Genetic snapshots of the Rhizobium species NGR234 genome

BACKGROUND: In nitrate-poor soils, many leguminous plants form nitrogen-fixing symbioses with members of the bacterial family Rhizobiaceae. We selected Rhizobium sp. NGR234 for its exceptionally broad host range, which includes more than I 12 genera of legumes. Unlike the genome of Bradyrhizobium japonicum, which is composed of a single 8.7 Mb chromosome, that of NGR234 is partitioned into three replicons: a chromosome of about 3.5 Mb, a megaplasmid of more than 2 Mb (pNGR234b) and pNGR234a, a 536,165 bp plasmid that carries most of the genes required for symbioses with legumes. Symbiotic loci represent only a small portion of all the genes coded by rhizobial genomes, however. To rapidly characterize the two largest replicons of NGR234, the genome of strain ANU265 (a derivative strain cured of pNGR234a) was analyzed by shotgun sequencing. RESULTS: Homology searches of public databases with 2,275 random sequences of strain ANU265 resulted in the identification of 1,130 putative protein-coding sequences, of which 922 (41%) could be classified into functional groups. In contrast to the 18% of insertion-like sequences (ISs) found on the symbiotic plasmid pNGR234a, only 2.2% of the shotgun sequences represent known ISs, suggesting that pNGR234a is enriched in such elements. Hybridization data also indicate that the density of known transposable elements is higher in pNGR234b (the megaplasmid) than on the chromosome. Rhizobium-specific intergenic mosaic elements (RIMEs) were found in 35 shotgun sequences, 6 of which carry RIME2 repeats previously thought to be present only in Rhizobium meliloti. As non-overlapping shotgun sequences together represent approximately 10% of ANU265 genome, the chromosome and megaplasmid may carry a total of over 200 RIMEs. CONCLUSIONS: 'Skimming' the genome of Rhizobium sp. NGR234 sheds new light on the fine structure and evolution of its replicons, as well as on the integration of symbiotic functions in the genome of a soil bacterium. Although most putative coding sequences could be distributed into functional classes similar to those in Bacillus subtilis, functions related to transposable elements were more abundant in NGR234. In contrast to ISs that accumulated in pNGR234a and pNGR234b, the hundreds of RIME elements seem mostly attributes of the chromosome

Outflows in rho Ophiuchi as Seen with the Spitzer Infrared Array Camera

Using the IRAC images from the Spitzer c2d program, we have made a survey of mid-infrared outflows in the rho Ophiuchi molecular cloud. Extended objects that have prominent emission in IRAC channel 2 (4.5 micron) compared to IRAC channel 1 (3.6 micron) and stand out as green objects in the three-color images (3.6 micron in blue, 4.5 micron in green, 8.0 micron in red) are identified as mid-infrared outflows. As a result, we detected 13 new outflows in the rho Ophiuchi molecular cloud that have not been previously observed in optical or near-infrared. In addition, at the positions of previously observed HH objects or near-infrared emission, we detected 31 mid-infrared outflows, among which seven correspond to previously observed HH objects and 30 to near-infrared emission. Most of the mid-infrared outflows detected in the rho Ophiuchi cloud are concentrated in the L1688 dense core region. In combination with the survey results for Young Stellar Objects (YSOs) and millimeter and sub-millimeter sources, the distribution of mid-infrared outflows in the rho Ophiuchi molecular complex hints a propagation of star formation in the cloud in the direction from the northwest to the southeast as suggested by previous studies of the region.Comment: 23 pages and 43 figure

A genome-wide map of aberrantly expressed chromosomal islands in colorectal cancer

BACKGROUND: Cancer development is accompanied by genetic phenomena like deletion and amplification of chromosome parts or alterations of chromatin structure. It is expected that these mechanisms have a strong effect on regional gene expression. RESULTS: We investigated genome-wide gene expression in colorectal carcinoma (CRC) and normal epithelial tissues from 25 patients using oligonucleotide arrays. This allowed us to identify 81 distinct chromosomal islands with aberrant gene expression. Of these, 38 islands show a gain in expression and 43 a loss of expression. In total, 7.892 genes (25.3% of all human genes) are located in aberrantly expressed islands. Many chromosomal regions that are linked to hereditary colorectal cancer show deregulated expression. Also, many known tumor genes localize to chromosomal islands of misregulated expression in CRC. CONCLUSION: An extensive comparison with published CGH data suggests that chromosomal regions known for frequent deletions in colon cancer tend to show reduced expression. In contrast, regions that are often amplified in colorectal tumors exhibit heterogeneous expression patterns: even show a decrease of mRNA expression. Because for several islands of deregulated expression chromosomal aberrations have never been observed, we speculate that additional mechanisms (like abnormal states of regional chromatin) also have a substantial impact on the formation of co-expression islands in colorectal carcinoma

Gesellschaftliche Integrität der Forschung: Wissenschaftsforschung Jahrbuch 2005

Gesellschaftliche Integrität von Forschung bezieht sich nach Hippokrates vor allem auf das Methodische bei der Problembearbeitung: ein forschender Arzt ist verpflichtet, sich nur solcher Methoden zu bedienen, die dem Patienten nutzen, auf keinen Fall aber schaden dürfen. In diesem Sinne wird auch in unserer Zeit auf Unangemessenheiten in der Art naturwissenschaftlicher Wissensproduktion hingewiesen. „Unangemessenheit“ ist dabei als relationaler Begriff zu verstehen. Vor jeder Wertung stellt sie zunächst nur ein Verhältnis zwischen Eigenschaften der Wissenschaft und Eigenschaften des makrosystemischen Kontextes dar. Ändern sich die Systeme, die zu den Umwelten der Wissenschaften gehören, dann können sich die Bedingungen und Bestimmungen gesellschaftlicher Integrität von Forschung ebenfalls verschieben. Dieses Problem stellt sich in analoger Weise für jedes andere System. Auch die Politik, die Ökonomie und gegebenfalls auch andere Systeme sind gezwungen, die Implikationen von Informationen aus der Wissenschaftsentwicklung für die Funktionsabläufe und Ziele des eigenen Systems zu überprüfen (eine Übersetzung der fremdsystemischen Information in den Eigencode des Systems anzufertigen) und gegebenenfalls zu handeln. Dabei gibt es nicht selten Friktionen. Nicht immer zeigt sich zum Beispiel die Politik offen für die Berücksichtigung der neuen Erkenntnisse. Es gibt Fälle, in denen sie sowohl die Gewinnung als auch die Ausnutzung neuer wissenschaftlicher Ansätze zu blockieren versucht – aus welchen Gründen auch immer. Für die Wissenschaftsforschung steht vor allem die gesellschaftliche Integrität der Forschung selbst zur Diskussion. Die Gesellschaft für Wissenschaftsforschung hat sich dieser Fragestellung angenommen und sie im Rahmen ihrer Jahrestagung im Wissenschaftszentrum Berlin für Sozialforschung am 18. März 2005 unter dem Thema „Die gesellschaftliche Integrität der Forschung“ analysiert und diskutiert. Dabei ist es gelungen, theoretische Überlegungen mit historischen und aktuellen Fakten zu verbinden. Die Ergebnisse dieser Tagung werden in diesem Jahrbuch der Gesellschaft für Wissenschaftsforschung dem interessierten Leser vorgestellt.Peer Reviewe

Genome-wide expression patterns of invasion front, inner tumor mass and surrounding normal epithelium of colorectal tumors

Colorectal tumors have characteristic genome-wide expression patterns that allow their distinction from normal colon epithelia and facilitate clinical prognosis. The expression heterogeneity within a primary colorectal tumor has not been studied on a genome scale yet. Here we investigated three compartments of colorectal tumors, the invasion front, the inner tumor mass, and surrounding normal epithelial tissue by microdissection and microarray-based expression profiling. In both tumor compartments many genes were differentially expressed when compared to normal epithelium. The sets of significantly deregulated genes in both compartments overlapped to a large extent and revealed various interesting known and novel pathways that could have contributed to tumorigenesis. Cells from the invasion front and inner tumor mass, however, did not show significant differences in their expression profile, neither on the single gene level nor on the pathway level. Instead, gene expression differences between individuals are more pronounced as all patient-matched tumor samples clustered in close proximity to each other. With respect to invasion front and inner tumor mass we conclude that the specific tumor cell micro-environment does not have a strong influence on expression patterns: largely similar genome-wide expression programs operate in the invasion front and interior compartment of a colorectal tumor

Newfoundland Neogene sediment drifts: transition from the Paleogene greenhouse to the modern icehouse

This workshop brought together specialists from various fields to develop a drilling proposal to fill the "Oligo-Miocene Gap" that exists in our understanding of the functions of Earth's systems. We propose to establish the first continuous high-deposition record of the Oligo-Miocene through new International Ocean Discovery Program (IODP) drilling in the North Atlantic to allow the development of a continuous Neogene cyclostratigraphy and to enhance our knowledge of Oligo-Miocene ocean–ice–climate dynamics. The workshop was held in Heidelberg from 15 to 17 September 2014 funded by ESF (EARTHTIME EU), NSF, and the ECORD MagellanPlus Workshop Series Program. A total of 24 participants from six different countries (Australia, France, Germany, the Netherlands, United Kingdom, and United States) attended the workshop, including several early career stage researchers. We discussed certain aspects of Cenozoic paleoceanography and paleoclimate and how the gaps in the Oligo-Miocene could be filled using scientific drilling. The ultimate goal of the workshop (to submit a pre-proposal to IODP) was achieved (IODP Proposal 874-pre was submitted 1 October 2014). Our workshop consisted of overview presentations followed by self-selected breakout groups that discussed different topics and produced text and figures for the proposal. Here, we give a short overview of the major topics discussed during the workshop and the scientific goals presented in the resulting IODP pre-proposal