Biology subjects

Chang, Y.

Publications and source records attributed to Chang, Y..

6 recordsLinked to original sources

bioRxiv2018

Snapshots of single particles from single cells using electron microscopy

Cryo-electron microscopy has become an indispensable tool for structural studies of biological macromolecules. There are two predominant methods for studying the architectures of multi-protein complexes: (1) single particle analysis of purified samples and (2) tomography of whole cells or cell sections. The former can produce high-resolution structures but is limited to highly purified samples, while the latter can capture proteins in their native state but is hindered by a low signal-to-noise ratio and results in lower-resolution structures. Here, we present a method combining microfluidic single cell extraction with single particle analysis by electron microscopy to characterize protein complexes from individual C. elegans embryos. Using this approach, we uncover three-dimensional structures of ribosomes directly from single embryo extracts. In addition, we investigate structural dynamics during development by counting the number of ribosomes per polysome in early and late embyros. This approach has significant potential applications for counting protein complexes and studying protein architectures from single cells in developmental, evolutionary and disease contexts.

biochemistry↗

bioRxiv2018

Comparative analysis of miR-155 tissue expression profiles of different breeds of chicken

miR-155 is an important microRNA which has multiple functions in many physiological and pathological processes. In this study, partial pri-miR-155 sequences were cloned from AA+ broiler, Sanhuang broiler and Hi-Line Brown layer, respectively. Stem-loop RT-qPCR was performed to detect the miR-155 spatiotemporal expression profiles of each chicken breed. The results showed that the partial pri-miR-155 sequences of different breeds of chicken were high conserved. The expression patterns of miR-155 between broiler and layer were basically similar, and miR-155 is expressed highly in immune related tissues. Interestingly, miR-155 expression activity had higher level in fat tissue of the three chicken breeds (14-day-old), but it decreased significantly in fat of the Hi-Line Brown layer (10-month-old and 24-month-old). In addition, the expression activities of miR-155 in 14-day-old broilers (AA+ broiler and Sanhuang broiler) were significantly lower than that of Hi-Line Brown layer (14-day-old) (P<0.05). Moreover, miR-155 expression activities in skeletal muscle of 14-day-old and 10-month-old Hi-Line Brown layer were also significantly lower than that of 24-month-old layer (P<0.05). The results indicated that miR-155 might be one of the important factors affecting the differences in skeletal muscle development and adipogenesis between different chicken breeds. These data can serve as a foundation for further study the functions and mechanisms of miR-155 in the physiological and pathological contexts.

molecular biology↗

bioRxiv2018

LRScaf: Improving Draft Genomes Using Long Noisy Reads

BackgroundThe advent of Third Generation Sequencing (TGS) technologies opens the door to improve genome assembly. Long reads are promised to enhance the quality of fragmental draft assemblies constructed from Next Generation Sequencing (NGS) technologies. To date, a few of algorithms, i.e., SSPACE-LongRead, OPERA-LG, SMIS, npScarf, DBG2OLC, Unicycler, and LINKS, have been released that are capable of improving draft assemblies. However, hybrid assembly on large genomes is still challenging.\n\nResultsWe develop a scalable and computationally efficient scaffolder, Long Reads Scaffolder (LRScaf), that is capable of boosting assembly contiguity to a large extent using long reads. In our experiment, our method significantly improves the contiguity of human draft assemblies, increasing the NG50 value of CHM1 from 127.5 Kb to 10.4 Mb using 20-fold coverage PacBio dataset and the NG50 value of NA12878 from 115.7 Kb to 17.4 Mb using 35-fold coverage Nanopore dataset. The run time for the scaffolding procedure using LRScaf is the shortest in all cases of our experiment. Compared with the run time of SSPACE-LongRead, LRScaf is faster 300 times for S. cerevisiae and 2,300 times for D. melanogaster. The peak RAM of LRScaf, by contrast, is more efficient than LINKS in our test. For the rice case, the peak RAM of LINKS (877.72 Gb) is about 196 times higher than LRScaf. For the experiment of human assembly, the peak RAM of LINKS is beyond the capacity of system memory (1 Tb) whereas LRScaf takes 20.28 and 41.20 Gb on CHM1 and NA12878 datasets.\n\nConclusionsThe new method, LRScaf, yields the best or at least moderate contiguity and accuracy of scaffolds in the shortest run time compared with the state-of-the-art methods. Furthermore, it offers a new opportunity for the hybrid assembly of large genomes.

bioinformatics↗

bioRxiv2018

Fungal polysaccharopeptides reduce obesity by richness of specific microbiota and modulation of lipid metabolism

The prevalence of obesity and related disorders has vastly increased throughout the world and prevention of such circumstances thus represents a major challenge. Here, we show that protein-bound {beta}-glucan (PBG), one representative of Coriolus versicolor polysaccharopeptides which are broadly used as immune boosters and clinically implicated in treatment of cancers and chronic hepatitis, could be a potent anti-obesity agent. PBG could reduce obesity and metabolic inflammation in mice fed with a high-fat diet (HFD). Gut microbiota analysis revealed that PBG markedly increased the abundance of Akkermansia muciniphila although it didnt rescue HFD-induced change in the Firmicutes to Bacteroidetes ratio. It appeared that PBG altered host physiology and created an intestinal microenvironment favorable for A. muciniphila colonization. Fecal transplants from PBG-treated animals in part reduced obesity in recipient HFD-fed mice. Further, PBG was shown to promote lipid metabolism in microbiota-depleted mice. Thus, our data highlights that PBG might exert its anti-obesity effects through a mirobiota-dependent (richness of specific microbiota) and -independent (modulation of lipid metabolism) manner. The fact that Coriolus versicolor polysaccharopeptides are approved oral immune boosters in cancers and chronic hepatitis with well-established safety profiles may accelerate the development of PBG as a novel drug for obesity treatment.

microbiology↗

bioRxiv2018

A compromised gsdf signaling leads to gamatogenesis confusion and subfertility in medaka

Summary statementGsdf signals trigger the gamatogenesis, alter the somatic expression of Fsh/Lh receptors and brain type aromatase in medaka brain and gonad.\n\nAbstractGonadal soma-derived factor (gsdf) and anti-Mullerian hormone (amh) are somatic male determinants in several species of teleosts, although the mechanisms by which they trigger the indifferent germ cells into the male pathway remain unknown. This study aimed to decipher the roles of gsdf/amh in directing the sexual fate of germ cells using medaka as a model. Transgenic lines (TgcryG) that restrictively and persistently express a Gsdf-Gfp fusion protein in the lens and the hypothalamus-pituitary-gonad (HPG) axis, were generated under the control of a mouse {gamma}F-crystallin promoter. A high frequency (44.4%) of XX male sex reversals was obtained in TgcryG lines, indicating that signals of gsdf-expressing cells in HPG were enough for the spermatogenesis activation in the genetic females. Furthermore, all TgcryG XY individuals with endogenous gsdf depletion (named Sissy) displayed intersex (100%) with enlarged ovotestis in contrast to a giant ovary developed in XY gsdf deficiency. The heterogeneous expression of gsdf led to the confusion of gamatogenesis and ovotestis development, similar to some hotei (amhr2) mutants, suggests that the signaling balance of gsdf/amh is essential for proper gamatogenesis, maintaining sex steroid production and gonadotropin secretion, which are evolutionarily conserved across phyla.

evolutionary biology↗

bioRxiv2017

CD-HIT-OTU-MiSeq, an Improved Approach for Clustering and Analyzing Paired End MiSeq 16S rRNA Sequences

In recent years, Illumina MiSeq sequencers replaced pyrosequencing platforms and became dominant in 16S rRNA sequencing. One unique feature of MiSeq technology, compared with Pyrosequencing, is the Paired End (PE) reads, with each read can be sequenced to 250-300 bases to cover multiple variable regions on the 16S rRNA gene. However, the PE reads need to be assembled into a single contig at the beginning of the analysis. Although there are many methods capable of assembling PE reads into contigs, a big portion of PE reads can not be accurately assembled because the poor quality at the 3 ends of both PE reads in the overlapping region. This causes that many sequences are discarded in the analysis. In this study, we developed a novel approach for clustering and annotation MiSeq-based 16S sequence data, CD-HIT-OTU-MiSeq. This new approach has four distinct novel features. (1) The package can clustering PE reads without joining them into contigs. (2) Users can choose a high quality portion of the PE reads for analysis (e.g. first 200 / 150 bases from forward / reverse reads), according to base quality profile. (3) We implemented a tool that can splice out the target region (e.g. V3-V4) from a full-length 16S reference database into the PE sequences. CD-HIT-OTU-MiSeq can cluster the spliced PE reference database together with samples, so we can derive Operational Taxonomic Units (OTUs) and annotate these OTUs concurrently. (4) Chimeric sequences are effectively identified through de novo approach. The package offers high speed and high accuracy. The software package is freely available as open source package and is distributed along with CD-HIT from http://cd-hit.org. Within the CD-HIT package, CD-HIT-OTU-MiSeq is within the usecase folder.

bioinformatics↗