Visualizing the Interface of Biotin and Fatty Acid Biosynthesis through SuFEx Probes

Site-specific covalent conjugation offers a powerful tool to identify and understand protein-protein interactions. In this study, we discover that sulfur fluoride exchange (SuFEx) warheads effectively crosslink the Escherichia coli acyl carrier protein (AcpP) with its partner BioF, a key pyridoxal 5′-phosphate (PLP)-dependent enzyme in the early steps of biotin biosynthesis by targeting a tyrosine residue proximal to the active site. We identify the site of crosslink by MS/MS analysis of the peptide originating from both partners. We further evaluate the BioF-AcpP interface through protein crystallography and mutational studies. Among the AcpP-interacting BioF surface residues, three critical arginine residues appear to be involved in AcpP recognition so that pimeloyl-AcpP can serve as the acyl donor for PLP-mediated catalysis. These findings validate an evolutionary gain-of-function for BioF, allowing the organism to build biotin directly from fatty acid biosynthesis through surface modifications selective for salt bridge formation with acidic AcpP residues.</p

Nitrogen oxides and PAN in plumes from boreal fires during ARCTAS-B and their impact on ozone: an integrated analysis of aircraft and satellite observations

We determine enhancement ratios for NO&lt;sub&gt;x&lt;/sub&gt;, PAN, and other NO&lt;sub&gt;y&lt;/sub&gt; species from boreal biomass burning using aircraft data obtained during the ARCTAS-B campaign and examine the impact of these emissions on tropospheric ozone in the Arctic. We find an initial emission factor for NO&lt;sub&gt;x&lt;/sub&gt; of 1.06 g NO per kg dry matter (DM) burned, much lower than previous observations of boreal plumes, and also one third the value recommended for extratropical fires. Our analysis provides the first observational confirmation of rapid PAN formation in a boreal smoke plume, with 40% of the initial NO&lt;sub&gt;x&lt;/sub&gt; emissions being converted to PAN in the first few hours after emission. We find little clear evidence for ozone formation in the boreal smoke plumes during ARCTAS-B in either aircraft or satellite observations, or in model simulations. Only a third of the smoke plumes observed by the NASA DC8 showed a correlation between ozone and CO, and ozone was depleted in the plumes as often as it was enhanced. Special observations from the Tropospheric Emission Spectrometer (TES) also show little evidence for enhanced ozone in boreal smoke plumes between 15 June and 15 July 2008. Of the 22 plumes observed by TES, only 4 showed ozone increasing within the smoke plumes, and even in those cases it was unclear that the increase was caused by fire emissions. Using the GEOS-Chem atmospheric chemistry model, we show that boreal fires during ARCTAS-B had little impact on the median ozone profile measured over Canada, and had little impact on ozone within the smoke plumes observed by TES

Reinforcement selection acting on the European house mouse hybrid zone

Behavioural isolation may lead to complete speciation when partial postzygotic isolation acts in the presence of divergent‐specific mate‐recognition systems. These conditions exist where Mus musculus musculus and M. m. domesticus come into contact and hybridize. We studied two mate‐recognition signal systems, based on urinary and salivary proteins, across a Central European portion of the mouse hybrid zone. Introgression of the genomic regions responsible for these signals: the major urinary proteins (MUPs) and androgen binding proteins (ABPs), respectively, was compared to introgression at loci assumed to be nearly neutral and those under selection against hybridization. The preference of individuals taken from across the zone regarding these signals was measured in Y mazes, and we develop a model for the analysis of the transition of such traits under reinforcement selection. The strongest assortative preferences were found in males for urine and females for ABP. Clinal analyses confirm nearly neutral introgression of an Abp locus and two loci closely linked to the Abp gene cluster, whereas two markers flanking the Mup gene region reveal unexpected introgression. Geographic change in the preference traits matches our reinforcement selection model significantly better than standard cline models. Our study confirms that behavioural barriers are important components of reproductive isolation between the house mouse subspecies.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/86873/1/j.1365-294X.2011.05106.x.pd

xclim: xarray-based climate data analytics

xclim is a Python library that enables computation of climate indicators over large, hetero- geneous data sets. It is built using xarray objects and operations, can seamlessly benefit from the parallelization handling provided by dask, and relies on community conventions for data formatting and metadata attributes. xclim is meant as a tool to facilitate both climate science research and the delivery of operational climate services and products. In addition to climate indicator calculations, xclim also includes utilities for bias correction and statistical adjustment, ensemble analytics, model diagnostics, data quality assurance, and metadata standards compliance

Knowledge-to-action processes in SHRTN collaborative communities of practice: A study protocol

<p>Abstract</p> <p>Background</p> <p>The Seniors Health Research Transfer Network (SHRTN) Collaborative is a network of networks that work together to improve the health and health care of Ontario seniors. The collaborative facilitates knowledge exchange through a library service, knowledge brokers (KBs), local implementation teams, collaborative technology, and, most importantly, Communities of Practice (CoPs) whose members work together to identify innovations, translate evidence, and help implement changes.</p> <p>This project aims to increase our understanding of knowledge-to-action (KTA) processes mobilized through SHRTN CoPs that are working to improve the health of Ontario seniors. For this research, KTA refers to the movement of research and experience-based knowledge between social contexts, and the use of that knowledge to improve practice. We will examine the KTA processes themselves, as well as the role of human agents within those processes. The conceptual framework we have adopted to inform our research is the Promoting Action on Research Implementation in Health Services (PARIHS) framework.</p> <p>Methods/design</p> <p>This study will use a multiple case study design (minimum of nine cases over three years) to investigate how SHRTN CoPs work and pursue knowledge exchange in different situations. Each case will yield a unique narrative, framed around the three PARIHS dimensions: evidence, context, and facilitation. Together, the cases will shed light on how SHRTN CoPs approach their knowledge exchange initiatives, and how they respond to challenges and achieve their objectives. Data will be collected using interviews, document analysis, and ethnographic observation.</p> <p>Discussion</p> <p>This research will generate new knowledge about the defining characteristics of CoPs operating in the health system, on leadership roles in CoPs, and on the nature of interaction processes, relationships, and knowledge exchange mechanisms. Our work will yield a better understanding of the factors that contribute to the success or failure of KTA initiatives, and create a better understanding of how local caregiving contexts interact with specific initiatives. Our participatory design will allow stakeholders to influence the practical usefulness of our findings and contribute to improved health services delivery for seniors.</p

Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study

Introduction: The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures. Methods: In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ≥18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025. Findings: Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5·0 months (IQR 4·2–6·3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p&lt;0·0001) and independently associated with COVID-19 status (odds ratio [OR] 2·9 [95% CI 1·5–5·8]; padjusted=0·0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0·0001; parenchymal abnormalities), brain abnormalities (p&lt;0·0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0·014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4–10]; mean age of 59·8 years [SD 11·7] with multiorgan abnormalities vs mean age of 52·8 years [11·9] without multiorgan abnormalities; p&lt;0·0001), more likely to have three or more comorbidities (OR 2·47 [1·32–4·82]; padjusted=0·0059), and more likely to have a more severe acute infection (acute CRP &gt;5mg/L, OR 3·55 [1·23–11·88]; padjusted=0·025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation. Interpretation: After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Intracellular Delivery of Protein Kinase C Beta II Peptide Inhibitor is Facilitated by Dual Conjugation with Myristic Acid and Trans Activator of Transcription to Attenuate Myocardial Ischemia/Reperfusion Injury

INTRODUCTION: Peptides conjugated to myristic acid (myr) or trans activator of transcription (tat) have long been used to increase cell permeability via simple diffusion and endocytosis, respectively. Previously myr-PKCβII inhibitor (myr-PKCβII-) exerted cardioprotective effects in myocardial ischemia/reperfusion (I/R) and inhibited superoxide (SO) release from rat leukocytes by 40% (20 µM). By contrast, dual conjugated myr-tat-PKCβII inhibitor (myr-tat-PKCβII-) inhibited SO release by 90% at the same concentration. OBJECTIVES: The purpose of this study was to determine the potency of myr-tat-PKCβII- compared to myr-PKCβII- in mitigating infarct size and restoring cardiac function in an ex-vivo rat model of myocardial I/R injury. METHODS: Isolated hearts from male Sprague-Dawley rats (~300g) were subjected to global I(30-min)/R(50-min). Left ventricular cardiac function was recorded using a pressure transducer. Treatments were infused during the first 5 min of R. After R, the hearts were sectioned (2 mm) and stained with 1% triphenyltetrazolium chloride. Infarcted tissue was excised to determine infarct size (i.e. infarct tissue weight/ total tissue weight). Data were analyzed using ANOVA Fisher’s LSD analysis. RESULTS: Compared to untreated controls (23.2±3.1%, n=17), myr-tat-PKCβII- exerted a significant and similar decrease in infarct size that was observed from 100 nM (9.7±0.59%, n=3, p\u3c0.05), 1 nM (10.0±2.3%, n=5, p\u3c0.05), to 100 pM (12.6±2.3%, n=5, p\u3c0.05); but not at 10 nM (13.8±3.6%, n=5). Cardiac function for all treatment groups did not significantly improve from control. However, at 100pM (1070±170 mmHg/s), +dP/dt max was significantly improved compared to all other treatment groups (p\u3c0.05). CONCLUSION: The addition of myr to tat-conjugated peptides improved the cardioprotective effects ~200-fold compared to myr-PKCβII- and ~2000-fold compared to native peptide presumably by enhanced intracellular delivery of cargo. The ~50% reduction in infarct size suggests that myr-tat-PKCβII- is cardioprotective in I/R. Future studies will test our most effective dose determined in ex vivo hearts in a porcine myocardial I/R model