Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray

pan-genome microarra

Draft genome sequence of the psychrophilic and alkaliphilic <em>Rhodonellum psychrophilum</em> strain GCM71^T

Rhodonellum psychrophilum GCM71(T), isolated from the cold and alkaline submarine ikaite columns in the Ikka Fjord in Greenland, displays optimal growth at 5 to 10°C and pH 10. Here, we report the draft genome sequence of this strain, which may provide insight into the mechanisms of adaptation to these extreme conditions

Bayesian prediction of bacterial growth temperature range based on genome sequences

<p>Abstract</p> <p>Background</p> <p>The preferred habitat of a given bacterium can provide a hint of which types of enzymes of potential industrial interest it might produce. These might include enzymes that are stable and active at very high or very low temperatures. Being able to accurately predict this based on a genomic sequence, would thus allow for an efficient and targeted search for production organisms, reducing the need for culturing experiments.</p> <p>Results</p> <p>This study found a total of 40 protein families useful for distinction between three thermophilicity classes (thermophiles, mesophiles and psychrophiles). The predictive performance of these protein families were compared to those of 87 basic sequence features (relative use of amino acids and codons, genomic and 16S rDNA AT content and genome size). When using naïve Bayesian inference, it was possible to correctly predict the optimal temperature range with a Matthews correlation coefficient of up to 0.68. The best predictive performance was always achieved by including protein families as well as structural features, compared to either of these alone. A dedicated computer program was created to perform these predictions.</p> <p>Conclusions</p> <p>This study shows that protein families associated with specific thermophilicity classes can provide effective input data for thermophilicity prediction, and that the naïve Bayesian approach is effective for such a task. The program created for this study is able to efficiently distinguish between thermophilic, mesophilic and psychrophilic adapted bacterial genomes.</p

Draft genome sequences of two protease-producing strains of <i>Arsukibacterium</i>, isolated from two cold and alkaline environments

Arsukibacterium ikkense GCM72(T) and a close relative, Arsukibacterium sp. MJ3, were isolated from two cold and alkaline environments as producers of extracellular proteolytic enzymes active at high pH and low temperature. This report describes the two draft genome sequences, which may serve as sources of future industrial enzymes

Ultraviolet Spectroscopy of Rapidly-Rotating Solar-Mass Stars: Emission Line Redshifts as a Test of the Solar-Stellar Connection

We compare high-resolution ultraviolet spectra of the Sun and thirteen solarmass main sequence stars with different rotational periods that serve as proxies for their different ages and magnetic field structures. In this the second paper in the series, we study the dependence of ultraviolet emission-line centroid velocities on stellar rotation period, as rotation rates decrease from that of the Pleiades star HII314 (Prot = 1.47 days) to Alpha Cen A (Prot = 28 days). Our stellar sample of F9 V to G5 V stars consists of six stars observed with the Cosmic Origins 1Guest Observer, NASA/ESA Hubble Space Telescope and User of the Data Archive at the Space Telescope Science Institute. Spectrograph on HST and eight stars observed with the Space Telescope Imaging Spectrograph on HST. We find a systematic trend of increasing redshift with more rapid rotation (decreasing rotation period) that is similar to the increase in line red shift between quiet and plage regions on the Sun. The fastest-rotating solar-mass star in our study, HII314, shows significantly enhanced redshifts at all temperatures above log T = 4.6, including the corona, which is very different from the redshift pattern observed in the more slowly-rotating stars. This difference in the redshift pattern suggests that a qualitative change in the magnetic-heating process occurs near Prot = 2 days. We propose that HII314 is an example of a solar-mass star with a magnetic heating rate too large for the physical processes responsible for the redshift pattern to operate in the same way as for the more slowly rotating stars. HII314 may therefore lie above the high activity end of the set of solar-like phenomena that is often called the "solar-stellar connection".Comment: 36 pages, 7 figures, 6 tables, to appear in the Astrophysical Journal July 201

GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes

We present an interactive web application for visualizing genomic data of prokaryotic chromosomes. The tool (GeneWiz browser) allows users to carry out various analyses such as mapping alignments of homologous genes to other genomes, mapping of short sequencing reads to a reference chromosome, and calculating DNA properties such as curvature or stacking energy along the chromosome. The GeneWiz browser produces an interactive graphic that enables zooming from a global scale down to single nucleotides, without changing the size of the plot. Its ability to disproportionally zoom provides optimal readability and increased functionality compared to other browsers. The tool allows the user to select the display of various genomic features, color setting and data ranges. Custom numerical data can be added to the plot allowing, for example, visualization of gene expression and regulation data. Further, standard atlases are pre-generated for all prokaryotic genomes available in GenBank, providing a fast overview of all available genomes, including recently deposited genome sequences. The tool is available online from http://www.cbs.dtu.dk/services/gwBrowser. Supplemental material including interactive atlases is available online at http://www.cbs.dtu.dk/services/gwBrowser/suppl/

Genomic Characterization of Campylobacter jejuni Strain M1

Campylobacter jejuni strain M1 (laboratory designation 99/308) is a rarely documented case of direct transmission of C. jejuni from chicken to a person, resulting in enteritis. We have sequenced the genome of C. jejuni strain M1, and compared this to 12 other C. jejuni sequenced genomes currently publicly available. Compared to these, M1 is closest to strain 81116. Based on the 13 genome sequences, we have identified the C. jejuni pan-genome, as well as the core genome, the auxiliary genes, and genes unique between strains M1 and 81116. The pan-genome contains 2,427 gene families, whilst the core genome comprised 1,295 gene families, or about two-thirds of the gene content of the average of the sequenced C. jejuni genomes. Various comparison and visualization tools were applied to the 13 C. jejuni genome sequences, including a species pan- and core genome plot, a BLAST Matrix and a BLAST Atlas. Trees based on 16S rRNA sequences and on the total gene families in each genome are presented. The findings are discussed in the background of the proven virulence potential of M1

Industry 4.0 readiness in manufacturing companies: challenges and enablers towards increased digitalization

Digitalization is changing the business environment and companies face challenges to make progress. A first step to support companies is to verify their digital readiness, capabilities, and developing clear plans for improvement. This paper aims to evaluate the digital readiness of seven companies through the application of a self-check tool, followed by a deeper investigation through a case study, to identify reasons, challenges/barriers and enablers towards digitalization. A workshop was conducted to evaluate the use of a self-check tool and collect other analysis. Results include the readiness level and comparison between companies, actions and practices towards increased digitalization

A study of velocity fields in the transition region of Epsilon Eri (K2 V)

Analyses of the widths and shifts of optically thin emission lines in the ultraviolet spectrum of the active dwarf Epsilon Eri (K2 V) are presented. The spectra were obtained using the Space Telescope Imaging Spectrograph on the Hubble Space Telescope and the Far Ultraviolet Spectroscopic Explorer. The line widths are used to find the non-thermal energy density and its variation with temperature from the chromosphere to the upper transition region. The energy fluxes that could be carried by Alfven and acoustic waves are investigated, to test their possible roles in coronal heating. Acoustic waves do not appear to be a viable means of coronal heating. There is, in principle, ample flux in Alfven waves, but detailed calculations of wave propagation are required before definite conclusions can be drawn about their viability. The high sensitivity and spectral resolution of the above instruments have allowed two-component Gaussian fits to be made to the profiles of the stronger transition region lines. The broad and narrow components which result share some similarities with those observed in the Sun, but in Epsilon Eri the broad component is redshifted relative to the narrow component and contributes more to the total line flux. The possible origins of the two components and the energy fluxes implied are discussed. On balance our results support the conclusion of Wood, Linsky & Ayres, that the narrow component is related to Alfven waves reaching to the corona, but the origin of the broad component is not clear.Comment: 19 pages, 16 figures. Accepted for publication by MNRA

Complimentary protein extraction methods increase the identification of the Park Grass Experiment metaproteome

Although the Park Grass Experiment is an important international reference soil for temperate grasslands, it still lacks the direct extraction of its metaproteome. The identification of these proteins can be crucial to our understanding of soil ecology and major biogeochemical processes. However, the extraction of protein from soil is a technically fraught process due to difficulties with co-extraction of humic material and lack of compatible databases to identify proteins. To address these issues, we combined two protein extraction techniques on Park Grass experiment soil, one based on humic acid removal, namely a modified freeze-dry, heat/thaw/phenol/chloroform (HTPC) method and another which co-extracts humic material, namely an established surfactant method. A broad range of proteins were identified by matching the mass spectra of extracted soil proteins against a tailored Park Grass proteome database. These were mainly in the categories of “protein metabolism”, “membrane transport”, “carbohydrate metabolism”, “respiration” “ribosomal and nitrogen cycle” proteins, enabling reconstitution of specific processes in grassland soil. Protein annotation using NCBI and EBI databases inferred that the Park Grass soil is dominated by Proteobacteria, Actinobacteria, Acidobacteria and Firmicutes at phylum level and Bradyrhizobium, Rhizobium, Acidobacteria, Streptomyces and Pseudolabrys at genus level. Further functional enrichment analysis enabled us to connect protein identities to regulatory and signalling networks of key biogeochemical cycles, notably the nitrogen cycle. The newly identified Park Grass metaproteome thus provides a baseline on which future targeted studies of important soil processes and their control can be built