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Recent Articles in Biomedical Engineering Online

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Alkjaer T, Larsen PK, Pedersen G, Nielsen LH, Simonsen EB
Biomechanical analysis of rollator walking.
Biomed Eng Online. 2006;52.
BACKGROUND: The rollator is a very popular walking aid. However, knowledge about how a rollator affects the walking patterns is limited. Thus, the purpose of the study was to investigate the biomechanical effects of walking with and without a rollator on the walking pattern in healthy subjects. METHODS: The walking pattern during walking with and without rollator was analyzed using a three-dimensional inverse dynamics method. Sagittal joint dynamics and kinematics of the ankle, knee and hip were calculated. In addition, hip joint dynamics and kinematics in the frontal plane were calculated. Seven healthy women participated in the study. RESULTS: The hip was more flexed while the knee and ankle joints were less flexed/dorsiflexed during rollator walking. The ROM of the ankle and knee joints was reduced during rollator-walking. Rollator-walking caused a reduction in the knee extensor moment by 50% when compared to normal walking. The ankle plantarflexor and hip abductor moments were smaller when walking with a rollator. In contrast, the angular impulse of the hip extensors was significantly increased during rollator-walking. CONCLUSION: Walking with a rollator unloaded the ankle and especially the knee extensors, increased the hip flexion and thus the contribution of hip extensors to produce movement. Thus, rollator walking did not result in an overall unloading of the muscles and joints of the lower extremities. However, the long-term effect of rollator walking is unknown and further investigation in this field is needed. [Abstract/Link to Full Text]

Ramasamy L, Sperelakis N
Action potential repolarization enabled by Ca++ channel deactivation in PSpice simulation of smooth muscle propagation.
Biomed Eng Online. 2005;4(1):71.
BACKGROUND: Previously, only the rising phase of the action potential (AP) in cardiac muscle and smooth muscle could be simulated due to the instability of PSpice upon insertion of a second black box (BB) into the K+ leg of the basic membrane unit. This restriction was acceptable because only the transmission of excitation from one cell to the next was investigated. METHODS: In the current work, the repolarization of the AP was accomplished by inserting a second BB into the Ca++ leg of the basic membrane unit. Repolarization of the AP was produced, not through an activation of the K+ channel conductance, but rather through a mimicking of the deactivation of the Ca++ channel conductance. Propagation of complete APs was studied in a chain (strand) of 10 smooth muscle cells, in which various numbers of gap-junction (gj) channels (assumed to be 100 pS each) were inserted across the cell junctions. RESULTS: The shunt resistance across the junctions produced by the gj-channels (Rgj) was varied from 100,000 MOmega (0 gj-channels) to 10,000 MOmega (1 gj-channel), to 1,000 MOmega (10 channels), to 100 MOmega (100 channels), to 10 MOmega (1000 channels), and to 1.0 MOmega (10,000 channels). Velocity of propagation (theta, in cm/sec) was calculated from the measured total propagation time (TPT, the time difference between when the AP rising phase of the first cell and the last cell crossed -20 mV), assuming a constant cell length of 200 microm. When there were no gj-channels, or only one, the transmission of excitation between cells was produced by the electric field (EF), i.e., the negative junctional cleft potential, that is generated in the narrow junctional clefts (e.g., 100 A) when the prejunctional membrane fires an AP (a fraction of a millisecond before the adjacent surface membrane). There were significant end-effects at the termination of the strand, such that the last cell (cell #10) failed to fire, or fired after a prolonged delay. This end-effect was abolished when the strand termination resistance (Rbt) was increased from 1.0 KOmega to 600 MOmega. When there were 1000 or 10,000 gj-channels, the transmission of excitation was produced by local-circuit current flow from one cell to the next through the gj-channels. DISCUSSION: In summary, it is now possible to simulate complete APs in smooth muscle cells that could propagate along a single chain of 10 cells, even when there were no gj-channels between the cells. [Abstract/Link to Full Text]

Ventura L, Jesus GT, Oliveira GC, Sousa SJ
Portable light transmission measuring system for preserved corneas.
Biomed Eng Online. 2005;470.
BACKGROUND: The authors have developed a small portable device for the objective measurement of the transparency of corneas stored in preservative medium, for use by eye banks in evaluation prior to transplantation. METHODS: The optical system consists of a white light, lenses, and pinholes that collimate the white light beams and illuminate the cornea in its preservative medium, and an optical filter (400-700 nm) that selects the range of the wavelength of interest. A sensor detects the light that passes through the cornea, and the average corneal transparency is displayed. In order to obtain only the tissue transparency, an electronic circuit was built to detect a baseline input of the preservative medium prior to the measurement of corneal transparency. The operation of the system involves three steps: adjusting the "0 %" transmittance of the instrument, determining the "100 %" transmittance of the system, and finally measuring the transparency of the preserved cornea inside the storage medium. RESULTS: Fifty selected corneas were evaluated. Each cornea was submitted to three evaluation methods: subjective classification of transparency through a slit lamp, quantification of the transmittance of light using a corneal spectrophotometer previously developed, and measurement of transparency with the portable device. CONCLUSION: By comparing the three methods and using the expertise of eye bank trained personnel, a table for quantifying corneal transparency with the new device has been developed. The correlation factor between the corneal spectrophotometer and the new device is 0,99813, leading to a system that is able to standardize transparency measurements of preserved corneas, which is currently done subjectively. [Abstract/Link to Full Text]

Beck TW, Housh TJ, Cramer JT, Weir JP, Johnson GO, Coburn JW, Malek MH, Mielke M
Mechanomyographic amplitude and frequency responses during dynamic muscle actions: a comprehensive review.
Biomed Eng Online. 2005;4(1):67.
The purpose of this review is to examine the literature that has investigated mechanomyographic (MMG) amplitude and frequency responses during dynamic muscle actions. To date, the majority of MMG research has focused on isometric muscle actions. Recent studies, however, have examined the MMG time and/or frequency domain responses during various types of dynamic activities, including dynamic constant external resistance (DCER) and isokinetic muscle actions, as well as cycle ergometry. Despite the potential influences of factors such as changes in muscle length and the thickness of the tissue between the muscle and the MMG sensor, there is convincing evidence that during dynamic muscle actions, the MMG signal provides valid information regarding muscle function. This argument is supported by consistencies in the MMG literature, such as the close relationship between MMG amplitude and power output and a linear increase in MMG amplitude with concentric torque production. There are still many issues, however, that have yet to be resolved, and the literature base for MMG during both dynamic and isometric muscle actions is far from complete. Thus, it is important to investigate the unique applications of MMG amplitude and frequency responses with different experimental designs/methodologies to continually reassess the uses/limitations of MMG. [Abstract/Link to Full Text]

Dotsinsky I
Suppression of AC railway power-line interference in ECG signals recorded by public access defibrillators.
Biomed Eng Online. 2005;465.
BACKGROUND: Public access defibrillators (PADs) are now available for more efficient and rapid treatment of out-of-hospital sudden cardiac arrest. PADs are used normally by untrained people on the streets and in sports centers, airports, and other public areas. Therefore, automated detection of ventricular fibrillation, or its exclusion, is of high importance. A special case exists at railway stations, where electric power-line frequency interference is significant. Many countries, especially in Europe, use 16.7 Hz AC power, which introduces high level frequency-varying interference that may compromise fibrillation detection. METHOD: Moving signal averaging is often used for 50/60 Hz interference suppression if its effect on the ECG spectrum has little importance (no morphological analysis is performed). This approach may be also applied to the railway situation, if the interference frequency is continuously detected so as to synchronize the analog-to-digital conversion (ADC) for introducing variable inter-sample intervals. A better solution consists of rated ADC, software frequency measuring, internal irregular re-sampling according to the interference frequency, and a moving average over a constant sample number, followed by regular back re-sampling. RESULTS: The proposed method leads to a total railway interference cancellation, together with suppression of inherent noise, while the peak amplitudes of some sharp complexes are reduced. This reduction has negligible effect on accurate fibrillation detection. CONCLUSION: The method is developed in the MATLAB environment and represents a useful tool for real time railway interference suppression. [Abstract/Link to Full Text]

Scotti CM, Shkolnik AD, Muluk SC, Finol EA
Fluid-structure interaction in abdominal aortic aneurysms: effects of asymmetry and wall thickness.
Biomed Eng Online. 2005;464.
BACKGROUND: Abdominal aortic aneurysm (AAA) is a prevalent disease which is of significant concern because of the morbidity associated with the continuing expansion of the abdominal aorta and its ultimate rupture. The transient interaction between blood flow and the wall contributes to wall stress which, if it exceeds the failure strength of the dilated arterial wall, will lead to aneurysm rupture. Utilizing a computational approach, the biomechanical environment of virtual AAAs can be evaluated to study the affects of asymmetry and wall thickness on this stress, two parameters that contribute to increased risk of aneurysm rupture. METHODS: Ten virtual aneurysm models were created with five different asymmetry parameters ranging from beta = 0.2 to 1.0 and either a uniform or variable wall thickness to study the flow and wall dynamics by means of fully coupled fluid-structure interaction (FSI) analyses. The AAA wall was designed to have a (i) uniform 1.5 mm thickness or (ii) variable thickness ranging from 0.5-1.5 mm extruded normally from the boundary surface of the lumen. These models were meshed with linear hexahedral elements, imported into a commercial finite element code and analyzed under transient flow conditions. The method proposed was then compared with traditional computational solid stress techniques on the basis of peak wall stress predictions and cost of computational effort. RESULTS: The results provide quantitative predictions of flow patterns and wall mechanics as well as the effects of aneurysm asymmetry and wall thickness heterogeneity on the estimation of peak wall stress. These parameters affect the magnitude and distribution of Von Mises stresses; varying wall thickness increases the maximum Von Mises stress by 4 times its uniform thickness counterpart. A pre-peak systole retrograde flow was observed in the AAA sac for all models, which is due to the elastic energy stored in the compliant arterial wall and the expansion force of the artery during systole. CONCLUSION: Both wall thickness and geometry asymmetry affect the stress exhibited by a virtual AAA. Our results suggest that an asymmetric AAA with regional variations in wall thickness would be exposed to higher mechanical stresses and an increased risk of rupture than a more fusiform AAA with uniform wall thickness. Therefore, it is important to accurately reproduce vessel geometry and wall thickness in computational predictions of AAA biomechanics. [Abstract/Link to Full Text]

Marx R, Qunaibi M, Wirtz DC, Niethard FU, Mumme T
Surface pretreatment for prolonged survival of cemented tibial prosthesis components: full- vs. surface-cementation technique.
Biomed Eng Online. 2005;461.
BACKGROUND: One of few persisting problems of cemented total knee arthroplasty (TKA) is aseptic loosening of tibial component due to degradation of the interface between bone cement and metallic tibial shaft component, particularly for surface cemented tibial components. Surface cementation technique has important clinical meaning in case of revision and for avoidance of stress shielding. Degradation of the interface between bone cement and bone may be a secondary effect due to excessive crack formation in bone cement starting at the opposite metallic surface. METHODS: This study was done to prove crack formation in the bone cement near the metallic surface when this is not coated. We propose a newly developed coating process by PVD layering with SiOx to avoid that crack formation in the bone cement. A biomechanical model for vibration fatigue test was done to simulate the physiological and biomechanical conditions of the human knee joint and to prove excessive crack formation. RESULTS: It was found that coated tibial components showed a highly significant reduction of cement cracking near the interface metal/bone cement (p < 0.01) and a significant reduction of gap formation in the interface metal-to-bone cement (p < 0.05). CONCLUSION: Coating dramatically reduces hydrolytic- and stress-related crack formation at the prosthesis interface metal/bone cement. This leads to a more homogenous load transfer into the cement mantle which should reduce the frequency of loosening in the interfaces metal/bone cement/bone. With surface coating of the tibial component it should become possible that surface cemented TKAs reveal similar loosening rates as TKAs both surface and stem cemented. This would be an important clinical advantage since it is believed that surface cementing reduces metaphyseal bone loss in case of revision and stress shielding for better bone health. [Abstract/Link to Full Text]

Hayano J, Barros AK, Kamiya A, Ohte N, Yasuma F
Assessment of pulse rate variability by the method of pulse frequency demodulation.
Biomed Eng Online. 2005;462.
BACKGROUND: Due to its easy applicability, pulse wave has been proposed as a surrogate of electrocardiogram (ECG) for the analysis of heart rate variability (HRV). However, its smoother waveform precludes accurate measurement of pulse-to-pulse interval by fiducial-point algorithms. Here we report a pulse frequency demodulation (PFDM) technique as a method for extracting instantaneous pulse rate function directly from pulse wave signal and its usefulness for assessing pulse rate variability (PRV). METHODS: Simulated pulse wave signals with known pulse interval functions and actual pulse wave signals obtained from 30 subjects with a trans-dermal pulse wave device were analyzed by PFDM. The results were compared with heart rate and HRV assessed from simultaneously recorded ECG. RESULTS: Analysis of simulated data revealed that the PFDM faithfully demodulates source interval function with preserving the frequency characteristics of the function, even when the intervals fluctuate rapidly over a wide range and when the signals include fluctuations in pulse height and baseline. Analysis of actual data revealed that individual means of low and high frequency components of PRV showed good agreement with those of HRV (intraclass correlation coefficient, 0.997 and 0.981, respectively). CONCLUSION: The PFDM of pulse wave signal provides a reliable assessment of PRV. Given the popularity of pulse wave equipments, PFDM may open new ways to the studies of long-term assessment of cardiovascular variability and dynamics. [Abstract/Link to Full Text]

Amann A, Tratnig R, Unterkofler K
Reliability of old and new ventricular fibrillation detection algorithms for automated external defibrillators.
Biomed Eng Online. 2005;460.
BACKGROUND: A pivotal component in automated external defibrillators (AEDs) is the detection of ventricular fibrillation by means of appropriate detection algorithms. In scientific literature there exists a wide variety of methods and ideas for handling this task. These algorithms should have a high detection quality, be easily implementable, and work in real time in an AED. Testing of these algorithms should be done by using a large amount of annotated data under equal conditions. METHODS: For our investigation we simulated a continuous analysis by selecting the data in steps of one second without any preselection. We used the complete BIH-MIT arrhythmia database, the CU database, and the files 7001-8210 of the AHA database. All algorithms were tested under equal conditions. RESULTS: For 5 well-known standard and 5 new ventricular fibrillation detection algorithms we calculated the sensitivity, specificity, and the area under their receiver operating characteristic. In addition, two QRS detection algorithms were included. These results are based on approximately 330,000 decisions (per algorithm). CONCLUSION: Our values for sensitivity and specificity differ from earlier investigations since we used no preselection. The best algorithm is a new one, presented here for the first time. [Abstract/Link to Full Text]

LaDisa JF, Olson LE, Hettrick DA, Warltier DC, Kersten JR, Pagel PS
Axial stent strut angle influences wall shear stress after stent implantation: analysis using 3D computational fluid dynamics models of stent foreshortening.
Biomed Eng Online. 2005;459.
INTRODUCTION: The success of vascular stents in the restoration of blood flow is limited by restenosis. Recent data generated from computational fluid dynamics (CFD) models suggest that the vascular geometry created by an implanted stent causes local alterations in wall shear stress (WSS) that are associated with neointimal hyperplasia (NH). Foreshortening is a potential limitation of stent design that may affect stent performance and the rate of restenosis. The angle created between axially aligned stent struts and the principal direction of blood flow varies with the degree to which the stent foreshortens after implantation. METHODS: In the current investigation, we tested the hypothesis that stent foreshortening adversely influences the distribution of WSS and WSS gradients using time-dependent 3D CFD simulations of normal arteries based on canine coronary artery measurements of diameter and blood flow. WSS and WSS gradients were calculated using conventional techniques in ideal (16 mm) and progressively foreshortened (14 and 12 mm) stented computational vessels. RESULTS: Stent foreshortening increased the intrastrut area of the luminal surface exposed to low WSS and elevated spatial WSS gradients. Progressive degrees of stent foreshortening were also associated with strut misalignment relative to the direction of blood flow as indicated by analysis of near-wall velocity vectors. CONCLUSION: The current results suggest that foreshortening may predispose the stented vessel to a higher risk of neointimal hyperplasia. [Abstract/Link to Full Text]

Sahba F, Tizhoosh HR, Salama MM
A coarse-to-fine approach to prostate boundary segmentation in ultrasound images.
Biomed Eng Online. 2005;458.
BACKGROUND: In this paper a novel method for prostate segmentation in transrectal ultrasound images is presented. METHODS: A segmentation procedure consisting of four main stages is proposed. In the first stage, a locally adaptive contrast enhancement method is used to generate a well-contrasted image. In the second stage, this enhanced image is thresholded to extract an area containing the prostate (or large portions of it). Morphological operators are then applied to obtain a point inside of this area. Afterwards, a Kalman estimator is employed to distinguish the boundary from irrelevant parts (usually caused by shadow) and generate a coarsely segmented version of the prostate. In the third stage, dilation and erosion operators are applied to extract outer and inner boundaries from the coarsely estimated version. Consequently, fuzzy membership functions describing regional and gray-level information are employed to selectively enhance the contrast within the prostate region. In the last stage, the prostate boundary is extracted using strong edges obtained from selectively enhanced image and information from the vicinity of the coarse estimation. RESULTS: A total average similarity of 98.76%(+/- 0.68) with gold standards was achieved. CONCLUSION: The proposed approach represents a robust and accurate approach to prostate segmentation. [Abstract/Link to Full Text]

Ramon C, Preissl H, Murphy P, Wilson JD, Lowery C, Eswaran H
Synchronization analysis of the uterine magnetic activity during contractions.
Biomed Eng Online. 2005;455.
BACKGROUND: Our objective was to quantify and compare the extent of synchronization of the spatial-temporal myometrial activity over the human uterus before and during a contraction using transabdominal magnetomyographic (MMG) recordings. Synchronization can be an important indicator for the quantification of uterine contractions. METHODS: The spatialtermporal myometrial activity recordings were performed using a 151-channel noninvasive magnetic sensor system called SARA. This device covers the entire pregnant abdomen and records the magnetic field corresponding to the electrical activity generated in the uterine myometrium. The data was collected at 250 samples/sec and was resampled with 25 samples/sec and then filtered in the band of 0.1-0.2 Hz to study the primary magnetic activity of the uterus related to contractions. The synchronization between a channel pair was computed. It was inferred from a statistical tendency to maintain a nearly constant phase difference over a given period of time even though the analytic phase of each channel may change markedly during that time frame. The analytic phase was computed after taking Hilbert transform of the magnetic field data. The process was applied on the pairs of magnetic field traces (240 sec length) with a stepping window of 20 sec duration which is long enough to cover two cycle of the lowest frequency of interest (0.1 Hz). The analysis was repeated by stepping the window at 10 sec intervals. The spatial patterns of the synchronization indices covering the anterior transabdominal area were computed. For this, regional coil-pairs were used. For a given coil, the coil pairs were constructed with the surrounding six coils. The synchronization indices were computed for each coil pair, averaged over the 21 coil-pairs and then assigned as the synchronization index to that particular coil. This procedure was tested on six pregnant subjects at the gestational age between 29 and 40 weeks admitted to the hospital for contractions. The RMS magnetic field for each coil was also computed. RESULTS: The results show that the spatial patterns of the synchronization indices change and follow the periodic pattern of the uterine contraction cycle. Spatial patterns of synchronization indices and the RMS magnetic fields show similarities in few window frames and also show large differences in few other windows. For six subjects, the average synchronization indices were: 0.346 +/- 0.068 for the quiescent baseline period and 0.545 +/- 0.022 at the peak of the contraction. DISCUSSION: These results show that synchronization indices and their spatial distributions depict uterine contractions and relaxations. [Abstract/Link to Full Text]

Clayton RH, Taggart P
Regional differences in APD restitution can initiate wavebreak and re-entry in cardiac tissue: a computational study.
Biomed Eng Online. 2005;454.
BACKGROUND: Regional differences in action potential duration (APD) restitution in the heart favour arrhythmias, but the mechanism is not well understood. METHODS: We simulated a 150 x 150 mm 2D sheet of cardiac ventricular tissue using a simplified computational model. We investigated wavebreak and re-entry initiated by an S1S2S3 stimulus protocol in tissue sheets with two regions, each with different APD restitution. The two regions had a different APD at short diastolic interval (DI), but similar APD at long DI. Simulations were performed twice; once with both regions having steep (slope > 1), and once with both regions having flat (slope < 1) APD restitution. RESULTS: Wavebreak and re-entry were readily initiated using the S1S2S3 protocol in tissue sheets with two regions having different APD restitution properties. Initiation occurred irrespective of whether the APD restitution slopes were steep or flat. With steep APD restitution, the range of S2S3 intervals resulting in wavebreak increased from 1 ms with S1S2 of 250 ms, to 75 ms (S1S2 180 ms). With flat APD restitution, the range of S2S3 intervals resulting in wavebreak increased from 1 ms (S1S2 250 ms), to 21 ms (S1S2 340 ms) and then 11 ms (S1S2 400 ms). CONCLUSION: Regional differences in APD restitution are an arrhythmogenic substrate that can be concealed at normal heart rates. A premature stimulus produces regional differences in repolarisation, and a further premature stimulus can then result in wavebreak and initiate re-entry. This mechanism for initiating re-entry is independent of the steepness of the APD restitution curve. [Abstract/Link to Full Text]

Richerson S, Ingram M, Perry D, Stecker MM
Classification of the extracellular fields produced by activated neural structures.
Biomed Eng Online. 2005;453.
BACKGROUND: Classifying the types of extracellular potentials recorded when neural structures are activated is an important component in understanding nerve pathophysiology. Varying definitions and approaches to understanding the factors that influence the potentials recorded during neural activity have made this issue complex. METHODS: In this article, many of the factors which influence the distribution of electric potential produced by a traveling action potential are discussed from a theoretical standpoint with illustrative simulations. RESULTS: For an axon of arbitrary shape, it is shown that a quadrupolar potential is generated by action potentials traveling along a straight axon. However, a dipole moment is generated at any point where an axon bends or its diameter changes. Next, it is shown how asymmetric disturbances in the conductivity of the medium surrounding an axon produce dipolar potentials, even during propagation along a straight axon. Next, by studying the electric fields generated by a dipole source in an insulating cylinder, it is shown that in finite volume conductors, the extracellular potentials can be very different from those in infinite volume conductors. Finally, the effects of impulses propagating along axons with inhomogeneous cable properties are analyzed. CONCLUSION: Because of the well-defined factors affecting extracellular potentials, the vague terms far-field and near-field potentials should be abandoned in favor of more accurate descriptions of the potentials. [Abstract/Link to Full Text]

Nagano A, Komura T, Yoshioka S, Fukashiro S
Contribution of non-extensor muscles of the leg to maximal-effort countermovement jumping.
Biomed Eng Online. 2005;452.
BACKGROUND: The purpose of this study was to determine the effects of non-extensor muscles of the leg (i.e., muscles whose primary function is not leg extension) on the kinematics and kinetics of human maximal-effort countermovement jumping. Although it is difficult to address this type of question through experimental procedures, the methodology of computer simulation can be a powerful tool. METHODS: A skeletal model that has nine rigid body segments and twenty degrees of freedom was developed. Two sets of muscle models were attached to this skeletal model: all (most of) major muscles in the leg ("All Muscles" model) and major extensor muscles in the leg (i.e., muscles whose primary function is leg extension; "Extensors Only" model). Neural activation input signal was represented by a series of step functions with a step duration of 0.05 s. Simulations were started from an identical upright standing posture. The optimal pattern of the activation input signal was searched through extensive random-search numerical optimization with a goal of maximizing the height reached by the mass centre of the body after jumping up. RESULTS: The simulated kinematics was almost two-dimensional, suggesting the validity of two-dimensional analyses when evaluating net mechanical outputs around the joints using inverse dynamics. A greater jumping height was obtained for the "All Muscles" model (0.386 m) than for the "Extensors Only" model (0.301 m). For the "All Muscles" model, flexor muscles developed force in the beginning of the countermovement. For the "All Muscles" model, the sum of the work outputs from non-extensor muscles was 47.0 J, which was 13% of the total amount (359.9 J). The quantitative distribution of the work outputs from individual muscles was markedly different between these two models. CONCLUSION: It was suggested that the contribution of non-extensor muscles in maximal-effort countermovement jumping is substantial. The use of a computer simulation model that includes non-extensor muscles seems to be more desirable for the assessment of muscular outputs during jumping. [Abstract/Link to Full Text]

Finlay DD, Nugent CD, McCullagh PJ, Black ND
Mining for diagnostic information in body surface potential maps: a comparison of feature selection techniques.
Biomed Eng Online. 2005;451.
BACKGROUND: In body surface potential mapping, increased spatial sampling is used to allow more accurate detection of a cardiac abnormality. Although diagnostically superior to more conventional electrocardiographic techniques, the perceived complexity of the Body Surface Potential Map (BSPM) acquisition process has prohibited its acceptance in clinical practice. For this reason there is an interest in striking a compromise between the minimum number of electrocardiographic recording sites required to sample the maximum electrocardiographic information. METHODS: In the current study, several techniques widely used in the domains of data mining and knowledge discovery have been employed to mine for diagnostic information in 192 lead BSPMs. In particular, the Single Variable Classifier (SVC) based filter and Sequential Forward Selection (SFS) based wrapper approaches to feature selection have been implemented and evaluated. Using a set of recordings from 116 subjects, the diagnostic ability of subsets of 3, 6, 9, 12, 24 and 32 electrocardiographic recording sites have been evaluated based on their ability to correctly asses the presence or absence of Myocardial Infarction (MI). RESULTS: It was observed that the wrapper approach, using sequential forward selection and a 5 nearest neighbour classifier, was capable of choosing a set of 24 recording sites that could correctly classify 82.8% of BSPMs. Although the filter method performed slightly less favourably, the performance was comparable with a classification accuracy of 79.3%. In addition, experiments were conducted to show how (a) features chosen using the wrapper approach were specific to the classifier used in the selection model, and (b) lead subsets chosen were not necessarily unique. CONCLUSION: It was concluded that both the filter and wrapper approaches adopted were suitable for guiding the choice of recording sites useful for determining the presence of MI. It should be noted however that in this study recording sites have been suggested on their ability to detect disease and such sites may not be optimal for estimating body surface potential distributions. [Abstract/Link to Full Text]

Levkov C, Mihov G, Ivanov R, Daskalov I, Christov I, Dotsinsky I
Removal of power-line interference from the ECG: a review of the subtraction procedure.
Biomed Eng Online. 2005 Aug 23;450.
BACKGROUND: Modern biomedical amplifiers have a very high common mode rejection ratio. Nevertheless, recordings are often contaminated by residual power-line interference. Traditional analogue and digital filters are known to suppress ECG components near to the power-line frequency. Different types of digital notch filters are widely used despite their inherent contradiction: tolerable signal distortion needs a narrow frequency band, which leads to ineffective filtering in cases of larger frequency deviation of the interference. Adaptive filtering introduces unacceptable transient response time, especially after steep and large QRS complexes. Other available techniques such as Fourier transform do not work in real time. The subtraction procedure is found to cope better with this problem. METHOD: The subtraction procedure was developed some two decades ago, and almost totally eliminates power-line interference from the ECG signal. This procedure does not affect the signal frequency components around the interfering frequency. Digital filtering is applied on linear segments of the signal to remove the interference components. These interference components are stored and further subtracted from the signal wherever non-linear segments are encountered. RESULTS: Modifications of the subtraction procedure have been used in thousands of ECG instruments and computer-aided systems. Other work has extended this procedure to almost all possible cases of sampling rate and interference frequency variation. Improved structure of the on-line procedure has worked successfully regardless of the multiplicity between the sampling rate and the interference frequency. Such flexibility is due to the use of specific filter modules. CONCLUSION: The subtraction procedure has largely proved advantageous over other methods for power-line interference cancellation in ECG signals. [Abstract/Link to Full Text]

Naidu MU, Reddy BM, Yashmaina S, Patnaik AN, Rani PU
Validity and reproducibility of arterial pulse wave velocity measurement using new device with oscillometric technique: a pilot study.
Biomed Eng Online. 2005;449.
BACKGROUND: Availability of a range of techniques and devices allow measurement of many variables related to the stiffness of large or medium sized arteries. There is good evidence that, pulse wave velocity is a relatively simple measurement and is a good indicator of changes in arterial properties. The pulse wave velocity calculated from pulse wave recording by other methods like doppler or tonometry is tedious, time-consuming and above all their reproducibility depends on the operator skills. It requires intensive resource involvement. For epidemiological studies these methods are not suitable. The aim of our study was to clinically evaluate the validity and reproducibility of a new automatic device for measurement of pulse wave velocity that can be used in such studies. METHODS: In 44 subjects including normal healthy control and patients with coronary artery disease, heart brachial, heart ankle, brachial ankle and carotid femoral pulse wave velocities were recorded by using a new oscillometric device. Lead I and II electrocardiogram and pressure curves were simultaneously recorded. Two observers recorded the pulse wave velocity for validation and one observer recorded the velocity on two occasions for reproducibility. RESULTS AND DISCUSSION: Pulse wave velocity and arterial stiffness index were recorded in 24 control and 20 coronary artery disease patients. All the velocities were significantly high in coronary artery disease patients. There was highly significant correlation between the values noted by the two observers with low standard deviation. The Pearson's correlation coefficient for various velocities ranged from (r = 0.88-0.90) with (p < 0.0001). The reproducibility was also very good as shown by Bland-Altman plot; most of the values were lying within 2 SD. The interperiod measurements of pulse wave velocity were also significantly correlated (r = 0.71-0.98) (P < 0.0001). Carotid-femoral pulse wave velocity was found to correlate significantly with heart brachial, heart ankle, brachial ankle pulse wave velocity and arterial stiffness index values. Reproducibility of our method was good with very low variability in both interobserver and interperiod analysis. CONCLUSION: The new device "PeriScope" based on oscillometric technique has been found to be a simple, non-invasive and reproducible device for the assessment of pulse wave velocity and can be used to determine arterial stiffness in large population based studies. [Abstract/Link to Full Text]

Treo EF, Herrera MC, Valentinuzzi ME
Algorithm for identifying and separating beats from arterial pulse records.
Biomed Eng Online. 2005;448.
BACKGROUND: This project was designed as an epidemiological aid-selecting tool for a small country health center with the general objective of screening out possible coronary patients. Peripheral artery function can be non-invasively evaluated by impedance plethysmography. Changes in these vessels appear as good predictors of future coronary behavior. Impedance plethysmography detects volume variations after simple occlusive maneuvers that may show indicative modifications in arterial/venous responses. Averaging of a series of pulses is needed and this, in turn, requires proper determination of the beginning and end of each beat. Thus, the objective here is to describe an algorithm to identify and separate out beats from a plethysmographic record. A secondary objective was to compare the output given by human operators against the algorithm. METHODS: The identification algorithm detected the beat's onset and end on the basis of the maximum rising phase, the choice of possible ventricular systolic starting points considering cardiac frequency, and the adjustment of some tolerance values to optimize the behavior. Out of 800 patients in the study, 40 occlusive records (supradiastolic- subsystolic) were randomly selected without any preliminary diagnosis. Radial impedance plethysmographic pulse and standard ECG were recorded digitizing and storing the data. Cardiac frequency was estimated with the Power Density Function and, thereafter, the signal was derived twice, followed by binarization of the first derivative and rectification of the second derivative. The product of the two latter results led to a weighing signal from which the cycles' onsets and ends were established. Weighed and frequency filters are needed along with the pre-establishment of their respective tolerances. Out of the 40 records, 30 seconds strands were randomly chosen to be analyzed by the algorithm and by two operators. Sensitivity and accuracy were calculated by means of the true/false and positive/negative criteria. Synchronization ability was measured through the coefficient of variation and the median value of correlation for each patient. These parameters were assessed by means of Friedman's ANOVA and Kendall Concordance test. RESULTS: Sensitivity was 97% and 91% for the two operators, respectively, while accuracy was cero for both of them. The synchronism variability analysis was significant (p < 0.01) for the two statistics, showing that the algorithm produced the best result. CONCLUSION: The proposed algorithm showed good performance as expressed by its high sensitivity. The correlation analysis demonstrated that, from the synchronism point of view, the algorithm performed the best detection. Patients with marked arrhythmic processes are not good candidates for this kind of analysis. At most, they would be singled out by the algorithm and, thereafter, to be checked by an operator. [Abstract/Link to Full Text]

Ganesh VK, Ramakrishna K, Ghista DN
Biomechanics of bone-fracture fixation by stiffness-graded plates in comparison with stainless-steel plates.
Biomed Eng Online. 2005;446.
BACKGROUND: In the internal fixation of fractured bone by means of bone-plates fastened to the bone on its tensile surface, an on-going concern has been the excessive stress-shielding of the bone by the excessively-stiff stainless-steel plate. The compressive stress-shielding at the fracture-interface immediately after fracture-fixation delays callus formation and bone healing. Likewise, the tensile stress-shielding of the layer of the bone underneath the plate can cause osteoporosis and decrease in tensile strength of this layer. METHOD: In order to address this problem, we propose to use stiffness-graded plates. Accordingly, we have computed (by finite-element analysis) the stress distribution in the fractured bone fixed by composite plates, whose stiffness is graded both longitudinally and transversely. RESULTS: It can be seen that the stiffness-graded composite-plates cause less stress-shielding (as an example: at 50% of the healing stage, stress at the fracture interface is compressive in nature i.e. 0.002 GPa for stainless steel plate whereas stiffness graded plates provides tensile stress of 0.002 GPa. This means that stiffness graded plate is allowing the 50% healed bone to participate in loadings). Stiffness-graded plates are more flexible, and hence permit more bending of the fractured bone. This results in higher compressive stresses induced at the fractured faces accelerate bone-healing. On the other hand, away from the fracture interface the reduced stiffness and elastic modulus of the plate causes the neutral axis of the composite structure to be lowered into the bone resulting in the higher tensile stress in the bone-layer underneath the plate, wherein is conducive to the bone preserving its tensile strength. CONCLUSION: Stiffness graded plates (with in-built variable stiffness) are deemed to offer less stress-shielding to the bone, providing higher compressive stress at the fractured interface (to induce accelerated healing) as well as higher tensile stress in the intact portion of the bone (to prevent bone remodeling and osteoporosis). [Abstract/Link to Full Text]

Haemmerich D, Webster JG
Automatic control of finite element models for temperature-controlled radiofrequency ablation.
Biomed Eng Online. 2005;4(1):42.
BACKGROUND: The finite element method (FEM) has been used to simulate cardiac and hepatic radiofrequency (RF) ablation. The FEM allows modeling of complex geometries that cannot be solved by analytical methods or finite difference models. In both hepatic and cardiac RF ablation a common control mode is temperature-controlled mode. Commercial FEM packages don't support automating temperature control. Most researchers manually control the applied power by trial and error to keep the tip temperature of the electrodes constant. METHODS: We implemented a PI controller in a control program written in C++. The program checks the tip temperature after each step and controls the applied voltage to keep temperature constant. We created a closed loop system consisting of a FEM model and the software controlling the applied voltage. The control parameters for the controller were optimized using a closed loop system simulation. RESULTS: We present results of a temperature controlled 3-D FEM model of a RITA model 30 electrode. The control software effectively controlled applied voltage in the FEM model to obtain, and keep electrodes at target temperature of 100 degrees C. The closed loop system simulation output closely correlated with the FEM model, and allowed us to optimize control parameters. DISCUSSION: The closed loop control of the FEM model allowed us to implement temperature controlled RF ablation with minimal user input. [Abstract/Link to Full Text]

Ekstrand V, Wiksell H, Schultz I, Sandstedt B, Rotstein S, Eriksson A
Influence of electrical and thermal properties on RF ablation of breast cancer: is the tumour preferentially heated?
Biomed Eng Online. 2005;441.
BACKGROUND: Techniques based on radio frequency (RF) energy have many applications in medicine, in particular tumour ablation. Today, mammography screening detects many breast cancers at an early stage, facilitating treatment by minimally invasive techniques such as radio frequency ablation (RFA). The breast cancer is mostly surrounded by fat, which during RFA-treatment could result in preferential heating of the tumour due to the substantial differences in electrical parameters. The object of this study was to investigate if this preferential heating existed during experimental in vitro protocols and during computer simulations. METHODS: Excised breast material from four patients with morphologically diagnosed breast cancers were treated with our newly developed RFA equipment. Subsequently, two finite element method (FEM) models were developed; one with only fat and one with fat and an incorporated breast cancer of varying size. The FEM models were solved using temperature dependent electrical conductivity versus constant conductivity, and transient versus steady-state analyses. RESULTS: Our experimental study performed on excised breast tissue showed a preferential heating of the tumour, even if associated with long tumour strands. The fat between these tumour strands was surprisingly unaffected. Furthermore, the computer simulations demonstrated that the difference in electrical and thermal parameters between fat and tumour tissue can cause preferential heating of the tumour. The specific absorption rate (SAR) distribution changed significantly when a tumour was present in fatty tissue. The degree of preferential heating depended on tissue properties, tumour shape, and placement relative to the electrode. Temperature dependent electrical conductivity increased the thermal lesion volume, but did not change the preferential heating. Transient solutions decreased the thermal lesion volume but increased the preferential heating of the tumour. CONCLUSION: Both the computer model and the in vitro study confirmed that preferential heating of the tumour during RFA exists in breast tissue. However, the observed preferential heating in the in vitro studies were more pronounced, indicating that additional effects other than the difference in tissue parameters might be involved. The existing septa layers between the cancer tissue and the fatty tissue could have an additional electrical or thermal insulating effect, explaining the discrepancy between the in vitro study and the computer model. [Abstract/Link to Full Text]

George K
A two-dimensional mathematical model of non-linear dual-sorption of percutaneous drug absorption.
Biomed Eng Online. 2005;440.
BACKGROUND: Certain drugs, for example scopolamine and timolol, show non-linear kinetic behavior during permeation process. This non-linear kinetic behavior is due to two mechanisms; the first mechanism being a simple dissolution producing mobile and freely diffusible molecules and the second being an adsorption process producing non-mobile molecules that do not participate in the diffusion process. When such a drug is applied on the skin surface, the concentration of the drug accumulated in the skin and the amount of the drug eliminated into the blood vessel depend on the value of a parameter, C, the donor concentration. The present paper studies the effect of the parameter value, C, when the region of the contact of the skin with drug, is a line segment on the skin surface. To confirm that dual-sorption process gives an explanation to non-linear kinetic behavior, the characteristic features that are used in one-dimensional models are (1) prolongation of half-life if the plot of flux versus time are straight lines soon after the vehicle removal, (2) the decrease in half-life with increase in donor concentration. This paper introduces another feature as a characteristic to confirm that dual-sorption model gives an explanation to the non-linear kinetic behavior of the drug. This new feature is "the prolongation of half-life is not a necessary feature if the plots of drug flux versus time is a non-linear curve, soon after the vehicle removal". METHODS: From biological point of view, a drug absorption model is said to be nonlinear if the sorption isotherm is non-linear. When a model is non-linear the relationship between lag-time and donor concentration is non-linear and the lag time decreases with increase in donor concentration. A two-dimensional dual-sorption model is developed for percutaneous absorption of a drug, which shows non-linear kinetic behavior in the permeation process. This model may be used when the diffusion of the drug in the direction parallel to the skin surface must be examined, as well as in the direction into the skin, examined in one-dimensional models. The dual-sorption model is an initial/boundary value problem which consists of (1) one non-linear, two-dimensional, second-order parabolic equation, (2) boundary conditions, (3) one initial condition. Note that, the number of boundary conditions are, six and four, respectively, if the permeation process under consideration is, during the application of the vehicle and during the removal of the vehicle. Adopting the approach of method of lines, the initial/boundary value problem is transformed into an initial-value problem, which consists of (1) a system of non-linear ordinary differential equations, (2) one initial condition. The system of non-linear ordinary differential equations contains time-dependent non-homogeneous terms, if the permeation process under consideration is, during the application of the vehicle. To solve this initial-value problem, an eight-stage sequential algorithm which is second-order accurate, and requires only tri-diagonal solvers, is developed. RESULTS: Simulation of the numerical methods described is carried out with various values of the parameter C. The illustrations are given in the form of figures. The concentration profiles are viewed as parabolas along the mesh lines parallel to x-axis or y-axis. The flow rates in different subregions of the skin-region are studied. The shapes of the concentration profiles are examined before and after the steady-state concentration is reached. The concentration reaches steady-state when the flux reaches the steady state. The plots of flux versus time and cumulative amount of drug eliminated into the receptor cell versus time are given. CONCLUSION: Based on the various values of the parameter, C, conclusions are drawn about (1) flow rate of the drug in different regions of the skin, (2) shape of the concentration profiles, (3) the time required to reach the steady-state value of the concentration, (4) concentration of the drug in different regions of the skin, when steady-state value of the concentration is reached, (5) the time required to reach the steady-state value of the flux, (6) time required to reach the steady-state value of the concentration of the drug, (7) half-life of the concentration of the drug and (8) lag-time. A comparison, between this two-dimensional model and the one-dimensional non-linear dual-sorption model that exists in the literature, is done based on (1) the shape of the concentration profiles at various time levels, (2) the time required to reach the steady-state value of the concentration, (3) lag-time and (4) half-life. [Abstract/Link to Full Text]

Saleh KY, Smith NB
A 63 element 1.75 dimensional ultrasound phased array for the treatment of benign prostatic hyperplasia.
Biomed Eng Online. 2005;4(1):39.
BACKGROUND: Prostate cancer and benign prostatic hyperplasia are very common diseases in older American men, thus having a reliable treatment modality for both diseases is of great importance. The currently used treating options, mainly surgical ones, have numerous complications, which include the many side effects that accompany such procedures, besides the invasive nature of such techniques. Focused ultrasound is a relatively new treating modality that is showing promising results in treating prostate cancer and benign prostatic hyperplasia. Thus this technique is gaining more attention in the past decade as a non-invasive method to treat both diseases. METHODS: In this paper, the design, construction and evaluation of a 1.75 dimensional ultrasound phased array to be used for treating prostate cancer and benign prostatic hyperplasia is presented. With this array, the position of the focus can be controlled by changing the electrical power and phase to the individual elements for electronically focusing and steering in a three dimensional volume. The array was designed with a maximum steering angle of +/- 13.5 degrees in the transverse direction and a maximum depth of penetration of 11 cm, which allows the treatment of large prostates. The transducer piezoelectric ceramic, matching layers and cable impedance have been designed for maximum power transfer to tissue. RESULTS: To verify the capability of the transducer for focusing and steering, exposimetry was performed and the results correlated well with the calculated field. Ex vivo experiments using bovine tissue were performed with various lesion sizes and indicated the capability of the transducer to ablate tissue using short sonications. CONCLUSION: A 1.75 dimensional array, that overcame the drawbacks associated with one-dimensional arrays, has been designed, built and successfully tested. Design issues, such as cable and ceramic capacitances, were taken into account when designing this array. The final prototype overcame also the problem of generating grating lobes at unwanted locations by tapering the array elements. [Abstract/Link to Full Text]

Litscher G
Infrared thermography fails to visualize stimulation-induced meridian-like structures.
Biomed Eng Online. 2005;4(1):38.
BACKGROUND: According to Traditional Chinese Medicine (TCM) the vital energy flows through a system of channels also called meridians. Generally accepted proof for meridians cannot be considered as being given. Goal of this study was to examine whether possible stimulation-induced meridian-like structures, as recently described by other authors, can be visualized and objectified simultaneously at different infrared wavelength ranges. METHODS: The study analyses evidence for the existence of acupuncture-specific, meridian-like artifacts in 6 healthy volunteers (mean age +/- SD 28.7 +/- 3.7 years; range 25 - 35 years). Two infrared cameras at different wavelength ranges were used for thermographic control of possible stimulation effects (moxibustion-cigar, infrared warmth stimulation, needle and laserneedle stimulation). In addition to thermography, temperature and microcirculatory parameters were registered at a selected point using laser-Doppler flowmetry. RESULTS AND CONCLUSION: After moxibustion (or infrared light stimulation) of the body at 2 - 5 microm and 7.5 - 13 microm ranges, different structures appear on thermographic images of the human body which are technical artifacts and which are not identical to what are known as meridians in all textbooks of TCM. Further scientific studies are required regarding the possible visualization of meridians. [Abstract/Link to Full Text]

Li Y, Jiang M, Wang G
Computational optical biopsy.
Biomed Eng Online. 2005;4(1):36.
Optical molecular imaging is based on fluorescence or bioluminescence, and hindered by photon scattering in the tissue, especially in patient studies. Here we propose a computational optical biopsy (COB) approach to localize and quantify a light source deep inside a subject. In contrast to existing optical biopsy techniques, our scheme is to collect optical signals directly from a region of interest along one or multiple biopsy paths in a subject, and then compute features of an underlying light source distribution. In this paper, we formulate this inverse problem in the framework of diffusion approximation, demonstrate the solution uniqueness properties in two representative configurations, and obtain analytic solutions for reconstruction of both optical properties and source parameters. [Abstract/Link to Full Text]

Sohn K, Warwick WJ, Lee YW, Lee J, Holte JE
Investigation of non-uniform airflow signal oscillation during high frequency chest compression.
Biomed Eng Online. 2005;4(1):34.
BACKGROUND: High frequency chest compression (HFCC) is a useful and popular therapy for clearing bronchial airways of excessive or thicker mucus. Our observation of respiratory airflow of a subject during use of HFCC showed the airflow oscillation by HFCC was strongly influenced by the nonlinearity of the respiratory system. We used a computational model-based approach to analyse the respiratory airflow during use of HFCC. METHODS: The computational model, which is based on previous physiological studies and represented by an electrical circuit analogue, was used for simulation of in vivo protocol that shows the nonlinearity of the respiratory system. Besides, airflow was measured during use of HFCC. We compared the simulation results to either the measured data or the previous research, to understand and explain the observations. RESULTS AND DISCUSSION: We could observe two important phenomena during respiration pertaining to the airflow signal oscillation generated by HFCC. The amplitudes of HFCC airflow signals varied depending on spontaneous airflow signals. We used the simulation results to investigate how the nonlinearity of airway resistance, lung capacitance, and inertance of air characterized the respiratory airflow. The simulation results indicated that lung capacitance or the inertance of air is also not a factor in the non-uniformity of HFCC airflow signals. Although not perfect, our circuit analogue model allows us to effectively simulate the nonlinear characteristics of the respiratory system. CONCLUSION: We found that the amplitudes of HFCC airflow signals behave as a function of spontaneous airflow signals. This is due to the nonlinearity of the respiratory system, particularly variations in airway resistance. [Abstract/Link to Full Text]

Korhonen RK, Koistinen A, Konttinen YT, Santavirta SS, Lappalainen R
The effect of geometry and abduction angle on the stresses in cemented UHMWPE acetabular cups--finite element simulations and experimental tests.
Biomed Eng Online. 2005;4(1):32.
BACKGROUND: Contact pressure of UHMWPE acetabular cup has been shown to correlate with wear in total hip replacement (THR). The aim of the present study was to test the hypotheses that the cup geometry, abduction angle, thickness and clearance can modify the stresses in cemented polyethylene cups. METHODS: Acetabular cups with different geometries (Link: IP and Lubinus eccentric) were tested cyclically in a simulator at 45 degrees and 60 degrees abduction angles. Finite element (FE) meshes were generated and two additional designs were reconstructed to test the effects of the cup clearance and thickness. Contact pressures at cup-head and cup-cement interfaces were calculated as a function of loading force at 45 degrees, 60 degrees and 80 degrees abduction angles. RESULTS: At the cup-head interface, IP experienced lower contact pressures than the Lubinus eccentric at low loading forces. However, at higher loading forces, much higher contact pressures were produced on the surface of IP cup. An increase in the abduction angle increased contact pressure in the IP model, but this did not occur to any major extent with the Lubinus eccentric model. At the cup-cement interface, IP experienced lower contact pressures. Increased clearance between cup and head increased contact pressure both at cup-head and cup-cement interfaces, whereas a decreased thickness of polyethylene layer increased contact pressure only at the cup-cement interface. FE results were consistent with experimental tests and acetabular cup deformations. CONCLUSION: FE analyses showed that geometrical design, thickness and abduction angle of the acetabular cup, as well as the clearance between the cup and head do change significantly the mechanical stresses experienced by a cemented UHMWPE acetabular cup. These factors should be taken into account in future development of THR prostheses. FE technique is a useful tool with which to address these issues. [Abstract/Link to Full Text]

Singh SS, Kim D, Mohler JL
Java Web Start based software for automated quantitative nuclear analysis of prostate cancer and benign prostate hyperplasia.
Biomed Eng Online. 2005;4(1):31.
BACKGROUND: Androgen acts via androgen receptor (AR) and accurate measurement of the levels of AR protein expression is critical for prostate research. The expression of AR in paired specimens of benign prostate and prostate cancer from 20 African and 20 Caucasian Americans was compared to demonstrate an application of this system. METHODS: A set of 200 immunopositive and 200 immunonegative nuclei were collected from the images using a macro developed in Image Pro Plus. Linear Discriminant and Logistic Regression analyses were performed on the data to generate classification coefficients. Classification coefficients render the automated image analysis software independent of the type of immunostaining or image acquisition system used. The image analysis software performs local segmentation and uses nuclear shape and size to detect prostatic epithelial nuclei. AR expression is described by (a) percentage of immunopositive nuclei; (b) percentage of immunopositive nuclear area; and (c) intensity of AR expression among immunopositive nuclei or areas. RESULTS: The percent positive nuclei and percent nuclear area were similar by race in both benign prostate hyperplasia and prostate cancer. In prostate cancer epithelial nuclei, African Americans exhibited 38% higher levels of AR immunostaining than Caucasian Americans (two sided Student's t-tests; P < 0.05). Intensity of AR immunostaining was similar between races in benign prostate. CONCLUSION: The differences measured in the intensity of AR expression in prostate cancer were consistent with previous studies. Classification coefficients are required due to non-standardized immunostaining and image collection methods across medical institutions and research laboratories and helps customize the software for the specimen under study. The availability of a free, automated system creates new opportunities for testing, evaluation and use of this image analysis system by many research groups who study nuclear protein expression. [Abstract/Link to Full Text]

Bozkurt A, Rosen A, Rosen H, Onaral B
A portable near infrared spectroscopy system for bedside monitoring of newborn brain.
Biomed Eng Online. 2005;4(1):29.
BACKGROUND: Newborns with critical health conditions are monitored in neonatal intensive care units (NICU). In NICU, one of the most important problems that they face is the risk of brain injury. There is a need for continuous monitoring of newborn's brain function to prevent any potential brain injury. This type of monitoring should not interfere with intensive care of the newborn. Therefore, it should be non-invasive and portable. METHODS: In this paper, a low-cost, battery operated, dual wavelength, continuous wave near infrared spectroscopy system for continuous bedside hemodynamic monitoring of neonatal brain is presented. The system has been designed to optimize SNR by optimizing the wavelength-multiplexing parameters with special emphasis on safety issues concerning burn injuries. SNR improvement by utilizing the entire dynamic range has been satisfied with modifications in analog circuitry. RESULTS AND CONCLUSION: As a result, a shot-limited SNR of 67 dB has been achieved for 10 Hz temporal resolution. The system can operate more than 30 hours without recharging when an off-the-shelf 1850 mAh-7.2 V battery is used. Laboratory tests with optical phantoms and preliminary data recorded in NICU demonstrate the potential of the system as a reliable clinical tool to be employed in the bedside regional monitoring of newborn brain metabolism under intensive care. [Abstract/Link to Full Text]

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Recent Articles in Journal of Biomedicine & Biotechnology

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Al-Ali AK, Al-Ateeq S, Imamwerdi BW, Al-Sowayan S, Al-Madan M, Al-Muhanna F, Bashaweri L, Qaw F
Molecular Bases of beta-Thalassemia in the Eastern Province of Saudi Arabia.
J Biomed Biotechnol. 2005;2005(4):322-5.
beta-thalassemia is a group of heterogeneous recessive disorders common in many parts of the world. Al-Qatif and Al-Hassa oases in the Eastern Province of Saudi Arabia are regions known for high frequency of these disorders. Using two molecular methods, based on multiplexing-amplification refractory system and reverse hybridization principles, the spectrum of beta-thalassemia in the region was studied. Sixty-nine subjects with known beta-thalassemia disease and volunteers with high hemoglobin $A(2)(HbA(2))$ and low mean corpuscular volume (MCV) were included in this study. Ten mutations were detected in 91% of the subjects under study. Six of these mutations had previously been observed while the other four mutations are reported here for the first time. In addition, four of the mutations accounted for 76.8% of the subjects studied. IVSII-1 (G > A), IVSI-5 (G > A), and codon 39 (C > T) mutations were found to be the most frequent. However, the frequencies of different mutations reported here are slightly different from those reported earlier. A number of these mutations were also found in the neighboring countries, which can be explained in terms of gene flow. [Abstract/Link to Full Text]

Haroun M
Bovine serum albumin antibodies as a disease marker for hepatitis e virus infection.
J Biomed Biotechnol. 2005;2005(4):316-21.
This report evaluates the significance of antibody/bovine serum albumin (BSA) interactions as a risk factor for the diagnosis of acute hepatitis E. Serum samples from 40 patients with acute hepatitis E and from 40 age/sex matched healthy adult subjects were tested for IgA, IgG, and IgM by ELISA and by turbidimetric assay. BSA was used as a target to characterize changes in levels of interacting immunoglobulins. Initial results obtained before removal of antibodies that interacted with BSA suggested that HEV patients had increased levels of IgM in their sera. It was found that normal individuals had mean IgA, IgG, and IgM levels of 2.55 mg/mL, 9.80 mg/mL, and 1.73 mg/mL, respectively while HEV patients had mean levels of 2.66 mg/mL, 10.04 mg/mL, and 2.01 mg/mL ($P < .26$ , $P < .32$, and $P < .0004$). However, the mean level of IgM in HEV-infected sera after purification from antibodies that interacted with BSA was determined to be 1.72 mg/mL indicating that there was no significant difference in IgM level in HEV patients compared to normal individuals ($P < .6$). The presence of antibodies that interact with BSA might serve as a diagnostic tool for detection of high-risk patients. [Abstract/Link to Full Text]

Ajib R, Janbazian L, Rahal E, Matar GM, Zaynoun S, Kibbi AG, Abdelnoor AM
HLA Allele Associations and V-Beta T-Lymphocyte Expansions in Patients With Psoriasis, Harboring Toxin-Producing Staphylococcus aureus.
J Biomed Biotechnol. 2005;2005(4):310-5.
HLA alleles have been associated with psoriasis. Toxin-producing strains of Staphylococcus aureus behave as superantigens, and if present in patients, might play a role in the exacerbation of psoriatic lesions by activating certain V-beta (V beta) T-lymphocyte subsets. Allele frequencies in 22 patients and 22 controls (alleles determined by DNA/SSP typing) were used to calculate a relative risk of $4.7$ ($P < .05$) for HLA-Cw6. S aureus was isolated from the throat of 11 patients. Enterotoxins A and C were detected by agglutination in the culture filtrate of one isolate. The enterotoxin A and/or C genes were detected by PCR in 9 isolates, and transcripts were detected by RT-PCR in 7 of them. None of the isolates from controls harbored enterotoxin genes. V beta expansions were detected by RT-PCR in all 22 patients. Low or no V beta expansions were obtained in controls. The association of HLA-Cw6 with psoriasis in Lebanese concurs with that reported for other ethnic groups. Toxin-producing isolates that colonize patients might play a role in the exacerbation of psoriatic lesions. [Abstract/Link to Full Text]

Sharma S, Pradhan A, Chauhan VS, Tuteja R
Isolation and characterization of type I signal peptidase of different malaria parasites.
J Biomed Biotechnol. 2005;2005(4):301-9.
Type I signal peptidases are important membrane-bound serine proteases responsible for the cleavage of the signal peptide of the proteins. These enzymes are unique serine proteases that carry out catalysis using a serine/lysine catalytic dyad. In the present study, we report the isolation of type I signal peptidase from the malaria parasites Plasmodium falciparum, Plasmodium knowlesi, and Plasmodium yoelii and some characterization of type I signal peptidase of Plasmodium falciparum. We show that these enzymes are homologous to signal peptidases from various sources and also contain the conserved boxes present in other type I signal peptidases. The type I signal peptidase from P falciparum is an intron-less and a single-copy gene. The results also show that the enzyme from Plasmodium falciparum is subject to self-cleavage and it has been demonstrated to possess type I signal peptidase activity in E coli preprotein processing in vivo by complementation assay. This study will be helpful in understanding one of the important metabolic pathways "the secretory pathway" in the parasite and should make an important contribution in understanding the complex process of protein targeting in the parasite. [Abstract/Link to Full Text]

Beebe SJ, Schoenbach KH
Nanosecond pulsed electric fields: a new stimulus to activate intracellular signaling.
J Biomed Biotechnol. 2005;2005(4):297-300. [Abstract/Link to Full Text]

Mulot C, Stücker I, Clavel J, Beaune P, Loriot MA
Collection of human genomic DNA from buccal cells for genetics studies: comparison between cytobrush, mouthwash, and treated card.
J Biomed Biotechnol. 2005;2005(3):291-6.
Alternative sources such as buccal cells have already been tested for genetic studies and epidemiological investigations. Thirty-seven volunteers participated in this study to compare cytology brushes, mouthwash, and treated cards for DNA collection. Quantity and quality of DNA and cost and feasibility were assessed. The mean DNA yield at 260 nm was found to be 3.5, 4, and 2.6 mu g for cytobrushes, mouthwashes, and treated cards, respectively. A second quantification technique by fluorescence showed differences in the DNA yield with 1.1 and 5.2 mu g for cytobrushes and mouthwash, respectively. All buccal samples allowed isolation of DNA suitable for polymerase chain reaction. According to the procedure of sample collection, the yield and purity of collected DNA, and storage conditions, the use of cytobrush appears to be the more appropriate method for DNA collection. This protocol has been validated and is currently applied in three large-scale multicentric studies including adults or children. [Abstract/Link to Full Text]

Tsui P, Rubenstein M, Guinan P
Correlation Between PSMA and VEGF Expression as Markers for LNCaP Tumor Angiogenesis.
J Biomed Biotechnol. 2005;2005(3):287-90.
Our aim is the identification and correlation of changes in tumor-associated protein expression which results from therapy. LNCaP tumors, excised from nude mice treated either by orchiectomy or with the chemotherapeutic agent paclitaxel, were evaluated for the expression of proteins and receptors associated with growth, differentiation, and angiogenesis using immunohistologic procedures. Compared to untreated control tumors, both treatments reduced the expression of vascular endothelial growth factor (VEGF), prostate-specific membrane antigen (PSMA), prostate-specific antigen (PSA), androgen receptor (AR), and epidermal growth factor receptor (EGFR). The effect of paclitaxel treatment on AR expression was the most significant ($P = .005$). Of particular interest was identifying a significant correlation ($P < .000801$) between PSMA and VEGF expression regardless of treatment modality. These altered expressions suggest that PSMA may also be a marker for angiogenesis and could represent a target for deliverable agents recognizing either prostatic tumors or endothelial development. Cell surface PSMA would then present a unique target for treatment of patients early in their development of prostatic metastases. [Abstract/Link to Full Text]

Mandal MD, Mandal S, Pal NK
Plasmid-Mediated Dimethoate Degradation by Bacillus licheniformis Isolated From a Fresh Water Fish Labeo rohita.
J Biomed Biotechnol. 2005;2005(3):280-6.
The Bacillus licheniformis strain isolated from the intestine of Labeo rohita by an enrichment technique showed capability of utilizing dimethoate as the sole source of carbon. The bacterium rapidly utilized dimethoate beyond 0.6 mg/mL and showed prolific growth in a mineral salts medium containing 0.45 mg/mL dimethoate. The isolated B licheniformis exhibited high level of tolerance of dimethoate (3.5 mg/mL) in nutrient broth, while its cured mutant did not tolerate dimethoate beyond 0.45 mg/mL and it was unable to utilize dimethoate. The wild B licheniformis strain transferred dimethoate degradation property to E coli C600 (Na(r), F( -)) strain. The transconjugant harbored a plasmid of the same molecular size (approximately 54 kb) as that of the donor plasmid; the cured strain was plasmid less. Thus a single plasmid of approximately 54 kb was involved in dimethoate degradation. Genes encoding resistance to antibiotic and heavy metal were also located on the plasmid. [Abstract/Link to Full Text]

Dhingra V, Li Q, Allison AB, Stallknecht DE, Fu ZF
Proteomic profiling and neurodegeneration in west-nile-virus-infected neurons.
J Biomed Biotechnol. 2005;2005(3):271-9.
West Nile virus, a mosquito-borne flavivirus, is a human, equine, and avian pathogen. High-resolution two-dimensional differential-gel electrophoresis (2D-DIGE) was used to characterize protein expression in primary rat neurons and to examine the proteomic profiling to understand the pathogenesis of West-Nile-associated meningoencephalitis. Three pH ranges, 3-10, 4-7, and 5-6, were used to analyze the protein spots. The proteins are labeled with fluorescent dyes Cy3 and Cy5 before being separated on the basis of charge and size respectively on a two-dimensional platform. About 55 proteins showed altered expression levels. These were then subsequently digested and identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis using peptide mass fingerprinting and database searching. These cellular proteins could represent distinct roles during infection related to apoptosis. Our findings show that two-dimensional differential gel electrophoresis combined with mass spectrometry is a powerful approach that permits the identification of proteins whose expression was altered due to West Nile virus infection. [Abstract/Link to Full Text]

Zibara K, Garin G, McGregor JL
Identification, Structural, and Functional Characterization of a New Early Gene (6A3-5, 7 kb): Implication in the Proliferation and Differentiation of Smooth Muscle Cells.
J Biomed Biotechnol. 2005;2005(3):254-70.
Arterial smooth muscle cells (SMCs) play a major role in atherosclerosis and restenosis. Differential display was used to compare transcription profiles of synthetic SMCs to proliferating rat cultured SMC line. An isolated cDNA band (6A3-5) was shown by northern (7 kb) to be upregulated in the proliferating cell line. A rat tissue northern showed differential expression of this gene in different tissues. Using 5' RACE and screening of a rat brain library, part of the cDNA was cloned and sequenced (5.4 kb). Sequence searches showed important similarities with a new family of transcription factors, bearing ARID motifs. A polyclonal antibody was raised and showed a protein band of 175 kd, which is localized intracellularly. We also showed that 6A3-5 is upregulated in dedifferentiated SMC (P9) in comparison to contractile SMC ex vivo (P0). This work describes cloning, structural, and functional characterization of a new early gene involved in SMC phenotype modulation. [Abstract/Link to Full Text]

Bodin L, Beaune PH, Loriot MA
Determination of Cytochrome P450 2D6 (CYP2D6) Gene Copy Number by Real-Time Quantitative PCR.
J Biomed Biotechnol. 2005;2005(3):248-53.
Gene dosage by real-time quantitative PCR has proved to be accurate for measuring gene copy number. The aim of this study was to apply this approach to the CYP2D6 gene to allow for rapid identification of poor and ultrarapid metabolizers (0, 1, or more than 2 gene copy number). Using the 2(-Delta Delta Ct) calculation method and a duplex reaction, the number of CYP2D6 gene copies was determined. Quantitative PCR was performed on 43 samples previously analyzed by Southern blotting and long PCR including 20 samples with a heterozygous deletion, 11 with normal copy number (2 copies), and 12 samples with duplicated genes. The average ratio ranged from 1.02 to 1.28, 1.85 to 2.21, and 2.55 to 3.30, respectively, for the samples with 1 copy, 2 copies, and 3 copies. This study shows that this method is sensitive enough to detect either a heterozygous gene deletion or duplication. [Abstract/Link to Full Text]

Paniagua-Pérez R, Madrigal-Bujaidar E, Reyes-Cadena S, Molina-Jasso D, Gallaga JP, Silva-Miranda A, Velazco O, Hernández N, Chamorro G
Genotoxic and cytotoxic studies of Beta-sitosterol and pteropodine in mouse.
J Biomed Biotechnol. 2005;2005(3):242-7.
Beta-sitosterol (BS) and pteropodine (PT) are constituents of various plants with pharmacological activities potentially useful to man. The chemicals themselves possess biomedical properties related to the modulation of the immune and the nervous systems, as well as to the inflammatory process. Therefore, safety evaluation of the compounds is necessary in regard to their probable beneficial use in human health. The present study evaluates their genotoxic and cytotoxic potential by determining the capacity of the compounds to induce sister chromatid exchanges (SCE), or to alter cellular proliferation kinetics (CPK) and the mitotic index (MI) in mouse bone marrow cells. Besides, it also determines their capacity to increase the rate of micronucleated polychromatic erythrocytes (MNPE) in peripheral mouse blood, and the relationship polychromatic erythrocytes/normochromatic erythrocytes (PE/NE) as an index of cytotoxicity. For the first assay, four doses of each compound were tested: 200, 400, 600, and 1000 mg/kg in case of BS, and 100, 200, 300, and 600 mg/kg for PT. The results in regard to both agents showed no SCE increase induced by any of the tested doses, as well as no alteration in the CPK, or in the MI. With respect to the second assay, the results obtained with the two agents were also negative for both the MNPE and the PE/NE index along the daily evaluation made for four days. In the present study, the highest tested dose corresponded to 80% of the LD(50) obtained for BS and to 78% in the case of PT. The results obtained establish that the studied agents have neither genotoxic nor cytotoxic effect on the model used, and therefore they encourage studies on their pharmacological properties. [Abstract/Link to Full Text]

El Astal Z
Increasing ciprofloxacin resistance among prevalent urinary tract bacterial isolates in gaza strip, palestine.
J Biomed Biotechnol. 2005;2005(3):238-41.
This article presents the incidence of ciprofloxacin resistance among 480 clinical isolates obtained from patients with urinary tract infection (UTI) during January to June 2004 in Gaza Strip, Palestine. The resistance rates observed were 15.0% to ciprofloxacin, 82.5% to amoxycillin, 64.4% to cotrimoxazole, 63.1% to doxycycline, 32.5% to cephalexin, 31.9% to nalidixic acid, and 10.0% to amikacin. High resistance to ciprofloxacin was detected among Acinetobacter haemolyticus (28.6%), Staphylococcus saprophyticus (25.0%),Pseudomonas aeruginosa (20.0%), Klebsiella pneumonia (17.6%), and Escherichia coli (12.0%). Minimal inhibitory concentration (MIC) of ciprofloxacin evenly ranged from 4 to 32 mu g/mL with a mean of 25.0 mu g/mL. This study indicates emerging ciprofloxacin resistance among urinary tract infection isolates. Increasing resistance against ciprofloxacin demands coordinated monitoring of its activity and rational use of the antibiotics. [Abstract/Link to Full Text]

Singh S, Bhattacherjee V, Mukhopadhyay P, Worth CA, Wellhausen SR, Warner CP, Greene RM, Pisano MM
Fluorescence-Activated Cell Sorting of EGFP-Labeled Neural Crest Cells From Murine Embryonic Craniofacial Tissue.
J Biomed Biotechnol. 2005;2005(3):232-7.
During the early stages of embryogenesis, pluripotent neural crest cells (NCC) are known to migrate from the neural folds to populate multiple target sites in the embryo where they differentiate into various derivatives, including cartilage, bone, connective tissue, melanocytes, glia, and neurons of the peripheral nervous system. The ability to obtain pure NCC populations is essential to enable molecular analyses of neural crest induction, migration, and/or differentiation. Crossing Wnt 1-Cre and Z/EG transgenic mouse lines resulted in offspring in which the Wnt 1-Cre transgene activated permanent EGFP expression only in NCC. The present report demonstrates a flow cytometric method to sort and isolate populations of EGFP-labeled NCC. The identity of the sorted neural crest cells was confirmed by assaying expression of known marker genes by TaqMan Quantitative Real-Time Polymerase Chain Reaction (QRT-PCR). The molecular strategy described in this report provides a means to extract intact RNA from a pure population of NCC thus enabling analysis of gene expression in a defined population of embryonic precursor cells critical to development. [Abstract/Link to Full Text]

Zemlo T
Steps towards developing a cure for autoimmunity.
J Biomed Biotechnol. 2005;2005(3):230-1. [Abstract/Link to Full Text]

Schulz W
Qualified promise: DNA methylation assays for the detection and classification of human cancers.
J Biomed Biotechnol. 2005;2005(3):227-9. [Abstract/Link to Full Text]

Hand DJ, Heard NA
Finding groups in gene expression data.
J Biomed Biotechnol. 2005 Jun 30;2005(2):215-25.
The vast potential of the genomic insight offered by microarray technologies has led to their widespread use since they were introduced a decade ago. Application areas include gene function discovery, disease diagnosis, and inferring regulatory networks. Microarray experiments enable large-scale, high-throughput investigations of gene activity and have thus provided the data analyst with a distinctive, high-dimensional field of study. Many questions in this field relate to finding subgroups of data profiles which are very similar. A popular type of exploratory tool for finding subgroups is cluster analysis, and many different flavors of algorithms have been used and indeed tailored for microarray data. Cluster analysis, however, implies a partitioning of the entire data set, and this does not always match the objective. Sometimes pattern discovery or bump hunting tools are more appropriate. This paper reviews these various tools for finding interesting subgroups. [Abstract/Link to Full Text]

Mungur R, Glass AD, Goodenow DB, Lightfoot DA
Metabolite fingerprinting in transgenic Nicotiana tabacum altered by the Escherichia coli glutamate dehydrogenase gene.
J Biomed Biotechnol. 2005 Jun 30;2005(2):198-214.
With about 200,000 phytochemicals in existence, identifying those of biomedical significance is a mammoth task. In the postgenomic era, relating metabolite fingerprints, abundances, and profiles to genotype is also a large task. Ion analysis using Fourier transformed ion cyclotron resonance mass spectrometry (FT-ICR-MS) may provide a high-throughput approach to measure genotype dependency of the inferred metabolome if reproducible techniques can be established. Ion profile inferred metabolite fingerprints are coproducts. We used FT-ICR-MS-derived ion analysis to examine gdhA (glutamate dehydrogenase (GDH; EC 1.4.1.1)) transgenic Nicotiana tabacum (tobacco) carrying out altered glutamate, amino acid, and carbon metabolisms, that fundamentally alter plant productivity. Cause and effect between gdhA expression, glutamate metabolism, and plant phenotypes was analyzed by (13) NH(4)(+) labeling of amino acid fractions, and by FT-ICR-MS analysis of metabolites. The gdhA transgenic plants increased (13)N labeling of glutamate and glutamine significantly. FT-ICR-MS detected 2,012 ions reproducible in 2 to 4 ionization protocols. There were 283 ions in roots and 98 ions in leaves that appeared to significantly change abundance due to the measured GDH activity. About 58% percent of ions could not be used to infer a corresponding metabolite. From the 42% of ions that inferred known metabolites we found that certain amino acids, organic acids, and sugars increased and some fatty acids decreased. The transgene caused increased ammonium assimilation and detectable ion variation. Thirty-two compounds with biomedical significance were altered in abundance by GDH including 9 known carcinogens and 14 potential drugs. Therefore, the GDH transgene may lead to new uses for crops like tobacco. [Abstract/Link to Full Text]

Corder EH, Ervin JF, Lockhart E, Szymanski MH, Schmechel DE, Hulette CM
Cardiovascular damage in Alzheimer disease: autopsy findings from the Bryan ADRC.
J Biomed Biotechnol. 2005 Jun 30;2005(2):189-97.
Autopsy information on cardiovascular damage was investigated for pathologically confirmed Alzheimer disease (AD) patients (n=84) and non-AD control patients (n=60). The 51 relevant items were entered into a grade-of-membership model to describe vascular damage in AD. Five latent groups were identified "I: early-onset AD," "II: controls, cancer," "III: controls, extensive atherosclerosis," "IV: late-onset AD, male," and "V: late-onset AD, female." Expectedly, Groups IV and V had elevated APOE epsilon 4 frequency. Unexpectedly, there was limited atherosclerosis and frequent myocardial valve and ventricular damage. The findings do not indicate a strong relationship between atherosclerosis and AD, although both are associated with the APOE epsilon 4. Instead, autopsy findings of extensive atherosclerosis were associated with possible, not probable or definite AD, and premature death. They are consistent with the hypothesis that brain hypoperfusion contributes to dementia, possibly to AD pathogenesis, and raise the possibility that the APOE allele epsilon 4 contributes directly to heart valve and myocardial damage. [Abstract/Link to Full Text]

Alkharouf NW, Jamison DC, Matthews BF
Online analytical processing (OLAP): a fast and effective data mining tool for gene expression databases.
J Biomed Biotechnol. 2005 Jun 30;2005(2):181-8.
Gene expression databases contain a wealth of information, but current data mining tools are limited in their speed and effectiveness in extracting meaningful biological knowledge from them. Online analytical processing (OLAP) can be used as a supplement to cluster analysis for fast and effective data mining of gene expression databases. We used Analysis Services 2000, a product that ships with SQLServer2000, to construct an OLAP cube that was used to mine a time series experiment designed to identify genes associated with resistance of soybean to the soybean cyst nematode, a devastating pest of soybean. The data for these experiments is stored in the soybean genomics and microarray database (SGMD). A number of candidate resistance genes and pathways were found. Compared to traditional cluster analysis of gene expression data, OLAP was more effective and faster in finding biologically meaningful information. OLAP is available from a number of vendors and can work with any relational database management system through OLE DB. [Abstract/Link to Full Text]

Baldwin NE, Chesler EJ, Kirov S, Langston MA, Snoddy JR, Williams RW, Zhang B
Computational, integrative, and comparative methods for the elucidation of genetic coexpression networks.
J Biomed Biotechnol. 2005 Jun 30;2005(2):172-80.
Gene expression microarray data can be used for the assembly of genetic coexpression network graphs. Using mRNA samples obtained from recombinant inbred Mus musculus strains, it is possible to integrate allelic variation with molecular and higher-order phenotypes. The depth of quantitative genetic analysis of microarray data can be vastly enhanced utilizing this mouse resource in combination with powerful computational algorithms, platforms, and data repositories. The resulting network graphs transect many levels of biological scale. This approach is illustrated with the extraction of cliques of putatively co-regulated genes and their annotation using gene ontology analysis and cis-regulatory element discovery. The causal basis for co-regulation is detected through the use of quantitative trait locus mapping. [Abstract/Link to Full Text]

Mao Y, Zhou X, Pi D, Sun Y, Wong ST
Multiclass cancer classification by using fuzzy support vector machine and binary decision tree with gene selection.
J Biomed Biotechnol. 2005 Jun 30;2005(2):160-71.
We investigate the problems of multiclass cancer classification with gene selection from gene expression data. Two different constructed multiclass classifiers with gene selection are proposed, which are fuzzy support vector machine (FSVM) with gene selection and binary classification tree based on SVM with gene selection. Using F test and recursive feature elimination based on SVM as gene selection methods, binary classification tree based on SVM with F test, binary classification tree based on SVM with recursive feature elimination based on SVM, and FSVM with recursive feature elimination based on SVM are tested in our experiments. To accelerate computation, preselecting the strongest genes is also used. The proposed techniques are applied to analyze breast cancer data, small round blue-cell tumors, and acute leukemia data. Compared to existing multiclass cancer classifiers and binary classification tree based on SVM with F test or binary classification tree based on SVM with recursive feature elimination based on SVM mentioned in this paper, FSVM based on recursive feature elimination based on SVM can find most important genes that affect certain types of cancer with high recognition accuracy. [Abstract/Link to Full Text]

Liu Z, Chen D, Bensmail H
Gene expression data classification with Kernel principal component analysis.
J Biomed Biotechnol. 2005 Jun 30;2005(2):155-9.
One important feature of the gene expression data is that the number of genes M far exceeds the number of samples N. Standard statistical methods do not work well when N < M. Development of new methodologies or modification of existing methodologies is needed for the analysis of the microarray data. In this paper, we propose a novel analysis procedure for classifying the gene expression data. This procedure involves dimension reduction using kernel principal component analysis (KPCA) and classification with logistic regression (discrimination). KPCA is a generalization and nonlinear version of principal component analysis. The proposed algorithm was applied to five different gene expression datasets involving human tumor samples. Comparison with other popular classification methods such as support vector machines and neural networks shows that our algorithm is very promising in classifying gene expression data. [Abstract/Link to Full Text]

Ghosh D, Chinnaiyan AM
Classification and selection of biomarkers in genomic data using LASSO.
J Biomed Biotechnol. 2005 Jun 30;2005(2):147-54.
High-throughput gene expression technologies such as microarrays have been utilized in a variety of scientific applications. Most of the work has been done on assessing univariate associations between gene expression profiles with clinical outcome (variable selection) or on developing classification procedures with gene expression data (supervised learning). We consider a hybrid variable selection/classification approach that is based on linear combinations of the gene expression profiles that maximize an accuracy measure summarized using the receiver operating characteristic curve. Under a specific probability model, this leads to the consideration of linear discriminant functions. We incorporate an automated variable selection approach using LASSO. An equivalence between LASSO estimation with support vector machines allows for model fitting using standard software. We apply the proposed method to simulated data as well as data from a recently published prostate cancer study. [Abstract/Link to Full Text]

Gao J, Qi Y, Cao Y, Tung WW
Protein coding sequence identification by simultaneously characterizing the periodic and random features of DNA sequences.
J Biomed Biotechnol. 2005 Jun 30;2005(2):139-46.
Most codon indices used today are based on highly biased nonrandom usage of codons in coding regions. The background of a coding or noncoding DNA sequence, however, is fairly random, and can be characterized as a random fractal. When a gene-finding algorithm incorporates multiple sources of information about coding regions, it becomes more successful. It is thus highly desirable to develop new and efficient codon indices by simultaneously characterizing the fractal and periodic features of a DNA sequence. In this paper, we describe a novel way of achieving this goal. The efficiency of the new codon index is evaluated by studying all of the 16 yeast chromosomes. In particular, we show that the method automatically and correctly identifies which of the three reading frames is the one that contains a gene. [Abstract/Link to Full Text]

Chen D, Liu Z, Ma X, Hua D
Selecting genes by test statistics.
J Biomed Biotechnol. 2005 Jun 30;2005(2):132-8.
Gene selection is an important issue in analyzing multiclass microarray data. Among many proposed selection methods, the traditional ANOVA F test statistic has been employed to identify informative genes for both class prediction (classification) and discovery problems. However, the F test statistic assumes an equal variance. This assumption may not be realistic for gene expression data. This paper explores other alternative test statistics which can handle heterogeneity of the variances. We study five such test statistics, which include Brown-Forsythe test statistic and Welch test statistic. Their performance is evaluated and compared with that of F statistic over different classification methods applied to publicly available microarray datasets. [Abstract/Link to Full Text]

Gambin A, Otto R
Contextual multiple sequence alignment.
J Biomed Biotechnol. 2005 Jun 30;2005(2):124-31.
In a recently proposed contextual alignment model, efficient algorithms exist for global and local pairwise alignment of protein sequences. Preliminary results obtained for biological data are very promising. Our main motivation was to adopt the idea of context dependency to the multiple-alignment setting. To this aim the relaxation of the model was developed (we call this new model averaged contextual alignment) and a new family of amino acids substitution matrices are constructed. In this paper we present a contextual multiple-alignment algorithm and report the outcomes of experiments performed for the BAliBASE test set. The contextual approach turned out to give much better results for the set of sequences containing orphan genes. [Abstract/Link to Full Text]

Samsa G, Hu G, Root M
Combining information from multiple data sources to create multivariable risk models: illustration and preliminary assessment of a new method.
J Biomed Biotechnol. 2005 Jun 30;2005(2):113-23.
A common practice of metanalysis is combining the results of numerous studies on the effects of a risk factor on a disease outcome. If several of these composite relative risks are estimated from the medical literature for a specific disease, they cannot be combined in a multivariate risk model, as is often done in individual studies, because methods are not available to overcome the issues of risk factor colinearity and heterogeneity of the different cohorts. We propose a solution to these problems for general linear regression of continuous outcomes using a simple example of combining two independent variables from two sources in estimating a joint outcome. We demonstrate that when explicitly modifying the underlying data characteristics (correlation coefficients, standard deviations, and univariate betas) over a wide range, the predicted outcomes remain reasonable estimates of empirically derived outcomes (gold standard). This method shows the most promise in situations where the primary interest is in generating predicted values as when identifying a high-risk group of individuals. The resulting partial regression coefficients are less robust than the predicted values. [Abstract/Link to Full Text]

Wren JD, Garner HR
Data-mining analysis suggests an epigenetic pathogenesis for type 2 diabetes.
J Biomed Biotechnol. 2005 Jun 30;2005(2):104-12.
The etiological origin of type 2 diabetes mellitus (T2DM) has long been controversial. The body of literature related to T2DM is vast and varied in focus, making a broad epidemiological perspective difficult, if not impossible. A data-mining approach was used to analyze all electronically available scientific literature, over 12 million Medline records, for "objects" such as genes, diseases, phenotypes, and chemical compounds linked to other objects within the T2DM literature but were not themselves within the T2DM literature. The goal of this analysis was to conduct a comprehensive survey to identify novel factors implicated in the pathology of T2DM by statistically evaluating mutually shared associations. Surprisingly, epigenetic factors were among the highest statistical scores in this analysis, strongly implicating epigenetic changes within the body as causal factors in the pathogenesis of T2DM. Further analysis implicates adipocytes as the potential tissue of origin, and cytokines or cytokine-like genes as the dysregulated factor(s) responsible for the T2DM phenotype. The analysis provides a wealth of literature supporting this hypothesis, which-if true-represents an important paradigm shift for researchers studying the pathogenesis of T2DM. [Abstract/Link to Full Text]

Joy MP, Brock A, Ingber DE, Huang S
High-betweenness proteins in the yeast protein interaction network.
J Biomed Biotechnol. 2005 Jun 30;2005(2):96-103.
Structural features found in biomolecular networks that are absent in random networks produced by simple algorithms can provide insight into the function and evolution of cell regulatory networks. Here we analyze "betweenness" of network nodes, a graph theoretical centrality measure, in the yeast protein interaction network. Proteins that have high betweenness, but low connectivity (degree), were found to be abundant in the yeast proteome. This finding is not explained by algorithms proposed to explain the scale-free property of protein interaction networks, where low-connectivity proteins also have low betweenness. These data suggest the existence of some modular organization of the network, and that the high-betweenness, low-connectivity proteins may act as important links between these modules. We found that proteins with high betweenness are more likely to be essential and that evolutionary age of proteins is positively correlated with betweenness. By comparing different models of genome evolution that generate scale-free networks, we show that rewiring of interactions via mutation is an important factor in the production of such proteins. The evolutionary and functional significance of these observations are discussed. [Abstract/Link to Full Text]

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Recent Articles in BMC Biotechnology

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Castillo B, Bansal V, Ganesan A, Halling P, Secundo F, Ferrer A, Griebenow K, Barletta G
On the activity loss of hydrolases in organic solvents: II. a mechanistic study of subtilisin Carlsberg.
BMC Biotechnol. 2006;651.
BACKGROUND: Enzymes have been extensively used in organic solvents to catalyze a variety of transformations of biological and industrial significance. It has been generally accepted that in dry aprotic organic solvents, enzymes are kinetically trapped in their conformation due to the high-energy barrier needed for them to unfold, suggesting that in such media they should remain catalytically active for long periods. However, recent studies on a variety of enzymes demonstrate that their initial high activity is severely reduced after exposure to organic solvents for several hours. It was speculated that this could be due to structural perturbations, changes of the enzyme's pH memory, enzyme aggregation, or dehydration due to water removal by the solvents. Herein, we systematically study the possible causes for this undesirable activity loss in 1,4-dioxane. RESULTS: As model enzyme, we employed the protease subtilisin Carlsberg, prepared by lyophilization and colyophilization with the additive methyl-beta-cyclodextrin (MbetaCD). Our results exclude a mechanism involving a change in ionization state of the enzyme, since the enzyme activity shows a similar pH dependence before and after incubation for 5 days in 1,4-dioxane. No apparent secondary or tertiary structural perturbations resulting from prolonged exposure in this solvent were detected. Furthermore, active site titration revealed that the number of active sites remained constant during incubation. Additionally, the hydration level of the enzyme does not seem to affect its stability. Electron paramagnetic resonance spectroscopy studies revealed no substantial increase in the rotational freedom of a paramagnetic nitroxide inhibitor bound to the active site (a spin-label) during incubation in neat 1,4-dioxane, when the water activity was kept constant using BaBr2 hydrated salts. Incubation was also accompanied by a substantial decrease in Vmax/KM. CONCLUSION: These results exclude some of the most obvious causes for the observed low enzyme storage stability in 1,4-dioxane, mainly structural, dynamics and ionization state changes. The most likely explanation is possible rearrangement of water molecules within the enzyme that could affect its dielectric environment. However, other mechanisms, such as small distortions around the active site or rearrangement of counter ions, cannot be excluded at this time. [Abstract/Link to Full Text]

Wang S, Shi Z, Liu W, Jules J, Feng X
Development and validation of vectors containing multiple siRNA expression cassettes for maximizing the efficiency of gene silencing.
BMC Biotechnol. 2006;650.
BACKGROUND: RNA interference (RNAi) was originally identified as a biological process in which short double-stranded RNA (dsRNA) suppress the expression of genes complimentary to the dsRNA. This cellular intrinsic gene silencing mechanism has subsequently been developed as a useful tool for studies of gene function. A major strategy for producing small interfering RNA (siRNA) in cultured cells involves the use of siRNA expression vectors in which a RNA polymerase III (Pol III) promoter and transcription stop signal are designed to constitute a functional siRNA expression cassette for production of siRNA. However, most of the available vectors contain only one siRNA expression cassette. RESULTS: In order to maximize the efficiency and versatility of the vector-based siRNA approach, we have developed vectors containing multiple (up to six) tandem siRNA expression cassettes. Moreover, we demonstrated that these vectors can be used not only to produce different siRNA to simultaneously suppress the expression of multiple genes but also to maximize the silencing of a single gene. CONCLUSION: The vectors containing multiple siRNA expression cassettes can serve as useful tools for maximizing the efficiency of gene silencing. [Abstract/Link to Full Text]

Chapple SD, Crofts AM, Shadbolt SP, McCafferty J, Dyson MR
Multiplexed expression and screening for recombinant protein production in mammalian cells.
BMC Biotechnol. 2006;649.
BACKGROUND: A variety of approaches to understanding protein structure and function require production of recombinant protein. Mammalian based expression systems have advantages over bacterial systems for certain classes of protein but can be slower and more laborious. Thus the availability of a simple system for production and rapid screening of constructs or conditions for mammalian expression would be of great benefit. To this end we have coupled an efficient recombinant protein production system based on transient transfection in HEK-293 EBNA1 (HEK-293E) suspension cells with a dot blot method allowing pre-screening of proteins expressed in cells in a high throughput manner. RESULTS: A nested PCR approach was used to clone 21 extracellular domains of mouse receptors as CD4 fusions within a mammalian GATEWAY expression vector system. Following transient transfection, HEK-293E cells grown in 2 ml cultures in 24-deep well blocks showed similar growth kinetics, viability and recombinant protein expression profiles, to those grown in 50 ml shake flask cultures as judged by western blotting. Following optimisation, fluorescent dot blot analysis of transfection supernatants was shown to be a rapid method for analysing protein expression yielding similar results as western blot analysis. Addition of urea enhanced the binding of glycoproteins to a nitrocellulose membrane. A good correlation was observed between the results of a plate based small scale transient transfection dot blot pre-screen and successful purification of proteins expressed at the 50 ml scale. CONCLUSION: The combination of small scale multi-well plate culture and dot blotting described here will allow the multiplex analysis of different mammalian expression experiments enabling a faster identification of high yield expression constructs or conditions prior to large scale protein production. The methods for parallel GATEWAY cloning and expression of multiple constructs in cell culture will also be useful for applications such as the generation of receptor protein microarrays. [Abstract/Link to Full Text]

Leitner NR, Strobl B, Bokor M, Painz R, Kolbe T, Rülicke T, Müller M, Karaghiosoff M
A time- and dose-dependent STAT1 expression system.
BMC Biotechnol. 2006;648.
BACKGROUND: The signal transducer and activator of transcription (STAT) family of transcription factors mediates a variety of cytokine dependent gene regulations. STAT1 has been mainly characterized by its role in interferon (IFN) type I and II signaling and STAT1 deficiency leads to high susceptibility to several pathogens. For fine-tuned analysis of STAT1 function we established a dimerizer-inducible system for STAT1 expression in vitro and in vivo. RESULTS: The functionality of the dimerizer-induced STAT1 system is demonstrated in vitro in mouse embryonic fibroblasts and embryonic stem cells. We show that this two-vector based system is highly inducible and does not show any STAT1 expression in the absence of the inducer. Reconstitution of STAT1 deficient cells with inducible STAT1 restores IFNgamma-mediated gene induction, antiviral responses and STAT1 activation remains dependent on cytokine stimulation. STAT1 expression is induced rapidly upon addition of dimerizer and expression levels can be regulated in a dose-dependent manner. Furthermore we show that in transgenic mice STAT1 can be induced upon stimulation with the dimerizer, although only at low levels. CONCLUSION: These results prove that the dimerizer-induced system is a powerful tool for STAT1 analysis in vitro and provide evidence that the system is suitable for the use in transgenic mice. To our knowledge this is the first report for inducible STAT1 expression in a time- and dose-dependent manner. [Abstract/Link to Full Text]

Saba R, Booth SA
Target labelling for the detection and profiling of microRNAs expressed in CNS tissue using microarrays.
BMC Biotechnol. 2006;647.
BACKGROUND: MicroRNAs (miRNA) are a novel class of small, non-coding, gene regulatory RNA molecules that have diverse roles in a variety of eukaryotic biological processes. High-throughput detection and differential expression analysis of these molecules, by microarray technology, may contribute to a greater understanding of the many biological events regulated by these molecules. In this investigation we compared two different methodologies for the preparation of labelled miRNAs from mouse CNS tissue for microarray analysis. Labelled miRNAs were prepared either by a procedure involving linear amplification of miRNAs (labelled-aRNA) or using a direct labelling strategy (labelled-cDNA) and analysed using a custom miRNA microarray platform. Our aim was to develop a rapid, sensitive methodology to profile miRNAs that could be adapted for use on limited amounts of tissue. RESULTS: We demonstrate the detection of an equivalent set of miRNAs from mouse CNS tissues using both amplified and non-amplified labelled miRNAs. Validation of the expression of these miRNAs in the CNS by multiplex real-time PCR confirmed the reliability of our microarray platform. We found that although the amplification step increased the sensitivity of detection of miRNAs, we observed a concomitant decrease in specificity for closely related probes, as well as increased variation introduced by dye bias. CONCLUSION: The data presented in this investigation identifies several important sources of systematic bias that must be considered upon linear amplification of miRNA for microarray analysis in comparison to directly labelled miRNA. [Abstract/Link to Full Text]

Martin CD, Rojas G, Mitchell JN, Vincent KJ, Wu J, McCafferty J, Schofield DJ
A simple vector system to improve performance and utilisation of recombinant antibodies.
BMC Biotechnol. 2006;646.
BACKGROUND: Isolation of recombinant antibody fragments from antibody libraries is well established using technologies such as phage display. Phage display vectors are ideal for efficient display of antibody fragments on the surface of bacteriophage particles. However, they are often inefficient for expression of soluble antibody fragments, and sub-cloning of selected antibody populations into dedicated soluble antibody fragment expression vectors can enhance expression. RESULTS: We have developed a simple vector system for expression, dimerisation and detection of recombinant antibody fragments in the form of single chain Fvs (scFvs). Expression is driven by the T7 RNA polymerase promoter in conjunction with the inducible lysogen strain BL21 (DE3). The system is compatible with a simple auto-induction culture system for scFv production. As an alternative to periplasmic expression, expression directly in the cytoplasm of a mutant strain with a more oxidising cytoplasmic environment (Origami 2 (DE3)) was investigated and found to be inferior to periplasmic expression in BL21 (DE3) cells. The effect on yield and binding activity of fusing scFvs to the N terminus of maltose binding protein (a solubility enhancing partner), bacterial alkaline phosphatase (a naturally dimeric enzymatic reporter molecule), or the addition of a free C-terminal cysteine was determined. Fusion of scFvs to the N-terminus of maltose binding protein increased scFv yield but binding activity of the scFv was compromised. In contrast, fusion to the N-terminus of bacterial alkaline phosphatase led to an improved performance. Alkaline phosphatase provides a convenient tag allowing direct enzymatic detection of scFv fusions within crude extracts without the need for secondary reagents. Alkaline phosphatase also drives dimerisation of the scFv leading to an improvement in performance compared to monovalent constructs. This is illustrated by ELISA, western blot and immunohistochemistry. CONCLUSION: Nine scFv expression vectors have been generated and tested. Three vectors showed utility for expression of functional scFv fragments. One vector, pSANG14-3F, produces scFv-alkaline phosphatase fusion molecules which offers a simple, convenient and sensitive way of determining the reactivity of recombinant antibody fragments in a variety of common assay systems. [Abstract/Link to Full Text]

Bestoso F, Ottaggio L, Armirotti A, Balbi A, Damonte G, Degan P, Mazzei M, Cavalli F, Ledda B, Miele M
In vitro cell cultures obtained from different explants of Corylus avellana produce Taxol and taxanes.
BMC Biotechnol. 2006;645.
BACKGROUND: Taxol is an effective antineoplastic agent, originally extracted from the bark of Taxus brevifolia with a low yield. Many attempts have been made to produce Taxol by chemical synthesis, semi-synthesis and plant tissue cultures. However, to date, the availability of this compound is not sufficient to satisfy the commercial requirements. The aim of the present work was to produce suspension cell cultures from plants not belonging to Taxus genus and to verify whether they produced Taxol and taxanes. For this purpose different explants of hazel (Corylus avellana species) were used to optimize the protocol for inducing in vitro callus, an undifferentiated tissue from which suspension cell cultures were established. RESULTS: Calli were successfully induced from stems, leaves and seeds grown in various hormone concentrations and combinations. The most suitable callus to establish suspension cell cultures was obtained from seeds. Media recovered from suspension cell cultures contained taxanes, and showed antiproliferative activity on human tumour cells. Taxol, 10-deacetyltaxol and 10-deacetylbaccatin III were the main taxanes identified. The level of Taxol recovered from the media of hazel cultures was similar to that found in yew cultures. Moreover, the production of taxanes in hazel cell cultures increased when elicitors were used. CONCLUSION: Here we show that hazel cell cultures produce Taxol and taxanes under controlled conditions. This result suggests that hazel possesses the enzymes for Taxol production, which until now was considered to be a pathway particular to Taxus genus. The main benefit of producing taxanes through hazel cell cultures is that hazel is widely available, grows at a much faster rate in vivo, and is easier to cultivate in vitro than yew. In addition, the production of callus directly from hazel seeds shortens the culture time and minimizes the probability of contamination. Therefore, hazel could become a commercial source of Taxol and taxanes, both to be used as new therapeutic agents or as new precursors for Taxol semi-synthesis. [Abstract/Link to Full Text]

Sanchez JA, Abramowitz JD, Salk JJ, Reis AH, Rice JE, Pierce KE, Wangh LJ
Two-temperature LATE-PCR endpoint genotyping.
BMC Biotechnol. 2006;644.
BACKGROUND: In conventional PCR, total amplicon yield becomes independent of starting template number as amplification reaches plateau and varies significantly among replicate reactions. This paper describes a strategy for reconfiguring PCR so that the signal intensity of a single fluorescent detection probe after PCR thermal cycling reflects genomic composition. The resulting method corrects for product yield variations among replicate amplification reactions, permits resolution of homozygous and heterozygous genotypes based on endpoint fluorescence signal intensities, and readily identifies imbalanced allele ratios equivalent to those arising from gene/chromosomal duplications. Furthermore, the use of only a single colored probe for genotyping enhances the multiplex detection capacity of the assay. RESULTS: Two-Temperature LATE-PCR endpoint genotyping combines Linear-After-The-Exponential (LATE)-PCR (an advanced form of asymmetric PCR that efficiently generates single-stranded DNA) and mismatch-tolerant probes capable of detecting allele-specific targets at high temperature and total single-stranded amplicons at a lower temperature in the same reaction. The method is demonstrated here for genotyping single-nucleotide alleles of the human HEXA gene responsible for Tay-Sachs disease and for genotyping SNP alleles near the human p53 tumor suppressor gene. In each case, the final probe signals were normalized against total single-stranded DNA generated in the same reaction. Normalization reduces the coefficient of variation among replicates from 17.22% to as little as 2.78% and permits endpoint genotyping with >99.7% accuracy. These assays are robust because they are consistent over a wide range of input DNA concentrations and give the same results regardless of how many cycles of linear amplification have elapsed. The method is also sufficiently powerful to distinguish between samples with a 1:1 ratio of two alleles from samples comprised of 2:1 and 1:2 ratios of the same alleles. CONCLUSION: SNP genotyping via Two-Temperature LATE-PCR takes place in a homogeneous closed-tube format and uses a single hybridization probe per SNP site. These assays are convenient, rely on endpoint analysis, improve the options for construction of multiplex assays, and are suitable for SNP genotyping, mutation scanning, and detection of DNA duplication or deletions. [Abstract/Link to Full Text]

Mullick A, Xu Y, Warren R, Koutroumanis M, Guilbault C, Broussau S, Malenfant F, Bourget L, Lamoureux L, Lo R, Caron AW, Pilotte A, Massie B
The cumate gene-switch: a system for regulated expression in mammalian cells.
BMC Biotechnol. 2006;643.
BACKGROUND: A number of expression systems have been developed where transgene expression can be regulated. They all have specific characteristics making them more suitable for certain applications than for others. Since some applications require the regulation of several genes, there is a need for a variety of independent yet compatible systems. RESULTS: We have used the regulatory mechanisms of bacterial operons (cmt and cym) to regulate gene expression in mammalian cells using three different strategies. In the repressor configuration, regulation is mediated by the binding of the repressor (CymR) to the operator site (CuO), placed downstream of a strong constitutive promoter. Addition of cumate, a small molecule, relieves the repression. In the transactivator configuration, a chimaeric transactivator (cTA) protein, formed by the fusion of CymR with the activation domain of VP16, is able to activate transcription when bound to multiple copies of CuO, placed upstream of the CMV minimal promoter. Cumate addition abrogates DNA binding and therefore transactivation by cTA. Finally, an adenoviral library of cTA mutants was screened to identify a reverse cumate activator (rcTA), which activates transcription in the presence rather than the absence of cumate. CONCLUSION: We report the generation of a new versatile inducible expression system. [Abstract/Link to Full Text]

Felsheim RF, Herron MJ, Nelson CM, Burkhardt NY, Barbet AF, Kurtti TJ, Munderloh UG
Transformation of Anaplasma phagocytophilum.
BMC Biotechnol. 2006;642.
BACKGROUND: Tick-borne pathogens cause emerging zoonoses, and include fastidious organisms such as Anaplasma phagocytophilum. Because of their obligate intracellular nature, methods for mutagenesis and transformation have not been available. RESULTS: To facilitate genetic manipulation, we transformed A. phagocytophilum (Ap) to express a green fluorescent protein (GFP) with the Himar1 transposase system and selection with the clinically irrelevant antibiotic spectinomycin. CONCLUSION: These transformed bacteria (GFP/Ap) grow at normal rates and are brightly fluorescent in human, monkey, and tick cell culture. Molecular characterization of the GFP/Ap genomic DNA confirmed transposition and the flanking genomic insertion locations were sequenced. Three mice inoculated with GFP/Ap by intraperitoneal injection became infected as demonstrated by the appearance of morulae in a peripheral blood neutrophil and re-isolation of the bacteria in culture. [Abstract/Link to Full Text]

Erkens T, Van Poucke M, Vandesompele J, Goossens K, Van Zeveren A, Peelman LJ
Development of a new set of reference genes for normalization of real-time RT-PCR data of porcine backfat and longissimus dorsi muscle, and evaluation with PPARGC1A.
BMC Biotechnol. 2006;641.
BACKGROUND: An essential part of using real-time RT-PCR is that expression results have to be normalized before any conclusions can be drawn. This can be done by using one or multiple, validated reference genes, depending on the desired accuracy of the results. In the pig however, very little information is available on the expression stability of reference genes. The aim of this study was therefore to develop a new set of reference genes which can be used for normalization of mRNA expression data of genes expressed in porcine backfat and longissimus dorsi muscle, both representing an economically important part of a pig's carcass. Because of its multiple functions in fat metabolism and muscle fibre type composition, peroxisome proliferative activated receptor gamma coactivator 1alpha (PPARGC1A) is a very interesting candidate gene for meat quality, and was an ideal gene to evaluate our developed set of reference genes for normalization of mRNA expression data of both tissue types. RESULTS: The mRNA expression stability of 10 reference genes was determined. The expression of RPL13A and SDHA appeared to be highly unstable. After normalization to the geometric mean of the three most stably expressed reference genes (ACTB, TBP and TOP2B), the results not only showed that the mRNA expression of PPARGC1A was significantly higher in each of the longissimus dorsi muscle samples than in backfat (P < 0.05), but also that the expression was significantly higher in the most cranial of the three muscle samples (P < 0.05). CONCLUSION: This study provides a new set of reference genes (ACTB, TBP and TOP2B) suitable for normalization of real-time RT-PCR data of backfat and longissimus dorsi muscle in the pig. The obtained PPARGC1A expression results, after application of this set of reference genes, are a first step in unravelling the PPARGC1A expression pattern in the pig and provide a basis for possible selection towards improved meat quality while maintaining a lean carcass. [Abstract/Link to Full Text]

Kuroda T, Martuza RL, Todo T, Rabkin SD
Flip-Flop HSV-BAC: bacterial artificial chromosome based system for rapid generation of recombinant herpes simplex virus vectors using two independent site-specific recombinases.
BMC Biotechnol. 2006;640.
BACKGROUND: Oncolytic herpes simplex virus (HSV) vectors that specifically replicate in and kill tumor cells sparing normal cells are a promising cancer therapy. Traditionally, recombinant HSV vectors have been generated through homologous recombination between the HSV genome and a recombination plasmid, which usually requires laborious screening or selection and can take several months. Recent advances in bacterial artificial chromosome (BAC) technology have enabled cloning of the whole HSV genome as a BAC plasmid and subsequent manipulation in E. coli. Thus, we sought a method to generate recombinant oncolytic HSV vectors more easily and quickly using BAC technology. RESULTS: We have developed an HSV-BAC system, termed the Flip-Flop HSV-BAC system, for the rapid generation of oncolytic HSV vectors. This system has the following features: (i) two site-specific recombinases, Cre and FLPe, are used sequentially to integrate desired sequences and to excise the BAC sequences, respectively; and (ii) the size of the HSV-BAC-insert genome exceeds the packaging limit of HSV so only correctly recombined virus grows efficiently. We applied this to the construction of an HSV-BAC plasmid that can be used for the generation of transcriptionally-targeted HSV vectors. BAC sequences were recombined into the UL39 gene of HSV ICP4-deletion mutant d120 to generate M24-BAC virus, from which HSV-BAC plasmid pM24-BAC was isolated. An ICP4 expression cassette driven by an exogenous promoter was re-introduced to pM24-BAC by Cre-mediated recombination and nearly pure preparations of recombinant virus were obtained typically in two weeks. Insertion of the ICP4 coding sequence alone did not restore viral replication and was only minimally better than an ICP4-null construct, whereas insertion of a CMVIE promoter-ICP4 transgene (bM24-CMV) efficiently drove viral replication. The levels of bM24-CMV replication in tumor cells varied considerably compared to hrR3 (UL39 mutant). CONCLUSION: Our Flip-Flop HSV-BAC system enables rapid generation of HSV vectors carrying transgene inserts. By introducing a tumor-specific-promoter-driven ICP4 cassette into pM24-BAC using this system, one should be able to generate transcriptionally-targeted oncolytic HSV vectors. We believe this system will greatly facilitate the screening of a plethora of clinically useful tumor-specific promoters in the context of oncolytic HSV vectors. [Abstract/Link to Full Text]

Gupta A, Chaudhary VK
Bifunctional recombinant fusion proteins for rapid detection of antibodies to both HIV-1 and HIV-2 in whole blood.
BMC Biotechnol. 2006;639.
BACKGROUND: Availability of accurate diagnostic tests has been helpful in curtailing the spread of HIV infection. Among these, simple, point of care, inexpensive tests which require only a drop of blood from finger-prick and give reliable results within minutes are a must for expansion of testing services and for reaching mobile and marginalized populations. Such tests will not only be a boon for the infrastructure-starved developing and underdeveloped countries but will also be extremely useful in developed countries where post-testing compliance is a major problem. Our laboratory has been involved in developing reagents for heamagglutination-based rapid detection of antibodies to HIV in whole blood using recombinant molecules specific for either HIV-1 or HIV-2. Since it is not required of a screening test to differentially detect HIV and HIV-2, it would useful to create a single molecule capable of simultaneous detection of both HIV-1 and HIV-2 in a drop of blood. RESULTS: The present paper describes designing, high-level expression and large-scale purification of new molecules comprising recombinant anti-RBC Fab fused to immunodominant regions of envelope sequences from both gp41 of HIV-1 and gp36 of HIV-2. These immunodominant regions of HIV envelope contain cysteine residues, which make disulfide bond and can interfere with the assembly of light chain and heavy chain fragment to make Fab molecule in vitro. To circumvent this problem, a series of fusion proteins having different combinations of native and mutant envelope sequences were constructed, purified and evaluated for their efficacy in detecting antibodies to HIV-1 and HIV-2. A chimeric molecule comprising native envelope sequence of gp41 of HIV-1 and modified envelope sequence of gp36 of HIV-2 gave good production yield and also detected both HIV-1 and HIV-2 samples with high sensitivity and specificity. CONCLUSION: The new bifunctional antibody fusion protein identified in this study detects both HIV-1 and HIV-2 infected samples efficiently and can be used in place of molecules that detect only HIV-1 or HIV-2. This will make reagent production more economical as only one molecule has to be produced in place of two molecules. Also, it will simplify the testing procedure allowing detection of both HIV-1 and HIV-2 infections in a single drop of blood. [Abstract/Link to Full Text]

Real SM, Marzese DM, Gomez LC, Mayorga LS, Roqué M
Development of a Premature Stop Codon-detection method based on a bacterial two-hybrid system.
BMC Biotechnol. 2006;638.
BACKGROUND: The detection of Premature Stop Codons (PSCs) in human genes is very useful for the genetic diagnosis of different hereditary cancers, e.g. Familial Breast Cancer and Hereditary Non-Polyposis Colorectal Cancer (HNPCC). The products of these PSCs are truncated proteins, detectable in vitro by the Protein Truncation Test and in vivo by using the living translation machinery of yeast or bacteria. These living strategies are based on the construction of recombinant plasmids where the human sequence of interest is inserted upstream of a reporter gene. Although simple, these assays have their limitations. The yeast system requires extensive work to enhance its specificity, and the bacterial systems yield many false results due to translation re-initiation events occurring post PSCs. Our aim was to design a recombinant plasmid useful for detecting PSCs in human genes and resistant to bacterial translation re-initiation interferences. RESULTS: A functional recombinant plasmid (pREAL) was designed based on a bacterial two-hybrid system. In our design, the in vivo translation of fused fragments of the Bordetella pertussis adenylate cyclase triggers the production of cAMP giving rise to a selectable bacterial phenotype. When a gene of interest is inserted between the two fragments, any PSC inhibits the enzymatic activity of the product, and translation re-initiation events post-PSC yield separated inactive fragments. We demonstrated that the system can accurately detect PSCs in human genes by inserting mutated fragments of the brca1 and msh2 gene. Western Blot assays revealed translation re-initiation events in all the tested colonies, implying that a simpler plasmid would not be resistant to this source of false negative results. The application of the system to a HNPCC family with a nonsense mutation in the msh2 gene correctly diagnosed wild type homozygous and heterozygous patients. CONCLUSION: The developed pREAL is applicable to the detection of PSCs in human genes related to different diseases and is resistant to translation re-initiation events. The diagnosis steps are easy, have a low cost, detect only pathologic mutations, and allow the analysis of separated alleles. [Abstract/Link to Full Text]

Cankar K, Stebih D, Dreo T, Zel J, Gruden K
Critical points of DNA quantification by real-time PCR--effects of DNA extraction method and sample matrix on quantification of genetically modified organisms.
BMC Biotechnol. 2006;637.
BACKGROUND: Real-time PCR is the technique of choice for nucleic acid quantification. In the field of detection of genetically modified organisms (GMOs) quantification of biotech products may be required to fulfil legislative requirements. However, successful quantification depends crucially on the quality of the sample DNA analyzed. Methods for GMO detection are generally validated on certified reference materials that are in the form of powdered grain material, while detection in routine laboratories must be performed on a wide variety of sample matrixes. Due to food processing, the DNA in sample matrixes can be present in low amounts and also degraded. In addition, molecules of plant origin or from other sources that affect PCR amplification of samples will influence the reliability of the quantification. Further, the wide variety of sample matrixes presents a challenge for detection laboratories. The extraction method must ensure high yield and quality of the DNA obtained and must be carefully selected, since even components of DNA extraction solutions can influence PCR reactions. GMO quantification is based on a standard curve, therefore similarity of PCR efficiency for the sample and standard reference material is a prerequisite for exact quantification. Little information on the performance of real-time PCR on samples of different matrixes is available. RESULTS: Five commonly used DNA extraction techniques were compared and their suitability for quantitative analysis was assessed. The effect of sample matrix on nucleic acid quantification was assessed by comparing 4 maize and 4 soybean matrixes. In addition 205 maize and soybean samples from routine analysis were analyzed for PCR efficiency to assess variability of PCR performance within each sample matrix. Together with the amount of DNA needed for reliable quantification, PCR efficiency is the crucial parameter determining the reliability of quantitative results, therefore it was chosen as the primary criterion by which to evaluate the quality and performance on different matrixes and extraction techniques. The effect of PCR efficiency on the resulting GMO content is demonstrated. CONCLUSION: The crucial influence of extraction technique and sample matrix properties on the results of GMO quantification is demonstrated. Appropriate extraction techniques for each matrix need to be determined to achieve accurate DNA quantification. Nevertheless, as it is shown that in the area of food and feed testing matrix with certain specificities is impossible to define strict quality controls need to be introduced to monitor PCR. The results of our study are also applicable to other fields of quantitative testing by real-time PCR. [Abstract/Link to Full Text]

Hoffmann D, Wildner O
Efficient generation of double heterologous promoter controlled oncolytic adenovirus vectors by a single homologous recombination step in Escherichia coli.
BMC Biotechnol. 2006;636.
BACKGROUND: Oncolytic adenoviruses are promising agents for the multimodal treatment of cancer. However, tumor-selectivity is crucial for their applicability in patients. Recent studies by several groups demonstrated that oncolytic adenoviruses with tumor-/tissue-specific expression of the E1 and E4 genes, which are pivotal for adenoviral replication, have a specificity profile that is superior to viruses that solely target the expression of E1 or E4 genes. Presently the E1 and E4 regions are modified in a time consuming sequential fashion. RESULTS: Based on the widely used adenoviral cloning system AdEasy we generated a novel transfer vector that allows efficient and rapid generation of conditionally replication-competent adenovirus type 5 based vectors with the viral E1 and E4 genes under the transcriptional control of heterologous promoters. For insertion of the promoters of interest our transfer vector has two unique multiple cloning sites. Additionally, our shuttle plasmid allows encoding of a transgene within the E1A transcription unit. The modifications, including E1 mutations, are introduced into the adenoviral genome by a single homologous recombination step in Escherichia coli. Subsequently infectious viruses are rescued from plasmids. As a proof-of-concept we generated two conditionally replication-competent adenoviruses Ad.Ki x COX and Ad.COX x Ki with the promoters of the Ki-67 protein and the cyclooxygenase-2 (COX-2) driving E1 and E4 and vice versa. CONCLUSION: We demonstrated with our cloning system efficient generation of double heterologous promoter controlled oncolytic adenoviral vectors by a single homologous recombination step in bacteria. The generated viruses showed preferential replication in tumor cells and in a subcutaneous HT-29 colon cancer xenograft model the viruses demonstrated significant oncolytic activity comparable with dl327. [Abstract/Link to Full Text]

Vivona S, Bernante F, Filippini F
NERVE: new enhanced reverse vaccinology environment.
BMC Biotechnol. 2006;635.
BACKGROUND: Since a milestone work on Neisseria meningitidis B, Reverse Vaccinology has strongly enhanced the identification of vaccine candidates by replacing several experimental tasks using in silico prediction steps. These steps have allowed scientists to face the selection of antigens from the predicted proteome of pathogens, for which cell culture is difficult or impossible, saving time and money. However, this good example of bioinformatics-driven immunology can be further developed by improving in silico steps and implementing biologist-friendly tools. RESULTS: We introduce NERVE (New Enhanced Reverse Vaccinology Environment), an user-friendly software environment for the in silico identification of the best vaccine candidates from whole proteomes of bacterial pathogens. The software integrates multiple robust and well-known algorithms for protein analysis and comparison. Vaccine candidates are ranked and presented in a html table showing relevant information and links to corresponding primary data. Information concerning all proteins of the analyzed proteome is not deleted along selection steps but rather flows into an SQL database for further mining and analyses. CONCLUSION: After learning from recent years' works in this field and analysing a large dataset, NERVE has been implemented and tuned as the first available tool able to rank a restricted pool (approximately 8-9% of the whole proteome) of vaccine candidates and to show high recall (approximately 75-80%) of known protective antigens. These vaccine candidates are required to be "safe" (taking into account autoimmunity risk) and "easy" for further experimental, high-throughput screening (avoiding possibly not soluble antigens). NERVE is expected to help save time and money in vaccine design and is available as an additional file with this manuscript; updated versions will be available at http://www.bio.unipd.it/molbinfo. [Abstract/Link to Full Text]

Geraerts M, Willems S, Baekelandt V, Debyser Z, Gijsbers R
Comparison of lentiviral vector titration methods.
BMC Biotechnol. 2006;634.
BACKGROUND: Lentiviral vectors are efficient vehicles for stable gene transfer in dividing and non-dividing cells. Several improvements in vector design to increase biosafety and transgene expression, have led to the approval of these vectors for use in clinical studies. Methods are required to analyze the quality of lentiviral vector production, the efficiency of gene transfer and the extent of therapeutic gene expression. RESULTS: We compared lentiviral vector titration methods that measure pg p24/ml, RNA equivalents/ml, transducing units (TU/ml) or mRNA equivalents. The amount of genomic RNA in vector particles proves to be reliable to assess the production quality of vectors encoding non-fluorescent proteins. However, the RNA and p24 titers of concentrated vectors are rather poor in predicting transduction efficiency, due to the high variability of vector production based on transient transfection. Moreover, we demonstrate that transgenic mRNA levels correlate well with TU and can be used for functional titration of non-fluorescent transgenes. CONCLUSION: The different titration methods have specific advantages and disadvantages. Depending on the experimental set-up one titration method should be preferred over the others. [Abstract/Link to Full Text]

Ellison SL, English CA, Burns MJ, Keer JT
Routes to improving the reliability of low level DNA analysis using real-time PCR.
BMC Biotechnol. 2006;633.
BACKGROUND: Accurate quantification of DNA using quantitative real-time PCR at low levels is increasingly important for clinical, environmental and forensic applications. At low concentration levels (here referring to under 100 target copies) DNA quantification is sensitive to losses during preparation, and suffers from appreciable valid non-detection rates for sampling reasons. This paper reports studies on a real-time quantitative PCR assay targeting a region of the human SRY gene over a concentration range of 0.5 to 1000 target copies. The effects of different sample preparation and calibration methods on quantitative accuracy were investigated. RESULTS: At very low target concentrations of 0.5-10 genome equivalents (g.e.) eliminating any replicates within each DNA standard concentration with no measurable signal (non-detects) compromised calibration. Improved calibration could be achieved by eliminating all calibration replicates for any calibration standard concentration with non-detects ('elimination by sample'). Test samples also showed positive bias if non-detects were removed prior to averaging; less biased results were obtained by converting to concentration, including non-detects as zero concentration, and averaging all values.Tube plastic proved to have a strongly significant effect on DNA quantitation at low levels (p = 1.8 x 10(-4)). At low concentrations (under 10 g.e.), results for assays prepared in standard plastic were reduced by about 50% compared to the low-retention plastic. Preparation solution (carrier DNA or stabiliser) was not found to have a significant effect in this study.Detection probabilities were calculated using logistic regression. Logistic regression over large concentration ranges proved sensitive to non-detected replicate reactions due to amplification failure at high concentrations; the effect could be reduced by regression against log (concentration) or, better, by eliminating invalid responses. CONCLUSION: Use of low-retention plastic tubes is advised for quantification of DNA solutions at levels below 100 g.e. For low-level calibration using linear least squares, it is better to eliminate the entire replicate group for any standard that shows non-detects reasonably attributable to sampling effects than to either eliminate non-detects or to assign arbitrary high Ct values. In calculating concentrations for low-level test samples with non-detects, concentrations should be calculated for each replicate, zero concentration assigned to non-detects, and all resulting concentration values averaged. Logistic regression is a useful method of estimating detection probability at low DNA concentrations. [Abstract/Link to Full Text]

Taylor MC, Kelly JM
pTcINDEX: a stable tetracycline-regulated expression vector for Trypanosoma cruzi.
BMC Biotechnol. 2006;632.
BACKGROUND: Trypanosoma cruzi is a protozoan pathogen of major medical importance in Latin America. It is also an early diverging eukaryote that displays many unusual biochemical features. The completion of the T. cruzi genome project has highlighted the need to extend the range of techniques available to study gene function. To this end we report the development of a stable tetracycline-dependent expression vector applicable to this parasite and describe in detail the parameters of the system. RESULTS: We first produced T. cruzi cell lines that constitutively expressed bacteriophage T7 RNA polymerase and the tetracycline repressor protein from a multicopy episome. An integrative vector with an inducible expression site under the control of a tetracycline-regulatable T7 promoter (pTcINDEX) was targeted to the transcriptionally silent ribosomal RNA spacer region of these parasites and transformants selected using a T7 RNA polymerase-dependent hygromycin resistance gene. To test the system we used two marker proteins, luciferase and red fluorescent protein (RFP), and an endogenous parasite protein (a mitochondrial superoxide dismutase). In each case we found that induction was both time and dose-dependent. Luciferase mRNA could be induced by at least 100-fold, and luciferase activity up to 60-fold, within 24 hours of the addition of tetracycline. When we examined RFP induction by confocal microscopy and fluorescence activated cell sorter, we observed very high levels of expression (>1000-fold increase in fluorescence intensity), although this was not synchronous throughout clonal populations. Induction of superoxide dismutase resulted in an 18-fold increase in cellular activity. The observation that a tagged version of the enzyme was correctly targeted to the mitochondrion demonstrates that our expression system may also provide a high-throughput strategy for subcellular localisation. CONCLUSION: Our results show that pTcINDEX represents a valuable addition to the genetic tools available for T. cruzi. The vector system is sufficiently flexible that it should have widespread uses including inducible expression of tagged proteins, generation of conditional knockout cell lines and the application of dominant-negative approaches. [Abstract/Link to Full Text]

Pinto FL, Svensson H, Lindblad P
Generation of non-genomic oligonucleotide tag sequences for RNA template-specific PCR.
BMC Biotechnol. 2006;631.
BACKGROUND: In order to overcome genomic DNA contamination in transcriptional studies, reverse template-specific polymerase chain reaction, a modification of reverse transcriptase polymerase chain reaction, is used. The possibility of using tags whose sequences are not found in the genome further improves reverse specific polymerase chain reaction experiments. Given the absence of software available to produce genome suitable tags, a simple tool to fulfill such need was developed. RESULTS: The program was developed in Perl, with separate use of the basic local alignment search tool, making the tool platform independent (known to run on Windows XP and Linux). In order to test the performance of the generated tags, several molecular experiments were performed. The results show that Tagenerator is capable of generating tags with good priming properties, which will deliberately not result in PCR amplification of genomic DNA. CONCLUSION: The program Tagenerator is capable of generating tag sequences that combine genome absence with good priming properties for RT-PCR based experiments, circumventing the effects of genomic DNA contamination in an RNA sample. [Abstract/Link to Full Text]

Geurts AM, Wilber A, Carlson CM, Lobitz PD, Clark KJ, Hackett PB, McIvor RS, Largaespada DA
Conditional gene expression in the mouse using a Sleeping Beauty gene-trap transposon.
BMC Biotechnol. 2006;630.
BACKGROUND: Insertional mutagenesis techniques with transposable elements have been popular among geneticists studying model organisms from E. coli to Drosophila and, more recently, the mouse. One such element is the Sleeping Beauty (SB) transposon that has been shown in several studies to be an effective insertional mutagen in the mouse germline. SB transposon vector studies have employed different functional elements and reporter molecules to disrupt and report the expression of endogenous mouse genes. We sought to generate a transposon system that would be capable of reporting the expression pattern of a mouse gene while allowing for conditional expression of a gene of interest in a tissue- or temporal-specific pattern. RESULTS: Here we report the systematic development and testing of a transposon-based gene-trap system incorporating the doxycycline-repressible Tet-Off (tTA) system that is capable of activating the expression of genes under control of a Tet response element (TRE) promoter. We demonstrate that the gene trap system is fully functional in vitro by introducing the "gene-trap tTA" vector into human cells by transposition and identifying clones that activate expression of a TRE-luciferase transgene in a doxycycline-dependent manner. In transgenic mice, we mobilize gene-trap tTA vectors, discover parameters that can affect germline mobilization rates, and identify candidate gene insertions to demonstrate the in vivo functionality of the vector system. We further demonstrate that the gene-trap can act as a reporter of endogenous gene expression and it can be coupled with bioluminescent imaging to identify genes with tissue-specific expression patterns. CONCLUSION: Akin to the GAL4/UAS system used in the fly, we have made progress developing a tool for mutating and revealing the expression of mouse genes by generating the tTA transactivator in the presence of a secondary TRE-regulated reporter molecule. A vector like the gene-trap tTA could provide a means for both annotating mouse genes and creating a resource of mice that express a regulable transcription factor in temporally- and tissue-specific patterns for conditional gene expression studies. These mice would be a valuable resource to the mouse genetics community for purpose of dissecting mammalian gene function. [Abstract/Link to Full Text]

Marconi G, Albertini E, Barone P, De Marchis F, Lico C, Marusic C, Rutili D, Veronesi F, Porceddu A
In planta production of two peptides of the Classical Swine Fever Virus (CSFV) E2 glycoprotein fused to the coat protein of potato virus X.
BMC Biotechnol. 2006;629.
BACKGROUND: Classical Swine Fever (CSFV) is one of the most important viral infectious diseases affecting wild boars and domestic pigs. The etiological agent of the disease is the CSF virus, a single stranded RNA virus belonging to the family Flaviviridae. All preventive measures in domestic pigs have been focused in interrupting the chain of infection and in avoiding the spread of CSFV within wild boars as well as interrupting transmission from wild boars to domestic pigs. The use of plant based vaccine against CSFV would be advantageous as plant organs can be distributed without the need of particular treatments such as refrigeration and therefore large areas, populated by wild animals, could be easily covered. RESULTS: We report the in planta production of peptides of the classical swine fever (CSF) E2 glycoprotein fused to the coat protein of potato virus X. RT-PCR studies demonstrated that the peptide encoding sequences are correctly retained in the PVX construct after three sequential passage in Nicotiana benthamiana plants. Sequence analysis of RT-PCR products confirmed that the epitope coding sequences are replicated with high fidelity during PVX infection. Partially purified virions were able to induce an immune response in rabbits. CONCLUSION: Previous reports have demonstrated that E2 synthetic peptides can efficiently induce an immunoprotective response in immunogenized animals. In this work we have showed that E2 peptides can be expressed in planta by using a modified PVX vector. These results are particularly promising for designing strategies for disease containment in areas inhabited by wild boars. [Abstract/Link to Full Text]

Du C, Ge B, Liu Z, Fu K, Chan WC, McKeithan TW
PCR-based generation of shRNA libraries from cDNAs.
BMC Biotechnol. 2006;628.
BACKGROUND: The use of small interfering RNAs (siRNAs) to silence target gene expression has greatly facilitated mammalian genetic analysis by generating loss-of-function mutants. In recent years, high-throughput, genome-wide screening of siRNA libraries has emerged as a viable approach. Two different methods have been used to generate short hairpin RNA (shRNA) libraries; one is to use chemically synthesized oligonucleotides, and the other is to convert complementary DNAs (cDNAs) into shRNA cassettes enzymatically. The high cost of chemical synthesis and the low efficiency of the enzymatic approach have hampered the widespread use of screening with shRNA libraries. RESULTS: We report here an improved method for constructing genome-wide shRNA libraries enzymatically. The method includes steps of cDNA fragmentation and endonuclease MmeI digestion to generate 19-bp fragments, capping the 19-bp cDNA fragments with a hairpin oligonucleotide, and amplification of the hairpin structures by PCR. The PCR step converts hairpins into double-stranded DNAs that contain head-to-head cDNA fragments that can be cloned into a vector downstream of a Pol III promoter. CONCLUSION: This method can readily be used to generate shRNA libraries from a small amount of mRNA and thus can be used to create cell- or tissue-specific libraries. [Abstract/Link to Full Text]

Sarkar A, Atapattu A, Belikoff EJ, Heinrich JC, Li X, Horn C, Wimmer EA, Scott MJ
Insulated piggyBac vectors for insect transgenesis.
BMC Biotechnol. 2006;627.
BACKGROUND: Germ-line transformation of insects is now a widely used method for analyzing gene function and for the development of genetically modified strains suitable for pest control programs. The most widely used transposable element for the germ-line transformation of insects is piggyBac. The site of integration of the transgene can influence gene expression due to the effects of nearby transcription enhancers or silent heterochromatic regions. Position effects can be minimized by flanking a transgene with insulator elements. The scs/scs' and gypsy insulators from Drosophila melanogaster as well as the chicken beta-globin HS4 insulator function in both Drosophila and mammalian cells. RESULTS: To minimize position effects we have created a set of piggyBac transformation vectors that contain either the scs/scs', gypsy or chicken beta-globin HS4 insulators. The vectors contain either fluorescent protein or eye color marker genes and have been successfully used for germ-line transformation of Drosophila melanogaster. A set of the scs/scs' vectors contains the coral reef fluorescent protein marker genes AmCyan, ZsGreen and DsRed that have not been optimized for translation in human cells. These marker genes are controlled by a combined GMR-3xP3 enhancer/promoter that gives particularly strong expression in the eyes. This is also the first report of the use of the ZsGreen and AmCyan reef fluorescent proteins as transformation markers in insects. CONCLUSION: The insulated piggyBac vectors should protect transgenes against position effects and thus facilitate fine control of gene expression in a wide spectrum of insect species. These vectors may also be used for transgenesis in other invertebrate species. [Abstract/Link to Full Text]

Couderc B, Penary M, Tohfe M, Pradines A, Casteignau A, Berg D, Favre G
Reversible inactivation of the transcriptional function of P53 protein by farnesylation.
BMC Biotechnol. 2006;626.
BACKGROUND: The use of integrating viral vectors in Gene therapy clinical trials has pointed out the problem of the deleterous effect of the integration of the ectopic gene to the cellular genome and the safety of this strategy. We proposed here a way to induce the death of gene modified cells upon request by acting on a pro-apoptotic protein cellular localization and on the activation of its apoptotic function. RESULTS: We constructed an adenoviral vector coding a chimeric p53 protein by fusing p53 sequence with the 21 COOH term amino acids sequence of H-Ras. Indeed, the translation products of Ras genes are cytosolic proteins that become secondarily associated with membranes through a series of post-translational modifications initiated by a CAAX motif present at the C terminus of Ras proteins. The chimeric p53HRCaax protein was farnesylated efficiently in transduced human osteosarcoma p53-/- cell line. The farnesylated form of p53 resided mainly in the cytosol, where it is non-functional. Farnesyl transferase inhibitors (FTIs) specifically inhibited farnesyl isoprenoid lipid modification of proteins. Following treatment of the cells with an FTI, p53HRCaax underwent translocation into the nucleus where it retained transcription factor activity. Shifting p53 into the nucleus resulted in the induction of p21waf1/CIP1 and Bax transcription, cell growth arrest, caspase activation and apoptosis. CONCLUSION: Artificial protein farnesylation impaired the transcriptional activity of p53. This could be prevented by Farnesyl transferase inhibition. These data highlight the fact that the artificial prenylation of proteins provides a novel system for controlling the function of a transactivating factor. [Abstract/Link to Full Text]

Bello-Rivero I, Torrez-Ruiz Y, Blanco-Garcés E, Pentón-Rol G, Fernández-Batista O, Javier-González L, Gerónimo-Perez H, López-Saura P
Construction, purification, and characterization of a chimeric TH1 antagonist.
BMC Biotechnol. 2006;625.
BACKGROUND: TH1 immune response antagonism is a desirable approach to mitigate some autoimmune and inflammatory reactions during the course of several diseases where IL-2 and IFN-gamma are two central players. Therefore, the neutralization of both cytokines could provide beneficial effects in patients suffering from autoimmune or inflammatory illnesses. RESULTS: A chimeric antagonist that can antagonize the action of TH1 immunity mediators, IFN-gamma and IL-2, was designed, engineered, expressed in E. coli, purified and evaluated for its in vitro biological activities. The TH1 antagonist molecule consists of the extracellular region for the human IFNgamma receptor chain 1 fused by a four-aminoacid linker peptide to human 60 N-terminal aminoacid residues of IL-2. The corresponding gene fragments were isolated by RT-PCR and cloned in the pTPV-1 vector. E. coli (W3110 strain) was transformed with this vector. The chimeric protein was expressed at high level as inclusion bodies. The protein was partially purified by pelleting and washing. It was then solubilized with strong denaturant and finally refolded by gel filtration. In vitro biological activity of chimera was demonstrated by inhibition of IFN-gamma-dependent HLA-DR expression in Colo 205 cells, inhibition of IFN-gamma antiproliferative effect on HEp-2 cells, and by a bidirectional effect in assays for IL-2 T-cell dependent proliferation: agonism in the absence versus inhibition in the presence of IL-2. CONCLUSION: TH1 antagonist is a chimeric protein that inhibits the in vitro biological activities of human IFN-gamma, and is a partial agonist/antagonist of human IL-2. With these attributes, the chimera has the potential to offer a new opportunity for the treatment of autoimmune and inflammatory diseases. [Abstract/Link to Full Text]

Bogaert L, Van Poucke M, De Baere C, Peelman L, Gasthuys F, Martens A
Selection of a set of reliable reference genes for quantitative real-time PCR in normal equine skin and in equine sarcoids.
BMC Biotechnol. 2006;624.
BACKGROUND: Real-time quantitative PCR can be a very powerful and accurate technique to examine gene transcription patterns in different biological conditions. One of the critical steps in comparing transcription profiles is accurate normalisation. In most of the studies published on real-time PCR in horses, normalisation occurred against only one reference gene, usually GAPDH or ACTB, without validation of its expression stability. This might result in unreliable conclusions, because it has been demonstrated that the expression levels of so called "housekeeping genes" may vary considerably in different tissues, cell types or disease stages, particularly in clinical samples associated with malignant disease. The goal of this study was to establish a reliable set of reference genes for studies concerning normal equine skin and equine sarcoids, which are the most common skin tumour in horses. RESULTS: In the present study the gene transcription levels of 6 commonly used reference genes (ACTB, B2M, HPRT1, UBB, TUBA1 and RPL32) were determined in normal equine skin and in equine sarcoids. After applying the geNorm applet to this set of genes, TUBA1, ACTB and UBB were found to be most stable in normal skin and B2M, ACTB and UBB in equine sarcoids. CONCLUSION: Based on these results, TUBA1, ACTB and UBB, respectively B2M, ACTB and UBB can be proposed as reference gene panels for accurate normalisation of quantitative data for normal equine skin, respectively equine sarcoids. When normal skin and equine sarcoids are compared, the use of the geometric mean of UBB, ACTB and B2M can be recommended as a reliable and accurate normalisation factor. [Abstract/Link to Full Text]

Jung HC, Kwon SJ, Pan JG
Display of a thermostable lipase on the surface of a solvent-resistant bacterium, Pseudomonas putida GM730, and its applications in whole-cell biocatalysis.
BMC Biotechnol. 2006;623.
BACKGROUND: Whole-cell biocatalysis in organic solvents has been widely applied to industrial bioprocesses. In two-phase water-solvent processes, substrate conversion yields and volumetric productivities can be limited by the toxicity of solvents to host cells and by the low mass transfer rates of the substrates from the solvent phase to the whole-cell biocatalysts in water. RESULTS: To solve the problem of solvent toxicity, we immobilized a thermostable lipase (TliA) from Pseudomonas fluorescens on the cell surface of a solvent-resistant bacterium, Pseudomonas putida GM730. Surface immobilization of enzymes eliminates the mass-transfer limitation imposed by the cell wall and membranes. TliA was successfully immobilized on the surface of P. putida cells using the ice-nucleation protein (INP) anchoring motif from Pseudomonas syrinage. The surface location was confirmed by flow cytometry, protease accessibility and whole-cell enzyme activity using a membrane-impermeable substrate. Three hundred and fifty units of whole-cell hydrolytic activity per gram dry cell mass were obtained when the enzyme was immobilized with a shorter INP anchoring motif (INPNC). The surface-immobilized TliA retained full enzyme activity in a two-phase water-isooctane reaction system after incubation at 37 degrees C for 12 h, while the activity of the free form enzyme decreased to 65% of its initial value. Whole cells presenting immobilized TliA were shown to catalyze three representative lipase reactions: hydrolysis of olive oil, synthesis of triacylglycerol and chiral resolution. CONCLUSION: In vivo surface immobilization of enzymes on solvent-resistant bacteria was demonstrated, and appears to be useful for a variety of whole-cell bioconversions in the presence of organic solvents. [Abstract/Link to Full Text]

Watts KT, Lee PC, Schmidt-Dannert C
Biosynthesis of plant-specific stilbene polyketides in metabolically engineered Escherichia coli.
BMC Biotechnol. 2006;622.
BACKGROUND: Phenylpropanoids are the precursors to a range of important plant metabolites such as the cell wall constituent lignin and the secondary metabolites belonging to the flavonoid/stilbene class of compounds. The latter class of plant natural products has been shown to function in a wide range of biological activities. During the last few years an increasing number of health benefits have been associated with these compounds. In particular, they demonstrate potent antioxidant activity and the ability to selectively inhibit certain tyrosine kinases. Biosynthesis of many medicinally important plant secondary metabolites, including stilbenes, is frequently not very well understood and under tight spatial and temporal control, limiting their availability from plant sources. As an alternative, we sought to develop an approach for the biosynthesis of diverse stilbenes by engineered recombinant microbial cells. RESULTS: A pathway for stilbene biosynthesis was constructed in Escherichia coli with 4-coumaroyl CoA ligase 1 4CL1) from Arabidopsis thaliana and stilbene synthase (STS) cloned from Arachis hypogaea. E. coli cultures expressing these enzymes together converted the phenylpropionic acid precursor 4-coumaric acid, added to the growth medium, to the stilbene resveratrol (>100 mg/L). Caffeic acid, added in the same way, resulted in the production of the expected dihydroxylated stilbene, piceatannol (>10 mg/L). Ferulic acid, however, was not converted to the expected stilbene product, isorhapontigenin. Substitution of 4CL1 with a homologous enzyme, 4CL4, with a preference for ferulic acid over 4-coumaric acid, had no effect on the conversion of ferulic acid. Accumulation of tri- and tetraketide lactones from ferulic acid, regardless of the CoA-ligase expressed in E. coli, suggests that STS cannot properly accommodate and fold the tetraketide intermediate to the corresponding stilbene structure. CONCLUSION: Phenylpropionic acids, such as 4-coumaric acid and caffeic acid, can be efficiently converted to stilbene compounds by recombinant E. coli cells expressing plant biosynthetic genes. Optimization of precursor conversion and cyclization of the bulky ferulic acid precursor by host metabolic engineering and protein engineering may afford the synthesis of even more structurally diverse stilbene compounds. [Abstract/Link to Full Text]

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