The ATP-Binding Cassette Proteins of the Deep-Branching Protozoan Parasite Trichomonas vaginalis

The ATP binding cassette (ABC) proteins are a family of membrane transporters and regulatory proteins responsible for diverse and critical cellular process in all organisms. To date, there has been no attempt to investigate this class of proteins in the infectious parasite Trichomonas vaginalis. We have utilized a combination of bioinformatics, gene sequence analysis, gene expression and confocal microscopy to investigate the ABC proteins of T. vaginalis. We demonstrate that, uniquely among eukaryotes, T. vaginalis possesses no intact full-length ABC transporters and has undergone a dramatic expansion of some ABC protein sub-families. Furthermore, we provide preliminary evidence that T. vaginalis is able to read through in-frame stop codons to express ABC transporter components from gene pairs in a head-to-tail orientation. Finally, with confocal microscopy we demonstrate the expression and endoplasmic reticulum localization of a number of T. vaginalis ABC transporters

Alien pathogens on the horizon: opportunities for predicting their threat to wildlife

According to the Convention on Biological Diversity, by 2020 invasive alien species (IAS) should be identified and their impacts assessed, so that species can be prioritized for implementation of appropriate control strategies and measures put in place to manage invasion pathways. For one quarter of the IAS listed as the “100 of the world's worst” environmental impacts are linked to diseases of wildlife (undomesticated plants and animals). Moreover, IAS are a significant source of “pathogen pollution” defined as the human-mediated introduction of a pathogen to a new host or region. Despite this, little is known about the biology of alien pathogens and their biodiversity impacts after introduction into new regions. We argue that the threats posed by alien pathogens to endangered species, ecosystems, and ecosystem services should receive greater attention through legislation, policy, and management. We identify 10 key areas for research and action, including those relevant to the processes of introduction and establishment of an alien pathogen and to prediction of the spread and associated impact of an alien pathogen on native biota and ecosystems. The development of interdisciplinary capacity, expertise, and coordination to identify and manage threats was seen as critical to address knowledge gaps

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Increasing frailty is associated with higher prevalence and reduced recognition of delirium in older hospitalised inpatients: results of a multi-centre study

Purpose: Delirium is a neuropsychiatric disorder delineated by an acute change in cognition, attention, and consciousness. It is common, particularly in older adults, but poorly recognised. Frailty is the accumulation of deficits conferring an increased risk of adverse outcomes. We set out to determine how severity of frailty, as measured using the CFS, affected delirium rates, and recognition in hospitalised older people in the United Kingdom. Methods: Adults over 65 years were included in an observational multi-centre audit across UK hospitals, two prospective rounds, and one retrospective note review. Clinical Frailty Scale (CFS), delirium status, and 30-day outcomes were recorded. Results: The overall prevalence of delirium was 16.3% (483). Patients with delirium were more frail than patients without delirium (median CFS 6 vs 4). The risk of delirium was greater with increasing frailty [OR 2.9 (1.8–4.6) in CFS 4 vs 1–3; OR 12.4 (6.2–24.5) in CFS 8 vs 1–3]. Higher CFS was associated with reduced recognition of delirium (OR of 0.7 (0.3–1.9) in CFS 4 compared to 0.2 (0.1–0.7) in CFS 8). These risks were both independent of age and dementia. Conclusion: We have demonstrated an incremental increase in risk of delirium with increasing frailty. This has important clinical implications, suggesting that frailty may provide a more nuanced measure of vulnerability to delirium and poor outcomes. However, the most frail patients are least likely to have their delirium diagnosed and there is a significant lack of research into the underlying pathophysiology of both of these common geriatric syndromes

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

Initial evaluations of a U.S. Navy Rapidly Relocatable Gulf of Mexico/Caribbean Ocean Forecast System in the Context of the Deepwater Horizon Oil Spill Disaster

In response to the Deepwater Horizon (DwH) oil spill event in 2010, the Naval Oceanographic Office deployed a nowcast-forecast system covering the Gulf of Mexico and adjacent Caribbean Sea that was designated Americas Seas, or AMSEAS, which is documented in this manuscript. The DwH disaster provided a challenge to the application of available ocean-forecast capabilities, and also generated a historically large observational dataset. AMSEAS was evaluated by four complementary efforts, each with somewhat different aims and approaches: a university research consortium within an Integrated Ocean Observing System (IOOS) testbed; a petroleum industry consortium, the Gulf of Mexico 3-D Operational Ocean Forecast System Pilot Prediction Project (GOMEX-PPP); a British Petroleum (BP) funded project at the Northern Gulf Institute in response to the oil spill; and the Navy itself. Validation metrics are presented in these different projects for water temperature and salinity profiles, sea surface wind, sea surface temperature, sea surface height, and volume transport, for different forecast time scales. The validation found certain geographic and time biases/errors, and small but systematic improvements relative to earlier regional and global modeling efforts. On the basis of these positive AMSEAS validation studies, an oil spill transport simulation was conducted using archived AMSEAS nowcasts to examine transport into the estuaries east of the Mississippi River. This effort captured the influences of Hurricane Alex and a non-tropical cyclone off the Louisiana coast, both of which pushed oil into the western Mississippi Sound, illustrating the importance of the atmospheric influence on oil spills such as DwH

The ABCE proteins of archaea and eukaroytes.

<p>Multiple sequence alignment and boot-strapping was performed as described in the material and methods. The boot-strap values (percentages) are displayed on all branches.</p

The absence of full length transporters from <i>T. vaginalis</i>.

<p><b>A, B</b> genomic context of combinations of open reading frames that could encode for an intact full-length ABC transporter. Formatting is as described in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001693#pntd-0001693-g002" target="_blank">Figure 2</a>, with pairs of primers used to verify the genomic organization displayed as blue and orange arrows (<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001693#pntd.0001693.s002" target="_blank">Table S1</a>). <b>C</b> The two genes TVAG_415980 and TVAG_415990 are separated only by an in-frame stop codon (TGA). RT-PCR analysis of mRNA with primers (black arrows) demonstrates that transcript containing both TVAG_415980 and TVAG_415990 sequences exists (lane 5, asterisk, at the same size as the genomic DNA control). Reactions lacking the RT step (lane 3), or containing primers only (lane 2) verify the specificity of the band in lane 5. <b>D</b> Confocal microscopy of <i>T. vaginalis</i> C1 cells. The four panels represent (left to right, scale bars 10 µm) bright-field images, detection of nuclear material by propidium iodide staining, overlay of the first pair, and finally, the lack of any anti-HA reactive signal in C1 cells. <b>E</b> Confocal microscopy of <i>T. vaginalis</i> C1 transformed with a plasmid containing the genomic DNA of TVAG_415980 and TVAG_415990 with the stop codon of the latter replaced by a double haemagluttinin (HA) tag. Parasites were fixed as described in the Methods, examined with a Zeiss LSM 710 confocal microscope, and visualization of HA-tagged ABC TVAG_415980_90 followed incubation with anti-HA primary and an Alexaflour-488 secondary antibody (green).</p

The classified ABC proteins of <i>T. vaginalis</i> compared with other eukaryotes.

<p>The classified ABC proteins of <i>T. vaginalis</i> compared with other eukaryotes.</p

Localization of ABCD transporters in <i>T. vaginalis</i>.

<p>Parasites were fixed, labelled and imaged as described in the legend to <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001693#pntd-0001693-g003" target="_blank">Figure 3</a>. The endoplasmic reticulum protein BiP in C1 (<b>A</b>) was detected with primary anti-BiP antibody, whilst the hydrogenosomal protein TOM40-3 (<b>B</b>) and two ABCD transformants (TVAG_470720; <b>C</b>; and TVAG_605460; <b>D</b>) were detected by reactivity to anti-HA antibodies. The distributions of BIP, TVAG_605460, and TVAG_470720 are all similar with a dispersed pattern of staining. In contrast, the hydrogenosome membrane protein TOM 40-3 (<b>B</b>) was detected in discrete spherical organelles, consistent with the size and shape of the hydrogenosome. <b>E</b> the ABCD transporters of eukaryotes for two distinct sub-families, one of which (grey boxed) has independent evidence to support endoplasmic reticulum localization, whereas the other sub-family are peroxisomal localized.</p