Protein-DNA charge transport: Redox activation of a DNA repair protein by guanine radical

DNA charge transport (CT) chemistry provides a route to carry out oxidative DNA damage from a distance in a reaction that is sensitive to DNA mismatches and lesions. Here, DNA-mediated CT also leads to oxidation of a DNA-bound base excision repair enzyme, MutY. DNA-bound Ru(III), generated through a flash/quench technique, is found to promote oxidation of the [4Fe-4S](2+) cluster of MutY to [4Fe-4S](3+) and its decomposition product [3Fe-4S](1+). Flash/quench experiments monitored by EPR spectroscopy reveal spectra with g = 2.08, 2.06, and 2.02, characteristic of the oxidized clusters. Transient absorption spectra of poly(dGC) and [Ru(phen)(2)dppz](3+) (dppz = dipyridophenazine), generated in situ, show an absorption characteristic of the guanine radical that is depleted in the presence of MutY with formation instead of a long-lived species with an absorption at 405 nm; we attribute this absorption also to formation of the oxidized [4Fe-4S](3+) and [3Fe4S](1+) clusters. In ruthenium-tethered DNA assemblies, oxidative damage to the 5'-G of a 5'-GG-3' doublet is generated from a distance but this irreversible damage is inhibited by MutY and instead EPR experiments reveal cluster oxidation. With ruthenium-tethered assemblies containing duplex versus single-stranded regions, MutY oxidation is found to be mediated by the DNA duplex, with guanine radical as an intermediate oxidant; guanine radical formation facilitates MutY oxidation. A model is proposed for the redox activation of DNA repair proteins through DNA CT, with guanine radicals, the first product under oxidative stress, in oxidizing the DNA-bound repair proteins, providing the signal to stimulate DNA repair

The effect of mixing entire male pigs prior to transport to slaughter on behaviour, welfare and carcass lesions

peer-reviewedData set for article is also provided.Research is needed to validate lesions recorded at meat inspection as indicators of pig welfare on farm. The aims were to determine the influence of mixing pigs on carcass lesions and to establish whether such lesions correlate with pig behaviour and lesions scored on farm. Aggressive and mounting behaviour of pigs in three single sex pens was recorded on Day −5, −2, and −1 relative to slaughter (Day 0). On Day 0 pigs were randomly allocated to 3 treatments (n = 20/group) over 5 replicates: males mixed with females (MF), males mixed with males (MM), and males unmixed (MUM). Aggressive and mounting behaviours were recorded on Day 0 at holding on farm and lairage. Skin/tail lesions were scored according to severity at the farm (Day −1), lairage, and on the carcass (Day 0). Effect of treatment and time on behaviour and lesions were analysed by mixed models. Spearman rank correlations between behaviour and lesion scores and between scores recorded at different stages were determined. In general, MM performed more aggressive behaviour (50.4 ± 10.72) than MUM (20.3 ± 9.55, P < 0.05) and more mounting (30.9 ± 9.99) than MF (11.4 ± 3.76) and MUM (9.8 ± 3.74, P < 0.05). Skin lesion scores increased between farm (Day −1) and lairage (P < 0.001), but this tended to be significant only for MF and MM (P = 0.08). There was no effect of treatment on carcass lesions and no associations were found with fighting/mounting. Mixing entire males prior to slaughter stimulated mounting and aggressive behaviour but did not influence carcass lesion scores. Carcass skin/tail lesions scores were correlated with scores recorded on farm (rskin = 0.21 and rtail = 0.18, P < 0.01) suggesting that information recorded at meat inspection could be used as indicators of pig welfare on farm.This study was part of the PIGWELFIND project funded by the Department of Agriculture, Food and the Marine (DAFM), Ireland

Archaeobotany in Australia and New Guinea: practice, potential and prospects

Archaeobotany is the study of plant remains from archaeological contexts. Despite Australasian research being at the forefront of several methodological innovations over the last three decades, archaebotany is now a relatively peripheral concern to most archaeological projects in Australia and New Guinea. In this paper, many practicing archaeobotanists working in these regions argue for a more central role for archaeobotany in standard archaeological practice. An overview of archaeobotanical techniques and applications is presented, the potential for archaeobotany to address key historical research questions is indicated, and initiatives designed to promote archaeobotany and improve current practices are outlined

Archaeobotany in Australia and New Guinea: practice, potential and prospects

Archaeobotany is the study of plant remains from archaeological contexts. Despite Australasian research being at the forefront of several methodological innovations over the last three decades, archaebotany is now a relatively peripheral concern to most archaeological projects in Australia and New Guinea. In this paper, many practicing archaeobotanists working in these regions argue for a more central role for archaeobotany in standard archaeological practice. An overview of archaeobotanical techniques and applications is presented, the potential for archaeobotany to address key historical research questions is indicated, and initiatives designed to promote archaeobotany and improve current practices are outlined

PRIMUS: Enhanced Specific Star Formation Rates In Close Galaxy Pairs

Tidal interactions between galaxies can trigger star formation, which contributes to the global star formation rate density of the universe and could be a factor in the transformation of blue, star-forming galaxies to red, quiescent galaxies over cosmic time. We investigate tidally-triggered star formation in isolated close galaxy pairs drawn from the Prism Multi-Object Survey (PRIMUS), a low-dispersion prism redshift survey that has measured ~120,000 robust galaxy redshifts over 9.1 deg^2 out to z ~ 1. We select a sample of galaxies in isolated galaxy pairs at redshifts 0.25 < z < 0.75, with no other objects within a projected separation of 300 h^-1 kpc and dz/(1+z) = 0.01, and compare them to a control sample of isolated galaxies to test for systematic differences in their rest-frame FUV-r and NUV-r colors as a proxy for relative specific SFR. We find that galaxies in r_p < 50 h^-1 kpc pairs have bluer dust-corrected UV-r colors on average than the control galaxies by -0.134 +/- 0.045 magnitudes in FUV-r and -0.075 +/- 0.038 magnitudes in NUV-r, corresponding to a ~15-20% increase in SSFR. This indicates an enhancement in SSFR due to tidal interactions. We also find that this relative enhancement is greater for a subset of r_p < 30 h^-1 kpc pair galaxies, for which the average colors offsets are -0.193 +/- 0.065 magnitudes in FUV-r and -0.159 +/- 0.048 magnitudes in NUV-r, corresponding to a ~25-30% increase in SSFR. We test for evolution in the enhancement of tidally-triggered star formation with redshift across our sample redshift range and find marginal evidence for a decrease in SSFR enhancement from 0.25 < z < 0.5 to 0.5 < z < 0.75. This indicates that a change in enhanced star formation triggered by tidal interactions in low density environments is not a contributor to the decline in the global star formation rate density across this redshift range.Comment: Accepted for publication in ApJ, emulateapj format, 12 pages, 9 figures, 2 table

Genome-Wide Association Study and Gene Expression Analysis Identifies CD84 as a Predictor of Response to Etanercept Therapy in Rheumatoid Arthritis

Anti-tumor necrosis factor alpha (anti-TNF) biologic therapy is a widely used treatment for rheumatoid arthritis (RA). It is unknown why some RA patients fail to respond adequately to anti-TNF therapy, which limits the development of clinical biomarkers to predict response or new drugs to target refractory cases. To understand the biological basis of response to anti-TNF therapy, we conducted a genome-wide association study (GWAS) meta-analysis of more than 2 million common variants in 2,706 RA patients from 13 different collections. Patients were treated with one of three anti-TNF medications: etanercept (n = 733), infliximab (n = 894), or adalimumab (n = 1,071). We identified a SNP (rs6427528) at the 1q23 locus that was associated with change in disease activity score (ΔDAS) in the etanercept subset of patients (P = 8×10-8), but not in the infliximab or adalimumab subsets (P>0.05). The SNP is predicted to disrupt transcription factor binding site motifs in the 3′ UTR of an immune-related gene, CD84, and the allele associated with better response to etanercept was associated with higher CD84 gene expression in peripheral blood mononuclear cells (P = 1×10-11 in 228 non-RA patients and P = 0.004 in 132 RA patients). Consistent with the genetic findings, higher CD84 gene expression correlated with lower cross-sectional DAS (P = 0.02, n = 210) and showed a non-significant trend for better ΔDAS in a subset of RA patients with gene expression data (n = 31, etanercept-treated). A small, multi-ethnic replication showed a non-significant trend towards an association among etanercept-treated RA patients of Portuguese ancestry (n = 139, P = 0.4), but no association among patients of Japanese ancestry (n = 151, P = 0.8). Our study demonstrates that an allele associated with response to etanercept therapy is also associated with CD84 gene expression, and further that CD84 expression correlates with disease activity. These findings support a model in which CD84 genotypes and/or expression may serve as a useful biomarker for response to etanercept treatment in RA patients of European ancestry. © 2013 Cui et al

Appraisal of quality and analysis of the similarities and differences between osteoarthritis Clinical Practice Guideline recommendations: A systematic review

Objective: Clinical Practice Guidelines (CPGs) aim to support management of hip and knee osteoarthritis (OA), but recommendations are often conflicting and implementation is poor, contributing to evidence-to-practice gaps. This systematic review investigated the contextual and methodological factors contributing to conflicting recommendations for hip and knee OA. Method: Our systematic review appraised CPGs for managing hip and knee OA in adults ≥18 years (PROSPERO CRD42021276635). We used AGREE-II and AGREE-REX to assess quality and extracted data on treatment gaps, conflicts, biases, and consensus. Heterogeneity of recommendations was determined using Weighted Fleiss Kappa (K). The relationship between (K) and AGREE-II/AGREE-REX scores was explored. Results: We identified 25 CPGs across eight countries and four international organisations. The ACR, EULAR, NICE, OARSI and RACGP guidelines scored highest for overall AGREE-II quality (83%). The highest overall AGREE-REX scores were for BMJ Arthroscopy (80%), RACGP (78%) and NICE (76%). CPGs with the least agreement for pharmacological recommendations were ESCEO and NICE (−0.14), ACR (−0.08), and RACGP (−0.01). The highest agreements were between RACGP and NICE (0.53), RACGP and ACR (0.61), and NICE and ACR (0.91). Decreased internal validity determined by low-quality AGREE scores(<60%) in editorial independence were associated with less agreement for pharmacological recommendations. Conclusion: There were associations between guideline quality and agreement scores. Future guideline development should be informed by robust evidence, editorial independence and methodological rigour to ensure a harmonisation of recommendations. End-users of CPGs must recognise the contextual factors associated with the development of OA CPGs and balance these factors with available evidence

Rapid cultural adaptation can facilitate the evolution of large-scale cooperation

Over the past several decades, we have argued that cultural evolution can facilitate the evolution of large-scale cooperation because it often leads to more rapid adaptation than genetic evolution, and, when multiple stable equilibria exist, rapid adaptation leads to variation among groups. Recently, Lehmann, Feldman, and colleagues have published several papers questioning this argument. They analyze models showing that cultural evolution can actually reduce the range of conditions under which cooperation can evolve and interpret these models as indicating that we were wrong to conclude that culture facilitated the evolution of human cooperation. In the main, their models assume that rates of cultural adaption are not strong enough compared to migration to maintain persistent variation among groups when payoffs create multiple stable equilibria. We show that Lehmann et al. reach different conclusions because they have made different assumptions. We argue that the assumptions that underlie our models are more consistent with the empirical data on large-scale cultural variation in humans than those of Lehmann et al., and thus, our models provide a more plausible account of the cultural evolution of human cooperation in large groups

Measurement of the cross-section and charge asymmetry of WW bosons produced in proton-proton collisions at s=8\sqrt{s}=8 TeV with the ATLAS detector

This paper presents measurements of the $W^+ \rightarrow \mu^+\nu$ and $W^- \rightarrow \mu^-\nu$ cross-sections and the associated charge asymmetry as a function of the absolute pseudorapidity of the decay muon. The data were collected in proton--proton collisions at a centre-of-mass energy of 8 TeV with the ATLAS experiment at the LHC and correspond to a total integrated luminosity of 20.2~\mbox{fb^{-1}}. The precision of the cross-section measurements varies between 0.8% to 1.5% as a function of the pseudorapidity, excluding the 1.9% uncertainty on the integrated luminosity. The charge asymmetry is measured with an uncertainty between 0.002 and 0.003. The results are compared with predictions based on next-to-next-to-leading-order calculations with various parton distribution functions and have the sensitivity to discriminate between them.Comment: 38 pages in total, author list starting page 22, 5 figures, 4 tables, submitted to EPJC. All figures including auxiliary figures are available at https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/STDM-2017-13

Search for chargino-neutralino production with mass splittings near the electroweak scale in three-lepton final states in √s=13 TeV pp collisions with the ATLAS detector

A search for supersymmetry through the pair production of electroweakinos with mass splittings near the electroweak scale and decaying via on-shell W and Z bosons is presented for a three-lepton final state. The analyzed proton-proton collision data taken at a center-of-mass energy of √s=13  TeV were collected between 2015 and 2018 by the ATLAS experiment at the Large Hadron Collider, corresponding to an integrated luminosity of 139  fb−1. A search, emulating the recursive jigsaw reconstruction technique with easily reproducible laboratory-frame variables, is performed. The two excesses observed in the 2015–2016 data recursive jigsaw analysis in the low-mass three-lepton phase space are reproduced. Results with the full data set are in agreement with the Standard Model expectations. They are interpreted to set exclusion limits at the 95% confidence level on simplified models of chargino-neutralino pair production for masses up to 345 GeV