Measurement of the ttbar Production Cross Section in ppbar Collisions at sqrt(s)=1.96 TeV using Lepton + Jets Events with Lifetime b-tagging

We present a measurement of the top quark pair ($t\bar{t}$) production cross section ($\sigma_{t\bar{t}}$) in $p\bar{p}$ collisions at $\sqrt{s}=1.96$ TeV using 230 pb$^{-1}$ of data collected by the D0 experiment at the Fermilab Tevatron Collider. We select events with one charged lepton (electron or muon), missing transverse energy, and jets in the final state. We employ lifetime-based b-jet identification techniques to further enhance the $t\bar{t}$ purity of the selected sample. For a top quark mass of 175 GeV, we measure $\sigma_{t\bar{t}}=8.6^{+1.6}_{-1.5}(stat.+syst.)\pm 0.6(lumi.)$ pb, in agreement with the standard model expectation.Comment: 7 pages, 2 figures, 3 tables Submitted to Phys.Rev.Let

Keratinocytes drive the epithelial hyperplasia key to sea lice resistance in coho salmon

Background Salmonid species have followed markedly divergent evolutionary trajectories in their interactions with sea lice. While sea lice parasitism poses significant economic, environmental, and animal welfare challenges for Atlantic salmon (Salmo salar) aquaculture, coho salmon (Oncorhynchus kisutch) exhibit near-complete resistance to sea lice, achieved through a potent epithelial hyperplasia response leading to rapid louse detachment. The molecular mechanisms underlying these divergent responses to sea lice are unknown. Results We characterized the cellular and molecular responses of Atlantic salmon and coho salmon to sea lice using single-nuclei RNA sequencing. Juvenile fish were exposed to copepodid sea lice (Lepeophtheirus salmonis), and lice attached pelvic fin and skin samples were collected 12 h, 24 h, 36 h, 48 h, and 60 h after exposure, along with control samples. Comparative analysis of control and treatment samples revealed an immune and wound-healing response that was common to both species, but attenuated in Atlantic salmon, potentially reflecting greater sea louse immunomodulation. Our results revealed unique but complementary roles of three layers of keratinocytes in the epithelial hyperplasia response leading to rapid sea lice rejection in coho salmon. Our results suggest that basal keratinocytes direct the expansion and mobility of intermediate and, especially, superficial keratinocytes, which eventually encapsulate the parasite. Conclusions Our results highlight the key role of keratinocytes in coho salmon’s sea lice resistance and the diverged biological response of the two salmonid host species when interacting with this parasite. This study has identified key pathways and candidate genes that could be manipulated using various biotechnological solutions to improve Atlantic salmon sea lice resistance.publishedVersio

Co-infections and multiple stressors in fish

Fish are typically exposed to multiple physical, chemical and biological stressors. The cumulative impact of co-infections between parasites, bacteria, viruses and (a)biotic environmental pressures may trigger complex interactions, eliciting different pathological and immunological outcomes than those classically assessed. New cross-disciplinary studies attempt to measure the impact of environmental stressors in modulating the host response to pathogens. Scientific advances are needed to reduce pressure on natural populations, improve fish stock management, and to design more efficient diagnostic tools or vaccination strategies. An EAFP-promoted workshop, held on 10th September 2019 in Porto, Portugal, was dedicated to sharing research experiences on the interaction between heterogenous pathogens and multiple stressors in fish. The workshop involved around 200 attendants, opened by a keynote talk (Fast), and followed by a further twelve oral presentations, including three in the format of lash poster presentations. Contributions illustrated cross-disciplinary approaches to study complex host-pathogen and stressors interactions

5A apolipoprotein mimetic peptide promotes cholesterol efflux and reduces atherosclerosis in mice

ABSTRACT Intravenous administration of apoA-I complexed with phospholipid has been shown to rapidly reduce plaque size in both animal models and in humans. Short synthetic amphipathic peptides can mimic the anti-atherogenic properties of apoA-I and have been proposed as alternative therapeutic agents. In this study, we investigated the atheroprotective effect of the 5A peptide, a bi-helical amphipathic peptide that specifically effluxes cholesterol from cells by the ABCA1 transporter. 5A stimulated a 3.5-fold increase in ABCA1 mediated efflux from cells and a further 2.5-fold increase after complexing it with phospholipid (5A:POPC [1:7 mol/mol]). 5A:POPC but not free 5A was also found to promote cholesterol efflux by ABCG1. When incubated with human serum, 5A-POPC primarily bound to HDL but also to LDL and promoted the transfer of cholesterol from LDL to HDL. 24 hours following IV injection of 5A-POPC (30 mg/kg) into apoE-KO mice, both the cholesterol (181%) and phospholipid (219%) content of HDL significantly increased. By an in vivo cholesterol isotope dilution stud

One thousand plant transcriptomes and the phylogenomics of green plants

Abstract: Green plants (Viridiplantae) include around 450,000–500,000 species1, 2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life

Prostaglandin E(2) modulation of gene expression in an Atlantic salmon (Salmo salar) macrophage-like cell line (SHK-1).

Following lipopolysaccharide (LPS)-stimulation of Atlantic salmon (Salmo salar) macrophage-like SHK-1 cells, prostaglandin E(2) (PGE(2)) exhibited dose-dependent inhibition of the antigen presenting molecules major histocompatability class I and II and the pro-inflammatory cytokine interleukin-1 beta gene expression. Prostaglandin E(2) was found to be stimulatory towards cyclooxygenase-2 (COX-2) expression at higher concentrations (1 x 10(-6) and 1 x 10(-8)M) and inhibitory at lower concentrations (1 x 10(-10) and 1 x 10(-12)M) after 4h exposure. After 24h exposure, however, LPS-induced COX-2 expression decreased and was completely inhibited by all PGE(2) concentrations (1 x 10(-6)-1 x 10(-10)M). Incubation of SHK-1 cells with LPS alone had no effect on tumour necrosis factor alpha (TNFalpha)-like gene or transforming growth factor beta-like gene expression after 4h, however, LPS and PGE(2) showed a synergistic effect on TNFalpha-like gene expression after 24h. This study provides evidence for the existence of a PGE(2)-mediated negative feedback mechanism in the control of PGs through down-regulation of COX-2, as well as for inflammatory responses by the down-regulation of both COX-2 and IL-1 beta. The differential regulation of immune-related genes under these conditions further demonstrates the usefulness of the SHK-1 cell line for studying aspects of salmonid immunology

Spatial patterns in markers of contaminant exposure, glucose and glycogen metabolism, and immunological response in juvenile winter flounder (Pseudopleuronectes americanus)

Inshore winter flounder (Pseudopleuronectes americanus) populations in NY, USA have reached record low numbers in recent years, and recruitment into the fishery appears to be limited by survival of post-settlement juvenile fish. In order to identify cellular pathways associated with site-specific variation in condition and mortality, we examined differential mRNA expression in juvenile winter flounder collected from six different bays across a gradient in human population density and sewage inputs. Illumina sequencing of pooled samples of flounder from contrasting degraded sites and less impacted sites was used to guide our choice of targets for qPCR analysis. 253 transcripts of > 100 bp were differentially expressed, with 60% showing strong homology to mostly teleost sequences within the NCBI database. Based on these data, transcripts representing nine genes of interest associated with contaminant exposure, immune response and glucose and glycogen metabolism were examined by qPCR in individual flounder from each site. Statistically significant site-specific differences were observed in expression of all but one gene, although patterns in expression were complex with only one, (vitellogenin) demonstrating a west to east gradient consistent with known loadings of municipal sewage effluent. Principal components analysis (PCA) identified relationships among the genes evaluated. Our data indicate that juvenile winter flounder are responding to estrogenic chemicals in more urbanized coastal bays, and suggests potential mechanistic links between immune response, contaminant exposure and energy metabolism