Abundance and Biomass from heterotrophic bacteria, Synechococcus, Prochlorococcus and Virus in the Aegean Sea in April 2008 during SES_GR1

The HCMR_SES_LAGRANGIAN_GR1_ MICROBIAL PARAMETERS dataset is based on samples collected in the framework of the project SESAME, in the North Aegean Sea during April 2008. The objectives were to measure the standing stocks and calculate the production of the microbial compartment of the food web, describe the vertical distribution pattern and characterize its structure and function through the water column as influenced by the BSW. Heterotrophic bacteria, Synechococcus, Prochlorococcus and Virus abundance: Subsamples for virus, heterotrophic bacteria and cyanobacteria (Synechococcus spp. and Prochlorococcus spp.) counting were analyzed using a FACSCalibur (Becton Dickinson) flow cytometer equipped with a standard laser (488 nm) and filter set and using deionized water as sheath fluid. Fluorescent beads with a diameter of 0.97 µm (Polysciences) were added to each sample as an internal standard, and all parameters were normalized to the beads and expressed as relative units. SYBRGreen I stain (Molecular Probe) was used to stain viral and heterotrophic bacterial DNA. Viruses were counted according to (Brussaard 1984). In order to avoid bulk consentrations of viruses samples we dilluted to Tris-EDTA (pH=8,0) buffer to a final sollution of 1/5 to 1/100. Total abundance and nucleid content classes were calculated using the Paint-A-Gate software (Becton Dickinson). Heterotrophic Nanoflagellate abundance: Subsamples (30-150 ml) were concentrated on 25mm black polycarbonate filters of porosity 0.6µm and stained with DAPI for 10 min (Porter and Feig 1980). Under epifluorescence microscopy heterotrophic nanoflagellates (HNAN) were distinguished using UV and blue excitation and enumerated. Nanoflagellates were classified in size categories and the biovolume was calculated. Ciliate abundance: For ciliate identification and enumeration, 100-3000 ml samples were left for 24h-4d for sedimentation and then observed under an inverted microscope. Ciliates were counted, distinguished into size-classes and major taxonomic groups and identified down to genus or species level where possible (Pitta et al. 2005). Heterotrophic bacteria, Synechococcus, Prochlorococcus biomass: Subsamples for virus, heterotrophic bacteria and cyanobacteria (Synechococcus spp. and Prochlorococcus spp.) counting were analyzed using a FACSCalibur (Becton Dickinson) flow cytometer equipped with a standard laser (488 nm) and filter set and using deionized water as sheath fluid. Fluorescent beads with a diameter of 0.97 µm (Polysciences) were added to each sample as an internal standard, and all parameters were normalized to the beads and expressed as relative units. SYBRGreen I stain (Molecular Probe) was used to stain viral and heterotrophic bacterial DNA. Viruses were counted according to (Brussaard 1984). In order to avoid bulk consentrations of viruses samples we dilluted to Tris-EDTA (pH=8,0) buffer to a final sollution of 1/5 to 1/100. Total abundance and nucleid content classes were calculated using the Paint-A-Gate software (Becton Dickinson). Abundance data were converted into C biomass using 250 fgC cell-1 (Kana & Glibert 1987) for Synechococcus, 50 fgC cell-1 (Campbell et al. 1994) for Prochlorococcus and 20fgC cell-1 (Lee & Fuhrman 1987) for heterotrophic bacteria. Heterotrophic Nanoflagellate biomass: Subsamples (30-150 ml) were concentrated on 25mm black polycarbonate filters of porosity 0.6µm and stained with DAPI for 10 min (Porter and Feig 1980). Under epifluorescence microscopy heterotrophic nanoflagellates (HNAN) were distinguished using UV and blue excitation and enumerated. Nanoflagellates were classified in size categories and the biovolume was calculated. Abundance data were converted into C biomass using 183 fgC µm**3 (Caron et al. 1995). Ciliate biomass: For ciliate identification and enumeration, 100-3000 ml samples were left for 24h-4d for sedimentation and then observed under an inverted microscope. Ciliates were counted, distinguished into size-classes and major taxonomic groups and identified down to genus or species level where possible (Pitta et al. 2005). Ciliate cell sizes were measured and converted into cell volumes using appropriate geometric formulae using image analysis. For biomass estimation, the conversion factor 190 fgC µm**3 was used (Putt and Stoecker 1989).

Nile River & Red Sea Region, 1884 (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: A map of the Nile, from the equatorial lakes to the Mediterranean : embracing the eastern Sûdan (Kordofan, Darfur &c.) and Abyssinia. It was published by E. Stanford in 1884. Scale [ca. 1:6,000,000). Covers the Nile River and Red Sea regions. The image inside the map neatline is georeferenced to the surface of the earth and fit to the Africa Sinusoidal projected coordinate system. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as drainage, cities and other human settlements, territorial boundaries, shoreline features, roads, railroads, exploration routes, and more. Relief shown by hachures. This layer is part of a selection of digitally scanned and georeferenced historic maps from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of originators, ground condition dates, scales, and map purposes.

Nile River & Red Sea Region, 1822 (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: Carte générale de l'Egypte et de l'Arabie Pétrée, par A. H. Brué, Géographe de S.A.R. Monsieur. It was published by Chez l'auteur, Rue des Maçons Sorbonne, No. 9 in Mai 1822. Scale [ca. 1:2,350,000]. Covers the Nile River and Red Sea regions. Map in French.The image inside the map neatline is georeferenced to the surface of the earth and fit to the Egypt Red Belt projected coordinate system. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as drainage, cities and other human settlements, territorial boundaries, shoreline features, historic sites and ruins, and more. Relief shown by hachures.This layer is part of a selection of digitally scanned and georeferenced historic maps from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of originators, ground condition dates, scales, and map purposes.

Nile River & Red Sea Region, 1828 (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: Carte historique, physique & politique de l'Egypte, dressée par le Ch.er Lapie, 1er Géographe du Roi, Officier supérieur au Corps Royal des Ingénieurs Géographes, d'après les itinéraires & les reconnaissances recueillis par MM. les Généraux Comtes Guilleminot, Tromelin & Fernig, ainsi que d'après ceux de MM. Pacho, Caillaud, Coste, Burckhardt, Irwin &c. et les travaux de la Commission d'Egypte, le tout appuyé sur les Observations Astronomiques de MM. Gauttier, Smith, Rüppel & Nouet ; gravé par Flahaut, Rue de l'Est, N°1 ; écrit par Hacq, Graveur du Dèpôt de la Guerre. It was published by Chez Ch. Picquet in 1828. Scale [ca 1:120,000]. Covers the Nile River and Red Sea regions. Map in French. The image inside the map neatline is georeferenced to the surface of the earth and fit to the Egypt Red Belt projected coordinate system. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as drainage, cities and other human settlements, territorial boundaries, shoreline features, roads, historic sites and ruins, and more. Relief shown by hachures. Includes insets: "Plan d'Alexandrie" (1:50,000) and "Plan du Caire" (1:50,000).This layer is part of a selection of digitally scanned and georeferenced historic maps from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of originators, ground condition dates, scales, and map purposes.

Nile River & Red Sea Region, ca. 1870 (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: Egypt, Arabia Petraea, and lower Nubia, by Keith Johnston. It was published by William Blackwood & Sons ; W. & K. Johnston, ca. 1870. Scale [ca. 1:2,854,868]. Covers the Nile River and Red Sea regions.The image inside the map neatline is georeferenced to the surface of the earth and fit to the Egypt Red Belt projected coordinate system. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as drainage, cities and other human settlements, territorial boundaries, shoreline features, roads, railroads, canals, wells, and more. Covers the Nile River and Red Sea regions.This layer is part of a selection of digitally scanned and georeferenced historic maps from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of originators, ground condition dates, scales, and map purposes.

Nile River & Red Sea Region, 1810 (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: Charte vom Nil Strome, oder Aegypten, Nubien und Habesch. It was published in 1810. Scale [ca. 1:7,000,000]. Covers the Nile River and Red Sea region. Map in German. The image inside the map neatline is georeferenced to the surface of the earth and fit to the Africa Lambert Conformal Conic projected coordinate system. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as drainage, cities and other human settlements, territorial and administrative boundaries, shoreline features, caravan routes, and more. Relief shown by hachures. Includes notes.This layer is part of a selection of digitally scanned and georeferenced historic maps from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of originators, ground condition dates, scales, and map purposes.

HIV infection, viral hepatitis and liver fibrosis among prison inmates in West Africa.

BACKGROUND Prisoners represent a vulnerable population for blood-borne and sexually transmitted infections which can potentially lead to liver fibrosis and ultimately cirrhosis. However, little is known about the prevalence of liver fibrosis and associated risk factors among inmates in sub-Saharan Africa. METHODS Screening of liver fibrosis was undertaken in a randomly selected sample of male inmates incarcerated in Lome, Togo and in Dakar, Senegal using transient elastography. A liver stiffness measurement ≥9.5 KPa was retained to define the presence of a severe liver fibrosis. All included inmates were also screened for HIV, Hepatitis B Virus (HBV) and Hepatitis C Virus (HCV) infection. Substances abuse including alcohol, tobacco and cannabis use were assessed during face-to-face interviews. Odds Ratio (OR) estimates were computed with their 95 % Confidence Interval (CI) to identify factors associated with severe liver fibrosis. RESULTS Overall, 680 inmates were included with a median age of 30 years [interquartile range: 24-35]. The prevalence of severe fibrosis was 3.1 % (4.9 % in Lome and 1.2 % in Dakar). Infections with HIV, HBV and HCV were identified in 2.6 %, 12.5 % and 0.5 % of inmates, respectively. Factors associated with a severe liver fibrosis were HIV infection (OR = 7.6; CI 1.8-32.1), HBV infection (OR = 4.8; CI 1.8-12.8), HCV infection (OR = 52.6; CI 4.1-673.8), use of traditional medicines (OR = 3.7; CI 1.4-10.1) and being incarcerated in Lome (OR = 3.3; CI 1.1-9.8) compared to Dakar. CONCLUSIONS HIV infection and viral hepatitis infections were identified as important and independent determinants of severe liver fibrosis. While access to active antiviral therapies against HIV and viral hepatitis expands in Africa, adapted strategies for the monitoring of liver disease need to be explored, especially in vulnerable populations such as inmates.

Limitations of microbial hydrocarbon degradation at the Amon Mud Volcano (Nile Deep Sea Fan)

The Amon mud volcano (MV), located at 1250 m water depth on the Nile Deep Sea Fan, is known for its active emission of methane and non-methane hydrocarbons into the hydrosphere. Previous investigations showed a low efficiency of hydrocarbon-degrading anaerobic microbial communities inhabiting the Amon MV center in the presence of sulphate and hydrocarbons in the seeping subsurface fluids. By comparing spatial and temporal patterns of in situ biogeochemical fluxes, temperature gradients, pore water composition and microbial activities over three years, we investigated why the activity of anaerobic hydrocarbon degraders can be low despite high energy supplies. We found that the central dome of the Amon MV, as well as a lateral mud flow at its base, showed signs of recent exposure of hot subsurface muds lacking active hydrocarbon degrading communities. In these highly disturbed areas, anaerobic degradation of methane was less than 2% of the methane flux. Rather high oxygen consumption rates compared to low sulphide production suggest a faster development of more rapidly growing aerobic hydrocarbon degraders in highly disturbed areas. In contrast, the more stabilized muds surrounding the central gas and fluid conduits hosted active anaerobic hydrocarbon-degrading microbial communities. Furthermore, within three years, cell numbers and hydrocarbon degrading activity increased at the gas-seeping sites. The low microbial activity in the hydrocarbon-vented areas of Amon mud volcano is thus a consequence of kinetic limitations by heat and mud expulsion, whereas most of the outer mud volcano area is limited by hydrocarbon transport.

Description of recent sediments of Nile Delta, Red Sea and Gulf of Aden (Table 1-3)

The study of textural, structural, chemical, and physical properties of fine-grained recent marine sediments leads to the conclusion that only a few compositional factors are responsible for significant changes in mass physical characteristics in the upper meters below sea bottom. Fossil-induced porosity increases water content and liquid limit. It also seems to have partially influenced the plastic limit and plasticity index of calcareous sandy silts from the Red Sea and the western Gulf of Aden so that they become similar to the montmorillonite rich prodelta clays from the Nile Delta. Diagrams based on liquid limit and plasticity loose their original meaning in these cases. Activity of sediments rich in microorganisms can be higher than that of montmorillonitic clay. The shear strength-depth relationship of normally consolidated sediments is surprisingly little influenced by changes in sand or clay content and clay mineralogy. Only high lime content, submarine erosion and beginning cementation increase the strength considerably. Erosional disconformities near the present surface can be deduced from the strength-depth curve when as little as 1 or 2 m sediment have been removed. Flat or irregular strength-depth curves indicate beginning cementation and probably discontinuous sedimentation, provided the composition of the material remains in some degree constant. In our samples diagenetic pyrite, but no recristallisation of carbonates could be detected under the microscope. Underconsolidation and excess pore-water pressure, factors which tend to foster submarine slides, mud lumps, and diapiric folding, seem to be restricted Varito areas with mainly rapidly deposited, homogeneous or layered sediments. But where an abundance of burrowing organisms increases the vertical permeability of the sediment, normal consolidation and stable deposits are to be expected, at least in the upper meters below the present surface. According to 14C-determinations on calcareous microorganisms the rate of deposition of the investigated sediments seems to range from 26 to 167 cm per 1000 years.

(Table 1) Heavy mineral content in sediments of the southern Mediterranean Ridge, Nile Cone and Egyptian Shelf

Petrographic analysis of Quaternary terrigenous sand layers in eastern Mediterranean cores reveals distinct mineralogical differences between the Egyptian Shelf-Nile Cone region and the southern part of the Mediterranean Ridge. A compositionally and texturally immature suite in Ridge cores, mixed with a Nile-derived assemblage, identifies a fresh non-recycled mineral component derived from proximal igneous and metamorphic surface or near-surface exposures, probably in the south-central Ridge area rather than from distal African sources. The presence of such basement terrains would be consistent with a compressive thrust-belt origin for this part of the Mediterranean Ridge.