Diversity of olfactomedin proteins in the sea urchin

AbstractOlfactomedin (OLF) domain proteins maintain extracellular protein-protein interactions in diverse phyla. Only one OLF family member, amassin-1, has been described from the sea urchin Strongylocentrotus purpuratus, a basal invertebrate deuterostome. Amassin-1 mediates intercellular adhesion of coelomocytes (immunocytes). Here we describe the protein structural features of four additional OLF proteins, the total for the genome being five. Phylogenetically, four of these proteins (the amassins) form a subgroup among previously identified OLF proteins. The fifth OLF protein is within the colmedin subfamily and contains a type II transmembrane domain, collagen repeats, and an OLF domain. Sea urchin OLF proteins represent an intermediate diversification between protostomes and vertebrates. Transcripts of all five OLF family members are in coelomocytes and adult radial nerve tissue. Transcripts for some OLF proteins increase during late larval stages. Transcript levels for amassin-1 increase 1,000,000-fold, coinciding with formation of the adult urchin rudiment within the larval body

The Weaklaw Vent, SE Scotland:Metasomatism of eruptive products by carbo-hydro-fluids of probable mantle origin

This is the author accepted manuscript. The final version is available from CUP via the DOI in this record The Weaklaw vent in SE Scotland (East Lothian coast), inferred to be Namurian, produced lava spatter and volcanic bombs. The latter commonly contained ultramafic xenoliths. All were metasomatised by carbonic fluids rich in incompatible elements. The lavas and xenoliths are inferred to have been basanites and lherzolites prior to metasomatism. The abundance and size of (carbonated) peridotite xenoliths at Weaklaw denotes unusual rapidity of magma ascent and high-energy eruption making Weaklaw exceptional in the British Isles. The lavas and xenoliths were altered subsequently by low-temperature (<200°C) carbo-hydrous fluids to carbonate, clay and quartz assemblages. A small irregular tuffisite 'dyke' that transects the ejecta is also composed dominantly of carbonates and clays. The peridotitic xenoliths are typically foliated, interpreted as originating as pre-entrainment mantle shear-planes. Analyses of the relic spinels shows them to be compositionally similar to spinels in local unaltered lherzolites from near-by basanitic occurrences. Chromium showed neither significant loss nor gain but was concentrated in a di-octahedral smectite allied to volkonskoite. It is in the complex association of smectite with other clays, chlorite and possibly fuchsite that the diverse incompatible elements are concentrated. We conclude that late Palaeozoic trans-tensional fault movement caused mantle shearing. Rapid ascent of basanite magma entrained large quantities of sheared lithospheric mantle. This was followed by ascent of an aggressive carbonate-/ hydroxyl-rich fluid causing pervasive metasomatism. The vent is unique in several ways: in its remarkable clay mineralogy and in displaying such high Cr-clays in a continental intra-plate setting; in being more productive in terms of its 'cargo' of peridotite xenoliths; in presenting an essentially un-eroded sequence of Namurian extrusives; and, not least, for giving evidence for post-eruptive, surface release of small-melt, deep-source fluids

Measuring nickel masses in Type Ia supernovae using cobalt emission in nebular phase spectra

The light curves of Type Ia supernovae (SNe Ia) are powered by the radioactive decay of $^{56}$Ni to $^{56}$Co at early times, and the decay of $^{56}$Co to $^{56}$Fe from ~60 days after explosion. We examine the evolution of the [Co III] 5892 A emission complex during the nebular phase for SNe Ia with multiple nebular spectra and show that the line flux follows the square of the mass of $^{56}$Co as a function of time. This result indicates both efficient local energy deposition from positrons produced in $^{56}$Co decay, and long-term stability of the ionization state of the nebula. We compile 77 nebular spectra of 25 SN Ia from the literature and present 17 new nebular spectra of 7 SNe Ia, including SN2014J. From these we measure the flux in the [Co III] 5892 A line and remove its well-behaved time dependence to infer the initial mass of $^{56}$Ni ($M_{Ni}$) produced in the explosion. We then examine $^{56}$Ni yields for different SN Ia ejected masses ($M_{ej}$ - calculated using the relation between light curve width and ejected mass) and find the $^{56}$Ni masses of SNe Ia fall into two regimes: for narrow light curves (low stretch s~0.7-0.9), $M_{Ni}$ is clustered near $M_{Ni}$ ~ 0.4$M_\odot$ and shows a shallow increase as $M_{ej}$ increases from ~1-1.4$M_\odot$; at high stretch, $M_{ej}$ clusters at the Chandrasekhar mass (1.4$M_\odot$) while $M_{Ni}$ spans a broad range from 0.6-1.2$M_\odot$. This could constitute evidence for two distinct SN Ia explosion mechanisms.Comment: 16 pages, 12 figures (main text), plus data tables in appendix. Spectra released on WISeREP. Submitted to MNRAS, comments welcom

Global Research Alliance N2O chamber methodology guidelines : Summary of modeling approaches

Acknowledgements Funding for this publication was provided by the New Zealand Government to support the objectives of the Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gases. Individual authors work contribute to the following projects for which support has been received: Climate smart use of Norwegian organic soils (MYR, 2017-2022) project funded by the Research Council of Norway (decision no. 281109); Scottish Government's Strategic Research Programme, SuperG (under EU Horizon 2020 programme); DEVIL (NE/M021327/1), Soils-R-GRREAT (NE/P019455/1) and the EU H2020 project under Grant Agreement 774378—Coordination of International Research Cooperation on Soil Carbon Sequestration in Agriculture (CIRCASA); to project J-001793, Science and Technology Branch, Agriculture and Agri-Food Canada; and New Zealand Ministry of Business, Innovation and Employment (MBIE) core funding. Thanks to Alasdair Noble and the anonymous reviewers for helpful comments on a draft of this paper and to Anne Austin for editing services.Peer reviewedPublisher PD

The Efficacy of Vaginal Clindamycin for the Treatment of Abnormal Genital Tract Flora in Pregnancy

Objective: To assess the efficacy of 2% clindamycin vaginal cream (CVC) to treat bacterial vaginosis (BV) in pregnancy. Methods: A prospective, randomized, double-blind, placebo-controlled, tricenter study. Four hundred and four women with BV on Gram stain at their first antenatal clinic visit were randomized to receive a 3-day course of 2% CVC or placebo. The outcome was assessed using an intention to treat analysis at 3 weeks and 6 weeks post-treatment according to three different diagnostic methods based on five criteria (Gram stain and all four elements of clinical composite criteria: vaginal discharge, abnormal vaginal pH, clue cells, amine odor), three criteria (vaginal pH, clue cells, amine odor) or two criteria (clue cells and amine odor) to reflect stringency of diagnosis, historical precedence and government agency recommendations respectively. Results: Using five diagnostic criteria, 18% of CVC patients were cured and 70.8% either cured and/or improved compared to 1.6% and 12% of placebo patients respectively (p < 0.0001). Using three diagnostic criteria, 44.8% of CVC patients were cured and 77.3% were either cured and/or improved compared to 9.3% and 28.8% of placebo patients respectively (p < 0.0001). Using two diagnostic criteria, 75.0% of CVC patients were cured compared to 18.0% of placebo patients (p < 0.0001). Recurrence rates in those CVC patients successfully treated were approximately 6% at 6 weeks post baseline and 10% at 28 to 34 weeks gestation. Conclusions: A 3-day course of CVC appears to be well tolerated by the mother and statistically significantly more efficacious than placebo in the treatment of BV during the second trimester of pregnancy

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms ( SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds ( a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines - in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases

Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster

Many animal species use a chromosome-based mechanism of sex determination, which has led to the coordinate evolution of dosage-compensation systems. Dosage compensation not only corrects the imbalance in the number of X chromosomes between the sexes but also is hypothesized to correct dosage imbalance within cells that is due to monoallelic X-linked expression and biallelic autosomal expression, by upregulating X-linked genes twofold (termed ‘Ohno’s hypothesis’). Although this hypothesis is well supported by expression analyses of individual X-linked genes and by microarray-based transcriptome analyses, it was challenged by a recent study using RNA sequencing and proteomics. We obtained new, independent RNA-seq data, measured RNA polymerase distribution and reanalyzed published expression data in mammals, C. elegans and Drosophila. Our analyses, which take into account the skewed gene content of the X chromosome, support the hypothesis of upregulation of expressed X-linked genes to balance expression of the genome

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication

Little is known about the genetic changes that distinguish domestic cat populations from their wild progenitors. Here we describe a high-quality domestic cat reference genome assembly and comparative inferences made with other cat breeds, wildcats, and other mammals. Based upon these comparisons, we identified positively selected genes enriched for genes involved in lipid metabolism that underpin adaptations to a hypercarnivorous diet. We also found positive selection signals within genes underlying sensory processes, especially those affecting vision and hearing in the carnivore lineage. We observed an evolutionary tradeoff between functional olfactory and vomeronasal receptor gene repertoires in the cat and dog genomes, with an expansion of the feline chemosensory system for detecting pheromones at the expense of odorant detection. Genomic regions harboring signatures of natural selection that distinguish domestic cats from their wild congeners are enriched in neural crest-related genes associated with behavior and reward in mouse models, as predicted by the domestication syndrome hypothesis. Our description of a previously unidentified allele for the gloving pigmentation pattern found in the Birman breed supports the hypothesis that cat breeds experienced strong selection on specific mutations drawn from random bred populations. Collectively, these findings provide insight into how the process of domestication altered the ancestral wildcat genome and build a resource for future disease mapping and phylogenomic studies across all members of the Felidae