The effects of endothelial lipase gene (LIPG) variants on inflammation marker levels and atherosclerosis development

Atherosclerosis is a major pathological process related with several important adverse vascular events including coronary artery disease, stroke, and peripheral arterial disease. Endothelial lipase is an enzyme the activity of which affects all of lipoproteins, whereas HDL is the main substrate. The purpose of our study was to investigate the effects of endothelial lipase gene polymorphism and inflammation markers (CRP, IL-1β, IL-6, IL-8 and TNF-α) in the atherosclerosis. 104 patients with atherosclerosis and 76 healthy individuals were included in the study. LIPG ?584C/T polymorphism gene polymorphisms were assessed with PCR–RFLP method. The serum CRP levels were measured by turbidimetric method using a biochemistry autoanalyzer, whereas serum IL-1β, IL-6, IL-8, TNF-α levels were determined by enzyme-linked immunosorbent assay. In this study, we found that the frequencies of TC genotype are more prevalent in patients than controls. We found a statistically significant difference of IL-6 levels between patient and control group. Our findings suggest that T allele might play a potential role in the susceptibility to atherogenesis in the Turkish population.     

Investigation of major gene for milk yield, milking speed, dry matter intake, and body weight in dairy cattle

The main aim of this study was to determine if there exist any major gene for milk yield (MY), milking speed (MS), dry matter intake (DMI), and body weight (BW) recorded at various stages of lactation in first-lactation dairy cows (2543 observations from 320 cows) kept at the research farm of the Swiss Federal Institute of Technology between April 1994 and April 2004. Data were modelled based a simple repeatability covariance structure and analysed by using Bayesian segregation analyses. Gibbs sampling was used to make statistical inferences on posterior distributions; inferences were based on a single run of the Markov chain for each trait with 500,000 samples, with each 10th sample collected because of the high correlation among the samples. The posterior mean (+/-SD) of major gene variance was 2.61 (+/-2.46) for MY, 0.83 (+/-1.26) for MS, 4.37 (+/-2.34) for DMI, and 2056.43 (+/-665.67) for BW. Highest posterior density regions for 3 of the 4 traits did not include 0 (except MS), which supported the evidence for major gene. With additional tests for agreement with Mendelian transmission probabilities, we could only confirm the existence of a major gene for MY, but not for MS, DMI, and BW. Expected Mendelian transmission probabilities and their model fits were also compared.     

Comparison of partial excision with simple section of the transverse carpal ligament in the treatment of carpal tunnel syndrome

In the surgical treatment of carpal tunnel syndrome, debate has commonly focused on whether decompression should be performed by open or blind techniques. Contrarily, the goal of the present study was to determine whether instead of simple section, partial excision of the transverse carpal ligament has contributed to better results. Because complete healing of the transverse carpal ligament observed during reoperations has been reported elsewhere, the charts of 75 carpal tunnel syndrome patients who had been treated with open technique at Dokuz Eylül University were reviewed. Statistical analysis was performed using the Fisher's exact test and Student's t test when appropriate. Thirty-five patients had been treated with simple section of the transverse carpal ligament, whereas 40 had been treated with partial excision. Internal neurolysis was also performed in 19 of the patients, 11 of whom were treated with partial excision. The average follow-up time was 3.8 years. The comparisons regarding the overall operative outcomes did not show any significant difference between the two different techniques of releasing the transverse carpal ligament. In patients treated without neurolysis, results of partial excision of the transverse carpal ligament improved when compared with those of simple section, but this superiority was not statistically significant. There seemed to be statistically higher reoperation rates and worse outcomes after neurolysis (p < 0.05). Reoperation was required in eight patients (11 percent). Five of the patients who underwent reoperation had initially been treated with partial excision and neurolysis, whereas two had been treated with simple section and neurolysis. Another patient who had undergone reoperation had initially undergone only simple section. The mean time to return to work or daily activities did not differ between the types of applied technique for releasing the transverse carpal ligament. However, neurolysis lengthened these periods significantly when performed (p < 0.05). In the present study, partial excision of the transverse carpal ligament without adding neurolysis offered relatively better results than simple section. Verification of this finding endoscopically, if applicable, may improve the success rate of surgical therapy in patients with carpal tunnel syndrome.     

Enzyme Inhibition and Antioxidant Activities of Asparagus officinalis L. and Analysis of Its Phytochemical Content by LC/MS/MS

In the study, water, ethanol, methanol, dichloromethane, and acetone extracts of Asparagus officinalis L. were obtained by maceration. DPPH⋅, ABTS⋅⁺, FRAP, and CUPRAC methods determined the antioxidant capacities of all extracts. Moreover, the in vitro effects of extracts on acetylcholinesterase (AChE), butyrylcholinesterase (BChE), carbonic anhydrase (CA)-I, CA-II and α-Glycosidase were investigated. At a 10 μg/ml concentration, the extract with the highest Fe³⁺ reduction capacity was ethanol (AE), and the extract with the highest Cu²⁺ reduction capacity was acetone (AA). AE for AChE (IC₅₀=21.19 μg/ml) and α-Glycosidase (IC₅₀: 70.00 μg/ml), methanol (AM) for BChE (IC₅₀=17.33 μg/ml), CA−I and II (IC₅₀=79.65 and 36.09 μg/ml, respectively) showed the most potent inhibition effect. The content analysis of acetone extract was performed with LC/MS-MS, the first three phytochemicals found most were p-Coumaric acid, rutin, and 4-hydroxybenzoic acid (284.29±3.97, 135.39±8.19, and 102.06±5.51 μg analyte/g extract, respectively).     

Expression of regulatory receptors on γδ T Cells and their cytokine production in Behcet's disease

Introduction

Behcet''s disease (BD) is a multi-systemic disorder with muco-cutaneous, ocular, arthritic, vascular or central nervous system involvement. The role of γδ T cells is implicated in BD. The activation status of γδ T cells and their cytokine secretion against phosphoantigens are evaluated in BD.

Methods

NKG2A, NKG2C, NKG2D, CD16 and CCR7 molecules on γδ T cells were analyzed in 70 BD, 27 tuberculosis (TB) patients and 26 healthy controls (HC). Peripheral γδ T cells were expanded with a phosphoantigen (BrHPP) and IL-2, restimulated with BrHPP and a TLR3 ligand, and cytokine production was measured.

Results

γδ T cells were not increased in both BD and TB patients, but the proportions of TCRVδ2⁺ T cells were lower (58.9 and 50.7 vs. 71.7%, P = 0.04 and P = 0.005) compared to HC. Higher proportion of TCRVδ2⁺ T cells were CD16⁺ (26.2 and 33.9 vs. 16.6%, P = 0.02 and P = 0.001) and CCR7^- (32.2 and 27.9 vs. 17.7%, P < 0.0001 and P = 0.014) in BD and TB patients compared to HC. NKG2C⁺ γδ⁺ T cells were relatively increased (0.5 and 0.6 vs. 0.3%, P = 0.008 and 0.018), whereas NKG2D positivity was decreased in patients with BD and TB (77.7 and 75.8 vs. 87.5%, P = 0.001 and 0.004). Expansion capacity of γδ T cells in BD and TB as well as production of IL-13, IFN-γ, granulocyte monocyte colony stimulating factor (GM-CSF), TNF-α, CCL4 and CCL5 in BD was lower compared to HC, when restimulated by TLR3 ligand and BrHPP.

Conclusion

The changes on γδ T cells of BD as well as TB patients implicate that γδ T cells have already been exposed to regulatory effects, which changed their activity. Lower cytokine response of γδ T cells implicates down modulation of these cells in BD.     

Structural and electrostatic characterization of Pariacoto virus: Implications for viral assembly

We present the first all‐atom model for the structure of a T = 3 virus, pariacoto virus (PaV), which is a nonenveloped, icosahedral RNA virus and a member of the Nodaviridae family. The model is an extension of the crystal structure, which reveals about 88% of the protein structure but only about 35% of the RNA structure. New modeling methods, combining coarse‐grained and all‐atom approaches, were required for developing the model. Evaluation of alternative models confirms our earlier observation that the polycationic N‐ and C‐terminal tails of the capsid proteins must penetrate deeply into the core of the virus, where they stabilize the structure by neutralizing a substantial fraction of the RNA charge. This leads us to propose a model for the assembly of small icosahedral RNA viruses: nonspecific binding of the protein tails to the RNA leads to a collapse of the complex, in a fashion reminiscent of DNA condensation. The globular protein domains are excluded from the condensed phase but are tethered to it, so they accumulate in a shell around the condensed phase, where their concentration is high enough to trigger oligomerization and formation of the mature virus. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 530–538, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

VitAL: Viterbi Algorithm for de novo Peptide Design

Background

Drug design against proteins to cure various diseases has been studied for several years. Numerous design techniques were discovered for small organic molecules for specific protein targets. The specificity, toxicity and selectivity of small molecules are hard problems to solve. The use of peptide drugs enables a partial solution to the toxicity problem. There has been a wide interest in peptide design, but the design techniques of a specific and selective peptide inhibitor against a protein target have not yet been established.

Methodology/Principal Findings

A novel de novo peptide design approach is developed to block activities of disease related protein targets. No prior training, based on known peptides, is necessary. The method sequentially generates the peptide by docking its residues pair by pair along a chosen path on a protein. The binding site on the protein is determined via the coarse grained Gaussian Network Model. A binding path is determined. The best fitting peptide is constructed by generating all possible peptide pairs at each point along the path and determining the binding energies between these pairs and the specific location on the protein using AutoDock. The Markov based partition function for all possible choices of the peptides along the path is generated by a matrix multiplication scheme. The best fitting peptide for the given surface is obtained by a Hidden Markov model using Viterbi decoding. The suitability of the conformations of the peptides that result upon binding on the surface are included in the algorithm by considering the intrinsic Ramachandran potentials.

Conclusions/Significance

The model is tested on known protein-peptide inhibitor complexes. The present algorithm predicts peptides that have better binding energies than those of the existing ones. Finally, a heptapeptide is designed for a protein that has excellent binding affinity according to AutoDock results.     

Vibrotactile thresholds of the Non-Pacinian I channel: II. Predicting the effects of contactor location on the phalanx

The firing-rate-based population model for rapidly-adapting (RA) mechanoreceptive fibers by Gü?lü and Bolanowski is extended by including temporal-response properties of RA fibers. This representation allows for the generation of action-potential (spike) times for each fiber when a sinusoidal, steady-state stimulus is applied onto the skin. Signal detection theory was used to predict human psychophysical thresholds. Specifically, the effects of sensorineural innervation pattern, stimulus-contactor location and selected decision rules on the model predictions were studied. The predicted thresholds were lowest when the decision rule was one spike and highest when many active fibers were required for detection. These predictions were empirically tested by measuring vibrotactile thresholds of the Non-Pacinian I (NP I) channel, which required the special techniques discussed in the preceding article. Although the model predicted thresholds to decrease distally due to the known innervation density which is higher distally, the thresholds of the NP I psychophysical channel were found to be approximately constant (20-25 dB re 1 microm peak amplitude) from the proximal site on the terminal phalanx to the most distal portion. Interestingly, the mechanical impedance of the skin was found not to be constant along the proximo-distal axis. This latter result implies that the space-invariant mechanical attenuation function used in the model may not be valid at every location on the fingertip. Because of this, the discrepancy between the model's predictions and the psychophysical results may be reconciled.     

Effects of glutamine on growth performance,nutrient content,fatty acid profile,and blood parameters of rainbow trout (Oncorhynchus mykiss)

In this study, different amounts of glutamine were added to the diet of rainbow trout, and they were then fed for a period of 90 days. The current research investigated the effects of glutamine on various aspects of rainbow trout, including growth performance, condition factor, viscerosomatic index, hepatosomatic index, carcass composition, fatty acid profile, hematological parameters, and biochemical parameters. The study's findings revealed that adding glutamine to the diet of rainbow trout had a beneficial impact on their growth features. The rainbow trout group that was fed a 2% concentration of glutamine experienced the most notable increase in growth rate. A statistically significant difference in growth was observed among all groups (p < 0.05). Adding glutamine to the diet increased the amount of protein and decreased the fat content in the flesh of the fish. Glutamine exerted an influence on the blood and biochemistry parameters of fish, as well as their fatty acid composition. In conclusion, the inclusion of glutamine in the diet of fish could potentially enhance their immune system, improve the quality of their muscles, and enhance their growth performance.     

Spatiotemporally controlled cardiac conduction block using high-frequency electrical stimulation

Background

Methods for the electrical inhibition of cardiac excitation have long been sought to control excitability and conduction, but to date remain largely impractical. High-amplitude alternating current (AC) stimulation has been known to extend cardiac action potentials (APs), and has been recently exploited to terminate reentrant arrhythmias by producing reversible conduction blocks. Yet, low-amplitude currents at similar frequencies have been shown to entrain cardiac tissues by generation of repetitive APs, leading in some cases to ventricular fibrillation and hemodynamic collapse in vivo. Therefore, an inhibition method that does not lead to entrainment – irrespective of the stimulation amplitude (bound to fluctuate in an in vivo setting) – is highly desirable.

Methodology/Principal Findings

We investigated the effects of broader amplitude and frequency ranges on the inhibitory effects of extracellular AC stimulation on HL-1 cardiomyocytes cultured on microelectrode arrays, using both sinusoidal and square waveforms. Our results indicate that, at sufficiently high frequencies, cardiac tissue exhibits a binary response to stimulus amplitude with either prolonged APs or no effect, thereby effectively avoiding the risks of entrainment by repetitive firing observed at lower frequencies. We further demonstrate the ability to precisely define reversible local conduction blocks in beating cultures without influencing the propagation activity in non-blocked areas. The conduction blocks were spatiotemporally controlled by electrode geometry and stimuli duration, respectively, and sustainable for long durations (300 s).

Conclusion/Significance

Inhibition of cardiac excitation induced by high-frequency AC stimulation exhibits a binary response to amplitude above a threshold frequency, enabling the generation of reversible conduction blocks without the risks of entrainment. This inhibition method could yield novel approaches for arrhythmia modeling in vitro, as well as safer and more efficacious tools for in vivo cardiac mapping and radio-frequency ablation guidance applications.