SAG/ROC2 E3 ligase regulates skin carcinogenesis by stage-dependent targeting of c-Jun/AP1 and IκB-α/NF-κB

Sensitive to apoptosis gene (SAG)/regulator of cullins-2–Skp1-cullin–F-box protein (SCF) E3 ubiquitin ligase regulates cellular functions through ubiquitination and degradation of protein substrates. We report that, when expressed in mouse epidermis driven by the K14 promoter, SAG inhibited TPA-induced c-Jun levels and activator protein-1 (AP-1) activity in both in vitro primary culture, in vivo transgenic mice, and an AP-1– luciferase reporter mouse model. After AP-1 inactivation, epidermal proliferation induced by 7,12-dimethylbenz(a)-anthracene/12-O-tetradecanoylphorbol-13-acetate at the early stage of carcinogenesis was substantially inhibited. Later stage tumor formation was also substantially inhibited with prolonged latency and reduced frequency of tumor formation. Interestingly, SAG expression increased tumor size, not because of accelerated proliferation, but caused by reduced apoptosis resulting, at least in part, from nuclear factor κB (NF-κB) activation. Thus, SAG, in a manner depending on the availability of F-box proteins, demonstrated early-stage suppression of tumor formation by promoting c-Jun degradation, thereby inhibiting AP-1, and later-stage enhancement of tumor growth, by promoting inhibitor of κBα degradation to activate NF-κB and inhibit apoptosis

Lymph node homing cells biologically enriched for γδ T cells express multiple genes from the T19 repertoire

Sheep γδ T cells have been shown serologically to express T19, a membrane protein of 180-200 kDa which is a member of the scavenger receptor superfamily. Previous work from this laboratory resulted in the detection of a multigene family of T19-like genes in the sheep genome. In this study nucleotide sequences from several T19 genes were determined and are reported along with the corresponding segments of a number of expressed mRNA molecules. A segment of a single sheep T19-like gene was sequenced and these data, along with the corresponding sequences from cloned T19-like cDNA molecules from sheep and cow, were used to design an ollgonucleotide primer system suitable for amplification of corresponding segments of many T19 genes and their cDNAs. Between 30 and 40% of cloned T19 genes were amenable to amplification using the selected primers, and sequence analysis of cloned PCR products confirmed that different T19 genes encode unique amino acid sequences. The expression of multiple T19 genes was established using cDNA molecules obtained from a single sample of sheep lymphocyte mRNA. The possible role of the T19 family of genes is discusse

Full-genome next-generation sequencing of hepatitis C virus to assess the accuracy of genotyping by the commercial assay LiPA and the prevalence of resistance-associated substitutions in a Belgian cohort

Funding Information: This work and KTC were supported by grants from the Fonds voor Wetenschappelijk Onderzoek Vlaanderen (FWO) ( G069214 , G0B2317N , 1S38819N ). LC acknowledges FWO travel grant for a research visit at University of Oxford ( V431117N ). The authors thank the staff in Oxford in their support of the laboratory work and the donation of the probes used for enrichment of HCV. Publisher Copyright: © 2022 Elsevier B.V.Background: Although most currently used regimens for Hepatitis C virus (HCV) infections can be initiated without prior knowledge of genotype and subtype, genotyping is still useful to identify patients who might benefit from a personalized treatment due to resistance to direct-acting antivirals (DAA). Objectives: To assess the utility of full-genome next-generation sequencing (FG-NGS) for HCV genotyping. Study design: 138 HCV plasma samples previously genotyped by VERSANT HCV Genotype Assay (LiPA) were subjected to FG-NGS and phylogenetically genotyped Genome Detective. Consensuses were analysed by HCV-GLUE for resistance-associated substitutions (RASs) and their impact on treatment response was investigated. Results: 102/138 (73.9%) samples were sequenced to a genome coverage and depth of >90% of the HCV open reading frame covered by >100 reads/site. Concordant genotype and subtype results were assigned in 97.1% and 79.4% of samples, respectively. FG-NGS resolved the subtype of 13.7% samples that had ambiguous calls by LiPA and identified one dual infection and one recombinant strain. At least one RAS was found for the HCV genes NS3, NS5A, and NS5B in 2.91%, 36.98% and 27.3% samples, respectively. Irrespective of the observed RAS, all patients responded well to DAA treatment, except for HCV1b-infected patients treated with Zepatier (33.3% failure rate (5/15)). Conclusion: While LiPA and FG-NGS showed overall good concordance, FG-NGS improved specificity for subtypes, recombinant and mixed infections. FG-NGS enabled the detection of RAS, but its predictive value for treatment outcome in DAA-naïve patients remains uncertain. With additional refinements, FG-NGS may be the way forward for HCV genotyping.publishersversionpublishe

People of the British Isles: preliminary analysis of genotypes and surnames in a UK control population

There is a great deal of interest in fine scale population structure in the UK, both as a signature of historical immigration events and because of the effect population structure may have on disease association studies. Although population structure appears to have a minor impact on the current generation of genome-wide association studies, it is likely to play a significant part in the next generation of studies designed to search for rare variants. A powerful way of detecting such structure is to control and document carefully the provenance of the samples involved. Here we describe the collection of a cohort of rural UK samples (The People of the British Isles), aimed at providing a well-characterised UK control population that can be used as a resource by the research community as well as providing fine scale genetic information on the British population. So far, some 4,000 samples have been collected, the majority of which fit the criteria of coming from a rural area and having all four grandparents from approximately the same area. Analysis of the first 3,865 samples that have been geocoded indicates that 75% have a mean distance between grandparental places of birth of 37.3km, and that about 70% of grandparental places of birth can be classed as rural. Preliminary genotyping of 1,057 samples demonstrates the value of these samples for investigating fine scale population structure within the UK, and shows how this can be enhanced by the use of surnames

Focused fluid seepage related to variations in accretionary wedge structure, Hikurangi margin, New Zealand

Hydrogeological processes influence the morphology, mechanical behavior, and evolution of subduction margins. Fluid supply, release, migration, and drainage control fluid pressure and collectively govern the stress state, which varies between accretionary and nonaccretionary systems. We compiled over a decade of published and unpublished acoustic data sets and seafloor observations to analyze the distribution of focused fluid expulsion along the Hikurangi margin, New Zealand. The spatial coverage and quality of our data are exceptional for subduction margins globally. We found that focused fluid seepage is widespread and varies south to north with changes in subduction setting, including: wedge morphology, convergence rate, seafloor roughness, and sediment thickness on the incoming Pacific plate. Overall, focused seepage manifests most commonly above the deforming backstop, is common on thrust ridges, and is largely absent from the frontal wedge despite ubiquitous hydrate occurrences. Focused seepage distribution may reflect spatial differences in shallow permeability architecture, while diffusive fluid flow and seepage at scales below detection limits are also likely. From the spatial coincidence of fluids with major thrust faults that disrupt gas hydrate stability, we surmise that focused seepage distribution may also reflect deeper drainage of the forearc, with implications for pore-pressure regime, fault mechanics, and critical wedge stability and morphology. Because a range of subduction styles is represented by 800 km of along-strike variability, our results may have implications for understanding subduction fluid flow and seepage globally

Indicators of ‘critical’ outcomes in 941 horses seen ‘out-of-hours’ for colic

Background: This study aimed to describe the presentation and outcomes of horses with signs of colic (abdominal pain) seen ‘out-of-hours’ in equine practice. Methods: This was a retrospective study of horses seen ‘out-of-hours’ with colic by two equine veterinary practices between 2011-2013. Case outcomes were categorised as ‘critical’ or ‘not critical’. A critical outcome was defined as requiring medical or surgical hospital treatment, or resulting in euthanasia or death. A non-critical outcome was defined as resolving with simple medical treatment. A hierarchical generalised linear model was used to identify ‘red flag’ parameters (aspects of signalment, history and presenting clinical signs) associated with critical outcomes.Results: Data were retrieved from 941 cases that presented with colic; 23.9% (n=225/941) were critical. Variables significantly associated with the likelihood of a critical outcome in the final multivariable mode were: increased heart rate (p [less than] 0.001), age of the horse (p=0.013) and abnormal mucous membrane colour (p [less than] 0.001). Overall 18% of cases (n=168/941) were euthanased.Conclusions: This study highlights the mortality associated with colic. The ‘red flag’ parameters identified should be considered an essential component of the primary assessment of horses with colic

Formation Flying and Change Detection for the UNSW Canberra Space ‘M2’ Low Earth Orbit Formation Flying CubeSat Mission

The University of New South Wales, Canberra (UNSW Canberra) embarked on an ambitious CubeSatellite research, development, and education program in 2017 through funding provided by the Royal Australian Air Force (RAAF). The program consisted of M1 (Mission 1), M2 Pathfinder, and concludes with the formation flying mission M2. M2 is the final mission comprising two 6U CubeSatellites flying in formation using differential aerodynamic drag control. The M2 satellites were launched in a conjoined 12U form factor on RocketLab’s ‘They Go Up So Fast’ launch in March 2021. On 10th September 2021 the spacecraft divided into two 6U CubeSats (M2-A and M2-B) under the action of a small spring force in their near-circular 550km, 45-degree inclination orbit. The formation is controlled by varying the spacecrafts’ attitude, which creates a large variation in the aerodynamic drag force due to the change in the cross-sectional area from the large, double-deployable, solar arrays located on the zenith face of the spacecraft. This paper presents the outcomes of the Formation Flying and Change Detection primary mission objectives for the mission. The results are generated by collecting and analysing optical and RF (Radio Frequency) space domain awareness sensor data from the ground and validating them against GPS (Global Positioning System) and attitude data downlinked from the spacecraft. The outcomes of the broader mission objectives, which include increasing the Technology Readiness Level for a suite of intelligent on-board optical and RF sensor technologies, will be presented in subsequent publications. The results presented here comprise two major campaigns: 1.) The spacecraft separation campaign when the original 12U form factor deployed following launch split in half to form the M2-A and M2-B satellites, and 2) the demonstration of active formation control of the spacecraft via differential aerodynamic drag. M2-A and M2-B underwent several major configuration changes during the spacecraft separation campaign. The results from ground-based sensors detecting the 12U spacecraft separating into two distinct (6U) objects are presented. The effect of the double-deployable solar arrays deployment on the relative orbital motion of the M2-A and M2-B spacecraft is illustrated and compared to data from optical and RF ground-based measurements taken during this window. The formation control campaign involved actively controlling the spacecraft via differential aerodynamic drag in order to significantly alter the separation distance. The mission demonstrated the capability to switch the leading spacecraft’s position between M2-A and M2-B and to actively control separation distance ranging from 130km down to 1km. Formation control is achieved via open-loop, pre-scheduled, commands issued from the UNSW Canberra Space ground station. A two-stage modelling and simulation process is used to derive the scheduled attitude states. Firstly, a batch least squares orbit determination algorithm is applied to GPS data from a steady-state differential drag actuation period (where one spacecraft is in maximum drag and the other in its minimum drag attitude configuration). The batch least squares orbit determination is conducted out using the NASA General Mission Analysis Tool (GMAT), resulting in precise state estimates for each spacecraft and drag coefficient (Cd) estimates for both the maximum and minimum drag configurations. Predictions of trajectory for various attitude profiles can be produced by tailoring the spacecraft’s drag coefficients between the maximum and minimum values generated by the batch least squares state estimation process. Ground-based optical and RF space domain awareness (SDA) sensor measurements collected during the manoeuvre campaign are compared to the spacecraft’s GPS and attitude telemetry data. The SDA sensors are actively seeking to detect changes in the separation distance between the spacecraft. Initial results from an investigation into whether changes observed in photometric light curve signatures can signal the commencement of a differential drag manoeuvre are presented

Phylogenetic Analysis of Hepatitis C Virus Infections in a Large Belgian Cohort Using Next-Generation Sequencing of Full-Length Genomes

Funding Information: This research and Kasper Thorhauge Christensen was funded by grants from the Fonds Wetenschappelijk Onderzoek Vlaanderen (FWO) (G069214, G0B2317N and 1S38819N). Lize Cuypers acknowledges FWO travel grant for a research visit at the University of Oxford (V431117N). Core funding to the Wellcome Centre for Human Genetics was provided by the Wellcome Trust (award 203141/Z/16/Z). The authors acknowledge the STOP-HCV consortium that was funded by a grant from the Medical Research Council, United Kingdom (MR/K01532X/1). Publisher Copyright: © 2023 by the authors.The hepatitis C virus (HCV) epidemic in Western countries is primarily perpetuated by the sub-populations of men who have sex with men (MSM) and people who inject drugs (PWID). Understanding the dynamics of transmission in these communities is crucial for removing the remaining hurdles towards HCV elimination. We sequenced 269 annotated HCV plasma samples using probe enrichment and next-generation sequencing, obtaining 224 open reading frames of HCV (OR497849-OR498072). Maximum likelihood phylogenies were generated on the four most prevalent subtypes in this study (HCV1a, 1b, 3a, 4d) with a subsequent transmission cluster analysis. The highest rate of clustering was observed for HCV4d samples (13/17 (76.47%)). The second highest rate of clustering was observed in HCV1a samples (42/78 (53.85%)) with significant association with HIV-positive MSM. HCV1b and HCV3a had very low rates of clustering (2/83 (2.41%) and (0/29)). The spread of the prevalent subtype HCV1b appears to have been largely curtailed, and we demonstrate the onwards transmission of HCV1a and HCV4d in the HIV-positive MSM population across municipal borders. More systematic data collection and sequencing is needed to allow a better understanding of the HCV transmission among the community of PWID and overcome the remaining barriers for HCV elimination in Belgium.publishersversionpublishe

Retrospective case series to identify the most common conditions seen ‘out-of-hours’ by first-opinion equine veterinary practitioners

Background: The study aim was to describe conditions seen ‘out-of-hours’ in equine practice. Methods: This was a retrospective case series of first opinion ‘out-of-hours’ cases seen at two equine practices between 2011-2013. Data was retrieved on case presentation, diagnostic testing, treatment administered and outcome, and diseases categorised using a systems-based coding system. A hierarchical logistic regression, formulated using a Generalised Linear Model, was used to identify clinical variables associated with a binary outcome of ‘critical’ cases (required hospitalisation or euthanasia or died).Results: Data from 2,602 cases were analysed. The most common reasons for ‘out-of-hours’ visits were colic (35%, n=923/2,620), wounds (20%, n=511/2,620) and lameness (11%, n=288/2,620). The majority of cases required a single treatment (58%, n=1,475/2,550), 26% (n=656/2,550) needed multiple treatments, and 13% (n=339/2,550) were euthanased. Eighteen percent (n=480/2602) of cases had a critical outcome. Increased heart rate at primary presentation was associated with critical outcome in both practices (Practice A, OR 1.07 (95%CI 1.06-1.09), Practice B OR 1.08 (95%CI 1.07-1.09; p [less than] 0.001)).Conclusion: Colic, wounds and lameness were the most common equine ‘out-of-hours’ conditions; 13% of cases were euthanased. Further research is required into out-of-hours euthanasia decision-making

A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance

OBJECTIVES: To investigate the prospects of newly available benchtop sequencers to provide rapid whole-genome data in routine clinical practice. Next-generation sequencing has the potential to resolve uncertainties surrounding the route and timing of person-to-person transmission of healthcare-associated infection, which has been a major impediment to optimal management. DESIGN: The authors used Illumina MiSeq benchtop sequencing to undertake case studies investigating potential outbreaks of methicillin-resistant Staphylococcus aureus (MRSA) and Clostridium difficile. SETTING: Isolates were obtained from potential outbreaks associated with three UK hospitals. PARTICIPANTS: Isolates were sequenced from a cluster of eight MRSA carriers and an associated bacteraemia case in an intensive care unit, another MRSA cluster of six cases and two clusters of C difficile. Additionally, all C difficile isolates from cases over 6 weeks in a single hospital were rapidly sequenced and compared with local strain sequences obtained in the preceding 3 years. MAIN OUTCOME MEASURE: Whole-genome genetic relatedness of the isolates within each epidemiological cluster. RESULTS: Twenty-six MRSA and 15 C difficile isolates were successfully sequenced and analysed within 5 days of culture. Both MRSA clusters were identified as outbreaks, with most sequences in each cluster indistinguishable and all within three single nucleotide variants (SNVs). Epidemiologically unrelated isolates of the same spa-type were genetically distinct (≥21 SNVs). In both C difficile clusters, closely epidemiologically linked cases (in one case sharing the same strain type) were shown to be genetically distinct (≥144 SNVs). A reconstruction applying rapid sequencing in C difficile surveillance provided early outbreak detection and identified previously undetected probable community transmission. CONCLUSIONS: This benchtop sequencing technology is widely generalisable to human bacterial pathogens. The findings provide several good examples of how rapid and precise sequencing could transform identification of transmission of healthcare-associated infection and therefore improve hospital infection control and patient outcomes in routine clinical practice