Phylogenetic detection of horizontal gene transfer during the step-wise genesis of Mycobacterium tuberculosis

<p>Abstract</p> <p>Background</p> <p>In the past decade, the availability of complete genome sequence data has greatly facilitated comparative genomic research aimed at addressing genetic variability within species. More recently, analysis across species has become feasible, especially in genera where genome sequencing projects of multiple species have been initiated. To understand the genesis of the pathogen <it>Mycobacterium tuberculosis </it>within a genus where the majority of species are harmless environmental organisms, we have used genome sequence data from 16 mycobacteria to look for evidence of horizontal gene transfer (HGT) associated with the emergence of pathogenesis. First, using multi-locus sequence analysis (MLSA) of 20 housekeeping genes across these species, we derived a phylogeny that serves as the basis for HGT assignments. Next, we performed alignment searches for the 3989 proteins of <it>M. tuberculosis </it>H37Rv against 15 other mycobacterial genomes, generating a matrix of 59835 comparisons, to look for genetic elements that were uniquely found in <it>M. tuberculosis </it>and closely-related pathogenic mycobacteria. To assign when foreign genes were likely acquired, we designed a bioinformatic program called mycoHIT (mycobacterial homologue investigation tool) to analyze these data in conjunction with the MLSA-based phylogeny.</p> <p>Results</p> <p>The bioinformatic screen predicted that 137 genes had been acquired by HGT at different phylogenetic strata; these included genes coding for metabolic functions and modification of mycobacterial lipids. For the majority of these genes, corroborating evidence of HGT was obtained, such as presence of phage or plasmid, and an aberrant GC%.</p> <p>Conclusion</p> <p><it>M. tuberculosis </it>emerged through vertical inheritance along with the step-wise addition of genes acquired via HGT events, a process that may more generally describe the evolution of other pathogens.</p

Simulating Photons and Plasmons in a Three-dimensional Lattice

Three-dimensional metallic photonic structures are studied using a newly developed mixed finite element-finite difference (FE-FD) code, Curly3d. The code solves the vector Helmholtz equation as an eigenvalue problem in the unit cell of a triply periodic lattice composed of conductors and/or dielectrics. The mixed FE-FD discretization scheme ensures rapid numerical convergence of the eigenvalue and allows the code to run at low resolution. Plasmon and photonic band structure calculations are presented

Spectral dynamic causal modelling in healthy women reveals brain connectivity changes along the menstrual cycle

Longitudinal menstrual cycle studies allow to investigate the effects of ovarian hormones on brain organization. Here, we use spectral dynamic causal modelling (spDCM) in a triple network model to assess effective connectivity changes along the menstrual cycle within and between the default mode, salience and executive control networks (DMN, SN, and ECN). Sixty healthy young women were scanned three times along their menstrual cycle, during early follicular, pre-ovulatory and mid-luteal phase. Related to estradiol, right before ovulation the left insula recruits the ECN, while the right middle frontal gyrus decreases its connectivity to the precuneus and the DMN decouples into anterior/posterior parts. Related to progesterone during the mid-luteal phase, the insulae (SN) engage to each other, while decreasing their connectivity to parietal ECN, which in turn engages the posterior DMN. When including the most confident connections in a leave-one out cross-validation, we find an above-chance prediction of the left-out subjects’ cycle phase. These findings corroborate the plasticity of the female brain in response to acute hormone fluctuations and may help to further understand the neuroendocrine interactions underlying cognitive changes along the menstrual cycle

Plasma Dielectric Tensor for Non-Maxwellian Distributions in the FLR Limit

Previous analytical and numerical studies have noted that the presence of fully non-Maxwellian plasma species can significantly alter the dynamics of electromagnetic waves in magnetized plasmas. In this paper, a general form for the hot plasma dielectric tensor for non-Maxwellian distributions is derived that is valid in the finite Larmor radius approximation. This model provides some insight into understanding the limitations on representing non-Maxwellian plasma species with equivalent Maxwellian components in modeling radio-frequency wave propagation and absorption

Switching between local and global aromaticity in a conjugated macrocycle for high-performance organic sodium-ion battery anodes

Aromatic organic compounds can be used as electrode materials in rechargeable batteries and are expected to advance the development of both anode and cathode materials for sodium-ion batteries (SIBs). However, most aromatic organic compounds assessed as anode materials in SIBs to date exhibit significant degradation issues under fast-charge/discharge conditions and unsatisfying long-term cycling performance. Now, a molecular design concept is presented for improving the stability of organic compounds for battery electrodes. The molecular design of the investigated compound, [2.2.2.2]paracyclophane-1,9,17,25-tetraene (PCT), can stabilize the neutral state by local aromaticity and the doubly reduced state by global aromaticity, resulting in an anode material with extraordinarily stable cycling performance and outstanding performance under fast-charge/discharge conditions, demonstrating an exciting new path for the development of electrode materials for SIBs and other types of batteries