Seismo-Stratigraphy and Sedimentology of Holocene Sediments off Grande Rivière de la Baleine, Southeastern Hudson Bay, Québec

The regional distribution of Holocene sediments of eastern Hudson Bay off the Grande Rivière de la Baleine mouth was mapped using a grid of reflection seismic lines (approximately 300 km long and covering an area of approximately 800 km2) and data from 7 piston cores. Based on the seismic records and piston cores, 4 stratigraphic units overlying the Proterozoic bedrock (unit 1) were defined and interpreted: (unit 2) glacial till deposited by a westward flowing ice sheet, (unit 3) rhythmically bedded clays and silts presumably deposited in glacial Lake Ojibway, (unit 4) postglacial marine muds deposited in the Tyrrell Sea overlain by undifferentiated modern marine muds, and (unit 5) distal fluviodeltaic sediments from Grande Rivière de la Baleine. Similar stratigraphie units have been described onshore. Textural and geochemical analyses suggest that unit 3 rhythmites are true varves; dark "summer" laminae were deposited mainly by underflows during the open water season, and light "winter" laminae were deposited by overflows-interflows along thermal stratifications under a seasonal ice cover. Unit 5 covers approximately 400 km2 and occurs as a deltaic constructional wedge protruding as far as 11 km offshore of the Grande Rivière de la Baleine entrance with thicknesses reaching 30 m along the coast. It was deposited between 3500 BP and the present from remobilization of glacial sediments farther upstream due to river downcutting during emergence.La répartition régionale des sédiments holocènes de l'est de la baie d'Hudson, face à l'embouchure de la Grande rivière de la Baleine, a été cartographiée à l'aide d'un grille de profils de sismique réflexion (d'environ 300 km de long et d'une superficie de 800 km2) et de données provenant de sept forages par carottier à piston. Quatre unités stratigraphiques reposant sur le socle protérozoïque (unité 1) ont été définies et interprétées : un till (unité 2) déposé par un glacier progressant vers l'ouest, des argiles et silts stratifiés (unité 3) probablement déposés dans le Lac glaciaire Ojibway, des boues marines postglaciaires (unité 4) déposés dans la Mer de Tyrrell auxquelles se superposent des boues marines récentes indifférenciées et des sédiments fluvio-deltaiques distaux (unité 5) provenant de la Grande rivière de la Baleine. Les mêmes unités stratigraphiques ont été décrites sur la côte. Les analyses granulométriques et géochimiques laissent croire que les rythmites de l'unité 3 sont des varves; les couches foncées d'été ont surtout été déposées par des courants de densité s'écoulant sur le fond pendant la période libre de glace et les couches pâles d'hiver ont été transportés en suspension le long de stratifications thermiques sous un couvert de glace saisonnier. L'unité 5 couvre environ 400 km2 et forme un prisme s'étendant jusqu'à 11 km de l'embouchure de la Grande rivière de la Baleine avec des épaisseurs atteignant 30 m le long de la côte. La mise en place de l'unité 5 s'est faite entre 3500 BP et aujourd'hui et résulte de l'érosion et de l'apport de sédiments d'origine glaciaire provenant de l'amont durant l'émergence du chenal fluvial.Man hat die régionale Verteilung von Holozàn-Sedimenten der ôstlichen Hudson Bay in offener See gegenùber der Mùndung von Grande Rivière de la Baleine kartographiert, mit Hilfe eines Rasters der seismischen Reflexionslinien (etwa 300 km lang und ein Gebiet von etwa 800 km2 bedeckend) und der Daten aus 7 Kernen von Kolbenbohrungen. Vier ùber dem anstehenden Gestein des Protero-zoikums (Einheit 1) liegende stratigraphische Einheiten wurden bestimmt und interprétiez: (Einheit 2) glaziales Till, das von einer westwàrts flieBenden Eisdecke abge-lagert wurde, (Einheit 3) rhythmisch geschichteter Lehm und Schlamm, der wohl in dem glazialen Ojibwaysee abgelagert worden war, (Einheit 4) postglazialer Meeresschlamm, der in der Tyrrell-See abgelagert wurde und uber dem undifferenzierter neuzeitlicher Meeresschlamm liegt, und (Einheit 5) distale FluB-Deltasedimente von Grande Rivière de la Baleine. Àhnliche stratigraphische Einheiten sind am Strand beschrieben worden. Die Analysen von Textur und Geochemie lassen vermuten, daB Rhythmite der Einheit 3 echte Warwen sind; die dun-klen "Sommer"-Schichten wurden hauptsâchlich durch Unterstrômungen wàhrend der Saison offenen Wassers abgelagert, und die hellen "Winter"-Schichten wurden durch Ùberlauf-Zwischenlauf entlang der therma-len Schichtungen unter der saisonbedingten Eisdecke abgelagert. Einheit 5 bedeckt etwa 400 km2 und hat die Form eines deltaartigen Keils, der bis zu 11 km in die Mundung von Grande Rivière de la Baleine hineinragt und eine Dicke bis zu 30 m entlang der Kûste erreicht

The SASSCAL contribution to climate observation, climate data management and data rescue in Southern Africa

A major task of the newly established "Southern African Science Service Centre for Climate Change and Adaptive Land Management" (SASSCAL; www.sasscal.org) and its partners is to provide science-based environmental information and knowledge which includes the provision of consistent and reliable climate data for Southern Africa. Hence, SASSCAL, in close cooperation with the national weather authorities of Angola, Botswana, Germany and Zambia as well as partner institutions in Namibia and South Africa, supports the extension of the regional meteorological observation network and the improvement of the climate archives at national level. With the ongoing rehabilitation of existing weather stations and the new installation of fully automated weather stations (AWS), altogether 105 AWS currently provide a set of climate variables at 15, 30 and 60 min intervals respectively. These records are made available through the SASSCAL WeatherNet, an online platform providing near-real time data as well as various statistics and graphics, all in open access. This effort is complemented by the harmonization and improvement of climate data management concepts at the national weather authorities, capacity building activities and an extension of the data bases with historical climate data which are still available from different sources. These activities are performed through cooperation between regional and German institutions and will provide important information for climate service related activities

A Global Overview of the Genetic and Functional Diversity in the Helicobacter pylori cag Pathogenicity Island

The Helicobacter pylori cag pathogenicity island (cagPAI) encodes a type IV secretion system. Humans infected with cagPAI–carrying H. pylori are at increased risk for sequelae such as gastric cancer. Housekeeping genes in H. pylori show considerable genetic diversity; but the diversity of virulence factors such as the cagPAI, which transports the bacterial oncogene CagA into host cells, has not been systematically investigated. Here we compared the complete cagPAI sequences for 38 representative isolates from all known H. pylori biogeographic populations. Their gene content and gene order were highly conserved. The phylogeny of most cagPAI genes was similar to that of housekeeping genes, indicating that the cagPAI was probably acquired only once by H. pylori, and its genetic diversity reflects the isolation by distance that has shaped this bacterial species since modern humans migrated out of Africa. Most isolates induced IL-8 release in gastric epithelial cells, indicating that the function of the Cag secretion system has been conserved despite some genetic rearrangements. More than one third of cagPAI genes, in particular those encoding cell-surface exposed proteins, showed signatures of diversifying (Darwinian) selection at more than 5% of codons. Several unknown gene products predicted to be under Darwinian selection are also likely to be secreted proteins (e.g. HP0522, HP0535). One of these, HP0535, is predicted to code for either a new secreted candidate effector protein or a protein which interacts with CagA because it contains two genetic lineages, similar to cagA. Our study provides a resource that can guide future research on the biological roles and host interactions of cagPAI proteins, including several whose function is still unknown

Protein Glycosylation in Helicobacter pylori: Beyond the Flagellins?

Glycosylation of flagellins by pseudaminic acid is required for virulence in Helicobacter pylori. We demonstrate that, in H. pylori, glycosylation extends to proteins other than flagellins and to sugars other than pseudaminic acid. Several candidate glycoproteins distinct from the flagellins were detected via ProQ-emerald staining and DIG- or biotin- hydrazide labeling of the soluble and outer membrane fractions of wild-type H. pylori, suggesting that protein glycosylation is not limited to the flagellins. DIG-hydrazide labeling of proteins from pseudaminic acid biosynthesis pathway mutants showed that the glycosylation of some glycoproteins is not dependent on the pseudaminic acid glycosylation pathway, indicating the existence of a novel glycosylation pathway. Fractions enriched in glycoprotein candidates by ion exchange chromatography were used to extract the sugars by acid hydrolysis. High performance anion exchange chromatography with pulsed amperometric detection revealed characteristic monosaccharide peaks in these extracts. The monosaccharides were then identified by LC-ESI-MS/MS. The spectra are consistent with sugars such as 5,7-diacetamido-3,5,7,9-tetradeoxy-L-glycero-L-manno-nonulosonic acid (Pse5Ac7Ac) previously described on flagellins, 5-acetamidino-7-acetamido-3,5,7,9-tetradeoxy-L-glycero-L-manno-nonulosonic acid (Pse5Am7Ac), bacillosamine derivatives and a potential legionaminic acid derivative (Leg5AmNMe7Ac) which were not previously identified in H. pylori. These data open the way to the study of the mechanism and role of protein glycosylation on protein function and virulence in H. pylori

CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes

BACKGROUND: The recent accumulation of closely related genomic sequences provides a valuable resource for the elucidation of the evolutionary histories of various organisms. However, although numerous alignment calculation and visualization tools have been developed to date, the analysis of complex genomic changes, such as large insertions, deletions, inversions, translocations and duplications, still presents certain difficulties. RESULTS: We have developed a comparative genome analysis tool, named CGAT, which allows detailed comparisons of closely related bacteria-sized genomes mainly through visualizing middle-to-large-scale changes to infer underlying mechanisms. CGAT displays precomputed pairwise genome alignments on both dotplot and alignment viewers with scrolling and zooming functions, and allows users to move along the pre-identified orthologous alignments. Users can place several types of information on this alignment, such as the presence of tandem repeats or interspersed repetitive sequences and changes in G+C contents or codon usage bias, thereby facilitating the interpretation of the observed genomic changes. In addition to displaying precomputed alignments, the viewer can dynamically calculate the alignments between specified regions; this feature is especially useful for examining the alignment boundaries, as these boundaries are often obscure and can vary between programs. Besides the alignment browser functionalities, CGAT also contains an alignment data construction module, which contains various procedures that are commonly used for pre- and post-processing for large-scale alignment calculation, such as the split-and-merge protocol for calculating long alignments, chaining adjacent alignments, and ortholog identification. Indeed, CGAT provides a general framework for the calculation of genome-scale alignments using various existing programs as alignment engines, which allows users to compare the outputs of different alignment programs. Earlier versions of this program have been used successfully in our research to infer the evolutionary history of apparently complex genome changes between closely related eubacteria and archaea. CONCLUSION: CGAT is a practical tool for analyzing complex genomic changes between closely related genomes using existing alignment programs and other sequence analysis tools combined with extensive manual inspection

More than a century of bathymetric observations and present-day shallow sediment characterization in Belfast Bay, Maine, USA: implications for pockmark field longevity

This paper is not subject to U.S. copyright. The definitive version was published in Geo-Marine Letters 31 (2011): 237-248, doi:10.1007/s00367-011-0228-0.Mechanisms and timescales responsible for pockmark formation and maintenance remain uncertain, especially in areas lacking extensive thermogenic fluid deposits (e.g., previously glaciated estuaries). This study characterizes seafloor activity in the Belfast Bay, Maine nearshore pockmark field using (1) three swath bathymetry datasets collected between 1999 and 2008, complemented by analyses of shallow box-core samples for radionuclide activity and undrained shear strength, and (2) historical bathymetric data (report and smooth sheets from 1872, 1947, 1948). In addition, because repeat swath bathymetry surveys are an emerging data source, we present a selected literature review of recent studies using such datasets for seafloor change analysis. This study is the first to apply the method to a pockmark field, and characterizes macro-scale (>5 m) evolution of tens of square kilometers of highly irregular seafloor. Presence/absence analysis yielded no change in pockmark frequency or distribution over a 9-year period (1999–2008). In that time pockmarks did not detectably enlarge, truncate, elongate, or combine. Historical data indicate that pockmark chains already existed in the 19th century. Despite the lack of macroscopic changes in the field, near-bed undrained shear-strength values of less than 7 kPa and scattered downcore 137Cs signatures indicate a highly disturbed setting. Integrating these findings with independent geophysical and geochemical observations made in the pockmark field, it can be concluded that (1) large-scale sediment resuspension and dispersion related to pockmark formation and failure do not occur frequently within this field, and (2) pockmarks can persevere in a dynamic estuarine setting that exhibits minimal modern fluid venting. Although pockmarks are conventionally thought to be long-lived features maintained by a combination of fluid venting and minimal sediment accumulation, this suggests that other mechanisms may be equally active in maintaining such irregular seafloor morphology. One such mechanism could be upwelling within pockmarks induced by near-bed currents.Graduate support for Brothers came from a Maine Economic Improvement Fund Dissertation Fellowship

Intestinal Microbiota Composition of Interleukin-10 Deficient C57BL/6J Mice and Susceptibility to Helicobacter hepaticus-Induced Colitis

The mouse pathobiont Helicobacter hepaticus can induce typhlocolitis in interleukin-10-deficient mice, and H. hepaticus infection of immunodeficient mice is widely used as a model to study the role of pathogens and commensal bacteria in the pathogenesis of inflammatory bowel disease. C57BL/6J Il10[superscript −/−] mice kept under specific pathogen-free conditions in two different facilities (MHH and MIT), displayed strong differences with respect to their susceptibilities to H. hepaticus-induced intestinal pathology. Mice at MIT developed robust typhlocolitis after infection with H. hepaticus, while mice at MHH developed no significant pathology after infection with the same H. hepaticus strain. We hypothesized that the intestinal microbiota might be responsible for these differences and therefore performed high resolution analysis of the intestinal microbiota composition in uninfected mice from the two facilities by deep sequencing of partial 16S rRNA amplicons. The microbiota composition differed markedly between mice from both facilities. Significant differences were also detected between two groups of MHH mice born in different years. Of the 119 operational taxonomic units (OTUs) that occurred in at least half the cecum or colon samples of at least one mouse group, 24 were only found in MIT mice, and another 13 OTUs could only be found in MHH samples. While most of the MHH-specific OTUs could only be identified to class or family level, the MIT-specific set contained OTUs identified to genus or species level, including the opportunistic pathogen, Bilophila wadsworthia. The susceptibility to H. hepaticus-induced colitis differed considerably between Il10[superscript −/−] mice originating from the two institutions. This was associated with significant differences in microbiota composition, highlighting the importance of characterizing the intestinal microbiome when studying murine models of IBD.National Institutes of Health (U.S.) (Grant NIH P01-CA26731)National Institutes of Health (U.S.) (Grant NIH P30ES0026731)National Institutes of Health (U.S.) (Grant NIH R01-OD011141

Effects of Helicobacter suis γ-glutamyl transpeptidase on lymphocytes: modulation by glutamine and glutathione supplementation and outer membrane vesicles as a putative delivery route of the enzyme

Helicobacter (H.) suis colonizes the stomach of the majority of pigs as well as a minority of humans worldwide. Infection causes chronic inflammation in the stomach of the host, however without an effective clearance of the bacteria. Currently, no information is available about possible mechanisms H. suis utilizes to interfere with the host immune response. This study describes the effect on various lymphocytes of the γ-glutamyl transpeptidase (GGT) from H. suis. Compared to whole cell lysate from wild-type H. suis, lysate from a H. suis ggt mutant strain showed a decrease of the capacity to inhibit Jurkat T cell proliferation. Incubation of Jurkat T cells with recombinantly expressed H. suis GGT resulted in an impaired proliferation, and cell death was shown to be involved. A similar but more pronounced inhibitory effect was also seen on primary murine CD4+ T cells, CD8+ T cells, and CD19+ B cells. Supplementation with known GGT substrates was able to modulate the observed effects. Glutamine restored normal proliferation of the cells, whereas supplementation with reduced glutathione strengthened the H. suis GGT-mediated inhibition of proliferation. H. suis GGT treatment abolished secretion of IL-4 and IL-17 by CD4+ T cells, without affecting secretion of IFN-γ. Finally, H. suis outer membrane vesicles (OMV) were identified as a possible delivery route of H. suis GGT to lymphocytes residing in the deeper mucosal layers. Thus far, this study is the first to report that the effects on lymphocytes of this enzyme, not only important for H. suis metabolism but also for that of other Helicobacter species, depend on the degradation of two specific substrates: glutamine and reduced glutatione. This will provide new insights into the pathogenic mechanisms of H. suis infection in particular and infection with gastric helicobacters in general