuclear ribosomal RNA genes and in organellar genomes. In contrast, they are rare in all other organisms and genomes, including bacteria. RESULTS: Here we report five group I introns, each containing a LAGLIDADG homing endonuclease gene (HEG), in large subunit (LSU) rRNA genes of cyanobacteria. Three of the introns are located in the LSU gene of Synechococcus sp. C9, and the other two are in the LSU gene of Synechococcus lividus strain C1. Phylogenetic analyses show that these introns and their HEGs are closely related to introns and HEGs located at homologous insertion sites in organellar and bacterial rDNA genes. We also present a compilation of group I introns with homing endonuclease genes in bacteria. CONCLUSION: We have discovered multiple HEG-containing group I introns in a single bacterial gene. To our knowledge, these are the first cases of multiple group I introns in the same bacterial gene (multiple group I introns have been reported in at least one phage gene and one prophage gene). The HEGs each contain one copy of the LAGLIDADG motif and presumably function as homodimers. Phylogenetic analysis, in conjunction with their patchy taxonomic distribution, suggests that these intron-HEG elements have been transferred horizontally among organelles and bacteria. However, the mode of transfer and the nature of the biological connections among the intron-containing organisms are unknown. [Abstract/Link to Full Text]

Gali�n J, Proen�a SJ, Vogler AP
Evolutionary dynamics of autosomal-heterosomal rearrangements in a multiple-X chromosome system of tiger beetles (Cicindelidae).
BMC Evol Biol. 2007;7158.
BACKGROUND: Genetic systems involving multiple X chromosomes have arisen repeatedly in sexually reproducing animals. Tiger beetles (Cicindelidae) exhibit a phylogenetically ancient multiple-X system typically consisting of 2-4 X chromosomes and a single Y. Because recombination rates are suppressed in sex chromosomes, changes in their numbers and movement of genes between sex chromosomes and autosomes, could have important consequences for gene evolution and rates of speciation induced by these rearrangements. However, it remains unclear how frequent these rearrangements are and which genes are affected. RESULTS: Karyotype analyses were performed for a total of 26 North American species in the highly diverse genus Cicindela, tallying the number of X chromosomes and autosomes during mitosis and meiosis. The chromosomal location of the ribosomal rRNA gene cluster (rDNA) was used as an easily scored marker for genic turnover between sex chromosomes or autosomes. The findings were assessed in the light of a recent phylogenetic analysis of the group. While autosome numbers remained constant throughout the lineage, sex chromosome numbers varied. The predominant karyotype was n = 9+X1X2X3Y which was also inferred to be the ancestral state, with several changes to X1X2Y and X1X2X3X4Y confined to phylogenetically isolated species. The total (haploid) numbers of rDNA clusters varied between two, three, and six (in one exceptional case), and clusters were localized either on the autosomes, the sex chromosomes, or both. Transitions in rDNA localization and in numbers of rDNA clusters varied independently of each other, and also independently of changes in sex chromosome numbers. CONCLUSION: Changes of X chromosome numbers and transposition of the rDNA locus (and presumably other genes) between autosomes and sex chromosomes in Cicindela occur frequently, and are likely to be the result of fusions or fissions between X chromosomes, rather than between sex chromosomes and autosomes. Yet, translocations between sex chromosomes and autosomes appear to be common, as indicated by the patterns of rDNA localization. Rearranged karyotypes involving multiple sex chromosomes would reduce recombination, and hybrid dysgenesis selects against polymorphic populations. Hence, the high frequency of these rearrangements could be a cause of the great species diversity in Cicindela. [Abstract/Link to Full Text]

Edwards CA, Rens W, Clarke O, Mungall AJ, Hore T, Graves JA, Dunham I, Ferguson-Smith AC, Ferguson-Smith MA
The evolution of imprinting: chromosomal mapping of orthologues of mammalian imprinted domains in monotreme and marsupial mammals.
BMC Evol Biol. 2007;7157.
BACKGROUND: The evolution of genomic imprinting, the parental-origin specific expression of genes, is the subject of much debate. There are several theories to account for how the mechanism evolved including the hypothesis that it was driven by the evolution of X-inactivation, or that it arose from an ancestrally imprinted chromosome. RESULTS: Here we demonstrate that mammalian orthologues of imprinted genes are dispersed amongst autosomes in both monotreme and marsupial karyotypes. CONCLUSION: These data, along with the similar distribution seen in birds, suggest that imprinted genes were not located on an ancestrally imprinted chromosome or associated with a sex chromosome. Our results suggest imprinting evolution was a stepwise, adaptive process, with each gene/cluster independently becoming imprinted as the need arose. [Abstract/Link to Full Text]

Pavoine S, Bailly X
New analysis for consistency among markers in the study of genetic diversity: development and application to the description of bacterial diversity.
BMC Evol Biol. 2007;7156.
BACKGROUND: The development of post-genomic methods has dramatically increased the amount of qualitative and quantitative data available to understand how ecological complexity is shaped. Yet, new statistical tools are needed to use these data efficiently. In support of sequence analysis, diversity indices were developed to take into account both the relative frequencies of alleles and their genetic divergence. Furthermore, a method for describing inter-population nucleotide diversity has recently been proposed and named the double principal coordinate analysis (DPCoA), but this procedure can only be used with one locus. In order to tackle the problem of measuring and describing nucleotide diversity with more than one locus, we developed three versions of multiple DPCoA by using three ordination methods: multiple co-inertia analysis, STATIS, and multiple factorial analysis. RESULTS: This combination of methods allows i) testing and describing differences in patterns of inter-population diversity among loci, and ii) defining the best compromise among loci. These methods are illustrated by the analysis of both simulated data sets, which include ten loci evolving under a stepping stone model and a locus evolving under an alternative population structure, and a real data set focusing on the genetic structure of two nitrogen fixing bacteria, which is influenced by geographical isolation and host specialization. All programs needed to perform multiple DPCoA are freely available. CONCLUSION: Multiple DPCoA allows the evaluation of the impact of various loci in the measurement and description of diversity. This method is general enough to handle a large variety of data sets. It complements existing methods such as the analysis of molecular variance or other analyses based on linkage disequilibrium measures, and is very useful to study the impact of various loci on the measurement of diversity. [Abstract/Link to Full Text]

Iannelli F, Griggio F, Pesole G, Gissi C
The mitochondrial genome of Phallusia mammillata and Phallusia fumigata (Tunicata, Ascidiacea): high genome plasticity at intra-genus level.
BMC Evol Biol. 2007 Aug 31;7(1):155.
ABSTRACT: BACKGROUND: Within Chordata, the subphyla Vertebrata and Cephalochordata (lancelets) are characterized by a remarkable stability of the mitochondrial (mt) genome, with constancy of gene content and almost invariant gene order, whereas the limited mitochondrial data on the subphylum Tunicata suggest frequent and extensive gene rearrangements, observed also within ascidians of the same genus. RESULTS: To confirm this evolutionary trend and to better understand the evolutionary dynamics of the mitochondrial genome in Tunicata Ascidiacea, we have sequenced and characterized the complete mt genome of two congeneric ascidian species, Phallusia mammillata and Phallusia fumigata (Phlebobranchiata, Ascidiidae). The two mtDNAs are surprisingly rearranged, both with respect to one another and relative to those of other tunicates and chordates, with gene rearrangements affecting both protein-coding and tRNA genes. The new data highlight the extraordinary variability of ascidian mt genome in base composition, tRNA secondary structure, tRNA gene content, and non-coding regions (number, size, sequence and location). Indeed, both Phallusia genomes lack the trnD gene, show loss/acquisition of DHU-arm in two tRNAs, and have a G+C content two-fold higher than other ascidians. Moreover, the mt genome of P. fumigata presents two identical copies of trnI, an extra tRNA gene with uncertain amino acid specificity, and four almost identical sequence regions. In addition, a truncated cytochrome b, lacking a C-terminal tail that commonly protrudes into the mt matrix, has been identified as a new mt feature probably shared by all tunicates. CONCLUSIONS: The frequent occurrence of major gene order rearrangements in ascidians both at high taxonomic level and within the same genus makes this taxon an excellent model to study the mechanisms of gene rearrangement, and renders the mt genome an invaluable phylogenetic marker to investigate molecular biodiversity and speciation events in this largely unexplored group of basal chordates. [Abstract/Link to Full Text]

Anisimova M, Bielawski J, Dunn K, Yang Z
Phylogenomic analysis of natural selection pressure in Streptococcus genomes.
BMC Evol Biol. 2007;7154.
BACKGROUND: In comparative analyses of bacterial pathogens, it has been common practice to discriminate between two types of genes: (i) those shared by pathogens and their non-pathogenic relatives (core genes), and (ii) those found exclusively in pathogens (pathogen-specific accessory genes). Rather than attempting to a priori delineate genes into sets more or less relevant to pathogenicity, we took a broad approach to the analysis of Streptococcus species by investigating the strength of natural selection in all clusters of homologous genes. The genus Streptococcus is comprised of a wide variety of both pathogenic and commensal lineages, and we relate our findings to the pre-existing knowledge of Streptococcus virulence factors. RESULTS: Our analysis of 1730 gene clusters revealed 136 cases of positive Darwinian selection, which we suggest is most likely to result from an antagonistic interaction between the host and pathogen at the molecular level. A two-step validation procedure suggests that positive selection was robustly identified in our genomic survey. We found no evidence to support the notion that pathogen specific accessory genes are more likely to be subject to positive selection than core genes. Indeed, we even uncovered a few cases of essential gene evolution by positive selection. Among the gene clusters subject to positive selection, a large fraction (29%) can be connected to virulence. The most striking finding was that a considerable fraction of the positively selected genes are also known to have tissue specific patterns of expression during invasive disease. As current expression data is far from comprehensive, we suggest that this fraction was underestimated. CONCLUSION: Our findings suggest that pathogen specific genes, although a popular focus of research, do not provide a complete picture of the evolutionary dynamics of virulence. The results of this study, and others, support the notion that the products of both core and accessory genes participate in complex networks that comprise the molecular basis of virulence. Future work should seek to understand the evolutionary dynamics of both core and accessory genes as a function of the networks in which they participate. [Abstract/Link to Full Text]

Stevens MI, Hogendoorn K, Schwarz MP
Evolution of sociality by natural selection on variances in reproductive fitness: evidence from a social bee.
BMC Evol Biol. 2007;7153.
BACKGROUND: The Central Limit Theorem (CLT) is a statistical principle that states that as the number of repeated samples from any population increase, the variance among sample means will decrease and means will become more normally distributed. It has been conjectured that the CLT has the potential to provide benefits for group living in some animals via greater predictability in food acquisition, if the number of foraging bouts increases with group size. The potential existence of benefits for group living derived from a purely statistical principle is highly intriguing and it has implications for the origins of sociality. RESULTS: Here we show that in a social allodapine bee the relationship between cumulative food acquisition (measured as total brood weight) and colony size accords with the CLT. We show that deviations from expected food income decrease with group size, and that brood weights become more normally distributed both over time and with increasing colony size, as predicted by the CLT. Larger colonies are better able to match egg production to expected food intake, and better able to avoid costs associated with producing more brood than can be reared while reducing the risk of under-exploiting the food resources that may be available. CONCLUSION: These benefits to group living derive from a purely statistical principle, rather than from ecological, ergonomic or genetic factors, and could apply to a wide variety of species. This in turn suggests that the CLT may provide benefits at the early evolutionary stages of sociality and that evolution of group size could result from selection on variances in reproductive fitness. In addition, they may help explain why sociality has evolved in some groups and not others. [Abstract/Link to Full Text]

Zuccolo A, Sebastian A, Talag J, Yu Y, Kim H, Collura K, Kudrna D, Wing RA
Transposable element distribution, abundance and role in genome size variation in the genus Oryza.
BMC Evol Biol. 2007;7152.
BACKGROUND: The genus Oryza is composed of 10 distinct genome types, 6 diploid and 4 polyploid, and includes the world's most important food crop - rice (Oryza sativa [AA]). Genome size variation in the Oryza is more than 3-fold and ranges from 357 Mbp in Oryza glaberrima [AA] to 1283 Mbp in the polyploid Oryza ridleyi [HHJJ]. Because repetitive elements are known to play a significant role in genome size variation, we constructed random sheared small insert genomic libraries from 12 representative Oryza species and conducted a comprehensive study of the repetitive element composition, distribution and phylogeny in this genus. Particular attention was paid to the role played by the most important classes of transposable elements (Long Terminal Repeats Retrotransposons, Long interspersed Nuclear Elements, helitrons, DNA transposable elements) in shaping these genomes and in their contributing to genome size variation. RESULTS: We identified the elements primarily responsible for the most strikingly genome size variation in Oryza. We demonstrated how Long Terminal Repeat retrotransposons belonging to the same families have proliferated to very different extents in various species. We also showed that the pool of Long Terminal Repeat Retrotransposons is substantially conserved and ubiquitous throughout the Oryza and so its origin is ancient and its existence predates the speciation events that originated the genus. Finally we described the peculiar behavior of repeats in the species Oryza coarctata [HHKK] whose placement in the Oryza genus is controversial. CONCLUSION: Long Terminal Repeat retrotransposons are the major component of the Oryza genomes analyzed and, along with polyploidization, are the most important contributors to the genome size variation across the Oryza genus. Two families of Ty3-gypsy elements (RIRE2 and Atlantys) account for a significant portion of the genome size variations present in the Oryza genus. [Abstract/Link to Full Text]

Moczek AP
Pupal remodeling and the evolution and development of alternative male morphologies in horned beetles.
BMC Evol Biol. 2007;7151.
BACKGROUND: How novel morphological traits originate and diversify represents a major frontier in evolutionary biology. Horned beetles are emerging as an increasingly popular model system to explore the genetic, developmental, and ecological mechanisms, as well as the interplay between them, in the genesis of novelty and diversity. The horns of beetles originate during a rapid growth phase during the prepupal stage of larval development. Differential growth during this period is either implicitly or explicitly assumed to be the sole mechanism underlying differences in horn expression within and between species. Here I focus on male horn dimorphisms, a phenomenon at the center of many studies in behavioral ecology and evolutionary development, and quantify the relative contributions of a previously ignored developmental process, pupal remodeling, to the expression of male dimorphism in three horned beetle species. RESULTS: Prepupal growth is not the only determinant of differences in male horn expression. Instead, following their initial prepupal growth phase, beetles may be extensively remodeled during the subsequent pupal stage in a sex and size-dependent manner. Specifically, male dimorphism in the three Onthophagus species studied here was shaped not at all, partly or entirely by such pupal remodeling rather than differential growth, suggesting that pupal remodeling is phylogenetically widespread, evolutionarily labile, and developmentally flexible. CONCLUSION: This study is the first to document that male dimorphism in horned beetles is the product of two developmentaly dissociated processes: prepupal growth and pupal remodeling. More generally, adult morphology alone appears to provide few clues, if any, as to the relative contributions of both processes to the expression of alternative male morphs, underscoring the importance of developmental studies in efforts aimed at understanding the evolution of adult diversity patterns. [Abstract/Link to Full Text]

Wu W, Niles EG, LoVerde PT
Thyroid hormone receptor orthologues from invertebrate species with emphasis on Schistosoma mansoni.
BMC Evol Biol. 2007;7150.
BACKGROUND: Thyroid hormone receptors (TRs) function as molecular switches in response to thyroid hormone to regulate gene transcription. TRs were previously believed to be present only in chordates. RESULTS: We isolated two TR genes from the Schistosoma mansoni and identified TR orthologues from other invertebrates: the platyhelminths, S. japonium and Schmidtea mediterranea, the mollusc, Lottia gigantean and the arthropod Daphnia pulex. Phylogenetic analysis of the DNA binding domain and/or ligand binding domain shows that invertebrate and vertebrate TRs cluster together, TRs from the vertebrates and from the jawless vertebrate (lamprey) clustered within separate subgroups, Platyhelminth TRs cluster outside of the vertebrate TR subgroups and that the schistosome TRs and S. mediterranea TRs clustered within separate subgroups. Alignment of the C-terminus of the A/B domain revealed a conserved TR-specific motif, termed TR 'N-terminus signature sequence', with a consensus sequence of (G/P)YIPSY(M/L)XXXGPE(D/E)X. Heterodimer formation between S. mansoni TRs and SmRXR1 suggests that the invertebrate TR protein gained the ability to form a heterodimer with RXR. ESMA analysis showed that SmTR alpha could bind to a conserved DNA core motif as a monomer or homodimer. CONCLUSION: Vertebrate TR genes originated from a common ancestor of the Bilateria. TR genes underwent duplication independently in the Protostomia and Deuterostomia. The duplication of TRs in deuterostomes occurred after the split of jawless and jawed vertebrates. In protostomes, TR genes underwent duplication in Platyhelminths, occurring independently in trematode and turbellarian lineages. Using S. mansoni TRs as an example, invertebrate TRs exhibited the ability to form a dimer with RXR prior to the emergence of the vertebrate TRs and were able to bind to vertebrate TR core DNA elements as a monomer or homodimer. [Abstract/Link to Full Text]

Kruithof EK, Satta N, Liu JW, Dunoyer-Geindre S, Fish RJ
Gene conversion limits divergence of mammalian TLR1 and TLR6.
BMC Evol Biol. 2007;7148.
BACKGROUND: Toll-like receptors (TLR) recognize pathogen-associated molecular patterns and are important mediators of the innate immune system. TLR1 and TLR6 are paralogs and located in tandem on the same chromosome in mammals. They form heterodimers with TLR2 and bind lipopeptide components of gram-positive and gram-negative bacterial cell walls. To identify conserved stretches in TLR1 and TLR6, that may be important for their function, we compared their protein sequences in nine mammalian species(Homo sapiens, Pan troglodytes, Macaca mulatta, Mus musculus, Rattus norvegicus; Erinaceus europaeus, Bos Taurus, Sus scrofa and Canis familiaris). RESULTS: The N-terminal sequences of the orthologous proteins showed greater similarity than corresponding paralog sequences. However, we identified a region of 300 amino acids towards the C-terminus of TLR1 and TLR6, where paralogs had a greater degree of sequence identity than orthologs. Preservation of DNA sequence identity of paralogs in this region was observed in all nine mammalian species investigated, and is due to independent gene conversion events. The regions having undergone gene conversion in each species are almost identical and encode the leucine-rich repeat motifs 16 to 19, the C-terminal cap motif, the transmembrane domain and most of the intracellular Toll/interleukin-1 receptor (TIR) domain. CONCLUSION: Our results show that, for a specific conserved region, divergence of TLR1 and TLR6 is limited by gene conversion, most likely because of the need for co-evolution with multiple intracellular and extracellular binding partners. Thus, gene conversion provides a mechanism for limiting the divergence of functional regions of protein paralogs, while allowing other domains to evolve diversified functions. [Abstract/Link to Full Text]

W�gele JW, Mayer C
Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects.
BMC Evol Biol. 2007;7147.
BACKGROUND: Published molecular phylogenies are usually based on data whose quality has not been explored prior to tree inference. This leads to errors because trees obtained with conventional methods suppress conflicting evidence, and because support values may be high even if there is no distinct phylogenetic signal. Tools that allow an a priori examination of data quality are rarely applied. RESULTS: Using data from published molecular analyses on the phylogeny of crustaceans it is shown that tree topologies and popular support values do not show existing differences in data quality. To visualize variations in signal distinctness, we use network analyses based on split decomposition and split support spectra. Both methods show the same differences in data quality and the same clade-supporting patterns. Both methods are useful to discover long-branch effects.We discern three classes of long branch effects. Class I effects consist of attraction of terminal taxa caused by symplesiomorphies, which results in a false monophyly of paraphyletic groups. Addition of carefully selected taxa can fix this effect. Class II effects are caused by drastic signal erosion. Long branches affected by this phenomenon usually slip down the tree to form false clades that in reality are polyphyletic. To recover the correct phylogeny, more conservative genes must be used. Class III effects consist of attraction due to accumulated chance similarities or convergent character states. This sort of noise can be reduced by selecting less variable portions of the data set, avoiding biases, and adding slower genes. CONCLUSION: To increase confidence in molecular phylogenies an exploratory analysis of the signal to noise ratio can be conducted with split decomposition methods. If long-branch effects are detected, it is necessary to discern between three classes of effects to find the best approach for an improvement of the raw data. [Abstract/Link to Full Text]

Barth�l�my RM, Chenuil A, Blanquart S, Casanova JP, Faure E
Translational machinery of the chaetognath Spadella cephaloptera: a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression.
BMC Evol Biol. 2007;7146.
BACKGROUND: Chaetognaths, or arrow worms, are small marine, bilaterally symmetrical metazoans. The objective of this study was to analyse ribosomal protein (RP) coding sequences from a published collection of expressed sequence tags (ESTs) from a chaetognath (Spadella cephaloptera) and to use them in phylogenetic studies. RESULTS: This analysis has allowed us to determine the complete primary structures of 23 out of 32 RPs from the small ribosomal subunit (SSU) and 32 out of 47 RPs from the large ribosomal subunit (LSU). Ten proteins are partially determined and 14 proteins are missing. Phylogenetic analyses of concatenated RPs from six animals (chaetognath, echinoderm, mammalian, insect, mollusc and sponge) and one fungal taxa do not resolve the chaetognath phylogenetic position, although each mega-sequence comprises approximately 5,000 amino acid residues. This is probably due to the extremely biased base composition and to the high evolutionary rates in chaetognaths. However, the analysis of chaetognath RP genes revealed three unique features in the animal Kingdom. First, whereas generally in animals one RP appeared to have a single type of mRNA, two or more genes are generally transcribed for one RP type in chaetognath. Second, cDNAs with complete 5'-ends encoding a given protein sequence can be divided in two sub-groups according to a short region in their 5'-ends: two novel and highly conserved elements have been identified (5'-TAATTGAGTAGTTT-3' and 5'-TATTAAGTACTAC-3') which could correspond to different transcription factor binding sites on paralog RP genes. And, third, the overall number of deduced paralogous RPs is very high compared to those published for other animals. CONCLUSION: These results suggest that in chaetognaths the deleterious effects of the presence of paralogous RPs, such as apoptosis or cancer are avoided, and also that in each protein family, some of the members could have tissue-specific and extra-ribosomal functions. These results are congruent with the hypotheses of an allopolyploid origin of this phylum and of a ribosome heterogeneity. [Abstract/Link to Full Text]

Sz�v�nyi P, Hock Z, Schneller JJ, T�th Z
Multilocus dataset reveals demographic histories of two peat mosses in Europe.
BMC Evol Biol. 2007;7144.
BACKGROUND: Revealing the past and present demographic history of populations is of high importance to evaluate the conservation status of species. Demographic data can be obtained by direct monitoring or by analysing data of historical and recent collections. Although these methods provide the most detailed information they are very time consuming. Another alternative way is to make use of the information accumulated in the species' DNA over its history. Recent development of the coalescent theory makes it possible to reconstruct the demographic history of species using nucleotide polymorphism data. To separate the effect of natural selection and demography, multilocus analysis is needed because these two forces can produce similar patterns of polymorphisms. In this study we investigated the amount and pattern of sequence variability of a Europe wide sample set of two peat moss species (Sphagnum fimbriatum and S. squarrosum) with similar distributions and mating systems but presumably contrasting historical demographies using 3 regions of the nuclear genome (appr. 3000 bps). We aimed to draw inferences concerning demographic, and phylogeographic histories of the species. RESULTS: All three nuclear regions supported the presence of an Atlantic and Non-Atlantic clade of S. fimbriatum suggesting glacial survival of the species along the Atlantic coast of Europe. Contrarily, S. squarrosum haplotypes showed three clades but no geographic structure at all. Maximum likelihood, mismatch and Bayesian analyses supported a severe historical bottleneck and a relatively recent demographic expansion of the Non-Atlantic clade of S. fimbriatum, whereas size of S. squarrosum populations has probably decreased in the past. Species wide molecular diversity of the two species was nearly the same with an excess of replacement mutations in S. fimbriatum. Similar levels of molecular diversity, contrasting phylogeographic patterns and excess of replacement mutations in S. fimbriatum compared to S. squarrosum mirror unexpected differences in the demography and population history of the species. CONCLUSION: This study represents the first detailed European wide phylodemographic investigation on bryophytes and shows how pattern of nucleotide polymorphism can reveal unexpected differences in the population history of haploid plants with seemingly similar characteristics. [Abstract/Link to Full Text]

Tanaka-Kunishima M, Ishida Y, Takahashi K, Honda M, Oonuma T
Ancient intron insertion sites and palindromic genomic duplication evolutionally shapes an elementally functioning membrane protein family.
BMC Evol Biol. 2007;7143.
BACKGROUND: In spite of the recent accumulation of genomic data, the evolutionary pathway in the individual genes of present-day living taxa is still elusive for most genes. Among ion channels, inward K+ rectifier (IRK) channels are the fundamental and well-defined protein group. We analyzed the genomic structures of this group and compared them among a phylogenetically wide range with our sequenced Halocynthia roretzi, a tunicate, IRK genomic genes. RESULTS: A total of 131 IRK genomic genes were analyzed. The phylogenic trees of amino acid sequences revealed a clear diversification of deuterostomic IRKs from protostomic IRKs and suggested that the tunicate IRKs are possibly representatives of the descendants of ancestor forms of three major groups of IRKs in the vertebrate. However, the exon-intron structures of the tunicate IRK genomes showed considerable similarities to those of Caenorhabditis. In the vertebrate clade, the members in each major group increased at least four times those in the tunicate by various types of global gene duplication. The generation of some major groups was inferred to be due to anti-tandem (palindromic) duplication in early history. The intron insertion points greatly decreased during the evolution of the vertebrates, remaining as a unique conservation of an intron insertion site in the portion of protein-protein interaction within the coding regions of all vertebrate G-protein-activated IRK genes. CONCLUSION: From the genomic survey of a family of IRK genes, it was suggested that the ancient intron insertion sites and the unique palindromic genomic duplication evolutionally shaped this membrane protein family. [Abstract/Link to Full Text]

Porcelli D, Barsanti P, Pesole G, Caggese C
WITHDRAWN: The nuclear OXPHOS genes in insecta: a common evolutionary origin, a common cis-regulatory motif, a common destiny for gene duplicates.
BMC Evol Biol. 2007;7142. [Abstract/Link to Full Text]

Nicolas P, Bessi�res P, Ehrlich SD, Maguin E, van de Guchte M
Extensive horizontal transfer of core genome genes between two Lactobacillus species found in the gastrointestinal tract.
BMC Evol Biol. 2007;7141.
BACKGROUND: While genes that are conserved between related bacterial species are usually thought to have evolved along with the species, phylogenetic trees reconstructed for individual genes may contradict this picture and indicate horizontal gene transfer. Individual trees are often not resolved with high confidence, however, and in that case alternative trees are generally not considered as contradicting the species tree, although not confirming it either. Here we conduct an in-depth analysis of 401 protein phylogenetic trees inferred with varying levels of confidence for three lactobacilli from the acidophilus complex. At present the relationship between these bacteria, isolated from environments as diverse as the gastrointestinal tract (Lactobacillus acidophilus and Lactobacillus johnsonii) and yogurt (Lactobacillus delbrueckii ssp. bulgaricus), is ambiguous due to contradictory phenotypical and 16S rRNA based classifications. RESULTS: Among the 401 phylogenetic trees, those that could be reconstructed with high confidence support the 16S-rRNA tree or one alternative topology in an astonishing 3:2 ratio, while the third possible topology is practically absent. Lowering the confidence threshold for trees to be taken into consideration does not significantly affect this ratio, and therefore suggests that gene transfer may have affected as much as 40% of the core genome genes. Gene function bias suggests that the 16S rRNA phylogeny of the acidophilus complex, which indicates that L. acidophilus and L. delbrueckii ssp. bulgaricus are the closest related of these three species, is correct. A novel approach of comparison of interspecies protein divergence data employed in this study allowed to determine that gene transfer most likely took place between the lineages of the two species found in the gastrointestinal tract. CONCLUSION: This case-study reports an unprecedented level of phylogenetic incongruence, presumably resulting from extensive horizontal gene transfer. The data give a first indication of the large extent of gene transfer that may take place in the gastrointestinal tract and its accumulated effect. For future studies, our results should encourage a careful weighing of data on phylogenetic tree topology, confidence and distribution to conclude on the absence or presence and extent of horizontal gene transfer. [Abstract/Link to Full Text]

Rasteiro R, Pereira-Leal JB
Multiple domain insertions and losses in the evolution of the Rab prenylation complex.
BMC Evol Biol. 2007;7140.
BACKGROUND: Rab proteins are regulators of vesicular trafficking, requiring a lipid modification for proper function, prenylation of C-terminal cysteines. This is catalysed by a complex of a catalytic heterodimer (Rab Geranylgeranyl Transferase - RabGGTase) and an accessory protein (Rab Escort Protein. REP). Components of this complex display domain insertions relative to paralogous proteins. The function of these inserted domains is unclear. RESULTS: We profiled the domain architecture of the components of the Rab prenylation complex in evolution. We identified the orthologues of the components of the Rab prenylation machinery in 43 organisms, representing the crown eukaryotic groups. We characterize in detail the domain structure of all these components and the phylogenetic relationships between the individual domains. CONCLUSION: We found different domain insertions in different taxa, in alpha-subunits of RGGTase and REP. Our results suggest that there were multiple insertions, expansions and contractions in the evolution of this prenylation complex. [Abstract/Link to Full Text]

Hoegg S, Meyer A
Phylogenomic analyses of KCNA gene clusters in vertebrates: why do gene clusters stay intact?
BMC Evol Biol. 2007;7139.
BACKGROUND: Gene clusters are of interest for the understanding of genome evolution since they provide insight in large-scale duplications events as well as patterns of individual gene losses. Vertebrates tend to have multiple copies of gene clusters that typically are only single clusters or are not present at all in genomes of invertebrates. We investigated the genomic architecture and conserved non-coding sequences of vertebrate KCNA gene clusters. KCNA genes encode shaker-related voltage-gated potassium channels and are arranged in two three-gene clusters in tetrapods. Teleost fish are found to possess four clusters. The two tetrapod KNCA clusters are of approximately the same age as the Hox gene clusters that arose through duplications early in vertebrate evolution. For some genes, their conserved retention and arrangement in clusters are thought to be related to regulatory elements in the intergenic regions, which might prevent rearrangements and gene loss. Interestingly, this hypothesis does not appear to apply to the KCNA clusters, as too few conserved putative regulatory elements are retained. RESULTS: We obtained KCNA coding sequences from basal ray-finned fishes (sturgeon, gar, bowfin) and confirmed that the duplication of these genes is specific to teleosts and therefore consistent with the fish-specific genome duplication (FSGD). Phylogenetic analyses of the genes suggest a basal position of the only intron containing KCNA gene in vertebrates (KCNA7). Sistergroup relationships of KCNA1/2 and KCNA3/6 support that a large-scale duplication gave rise to the two clusters found in the genome of tetrapods. We analyzed the intergenic regions of KCNA clusters in vertebrates and found that there are only a few conserved sequences shared between tetrapods and teleosts or between paralogous clusters. The orthologous teleost clusters, however, show sequence conservation in these regions. CONCLUSION: The lack of overall conserved sequences in intergenic regions suggests that there are either other processes than regulatory evolution leading to cluster conservation or that the ancestral regulatory relationships among genes in KCNA clusters have been changed together with their regulatory sites. [Abstract/Link to Full Text]

Teske PR, Hamilton H, Matthee CA, Barker NP
Signatures of seaway closures and founder dispersal in the phylogeny of a circumglobally distributed seahorse lineage.
BMC Evol Biol. 2007;7138.
BACKGROUND: The importance of vicariance events on the establishment of phylogeographic patterns in the marine environment is well documented, and generally accepted as an important cause of cladogenesis. Founder dispersal (i.e. long-distance dispersal followed by founder effect speciation) is also frequently invoked as a cause of genetic divergence among lineages, but its role has long been challenged by vicariance biogeographers. Founder dispersal is likely to be common in species that colonize remote habitats by means of rafting (e.g. seahorses), as long-distance dispersal events are likely to be rare and subsequent additional recruitment from the source habitat is unlikely. In the present study, the relative importance of vicariance and founder dispersal as causes of cladogenesis in a circumglobally distributed seahorse lineage was investigated using molecular dating. A phylogeny was reconstructed using sequence data from mitochondrial and nuclear markers, and the well-documented closure of the Central American seaway was used as a primary calibration point to test whether other bifurcations in the phylogeny could also have been the result of vicariance events. The feasibility of three other vicariance events was explored: a) the closure of the Indonesian Seaway, resulting in sister lineages associated with the Indian Ocean and West Pacific, respectively; b) the closure of the Tethyan Seaway, resulting in sister lineages associated with the Indo-Pacific and Atlantic Ocean, respectively, and c) continental break-up during the Mesozoic followed by spreading of the Atlantic Ocean, resulting in pairs of lineages with amphi-Atlantic distribution patterns. RESULTS: Comparisons of pairwise genetic distances among the seahorse species hypothesized to have diverged as a result of the closure of the Central American Seaway with those of published teleost sequences having the same distribution patterns show that the seahorses were among the last to diverge. This suggests that their cladogenesis was associated with the final closure of this seaway. Although two other divergence events in the phylogeny could potentially have arisen as a result of the closures of the Indonesian and Tethyan seaways, respectively, the timing of the majority of bifurcations in the phylogeny differed significantly from the dates of vicariance events suggested in the literature. Moreover, several divergence events that resulted in the same distribution patterns of lineages at different positions in the phylogeny did not occur contemporaneously. For that reason, they cannot be the result of the same vicariance events, a result that is independent of molecular dating. CONCLUSION: Interpretations of the cladogenetic events in the seahorse phylogeny based purely on vicariance biogeographic hypotheses are problematic. We conclude that the evolution of the circumglobally distributed seahorse lineage was strongly influenced by founder dispersal, and suggest that this mode of speciation may be particularly important in marine organisms that lack a pelagic dispersal phase and instead disperse by means of rafting. [Abstract/Link to Full Text]

Egger B, Koblm�ller S, Sturmbauer C, Sefc KM
Nuclear and mitochondrial data reveal different evolutionary processes in the Lake Tanganyika cichlid genus Tropheus.
BMC Evol Biol. 2007;7137.
BACKGROUND: Cichlid fishes are notorious for their wealth of intra- and interspecific colour pattern diversity. In Lake Tanganyika, the endemic genus Tropheus represents the most impressive example for geographic variation in the pattern and hue of integument colouration, but the taxonomy of the over 100 mostly allopatric colour morphs remains to a large degree unresolved. Previous studies of mitochondrial DNA sequence data revealed polyphyly of the six nominally described species and complex phylogeographic patterns influenced by lake level fluctuations and population admixture, and suggested the parallel evolution of similar colour patterns in divergent evolutionary lineages. A gene tree of a rapidly radiating group may be subject to incomplete and stochastic lineage sorting, and to overcome this problem we used multi-locus, nuclear AFLP data in comparison with mtDNA sequences to study diversification, migration and introgression in Tropheus colour morphs in Lake Tanganyika. RESULTS: Significant incongruence between phylogenetic reconstructions from mitochondrial and AFLP data suggested incomplete sorting of mitochondrial haplotypes as well as frequent introgression between differentiated lineages. In contrast to the mitochondrial phylogeny, the AFLP phenogram was largely congruent with species classifications, colour pattern similarities, and in many cases also with the current geographic distribution of populations, and did not produce evidence of convergent colour pattern evolution. Homoplasy in the AFLP data was used to identify populations that were strongly affected by introgression. CONCLUSION: Different evolutionary processes were distinguished by the combination of mitochondrial and AFLP data. Mitochondrial phylogeographic patterns retained signals of large-scale migration events triggered by historical, major lake level fluctuations, whereas AFLP data indicated genetic cohesion among local groups of populations resulting from secondary contact of adjacent populations in the course of the more frequently occurring, minor lake level fluctuations. There was no support for the parallel evolution of similar colour patterns in the AFLP data. Genetic signatures of introgression and hybridisation detected in several populations suggest that lake level fluctuations drove the stunning diversification of Tropheus morphs not only through population fragmentation, but also by promoting hybridisation between differentiated morphs in secondary contact. [Abstract/Link to Full Text]

May-Collado LJ, Agnarsson I, Wartzok D
Phylogenetic review of tonal sound production in whales in relation to sociality.
BMC Evol Biol. 2007;7136.
BACKGROUND: It is widely held that in toothed whales, high frequency tonal sounds called 'whistles' evolved in association with 'sociality' because in delphinids they are used in a social context. Recently, whistles were hypothesized to be an evolutionary innovation of social dolphins (the 'dolphin hypothesis'). However, both 'whistles' and 'sociality' are broad concepts each representing a conglomerate of characters. Many non-delphinids, whether solitary or social, produce tonal sounds that share most of the acoustic characteristics of delphinid whistles. Furthermore, hypotheses of character correlation are best tested in a phylogenetic context, which has hitherto not been done. Here we summarize data from over 300 studies on cetacean tonal sounds and social structure and phylogenetically test existing hypotheses on their co-evolution. RESULTS: Whistles are 'complex' tonal sounds of toothed whales that demark a more inclusive clade than the social dolphins. Whistles are also used by some riverine species that live in simple societies, and have been lost twice within the social delphinoids, all observations that are inconsistent with the dolphin hypothesis as stated. However, cetacean tonal sounds and sociality are intertwined: (1) increased tonal sound modulation significantly correlates with group size and social structure; (2) changes in tonal sound complexity are significantly concentrated on social branches. Also, duration and minimum frequency correlate as do group size and mean minimum frequency. CONCLUSION: Studying the evolutionary correlation of broad concepts, rather than that of their component characters, is fraught with difficulty, while limits of available data restrict the detail in which component character correlations can be analyzed in this case. Our results support the hypothesis that sociality influences the evolution of tonal sound complexity. The level of social and whistle complexity are correlated, suggesting that complex tonal sounds play an important role in social communication. Minimum frequency is higher in species with large groups, and correlates negatively with duration, which may reflect the increased distances over which non-social species communicate. Our findings are generally stable across a range of alternative phylogenies. Our study points to key species where future studies would be particularly valuable for enriching our understanding of the interplay of acoustic communication and sociality. [Abstract/Link to Full Text]

Mower JP, Touzet P, Gummow JS, Delph LF, Palmer JD
Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants.
BMC Evol Biol. 2007;7135.
BACKGROUND: It has long been known that rates of synonymous substitutions are unusually low in mitochondrial genes of flowering and other land plants. Although two dramatic exceptions to this pattern have recently been reported, it is unclear how often major increases in substitution rates occur during plant mitochondrial evolution and what the overall magnitude of substitution rate variation is across plants. RESULTS: A broad survey was undertaken to evaluate synonymous substitution rates in mitochondrial genes of angiosperms and gymnosperms. Although most taxa conform to the generality that plant mitochondrial sequences evolve slowly, additional cases of highly accelerated rates were found. We explore in detail one of these new cases, within the genus Silene. A roughly 100-fold increase in synonymous substitution rate is estimated to have taken place within the last 5 million years and involves only one of ten species of Silene sampled in this study. Examples of unusually slow sequence evolution were also identified. Comparison of the fastest and slowest lineages shows that synonymous substitution rates vary by four orders of magnitude across seed plants. In other words, some plant mitochondrial lineages accumulate more synonymous change in 10,000 years than do others in 100 million years. Several perplexing cases of gene-to-gene variation in sequence divergence within a plant were uncovered. Some of these probably reflect interesting biological phenomena, such as horizontal gene transfer, mitochondrial-to-nucleus transfer, and intragenomic variation in mitochondrial substitution rates, whereas others are likely the result of various kinds of errors. CONCLUSION: The extremes of synonymous substitution rates measured here constitute by far the largest known range of rate variation for any group of organisms. These results highlight the utility of examining absolute substitution rates in a phylogenetic context rather than by traditional pairwise methods. Why substitution rates are generally so low in plant mitochondrial genomes yet occasionally increase dramatically remains mysterious. [Abstract/Link to Full Text]

Kuramae EE, Robert V, Echavarri-Erasun C, Boekhout T
Cophenetic correlation analysis as a strategy to select phylogenetically informative proteins: an example from the fungal kingdom.
BMC Evol Biol. 2007;7134.
BACKGROUND: The construction of robust and well resolved phylogenetic trees is important for our understanding of many, if not all biological processes, including speciation and origin of higher taxa, genome evolution, metabolic diversification, multicellularity, origin of life styles, pathogenicity and so on. Many older phylogenies were not well supported due to insufficient phylogenetic signal present in the single or few genes used in phylogenetic reconstructions. Importantly, single gene phylogenies were not always found to be congruent. The phylogenetic signal may, therefore, be increased by enlarging the number of genes included in phylogenetic studies. Unfortunately, concatenation of many genes does not take into consideration the evolutionary history of each individual gene. Here, we describe an approach to select informative phylogenetic proteins to be used in the Tree of Life (TOL) and barcoding projects by comparing the cophenetic correlation coefficients (CCC) among individual protein distance matrices of proteins, using the fungi as an example. The method demonstrated that the quality and number of concatenated proteins is important for a reliable estimation of TOL. Approximately 40-45 concatenated proteins seem needed to resolve fungal TOL. RESULTS: In total 4852 orthologous proteins (KOGs) were assigned among 33 fungal genomes from the Asco- and Basidiomycota and 70 of these represented single copy proteins. The individual protein distance matrices based on 531 concatenated proteins that has been used for phylogeny reconstruction before 14 were compared one with another in order to select those with the highest CCC, which then was used as a reference. This reference distance matrix was compared with those of the 70 single copy proteins selected and their CCC values were calculated. Sixty four KOGs showed a CCC above 0.50 and these were further considered for their phylogenetic potential. Proteins belonging to the cellular processes and signaling KOG category seem more informative than those belonging to the other three categories: information storage and processing; metabolism; and the poorly characterized category. After concatenation of 40 proteins the topology of the phylogenetic tree remained stable, but after concatenation of 60 or more proteins the bootstrap support values of some branches decreased, most likely due to the inclusion of proteins with lowers CCC values. The selection of protein sequences to be used in various TOL projects remains a critical and important process. The method described in this paper will contribute to a more objective selection of phylogenetically informative protein sequences. CONCLUSION: This study provides candidate protein sequences to be considered as phylogenetic markers in different branches of fungal TOL. The selection procedure described here will be useful to select informative protein sequences to resolve branches of TOL that contain few or no species with completely sequenced genomes. The robust phylogenetic trees resulting from this method may contribute to our understanding of organismal diversification processes. The method proposed can be extended easily to other branches of TOL. [Abstract/Link to Full Text]

Recent Articles in BMC Structural Biology

Huang B, Schroeder M
LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation.
BMC Struct Biol. 2006;619.
BACKGROUND: Identifying pockets on protein surfaces is of great importance for many structure-based drug design applications and protein-ligand docking algorithms. Over the last ten years, many geometric methods for the prediction of ligand-binding sites have been developed. RESULTS: We present LIGSITEcsc, an extension and implementation of the LIGSITE algorithm. LIGSITEcsc is based on the notion of surface-solvent-surface events and the degree of conservation of the involved surface residues. We compare our algorithm to four other approaches, LIGSITE, CAST, PASS, and SURFNET, and evaluate all on a dataset of 48 unbound/bound structures and 210 bound-structures. LIGSITEcsc performs slightly better than the other tools and achieves a success rate of 71% and 75%, respectively. CONCLUSION: The use of the Connolly surface leads to slight improvements, the prediction re-ranking by conservation to significant improvements of the binding site predictions. A web server for LIGSITEcsc and its source code is available at scoppi.biotec.tu-dresden.de/pocket [Abstract/Link to Full Text]

Chen L, Wu LY, Wang Y, Zhang S, Zhang XS
Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison.
BMC Struct Biol. 2006;618.
BACKGROUND: Protein structure comparison is one of the most important problems in computational biology and plays a key role in protein structure prediction, fold family classification, motif finding, phylogenetic tree reconstruction and protein docking. RESULTS: We propose a novel method to compare the protein structures in an accurate and efficient manner. Such a method can be used to not only reveal divergent evolution, but also identify circular permutations and further detect active-sites. Specifically, we define the structure alignment as a multi-objective optimization problem, i.e., maximizing the number of aligned atoms and minimizing their root mean square distance. By controlling a single distance-related parameter, theoretically we can obtain a variety of optimal alignments corresponding to different optimal matching patterns, i.e., from a large matching portion to a small matching portion. The number of variables in our algorithm increases with the number of atoms of protein pairs in almost a linear manner. In addition to solid theoretical background, numerical experiments demonstrated significant improvement of our approach over the existing methods in terms of quality and efficiency. In particular, we show that divergent evolution, circular permutations and active-sites (or structural motifs) can be identified by our method. The software SAMO is available upon request from the authors, or from http://zhangroup.aporc.org/bioinfo/samo/ and http://intelligent.eic.osaka-sandai.ac.jp/chenen/samo.htm. CONCLUSION: A novel formulation is proposed to accurately align protein structures in the framework of multi-objective optimization, based on a sequence order-independent strategy. A fast and accurate algorithm based on the bipartite matching algorithm is developed by exploiting the special features. Convergence of computation is shown in experiments and is also theoretically proven. [Abstract/Link to Full Text]

Colacino S, Tiana G, Colombo G
Similar folds with different stabilization mechanisms: the cases of Prion and Doppel proteins.
BMC Struct Biol. 2006;617.
BACKGROUND: Protein misfolding is the main cause of a group of fatal neurodegenerative diseases in humans and animals. In particular, in Prion-related diseases the normal cellular form of the Prion Protein PrP (PrPC) is converted into the infectious PrPSc through a conformational process during which it acquires a high beta-sheet content. Doppel is a protein that shares a similar native fold, but lacks the scrapie isoform. Understanding the molecular determinants of these different behaviours is important both for biomedical and biophysical research. RESULTS: In this paper, the dynamical and energetic properties of the two proteins in solution is comparatively analyzed by means of long time scale explicit solvent, all-atom molecular dynamics in different temperature conditions. The trajectories are analyzed by means of a recently introduced energy decomposition approach (Tiana et al, Prot. Sci. 2004) aimed at identifying the key residues for the stabilization and folding of the protein. Our analysis shows that Prion and Doppel have two different cores stabilizing the native state and that the relative contribution of the nucleus to the global stability of the protein for Doppel is sensitively higher than for PrP. Moreover, under misfolding conditions the Doppel core is conserved, while the energy stabilization network of PrP is disrupted. CONCLUSION: These observations suggest that different sequences can share similar native topology with different stabilizing interactions and that the sequences of the Prion and Doppel proteins may have diverged under different evolutionary constraints resulting in different folding and stabilization mechanisms. [Abstract/Link to Full Text]

Kachel N, Kremer W, Zahn R, Kalbitzer HR
Observation of intermediate states of the human prion protein by high pressure NMR spectroscopy.
BMC Struct Biol. 2006;616.
BACKGROUND: Prions as causative agents of transmissible spongiform encephalopathies (TSEs) in humans and animals are composed of the infectious isomer, PrPSc, of the cellular prion protein, PrPC. The conversion and thus the propensity of PrPC to adopt alternative folds leads to the species-specific propagation of the disease. High pressure is a powerful tool to study the physico-chemical properties of proteins as well as the dynamics and structure of folding intermediates. RESULTS: Conformational intermediates of the human prion protein huPrPC were characterized by a combination of hydrostatic pressure (up to 200 MPa) with two-dimensional NMR spectroscopy. All pressure effects showed to be reversible and there is virtually no difference in the overall pressure response between the folded core of the N-terminal truncated huPrPC(121-230) and the full-length huPrPC(23-230). The only significant differences in the pressure response of full-length and truncated PrP suggest that E168, H187, T192, E207, E211 and Y226 are involved in a transient interaction with the unfolded N-terminus. High-pressure NMR spectroscopy indicates that the folded core of the human prion protein occurs in two structural states N1 and N2 in solution associated with rather small differences in free enthalpies (3.0 kJ/mol). At atmospheric pressure approximately 29% of the protein are already in the pressure favored conformation N2. There is a second process representing two possible folding intermediates I1 and I2 with corresponding average free enthalpies of 10.8 and 18.6 kJ/mol. They could represent preaggregation states of the protein that coexist at ambient pressure with a very small population of approximately 1.2% and less than 0.1%. Further the pressure response of the N-terminus indicates that four different regions are in a fast equilibrium with non-random structural states whose populations are shifted by pressure. CONCLUSION: We identified pressure stabilized folding intermediates of the human prion protein. The regions reflecting most strongly the transition to the intermediate states are the beta1/alpha1-loop and the solvent exposed side of alpha3. The most pressure-sensitive region (representing mainly intermediate I1) is the loop between beta-strand 1 and alpha-helix 1 (residue 139-141), indicating that this region might be the first entry point for the infectious conformer to convert the cellular protein. [Abstract/Link to Full Text]

Fernandez-Fuentes N, Fiser A
Saturating representation of loop conformational fragments in structure databanks.
BMC Struct Biol. 2006;615.
BACKGROUND: Short fragments of proteins are fundamental starting points in various structure prediction applications, such as in fragment based loop modeling methods but also in various full structure build-up procedures. The applicability and performance of these approaches depend on the availability of short fragments in structure databanks. RESULTS: We studied the representation of protein loop fragments up to 14 residues in length. All possible query fragments found in sequence databases (Sequence Space) were clustered and cross referenced with available structural fragments in Protein Data Bank (Structure Space). We found that the expansion of PDB in the last few years resulted in a dense coverage of loop conformational fragments. For each loops of length 8 in the current Sequence Space there is at least one loop in Structure Space with 50% or higher sequence identity. By correlating sequence and structure clusters of loops we found that a 50% sequence identity generally guarantees structural similarity. These percentages of coverage at 50% sequence cutoff drop to 96, 94, 68, 53, 33 and 13% for loops of length 9, 10, 11, 12, 13, and 14, respectively. There is not a single loop in the current Sequence Space at any length up to 14 residues that is not matched with a conformational segment that shares at least 20% sequence identity. This minimum observed identity is 40% for loops of 12 residues or shorter and is as high as 50% for 10 residue or shorter loops. We also assessed the impact of rapidly growing sequence databanks on the estimated number of new loop conformations and found that while the number of sequentially unique sequence segments increased about six folds during the last five years there are almost no unique conformational segments among these up to 12 residues long fragments. CONCLUSION: The results suggest that fragment based prediction approaches are not limited any more by the completeness of fragments in databanks but rather by the effective scoring and search algorithms to locate them. The current favorable coverage and trends observed will be further accentuated with the progress of Protein Structure Initiative that targets new protein folds and ultimately aims at providing an exhaustive coverage of the structure space. [Abstract/Link to Full Text]

Brunner K, Gronwald W, Trenner JM, Neidig KP, Kalbitzer HR
A general method for the unbiased improvement of solution NMR structures by the use of related X-ray data, the AUREMOL-ISIC algorithm.
BMC Struct Biol. 2006;614.
BACKGROUND: Rapid and accurate three-dimensional structure determination of biological macromolecules is mandatory to keep up with the vast progress made in the identification of primary sequence information. During the last few years the amount of data deposited in the protein data bank has substantially increased providing additional information for novel structure determination projects. The key question is how to combine the available database information with the experimental data of the current project ensuring that only relevant information is used and a correct structural bias is produced. For this purpose a novel fully automated algorithm based on Bayesian reasoning has been developed. It allows the combination of structural information from different sources in a consistent way to obtain high quality structures with a limited set of experimental data. The new ISIC (Intelligent Structural Information Combination) algorithm is part of the larger AUREMOL software package. RESULTS: Our new approach was successfully tested on the improvement of the solution NMR structures of the Ras-binding domain of Byr2 from Schizosaccharomyces pombe, the Ras-binding domain of RalGDS from human calculated from a limited set of NMR data, and the immunoglobulin binding domain from protein G from Streptococcus by their corresponding X-ray structures. In all test cases clearly improved structures were obtained. The largest danger in using data from other sources is a possible bias towards the added structure. In the worst case instead of a refined target structure the structure from the additional source is essentially reproduced. We could clearly show that the ISIC algorithm treats these difficulties properly. CONCLUSION: In summary, we present a novel fully automated method to combine strongly coupled knowledge from different sources. The combination with validation tools such as the calculation of NMR R-factors strengthens the impact of the method considerably since the improvement of the structures can be assessed quantitatively. The ISIC method can be applied to a large number of similar problems where the quality of the obtained three-dimensional structures is limited by the available experimental data like the improvement of large NMR structures calculated from sparse experimental data or the refinement of low resolution X-ray structures. Also structures may be refined using other available structural information such as homology models. [Abstract/Link to Full Text]

Adamian L, Liang J
Prediction of transmembrane helix orientation in polytopic membrane proteins.
BMC Struct Biol. 2006;613.
BACKGROUND: Membrane proteins compose up to 30% of coding sequences within genomes. However, their structure determination is lagging behind compared with soluble proteins due to the experimental difficulties. Therefore, it is important to develop reliable computational methods to predict structures of membrane proteins. RESULTS: We present a method for prediction of the TM helix orientation, which is an essential step in ab initio modeling of membrane proteins. Our method is based on a canonical model of the heptad repeat originally developed for coiled coils. We identify the helical surface patches that interface with lipid molecules at an accuracy of about 88% from the sequence information alone, using an empirical scoring function LIPS (LIPid-facing Surface), which combines lipophilicity and conservation of residues in the helix. We test and discuss results of prediction of helix-lipid interfaces on 162 transmembrane helices from 18 polytopic membrane proteins and present predicted orientations of TM helices in TRPV1 channel. We also apply our method to two structures of homologous cytochrome b6f complexes and find discrepancy in the assignment of TM helices from subunits PetG, PetN and PetL. The results of LIPS calculations and analysis of packing and H-bonding interactions support the helix assignment found in the cytochrome b6f structure from green alga but not the assignment of TM helices in the cyanobacterium b6f structure. CONCLUSION: LIPS calculations can be used for the prediction of helix orientation in ab initio modeling of polytopic membrane proteins. We also show with the example of two cytochrome b6f structures that our method can identify questionable helix assignments in membrane proteins. The LIPS server is available online at http://gila.bioengr.uic.edu/lab/larisa/lips.html. [Abstract/Link to Full Text]

Zotenko E, O'Leary DP, Przytycka TM
Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification.
BMC Struct Biol. 2006;612.
BACKGROUND: Recently a new class of methods for fast protein structure comparison has emerged. We call the methods in this class projection methods as they rely on a mapping of protein structure into a high-dimensional vector space. Once the mapping is done, the structure comparison is reduced to distance computation between corresponding vectors. As structural similarity is approximated by distance between projections, the success of any projection method depends on how well its mapping function is able to capture the salient features of protein structure. There is no agreement on what constitutes a good projection technique and the three currently known projection methods utilize very different approaches to the mapping construction, both in terms of what structural elements are included and how this information is integrated to produce a vector representation. RESULTS: In this paper we propose a novel projection method that uses secondary structure information to produce the mapping. First, a diverse set of spatial arrangements of triplets of secondary structure elements, a set of structural models, is automatically selected. Then, each protein structure is mapped into a high-dimensional vector of "counts" or footprint, where each count corresponds to the number of times a given structural model is observed in the structure, weighted by the precision with which the model is reproduced. We perform the first comprehensive evaluation of our method together with all other currently known projection methods. CONCLUSION: The results of our evaluation suggest that the type of structural information used by a projection method affects the ability of the method to detect structural similarity. In particular, our method that uses the spatial conformations of triplets of secondary structure elements outperforms other methods in most of the tests. [Abstract/Link to Full Text]

Saha RP, Bahadur RP, Pal A, Mandal S, Chakrabarti P
ProFace: a server for the analysis of the physicochemical features of protein-protein interfaces.
BMC Struct Biol. 2006;611.
BACKGROUND: Molecular recognition is all pervasive in biology. Protein molecules are involved in enzyme regulation, immune response, signal transduction, oligomer assembly, etc. Delineation of physical and chemical features of the interface formed by protein-protein association would allow us to better understand protein interaction networks on one hand, and to design molecules that can engage a given interface and thereby control protein function on the other hand. RESULTS: ProFace is a suite of programs that uses a file, containing atomic coordinates of a multi-chain molecule, as input and analyzes the interface between any two or more subunits. The interface residues are shown segregated into spatial patches (if such a clustering is possible based on an input threshold distance) and/or core and rim regions. A number of physicochemical parameters defining the interface is tabulated. Among the different output files, one contains the list of interacting residues across the interface. Results can be used to infer if a particular interface belongs to a homodimeric molecule. CONCLUSION: A web-server, ProFace (available at http://www.boseinst.ernet.in/resources/bioinfo/stag.html) has been developed for dissecting protein-protein interfaces and deriving various physicochemical parameters. [Abstract/Link to Full Text]

Roosild TP, Vega M, Castronovo S, Choe S
Characterization of the family of Mistic homologues.
BMC Struct Biol. 2006;610.
BACKGROUND: Mistic is a unique Bacillus subtilis protein with virtually no detectable homologues in GenBank, which appears to integrate into the bacterial membrane despite an overall hydrophilic composition. These unusual properties have been shown to be useful for high-yield recombinant expression of other membrane proteins through fusion to the C-terminus of Mistic. To better understand the structure and function of Mistic, we systematically searched for and characterized homologous proteins among closely related bacteria. RESULTS: Three homologues of Mistic were found with 62% to 93% residue identity, all only 84 residues in length, corresponding to the C-terminal residues of B. subtilis Mistic. In every case, the Mistic gene was found partially overlapping a downstream gene for a K+ channel protein. Residue variation amongst these sequences is restricted to loop regions of the protein's structure, suggesting that secondary structure elements and overall fold have been conserved. Additionally, all three homologues retain the functional ability to chaperone fusion partners to the membrane. CONCLUSION: The functional core of Mistic consists of 84 moderately conserved residues that are sufficient for membrane targeting and integration. Understanding the minimal structural and chemical complexity of Mistic will lead to insights into the mechanistic underpinnings of Mistic-chaperoned membrane integration, as well as how to optimize its use for the recombinant heterologous expression of other integral membrane proteins of interest. [Abstract/Link to Full Text]

Sujatha MS, Balaji PV
Fold-recognition and comparative modeling of human alpha2,3-sialyltransferases reveal their sequence and structural similarities to CstII from Campylobacter jejuni.
BMC Struct Biol. 2006;69.
BACKGROUND: The 3-D structure of none of the eukaryotic sialyltransferases (SiaTs) has been determined so far. Sequence alignment algorithms such as BLAST and PSI-BLAST could not detect a homolog of these enzymes from the protein databank. SiaTs, thus, belong to the hard/medium target category in the CASP experiments. The objective of the current work is to model the 3-D structures of human SiaTs which transfer the sialic acid in alpha2,3-linkage viz., ST3Gal I, II, III, IV, V, and VI, using fold-recognition and comparative modeling methods. The pair-wise sequence similarity among these six enzymes ranges from 41 to 63%. RESULTS: Unlike the sequence similarity servers, fold-recognition servers identified CstII, a alpha2,3/8 dual-activity SiaT from Campylobacter jejuni as the homolog of all the six ST3Gals; the level of sequence similarity between CstII and ST3Gals is only 15-20% and the similarity is restricted to well-characterized motif regions of ST3Gals. Deriving template-target sequence alignments for the entire ST3Gal sequence was not straightforward: the fold-recognition servers could not find a template for the region preceding the L-motif and that between the L- and S-motifs. Multiple structural templates were identified to model these regions and template identification-modeling-evaluation had to be performed iteratively to choose the most appropriate templates. The modeled structures have acceptable stereochemical properties and are also able to provide qualitative rationalizations for some of the site-directed mutagenesis results reported in literature. Apart from the predicted models, an unexpected but valuable finding from this study is the sequential and structural relatedness of family GT42 and family GT29 SiaTs. CONCLUSION: The modeled 3-D structures can be used for docking and other modeling studies and for the rational identification of residues to be mutated to impart desired properties such as altered stability, substrate specificity, etc. Several studies in literature have focused on the development of tools and/or servers for the large-scale/automated modeling of 3-D structures of proteins. In contrast, the present study focuses on modeling the 3-D structure of a specific protein of interest to a biochemist and illustrates the associated difficulties. It is also able to establish a sequence/structure relationship between sialyltransferases of two distinct families. [Abstract/Link to Full Text]

Krishna SS, Sadreyev RI, Grishin NV
A tale of two ferredoxins: sequence similarity and structural differences.
BMC Struct Biol. 2006;68.
BACKGROUND: Sequence similarity between proteins is usually considered a reliable indicator of homology. Pyruvate-ferredoxin oxidoreductase and quinol-fumarate reductase contain ferredoxin domains that bind [Fe-S] clusters and are involved in electron transport. Profile-based methods for sequence comparison, such as PSI-BLAST and HMMer, suggest statistically significant similarity between these domains. RESULTS: The sequence similarity between these ferredoxin domains resides in the area of the [Fe-S] cluster-binding sites. Although overall folds of these ferredoxins bear no obvious similarity, the regions of sequence similarity display a remarkable local structural similarity. These short regions with pronounced sequence motifs are incorporated in completely different structural environments. In pyruvate-ferredoxin oxidoreductase (bacterial ferredoxin), the hydrophobic core of the domain is completed by two beta-hairpins, whereas in quinol-fumarate reductase (alpha-helical ferredoxin), the cluster-binding motifs are part of a larger all-alpha-helical globin-like fold core. CONCLUSION: Functionally meaningful sequence similarity may sometimes be reflected only in local structural similarity, but not in global fold similarity. If detected and used naively, such similarities may lead to incorrect fold predictions. [Abstract/Link to Full Text]

Chandonia JM, Kim SH
Structural proteomics of minimal organisms: conservation of protein fold usage and evolutionary implications.
BMC Struct Biol. 2006;67.
BACKGROUND: Determining the complete repertoire of protein structures for all soluble, globular proteins in a single organism has been one of the major goals of several structural genomics projects in recent years. RESULTS: We report that this goal has nearly been reached for several "minimal organisms"--parasites or symbionts with reduced genomes--for which over 95% of the soluble, globular proteins may now be assigned folds, overall 3-D backbone structures. We analyze the structures of these proteins as they relate to cellular functions, and compare conservation of fold usage between functional categories. We also compare patterns in the conservation of folds among minimal organisms and those observed between minimal organisms and other bacteria. CONCLUSION: We find that proteins performing essential cellular functions closely related to transcription and translation exhibit a higher degree of conservation in fold usage than proteins in other functional categories. Folds related to transcription and translation functional categories were also overrepresented in minimal organisms compared to other bacteria. [Abstract/Link to Full Text]

Sadreyev RI, Grishin NV
Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds.
BMC Struct Biol. 2006;66.
BACKGROUND: As tertiary structure is currently available only for a fraction of known protein families, it is important to assess what parts of sequence space have been structurally characterized. We consider protein domains whose structure can be predicted by sequence similarity to proteins with solved structure and address the following questions. Do these domains represent an unbiased random sample of all sequence families? Do targets solved by structural genomic initiatives (SGI) provide such a sample? What are approximate total numbers of structure-based superfamilies and folds among soluble globular domains? RESULTS: To make these assessments, we combine two approaches: (i) sequence analysis and homology-based structure prediction for proteins from complete genomes; and (ii) monitoring dynamics of the assigned structure set in time, with the accumulation of experimentally solved structures. In the Clusters of Orthologous Groups (COG) database, we map the growing population of structurally characterized domain families onto the network of sequence-based connections between domains. This mapping reveals a systematic bias suggesting that target families for structure determination tend to be located in highly populated areas of sequence space. In contrast, the subset of domains whose structure is initially inferred by SGI is similar to a random sample from the whole population. To accommodate for the observed bias, we propose a new non-parametric approach to the estimation of the total numbers of structural superfamilies and folds, which does not rely on a specific model of the sampling process. Based on dynamics of robust distribution-based parameters in the growing set of structure predictions, we estimate the total numbers of superfamilies and folds among soluble globular proteins in the COG database. CONCLUSION: The set of currently solved protein structures allows for structure prediction in approximately a third of sequence-based domain families. The choice of targets for structure determination is biased towards domains with many sequence-based homologs. The growing SGI output in the future should further contribute to the reduction of this bias. The total number of structural superfamilies and folds in the COG database are estimated as approximately 4000 and approximately 1700. These numbers are respectively four and three times higher than the numbers of superfamilies and folds that can currently be assigned to COG proteins. [Abstract/Link to Full Text]

Davies MN, Hattotuwagama CK, Moss DS, Drew MG, Flower DR
Statistical deconvolution of enthalpic energetic contributions to MHC-peptide binding affinity.
BMC Struct Biol. 2006;65.
BACKGROUND: MHC Class I molecules present antigenic peptides to cytotoxic T cells, which forms an integral part of the adaptive immune response. Peptides are bound within a groove formed by the MHC heavy chain. Previous approaches to MHC Class I-peptide binding prediction have largely concentrated on the peptide anchor residues located at the P2 and C-terminus positions. RESULTS: A large dataset comprising MHC-peptide structural complexes was created by re-modelling pre-determined x-ray crystallographic structures. Static energetic analysis, following energy minimisation, was performed on the dataset in order to characterise interactions between bound peptides and the MHC Class I molecule, partitioning the interactions within the groove into van der Waals, electrostatic and total non-bonded energy contributions. CONCLUSION: The QSAR techniques of Genetic Function Approximation (GFA) and Genetic Partial Least Squares (G/PLS) algorithms were used to identify key interactions between the two molecules by comparing the calculated energy values with experimentally-determined BL50 data. Although the peptide termini binding interactions help ensure the stability of the MHC Class I-peptide complex, the central region of the peptide is also important in defining the specificity of the interaction. As thermodynamic studies indicate that peptide association and dissociation may be driven entropically, it may be necessary to incorporate entropic contributions into future calculations. [Abstract/Link to Full Text]

Peters B, Moad C, Youn E, Buffington K, Heiland R, Mooney S
Identification of similar regions of protein structures using integrated sequence and structure analysis tools.
BMC Struct Biol. 2006;64.
BACKGROUND: Understanding protein function from its structure is a challenging problem. Sequence based approaches for finding homology have broad use for annotation of both structure and function. 3D structural information of protein domains and their interactions provide a complementary view to structure function relationships to sequence information. We have developed a web site http://www.sblest.org/ and an API of web services that enables users to submit protein structures and identify statistically significant neighbors and the underlying structural environments that make that match using a suite of sequence and structure analysis tools. To do this, we have integrated S-BLEST, PSI-BLAST and HMMer based superfamily predictions to give a unique integrated view to prediction of SCOP superfamilies, EC number, and GO term, as well as identification of the protein structural environments that are associated with that prediction. Additionally, we have extended UCSF Chimera and PyMOL to support our web services, so that users can characterize their own proteins of interest. RESULTS: Users are able to submit their own queries or use a structure already in the PDB. Currently the databases that a user can query include the popular structural datasets ASTRAL 40 v1.69, ASTRAL 95 v1.69, CLUSTER50, CLUSTER70 and CLUSTER90 and PDBSELECT25. The results can be downloaded directly from the site and include function prediction, analysis of the most conserved environments and automated annotation of query proteins. These results reflect both the hits found with PSI-BLAST, HMMer and with S-BLEST. We have evaluated how well annotation transfer can be performed on SCOP ID's, Gene Ontology (GO) ID's and EC Numbers. The method is very efficient and totally automated, generally taking around fifteen minutes for a 400 residue protein. CONCLUSION: With structural genomics initiatives determining structures with little, if any, functional characterization, development of protein structure and function analysis tools are a necessary endeavor. We have developed a useful application towards a solution to this problem using common structural and sequence based analysis tools. These approaches are able to find statistically significant environments in a database of protein structure, and the method is able to quantify how closely associated each environment is to a predicted functional annotation. [Abstract/Link to Full Text]

Jeong J, Berman P, Przytycka T
Fold classification based on secondary structure--how much is gained by including loop topology?
BMC Struct Biol. 2006;63.
BACKGROUND: It has been proposed that secondary structure information can be used to classify (to some extend) protein folds. Since this method utilizes very limited information about the protein structure, it is not surprising that it has a higher error rate than the approaches that use full 3D fold description. On the other hand, the comparing of 3D protein structures is computing intensive. This raises the question to what extend the error rate can be decreased with each new source of information, especially if the new information can still be used with simple alignment algorithms. We consider the question whether the information about closed loops can improve the accuracy of this approach. While the answer appears to be obvious, we had to overcome two challenges. First, how to code and to compare topological information in such a way that local alignment of strings will properly identify similar structures. Second, how to properly measure the effect of new information in a large data sample. We investigate alternative ways of computing and presenting this information. RESULTS: We used the set of beta proteins with at most 30% pairwise identity to test the approach; local alignment scores were used to build a tree of clusters which was evaluated using a new log-odd cluster scoring function. In particular, we derive a closed formula for the probability of obtaining a given score by chance.Parameters of local alignment function were optimized using a genetic algorithm. Of 81 folds that had more than one representative in our data set, log-odds scores registered significantly better clustering in 27 cases and significantly worse in 6 cases, and small differences in the remaining cases. Various notions of the significant change or average change were considered and tried, and the results were all pointing in the same direction. CONCLUSION: We found that, on average, properly presented information about the loop topology improves noticeably the accuracy of the method but the benefits vary between fold families as measured by log-odds cluster score. [Abstract/Link to Full Text]

Argiriadi MA, Goedken ER, Bruck I, O'Donnell M, Kuriyan J
Crystal structure of a DNA polymerase sliding clamp from a Gram-positive bacterium.
BMC Struct Biol. 2006;62.
BACKGROUND: Sliding DNA clamps are processivity factors that are required for efficient DNA replication. DNA polymerases maintain proximity to nucleic acid templates by interacting with sliding clamps that encircle DNA and thereby link the polymerase enzyme to the DNA substrate. Although the structures of sliding clamps from Gram-negative bacteria (E. coli), eukaryotes, archaea, and T4-like bacteriophages are well-known, the structure of a sliding clamp from Gram-positive bacteria has not been reported previously. RESULTS: We have determined the crystal structure of the dimeric beta subunit of the DNA polymerase III holoenzyme of Streptococcus pyogenes. The sliding clamp from this Gram-positive organism forms a ring-shaped dimeric assembly that is similar in overall structure to that of the sliding clamps from Gram-negative bacteria, bacteriophage T4, eukaryotes and archaea. The dimer has overall dimensions of approximately 90 A x approximately 70 A x approximately 25 A with a central chamber that is large enough to accommodate duplex DNA. In comparison to the circular shape of other assemblies, the S. pyogenes clamp adopts a more elliptical structure. CONCLUSION: The sequences of sliding clamps from S. pyogenes and E. coli are only 23% identical, making the generation of structural models for the S. pyogenes clamp difficult in the absence of direct experimental information. Our structure of the S. pyogenes beta subunit completes the catalog of clamp structures from all the major sequence grouping of sliding clamps. The more elliptical rather than circular structure of the S. pyogenes clamp implies that the topological nature of encircling DNA, rather than a precise geometric shape, is the most conserved aspect for this family of proteins. [Abstract/Link to Full Text]

Pugh DJ, Ab E, Faro A, Lutya PT, Hoffmann E, Rees DJ
DWNN, a novel ubiquitin-like domain, implicates RBBP6 in mRNA processing and ubiquitin-like pathways.
BMC Struct Biol. 2006;61.
BACKGROUND: RBBP6 is a 250 kDa splicing-associated protein that has been identified as an E3 ligase due to the presence of a RING finger domain. In humans and mice it interacts with both p53 and Rb, and plays a role in the induction of apoptosis and regulation of the cell cycle. RBBP6 has recently been shown to be highly up-regulated in oesophageal cancer, and to be a promising target for immunotherapy against the disease. RESULTS: We show here using heteronuclear NMR that the N-terminal 81 amino acids of RBBP6 constitute a novel ubiquitin-like domain, which we have called the DWNN domain. The domain lacks conserved equivalents of K48 and K63, although the equivalents of K6 and K29 are highly, although not absolutely, conserved. The di-glycine motif that is characteristic of proteins involved in ubiquitination is found in the human and mouse form of the domain, although it is not present in all organisms. It forms part of a three-domain form of RBBP6 containing the DWNN domain, a zinc knuckle and a RING finger domain, which is found in all eukaryotic genomes so far examined, in the majority of cases at single copy number. The domain is also independently expressed in vertebrates as a single domain protein. CONCLUSION: DWNN is a novel ubiquitin-like domain found only at the N-terminus of the RBBP6 family of splicing-associated proteins. The ubiquitin-like structure of the domain greatly increases the likelihood that RBBP6 functions through some form of ubiquitin-like modification. Furthermore, the fact that the DWNN domain is independently expressed in higher vertebrates leads us to propose that the domain may itself function as a novel ubiquitin-like modifier of other proteins. [Abstract/Link to Full Text]

Manjasetty BA, Niesen FH, Scheich C, Roske Y, Goetz F, Behlke J, Sievert V, Heinemann U, B�ssow K
X-ray structure of engineered human Aortic Preferentially Expressed Protein-1 (APEG-1).
BMC Struct Biol. 2005;521.
BACKGROUND: Human Aortic Preferentially Expressed Protein-1 (APEG-1) is a novel specific smooth muscle differentiation marker thought to play a role in the growth and differentiation of arterial smooth muscle cells (SMCs). RESULTS: Good quality crystals that were suitable for X-ray crystallographic studies were obtained following the truncation of the 14 N-terminal amino acids of APEG-1, a region predicted to be disordered. The truncated protein (termed DeltaAPEG-1) consists of a single immunoglobulin (Ig) like domain which includes an Arg-Gly-Asp (RGD) adhesion recognition motif. The RGD motif is crucial for the interaction of extracellular proteins and plays a role in cell adhesion. The X-ray structure of DeltaAPEG-1 was determined and was refined to sub-atomic resolution (0.96 A). This is the best resolution for an immunoglobulin domain structure so far. The structure adopts a Greek-key beta-sandwich fold and belongs to the I (intermediate) set of the immunoglobulin superfamily. The residues lying between the beta-sheets form a hydrophobic core. The RGD motif folds into a 310 helix that is involved in the formation of a homodimer in the crystal which is mainly stabilized by salt bridges. Analytical ultracentrifugation studies revealed a moderate dissociation constant of 20 microM at physiological ionic strength, suggesting that APEG-1 dimerisation is only transient in the cell. The binding constant is strongly dependent on ionic strength. CONCLUSION: Our data suggests that the RGD motif might play a role not only in the adhesion of extracellular proteins but also in intracellular protein-protein interactions. However, it remains to be established whether the rather weak dimerisation of APEG-1 involving this motif is physiologically relevant. [Abstract/Link to Full Text]

Silverman BD
Asymmetry in the burial of hydrophobic residues along the histone chains of eukarya, archaea and a transcription factor.
BMC Struct Biol. 2005;520.
BACKGROUND: The histone fold is a common structural motif of proteins involved in the chromatin packaging of DNA and in transcription regulation. This single chain fold is stabilized by either homo- or hetero-dimer formation in archaea and eukarya. X-ray structures at atomic resolution have shown the eukaryotic nucleosome core particle to consist of a central tetramer of two bound H3-H4 dimers flanked by two H2A-H2B dimers. The c-terminal region of the H3 histone fold involved in coupling the two eukaryotic dimers of the tetramer, through a four-fold helical bundle, had previously been shown to be a region of reduced burial of hydrophobic residues within the dimers, and thereby provide a rationale for the observed reduced stability of the H3-H4 dimer compared with that of the H2A-H2B dimer. Furthermore, comparison between eukaryal and archaeal histones had suggested that this asymmetry in the distribution of hydrophobic residues along the H3 histone chains could be due to selective evolution that enhanced the coupling between the eukaryotic dimers of the tetramer. RESULTS AND DISCUSSION: The present work describes calculations utilizing the X-ray structures at atomic resolution of a hyperthermophile from Methanopyrus kandleri (HMk) and a eukaryotic transcription factor from Drosophila melanogaster (DRm), that are structurally homologous to the eukaryotic (H3-H4)2 tetramer. The results for several other related structures are also described. Reduced burial of hydrophobic residues, at the homologous H3 c-terminal regions of these structures, is found to parallel the burial at the c-terminal regions of the H3 histones and is, thereby, expected to affect dimer stability and the processes involving histone structural rearrangement. Significantly different sequence homology between the two histones of the HMk doublet with other archaeal sequences is observed, and how this might have occurred during selection to enhance tetramer stability is described. [Abstract/Link to Full Text]

Kozbial PZ, Mushegian AR
Natural history of S-adenosylmethionine-binding proteins.
BMC Struct Biol. 2005;519.
BACKGROUND: S-adenosylmethionine is a source of diverse chemical groups used in biosynthesis and modification of virtually every class of biomolecules. The most notable reaction requiring S-adenosylmethionine, transfer of methyl group, is performed by a large class of enzymes, S-adenosylmethionine-dependent methyltransferases, which have been the focus of considerable structure-function studies. Evolutionary trajectories of these enzymes, and especially of other classes of S-adenosylmethionine-binding proteins, nevertheless, remain poorly understood. We addressed this issue by computational comparison of sequences and structures of various S-adenosylmethionine-binding proteins. RESULTS: Two widespread folds, Rossmann fold and TIM barrel, have been repeatedly used in evolution for diverse types of S-adenosylmethionine conversion. There were also cases of recruitment of other relatively common folds for S-adenosylmethionine binding. Several classes of proteins have unique unrelated folds, specialized for just one type of chemistry and unified by the theme of internal domain duplications. In several cases, functional divergence is evident, when evolutionarily related enzymes have changed the mode of binding and the type of chemical transformation of S-adenosylmethionine. There are also instances of functional convergence, when biochemically similar processes are performed by drastically different classes of S-adenosylmethionine-binding proteins. Comparison of remote sequence similarities and analysis of phyletic patterns suggests that the last universal common ancestor of cellular life had between 10 and 20 S-adenosylmethionine-binding proteins from at least 5 fold classes, providing for S-adenosylmethionine formation, polyamine biosynthesis, and methylation of several substrates, including nucleic acids and peptide chain release factor. CONCLUSION: We have observed several novel relationships between families that were not known to be related before, and defined 15 large superfamilies of SAM-binding proteins, at least 5 of which may have been represented in the last common ancestor. [Abstract/Link to Full Text]

S�nchez de Groot N, Pallar�s I, Avil�s FX, Vendrell J, Ventura S
Prediction of "hot spots" of aggregation in disease-linked polypeptides.
BMC Struct Biol. 2005;518.
BACKGROUND: The polypeptides involved in amyloidogenesis may be globular proteins with a defined 3D-structure or natively unfolded proteins. The first class includes polypeptides such as beta2-microglobulin, lysozyme, transthyretin or the prion protein, whereas beta-amyloid peptide, amylin or alpha-synuclein all belong to the second class. Recent studies suggest that specific regions in the proteins act as "hot spots" driving aggregation. This should be especially relevant for natively unfolded proteins or unfolded states of globular proteins as they lack significant secondary and tertiary structure and specific intra-chain interactions that can mask these aggregation-prone regions. Prediction of such sequence stretches is important since they are potential therapeutic targets. RESULTS: In this study we exploited the experimental data obtained in an in vivo system using beta-amyloid peptide as a model to derive the individual aggregation propensities of natural amino acids. These data are used to generate aggregation profiles for different disease-related polypeptides. The approach detects the presence of "hot spots" which have been already validated experimentally in the literature and provides insights into the effect of disease-linked mutations in these polypeptides. CONCLUSION: The proposed method might become a useful tool for the future development of sequence-targeted anti-aggregation pharmaceuticals. [Abstract/Link to Full Text]

Martin J, Letellier G, Marin A, Taly JF, de Brevern AG, Gibrat JF
Protein secondary structure assignment revisited: a detailed analysis of different assignment methods.
BMC Struct Biol. 2005;517.
BACKGROUND: A number of methods are now available to perform automatic assignment of periodic secondary structures from atomic coordinates, based on different characteristics of the secondary structures. In general these methods exhibit a broad consensus as to the location of most helix and strand core segments in protein structures. However the termini of the segments are often ill-defined and it is difficult to decide unambiguously which residues at the edge of the segments have to be included. In addition, there is a "twilight zone" where secondary structure segments depart significantly from the idealized models of Pauling and Corey. For these segments, one has to decide whether the observed structural variations are merely distorsions or whether they constitute a break in the secondary structure. METHODS: To address these problems, we have developed a method for secondary structure assignment, called KAKSI. Assignments made by KAKSI are compared with assignments given by DSSP, STRIDE, XTLSSTR, PSEA and SECSTR, as well as secondary structures found in PDB files, on 4 datasets (X-ray structures with different resolution range, NMR structures). RESULTS: A detailed comparison of KAKSI assignments with those of STRIDE and PSEA reveals that KAKSI assigns slightly longer helices and strands than STRIDE in case of one-to-one correspondence between the segments. However, KAKSI tends also to favor the assignment of several short helices when STRIDE and PSEA assign longer, kinked, helices. Helices assigned by KAKSI have geometrical characteristics close to those described in the PDB. They are more linear than helices assigned by other methods. The same tendency to split long segments is observed for strands, although less systematically. We present a number of cases of secondary structure assignments that illustrate this behavior. CONCLUSION: Our method provides valuable assignments which favor the regularity of secondary structure segments. [Abstract/Link to Full Text]

Li B, Gallin WJ
Computational identification of residues that modulate voltage sensitivity of voltage-gated potassium channels.
BMC Struct Biol. 2005;516.
BACKGROUND: Studies of the structure-function relationship in proteins for which no 3D structure is available are often based on inspection of multiple sequence alignments. Many functionally important residues of proteins can be identified because they are conserved during evolution. However, residues that vary can also be critically important if their variation is responsible for diversity of protein function and improved phenotypes. If too few sequences are studied, the support for hypotheses on the role of a given residue will be weak, but analysis of large multiple alignments is too complex for simple inspection. When a large body of sequence and functional data are available for a protein family, mature data mining tools, such as machine learning, can be applied to extract information more easily, sensitively and reliably. We have undertaken such an analysis of voltage-gated potassium channels, a transmembrane protein family whose members play indispensable roles in electrically excitable cells. RESULTS: We applied different learning algorithms, combined in various implementations, to obtain a model that predicts the half activation voltage of a voltage-gated potassium channel based on its amino acid sequence. The best result was obtained with a k-nearest neighbor classifier combined with a wrapper algorithm for feature selection, producing a mean absolute error of prediction of 7.0 mV. The predictor was validated by permutation test and evaluation of independent experimental data. Feature selection identified a number of residues that are predicted to be involved in the voltage sensitive conformation changes; these residues are good target candidates for mutagenesis analysis. CONCLUSION: Machine learning analysis can identify new testable hypotheses about the structure/function relationship in the voltage-gated potassium channel family. This approach should be applicable to any protein family if the number of training examples and the sequence diversity of the training set that are necessary for robust prediction are empirically validated. The predictor and datasets can be found at the VKCDB web site. [Abstract/Link to Full Text]

De S, Krishnadev O, Srinivasan N, Rekha N
Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different.
BMC Struct Biol. 2005;515.
BACKGROUND: A polypeptide chain of a protein-protein complex is said to be obligatory if it is bound to another chain throughout its functional lifetime. Such a chain might not adopt the native fold in the unbound form. A non-obligatory polypeptide chain associates with another chain and dissociates upon molecular stimulus. Although conformational changes at the interaction interface are expected, the overall 3-D structure of the non-obligatory chain is unaltered. The present study focuses on protein-protein complexes to understand further the differences between obligatory and non-obligatory interfaces. RESULTS: A non-obligatory chain in a complex of known 3-D structure is recognized by its stable existence with same fold in the bound and unbound forms. On the contrary, an obligatory chain is detected by its existence only in the bound form with no evidence for the native-like fold of the chain in the unbound form. Various interfacial properties of a large number of complexes of known 3-D structures thus classified are comparatively analyzed with an aim to identify structural descriptors that distinguish these two types of interfaces. We report that the interaction patterns across the interfaces of obligatory and non-obligatory components are different and contacts made by obligatory chains are predominantly non-polar. The obligatory chains have a higher number of contacts per interface (20 +/- 14 contacts per interface) than non-obligatory chains (13 +/- 6 contacts per interface). The involvement of main chain atoms is higher in the case of obligatory chains (16.9 %) compared to non-obligatory chains (11.2 %). The beta-sheet formation across the subunits is observed only among obligatory protein chains in the dataset. Apart from these, other features like residue preferences and interface area produce marginal differences and they may be considered collectively while distinguishing the two types of interfaces. CONCLUSION: These results can be useful in distinguishing the two types of interfaces observed in structures determined in large-scale in the structural genomics initiatives, especially for those multi-component protein assemblies for which the biochemical characterization is incomplete. [Abstract/Link to Full Text]

Ho BK, Brasseur R
The Ramachandran plots of glycine and pre-proline.
BMC Struct Biol. 2005;514.
BACKGROUND: The Ramachandran plot is a fundamental tool in the analysis of protein structures. Of the 4 basic types of Ramachandran plots, the interactions that determine the generic and proline Ramachandran plots are well understood. The interactions of the glycine and pre-proline Ramachandran plots are not. RESULTS: In glycine, the psi angle is typically clustered at psi = 180 degrees and psi = 0 degrees. We show that these clusters correspond to conformations where either the N(i+1) or O atom is sandwiched between the two Halpha atoms of glycine. We show that the shape of the 5 distinct regions of density (the alpha, alphaL, betaS, betaP and betaPR regions) can be reproduced with electrostatic dipole-dipole interactions. In pre-proline, we analyse the origin of the zeta region of the Ramachandran plot, a region unique to pre-proline. We show that it is stabilized by a CO(i-1)...CdeltaHdelta(i+1) weak hydrogen bond. This is analogous to the CO(i-1)...NH(i+1) hydrogen bond that stabilizes the gamma region in the generic Ramachandran plot. CONCLUSION: We have identified the specific interactions that affect the backbone of glycine and pre-proline. Knowledge of these interactions will improve current force-fields, and help understand structural motifs containing these residues. [Abstract/Link to Full Text]

Ren J, Sainsbury S, Berrow NS, Alderton D, Nettleship JE, Stammers DK, Saunders NJ, Owens RJ
Crystal structure of nitrogen regulatory protein IIANtr from Neisseria meningitidis.
BMC Struct Biol. 2005;513.
BACKGROUND: The NMB0736 gene of Neisseria meningitidis serogroup B strain MC58 encodes the putative nitrogen regulatory protein, IIANtr (abbreviated to NM-IIANtr). The homologous protein present in Escherichia coli is implicated in the control of nitrogen assimilation. As part of a structural proteomics approach to the study of pathogenic Neisseria spp., we have selected this protein for structure determination by X-ray crystallography. RESULTS: The NM-IIANtr was over-expressed in E. coli and was shown to be partially mono-phosphorylated, as assessed by mass spectrometry of the purified protein. Crystals of un-phosphorylated protein were obtained and diffraction data collected to 2.5 A resolution. The structure of NM-IIANtr was solved by molecular replacement using the coordinates of the E. coli nitrogen regulatory protein IIAntr [PDB: 1A6J] as the starting model. The overall fold of the Neisseria enzyme shows a high degree of similarity to the IIANtr from E. coli, and the position of the phosphoryl acceptor histidine residue (H67) is conserved. The orientation of an adjacent arginine residue (R69) suggests that it may also be involved in coordinating the phosphate group. Comparison of the structure with that of E. coli IIAmtl complexed with HPr [PDB: 1J6T] indicates that NM-IIANtr binds in a similar way to the HPr-like enzyme in Neisseria. CONCLUSION: The structure of NM-IIANtr confirms its assignment as a homologue of the IIANtr proteins found in a range of other Gram-negative bacteria. We conclude that the NM- IIANtr protein functions as part of a phosphorylation cascade which, in contrast to E. coli, shares the upstream phosphotransfer protein with the sugar uptake phosphoenolpyruvate:sugar phosphotransferase system (PTS), but in common with E. coli has a distinct downstream effector mechanism. [Abstract/Link to Full Text]

Thiruv B, Quon G, Saldanha SA, Steipe B
Nh3D: a reference dataset of non-homologous protein structures.
BMC Struct Biol. 2005;512.
BACKGROUND: The statistical analysis of protein structures requires datasets in which structural features can be considered independently distributed, i.e. not related through common ancestry, and that fulfil minimal requirements regarding the experimental quality of the structures it contains. However, non-redundant datasets based on sequence similarity invariably contain distantly related homologues. Here we provide a reference dataset of non-homologous protein domains, assuming that structural dissimilarity at the topology level is incompatible with recognizable common ancestry. The dataset is based on domains at the Topology level of the CATH database which hierarchically classifies all protein structures. It contains the best refined representatives of each Topology level, validates structural dissimilarity and removes internally duplicated fragments. The compilation of Nh3D is fully scripted. RESULTS: The current Nh3D list contains 570 domains with a total of 90780 residues. It covers more than 70% of folds at the Topology level of the CATH database and represents more than 90% of the structures in the PDB that have been classified by CATH. We observe that even though all protein pairs are structurally dissimilar, some pairwise sequence identities after global alignment are greater than 30%. CONCLUSION: Nh3D is freely available as a reference dataset for the statistical analysis of sequence and structure features of proteins in the PDB. Regularly updated versions of Nh3D and the corresponding PDB-formatted coordinate sets are accessible from our Web site http://www.schematikon.org. [Abstract/Link to Full Text]

Pletnev S, Magracheva E, Wlodawer A, Zdanov A
A model of the ternary complex of interleukin-10 with its soluble receptors.
BMC Struct Biol. 2005;510.
BACKGROUND: Interleukin-10 (IL-10) is a cytokine whose main biological function is to suppress the immune response by induction of a signal(s) leading to inhibition of synthesis of a number of cytokines and their cellular receptors. Signal transduction is initiated upon formation of a ternary complex of IL-10 with two of its receptor chains, IL-10R1 and IL-10R2, expressed on the cell membrane. The affinity of IL-10R1 toward IL-10 is very high, which allowed determination of the crystal structure of IL-10 complexed with the extracellular/soluble domain of IL-10R1, while the affinity of IL-10R2 toward either IL-10 or IL-10/sIL-10R1 complex is quite low. This so far has prevented any attempts to obtain structural information about the ternary complex of IL-10 with its receptor chains. RESULTS: Structures of the second soluble receptor chain of interleukin-10 (sIL-10R2) and the ternary complex of IL-10/sIL-10R1/sIL-10R2 have been generated by homology modeling, which allowed us to identify residues involved in ligand-receptor and receptor-receptor interactions. CONCLUSION: The previously experimentally determined structure of the intermediate/binary complex IL-10/sIL-10R1 is the same in the ternary complex. There are two binding sites for the second receptor chain on the surface of the IL-10/sIL-10R1 complex, involving both IL-10 and sIL-10R1. Most of the interactions are hydrophilic in nature, although each interface includes two internal hydrophobic clusters. The distance between C-termini of the receptor chains is 25 A, which is common for known structures of ternary complexes of other cytokines. The structure is likely to represent the biologically active signaling complex of IL-10 with its receptor on the surface of the cell membrane. [Abstract/Link to Full Text]