Criblamydia sequanensis Harbors a Megaplasmid Encoding Arsenite Resistance.

Criblamydia sequanensis is an amoeba-resisting bacterium recently isolated from the Seine River. This Chlamydia-related bacterium harbors a genome of approximately 3 Mbp and a megaplasmid of 89,525 bp. The plasmid encodes several efflux systems and an operon for arsenite resistance. This first genome sequence within the Criblamydiaceae family enlarges our view on the evolution and the ecology of this important bacterial clade largely understudied so far

Complete Genome Sequence of Bacteroides ovatus V975

The complete genome sequence of Bacteroides ovatus V975 was determined. The genome consists of a single circular chromosome of 6,475,296 bp containing five rRNA operons, 68 tRNA genes, and 4,959 coding genes

Organics in comet 67P – a first comparative analysis of mass spectra from ROSINA–DFMS, COSAC and Ptolemy

The ESA Rosetta spacecraft followed comet 67P at a close distance for more than 2 yr. In addition, it deployed the lander Philae on to the surface of the comet. The (surface) composition of the comet is of great interest to understand the origin and evolution of comets. By combining measurements made on the comet itself and in the coma, we probe the nature of this surface material and compare it to remote sensing observations. We compare data from the double focusing mass spectrometer (DFMS) of the ROSINA experiment on ESA's Rosetta mission and previously published data from the two mass spectrometers COSAC (COmetary Sampling And Composition) and Ptolemy on the lander. The mass spectra of all three instruments show very similar patterns of mainly CHO-bearing molecules that sublimate at temperatures of 275 K. The DFMS data also show a great variety of CH-, CHN-, CHS-, CHO2- and CHNO-bearing saturated and unsaturated species. Methyl isocyanate, propanal and glycol aldehyde suggested by the earlier analysis of the measured COSAC spectrum could not be confirmed. The presence of polyoxymethylene in the Ptolemy spectrum was found to be unlikely. However, the signature of the aromatic compound toluene was identified in DFMS and Ptolemy data. Comparison with remote sensing instruments confirms the complex nature of the organics on the surface of 67P, which is much more diverse than anticipated

Philae Landing on Comet 67P/Churyumov-Gerasimenko – Planned Chirality Measurements and Ideas for the Future

Philae is a comet Lander, part of the ESA Rosetta Mission to comet 67P/Churyumov-Gerasimenko. After a ten year cruise through the solar system it successfully landed on the nucleus of the comet on November 12, 2014. Philae's payload consists of ten scientific instruments, including COSAC, an evolved gas analyser with the capability to differentiate chiral molecules. After the touchdown of Philae, the anchoring harpoons, which were expected to fix the lander to ground, did not work, Philae bounced in the low gravity environment, and only came to rest after a 2 hours " hop " in an unforeseen area on the comet surface. Although, the scientific instruments, including cameras, mass spectrometers (including the one of COSAC), a magnetometer and a radar instrument could be operated, and fascinating, unprecedented scientific results were obtained, it was not possible to collect a sample of the surface material and no gas chromatography measurement could be performed. Thus, the measurement of the chirality of molecules on comets is still to be done in the future. The paper gives an overview of the Philae mission and the attempts to measure chiral molecules with COSAC, and suggests future measurements with returned samples from the primitive asteroids (162173) Ryugu and (101955) Bennu with the spacecraft Hayabusa 2 (JAXA) and OSIRIS-REx (NASA), respectively. Both will reach their targets in 2018

The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract

Background Lactobacillus reuteri is a gut symbiont of a wide variety of vertebrate species that has diversified into distinct phylogenetic clades which are to a large degree host-specific. Previous work demonstrated host specificity in mice and begun to determine the mechanisms by which gut colonisation and host restriction is achieved. However, how L. reuteri strains colonise the gastrointestinal (GI) tract of pigs is unknown. Results To gain insight into the ecology of L. reuteri in the pig gut, the genome sequence of the porcine small intestinal isolate L. reuteri ATCC 53608 was completed and consisted of a chromosome of 1.94 Mbp and two plasmids of 138.5 kbp and 9.09 kbp, respectively. Furthermore, we generated draft genomes of four additional L. reuteri strains isolated from pig faeces or lower GI tract, lp167-67, pg-3b, 20-2 and 3c6, and subjected all five genomes to a comparative genomic analysis together with the previously completed genome of strain I5007. A phylogenetic analysis based on whole genomes showed that porcine L. reuteri strains fall into two distinct clades, as previously suggested by multi-locus sequence analysis. These six pig L. reuteri genomes contained a core set of 1364 orthologous gene clusters, as determined by OrthoMCL analysis, that contributed to a pan-genome totalling 3373 gene clusters. Genome comparisons of the six pig L. reuteri strains with 14 L. reuteri strains from other host origins gave a total pan-genome of 5225 gene clusters that included a core genome of 851 gene clusters but revealed that there were no pig-specific genes per se. However, genes specific for and conserved among strains of the two pig phylogenetic lineages were detected, some of which encoded cell surface proteins that could contribute to the diversification of the two lineages and their observed host specificity. Conclusions This study extends the phylogenetic analysis of L. reuteri strains at a genome-wide level, pointing to distinct evolutionary trajectories of porcine L. reuteri lineages, and providing new insights into the genomic events in L. reuteri that occurred during specialisation to their hosts. The occurrence of two distinct pig-derived clades may reflect differences in host genotype, environmental factors such as dietary components or to evolution from ancestral strains of human and rodent origin following contact with pig populations

Medizinische und gesundheitsökonomische Bewertung der Radiochirurgie zur Behandlung von Hirnmetastasen

Background: Expressed Sequence Tags (ESTs) are in general used to gain a first insight into gene activities from a species of interest. Subsequently, and typically based on a combination of EST and genome sequences, microarray-based expression analyses are performed for a variety of conditions. In some cases, a multitude of EST and microarray experiments are conducted for one species, covering different tissues, cell states, and cell types. Under these circumstances, the challenge arises to combine results derived from the different expression profiling strategies, with the goal to uncover novel information on the basis of the integrated datasets. Findings: Using our new analysis tool, MediPlEx (MEDIcago truncatula multiPLe EXpression analysis), expression data from EST experiments, oligonucleotide microarrays and Affymetrix GeneChips® can be combined and analyzed, leading to a novel approach to integrated transcriptome analysis. We have validated our tool via the identification of a set of well-characterized AM-specific and AM-induced marker genes, identified by MediPlEx on the basis of in silico and experimental gene expression profiles from roots colonized with AM fungi. Conclusions: MediPlEx offers an integrated analysis pipeline for different sets of expression data generated for the model legume Medicago truncatula. As expected, in silico and experimental gene expression data that cover the same biological condition correlate well. The collection of differentially expressed genes identified via MediPlEx provides a starting point for functional studies in plant mutants

Therapieergebnisse beim aggressiven Non-Hodgkin-Lymphom mit Hodenbefall

Einleitung: Primäre Hodenlymphome haben einen Anteil von ca. neun Prozent an allen Hodentumoren und machen ein bis zwei Prozent aller Non-Hodgkin- Lymphome aus (Vitolo, Ferreri et al. 2008). In den letzten 15 Jahren hat sich ihre ungünstige Prognose dank eines multimodalen Therapiekonzepts für die Patienten verbessert (Ahmad, Idris et al. 2012, Cheah, Wirth et al. 2014). Die meisten Rezidive finden sich im ZNS und dem kontralateralen Hoden (Ahmad, Idris et al. 2012). Über die Jahre etablierte sich ein Therapiekonzept aus einer Orchiektomie, einer Anthrazyklin-basierten Chemotherapie mit Cyclophosphamid, Hydoxorubicin, Vincristine und Prednisolon (CHOP) plus einer monoklonalen Antikörpertherapie mit Rituximab (R), einer prophylaktischen Hodenbestrahlung mit einer Gesamtdosis von 30,6 bis 36 Gray, einer Einzeldosis von 1,8 bis zwei Gy, und einer Methotrexat-ZNS-Prophylaxe (Cheah, Wirth et al. 2014, Ahmad, Idris et al. 2012). Zielsetzung: In einer retrospektiven Auswertung wurde eine deskriptive Statistik anhand verschiedener Merkmale von 111 Patienten mit einem medianen Alter von 67 Jahren (Range: 34- 80) aus fünf Studien der Deutschen Studiengruppe für Hochmaligne Non-Hodgkin-Lymphome (DSHNHL) erstellt. Von diesen Patienten wurde für 103 Patienten eine Überlebensanalyse erstellt und verschiedene Einflussfaktoren auf das OS untersucht und durch Subgruppen verglichen. Zudem wurde das progressionsfreie Überleben und das Mortalitätsrisiko durch eine Competing Risk Analyse untersucht. Material und Methode: Eine deskriptive Statistik, eine Überlebens-, eine Rezidiv- und Competing Risks-analyse wurden durch den Vergleich verschiedener Subkollektive (CHOP vs. R-CHOP, Ann Arbor Stadium I/II vs. III/IV, RT+ vs. RT- und aaIPI 0 vs. 1) erstellt. 75 Patienten erhielten eine Systemtherapie mit Rituximab, 78 Patienten befanden sich in einem Ann Arbor Stadium Ⅰ/Ⅱ und 98 Patienten hatten einen aaIPI von 0 oder 1. 40 Pat. erhielten eine RT des kontralateralen Hoden. 32 Patienten wurden mit einer Gesamtdosis von 30,6 -36 Gy bestrahlt, die übrigen erhielten abweichende Dosierungen.   Ergebnis: Die mediane Überlebenszeit lag bei 7,92 Jahren für das gesamte Kollektiv. Das OS der 103 eingeschlossenen Patienten betrug nach drei Jahren 78,2 % und nach fünf Jahren 70,9 % (Abbildung 1/ Tabelle 6). Das OS in der Gruppe CHOP betrug nach fünf Jahren 70,1 %, in der Gruppe R-CHOP 63,8 % (95% CI 0,701-3,693, p=0,262). Das OS in der Gruppe Stadium I/II lag nach fünf Jahren bei 77,8 %, im Stadium III/IV bei 54,4 %. Patienten im Stadium Ⅲ/Ⅳ haben ein statistisch nicht signifikant erhöhtes Sterberisiko gegenüber Patienten im Stadium Ⅰ/Ⅱ (95% CI 0,754-3,402, p=0,220). Das OS des Subkollektiv ohne RT betrug nach einem Jahr 87,7 %, nach drei Jahren 75,5 % und nach fünf Jahren 69,4 %, im Vergleich dazu im Subkollektiv mit RT nach einem Jahr 97,3 %, nach drei Jahren 82,6 % und nach fünf Jahren 70,8 % (95% CI 0,250-1,381, p=0,222). Das statistisch signifikante OS in der Gruppe aaIPI 0 lag nach fünf Jahren bei 82,4 %, in der Gruppe aaIPI 1 bei 48,5 % (95% CI 3,417-8,021, p=0,005). In der Competing Risks Analyse verringerten die RT, ein Ann Arbor Stadium I/II und ein aaIPI 0 das Risiko eines Rezidivs und die Mortalität. Das Ann Arbor Stadium III/IV und ein aaIPI 1 erhöhten das Rezidiv- und Mortalitätsrisiko. Ein Rezidiv trat bei 19/111 Pat. auf. In vier Fällen war der kontralaterale Hoden betroffen, viermal das ZNS, sechsmal die Lymphknoten und fünfmal lag der Befall einer anderen extranodalen Region vor. In der Gruppe mit prophylaktischer Radiatio war das Rezidivrisiko im Vergleich zum Kollektiv ohne Bestrahlung erhöht. Unter diesen Rezidiven in dem Kollektiv ohne Radiatio ereignete sich nur ein Rezidiv am kontralateralen Hoden. Die RT senkte das Risiko der Mortalität. Schlussfolgerung: Die Ergebnisse zeigen, dass ein multimodaler Therapieansatz und eine risikoadaptierte Strategie zu einem verbesserten OS und einem sinkenden Rezidiv- und Mortalitätsrisiko beitragen. Die RT verhindert nachweißlich Lokalrezidive. In der Gruppe der bestrahlten Patienten ereignete sich nur ein Rezidiv am kontralateralen Hoden. Die restlichen Rezidive befanden sich in nicht bestrahlten Regionen.Introduction: Primary testicular lymphomas have a share of approximately nine percent of all testicular tumors and one to two percent of all non-Hodgkin lymphomas (Vitolo, Ferreri et al. 2008). In the last 15 years their unfavourable prognosis has improved thanks to a multimodal therapy concept for the patients (Ahmad, Idris et al. 2012, Cheah, Wirth et al. 2014). Most recurrences are found in the CNS and the contralateral testis (Ahmad, Idris et al. 2012). Over the years, a therapeutic concept consisting of an orchiectomy, an anthracycline-based chemotherapy with cyclophosphamide, hydroxydaunorubicin, vincristine and prednisolone (CHOP) plus a monoclonal antibody therapy with rituximab (R) has been established, prophylactic testicular irradiation with a total dose of 30.6 to 36 Gy, a single dose of 1.8 to two Gy, and methotrexate CNS prophylaxis (Cheah, Wirth et al. 2014, Ahmad, Idris et al. 2012). Purpose: In a retrospective evaluation, descriptive statistics has been based on various characteristics of 111 patients with a median age of 67 years (range: 34-80) from five studies of the German Study Group for Highly Modified Non-Hodgkin's Lymphoma (DSHNHL). Out of these patients, a survival analysis has been performed for 103 patients and various factors influencing the OS has been investigated and compared by subgroups. In addition, progression-free survival and mortality risk has been analysed in a Competing Risk Analysis. Materials and Method: A descriptive statistic, a survival, a recurrence and competing risks analysis had been established by comparing different sub collectives (CHOP vs. R-CHOP, Ann Arbor stage I/II vs. III/IV, RT+ vs. RT- and aaIPI 0 vs. 1). 75 patients received systemic therapy with rituximab, 78 patients had been in an Ann Arbor stage Ⅱ/Ⅱ and 98 patients had an aaIPI of zero or one. 40 patients received an RT of the contralateral testis. 32 patients has been irradiated with a total dose of 30.6 -36 Gy, the others received different doses. Results: The median survival time was 7.92 years for the entire collective. The OS of the 103 included patients was 78.2% after 3 years and 70.9% after five years (Figure 1/ Table 6). The OS in the group CHOP was 70.1% after five years and 63.8% in the group R-CHOP (95% CI 0.701-3.693, p=0.262). The OS in the group stage I/II was 77.8% after five years, in stage III/IV 54.4%. Patients in stage Ⅰ/Ⅳ have a statistically not significantly increased mortality risk compared to patients in stage Ⅱ/Ⅱ (95% CI 0.754-3.402, p=0.220). The OS of the subcollective without Radiotherapy was 87.7% after one year, 75.5% after three years and 69.4% after five years, compared to 97.3% after one year, 82.6% after three Zusammenfassung 8 years and 70.8% after five years in the subcollective with prophylactic irradiation (95% CI 0.25-1.381, p=0.222). The statistically significantly OS in group aaIPI 0 was 82.4% after five years, in group aaIPI 1 48.5% (95% CI 1.456-8.021, p=0.005). In the Competing Risks analysis, the irradiation, an Ann Arbor stage I/II and an aaIPI 0 reduced the risk of recurrence and mortality. The Ann Arbor stage III/IV and an aaIPI 1 increased the risk of relapse and mortality. A recurrence occurred in 19/111 patients. In four cases the contralateral testis was affected, four times the CNS, six times the lymph nodes and five times another extranodal region was affected. In the group of irradiation the risk of recurrence was increased compared to the collective without irradiation. Among these recurrences in the group without irradiation only one recurrence occurred on the contralateral testis. Irradiation RT reduced the risk of mortality. Conclusion: The results show that a multimodal therapy approach and a risk adapted strategy contribute to an improved OS and a reduced risk of recurrence and mortality. Irradiation has been shown to prevent local recurrences. In the group of irradiated patients only one recurrence occurred at the contralateral testis. The remaining recurrences were in non-irradiated regions

EDGAR 2.0: an enhanced software platform for comparative gene content analyses.

The rapidly increasing availability of microbial genome sequences has led to a growing demand for bioinformatics software tools that support the functional analysis based on the comparison of closely related genomes. By utilizing comparative approaches on gene level it is possible to gain insights into the core genes which represent the set of shared features for a set of organisms under study. Vice versa singleton genes can be identified to elucidate the specific properties of an individual genome. Since initial publication, the EDGAR platform has become one of the most established software tools in the field of comparative genomics. Over the last years, the software has been continuously improved and a large number of new analysis features have been added. For the new version, EDGAR 2.0, the gene orthology estimation approach was newly designed and completely re-implemented. Among other new features, EDGAR 2.0 provides extended phylogenetic analysis features like AAI (Average Amino Acid Identity) and ANI (Average Nucleotide Identity) matrices, genome set size statistics and modernized visualizations like interactive synteny plots or Venn diagrams. Thereby, the software supports a quick and user-friendly survey of evolutionary relationships between microbial genomes and simplifies the process of obtaining new biological insights into their differential gene content. All features are offered to the scientific community via a web-based and therefore platform-independent user interface, which allows easy browsing of precomputed datasets. The web server is accessible at http://edgar.computational.bio

Degradation of microbial fluorescence biosignatures by solar ultraviolet radiation on Mars

Recent and proposed robotic missions to Mars are equipped with implements to expose or excavate fresh material from beneath the immediate surface. Once brought into the open, any organic molecules or potential biosignatures of present or past life will be exposed to the unfiltered solar ultraviolet (UV) radiation and face photolytic degradation over short time courses. The key question, then, is what is the window of opportunity for detection of recently exposed samples during robotic operations? Detection of autofluorescence has been proposed as a simple method for surveying or triaging samples for organic molecules. Using a Mars simulation chamber we conduct UV exposures on thin frozen layers of two model microorganisms, the radiation-resistant polyextremophile Deinococcus radiodurans and the cyanobacterium Synechocystis sp. PCC 6803. Excitation–emission matrices (EEMs) are generated of the full fluorescence response to quantify the change in signal of different cellular fluorophores over Martian equivalent time. Fluorescence of Deinococcus cells, protected by a high concentration of carotenoid pigments, was found to be relatively stable over 32 h of Martian UV irradiation, with around 90% of the initial signal remaining. By comparison, fluorescence from protein-bound tryptophan in Synechocystis is much more sensitive to UV photodegradation, declining to 50% after 64 h exposure. The signal most readily degraded byUV irradiation is fluorescence of the photosynthetic pigments – diminished to only 35% after 64 h. This sensitivity may be expected as the biological function of chlorophyll and phycocyanin is to optimize the harvesting of light energy and so they are readily photobleached. A significant increase in a *450 nm emission feature is interpreted as accumulation of fluorescent cellular degradation products from photolysis. Accounting for diurnal variation in Martian sunlight, this study calculates that frozen cellular biosignatures would remain detectable by fluorescence for at least several sols; offering a sufficient window for robotic exploration operations

mRNA Inventory of Extracellular Vesicles from Ustilago maydis

Extracellular vesicles (EVs) can transfer diverse RNA cargo for intercellular communication. EV-associated RNAs have been found in diverse fungi and were proposed to be relevant for pathogenesis in animal hosts. In plant-pathogen interactions, small RNAs are exchanged in a cross-kingdom RNAi warfare and EVs were considered to be a delivery mechanism. To extend the search for EV-associated molecules involved in plant-pathogen communication, we have characterised the repertoire of EV-associated mRNAs secreted by the maize smut pathogen, Ustilago maydis. For this initial survey, we examined EV-enriched fractions from axenic filamentous cultures that mimic infectious hyphae. EV-associated RNAs were resistant to degradation by RNases and the presence of intact mRNAs was evident. The set of mRNAs enriched inside EVs relative to the fungal cells are functionally distinct from those that are depleted from EVs. mRNAs encoding metabolic enzymes are particularly enriched. Intriguingly, mRNAs of some known effectors and other proteins linked to virulence were also found in EVs. Furthermore, several mRNAs enriched in EVs are also upregulated during infection, suggesting that EV-associated mRNAs may participate in plant-pathogen interactions