Biology subjects

Liang, S.

Publications and source records attributed to Liang, S..

7 recordsLinked to original sources

bioRxiv2018

Mating system of Ustilago esculenta and its polymorphism

Zizania latifolia Turcz., which is mainly distributed in Asia, has had a long cultivation history as a cereal and vegetable crop. On infection with the smut fungus Ustilago esculenta, Z. latifolia becomes an edible vegetable, water bamboo. Two main cultivars, with a green shell and red shell, are cultivated for commercial production in Taiwan. Previous studies indicated that cultivars of Z. latifolia may be related to infection with U. esculenta isolates. However, related research is limited. The infection process of the corn smut fungus Ustilago maydis is coupled with sexual development and under control of the mating type locus. Thus, we aimed to use knowledge of U. maydis to reveal the mating system of U. esculenta. We collected water bamboo and isolated 145 U. esculenta strains from Taiwans major production areas. By using PCR and idiomorph screening among meiotic offspring and field isolates, we identified three idiomorphs of the mating type locus and found no sequence recombination between them. Whole-genome sequencing (Illumina and Pacbio) suggested that the mating system of U. esculenta was bipolar. Mating type locus 1 (MAT-1) was 555,862 bp, and contained 44% repeated sequences. Sequence comparison revealed that U. esculenta MAT-1 shared better conservation with the sex chromosome of U. maydis than U. hordei. These results can be utilized to further explore the genomic diversity of U. esculenta isolates and their application for water bamboo breeding.

microbiology↗

bioRxiv2018

Introduce a New Approach to Detect Genes Associated to Oral Squamous Cell Carcinoma

Oral squamous cell carcinoma (OSCC) represents the most frequent of all oral neoplasms in the world. Genetics plays an important role in the etiopathogenesis of OSCC. However, the investigation of the molecular mechanism of OSCC is still incomplete. In this article, we introduced a new approach to detect OSCC-associated genes, in which we not only compare mean difference, but also variance difference between cases and controls. Based on two OSCC datasets from Gene Expression Omnibus, we identified 456 differentially variable (DV) gene probes, in addition to 2,375 differentially expressed (DE) gene probes. There are 2,193 DE-only probes, 274 DV-only probes, and 182 DE-and-DV probes. DAVID functional analysis showed that genes corresponding to DE-only, DV-only, and DE-and-DV probes were enriched in different KEGG pathways, indicating they play different roles in OSCC. This new approach can be used to investigate the genetic risk factors for other complex human diseases.

genetics↗

bioRxiv2018

Posttranscriptional regulation of intestinal epithelial cell repair by RNA binding protein IMP1

RNA binding proteins, such as IMP1, are emerging as essential regulators of intestinal development and cancer. IMP1 hypomorphic mice exhibit severe intestinal growth defects, yet its role in adult intestinal epithelium is unclear. We employed ribosome profiling to test the effect of IMP1 loss on the \"translatome\" in colon cancer cell lines. In parallel, we evaluated mice with intestinal epithelial-specific Imp1 deletion (Imp1{Delta}IEC) following irradiation or colitis models. Ribosome-profiling revealed translation efficiency changes for multiple pathways important for intestinal homeostasis, including autophagy, in IMP1 knockout cells. We found increased autophagy flux in Imp1{Delta}IEC mice, reinforced through in silico and biochemical analyses revealing direct binding of IMP1 to autophagy transcripts MAP1LC3B and ATG3. We found that Imp1{Delta}IEC mice exhibit enhanced recovery following irradiation, which is attenuated with genetic deletion of autophagy gene Atg7. Finally, we demonstrated that IMP1 is upregulated in Crohns disease patients and Imp1 loss lessened colitis severity in mice. These studies demonstrate that IMP1 acts as a posttranscriptional regulator of gut epithelial repair post-irradiation and colitis, in part through modulation of autophagy.

physiology↗

bioRxiv2018

SCMarker: ab initio marker selection for single cell transcriptome profiling

Single-cell RNA-sequencing data generated by a variety of technologies, such as Drop-seq and SMART-seq, can reveal simultaneously the mRNA transcript levels of thousands of genes in thousands of cells. It is often important to identify informative genes or cell-type-discriminative markers to reduce dimensionality and achieve informative cell typing results. We present an ab initio method that performs unsupervised marker selection by identifying genes that have subpopulation-discriminative expression levels and are co- or mutually-exclusively expressed with other genes. Consistent improvements in cell-type classification and biologically meaningful marker selection are achieved by applying SCMarker on various datasets in multiple tissue types, followed by a variety of clustering algorithms. The source code of SCMarker is publicly available at https://github.com/KChen-lab/SCMarker.\n\nAuthor SummarySingle cell RNA-sequencing technology simultaneously provides the mRNA transcript levels of thousands of genes in thousands of cells. A frequent requirement of single cell expression analysis is the identification of markers which may explain complex cellular states or tissue composition. We propose a new marker selection strategy (SCMarker) to accurately delineate cell types in single cell RNA-sequencing data by identifying genes that have bi/multi-modally distributed expression levels and are co- or mutually-exclusively expressed with some other genes. Our method can determine the cell-type-discriminative markers without referencing to any known transcriptomic profiles or cell ontologies, and consistently achieves accurate cell-type-discriminative marker identification in a variety of scRNA-seq datasets.

bioinformatics↗

bioRxiv2017

Synthesis-Free PET Imaging Of Brown Adipose Tissue And TSPO Via Combination Of Disulfiram And 64CuCl2

PET imaging is a widely applicable but a very expensive technology. Strategies that can significantly reduce the high cost of PET imaging are highly desirable both for research and commercialization. On-site synthesis is one important contributor to the high cost. In this report, we demonstrated the feasibility of a synthesis-free method for PET imaging of brown adipose tissue (BAT) and translocator protein 18kDa (TSPO) via a combination of Disulfiram, an FDA approved drug for alcoholism, and 64CuCl2 (termed 64Cu-Dis). Our blocking studies, Western blot, and tissue histological imaging suggested that the observed BAT contrast was due to 64Cu-Dis binding to TSPO, which was further confirmed as a specific biomarker for BAT imaging using [18F]-F-DPA, a TSPO-specific PET tracer. Our studies, for the first time, demonstrated that TSPO could serve as a potential imaging biomarker for BAT. Furthermore, since imaging contrast obtained with both 64Cu-Dis and [18F]-F-DPA was not dependent on BAT activation, these agents could be used for reliably imaging BAT mass. Additional value of our synthesis-free approach could be applied to imaging TSPO in other tissues as it is an established biomarker of neuro-inflammation in activated microglia and plays a role in immune response, steroid synthesis, and apoptosis. Although here we applied 64Cu-Dis for a synthesis-free PET imaging of BAT, we believe that our strategy could be extended to other targets while significantly reducing the cost of PET imaging.\n\nSignificanceBrown adipose tissue (BAT) has been considered as \"good fat,\" and large-scale analysis has undoubtedly validated its clinical significance. BAT tightly correlates with body-mass index (BMI), suggesting that BAT bears clear significance for metabolic disorders such as obesity and diabetes. BAT imaging with [18F]-FDG, the most used method for visualizing BAT, primarily reflects BAT activation, but not BAT mass. A convenient imaging method that can consistently reflect BAT mass is still lacking. In this report, we demonstrated that BAT mass can be reliably imaged with a synthesis-free method using the combination of Disulfiram and 64CuCl2 (64Cu-Dis) via TSPO binding. We further demonstrated for the first time that TSPO is a specific imaging biomarker for BAT.

pharmacology and toxicology↗

bioRxiv2017

Interactome INSIDER: A Multi-Scale Structural Interactome Browser For Genomic Studies

Protein interactions underlie nearly all known cellular function, making knowledge of their binding conformations paramount to understanding the physical workings of the cell. Studying binding conformations has allowed scientists to explore some of the mechanistic underpinnings of disease caused by disruption of protein interactions. However, since experimentally determined interaction structures are only available for a small fraction of the known interactome such inquiry has largely excluded functional genomic studies of the human interactome and broad observations of the inner workings of disease. Here we present Interactome INSIDER, an information center for genomic studies using the first full-interactome map of human interaction interfaces. We applied a new, unified framework to predict protein interaction interfaces for 184,605 protein interactions with previously unresolved interfaces in human and 7 model organisms, including the entire experimentally determined human binary interactome. We find that predicted interfaces share several known functional properties of interfaces, including an enrichment for disease mutations and recurrent cancer mutations, suggesting their applicability to functional genomic studies. We also performed 2,164 de novo mutagenesis experiments and show that mutations of predicted interface residues disrupt interactions at a similar rate to known interface residues and at a much higher rate than mutations outside of predicted interfaces. To spur functional genomic studies in the human interactome, Interactome INSIDER (http://interactomeinsider.yulab.org) allows users to explore known population variants, disease mutations, and somatic cancer mutations, or upload their own set of mutations to find enrichment at the level of protein domains, residues, and 3D atomic clustering in known and predicted interaction interfaces.

genomics↗

bioRxiv2017

Polysome-profiling in small tissue samples

Polysome-profiling is commonly used to study genome wide patterns of translational efficiency, i.e. the translatome. The standard approach for collecting efficiently translated polysome-associated RNA results in laborious extraction of RNA from a large volume spread across multiple fractions. This property makes polysome-profiling inconvenient for larger experimental designs or samples with low RNA amounts such as primary cells or frozen tissues. To address this we optimized a non-linear sucrose gradient which reproducibly enriches for mRNAs associated with >3 ribosomes in only one or two fractions, thereby reducing sample handling 5-10 fold. The technique can be applied to cells and frozen tissue samples from biobanks, and generates RNA with a quality reflecting the starting material. When coupled with smart-seq2, a single-cell RNA sequencing technique, translatomes from small tissue samples can be obtained. Translatomes acquired using optimized non-linear gradients are very similar to those obtained when applying linear gradients. Polysome-profiling using optimized nonlinear gradients in HCT-116 cells with or without p53 identified a translatome associated with p53 status under serum starvation. Thus, here we present a polysome-profiling technique applicable to larger studies, primary cells where RNA amount is low and frozen tissue samples.

molecular biology↗