Combined experimental and theoretical study of Type-II toxin-antitoxin system response to antibiotics

Bacterial Type-II toxin-antitoxin (TA) systems, including kacAT in Klebsiella pneumoniae, respond to antibiotics. We investigated kacAT’s regulation relevant to antibiotic persistence, which refers to the survival of antibiotic exposure by dormant bacterial cells. Elevated toxin levels may induce dormancy. KacAT complex binds and represses the kacAT promoter cooperatively, leading to highly non-linear negative feedback. Antibiotics increase transcription of the kacA and kacT genes by inducing KacA degradation and consequently reducing the KacA:KacT ratio. Our model reproduced experimental findings, explaining increased kacAT transcription and reduced [KacA]:[KacT] ratio. Interestingly, KacAT overexpression induces antibiotic stress tolerance, while deleting kacAT has no effect, which our model can also explain. KacAT, therefore, cannot induce spontaneous (in the absence of antibiotics) persister formation. Earlier theoretical models, which predicted spontaneous persistence in Type-II TA systems, assumed the cooperative action of multiple TA systems. Our bioinformatics analysis, however, reveals a limited occurrence of multiple TA instances within clades and that cross-talk between clades is disfavored. These challenges the assumption of cooperativity in TA action, possibly explaining the absence of spontaneous persister generation in kacAT.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202

Expression, Purification and Bioactivities Analysis of Recombinant Active Peptide from Shark Liver

The Active Peptide from Shark Liver (APSL) was expressed in E. coli BL21 cells. The cDNA encoding APSL protein was obtained from shark regenerated hepatic tissue by RT-PCR, then it was cloned in the pET-28a expression vector. The expressed fusion protein was purified by Ni-IDA affinity chromatography. SDS-PAGE and HPLC analysis showed the purity of the purified fusion protein was more than 98%. The recombinant APSL (rAPSL) was tested for its biological activity both in vitro, by its ability to improve the proliferation of SMMC7721 cells, and in vivo, by its significant protective effects against acute hepatic injury induced by CCl4 and AAP (acetaminophen) in mice. In addition, the rAPSL could decrease the blood glucose concentration of mice with diabetes mellitus induced by alloxan. Paraffin sections of mouse pancreas tissues showed that rAPSL (3 mg/kg) could effectively protect mouse islets from lesions induced by alloxan, which indicated its potential application in theoretical research and industry

mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes

mGenomeSubtractor performs an mpiBLAST-based comparison of reference bacterial genomes against multiple user-selected genomes for investigation of strain variable accessory regions. With parallel computing architecture, mGenomeSubtractor is able to run rapid BLAST searches of the segmented reference genome against multiple subject genomes at the DNA or amino acid level within a minute. In addition to comparison of protein coding sequences, the highly flexible sliding window-based genome fragmentation approach offered can be used to identify short unique sequences within or between genes. mGenomeSubtractor provides powerful schematic outputs for exploration of identified core and accessory regions, including searches against databases of mobile genetic elements, virulence factors or bacterial essential genes, examination of G+C content and binucleotide distribution bias, and integrated primer design tools. mGenomeSubtractor also allows for the ready definition of species-specific gene pools based on available genomes. Pan-genomic arrays can be easily developed using the efficient oligonucleotide design tool. This simple high-throughput in silico ‘subtractive hybridization’ analytical tool will support the rapidly escalating number of comparative bacterial genomics studies aimed at defining genomic biomarkers of evolutionary lineage, phenotype, pathotype, environmental adaptation and/or disease-association of diverse bacterial species. mGenomeSubtractor is freely available to all users without any login requirement at: http://bioinfo-mml.sjtu.edu.cn/mGS/

ArrayOme: a program for estimating the sizes of microarray-visualized bacterial genomes

ArrayOme is a new program that calculates the size of genomes represented by microarray-based probes and facilitates recognition of key bacterial strains carrying large numbers of novel genes. Protein-coding sequences (CDS) that are contiguous on annotated reference templates and classified as ‘Present’ in the test strain by hybridization to microarrays are merged into ICs (ICs). These ICs are then extended to account for flanking intergenic sequences. Finally, the lengths of all extended ICs are summated to yield the ‘microarray-visualized genome (MVG)’ size. We tested and validated ArrayOme using both experimental and in silico-generated genomic hybridization data. MVG sizing of five sequenced Escherichia coli and Shigella strains resulted in an accuracy of 97–99%, as compared to true genome sizes, when the comprehensive ShE.coli meta-array gene sequences (6239 CDS) were used for in silico hybridization analysis. However, the E.coli CFT073 genome size was underestimated by 14% as this meta-array lacked probes for many CFT073 CDS. ArrayOme permits rapid recognition of discordances between PFGE-measured genome and MVG sizes, thereby enabling high-throughput identification of strains rich in novel genes. Gene discovery studies focused on these strains will greatly facilitate characterization of the global gene pool accessible to individual bacterial species

Electronic structure of Fe1.04(Te0.66Se0.34)

We report the electronic structure of the iron-chalcogenide superconductor, Fe1.04(Te0.66Se0.34), obtained with high resolution angle-resolved photoemission spectroscopy and density functional calculations. In photoemission measurements, various photon energies and polarizations are exploited to study the Fermi surface topology and symmetry properties of the bands. The measured band structure and their symmetry characters qualitatively agree with our density function theory calculations of Fe(Te0.66Se0.34), although the band structure is renormalized by about a factor of three. We find that the electronic structures of this iron-chalcogenides and the iron-pnictides have many aspects in common, however, significant differences exist near the Gamma-point. For Fe1.04(Te0.66Se0.34), there are clearly separated three bands with distinct even or odd symmetry that cross the Fermi energy (EF) near the zone center, which contribute to three hole-like Fermi surfaces. Especially, both experiments and calculations show a hole-like elliptical Fermi surface at the zone center. Moreover, no sign of spin density wave was observed in the electronic structure and susceptibility measurements of this compound.Comment: 7 pages, 9 figures. submitted to PRB on November 15, 2009, and accepted on January 6, 201

CAE Analysis of Primary Shaft Systems in Great Five-Axis Turning-Milling Complex CNC Machine

The design and analysis of primary shaft systems by using the commercial software of computer aided engineering (CAE) in the heavy industry field are novel. The research purpose is to provide the computational results for the construction of primary shaft systems in the five-axis turning-milling complex machine. The CAE with commercial software is used to analyze the linear static construction, stress and deformation for primary shaft systems in the great five-axis turning-milling complex computer numerical control (CNC) machine. It is desirable to compute and find the most external loads of primary shaft systems in the CNC machine which can be used to operate in safety condition and under its yield stress value of materials. The linear computational results of static stresses and displacements in primary shaft systems are obtained and investigated with the commercial SOLIDWORKS® 2014 simulation module

Adolescent Exercise in Association with Mortality from All Causes, Cardiovascular Disease, and Cancer among Middle-Aged and Older Chinese Women

Background: Little is known regarding the role of early-life exercise, a potentially modifiable factor, in long-term adult morbidity and mortality. We utilized the Shanghai Women\u27s Health Study (SWHS) to investigate adolescent exercise in association with cancer, cardiovascular disease (CVD), and all-cause mortality among middle-aged and older women. Methods: The SWHS is a prospective cohort of 74,941 Chinese women ages 40 to 70 years recruited from 1996 to 2000. In-person interviews at enrollment assessed adolescent and adult exercise history, medical and reproductive history, and other lifestyle and socioeconomic (SES) factors. Mortality follow-up occurs via annual linkage to the Shanghai Vital Statistics Registry. Adjusted hazard ratios (HR) and 95% confidence intervals (CI) were derived from Cox regression models. Results: Adjusting for birth year and other adolescent factors, adolescent exercise was associated with reduced risk of cancer, CVD, and total mortality [HRs (95% CI), 0.83 (0.72–0.95), 0.83 (0.70–0.98), and 0.78 (0.71–0.85), respectively for ≤1.33 hours (h)/week, and 0.83 (0.74–0.93), 0.62 (0.53–0.72), and 0.71 (0.66–0.77), respectively for \u3e1.33 h/week (reference = none)]. Results were attenuated after adjustment for adult SES and lifestyle factors. Participation in sports teams was inversely associated with cancer mortality [HR (95% CI), 0.86 (0.76–0.97)]. Joint adolescent and adult exercise was associated with reduced risk of all-cause, CVD, and cancer mortality [HRs (95% CIs), 0.80 (0.72–0.89), 0.83 (0.69–1.00), and 0.87 (0.74–1.01), respectively], adjusting for adult/adolescent factors, and adolescence exercise only was inversely associated with cancer mortality [HR (95% CI), 0.84 (0.71–0.98)]. Conclusions: Adolescent exercise participation, independent of adult exercise, was associated with reduced risk of cancer, CVD, and all-cause mortality. Impact: Results support promotion of exercise in adolescence to reduce mortality in later life

Monogamous property of generalized W states in three-qubit systems in terms of relative entropy of entanglement

Because of the difficulty in getting the analytic formula of relative entropy of entanglement, it becomes troublesome to study the monogamy relations of relative entropy of entanglement for three-qubit pure states. However, we find that all generalized W states have the monogamous property for relative entropy of entanglement by calculating the relative entropy of entanglement for the reduced states of the generalized W states in three-qubit systems.Comment: 9 pages, 1 figur