Three-Dimensional Lattice Boltzmann Model Results for Complex Fluids Ordering

The kinetics of domain growth of fluid mixtures quenched from a disordered to a lamellar phase has been studied in three dimensions. We use a numerical approach based on the lattice Boltzmann method (LBM). A novel implementation for LBM which "fuses" the collision and streaming steps is used in order to reduce memory and bandwidth requirements. We find that extended defects between stacks of lamellae with different orientation dominate the late time dynamics

Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

Background Obligate sulfur oxidizing chemolithoauthotrophic strains of Hydrogenovibrio crunogenus have been isolated from multiple hydrothermal vent associated habitats. However, a hydrogenase gene cluster (encoding the hydrogen converting enzyme and its maturation/assembly machinery) detected on the first sequenced H. crunogenus strain (XCL-2) suggested that hydrogen conversion may also play a role in this organism. Yet, numerous experiments have underlined XCL-2’s inability to consume hydrogen under the tested conditions. A recent study showed that the closely related strain SP-41 contains a homolog of the XCL-2 hydrogenase (a group 1b [NiFe]-hydrogenase), but that it can indeed use hydrogen. Hence, the question remained unresolved, why SP-41 is capable of using hydrogen, while XCL-2 is not. Results Here, we present the genome sequence of the SP-41 strain and compare it to that of the XCL-2 strain. We show that the chromosome of SP-41 codes for a further hydrogenase gene cluster, including two additional hydrogenases: the first appears to be a group 1d periplasmic membrane-anchored hydrogenase, and the second a group 2b sensory hydrogenase. The region where these genes are located was likely acquired horizontally and exhibits similarity to other Hydrogenovibrio species (H. thermophilus MA2-6 and H. marinus MH-110 T) and other hydrogen oxidizing Proteobacteria (Cupriavidus necator H16 and Ghiorsea bivora TAG-1 T). The genomes of XCL-2 and SP-41 show a strong conservation in gene order. However, several short genomic regions are not contained in the genome of the other strain. These exclusive regions are often associated with signs of DNA mobility, such as genes coding for transposases. They code for transport systems and/or extend the metabolic potential of the strains. Conclusions Our results suggest that horizontal gene transfer plays an important role in shaping the genomes of these strains, as a likely mechanism for habitat adaptation, including, but not limited to the transfer of the hydrogen conversion ability

Parameters Governing the Community Structure and Element Turnover in Kermadec Volcanic Ash and Hydrothermal Fluids as Monitored by Inorganic Electron Donor Consumption, Autotrophic CO2 Fixation and 16S Tags of the Transcriptome in Incubation Experiments

The microbial community composition and its functionality was assessed for hydrothermal fluids and volcanic ash sediments from Haungaroa and hydrothermal fluids from the Brothers volcano in the Kermadec island arc (New Zealand). The Haungaroa volcanic ash sediments were dominated by epsilonproteobacterial Sulfurovum sp. Ratios of electron donor consumption to CO2 fixation from respective sediment incubations indicated that sulfide oxidation appeared to fuel autotrophic CO2 fixation, coinciding with thermodynamic estimates predicting sulfide oxidation as the major energy source in the environment. Transcript analyses with the sulfide-supplemented sediment slurries demonstrated that Sulfurovum prevailed in the experiments as well. Hence, our sediment incubations appeared to simulate environmental conditions well suggesting that sulfide oxidation catalyzed by Sulfurovum members drive biomass synthesis in the volcanic ash sediments. For the Haungaroa fluids no inorganic electron donor and responsible microorganisms could be identified that clearly stimulated autotrophic CO2 fixation. In the Brothers hydrothermal fluids Sulfurimonas (49%) and Hydrogenovibrio/Thiomicrospira (15%) species prevailed. Respective fluid incubations exhibited highest autotrophic CO2 fixation if supplemented with iron(II) or hydrogen. Likewise catabolic energy calculations predicted primarily iron(II) but also hydrogen oxidation as major energy sources in the natural fluids. According to transcript analyses with material from the incubation experiments Thiomicrospira/Hydrogenovibrio species dominated, outcompeting Sulfurimonas. Given that experimental conditions likely only simulated environmental conditions that cause Thiomicrospira/Hydrogenovibrio but not Sulfurimonas to thrive, it remains unclear which environmental parameters determine Sulfurimonas’ dominance in the Brothers natural hydrothermal fluids

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

TextFormats: Simplifying the definition and parsing of text formats in bioinformatics.

Text formats are common in bioinformatics, as they allow for editing and filtering using standard tools, as well as, since text formats are often human readable, manual inspection and evaluation of the data. Bioinformatics is a rapidly evolving field, hence, new techniques, new software tools, new kinds of data often require the definition of new formats. Often new formats are not formally described in a standard or specification document. Although software libraries are available for accessing the most common formats, writing parsers for text formats, for which no library is currently available, is a very common though tedious task, utilized by many researchers in the field. This manuscript presents the open source software library and toolset TextFormats (available at https://github.com/ggonnella/textformats), which aims at simplifying the definition and parsing of text formats. Formats specifications are written in a simple data description format using an interactive wizard. Automatic generation of data examples and automatic testing of specifications allow for checking for correctness. Given the specification for a text format, TextFormats allows parsing and writing data in that format, using several programming languages (Nim, Python, C/C++) or the provided command line and graphical user interface tools. Although designed as a general purpose software, the main target application field, for the above mentioned reasons, is expected to be in bioinformatics: Thus, the specifications of several common existing bioinformatics formats are included

EGC: a format for expressing prokaryotic genomes content expectations

The number of available genomes of prokaryotic organisms is rapidly growing enabling comparative genomics studies. The comparison of genomes of organisms with a common phenotype, habitat or phylogeny often shows that these genomes share some common contents. Collecting rules expressing common genome traits depending on given factors is useful, as such rules could be used for quality control or for identifying interesting exceptions and formulating hypothesis. Automatizing the rules verification using computation tools requires the definition of a representation schema. In this study, we present EGC (Expected Genome Contents), a flat-text file format for the representation of expectation rules about the content of prokaryotic genomes. A parser for the EGC format has been implemented using the TextFormats software library, accompanied by a set of related Python packages

Charakterisierung der neuen putativen Aminosäuretransporters der ATF1-Überfamilie aus Arabidopsis thaliana

The uptake of nitrogen and its translocation in the plant involve the transport of organic nitrogen in the form of amino acids. During the last years, the focus of the studies on amino acid transport in plants moved from biochemical to molecular characterization of the carrier proteins required for this process. Not all the predicted transport fluxes through the membranes of plant cells have already been assigned to a particular carrier protein, although many carrier proteins were functionally characterized. Moreover, many other proteins, whose existence was predicted by genome sequencing and large scale EST projects, were suggested to function as amino acid transporters on the base of sequence similarity and predicted structural features. However, many of such putative transport proteins have not yet been functionally characterized. In this study a group of related Arabidopsis genes encoding putative amino acid transporters have been analyzed in detail. The in silico analysis grouped these genes to the ATF1 superfamily, suggesting a function as amino acid transporters. These proteins have been called AT, for Amino acid Transporters. Attempts to study these proteins by heterologous expression in Saccharomyces cerevisiae and complementation of yeast mutants defective in amino acid uptake, did not allow their functional characterization. The AT proteins are closely related to the yeast AVTs, that have been described as vacuolar transporters of amino acids. Thus, a hypothesis was raised that the AT proteins act as intracellular transporters of amino acids, located on the tonoplast. A yeast mutant strain, G119, was constructed to study vacuolar asparagine transporters which requires further optimization. The subcellular localization of AT1 and AT12 was determined by fusions with GFP and expression in Arabidopsis protoplasts. In these assays, both AT1 and AT12 were localized in endomembranes. Therefore, an alternative hypothesis on the function of the AT proteins was postulated: they may act as vesicular transporters of amino acids, involved in export processes from the cell, in a similar way to the mechanism suggested for the phylogenetically related RnVGAT, exporter in rat synapsis. To provide evidence for the possible physiological processes in which these proteins are involved, the activity of the promoter of AT4, AT5, AT9 and AT12 was analysed by promoter-GUS fusions. AT4 was expressed in the hypocotyl and in the petiole of young leaves and might play a role during the rapid cell elongation found in these organs. AT5 was not expressed under standard growth conditions. AT9 and AT12 were expressed in cotyledons and young leaves, suggesting a role in the supply of nitrogen to sink organs in young seedlings. They were also expressed in the pollen, therefore these proteins might have a role in the gametogenesis. AT9 was in addition also expressed in roots of developing seedlings and in the lateral roots of adult plants. A role of AT9 in the uptake of amino acids from the soil can therefore be postulated. The analysis of T-DNA insertion lines has revealed that the knock-out mutants in the AT7 gene are sterile. This might suggest an essential role of AT7 in the gametogenesis.Die Aufnahme und Verteilung von Stickstoff in Pflanzen beinhaltet den Transport von organischem Stickstoff in Form von Aminosäuren. In den letzten Jahren hat sich der Schwerpunkt der Forschung im Bereich des Aminosäuretransports von biochemischen Studien in Richtung der molekularen Charakterisierung an diesem Prozess beteiligter Transportproteine verschoben. Noch wurden nicht alle vorhergesagten Transportströme durch die Zellmembranen von Pflanzen einem bestimmten Protein zugeordnet. Viele Transportproteine wurden funktionell charakterisiert. Vielen anderen Proteinen, deren Existenz durch genomisches Sequenzieren und EST Projekten vorhergesagt wurde, kann aufgrund von Sequenzenähnlichkeiten und strukturellen Merkmalen eine Funktion als Aminosäuretransporter zugeordnet werden. Viele dieser Proteine sind zurzeit noch nicht charakterisiert. In dieser Arbeit wurden einige Gene aus Arabidopsis detailliert analysiert, die vermeintlich Aminosäuretransporter kodieren. Die in silico Analyse ermöglichte, diese Gene der ATF1-Überfamilie zuzuordnen und eine Funktion als Aminosäuretransporter vorherzusagen. Diese Proteine wurden AT genannt, für Aminosäuretransporter. Versuche, die Funktion dieser Proteine durch heterologe Expression in Saccharomyces cerevisiae und Komplementation von Hefemutanten, deren Aminosäureaufnahme gestört war, zu bestimmen, haben keine funktionelle Charakterisierung ermöglicht. Die AT Proteine sind eng verwandt mit den AVTs in Hefe, die als vakuoläre Aminosäuretransporter beschrieben wurden. Eine Hypothese zur Funktion der Gene ist also, dass die AT-Proteine als intrazelluläre Aminosäuretransporter agieren und im Tonoplasten lokalisiert sind. Eine Hefemutante, G119, wurde hergestellt, um vakuolären Asparagintransportern zu untersuchen was weiterer Optimierung bedarf. Die subzelluläre Lokalisierung von AT1 und AT2 wurde durch Fusionen mit GFP und Expression in Arabidopsis Protoplasten bestimmt. Diese Untersuchungen zeigten, dass AT1 und AT12 in Endomembranen lokalisiert sind. Daher wurde eine alternative Hypothese der Funktion dieser Proteine aufgestellt: Sie könnten als vesikuläre Aminosäuretransporter am Exportsystem der Zelle beteiligt sein, ähnlich dem Mechanismus, der für die phylogenetisch verwandten RnVGAT, Exporter in Rattensynapsen, vorgeschlagen wurde. Um Beweise für die möglichen physiologischen Prozesse zu finden, an denen diese Proteine beteiligt sind, wurde die Promotoraktivität von AT4, AT5, AT9 and AT12 durch Promotor-GUS-Fusionen untersucht. AT4 wurde im Hypokotyl und in den Petiolen junger Blätter exprimiert und könnte während der schnellen Zellstreckung dieser Organe eine Rolle spielen. AT5 wurde unter Standardbedingungen nicht exprimiert. AT9 und AT12 werden in Keimblättern und jungen Blättern exprimiert, was für eine Rolle bei der Stickstoffversorgung von Sinkorganen junger Keimlinge spricht. Sie werden außerdem im Pollen exprimiert und könnten eine Rolle bei der Gametogenese spielen. AT9 wird zusätzlich in Wurzeln sich entwickelnder Keimlinge und in den Lateralwurzeln adulter Pflanzen exprimiert. Daher kann eine Rolle bei der Aufnahme von Aminosäuren aus dem Boden postuliert werden. Die Analyse von T-DNA-Insertionslinien zeigt, dass Linien, die eine Knock-Out-Mutation im AT7-Gen tragen, steril sind. Das spricht für eine essentielle Rolle dieses Gens während der Gametogenese

Unambiguosly expressing expectations about the content of prokaryotic genomes

In recent years, the sequencing, assembling and annotation of prokaryotic genomes has become increasingly easy and cheap. Thus it becomes increasingly feasible and interesting to perform comparative genomics analyses of new genomes to those of related organisms. Thereby related organisms can be defined by different criteria, such as taxonomy or phenotype. Expectations regarding the contents of genomes are often expressed in scientific articles describing group of organisms. Evaluating such expectations, when a new genome becomes available, requires analysing the text snippets which express such expectations, extracting the logical elements of the text and enabling a formal expression, more suitable for further automated analyses. Hereby we present a theoretical framework, alongside practical consideration for expressing expectations about the content of genomes, with the purpose of enabling such comparative genomics analyses. The components of the framework include a system for the definition of groups of organisms, supported by a Prokaryotic Group Types Ontology, a system for the definition of genomic contents, supported by a Prokaryotic Genomic Contents Definition Ontology. Finally we discuss how the combination of these two systems may enable an unambiguous definition of absolute and relative genome content expectation rules

RGFA: powerful and convenient handling of assembly graphs

The “Graphical Fragment Assembly” (GFA) is an emerging format for the representation of sequence assembly graphs, which can be adopted by both de Bruijn graph- and string graph-based assemblers. Here we present RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex operations such as the separation of the implicit instances of repeats and the merging of linear paths can be performed. A typical application of RGFA is the editing of a graph, to finish the assembly of a sequence, using information not available to the assembler. We illustrate a use case, in which the assembly of a repetitive metagenomic fosmid insert was completed using a script based on RGFA. Furthermore, we show how the API provided by RGFA can be employed to design complex graph editing algorithms. As an example, we developed a detection algorithm for CRISPRs in a de Bruijn graph. Finally, RGFA can be used for comparing assembly graphs, e.g., to document the changes in a graph after applying a GUI editor. A program, GFAdiff is provided, which compares the information in two graphs, and generate a report or a Ruby script documenting the transformation steps between the graphs

Strategie terapeutiche nelle neoplasie della via biliare distale e dell’ampolla di Vater

I tumori maligni della via biliare distale e dell’ampolla di Vater rappresentano un’entità anatomo-clinica di complesso approccio chirurgico a causa delle difficoltà di porre una diagnosi precoce, dovuta alla scarsa sintomatologia di questi tumori nei primi stadi. Gli Autori, sulla base di 19 casi osservati tra il 1990 e il 2001 nel Dipartimento di Scienze Chirurgiche e Tecnologie Mediche Applicate “F. D u r a n t e ” dell’Università degli Studi di Roma “La Sapienza”, espongono i loro risultati nel trattamento chirurgico di queste neoplasie. Dall’analisi della loro casistica emerge che la sopravvivenza a distanza è condizionata principalmente dalla precocità della diagnosi, dallo stadio della neoplasia e dalle condizioni generali in cui il paziente giunge al tavolo operatorio