New V. cholerae atypical El Tor variant emerged during the 2006 epidemic outbreak in Angola

<p>Abstract</p> <p>Background</p> <p><it>V. cholerae </it>is the etiological agent of cholera, a major public health concern in most developing countries. Virulence of <it>V. cholerae </it>relies on the powerful cholera toxin, encoded by the CTX prophage. The emergence of new pathogenic variants in the recent years has been mostly associated with new CTX prophage rearrangements.</p> <p>Results</p> <p>In this retrospective study, we show that the epidemic <it>V. cholerae </it>O1 El Tor strain responsible for the 2006 outbreak in Angola is clonally and genetically different from El Tor strains circulating in the 1990s in the same area. Strains from 2006 carry ICE<it>Vch</it>Ang3 of the SXT/R391 family. This ICE is associated with a narrower multidrug resistance profile compared to the one conferred by plasmid p3iANG to strains of the 1990s. The CTX prophage carried by 2006 El Tor strains is characterized by <it>rstR^ET</it>and <it>ctxB^Cla</it>alleles organized in a RS1-RS2-Core array on chromosome I. Interestingly, the newly emerging atypical strain belongs to a clade previously known to comprise only clinical isolates from the Indian subcontinent that also contain the same ICE of the SXT/R391 family.</p> <p>Conclusions</p> <p>Our findings remark the appearance of a novel <it>V. cholerae </it>epidemic variant in Africa with a new CTXΦ arrangement previously described only in the Indian Subcontinent.</p

How to meet new global targets in the offshore realms: biophysical guidelines for offshore networks of no-take marine protected areas

Networks of no-take marine protected areas (MPAs), where all extractive activities are prohibited, are the most effective tool to directly protect marine ecosystems from destructive and unsustainable human activities. No-take MPAs and MPA networks have been globally implemented in coastal seas, and their success has been significantly enhanced where science-based biophysical guidelines have informed their design. Increasingly, as human pressure on marine ecosystems is expanding further offshore, governments are establishing offshore MPAs—some very large—or MPA networks. Globally, there are growing calls from scientists, non-government organisations, and national governments to set global conservation targets upwards of 30%. Given that most of the ocean is found either in the high seas or offshore within national Exclusive Economic Zones, large offshore MPAs or networks of MPAs must be a major component of these global targets for ocean protection. However, without adequate design, these offshore MPAs risk being placed to minimise conflict with economic interests, rather than to maximise biodiversity protection. This paper describes detailed biophysical guidelines that managers can use to design effective networks of no-take MPAs in offshore environments. We conducted a systematic review of existing biophysical design guidelines for networks of MPAs in coastal seas, and found consistent elements relating to size, shape, connectivity, timeframes, and representation of biophysical features. However, few of the guidelines are tailored to offshore environments, and few of the large offshore MPAs currently in place were designed systematically. We discuss how the common inshore design guidelines should be revised to be responsive to the characteristics of offshore ecosystems, including giving consideration of issues of scale, data availability, and uncertainty. We propose 10 biophysical guidelines that can be used to systematically design offshore networks of MPAs which will also contribute to the global goal of at least 30% protection globally. Finally, we offer three priority guidelines that reflect the unique conservation needs of offshore ecosystems: emphasising the need for larger MPAs; maximising the inclusion of special features that are known and mapped; and representing minimum percentages of habitats, or, where mapped, bioregions. Ultimately, MPA guidelines need to be embedded within an adaptive management framework, and have the flexibility to respond to emerging knowledge and new challenges

Crystal structures of Leptospira interrogans FAD-containing ferredoxin-NADP+ reductase and its complex with NADP+

<p>Abstract</p> <p>Background</p> <p>Ferredoxin-NADP(H) reductases (FNRs) are flavoenzymes that catalyze the electron transfer between NADP(H) and the proteins ferredoxin or flavodoxin. A number of structural features distinguish plant and bacterial FNRs, one of which is the mode of the cofactor FAD binding. <it>Leptospira interrogans </it>is a spirochaete parasitic bacterium capable of infecting humans and mammals in general. <it>Leptospira interrogans </it>FNR (LepFNR) displays low sequence identity with plant (34% with <it>Zea mays</it>) and bacterial (31% with <it>Escherichia coli</it>) FNRs. However, LepFNR contains all consensus sequences that define the plastidic class FNRs.</p> <p>Results</p> <p>The crystal structures of the FAD-containing LepFNR and the complex of the enzyme with NADP⁺, were solved and compared to known FNRs. The comparison reveals significant structural similarities of the enzyme with the plastidic type FNRs and differences with the bacterial enzymes. Our small angle X-ray scattering experiments show that LepFNR is a monomeric enzyme. Moreover, our biochemical data demonstrate that the LepFNR has an enzymatic activity similar to those reported for the plastidic enzymes and that is significantly different from bacterial flavoenzymes, which display lower turnover rates.</p> <p>Conclusion</p> <p>LepFNR is the first plastidic type FNR found in bacteria and, despite of its low sequence similarity with plastidic FNRs still displays high catalytic turnover rates. The typical structural and biochemical characteristics of plant FNRs unveiled for LepFNR support a notion of a putative lateral gene transfer which presumably offers <it>Leptospira interrogans </it>evolutionary advantages. The wealth of structural information about LepFNR provides a molecular basis for advanced drugs developments against leptospirosis.</p

Discriminating Catch Composition and Fishing Modes in an Artisanal Multispecies Fishery

Many small-scale fisheries are multi-species, and the catch composition can vary according to available habitats, fishing modes, and fisher groups. Here, we applied novel analyses for understanding the factors affecting differences in catch composition among fishers, which should be useful for planning regulatory measures and fishery development initiatives. Interviews with 235 artisanal fishers in Fiji were used to analyse how fishers' catch composition of 22 species of sea cucumbers varied across geographic scales (locations and villages within locations), genders, and fishing modes. Venn diagrams illustrated that gleaning and SCUBA diving were practiced to varying extents among locations and genders, whereas fishers used breath-hold diving more uniformly across the fishery. Segmented bubble plots revealed spatial variations in catch composition across the fishery. A PERMANOVA analysis found that species catch composition varied most across the two geographic scales and, secondarily, among fishing modes and between men and women. Gendered differences in catch composition were variable from one village to another, and so should not be generalized. SIMPER analyses showed that gleaners and SCUBA divers caught significantly different suites of sea cucumber species. Species threatened with extinction were among those typifying catches of SCUBA divers. Our novel graphical techniques are useful for visualizing fishing modes and catches across other fisheries. Artisanal fisheries may exhibit strong heterogeneity in catches at multiple spatial scales. Planning of regulatory measures that limit certain fishing modes or species should take into account the likely differential impacts on different fishing communities and genders

Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma

Therapy development for adult diffuse glioma is hindered by incomplete knowledge of somatic glioma driving alterations and suboptimal disease classification. We defined the complete set of genes associated with 1,122 diffuse grade II-III-IV gliomas from The Cancer Genome Atlas and used molecular profiles to improve disease classification, identify molecular correlations, and provide insights into the progression from low- to high-grade disease. Whole-genome sequencing data analysis determined that ATRX but not TERT promoter mutations are associated with increased telomere length. Recent advances in glioma classification based on IDH mutation and 1p/19q co-deletion status were recapitulated through analysis of DNA methylation profiles, which identified clinically relevant molecular subsets. A subtype of IDH mutant glioma was associated with DNA demethylation and poor outcome; a group of IDH-wild-type diffuse glioma showed molecular similarity to pilocytic astrocytoma and relatively favorable survival. Understanding of cohesive disease groups may aid improved clinical outcomes

Development and validation of HERWIG 7 tunes from CMS underlying-event measurements

This paper presents new sets of parameters (“tunes”) for the underlying-event model of the HERWIG7 event generator. These parameters control the description of multiple-parton interactions (MPI) and colour reconnection in HERWIG7, and are obtained from a fit to minimum-bias data collected by the CMS experiment at s=0.9, 7, and 13Te. The tunes are based on the NNPDF 3.1 next-to-next-to-leading-order parton distribution function (PDF) set for the parton shower, and either a leading-order or next-to-next-to-leading-order PDF set for the simulation of MPI and the beam remnants. Predictions utilizing the tunes are produced for event shape observables in electron-positron collisions, and for minimum-bias, inclusive jet, top quark pair, and Z and W boson events in proton-proton collisions, and are compared with data. Each of the new tunes describes the data at a reasonable level, and the tunes using a leading-order PDF for the simulation of MPI provide the best description of the dat

Measurement of B-c(2S)(+) and B-c*(2S)(+) cross section ratios in proton-proton collisions at root s=13 TeV

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