Identification of sample-specific sequences in mammalian cDNA and genomic DNA by the novel ligation-mediated subtraction (Limes)

The representational difference analysis (RDA) and other subtraction techniques are used to enrich sample-specific sequences by elimination of ubiquitous sequences existing in both the sample of interest (tester) and the subtraction partner (driver). While applying the RDA to genomic DNA of cutaneous lymphoma cells in order to identify tumor relevant alterations, we predominantly isolated repetitive sequences and artificial repeat-mediated fusion products of otherwise independent PCR fragments (PCR hybrids). Since these products severely interfered with the isolation of tester-specific fragments, we developed a considerably more robust and efficient approach, termed ligation-mediated subtraction (Limes). In first applications of Limes, genomic sequences and/or transcripts of genes involved in the regulation of transcription, such as transforming growth factor β stimulated clone 22 related gene (TSC-22R), cell death and cytokine production (caspase-1) or antigen presentation (HLA class II sequences), were found to be completely absent in a cutaneous lymphoma line. On the assumption that mutations in tumor-relevant genes can affect their transcription pattern, a protocol was developed and successfully applied that allows the identification of such sequences. Due to these results, Limes may substitute/supplement other subtraction/comparison techniques such as RDA or DNA microarray techniques in a variety of different research fields.

Gulf of Mexico and Caribbean Sea Region, ca. 1715 (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: A map of the West-Indies or the islands of America in the North Sea : with ye adjacent countries, explaning [sic] what belongs to Spain, England, France, Holland &c. also ye trade winds, and ye several tracts made by ye galeons and flota from place to place : according to ye newest and most exact observations, by Herman Moll, geographer. It was printed for Tho. Bowles in St. Pauls Church Yard and John Bowles at the Black Horse in Cornhill ca. 1715. Scale [ca. 1:4,300,000]. Covers the Gulf of Mexico and Caribbean Sea Region including parts of southern United States, Mexico, Central America, West Indies, and northern South America.The image inside the map neatline is georeferenced to the surface of the earth and fit to the North American Lambert Conformal Conic 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, and more. Relief shown pictorially. Includes also historical notes and insets.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.

Distribution of clay minerals in surface sediments of the Eurasian Arctic Ocean

Clay-mineral distributions in the Arctic Ocean and the adjacent Eurasian shelf areas are discussed to identify source areas and transport pathways of terrigenous material in the Arctic Ocean. The main clay minerals in Eurasian Arctic Ocean sediments are illite and chlorite. Smectite and kaolinite occur in minor amounts in these sediments, but show strong variations in the shelf areas. These two minerals are therefore reliable in reconstructions of source areas of sediments from the Eurasian Arctic. The Kara Sea and the western part of the Laptev Sea are enriched in smectite, with highest values of up to 70% in the deltas of the Ob and Yenisey rivers. Illite is the dominant clay mineral in all the investigated sediments except for parts of the Kara Sea. The highest concentrations with more than 70% illite occur in the East Siberian Sea and around Svalbard. Chlorite represents the clay mineral with lowest concentration changes in the Eastern Arctic, ranging between 10 and 25%. The main source areas for kaolinite in the Eurasian Arctic are Mesozoic sedimentary rocks on Franz-Josef Land islands. Based on clay-mineral data, transport of the clay fraction via sea ice is of minor importance for the modern sedimentary budget in the Arctic basins.

Accumulation of particulate organic carbon at the Eurasian continental margin during late Quaternary times

Data on the amount and composition of organic carbon were determined in sediment cores from the Kara and Laptev Sea continental margin, representing oxygen isotope stages 1-6. The characterization of organic matter is based on hydrogen index (HI) values, n-alkanes and maceral composition, indicating the predominance of terrigenous organic matter through space and time. The variations in the amount and composition of organic carbon are mainly influenced by changes in fluvial sediment supply, Atlantic water inflow, and continental ice sheets. During oxygen isotope stage (OIS) 6, high organic carbon contents in sediments from the Laptev Sea and western East Siberian Sea continental margin were probably caused by the increased glacial erosion and further transport in the eastward-flowing boundary current along the continental margin. During OIS 5 and early OIS 3, some increased amounts of marine organic matter were preserved in sediments east of the Lomonosov Ridge, suggesting an influence of nutrient-rich Pacific waters. During OIS 2, terrigenous organic carbon supply was increased along the Barents and western Kara Sea continental margin caused by extended continental ice sheets in the Barents Sea (Svalbard to Franz Josef Land) area and increased glacial erosion. Along the Laptev Sea continental margin, on the other hand, the supply of terrigenous (organic) matter was significantly reduced due to the lack of major ice sheets and reduced river discharge. Towards the Holocene, the amount of total organic carbon (TOC) increased along the Kara and Laptev Sea continental margin, reaching average values of up to 0.5 g C/cm**2/ky. Between about 8 and 10 ka (9 and 11 Cal ka), i.e., during times when the inner shallow Kara and Laptev seas became largely flooded for the first time after the Last Glacial Maximum, maximum supply of terrigenous organic carbon occurred, which is related to an increase in coastal erosion and Siberian river discharge. During the last 8000 years, the increased amount of marine organic carbon preserved in the sediments from the Kara and Laptev Sea continental margin is interpreted as a result of the intensification of Atlantic water inflow along the Eurasian continental margin.

Organic matter deposition along the Kara and Laptev Seas continental margin (eastern Arctic Ocean) during last deglaciation and Holocene

Organic petrologic (maceral analysis) and bulk organic-geochemical studies were performed on five sediment cores from the Eurasian continental margin to reconstruct the environmental changes during the last not, vert, similar13 000 yr. The core stratigraphy is based on AMS-14C dating, and correlation by magnetic susceptibility and lithostratigraphic characteristics. Variations in terrigenous, freshwater, and marine organic matter deposition document paleoceanographic and paleoclimatic changes during the transition from the last deglaciation to the Holocene. Glacigenic diamictons deposited in the St. Anna Trough (northern Kara Sea) during the Last Glacial Maximum (LGM) are characterized by reworked terrigenous organic matter. In contrast, the Laptev Sea shelf was not covered by an ice-sheet, but was exposed by the lowered sea level. Increased deposition of marine organic matter (MOM) during deglaciation indicates enhanced surface-water productivity, possibly related to influence of Atlantic waters. The occurrence of freshwater alginite gives evidence for river discharge to the Kara and Laptev Seas after the LGM. At the eastern Laptev Sea slope, the first influence of Atlantic water masses is indicated by an increase in the contents of MOM and dinoflagellate cysts, with Operculodinium centrocarpum prior to not, vert, similar10 000 yr BP. High sedimentation rates in the Kara and the Laptev Seas with the adjacent slope at the beginning of the Holocene are presumably related to increased freshwater and sediment discharge from the Siberian rivers. Evidence for elevated Holocene freshwater discharge to the Laptev Sea has been found between not, vert, similar9.8 and 9 kyr BP, at not, vert, similar5 kyr BP and at not, vert, similar2.5 kyr BP. In the Kara Sea, an increased freshwater signal is obvious at not, vert, similar8.5 kyr BP and at not, vert, similar5 kyr BP. Higher portions of MOM were accumulated in the St. Anna Trough and at the Eurasian continental margin at several intervals during the Holocene. Increased primary productivity during these intervals is explained by seasonally ice-free conditions possibly associated with increased inflow of Atlantic waters.