An Oxidative Stress Response Mechanism By The Vibrio Cholerae Arcab Two-Component System

Vibrio cholerae, the causative agent of the infectious disease, cholera, is a water-borne pathogen with a dynamic lifestyle across physical environments of different oxygen levels with various sources of oxidative stress. The anaerobic respiratory control (ArcB/A) two-component system is a global regulator that facilitates the transition between different electron transport strategies with respect to the redox environment. Upon sensing a more anoxic quinone pool at the inner membrane, the histidine kinase ArcB activates the response regulator ArcA’s regulatory functions by phosphorylation. ArcA has been reported in Escherichia coli and Salmonella enterica to be important for oxidative stress resistance, yet the mechanism through which ArcA respond to this stress is unknown. Here we report ArcA’s regulatory functions being partially retained in V. cholerae upon oxidative stress. This additional redox-sensing under oxidative stress is dependent on a cysteine residue, C173, in ArcA’s C-terminal DNA-binding domain. C173 is crucial in sustaining in vitro oxidative stress challenges and during colonization of mouse intestines. Phosphorylation state analysis indicates that ArcA phosphorylation is compromised when V. cholerae is challenged by oxidative stress. In vitro biochemical assays reveal that C173- dependent oxidation initiates ArcA binding to DNA containing an ArcA-binding motif. C173- dependent oxidation also promotes ArcA-ArcA interaction, similar to the effect from a microaerobic induction of ArcA. ArcA C173 is conserved in various Gram-negative pathogens. In vitro oxidative stress challenges and human intestinal epithelial cell invasion experiments with S. enterica further underscore the importance of ArcA C173 for bacterial survival. This work uncovers a new post-translational modification, oxidation, in addition to phosphorylation, that serves as an activating signal for ArcA. The redox response from ArcA couples a stress response to other ArcA-mediated transitions for an adaptation to a new environment, demonstrating theintricacy of bacterial stress responses and their close association to basic energy metabolism

Hybrid Data-driven Framework for Shale Gas Production Performance Analysis via Game Theory, Machine Learning and Optimization Approaches

A comprehensive and precise analysis of shale gas production performance is crucial for evaluating resource potential, designing field development plan, and making investment decisions. However, quantitative analysis can be challenging because production performance is dominated by a complex interaction among a series of geological and engineering factors. In this study, we propose a hybrid data-driven procedure for analyzing shale gas production performance, which consists of a complete workflow for dominant factor analysis, production forecast, and development optimization. More specifically, game theory and machine learning models are coupled to determine the dominating geological and engineering factors. The Shapley value with definite physical meanings is employed to quantitatively measure the effects of individual factors. A multi-model-fused stacked model is trained for production forecast, on the basis of which derivative-free optimization algorithms are introduced to optimize the development plan. The complete workflow is validated with actual production data collected from the Fuling shale gas field, Sichuan Basin, China. The validation results show that the proposed procedure can draw rigorous conclusions with quantified evidence and thereby provide specific and reliable suggestions for development plan optimization. Comparing with traditional and experience-based approaches, the hybrid data-driven procedure is advanced in terms of both efficiency and accuracy.Comment: 37 pages, 15 figures, 6 table

Computational Methods for the Pharmacogenetic Interpretation of Next Generation Sequencing Data

Up to half of all patients do not respond to pharmacological treatment as intended. A substantial fraction of these inter-individual differences is due to heritable factors and a growing number of associations between genetic variations and drug response phenotypes have been identified. Importantly, the rapid progress in Next Generation Sequencing technologies in recent years unveiled the true complexity of the genetic landscape in pharmacogenes with tens of thousands of rare genetic variants. As each individual was found to harbor numerous such rare variants they are anticipated to be important contributors to the genetically encoded inter-individual variability in drug effects. The fundamental challenge however is their functional interpretation due to the sheer scale of the problem that renders systematic experimental characterization of these variants currently unfeasible. Here, we review concepts and important progress in the development of computational prediction methods that allow to evaluate the effect of amino acid sequence alterations in drug metabolizing enzymes and transporters. In addition, we discuss recent advances in the interpretation of functional effects of non-coding variants, such as variations in splice sites, regulatory regions and miRNA binding sites. We anticipate that these methodologies will provide a useful toolkit to facilitate the integration of the vast extent of rare genetic variability into drug response predictions in a precision medicine framework

Discovery of Novel Bacterial Cell-Penetrating Phylloseptins in Defensive Skin Secretions of the South American Hylid Frogs, Phyllomedusa duellmani and Phyllomedusa coelestis

Phylloseptin (PS) peptides, derived from South American hylid frogs (subfamily Phyllomedusinae), have been found to have broad-spectrum antimicrobial activities and relatively low haemolytic activities. Although PS peptides have been identified from several well-known and widely-distributed species of the Phyllomedusinae, there remains merit in their study in additional, more obscure and specialised members of this taxon. Here, we report the discovery of two novel PS peptides, named PS-Du and PS-Co, which were respectively identified for the first time and isolated from the skin secretions of Phyllomedusa duellmani and Phyllomedusa coelestis. Their encoding cDNAs were cloned, from which it was possible to deduce the entire primary structures of their biosynthetic precursors. Reversed-phase high-performance liquid chromatography (RP-HPLC) and tandem mass spectrometry (MS/MS) analyses were employed to isolate and structurally-characterise respective encoded PS peptides from skin secretions. The peptides had molecular masses of 2049.7 Da (PS-Du) and 1972.8 Da (PS-Co). They shared typical N-terminal sequences and C-terminal amidation with other known phylloseptins. The two peptides exhibited growth inhibitory activity against E. coli (NCTC 10418), as a standard Gram-negative bacterium, S. aureus (NCTC 10788), as a standard Gram-positive bacterium and C. albicans (NCPF 1467), as a standard pathogenic yeast, all as planktonic cultures. Moreover, both peptides demonstrated the capability of eliminating S. aureus biofilm

Baltikinin: A New Myotropic Tryptophyllin-3 Peptide Isolated from the Skin Secretion of the Purple-Sided Leaf Frog, Phyllomedusa baltea

Here we report the identification of a novel tryptophyllin-3 peptide with arterial smooth muscle relaxation activity from the skin secretion of the purple-sided leaf frog, Phyllomedusa baltea. This new peptide was named baltikinin and had the following primary structure, pGluDKPFGPPPIYPV, as determined by tandem mass spectrometry (MS/MS) fragmentation sequencing and from cloned skin precursor-encoding cDNA. A synthetic replicate of baltikinin was found to have a similar potency to bradykinin in relaxing arterial smooth muscle (half maximal effective concentration (EC50) is 7.2 nM). These data illustrate how amphibian skin secretions can continue to provide novel potent peptides that act through functional targets in mammalian tissues