Synonymous co-variation across the E1/E2 gene junction of hepatitis C virus defines virion fitness

Hepatitis C virus is a positive-sense single-stranded RNA virus. The gene junction partitioning the viral glycoproteins E1 and E2 displays concurrent sequence evolution with the 3′-end of E1 highly conserved and the 5′-end of E2 highly heterogeneous. This gene junction is also believed to contain structured RNA elements, with a growing body of evidence suggesting that such structures can act as an additional level of viral replication and transcriptional control. We have previously used ultradeep pyrosequencing to analyze an amplicon library spanning the E1/E2 gene junction from a treatment naïve patient where samples were collected over 10 years of chronic HCV infection. During this timeframe maintenance of an in-frame insertion, recombination and humoral immune targeting of discrete virus sub-populations was reported. In the current study, we present evidence of epistatic evolution across the E1/E2 gene junction and observe the development of co-varying networks of codons set against a background of a complex virome with periodic shifts in population dominance. Overtime, the number of codons actively mutating decreases for all virus groupings. We identify strong synonymous co-variation between codon sites in a group of sequences harbouring a 3 bp in-frame insertion and propose that synonymous mutation acts to stabilize the RNA structural backbone

Neutral silicon vacancy centers in undoped diamond via surface control

Neutral silicon vacancy centers (SiV0) in diamond are promising candidates for quantum networks because of their long spin coherence times and stable, narrow optical transitions. However, stabilizing SiV0 requires high purity, boron doped diamond, which is not a readily available material. Here, we demonstrate an alternative approach via chemical control of the diamond surface. We use low-damage chemical processing and annealing in a hydrogen environment to realize reversible and highly stable charge state tuning in undoped diamond. The resulting SiV0 centers display optically detected magnetic resonance and bulk-like optical properties. Controlling the charge state tuning via surface termination offers a route for scalable technologies based on SiV0 centers, as well as charge state engineering of other defects

Seven centuries of reconstructed Brahmaputra River discharge demonstrate underestimated high discharge and flood hazard frequency

The lower Brahmaputra River in Bangladesh and Northeast India often floods during the monsoon season, with catastrophic consequences for people throughout the region. While most climate models predict an intensified monsoon and increase in flood risk with warming, robust baseline estimates of natural climate variability in the basin are limited by the short observational record. Here we use a new seven-century (1309–2004 C.E) tree-ring reconstruction of monsoon season Brahmaputra discharge to demonstrate that the early instrumental period (1956–1986 C.E.) ranks amongst the driest of the past seven centuries (13th percentile). Further, flood hazard inferred from the recurrence frequency of high discharge years is severely underestimated by 24–38% in the instrumental record compared to previous centuries and climate model projections. A focus on only recent observations will therefore be insufficient to accurately characterise flood hazard risk in the region, both in the context of natural variability and climate change

Ultra-high resolution X-ray structures of two forms of human recombinant insulin at 100 K

The crystal structure of a commercially available form of human recombinant (HR) insulin, Insugen (I), used in the treatment of diabetes has been determined to 0.92 Å resolution using low temperature, 100 K, synchrotron X-ray data collected at 16,000 keV (λ = 0.77 Å). Refinement carried out with anisotropic displacement parameters, removal of main-chain stereochemical restraints, inclusion of H atoms in calculated positions, and 220 water molecules, converged to a final value of R = 0.1112 and Rfree = 0.1466. The structure includes what is thought to be an ordered propanol molecule (POL) only in chain D(4) and a solvated acetate molecule (ACT) coordinated to the Zn atom only in chain B(2). Possible origins and consequences of the propanol and acetate molecules are discussed. Three types of amino acid representation in the electron density are examined in detail: (i) sharp with very clearly resolved features; (ii) well resolved but clearly divided into two conformations which are well behaved in the refinement, both having high quality geometry; (iii) poor density and difficult or impossible to model. An example of type (ii) is observed for the intra-chain disulphide bridge in chain C(3) between Sγ6–Sγ11 which has two clear conformations with relative refined occupancies of 0.8 and 0.2, respectively. In contrast the corresponding S–S bridge in chain A(1) shows one clearly defined conformation. A molecular dynamics study has provided a rational explanation of this difference between chains A and C. More generally, differences in the electron density features between corresponding residues in chains A and C and chains B and D is a common observation in the Insugen (I) structure and these effects are discussed in detail. The crystal structure, also at 0.92 Å and 100 K, of a second commercially available form of human recombinant insulin, Intergen (II), deposited in the Protein Data Bank as 3W7Y which remains otherwise unpublished is compared here with the Insugen (I) structure. In the Intergen (II) structure there is no solvated propanol or acetate molecule. The electron density of Intergen (II), however, does also exhibit the three types of amino acid representations as in Insugen (I). These effects do not necessarily correspond between chains A and C or chains B and D in Intergen (II), or between corresponding residues in Insugen (I). The results of this comparison are reported

An eleven year record of XCO2 estimates derived from GOSAT measurements using the NASA ACOS version 9 retrieval algorithm

The Thermal And Near infrared Sensor for carbon Observation – Fourier Transform Spectrometer (TANSO-FTS) on the Japanese Greenhouse gases Observing SATellite (GOSAT) has been returning data since April 2009. The version 9 (v9) Atmospheric Carbon Observations from Space (ACOS) Level 2 Full Physics (L2FP) retrieval algorithm (Kiel et al., 2019) was used to derive estimates of carbon dioxide (CO2) dry air mole fraction (XCO2) from the TANSO-FTS measurements collected over it's first eleven years of operation. The bias correction and quality filtering of the L2FP XCO2 product were evaluated using estimates derived from the Total Carbon Column Observing Network (TCCON) as well as values simulated from a suite of global atmospheric inverse modeling systems (models). In addition, the v9 ACOS GOSAT XCO2 results were compared with collocated XCO2 estimates derived from NASA's Orbiting Carbon Observatory-2 (OCO-2), using the version 10 (v10) ACOS L2FP algorithm. These tests indicate that the v9 ACOS GOSAT XCO2 product has improved throughput, scatter and bias, when compared to the earlier v7.3 ACOS GOSAT product, which extended through mid 2016. Of the 37 million (M) soundings collected by GOSAT through June 2020, approximately 20 % were selected for processing by the v9 L2FP algorithm after screening for clouds and other artifacts. After post-processing, 5.4 % of the soundings (2M out of 37M) were assigned a “good” XCO2 quality flag, as compared to 3.9 % in v7.3 (< 1M out of 24M). After quality filtering and bias correction, the differences in XCO2 between ACOS GOSAT v9 and both TCCON and models have a scatter (one sigma) of approximately 1 ppm for ocean-glint observations and 1 to 1.5 ppm for land observations. Similarly, global mean biases are less than approximately 0.2 ppm. Seasonal mean biases relative to the v10 OCO-2 XCO2 product are of order 0.1 ppm for observations over land. However, for ocean-glint observations, seasonal mean biases relative to OCO-2 range from 0.2 to 0.6 ppm, with substantial variation in time and latitude. The ACOS GOSAT v9 XCO2 data are available on the NASA Goddard Earth Science Data and Information Services Center (GES-DISC). The v9 ACOS Data User's Guide (DUG) describes best-use practices for the data. This dataset should be especially useful for studies of carbon cycle phenomena that span a full decade or more, and may serve as a useful complement to the shorter OCO-2 v10 dataset, which begins in September 2014

Genome-Wide Association Study of Coronary Heart Disease and Its Risk Factors in 8,090 African Americans: The NHLBI CARe Project

Coronary heart disease (CHD) is the leading cause of mortality in African Americans. To identify common genetic polymorphisms associated with CHD and its risk factors (LDL- and HDL-cholesterol (LDL-C and HDL-C), hypertension, smoking, and type-2 diabetes) in individuals of African ancestry, we performed a genome-wide association study (GWAS) in 8,090 African Americans from five population-based cohorts. We replicated 17 loci previously associated with CHD or its risk factors in Caucasians. For five of these regions (CHD: CDKN2A/CDKN2B; HDL-C: FADS1-3, PLTP, LPL, and ABCA1), we could leverage the distinct linkage disequilibrium (LD) patterns in African Americans to identify DNA polymorphisms more strongly associated with the phenotypes than the previously reported index SNPs found in Caucasian populations. We also developed a new approach for association testing in admixed populations that uses allelic and local ancestry variation. Using this method, we discovered several loci that would have been missed using the basic allelic and global ancestry information only. Our conclusions suggest that no major loci uniquely explain the high prevalence of CHD in African Americans. Our project has developed resources and methods that address both admixture- and SNP-association to maximize power for genetic discovery in even larger African-American consortia

Gene-centric approach identifies new and known loci for FVIII activity and VWF antigen levels in European Americans and African Americans: Genetic associations for FVIII:C and VWF:ag

Coagulation factor VIII and von Willebrand factor (VWF) are key proteins in procoagulant activation. Higher FVIII coagulant activity (FVIII:C) and VWF antigen (VWF:Ag) are risk factors for cardiovascular disease and venous thromboembolism. Beyond associations with ABO blood group, genetic determinants of FVIII and VWF are not well understood, especially in non European-American populations. We performed a genetic association study of FVIII:C and VWF:Ag that assessed 50,000 gene-centric single nucleotide polymorphisms (SNPs) in 18,556 European Americans (EAs) and 5,047 African Americans (AAs) from five population-based cohorts. Previously unreported associations for FVIII:C were identified in both AAs and EAs with KNG1 (most significantly associated SNP rs710446, Ile581Thr, P=5.10 × 10−7 in EAs and P=3.88 × 10−3 in AAs) and VWF rs7962217 (Gly2705Arg, P=6.30 × 10−9 in EAs and P=2.98 × 10−2 in AAs). Significant associations for FVIII:C were also observed with F8/TMLHE region SNP rs12557310 in EAs (P=8.02 × 10−10), with VWF rs1800380 in AAs (P=5.62 × 10−11), and with MAT1A rs2236568 in AAs (P=1.69 × 10−6). We replicated previously reported associations of FVIII:C and VWF:Ag with the ABO blood group, VWF rs1063856 (Thr789Ala), rs216321 (Ala852Gln), and VWF rs2229446 (Arg2185Gln). Findings from this study expand our understanding of genetic influences for FVIII:C and VWF:Ag in both EAs and AAs