Genome wide analysis of the complete GlnR nitrogen-response regulon in Mycobacterium smegmatis

BACKGROUND: Nitrogen is an essential element for bacterial growth and an important component of biological macromolecules. Consequently, responding to nitrogen limitation is critical for bacterial survival and involves the interplay of signalling pathways and transcriptional regulation of nitrogen assimilation and scavenging genes. In the soil dwelling saprophyte Mycobacterium smegmatis the OmpR-type response regulator GlnR is thought to mediate the transcriptomic response to nitrogen limitation. However, to date only ten genes have been shown to be in the GlnR regulon, a vastly reduced number compared to other organisms. RESULTS: We investigated the role of GlnR in the nitrogen limitation response and determined the entire GlnR regulon, by combining expression profiling of M. smegmatis wild type and glnR deletion mutant, with GlnR-specific chromatin immunoprecipitation and high throughput sequencing. We identify 53 GlnR binding sites during nitrogen limitation that control the expression of over 100 genes, demonstrating that GlnR is the regulator controlling the assimilation and utilisation of nitrogen. We also determine a consensus GlnR binding motif and identify key residues within the motif that are required for specific GlnR binding. CONCLUSIONS: We have demonstrated that GlnR is the global nitrogen response regulator in M. smegmatis, directly regulating the expression of more than 100 genes. GlnR controls key nitrogen stress survival processes including primary nitrogen metabolism pathways, the ability to utilise nitrate and urea as alternative nitrogen sources, and the potential to use cellular components to provide a source of ammonium. These studies further our understanding of how mycobacteria survive nutrient limiting conditions

Late Quaternary Marine and Terrestrial Environments, Northwestern Baffin Island, Northwest Territories

Paleoenvironmental data were analyzed from terrestrial, lake, and marine sediments collected near Arctic Bay, Baffin Island, N.W.T. Eighteen new radiocarbon dates provide chronological control, superseding earlier results. Spuriously old dates were obtained from both sandy peats and low-organic lake sediments. The most reliable dates were from marine shells and foraminifera. They indicate that déglaciation was underway by 9000 BP rather than 16,000 BP. Over the period of the record, the local environment was characterized by a high arctic pollen assemblage dominated by grass, sedge, and willow; a middle Holocene warm period is indicated by increased willow, herb, and moss values. Sea-ice conditions were severe enough to inhibit the growth of diatoms until ca. 6300 BP and ice proximal and deglacial conditions prevailed in the fiords until ca. 6000 BP. Diatom productivity increased between 3000 BP and 2500 BP, suggesting warmer surface waters and less sea ice. After 2000 BP diatom accumulation decreased sharply, due to a cooling of climate. The foraminifera indicate a major change in bottom water conditions ca. 4000 BP as the benthic species shift from a calcareous to an arenaceous assemblage.On a procédé à l'analyse des données paléoenvironnementales tirées de sédiments terrestres, marins et lacustres, près de Arctic Bay. Dix-huit nouvelles dates au radiocarbone ont permis d'établir une nouvelle chronologie. Les dates les plus anciennes, et les moins fiables, ont été obtenus dans des tourbes sableuses et des sédiments lacustres à basse teneur organique. Les dates les plus sûres proviennent de coquillages marins et des foraminifères. Elles indiquent que la déglaciation était en cours dès 9000 BP plutôt qu'à 16 000 BP. Pendant la période relevée, l'environnement dans le haut Arctique était caractérisé au niveau local par un assemblage pollinique dominé par l'herbe, le carex et le saule; à l'Holocène moyen, les valeurs croissantes du saule, de l'herbe et de la mousse reflètent une période chaude. La densité de la glace marine était assez forte pour empêcher la croissance des diatomées jusqu'à 6300 BP; la déglaciation s'est poursuivie jusque vers 6000 BP dans les fjords. La reproduction des diatomées a augmenté entre 3000 et 2500 BP en raison de températures de surface plus chaudes et une diminution des glaces marines. Après 2000 BP, l'accumulation des diatomées a décru abruptement en raison d'un refroidissement climatique. Les foraminifères démontrent un changement important survenu dans l'état des eaux profondes vers 4000 BP puisqu'il y a eu remplacement des espèces benthoniques à test calcaire par des espèces à test agglutiné.Man hat Palâoumweltdaten von Erd-, See- und Meeres-Sedimenten analysiert, die man in der Nâhe der Arctic Bay, lnsel Baffin, Nordwest-Territorien gesammelt hat. Achtzehn neue Radiocarbondaten liefern eine chronologische Kontrolle und ersetzen so fruhere Resultate. Faische alte Daten hat man sowohi aus sandigem Ton1 wie auch aus Seesedimenten mit niedrigem organischem Gehalt gewonnen. Die zuver-làssigsten Daten stammen von Meeres-muscheln und Foraminiferen. Sie zeigen, dass die Enteisung urn 9000 v.u.Z. und nicht um 16,000 v.u.Z. im Gange war. Liber den Zeitraum des Belegs charakterisierte sich die lokale Umwelt durch eine Pollen-Zusammensetzung der hohen Arktis, die von Gras, Schilfgras und Weide beherrscht war; auf eine warme Période wâhrend des mittleren Holozàns weisen zunehmende Weiden-, Gras- und Mooswerte. Die Meereseisbedingungen waren streng genug, um das Wachstum von Diatomeen bis etwa 6300 v.u.Z. zu verhindern und Proximaleis und Enteisungsbedingungen herrschten in den Fjords bis etwa 6000 v.u.Z. vor. Die Reproduktion von Diatomeen nahm zwischen 3000 v.u.Z. und 2500 v.u.Z. zu, was auf wàrmeres Oberflàchenwasser und weniger Meereseis schliessen làsst. Nach 2000 v.u.Z. nahm die Diatomeen-Akkumulation wegen einer Klimaabkuhlung plôtzlich ab. Die Foraminiferen zeigen einen betràchtlichen Wechsel der Bedingungen im tiefen Wasser um etwa 4000 v.u.Z., wenn die benthonischen Spezies von einer kalkartigen zu einer sandigen Zusammensetzung ubergehen

Fabrication of low-cost, large-area prototype Si(Li) detectors for the GAPS experiment

A Si(Li) detector fabrication procedure has been developed with the aim of satisfying the unique requirements of the GAPS (General Antiparticle Spectrometer) experiment. Si(Li) detectors are particularly well-suited to the GAPS detection scheme, in which several planes of detectors act as the target to slow and capture an incoming antiparticle into an exotic atom, as well as the spectrometer and tracker to measure the resulting decay X-rays and annihilation products. These detectors must provide the absorption depth, energy resolution, tracking efficiency, and active area necessary for this technique, all within the significant temperature, power, and cost constraints of an Antarctic long-duration balloon flight. We report here on the fabrication and performance of prototype 2"-diameter, 1-1.25 mm-thick, single-strip Si(Li) detectors that provide the necessary X-ray energy resolution of $\sim$4 keV for a cost per unit area that is far below that of previously-acquired commercial detectors. This fabrication procedure is currently being optimized for the 4"-diameter, 2.5 mm-thick, multi-strip geometry that will be used for the GAPS flight detectors.Comment: Accepted for publication at Nuclear Instrumentation and Methods A, 12 pages, 11 figure

Two Distinctly HLA-Associated Contiguous Linear Epitopes Uniquely Expressed Within the Islet Antigen 2 Molecule Are Major Autoantibody Epitopes of the Diabetes-Specific Tyrosine Phosphatase-Like Protein Autoantigens

AbstractThe related tyrosine phosphatase-like proteins islet Ag (IA)-2 and IA-2β are autoantigens of type 1 diabetes in humans. Autoantibodies are predominantly against IA-2, and IA-2-specific epitopes are major autoantibody targets. We used the close homology of IA-2 and IA-2β to design chimeras and mutants to identify humoral IA-2-specific epitopes. Two major IA-2 epitopes that are absent from the related autoantigens IA-2β and IA-2Δ 13 splice variant ICA512.bdc were found contiguous to each other within IA-2 juxtamembrane amino acids 611–620 (epitope JM1) and 621–630 (epitope JM2). JM1 and JM2 are recognized by sera from 67% of patients with IA-2 Abs, and relatives of patients with type 1 diabetes having Abs to either JM epitope had a >50% risk for developing type 1 diabetes within 6 years, even in the absence of diabetes-associated HLA genotypes. Remarkably, the presence of Abs to one of these two epitopes was mutually exclusive of the other; JM2 Abs and not JM1 Abs were found in relatives with HLA DR3/4, DR4/13, or DR1/4 genotypes; and the binding of autoantibodies to the JM2 epitope, but not the JM1 epitope, markedly affected proteolysis of IA-2. This is a unique demonstration of HLA-associated B cell responses to epitopes within a single autoantigen in humans and is consistent with modification of Ag processing by specific Ab-influencing peptide presentation by HLA molecules

A modified agar pad method for mycobacterial live-cell imaging

<p>Abstract</p> <p>Background</p> <p>Two general approaches to prokaryotic live-cell imaging have been employed to date, growing bacteria on thin agar pads or growing bacteria in micro-channels. The methods using agar pads 'sandwich' the cells between the agar pad on the bottom and a glass cover slip on top, before sealing the cover slip. The advantages of this technique are that it is simple and relatively inexpensive to set up. However, once the cover slip is sealed, the environmental conditions cannot be manipulated. Furthermore, desiccation of the agar pad, and the growth of cells in a sealed environment where the oxygen concentration will be in gradual decline, may not permit longer term studies such as those required for the slower growing mycobacteria.</p> <p>Findings</p> <p>We report here a modified agar pad method where the cells are sandwiched between a cover slip on the bottom and an agar pad on top of the cover slip (rather than the reverse) and the cells viewed from below using an inverted microscope. This critical modification overcomes some of the current limitations with agar pad methods and was used to produce time-lapse images and movies of cell growth for <it>Mycobacterium smegmatis </it>and <it>Mycobacterium bovis </it>BCG.</p> <p>Conclusions</p> <p>This method offers improvement on the current agar pad methods in that long term live cell imaging studies can be performed and modification of the media during the experiment is permitted.</p

Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source

Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a wellcharacterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 mu m diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 angstrom ngstrom were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here.11Ysciescopu

The gene-rich genome of the scallop Pecten maximus.

BACKGROUND: The king scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms the basis of a valuable commercial fishery and plays a key role in coastal ecosystems and food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which it has evolved some immunity. The molecular origins of this immunity are of interest to evolutionary biologists, pharmaceutical companies, and fisheries management. FINDINGS: Here we report the genome assembly of this species, conducted as part of the Wellcome Sanger 25 Genomes Project. This genome was assembled from PacBio reads and scaffolded with 10X Chromium and Hi-C data. Its 3,983 scaffolds have an N50 of 44.8 Mb (longest scaffold 60.1 Mb), with 92% of the assembly sequence contained in 19 scaffolds, corresponding to the 19 chromosomes found in this species. The total assembly spans 918.3 Mb and is the best-scaffolded marine bivalve genome published to date, exhibiting 95.5% recovery of the metazoan BUSCO set. Gene annotation resulted in 67,741 gene models. Analysis of gene content revealed large numbers of gene duplicates, as previously seen in bivalves, with little gene loss, in comparison with the sequenced genomes of other marine bivalve species. CONCLUSIONS: The genome assembly of P. maximus and its annotated gene set provide a high-quality platform for studies on such disparate topics as shell biomineralization, pigmentation, vision, and resistance to algal toxins. As a result of our findings we highlight the sodium channel gene Nav1, known to confer resistance to saxitoxin and tetrodotoxin, as a candidate for further studies investigating immunity to domoic acid

Major flaws in conflict prevention policies towards Africa : the conceptual deficits of international actors’ approaches and how to overcome them

Current thinking on African conflicts suffers from misinterpretations oversimplification, lack of focus, lack of conceptual clarity, state-centrism and lack of vision). The paper analyses a variety of the dominant explanations of major international actors and donors, showing how these frequently do not distinguish with sufficient clarity between the ‘root causes’ of a conflict, its aggravating factors and its triggers. Specifically, a correct assessment of conflict prolonging (or sustaining) factors is of vital importance in Africa’s lingering confrontations. Broader approaches (e.g. “structural stability”) offer a better analytical framework than familiar one-dimensional explanations. Moreover, for explaining and dealing with violent conflicts a shift of attention from the nation-state towards the local and sub-regional level is needed.Aktuelle Analysen afrikanischer Gewaltkonflikte sind häufig voller Fehlinterpretationen (Mangel an Differenzierung, Genauigkeit und konzeptioneller Klarheit, Staatszentriertheit, fehlende mittelfristige Zielvorstellungen). Breitere Ansätze (z. B. das Modell der Strukturellen Stabilität) könnten die Grundlage für bessere Analyseraster und Politiken sein als eindimensionale Erklärungen. häufig differenzieren Erklärungsansätze nicht mit ausreichender Klarheit zwischen Ursachen, verschärfenden und auslösenden Faktoren. Insbesondere die richtige Einordnung konfliktverlängernder Faktoren ist in den jahrzehntelangen gewaltsamen Auseinandersetzungen in Afrika von zentraler Bedeutung. Das Diskussionspapier stellt die große Variationsbreite dominanter Erklärungsmuster der wichtigsten internationalen Geber und Akteure gegenüber und fordert einen Perspektivenwechsel zum Einbezug der lokalen und der subregionalen Ebene für die Erklärung und Bearbeitung gewaltsamer Konflikte

Mucosal barrier and Th2 immune responses are enhanced by dietary inulin in pigs infected with <i>trichuris suis</i>

Diet composition may play a crucial role in shaping host immune responses and commensal gut microbiota populations. Bioactive dietary components, such as inulin, have been extensively studied for their bioactive properties, particularly in modulating gut immune function and reducing inflammation. It has been shown that colonization with gastrointestinal parasitic worms (helminths) may alleviate chronic inflammation through promotion of T-helper cell type (Th) 2 and T-regulatory immune responses and alterations in the gut microbiome. In this study, we investigated if dietary inulin could modulate mucosal immune function in pigs during colonization with the porcine whipworm Trichuris suis. T. suis infection induced a typical Th2-biased immune response characterized by transcriptional changes in Th2- and barrier function-related genes, accompanied by intestinal remodeling through increased epithelial goblet and tuft cell proliferation. We observed that inulin also up-regulated Th2-related immune genes (IL13, IL5), and suppressed Th1-related pro-inflammatory genes (IFNG, IL1A, IL8) in the colon. Notably, inulin augmented the T. suis-induced responses with increased transcription of key Th2 and mucosal barrier genes (e.g., IL13, TFF3), and synergistically suppressed pro-inflammatory genes, such as IFNG and CXCL9. 16S rRNA sequencing of proximal colon digesta samples revealed that inulin supplementation reduced the abundance of bacterial phyla linked to inflammation, such as Proteobacteria and Firmicutes, and simultaneously increased Actinobacteria and Bacteroidetes. Interestingly, pigs treated with both inulin and T. suis displayed the highest Bacteroidetes: Firmicutes ratio and the lowest gut pH, suggesting an interaction of diet and helminth infection that stimulates the growth of beneficial bacterial species. Overall, our data demonstrate that T. suis infection and inulin co-operatively enhance anti-inflammatory immune responses, which is potentially mediated by changes in microbiota composition. Our results highlight the intricate interactions between diet, immune function and microbiota composition in a porcine helminth infection model. This porcine model should facilitate further investigations into the use of bioactive diets as immunomodulatory mediators against inflammatory conditions, and how diet and parasites may influence gut health