The spillovers of betacoronaviruses in humans and the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants highlight the need for broad coronavirus countermeasures. We ...describe five monoclonal antibodies (mAbs) cross-reacting with the stem helix of multiple betacoronavirus spike glycoproteins isolated from COVID-19 convalescent individuals. Using structural and functional studies, we show that the mAb with the greatest breadth (S2P6) neutralizes pseudotyped viruses from three different subgenera through the inhibition of membrane fusion, and we delineate the molecular basis for its cross-reactivity. S2P6 reduces viral burden in hamsters challenged with SARS-CoV-2 through viral neutralization and Fc-mediated effector functions. Stem helix antibodies are rare, oftentimes of narrow specificity, and can acquire neutralization breadth through somatic mutations. These data provide a framework for structure-guided design of pan-betacoronavirus vaccines eliciting broad protection.
Sequence variation data of the human proteome can be used to analyze 3D protein structures to derive functional insights.We used genetic variant data from nearly 140,000 individuals to analyze 3D ...positional conservation in 4,715 proteins and 3,951 homology models using 860,292 missense and 465,886 synonymous variants. Sixty percent of protein structures harbor at least one intolerant 3D site as defined by significant depletion of observed over expected missense variation. Structural intolerance data correlated with deep mutational scanning functional readouts for PPARG, MAPK1/ERK2, UBE2I, SUMO1, PTEN, CALM1, CALM2, and TPK1 and with shallow mutagenesis data for 1,026 proteins. The 3D structural intolerance analysis revealed different features for ligand binding pockets and orthosteric and allosteric sites. Large-scale data on human genetic variation support a definition of functional 3D sites proteome-wide.
Reducing premature mortality associated with age-related chronic diseases, such as cancer and cardiovascular disease, is an urgent priority. We report early results using genomics in combination with ...advanced imaging and other clinical testing to proactively screen for age-related chronic disease risk among adults. We enrolled active, symptom-free adults in a study of screening for age-related chronic diseases associated with premature mortality. In addition to personal and family medical history and other clinical testing, we obtained whole-genome sequencing (WGS), noncontrast whole-bodyMRI, dual-energy X-ray absorptiometry (DXA), global metabolomics, a new blood test for prediabetes (Quantose IR), echocardiography (ECHO), ECG, and cardiac rhythm monitoring to identify age-related chronic disease risks. Precision medicine screening using WGS and advanced imaging along with other testing among active, symptom-free adults identified a broad set of complementary age-related chronic disease risks associated with premature mortality and strengthened WGS variant interpretation. This and other similarly designed screening approaches anchored by WGS and advanced imaging may have the potential to extend healthy life among active adults through improved prevention and early detection of age-related chronic diseases (and their risk factors) associated with premature mortality.
Many hierarchical schemes have been developed to describe multiple-scale cut-and-fill architecture of deep-water channel systems and analyse their evolution. A widely applicable genetical-based ...scheme is not on the horizon yet. Near seismic-scale exposures of two deep-water channel systems from the late Miocene of the Transylvanian Basin, Romania offer a fresh insight into the dynamics of erosional and depositional processes. Both channel systems are underlain by mudstone-prone successions; the channel-complex scale incisional surface can only be observed at Tău. Channel-form surfaces interpreted as the base of channel elements and storeys are present in both outcrops. At Tău, the shallow, base-of-slope channel complex consists of amalgamated sandstones separated by thin mudstones. The axis of the deep, slope channel at Daia is characterized by pebble lags, thick amalgamated sandstones that thin towards the margin, and thin mudstones. Backsets, possible cyclic steps, and erosional features, such as rip-up mud-boulders, detachment edges, and ghost bedding also occur. Cycles of incision, bypass with coarse lag accumulation, deposition from gravelly then sandy turbidity currents were repeated numerous times with differing amplitudes, which were followed by the abandonment of the channel complex. Novel incision-infill graphs were created to analyse and compare the cyclicity pattern of deep-water channels. Successive incision depth of channel-form surfaces, and infill height of channel-form bodies aids in distinguishing hierarchical levels, vertical and lateral offsets. Daia and Tău channel complexes show a remarkably similar cyclicity pattern, which might indicate an inherent character of this turbidite system. To investigate whether this pattern is universal, incision-infill graphs of two Laingsburg Karoo channel systems were constructed, based on published data. In all the four examples, a pattern of lateral-then-vertical offset of channel elements was present, and a similarity between channel element-complex and channel storey-element aggradation was found, suggesting a fractal behaviour. Two models are applicable to interpret the revealed pattern of incision-infill graphs, for the Tău and Daia channels: 1) three scales of waxing-waning flow magnitude cyclicity could create the architecture of channel complexes, or 2) the presence of autocyclic channel element incision-infill could eliminate one scale of flow magnitude changes, but two still need to be governed by allocyclic factors. The late Miocene turbidite system in the Transylvanian Basin developed in Lake Pannon, in close relationship with the uplifting Carpathians fringing the basin. As the duration of cycles is shorter than the time range of possible changes in uplift rate or fault activity, tectonically induced cyclicity is discarded. Climatically induced cycles are the most probable controls on varying the flow magnitude that created the complex architecture of channel systems in this lacustrine setting.
•Channel storey, channel element and channel complex scales all show cyclicity.•Laterally offset erosion, bypass, and deposition phases create one channel element.•Novel incision-infill graphs aid in cyclicity analysis, distinction of hierarchies.•Incision-infill pattern similarity at different scales suggests fractal character.•Climate-induced waxing-waning cycles affected evolution in this lacustrine setting.
Sequencing projects have identified large numbers of rare stop-gain and frameshift variants in the human genome. As most of these are observed in the heterozygous state, they test a gene's tolerance ...to haploinsufficiency and dominant loss of function. We analyzed the distribution of truncating variants across 16,260 autosomal protein coding genes in 11,546 individuals. We observed 39,893 truncating variants affecting 12,062 genes, which significantly differed from an expectation of 12,916 genes under a model of neutral de novo mutation (p<10-4). Extrapolating this to increasing numbers of sequenced individuals, we estimate that 10.8% of human genes do not tolerate heterozygous truncating variants. An additional 10 to 15% of truncated genes may be rescued by incomplete penetrance or compensatory mutations, or because the truncating variants are of limited functional impact. The study of protein truncating variants delineates the essential genome and, more generally, identifies rare heterozygous variants as an unexplored source of diversity of phenotypic traits and diseases.
A gene can be defined as essential when loss of its function compromises viability of the individual (for example, embryonic lethality) or results in profound loss of fitness. At the population ...level, identification of essential genes is accomplished by observing intolerance to loss-of-function variants. Several computational methods are available to score gene essentiality, and recent progress has been made in defining essentiality in the non-coding genome. Haploinsufficiency is emerging as a critical aspect of gene essentiality: approximately 3,000 human genes cannot tolerate loss of one of the two alleles. Genes identified as essential in human cell lines or knockout mice may be distinct from those in living humans. Reconciling these discrepancies in how we evaluate gene essentiality has applications in clinical genetics and may offer insights for drug development.
Hospital healthcare workers (HCW), in particular those involved in the clinical care of COVID-19 cases, are presumably exposed to a higher risk of acquiring the disease than the general population.
...Between April 16 and 30, 2020 we conducted a prospective, SARS-CoV-2 seroprevalence study in HCWs in Southern Switzerland. Participants were hospital personnel with varying COVID-19 exposure risk depending on job function and working site. They provided personal information (including age, sex, occupation, and medical history) and self-reported COVID-19 symptoms. Odds ratio (OR) of seropositivity to IgG antibodies was estimated by univariate and multivariate logistic regressions.
Among 4726 participants, IgG antibodies to SARS-CoV-2 were detected in 9.6% of the HCWs. Seropositivity was higher among HCWs working on COVID-19 wards (14.1% (11.9–16.5)) compared to other hospital areas at medium (10.7% (7.6–14.6)) or low risk exposure (7.3% (6.4–8.3)). OR for high vs. medium wards risk exposure was 1.42 (0.91–2.22), P = 0.119, and 1.98 (1.55–2.53), P<0.001 for high vs. low wards risk exposure. The same was for true for doctors and nurses (10.1% (9.0–11.3)) compared to other employees at medium (7.1% (4.8–10.0)) or low risk exposure (6.6% (5.0–8.4)). OR for high vs. medium profession risk exposure was 1.37 (0.89–2.11), P = 0.149, and 1.75 (1.28–2.40), P = 0.001 for high vs. low profession risk exposure. Moreover, seropositivity was higher among HCWs who had household exposure to COVID-19 cases compared to those without (18.7% (15.3–22.5) vs. 7.7% (6.9–8.6), OR 2.80 (2.14–3.67), P<0.001).
SARS-CoV-2 antibodies are detectable in up to 10% of HCWs from acute care hospitals in a region with high incidence of COVID-19 in the weeks preceding the study. HCWs with exposure to COVID-19 patients have only a slightly higher absolute risk of seropositivity compared to those without, suggesting that the use of PPE and other measures aiming at reducing nosocomial viral transmission are effective. Household contact with known COVID-19 cases represents the highest risk of seropositivity.
Henry Krenter Foundation, Ente Ospedaliero Cantonale and Vir Biotechnology.
The 20 residue long Trp‐cage is the smallest protein known, and thus has been the subject of several in vitro and in silico folding studies. Here, we report the multistate folding scenario of the ...miniprotein in atomic detail. We detected and characterized different intermediate states by temperature dependent NMR measurements of the 15N and 13C/15N labeled protein, both at neutral and acidic pH values. We developed a deconvolution technique to characterize the invisible—fully folded, unfolded and intermediate—fast exchanging states. Using nonlinear fitting methods we can obtain both the thermodynamic parameters (ΔHF–I, TmF–I, ΔCpF–I and ΔHI–U, TmI–U, ΔCpI–U) and the NMR chemical shifts of the conformers of the multistate unfolding process. During the unfolding of Trp‐cage distinct intermediates evolve: a fast‐exchanging intermediate is present under neutral conditions, whereas a slow‐exchanging intermediate‐pair emerges at acidic pH. The fast‐exchanging intermediate has a native‐like structure with a short α‐helix in the G11–G15 segment, whereas the slow‐exchanging intermediate‐pair presents elevated dynamics, with no detectable native‐like residue contacts in which the G11P12 peptide bond has either cis or trans conformation. Heteronuclear relaxation studies combined with MD simulations revealed the source of backbone mobility and the nature of structural rearrangements during these transitions. The ability to detect structural and dynamic information about folding intermediates in vitro provides an excellent opportunity to gain new insights into the energetic aspects of the energy landscape of protein folding. Our new experimental data offer exceptional testing ground for further computational simulations.
Számos in vitro és in silico feltekeredési tanulmány tárgyát képezte már kis méretének köszönhetően a mindössze 20 aminosavból felépülő Trp‐kalitka mini‐fehérje. Elsőként itt számolunk be és adunk atomi felbontású képet ezen természetes polimer több‐lépésben történő feltekeredéséről. A 15N és 13C/15N jelölt fehérjék hőmérsékletfüggő NMR mérései alapján különböző köztes‐állapokat figyeltünk meg és jellemeztünk mind semleges, mind savas pH‐n. A spektrumok elemzésére egy új dekonvolúciós eljárást dolgoztunk ki, olyat amellyel egyaránt jellemezni tudtuk az egymással gyorsan cserélődő s ezért tiszta formáikban „láthatatlan“ fel‐ és letekeredett, valamint közbülső állapotokat. Egy alkalmas nem‐lineáris illesztési módszert használva meghatároztuk a több‐lépéses feltekeredési folyamat termodinamikai paramétereit (ΔHF–I, TmF–I, ΔCpF–I és ΔHI–U, TmI–U, ΔCpI–U), valamint a „láthatatlan” teljesen tiszta állapotok NMR kémiai‐eltolódásértékeit. A Trp‐kalitka feltekeredése során több megkülönböztethető közbülső állapot kialakulását tapasztaljuk. Semleges közegben egy, az NMR időskálán mérve gyorsan cserét mutató, míg savas közegben két lassabban cserélődő intermedier figyelhető meg. A gyorsan cserélődő köztiállapot térszerkezete hasonlít a natív térszerkezethez, a különbség mindössze a G11G15 újonnan kialakuló α‐helikális szegmensre korlátozódik. A lassan cserélődő intermedier belső dinamikájára nézve mozgékony, térszerkezetét tekintve majdnem teljesen rendezetlen. Itt a G11P12 peptidkötés konformációja lehet akár cisz, akár transz térállású. Heteronukleáris relaxációs mérések, illetve molekuladinamikai szimulációk segítségével feltártuk a fehérjegerinc belső mozgékonyságának és a téralkat‐átrendeződésnek molekuláris hátterét. Az a tény, hogy in vitro atomi szintű szerkezeti és dinamikai információk gyűjthetők a Trp‐kalitka minifehérje intermedierjeiről egyben explicit utalást is ad arról, hogy milyen is e fehérje‐feltekeredésének potenciális energiafelülete. Az általunk most bemutatott kísérleti eredmények további in silico szimulációkhoz szolgáltatnak értékes adatsorokat.
Observing the invisible: The Trp‐cage miniprotein folds in a multistate process into its native structure. Heteronuclear NMR spectroscopy studies combined with molecular dynamics simulations provide direct evidence for the 310‐ to α‐helix rearrangement as an initial step during the unfolding. The G11P12 peptide bond isomerization slows down the folding under acidic conditions (see figure; F=folded, I=intermediate, and U=unfolded structures).
Studies of host genetic determinants of pathogen sequence variations can identify sites of genomic conflicts, by highlighting variants that are implicated in immune response on the host side and ...adaptive escape on the pathogen side. However, systematic genetic differences in host and pathogen populations can lead to inflated type I (false positive) and type II (false negative) error rates in genome-wide association analyses. Here, we demonstrate through a simulation that correcting for both host and pathogen stratification reduces spurious signals and increases power to detect real associations in a variety of tested scenarios. We confirm the validity of the simulations by showing comparable results in an analysis of paired human and HIV genomes.
Loss-of-function variants in innate immunity genes are associated with Mendelian disorders in the form of primary immunodeficiencies. Recent resequencing projects report that stop-gains and ...frameshifts are collectively prevalent in humans and could be responsible for some of the inter-individual variability in innate immune response. Current computational approaches evaluating loss-of-function in genes carrying these variants rely on gene-level characteristics such as evolutionary conservation and functional redundancy across the genome. However, innate immunity genes represent a particular case because they are more likely to be under positive selection and duplicated. To create a ranking of severity that would be applicable to innate immunity genes we evaluated 17,764 stop-gain and 13,915 frameshift variants from the NHLBI Exome Sequencing Project and 1,000 Genomes Project. Sequence-based features such as loss of functional domains, isoform-specific truncation and nonsense-mediated decay were found to correlate with variant allele frequency and validated with gene expression data. We integrated these features in a Bayesian classification scheme and benchmarked its use in predicting pathogenic variants against Online Mendelian Inheritance in Man (OMIM) disease stop-gains and frameshifts. The classification scheme was applied in the assessment of 335 stop-gains and 236 frameshifts affecting 227 interferon-stimulated genes. The sequence-based score ranks variants in innate immunity genes according to their potential to cause disease, and complements existing gene-based pathogenicity scores. Specifically, the sequence-based score improves measurement of functional gene impairment, discriminates across different variants in a given gene and appears particularly useful for analysis of less conserved genes.
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