Biology subjects

Jiang, Y.

Publications and source records attributed to Jiang, Y..

617 records · Page 35Linked to original sources

bioRxiv2017

Parsing Of Compositions And Microstructure Characteristics For Rust-Spots Of Pear Pericarp

The commercial value of Kurles pears pericarp, a popular and favored fruit for its unique aroma and refreshingly crisp texture, had sharply decreased because of a rust breakout of the beloved pear in China during the atmosphere-controlled storage. High performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC-MS) were used to analyze rust spots on the pericarp of Kurle pears. Therefore, the chemical compounds of four various eluates, originating from the rust-colored substance collected from the pears pericarp effected, were identified successfully for the first time, which were just rhein, aloe-emodin, chrysophanol and emodin, respectively. Taken together with microstructure characteristics for rust-spots of Kurle pear pericarp, it was no doubt that these eluates were the main factors affecting the rust spots on the pericarp of the Kurle pears during the atmosphere-controlled storage, which was a sign and consequence resisting the undesirable stress of the external environment.

plant biology↗

bioRxiv2017

FCS In Closed Systems And Application For Membrane Nanotubes

In the present study, we developed the fluorescence correlation spectroscopy theory for closed systems with either periodic or reflective boundaries. The illumination could be any arbitrary function. We tested our theory with simulated data of both boundary conditions. We also tested the theory with experimental data of membrane nanotubes, whose circular direction is a closed system. The result shows that the correlation function for nanotubes falls between 1D and 2D diffusion model. The fitting with our model gives an accurate recovery of the diffusion time and nanotube radius. We also give some examples of single molecule experiments for which our theory can be potentially useful.

biophysics↗

bioRxiv2017

Co-localization of Conditional eQTL and GWAS Signatures in Schizophrenia

Causal genes and variants within genome-wide association study (GWAS) loci can be identified by integrating GWAS statistics with expression quantitative trait loci (eQTL) and determining which SNPs underlie both GWAS and eQTL signals. Most analyses, however, consider only the marginal eQTL signal, rather than dissecting this signal into multiple independent eQTL for each gene. Here we show that analyzing conditional eQTL signatures, which could be important under specific cellular or temporal contexts, leads to improved fine mapping of GWAS associations. Using genotypes and gene expression levels from post-mortem human brain samples (N=467) reported by the CommonMind Consortium (CMC), we find that conditional eQTL are widespread; 63% of genes with primary eQTL also have conditional eQTL. In addition, genomic features associated with conditional eQTL are consistent with context specific (i.e. tissue, cell type, or developmental time point specific) regulation of gene expression. Integrating the Psychiatric Genomics Consortium schizophrenia (SCZ) GWAS and CMC conditional eQTL data reveals forty loci with strong evidence for co-localization (posterior probability >0.8), including six loci with co-localization of conditional eQTL. Our co-localization analyses support previously reported genes and identify novel genes for schizophrenia risk, and provide specific hypotheses for their functional follow-up.

genetics↗

bioRxiv2017

Modeling allele-specific gene expression by single-cell RNA sequencing

Allele-specific expression is traditionally studied by bulk RNA sequencing, which measures average expression across cells. Single-cell RNA sequencing (scRNA-seq) allows the comparison of expression distribution between the two alleles of a diploid organism and thus the characterization of allele-specific bursting. We propose SCALE to analyze genome-wide allele-specific bursting, with adjustment of technical variability. SCALE detects genes exhibiting allelic differences in bursting parameters, and genes whose alleles burst non-independently. We apply SCALE to mouse blastocyst and human fibroblast cells and find that, globally, cis control in gene expression overwhelmingly manifests as differences in burst frequency.

genomics↗

bioRxiv2017

Structural basis of Mycobacterium tuberculosis transcription and transcription inhibition

One Sentence SummaryStructures of Mycobacterium tuberculosis RNA polymerase reveal taxon-specific properties and binding sites of known and new antituberculosis agents\n\nAbstractMycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, which kills 1.8 million annually. Mtb RNA polymerase (RNAP) is the target of the first-line antituberculosis drug rifampin (Rif). We report crystal structures of Mtb RNAP, alone and in complex with Rif. The results identify an Mtb-specific structural module of Mtb RNAP and establish that Rif functions by a steric-occlusion mechanism that prevents extension of RNA. We also report novel non-Rif-related compounds-N-aroyl-N-aryl-phenylalaninamides (AAPs)-that potently and selectively inhibit Mtb RNAP and Mtb growth, and we report crystal structures of Mtb RNAP in complex with AAPs. AAPs bind to a different site on Mtb RNAP than Rif, exhibit no cross-resistance with Rif, function additively when co-administered with Rif, and suppress resistance emergence when co-administered with Rif.

molecular biology↗