The Electromotive Protein Prestin as a Sensitive Core of the Fluorescent Voltage Indicator

Russian Journal of Bioorganic Chemistry - In this study, we first used prestin, an electromotive protein of the mammalian auditory analyzer, as a voltage-sensitive core of a genetically encoded...     

An Adiabatic Calorimetry Method to Determine the Thermodynamic Characteristics of Cryoprotectants

Biophysics - Abstract—The efficiency of cryoprotectants used to protect cells from damage is usually evaluated by the changes in vital cell parameters after a freezing–thawing cycle....     

The Generation of Superoxide Radicals by Cardiac Mitochondria and the Antioxidant Effect of the Water-Soluble Form of Ubiquinol-10

Biophysics - We have studied the effect of the water-soluble form of ubiquinol-10 (CoQ10-H2) on the processes of electron transport, oxidative phosphorylation, and the formation of reactive oxygen...     

青藏高原丽蝇科昆虫物种多样性初探

本文从种数、特有物种和区系构成等角度分析了青藏高原丽蝇科昆虫的物种多样性。青藏高原已知丽蝇5亚科35属120种,占中国已知种数的44.28%,其中特有种55种,占该地区总种数的45.83%;区系构成以特有种、古北界 东洋界共同种及典型的东洋界种和古北界种为主,但澳洲界、新北界、非洲界和新热带界共同种也占一定比例。文中讨论了该地区特有种丰富的原因及地质历史环境对其的影响,分析了区系构成中各种区系成分的比例及形成原因。     

Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes

Plasmids are mobile genetic elements that play a key role in microbial ecology and evolution by mediating horizontal transfer of important genes, such as antimicrobial resistance genes. Many microbial genomes have been sequenced by short read sequencers and have resulted in a mix of contigs that derive from plasmids or chromosomes. New tools that accurately identify plasmids are needed to elucidate new plasmid-borne genes of high biological importance. We have developed Deeplasmid, a deep learning tool for distinguishing plasmids from bacterial chromosomes based on the DNA sequence and its encoded biological data. It requires as input only assembled sequences generated by any sequencing platform and assembly algorithm and its runtime scales linearly with the number of assembled sequences. Deeplasmid achieves an AUC–ROC of over 89%, and it was more accurate than five other plasmid classification methods. Finally, as a proof of concept, we used Deeplasmid to predict new plasmids in the fish pathogen Yersinia ruckeri ATCC 29473 that has no annotated plasmids. Deeplasmid predicted with high reliability that a long assembled contig is part of a plasmid. Using long read sequencing we indeed validated the existence of a 102 kb long plasmid, demonstrating Deeplasmid''s ability to detect novel plasmids.     

Maximum antigen diversification in a lyme bacterial population and evolutionary strategies to overcome pathogen diversity

Natural populations of pathogens and their hosts are engaged in an arms race in which the pathogens diversify to escape host immunity while the hosts evolve novel immunity. This co-evolutionary process poses a fundamental challenge to the development of broadly effective vaccines and diagnostics against a diversifying pathogen. Based on surveys of natural allele frequencies and experimental immunization of mice, we show high antigenic specificities of natural variants of the outer surface protein C (OspC), a dominant antigen of a Lyme Disease-causing bacterium (Borrelia burgdorferi). To overcome the challenge of OspC antigenic diversity to clinical development of preventive measures, we implemented a number of evolution-informed strategies to broaden OspC antigenic reactivity. In particular, the centroid algorithm—a genetic algorithm to generate sequences that minimize amino-acid differences with natural variants—generated synthetic OspC analogs with the greatest promise as diagnostic and vaccine candidates against diverse Lyme pathogen strains co-existing in the Northeast United States. Mechanistically, we propose a model of maximum antigen diversification (MAD) mediated by amino-acid variations distributed across the hypervariable regions on the OspC molecule. Under the MAD hypothesis, evolutionary centroids display broad cross-reactivity by occupying the central void in the antigenic space excavated by diversifying natural variants. In contrast to vaccine designs based on concatenated epitopes, the evolutionary algorithms generate analogs of natural antigens and are automated. The novel centroid algorithm and the evolutionary antigen designs based on consensus and ancestral sequences have broad implications for combating diversifying pathogens driven by pathogen–host co-evolution.Subject terms: Population genetics, Bacterial genetics     

Radiation mapping of the short arm of swine chromosome 2

In recent years, maps of mammalian genomes have been acquiring increasingly higher resolution. Integration of maps of different types has become possible. As a tool in integrating maps of mammalian genomes of different types, high-resolution mapping with radiation-induced hybrids (RH) is used. Here, we present an RH6000 map of the short arm of porcine chromosome 2. The map contains 15 microsatellites and five genes (for parathyroid hormone, lactate dehydrogenase A, myogenic factor, follicle-stimulating hormone beta, and calpain I). The RH panel was obtained on the basis of a hybrid cell line bearing the single porcine chromosome 2 against the background of mink chromosomes. The mean frequency of preserving markers examined in the panel was 18.3%. Integration of four genes in the panel and a comparison of gene order in homologous regions of human and porcine chromosomes are presented.     

A viscosimetric study of thermally induced release of ds-DNA from Un phage

The thermally induced ejection of DNA from the head of the Un phage was studied by viscosimetry, pH was used as a variable external factor. The results obtained suggest that the infection of the bacterium by the phage occurs in the pH range 6-10 rather than in the acidic medium (pH 4-5) because the infection can take place only if the DNA is completely ejected from the phage head. It was shown that the ejection of DNA upon dilution of the initial concentration of the phage depends on the time required for the equilibrium of the phage suspension in the corresponding buffer solution to be established after which the measurements can be performed. In our experiments, this time interval was 24 h.