73 research outputs found
The dUTPase Enzyme Is Essential in Mycobacterium smegmatis
No full textPubMed ID: 22655049This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Single cell genomics-based analysis of gene content and expression of prophages in a diffuse-flow deep-sea hydrothermal system
No full text© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Labonte, J. M., Pachiadaki, M., Fergusson, E., McNichol, J., Grosche, A., Gulmann, L. K., Vetriani, C., Sievert, S. M., & Stepanauskas, R. Single cell genomics-based analysis of gene content and expression of prophages in a diffuse-flow deep-sea hydrothermal system. Frontiers in Microbiology, 10, (2019): 1262, doi:10.3389/fmicb.2019.01262.Phage–host interactions likely play a major role in the composition and functioning of many microbiomes, yet remain poorly understood. Here, we employed single cell genomics to investigate phage–host interactions in a diffuse-flow, low-temperature hydrothermal vent that may be reflective of a broadly distributed biosphere in the subseafloor. We identified putative prophages in 13 of 126 sequenced single amplified genomes (SAGs), with no evidence for lytic infections, which is in stark contrast to findings in the surface ocean. Most were distantly related to known prophages, while their hosts included bacterial phyla Campylobacterota, Bacteroidetes, Chlorobi, Proteobacteria, Lentisphaerae, Spirochaetes, and Thermotogae. Our results suggest the predominance of lysogeny over lytic interaction in diffuse-flow, deep-sea hydrothermal vents, despite the high activity of the dominant Campylobacteria that would favor lytic infections. We show that some of the identified lysogens have co-evolved with their host over geological time scales and that their genes are transcribed in the environment. Functional annotations of lysogeny-related genes suggest involvement in horizontal gene transfer enabling host’s protection against toxic metals and antibacterial compounds.This work was supported by the U.S. National Science Foundation’s Dimensions of Biodiversity Program [OCE-1136488 (to RS), OCE-1136727 (to SMS) and OCE-1136451 (to CV)], as well as DEB-1441717 and OCE-1335810 (to RS), and the DOE JGI CSP project 1477
The emergence of magnetic flux through a partially ionised solar atmosphere
No full textWe present results from 2.5D numerical simulations of the emergence of magnetic flux from the upper convection zone through the photosphere and chromosphere into the corona. Certain regions of the solar atmosphere are at sufficiently low temperatures to be only partially ionised, in particular the lower chromosphere. This leads to Cowling resistivities orders of magnitude larger than the Coulomb values, and thus to anisotropic dissipation in Ohm’s law. This also leads to localised low magnetic Reynolds numbers (R m < 1). We find that the rates of emergence of magnetic field are greatly increased by the partially ionised regions of the model atmosphere, and the resultant magnetic field is more diffuse. More importantly, the only currents associated with the magnetic field to emerge into the corona are aligned with the field, and thus the newly formed coronal field is force-free
Electron acceleration sites in a large-scale coronal structure
No full textRadio observations and interplanetary particle measurements have
shown that even in the absence of conspicuous violent processes in the low
atmosphere (such as Hα flares) electrons are accelerated in the corona, most
likely at higher altitudes than during flares (≥0.5 R above the
photosphere). The paper presents direct evidence on the acceleration sites from
a case study of radio, visible light and soft X-ray observations: electrons are
repeatedly accelerated in a large-scale coronal structure which is identified
with a streamer in coronographic observations. Energy is simultaneously
released in an active region near the base of the structure and at a height of
∼1 R , over several hours before the large-scale structure erupts. Energy
input is observed in at least two emerging active regions underneath the
streamer. The coronal configuration is three-dimensional, overlying a whole
quadrant of the Sun. It is argued that the observations trace multiple sites of
energy release presumably in current sheets embedded within the streamer, in
agreement with scenarios developed for the acceleration of electrons seen in
the corona and at 1 AU, and for the evolution of large-scale coronal structures
towards eruption
The role of nitrogen on the flotation performance of a complex sulphide ore
No full textBibliography: leaves 94-99.This thesis focuses on the role of nitrogen on flotation performance of a sulphide PGM ore. Merensky ore obtained from Impala Platinum mine, Rustenburg, was used in laboratory batch flotation tests. Nitrogen addition was implemented during the conditioning and / or flotation stages of the test. In order to further evaluate the consistency of the role of nitrogen, tests were conducted using both stainless steel and mild steel as the milling media during the milling step prior to batch flotation. Specifically, the objectives of this thesis were as follows: To investigate the effect of nitrogen on the metallurgical flotation performance of the complex sulphide ore, as measured by mineral recoveries and grades of the major sulphide elements, copper, nickel and iron. These represent the major sulphides present in the ore; chalcopyrite (Cu), pentlandite (Ni) and pyrrhotite (Fe, as an approximate representative since Fe occurs in pyrrhotite, chalcopyrite, pentlandite as well as nonsulphide gangue). Secondly, to develop an understanding of the mechanisms of nitrogen addition on the relevant sub processes and interactions in froth flotation. The elucidation of these mechanisms was carried out with aid of complementary investigative studies which focused on the issues relating to the mechanistic role of nitrogen in flotation, as identified by the literature review. The first of these involved the evaluation of the role of nitrogen on the pulp chemical environment. The pulp chemical environment is defined here as the water - ore - reagent medium in which the valuable particle resides during the froth flotation process. Profiles of pH, temperature, dissolved oxygen (DO) and oxidation reduction potential (ORP, measured with a Pt - Ag/AgCI electrode) were recorded for each flotation test so as to monitor the changes in the pulp chemical environment, as a response to changes in milling media, reagent addition and gas addition. The second complimentary investigation involved the evaluation of the role of nitrogen on mineral surface oxidation. This involved the measurement of the level of metal hydroxide on the minerals' surface with a technique employing EDTA (ethylene diamine tetra acetic acid) for the purposes of extraction. This was to ascertain whether the addition of nitrogen during flotation tests resulted in reduced mineral surface oxidation either as a result of the direct effect of nitrogen or an indirect effect via galvanic interaction protection mechanisms. The final complimentary investigation involved an evaluation of the role of nitrogen on the collector-mineral and collector-mineral-activator interactions. This entailed the measurement of residual xanthate by UV spectroscopy. This was to ascertain whether any change in flotation response with nitrogen addition was attributable to a shift in the collector-activator-mineral interaction scheme
Clustering and module formation of DE gene signatures in CD14<sup>+</sup> and CD33<sup>+</sup> MC isolated from SLE Patients.
No full text(A) DE genes from active and inactive CD14+ MC were analyzed by GSVA to determine pathway enrichment using functional definitions provided from the BIG-C (Biologically Informed Gene Clustering) annotation library. Samples were successfully sorted by disease cohort via this method in both active and inactive MC. Starred BIG-C categories only appeared in the active or inactive analysis, respectively. (B) WGCNA of CD14+ and CD33+ MC isolated from SLE patients. Dendrograms show hierarchy of modules formed by unsupervised WGCNA clustering of DE genes from CD14+ and CD33+ MC isolated from active and inactive SLE patients.</p
Differential expression of CD14<sup>+</sup> monocyte genes in active and inactive SLE.
No full text(A) Number of differentially expressed (DE) genes detected by LIMMA analysis in MC, CD4+ T cells, and B cells isolated from inactive (SLEDAI+ MC isolated from inactive (SLEDAI52] (C) Fold change variation of genes found to be upregulated in both active and inactive SLE MC. Polarization-related genes are shown in bold and M1 genes are represented by a black wedge while M2 genes are represented with a white wedge. Genes not associated with M1 or M2 pathways are represented with a gray wedge.</p
Protein interaction-based clustering of genes in WGCNA modules significantly correlated to SLEDAI.
No full textProtein-protein interaction networks and clusters generated via CytoScape using the STRING and MCODE plugins. Networks were constructed of the gene lists of WGCNA modules positively (A, above) or negatively (B, below) correlated to SLEDAI from CD14+ MC (a) or CD33+ MC (b, c). MCODE clusters are determined by the strength of protein-protein interactions, calculated by pooling information from publicly available literature. Top half of diagrams show the cluster metastructure of each network while bottom half shows the specific genes that make up each cluster. M1-related genes are indicated by red arrows and M2-related genes are indicated by blue arrows.</p
3rd Annual Conference of the Leverhulme Centre for Integrative Research on Agriculture and Health (LCIRAH), Developing methods in agriculture and health research, London, 13–14 June 2013
No full textNon-PRIFPRI3; ISI; CRP4; B Promoting healthy food systemsPHND; A4NHCGIAR Research Program on Agriculture for Nutrition and Health (A4NH
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