Effective epitope identification employing phylogenetic,mutational variability,sequence entropy,and correlated mutation analysis targeting NS5B protein of hepatitis C virus: from bioinformatics to therapeutics

Hepatitis C virus (HCV) is considered as a foremost cause affecting numerous human liver‐related disorders. An effective immuno‐prophylactic measure (like stable vaccine) is still unavailable for HCV. We perform an in silico analysis of nonstructural protein 5B (NS5B) based CD4 and CD8 epitopes that might be implicated in improvement of treatment strategies for efficient vaccine development programs against HCV. Here, we report on effective utilization of knowledge obtained from multiple sequence alignment and phylogenetic analysis for investigation and evaluation of candidate epitopes that have enormous potential to be used in formulating proficient vaccine, embracing multiple strains prevalent among major geographical locations. Mutational variability data discussed herein focus on discriminating the region under active evolutionary pressure from those having lower mutational potential in existing experimentally verified epitopes, thus, providing a concrete framework for designing an effective peptide‐based vaccine against HCV. Additionally, we measured entropy distribution in NS5B residues and pinpoint the positions in epitopes that are more susceptible to mutations and, thus, account for virus strategy to evade the host immune system. Findings from this study are expected to add more details on the sequence and structural aspects of NS5B protein, ultimately facilitating our understanding about the pathophysiology of HCV and assisting advance studies on the function of NS5B antigen on the epitope level. We also report on the mutational crosstalk between functionally important coevolving residues, using correlated mutation analysis, and identify networks of coupled mutations that represent pathways of allosteric communication inside and among NS5B thumb, finger, and palm domains. Copyright © 2015 John Wiley & Sons, Ltd.     

Inferring causal factors for a declining population of bottlenose dolphins via temporal symmetry capture–recapture modeling

We applied temporal symmetry capture–recapture (TSCR) models to assess the strength of evidence for factors potentially responsible for population decline in bottlenose dolphins (Tursiops truncatus) in Doubtful Sound, New Zealand from 1995 to 2008. Model selection was conducted to estimate recruitment and population growth rates. There were similar levels of support for three different models, each reflecting distinct trends in recruitment. Modeling yielded low overall estimates of recruitment (0.0249, 95% CI: 0.0174–0.0324) and population growth rate (0.9642, 95% CI: 0.9546–0.9737). The TSCR rate of population decline was consistent with an estimate derived from trends in abundance (lambda = 0.9632, 95% CI: 0.9599–0.9665). The TSCR model selection confirmed the influence of a decline in the survival of calves (<1 yr old) since 2002 for population trends. However, TSCR population growth rates did not exceed 1 in any year between 1995 and 2008, indicating the population was declining prior to 2002. A separate reduction in juvenile survival (1–3 yr old) prior to 2002 was identified as a likely contributing factor in the population decline. Thus, TSCR modeling indicated the potential cause of the population decline in Doubtful Sound: cumulative impacts on individuals <3 yr old resulting in a reduced recruitment.     

Developing the readiness to alter sun-protective behaviour questionnaire (RASP-B)

Background: Australia has the highest incidence of skin cancer of any country in the world, even though the risk of contracting the disease can be lowered considerably by engaging in appropriate sun-protective behaviours. We aimed to construct and validate a questionnaire to assess the readiness of a group of mostly young people to change their levels of sun-protective behaviour by assigning them to a stage of change based on the transtheoretical model of behaviour change. Method: A sample of 122 undergraduate students in Queensland, Australia completed the readiness to alter sun-protective behaviour questionnaire (the RASP-B, a 12-item questionnaire about their attitudes toward sun-protection), in addition to a short questionnaire about their current sun-protective behaviours. Results: A principal component analysis revealed a clear three-factor structure corresponding to the precontemplation, contemplation, and action stages of the transtheoretical model. Participants in the action stage reported engaging in significantly higher levels of sun-protective behaviour than participants in the earlier precontemplation and contemplation stages. These behaviours included avoiding exposure to direct sunlight by wearing long-sleeved clothing and remaining in the shade or indoors. Participants in the different stages reported no significant differences in the reported frequency of sunscreen use, although respondents across all three stages reported using sunscreen infrequently. Conclusion: The RASP-B requires approximately 5 min to complete, can be self-administered and has satisfactory psychometric properties, and thus has utility in primary health care settings where time and client–practitioner contact are often limited.     

Patterns of reproductive‐mode evolution in Old World tree frogs (Anura,Rhacophoridae)

The Old World tree frogs (Anura: Rhacophoridae), with 387 species, display a remarkable diversity of reproductive modes – aquatic breeding, terrestrial gel nesting, terrestrial foam nesting and terrestrial direct development. The evolution of these modes has until now remained poorly studied in the context of recent phylogenies for the clade. Here, we use newly obtained DNA sequences from three nuclear and two mitochondrial gene fragments, together with previously published sequence data, to generate a well‐resolved phylogeny from which we determine major patterns of reproductive‐mode evolution. We show that basal rhacophorids have fully aquatic eggs and larvae. Bayesian ancestral‐state reconstructions suggest that terrestrial gel‐encapsulated eggs, with early stages of larval development completed within the egg outside of water, are an intermediate stage in the evolution of terrestrial direct development and foam nesting. The ancestral forms of almost all currently recognized genera (except the fully aquatic basal forms) have a high likelihood of being terrestrial gel nesters. Direct development and foam nesting each appear to have evolved at least twice within Rhacophoridae, suggesting that reproductive modes are labile and may arise multiple times independently. Evolution from a fully aquatic reproductive mode to more terrestrial modes (direct development and foam nesting) occurs through intermediate gel nesting ancestral forms. This suggests that gel nesting is not only a possible transitional state for the evolution of terrestriality, but also that it is a versatile reproductive mode that may give rise to other terrestrial reproductive modes. Evolution of foam nesting may have enabled rhacophorids to lay a larger number of eggs in more open and drier habitats, where protection from desiccation is important. Terrestrial direct development allows frogs to lay eggs independent of bodies of water, in a diversity of humid habitats, and may represent a key innovation that facilitated the evolution of nearly half of all known rhacophorid species.     

LC/ESI-MS/MS detection of FAs by charge reversal derivatization with more than four orders of magnitude improvement in sensitivity

Quantitative analysis of fatty acids (FAs) is an important area of analytical biochemistry. Ultra high sensitivity FA analysis usually is done with gas chromatography of pentafluorobenzyl esters coupled to an electron-capture detector. With the popularity of electrospray ionization (ESI) mass spectrometers coupled to liquid chromatography, it would be convenient to develop a method for ultra high sensitivity FA detection using this equipment. Although FAs can be analyzed by ESI in negative ion mode, this method is not very sensitive. In this study, we demonstrate a new method of FA analysis based on conversion of the carboxylic acid to an amide bearing a permanent positive charge, N-(4-aminomethylphenyl)pyridinium (AMPP) combined with analysis on a reverse-phase liquid chromatography column coupled to an ESI mass spectrometer operating in positive ion mode. This leads to an ∼60,000-fold increase in sensitivity compared with the same method carried out with underivatized FAs. The new method is about 10-fold more sensitive than the existing method of gas chromatography/electron-capture mass spectrometry of FA pentafluorobenzyl esters. Furthermore, significant fragmentation of the precursor ions in the nontag portion improves analytical specificity. We show that a large number of FA molecular species can be analyzed with this method in complex biological samples such as mouse serum.     

The effect of explosive blast loading on human neuroblastoma cells

Diagnosis of mild to moderate traumatic brain injury is challenging because brain tissue damage progresses slowly and is not readily detectable by conventional imaging techniques. We have developed a novel in vitro model to study primary blast loading on dissociated neurons using nitroamine explosives such as those used on the battlefield. Human neuroblastoma cells were exposed to single and triple 50-psi explosive blasts and single 100-psi blasts. Changes in membrane permeability and oxidative stress showed a significant increase for the single and triple 100-psi blast conditions compared with single 50-psi blast and controls.     

In vitro identification and characterisation of iron chelating catechol-containing natural products and derivatives

BioMetals - Iron is an essential component for multiple biological processes. Its regulation within the body is thus tightly controlled. Dysregulation of iron levels within the body can result in...