Draft Genome Sequence of Gordonia lacunae BS2T

We report here the draft genome sequence of the soil bacterium Gordonia lacunae BS2T ( DSM 45085T JCM 14873T NRRL B-24551T), isolated from an estuary in Plettenberg Bay, South Africa. Analysis of the draft genome revealed that more than 40% of the secondary metabolite biosynthetic genes encode new compounds

OcculterCut: A comprehensive survey of AT-rich regions in fungal genomes.

We present a novel method to measure the local GC-content bias in genomes and a survey of published fungal species. The method, enacted as "OcculterCut" (https://sourceforge.net/projects/occultercut), identified species containing distinct AT-rich regions. In most fungal taxa, AT-rich regions are a signature of repeat-induced point mutation (RIP), which targets repetitive DNA and decreases GC-content though the conversion of cytosine to thymine bases. RIP has in turn been identified as a driver of fungal genome evolution, as RIP mutations can also occur in single-copy genes neighbouring repeat-rich regions. Over time RIP perpetuates 'two speeds' of gene evolution in the GC-equilibrated and AT-rich regions of fungal genomes. In this study, genomes showing evidence of this process are found to be common, particularly among the Pezizomycotina. Further analysis highlighted differences in amino acid composition and putative functions of genes from these regions, supporting the hypothesis that these regions play an important role in fungal evolution. OcculterCut can also be used to identify genes undergoing RIP-assisted diversifying selection, such as small, secreted effector proteins that mediate host-microbe disease interactions

Construction of antimicrobial peptide-drug combination networks from scientific literature based on a semi-automated curation workflow

Considerable research efforts are being invested in the development of novel antimicrobial therapies effective against the growing number of multi-drug resistant (MDR) pathogens. Notably, the combination of different agents is increasingly explored as means to exploit and improve individual agent actions while minimising microorganism resistance. Although there are several databases on antimicrobial agents, scientific literature is the primary source of information on experimental antimicrobial combination testing. This work presents a semi-automated database curation workflow that supports the mining of scientific literature and enables the reconstruction of recently documented antimicrobial combinations. Currently, the database contains data on antimicrobial combinations that have been experimentally tested against Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli, Listeria monocytogenes and Candida albicans, which are prominent pathogenic organisms and are well-known for their wide and growing resistance to conventional antimicrobials. Researchers are able to explore the experimental results for a single organism or across organisms. Likewise, researchers may look into indirect network associations and identify new potential combinations to be tested. The database is available without charges. Database URL: http://sing.ei.uvigo.es/antimicrobialCombination/This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145FEDER-006684), and support by FCT and the European Community fund FEDER, through the Programme COMPETE, under the scope of the Projects AntiPep PTDC/SAU-SAP/113196/2009 (FCOMP-01-0124-FEDER-016012) and RECI/BBB-EBI/0179/2012 (FCOMP-01-0124-FEDER-027462). Authors acknowledge the PhD Grant of Paula Jorge, funded by FCT Ref. SFRH/BD/ 88192/2012, and the PhD grants of Martin Pérez-Pérez and Gael Pe´rez-Rodriguez, funded by the University of Vigo. Finally, this study was partially funded by the [15VI013] Contract-Programme from the University of Vigo and the Agrupamento INBIOMED from DXPCTSUG-FEDER unha maneira de facer Europa (2012/273). This document reflects only the authors views and the European Union is not liable for any use that may be made of the information contained herein

Minimum information about a biofilm experiment (MIABiE) : standards for reporting experiments and data on sessile microbial communities living at interfaces

The minimum information about a biofilm experiment (MIABiE) initiative has arisen from the need to find an adequate and scientifically sound way to control the quality of the documentation accompanying the public deposition of biofilm-related data, particularly those obtained using high-throughput devices and techniques. Thereby, the MIABiE consortium has initiated the identification and organization of a set of modules containing the minimum information that needs to be reported to guarantee the interpretability and independent verification of experimental results and their integration with knowledge coming from other fields. MIABiE does not intend to propose specific standards on how biofilms experiments should be performed, because it is acknowledged that specific research questions require specific conditions which may deviate from any standardization. Instead, MIABiE presents guidelines about the data to be recorded and published in order for the procedure and results to be easily and unequivocally interpreted and reproduced. Overall, MIABiE opens up the discussion about a number of particular areas of interest and attempts to achieve a broad consensus about which biofilm data and metadata should be reported in scientific journals in a systematic, rigorous and understandable manner.The authors would like to thank Thomas Bjarnsholt and Adyary Fallarero for a critical revision of the manuscript. This work was supported by IBB-CEB; Fundacao para a Ciencia e Tecnologia (FCT); the European Community fund FEDER, through Program COMPETE, in the ambit of the FCT Project PTDC/SAU-SAP/113196/2009/FCOMP-01-0124-FEDER-0 16012; the European Union Seventh Framework Programme [FP7/REGPOT-2012-2013.1] under Grant Agreement No. 316265, BIOCAPS; the Agrupamento INBIOMED from DXPCTSUG-FEDER unha maneira de facer Europa (2012/273). T. C. would like to thank FWO Vlaanderen and the Interuniversity Attraction Poles Programme initiated by the Belgian Science Policy Office for funding

RNA binding protein Caprin-2 is a pivotal regulator of the central osmotic defense response

In response to an osmotic challenge, the synthesis of the antidiuretic hormone arginine vasopressin (AVP) increases in the hypothalamus, and this is accompanied by extension of the 3′ poly(A) tail of the AVP mRNA, and the up-regulation of the expression of RNA binding protein Caprin-2. Here we show that Caprin-2 binds to AVP mRNAs, and that lentiviral mediated shRNA knockdown of Caprin-2 in the osmotically stimulated hypothalamus shortens the AVP mRNA poly(A) tail at the same time as reducing transcript abundance. In a recapitulated in vitro system, we confirm that Caprin-2 over-expression enhances AVP mRNA abundance and poly(A) tail length. Importantly, we show that Caprin-2 knockdown in the hypothalamus decreases urine output and fluid intake, and increases urine osmolality, urine sodium concentration, and plasma AVP levels. Thus Caprin-2 controls physiological mechanisms that are essential for the body's response to osmotic stress. DOI: http://dx.doi.org/10.7554/eLife.09656.00

ProteomeScout: A repository and analysis resource for post-translational modifications and proteins

ProteomeScout (https://proteomescout.wustl.edu) is a resource for the study of proteins and their post-translational modifications (PTMs) consisting of a database of PTMs, a repository for experimental data, an analysis suite for PTM experiments, and a tool for visualizing the relationships between complex protein annotations. The PTM database is a compendium of public PTM data, coupled with user-uploaded experimental data. ProteomeScout provides analysis tools for experimental datasets, including summary views and subset selection, which can identify relationships within subsets of data by testing for statistically significant enrichment of protein annotations. Protein annotations are incorporated in the ProteomeScout database from external resources and include terms such as Gene Ontology annotations, domains, secondary structure and non-synonymous polymorphisms. These annotations are available in the database download, in the analysis tools and in the protein viewer. The protein viewer allows for the simultaneous visualization of annotations in an interactive web graphic, which can be exported in Scalable Vector Graphics (SVG) format. Finally, quantitative data measurements associated with public experiments are also easily viewable within protein records, allowing researchers to see how PTMs change across different contexts. ProteomeScout should prove useful for protein researchers and should benefit the proteomics community by providing a stable repository for PTM experiments

Identification and characterization of a novel zebrafish (Danio rerio) pentraxin–carbonic anhydrase

Background Carbonic anhydrases (CAs) are ubiquitous, essential enzymes which catalyze the conversion of carbon dioxide and water to bicarbonate and H+ ions. Vertebrate genomes generally contain gene loci for 15–21 different CA isoforms, three of which are enzymatically inactive. CA VI is the only secretory protein of the enzymatically active isoforms. We discovered that non-mammalian CA VI contains a C-terminal pentraxin (PTX) domain, a novel combination for both CAs and PTXs. Methods We isolated and sequenced zebrafish (Danio rerio) CA VI cDNA, complete with the sequence coding for the PTX domain, and produced the recombinant CA VI–PTX protein. Enzymatic activity and kinetic parameters were measured with a stopped-flow instrument. Mass spectrometry, analytical gel filtration and dynamic light scattering were used for biophysical characterization. Sequence analyses and Bayesian phylogenetics were used in generating hypotheses of protein structure and CA VI gene evolution. A CA VI–PTX antiserum was produced, and the expression of CA VI protein was studied by immunohistochemistry. A knock-down zebrafish model was constructed, and larvae were observed up to five days post-fertilization (dpf). The expression of ca6 mRNA was quantitated by qRT-PCR in different developmental times in morphant and wild-type larvae and in different adult fish tissues. Finally, the swimming behavior of the morphant fish was compared to that of wild-type fish. Results The recombinant enzyme has a very high carbonate dehydratase activity. Sequencing confirms a 530-residue protein identical to one of the predicted proteins in the Ensembl database (ensembl.org). The protein is pentameric in solution, as studied by gel filtration and light scattering, presumably joined by the PTX domains. Mass spectrometry confirms the predicted signal peptide cleavage and disulfides, and N-glycosylation in two of the four observed glycosylation motifs. Molecular modeling of the pentamer is consistent with the modifications observed in mass spectrometry. Phylogenetics and sequence analyses provide a consistent hypothesis of the evolutionary history of domains associated with CA VI in mammals and non-mammals. Briefly, the evidence suggests that ancestral CA VI was a transmembrane protein, the exon coding for the cytoplasmic domain was replaced by one coding for PTX domain, and finally, in the therian lineage, the PTX-coding exon was lost. We knocked down CA VI expression in zebrafish embryos with antisense morpholino oligonucleotides, resulting in phenotype features of decreased buoyancy and swim bladder deflation in 4 dpf larvae. Discussion These findings provide novel insights into the evolution, structure, and function of this unique CA form