Conserved phosphoryl transfer mechanisms within kinase families and the role of the C8 proton of ATP in the activation of phosphoryl transfer

<p>Abstract</p> <p>Background</p> <p>The kinome is made up of a large number of functionally diverse enzymes, with the classification indicating very little about the extent of the conserved kinetic mechanisms associated with phosphoryl transfer. It has been demonstrated that C8-H of ATP plays a critical role in the activity of a range of kinase and synthetase enzymes.</p> <p>Results</p> <p>A number of conserved mechanisms within the prescribed kinase fold families have been identified directly utilizing the C8-H of ATP in the initiation of phosphoryl transfer. These mechanisms are based on structurally conserved amino acid residues that are within hydrogen bonding distance of a co-crystallized nucleotide. On the basis of these conserved mechanisms, the role of the nucleotide C8-H in initiating the formation of a pentavalent intermediate between the γ-phosphate of the ATP and the substrate nucleophile is defined. All reactions can be clustered into two mechanisms by which the C8-H is induced to be labile via the coordination of a backbone carbonyl to C6-NH₂of the adenyl moiety, namely a "push" mechanism, and a "pull" mechanism, based on the protonation of N7. Associated with the "push" mechanism and "pull" mechanisms are a series of proton transfer cascades, initiated from C8-H, via the tri-phosphate backbone, culminating in the formation of the pentavalent transition state between the γ-phosphate of the ATP and the substrate nucleophile.</p> <p>Conclusions</p> <p>The "push" mechanism and a "pull" mechanism are responsible for inducing the C8-H of adenyl moiety to become more labile. These mechanisms and the associated proton transfer cascades achieve the proton transfer via different family-specific conserved sets of amino acids. Each of these mechanisms would allow for the regulation of the rate of formation of the pentavalent intermediate between the ATP and the substrate nucleophile. Phosphoryl transfer within kinases is therefore a specific event mediated and regulated via the coordination of the adenyl moiety of ATP and the C8-H of the adenyl moiety.</p

Aggregation and settling in aqueous polydisperse alumina nanoparticle suspensions

Nanoparticle suspensions (also called nanofluids) are often polydisperse and tend to settle with time. Settling kinetics in these systems are known to be complex and hence challenging to understand. In this work, polydisperse spherical alumina (Al2O3) nanoparticles in the size range of ~10-100nm were dispersed in water and examined for aggregation and settling behaviour near its isoelectric point (IEP). A series of settling experiments were conducted and the results were analysed by photography and by Small Angle X-ray Scattering (SAXS). The settling curve obtained from standard bed height measurement experiments indicated two different types of behaviour, both of which were also seen in the SAXS data. But the SAXS data were remarkably able to pick out the rapid settling regime as a result of the high temporal resolution (10s) used. By monitoring the SAXS intensity, it was further possible to record the particle aggregation process for the first time. Optical microscopy images were produced on drying and dried droplets extracted from the suspension at various times. Dried deposits showed the rapid decrease in the number of very large particles with time which qualitatively validates the SAXS prediction, and therefore its suitability as a tool to study unstable polydisperse colloids. Keywords: Nanoparticles, nanofluids, polydisperse, aggregation, settling, alumina, microscopy, SAX

Theory, Phenomenology, and Prospects for Detection of Supersymmetric Dark Matter

One of the great attractions of minimal super-unified supersymmetric models is the prediction of a massive, stable, weakly interacting particle (the lightest supersymmetric partner, LSP) which can have the right relic abundance to be a cold dark matter candidate. In this paper we investigate the identity, mass, and properties of the LSP after requiring gauge coupling unification, proper electroweak symmetry breaking, and numerous phenomenological constraints. We then discuss the prospects for detecting the LSP from (1) LSP annihilations into positrons, anti-protons, and gamma rays in the galactic halo, (2) large underground arrays to detect upward going muons arising from LSP capture and annihilation in the sun and earth, (3) elastic collisions on matter in a table top apparatus, and (4) production of LSPs or decays into LSPs at high energy colliders. Our conclusions are that space annihilation experiments and large underground detectors are of limited help in initially detecting the LSP although perhaps they could provide confirmation of a signal seen in other experiments, while table top detectors have considerable discovery potential. Colliders, however, might be the best dark matter detectors of all.Comment: 32 pages, 18 figures (not included). Full postscript version available via anonymous ftp at ftp://141.211.96.66/pub/preprint

Proceedings of the Thirteenth International Society of Sports Nutrition (ISSN) Conference and Expo

Meeting Abstracts: Proceedings of the Thirteenth International Society of Sports Nutrition (ISSN) Conference and Expo Clearwater Beach, FL, USA. 9-11 June 201

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Convalescent plasma in patients admitted to hospital with COVID-19 (RECOVERY): a randomised controlled, open-label, platform trial

SummaryBackground Azithromycin has been proposed as a treatment for COVID-19 on the basis of its immunomodulatoryactions. We aimed to evaluate the safety and efficacy of azithromycin in patients admitted to hospital with COVID-19.Methods In this randomised, controlled, open-label, adaptive platform trial (Randomised Evaluation of COVID-19Therapy [RECOVERY]), several possible treatments were compared with usual care in patients admitted to hospitalwith COVID-19 in the UK. The trial is underway at 176 hospitals in the UK. Eligible and consenting patients wererandomly allocated to either usual standard of care alone or usual standard of care plus azithromycin 500 mg once perday by mouth or intravenously for 10 days or until discharge (or allocation to one of the other RECOVERY treatmentgroups). Patients were assigned via web-based simple (unstratified) randomisation with allocation concealment andwere twice as likely to be randomly assigned to usual care than to any of the active treatment groups. Participants andlocal study staff were not masked to the allocated treatment, but all others involved in the trial were masked to theoutcome data during the trial. The primary outcome was 28-day all-cause mortality, assessed in the intention-to-treatpopulation. The trial is registered with ISRCTN, 50189673, and ClinicalTrials.gov, NCT04381936.Findings Between April 7 and Nov 27, 2020, of 16 442 patients enrolled in the RECOVERY trial, 9433 (57%) wereeligible and 7763 were included in the assessment of azithromycin. The mean age of these study participants was65·3 years (SD 15·7) and approximately a third were women (2944 [38%] of 7763). 2582 patients were randomlyallocated to receive azithromycin and 5181 patients were randomly allocated to usual care alone. Overall,561 (22%) patients allocated to azithromycin and 1162 (22%) patients allocated to usual care died within 28 days(rate ratio 0·97, 95% CI 0·87–1·07; p=0·50). No significant difference was seen in duration of hospital stay (median10 days [IQR 5 to >28] vs 11 days [5 to >28]) or the proportion of patients discharged from hospital alive within 28 days(rate ratio 1·04, 95% CI 0·98–1·10; p=0·19). Among those not on invasive mechanical ventilation at baseline, nosignificant difference was seen in the proportion meeting the composite endpoint of invasive mechanical ventilationor death (risk ratio 0·95, 95% CI 0·87–1·03; p=0·24).Interpretation In patients admitted to hospital with COVID-19, azithromycin did not improve survival or otherprespecified clinical outcomes. Azithromycin use in patients admitted to hospital with COVID-19 should be restrictedto patients in whom there is a clear antimicrobial indication

Origins of modern human ancestry

New finds in the palaeoanthropological and genomic records have changed our view of the origins of modern human ancestry. Here we review our current understanding of how the ancestry of modern humans around the globe can be traced into the deep past, and which ancestors it passes through during our journey back in time. We identify three key phases that are surrounded by major questions, and which will be at the frontiers of future research. The most recent phase comprises the worldwide expansion of modern humans between 40 and 60 thousand years ago (ka) and their last known contacts with archaic groups such as Neanderthals and Denisovans. The second phase is associated with a broadly construed African origin of modern human diversity between 60 and 300 ka. The oldest phase comprises the complex separation of modern human ancestors from archaic human groups from 0.3 to 1 million years ago. We argue that no specific point in time can currently be identified at which modern human ancestry was confined to a limited birthplace, and that patterns of the first appearance of anatomical or behavioural traits that are used to define Homo sapiens are consistent with a range of evolutionary histories. A Review describes the three key phases that define the origins of modern human ancestry, and highlights the importance of analysing both palaeoanthropological and genomic records to further improve our understanding of our evolutionary history

Aliens in Antarctica: Assessing transfer of plant propagules by human visitors to reduce invasion risk

Despite considerable research on biological invasions, key areas remain poorly explored, especially ways to reduce unintentional propagule transfer. The Antarctic represents a microcosm of the situation, with the numbers of established non-native species growing. Information to help reduce potential impacts is therefore critical. We measured the propagule load of seeds, and fragments of bryophytes and lichens (the number of other plant or animal fragments was too low to draw any conclusions) carried in the clothing and gear of visitors to the Antarctic, during the 2007/08 austral summer. Samples were collected from different categories of visitors associated with national research programs and tourism and different categories of clothing and gear, new as well as used. We also collected information about the timing of travel and the regions visitors had travelled to prior to Antarctic travel. Seeds were found in 20% and 45% of tourist and science visitor samples, respectively. For bryophyte and lichen fragments the proportions were 11% and 20%, respectively. Footwear, trousers and bags belonging to field scientists were the highest risk items, especially of those personnel which had previously visited protected areas, parklands/botanic gardens or alpine areas. Tourists who visited rural/agricultural areas prior to travel, and/or travel with national programs or on smaller tourist vessels had the highest probability of transferring plant propagules. Travel either during the boreal or austral autumn months increased the probability of propagule presence. Our assessment is applicable to other areas given evidence of propagule transfer patterns in those areas that are broadly similar to those documented here. The current work provides a sound evidence base for both self-regulation (e.g. taking care of personal equipment) and organization-based regulation (e.g. issuing guidelines and holding regular inspections) to reduce propagule transfer of plants to the Antarctic