Amino acid size, charge, hydropathy indices and matrices for protein structure analysis

Background  

Prediction of protein folding and specific interactions from only the sequence (ab initio) is a major challenge in bioinformatics. It is believed that such prediction will prove possible if Anfinsen's thermodynamic principle is correct for all kinds of proteins, and all the information necessary to form a concrete 3D structure is indeed present in the sequence.     

Experimental evaluation of the relationship between lethal or non-lethal virulence and transmission success in malaria parasite infections

Background

Theoretical studies suggest that direct and indirect selection have the potential to cause substantial evolutionary change in female mate choice. Similarly, sexual selection is considered a strong force in the evolution of male attractiveness and the exaggeration of secondary sexual traits. Few studies have, however, directly tested how female mate choice and male attractiveness respond to selection. Here we report the results of a selection experiment in which we selected directly on female mating preference for attractive males and, independently, on male attractiveness in the guppy, Poecilia reticulata. We measured the direct and correlated responses of female mate choice and male attractiveness to selection and the correlated responses of male ornamental traits, female fecundity and adult male and female survival.

Results

Surprisingly, neither female mate choice nor male attractiveness responded significantly to direct or to indirect selection. Fecundity did differ significantly among lines in a way that suggests a possible sexually-antagonistic cost to male attractiveness.

Conclusions

The opportunity for evolutionary change in female mate choice and male attractiveness may be much smaller than predicted by current theory, and may thus have important consequences for how we understand the evolution of female mate choice and male attractiveness. We discuss a number of factors that may have constrained the response of female choice and male attractiveness to selection, including low heritabilities, low levels of genetic (co)variation in the multivariate direction of selection, sexually-antagonistic constraint on sexual selection and the "environmental covariance hypothesis".

     

The effect of contrast water therapy on symptoms of delayed onset muscle soreness

This study examined the effect of contrast water therapy (CWT) on the physiological and functional symptoms of delayed onset muscle soreness (DOMS) following DOMS-inducing leg press exercise. Thirteen recreational athletes performed 2 experimental trials separated by 6 weeks in a randomized crossover design. On each occasion, subjects performed a DOMS-inducing leg press protocol consisting of 5 x 10 eccentric contractions (180 seconds recovery between sets) at 140% of 1 repetition maximum (1RM). This was followed by a 15-minute recovery period incorporating either CWT or no intervention, passive recovery (PAS). Creatine kinase concentration (CK), perceived pain, thigh volume, isometric squat strength, and weighted jump squat performance were measured prior to the eccentric exercise, immediately post recovery, and 24, 48, and 72 hours post recovery. Isometric force production was not reduced below baseline measures throughout the 72-hour data collection period following CWT ( approximately 4-10%). However, following PAS, isometric force production (mean +/- SD) was 14.8 +/- 11.4% below baseline immediately post recovery (p < 0.05), 20.8 +/- 15.6% 24 hours post recovery (p < 0.05), and 22.5 +/- 12.3% 48 hours post recovery (p < 0.05). Peak power produced during the jump squat was significantly reduced (p < 0.05) following both PAS (20.9 +/- 13.4%) and CWT (12.8 +/- 8.0%), with the mean reduction in power for PAS being marginally (not significantly) greater than for CWT (effect size = 0.76). Thigh volume measured immediately following CWT was significantly less than PAS. No significant differences in the changes in CK were found; in addition, there were no significant (p > 0.01) differences in perceived pain between treatments. Contrast water therapy was associated with a smaller reduction, and faster restoration, of strength and power measured by isometric force and jump squat production following DOMS-inducing leg press exercise when compared to PAS. Therefore, CWT seems to be effective in reducing and improving the recovery of functional deficiencies that result from DOMS, as opposed to passive recovery.     

Haptoglobin and CCR2 receptor expression in ovarian cancer cells that were exposed to ascitic fluid: Exploring a new role of haptoglobin in the tumoral microenvironment

Haptoglobin (Hp) is an acute-phase protein that is produced by the liver to capture the iron that is present in the blood circulation, thus avoiding its accumulation in the blood. Moreover, Hp has been detected in a wide variety of tissues, in which it performs various functions. In addition, this protein is considered a potential biomarker in many diseases, such as cancer, including ovarian carcinoma; however, its participation in the cancerous processes has not yet been determined. The objective of this work was to demonstrate the expression of Hp and its receptor CCR2 in the ovarian cancer cells and its possible involvement in the process of cell migration through changes in the rearrangement of the actin cytoskeleton using western blot and wound-healing assays and confirming by confocal microscopy. Ovarian cancer cells express both Hp and its receptor CCR2 but only after exposure to ascitic fluid, inducing moderated cell migration. However, when the cells are exposed to exogenous Hp, the expression of CCR2 is induced together with drastic changes in the actin cytoskeleton rearrangement. At the same time, Hp induced cell migration in a much more efficient manner than did ascitic fluid. These effects were blocked when the CCR2 synthetic antagonist RS102895 was used to pretreat the cells. These results suggest that Hp-induced changes in the cell morphology, actin cytoskeleton structure, and migration ability of tumor cells, is possibly “preparing” these cells for the potential induction of the metastatic phenotype.     

An optimized microarray platform for assaying genomic variation in <Emphasis Type="Italic">Plasmodium falciparum</Emphasis> field populations

We present an optimized probe design for copy number variation (CNV) and SNP genotyping in the Plasmodium falciparum genome. We demonstrate that variable length and isothermal probes are superior to static length probes. We show that sample preparation and hybridization conditions mitigate the effects of host DNA contamination in field samples. The microarray and workflow presented can be used to identify CNVs and SNPs with 95% accuracy in a single hybridization, in field samples containing up to 92% human DNA contamination.