Novel Evidence of HBV Recombination in Family Cluster Infections in Western China

Two hepatitis B virus (HBV) C/D recombinants were isolated from western China. No direct evidence indicates that these new viruses arose as a result of recombination between genotype C and D or a result of convergence. In this study, we search for evidence of intra-individual recombination in the family cluster cases with co-circulation of genotype C, D and C/D recombinants. We studied 68 individuals from 15 families with HBV infections in 2006, identified individuals with mixed HBV genotype co-infections by restriction fragment length polymorphism and proceeded with cloning and DNA sequencing. Recombination signals were detected by RDP3 software and confirmed by split phylogenetic trees. Families with mixed HBV genotype co-infections were resampled in 2007. Three of 15 families had individuals with different HBV genotype co-infections in 2006. One individual (Y2) had a triple infection of HBV genotype C, D and C/D recombinant in 2006, but only genotype D in 2007. Further clonal analysis of this patient indicated that the C/D recombinant was not identical to previously isolated CD1 or CD2, but many novel recombinants with C2, D1 and CD1 were simultaneously found. All parental strains could recombine with each other to form new recombinant in this patient. This indicates that the detectable mixed infection and recombination have a limited time window. Also, as the recombinant nature of HBV precludes the possibility of a simple phylogenetic taxonomy, a new standard may be required for classifying HBV sequences

Identification of Serum MicroRNAs as Novel Non-Invasive Biomarkers for Early Detection of Gastric Cancer

BACKGROUND: To investigate the potential of serum miRNAs as biomarkers for early detection of gastric cancer (GC), a population-based study was conducted in Linqu, a high-risk area of GC in China. METHODOLOGY/PRINCIPAL FINDINGS: All subjects were selected from two large cohort studies. Differential miRNAs were identified in serum pools of GC and control using TaqMan low density array, and validated in individual from 82 pairs of GC and control, and 46 pairs of dysplasia and control by real-time quantitative reverse transcription-polymerase chain reaction. The temporal trends of identified serum miRNA expression were further explored in a retrospective study on 58 GC patients who had at least one pre-GC diagnosis serum sample based on the long-term follow-up population. The miRNA profiling results demonstrated that 16 miRNAs were markedly upregulated in GC patients compared to controls. Further validation identified a panel of three serum miRNAs (miR-221, miR-744, and miR-376c) as potential biomarkers for GC detection, and receiver operating characteristic (ROC) curve-based risk assessment analysis revealed that this panel could distinguish GCs from controls with 82.4% sensitivity and 58.8% specificity. MiR-221 and miR-376c demonstrated significantly positive correlation with poor differentiation of GC, and miR-221 displayed higher level in dysplasia than in control. Furthermore, the retrospective study revealed an increasing trend of these three miRNA levels during GC development (P for trend<0.05), and this panel could classify serum samples collected up to 5 years ahead of clinical GC diagnosis with 79.3% overall accuracy. CONCLUSIONS/SIGNIFICANCE: These data suggest that serum miR-221, miR-376c and miR-744 have strong potential as novel non-invasive biomarkers for early detection of GC

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

The “Singular” Behavior of the Solar Wind Scaling Features during Parker Solar Probe–BepiColombo Radial Alignment

International audienceAt the end of 2020 September, the Parker Solar Probe (PSP) and BepiColombo were radially aligned: PSP was orbiting near 0.17 au and BepiColombo near 0.6 au. This geometry is of particular interest for investigating the evolution of solar wind properties at different heliocentric distances by observing the same solar wind plasma parcels. In this work, we use the magnetic field observations from both spacecraft to characterize both the topology of the magnetic field at different heliocentric distances (scalings, high-order statistics, and multifractal features) and its evolution when moving from near-Sun to far-Sun locations. We observe a breakdown of the statistical self-similar nature of the solar wind plasma with an increase in the efficiency of the nonlinear energy cascade mechanism when moving away from the Sun. We find a complex organization of large field gradients to dissipate the excess of kinetic energy across the inertial range near the Sun, whereas the topological organization of small fluctuations is still primarily responsible for the energy transfer rate at 0.6 au. These results provide, for the first time, evidence of the different roles of dissipation mechanisms near and far away from the Sun

Detection of phosphates originating from Enceladus’s ocean

Abstract Saturn’s moon Enceladus harbours a global ice-covered water ocean. The Cassini spacecraft investigated the composition of the ocean by analysis of material ejected into space by the moon’s cryovolcanic plume. The analysis of salt-rich ice grains by Cassini’s Cosmic Dust Analyzer10 enabled inference of major solutes in the ocean water (Na+, K+, Cl-, HCO3-, CO32-) and its alkaline pH. Phosphorus, the least abundant of the bio-essential elements, has not yet been detected in an ocean beyond Earth. Earlier geochemical modelling studies suggest that phosphate might be scarce in the ocean of Enceladus and other icy ocean worlds. However, more recent modelling of mineral solubilities in Enceladus’s ocean indicates that phosphate could be relatively abundant. Here we present Cassini’s Cosmic Dust Analyzer mass spectra of ice grains emitted by Enceladus that show the presence of sodium phosphates. Our observational results, together with laboratory analogue experiments, suggest that phosphorus is readily available in Enceladus’s ocean in the form of orthophosphates, with phosphorus concentrations at least 100-fold higher in the moon’s plume-forming ocean waters than in Earth’s oceans. Furthermore, geochemical experiments and modelling demonstrate that such high phosphate abundances could be achieved in Enceladus and possibly in other icy ocean worlds beyond the primordial CO2 snowline, either at the cold seafloor or in hydrothermal environments with moderate temperatures. In both cases the main driver is probably the higher solubility of calcium phosphate minerals compared with calcium carbonate in moderately alkaline solutions rich in carbonate or bicarbonate ions