Coronavirus-like Core-Shell-Structured Co@C for Hydrogen Evolution via Hydrolysis of Sodium Borohydride.

Constructing a reliable and robust cobalt-based catalyst for hydrogen evolution via hydrolysis of sodium borohydride is appealing but challenging due to the deactivation caused by the metal leaching and re-oxidization of metallic cobalt. A unique core-shell-structured coronavirus-like Co@C microsphere was prepared via pyrolysis of Co-MOF. This special Co@C had a microporous carbon coating to retain the reduced state of cobalt and resist the metal leaching.

Facile fabrication and characterization of highly stretchable lignin-based hydroxyethyl cellulose self-healing hydrogel.

In this study, hydroxyethyl cellulose (HEC) and polyvinyl alcohol (PVA) as the framework, borax as the cross-linker, and biomass lignin from pulping black liquors and biorefinery as the plasticizer were used to synthesize the lignin-based HEC-PVA (LCP) self-healing conductive hydrogel with highly stretchable and thermosensitive properties by the one-step fabrication method. Compared with the PVA hydrogel, the maximum storage modulus and the elongation rate was increased by 7 times and 20 times, respectively. Uniformly distributed lignin could increase the mobility and distance of polymer molecular chains, therefore improve the viscoelasticity and stretchability of the LCP self-healing hydrogel.

Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers.

Background: The yield obtained from next generation sequencers has increased almost exponentially in recent years, making sample multiplexing common practice. While barcodes (known sequences of fixed length) primarily encode the sample identity of sequenced DNA fragments, barcodes made of random sequences (Unique Molecular Identifier or UMIs) are often used to distinguish between PCR duplicates and transcript abundance in, for example, single-cell RNA sequencing (scRNA-seq). In paired-end sequencing, different barcodes can be inserted at each fragment end to either increase the number of multiplexed samples in the library or to use one of the barcodes as UMI.

Peripheral fibroblast metabolic pathway alterations in juvenile rhesus monkeys undergoing long-term fluoxetine administration.

We report on biochemical pathways perturbed upon chronic fluoxetine administration to juvenile macaques using global metabolomics analyses of fibroblasts derived from skin biopsies. After exposure to tissue culture conditions confounding environmental factors are eliminated and identification of metabolites whose levels are affected by the drug become apparent with a better signal-to-noise ratio compared to data obtained from plasma and cerebrospinal fluid (CSF). Levels of more than 200 metabolites were analyzed to interrogate affected molecular pathways and identify biomarkers of drug response.

Fe-S cluster biosynthesis controls uptake of aminoglycosides in a ROS-less death pathway.

All bactericidal antibiotics were recently proposed to kill by inducing reactive oxygen species (ROS) production, causing destabilization of iron-sulfur (Fe-S) clusters and generating Fenton chemistry. We find that the ROS response is dispensable upon treatment with bactericidal antibiotics. Furthermore, we demonstrate that Fe-S clusters are required for killing only by aminoglycosides.

Detection of identity by descent using next-generation whole genome sequencing data.

Background: Identity by descent (IBD) has played a fundamental role in the discovery of genetic loci underlying human diseases. Both pedigree-based and population-based linkage analyses rely on estimating recent IBD, and evidence of ancient IBD can be used to detect population structure in genetic association studies. Various methods for detecting IBD, including those implemented in the soft- ware programs fastIBD and GERMLINE, have been developed in the past several years using population genotype data from microarray platforms.

Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.

We present a novel pipeline and methodology for simultaneously estimating isoform expression and allelic imbalance in diploid organisms using RNA-seq data. We achieve this by modeling the expression of haplotype-specific isoforms. If unknown, the two parental isoform sequences can be individually reconstructed.

Inferring combined CNV/SNP haplotypes from genotype data.

Motivation: Copy number variations (CNVs) are increasingly recognized as an substantial source of individual genetic variation, and hence there is a growing interest in investigating the evolutionary history of CNVs as well as their impact on complex disease susceptibility. CNV/SNP haplotypes are critical for this research, but although many methods have been proposed for inferring integer copy number, few have been designed for inferring CNV haplotypic phase and none of these are applicable at genome-wide scale. Here, we present a method for inferring missing CNV genotypes, predicting CNV allelic configuration and for inferring CNV haplotypic phase from SNP/CNV genotype data.

Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions.

Background: The power of haplotype-based methods for association studies, identification of regions under selection, and ancestral inference, is well-established for diploid organisms. For polyploids, however, the difficulty of determining phase has limited such approaches. Polyploidy is common in plants and is also observed in animals.

Disease association tests by inferring ancestral haplotypes using a hidden markov model.

Motivation: Most genome-wide association studies rely on single nucleotide polymorphism (SNP) analyses to identify causal loci. The increased stringency required for genome-wide analyses (with per-SNP significance threshold typically approximately 10(-7)) means that many real signals will be missed. Thus it is still highly relevant to develop methods with improved power at low type I error.