Biology subjects

Chen, B.

Publications and source records attributed to Chen, B..

25 records · Page 2Linked to original sources

bioRxiv2018

A learning-based framework for miRNA-disease association prediction using neural networks

MotivationA microRNA (miRNA) is a type of non-coding RNA, which plays important roles in many bio-logical processes. Lots of studies have shown that miRNAs were implicated in human diseases, indicating that miRNAs might be potential biomarkers for various types of diseases. Therefore, it is important to reveal the relationships between miRNAs and diseases/phenotypes.\n\nResultsWe proposed a novel learning-based framework, MDA-CNN, for miRNA-disease association identification. The model first captures richer interaction features between diseases and miRNAs based on a three-layer network with an additional gene layer. An auto-encoder is then employed to identify the essential feature combination for each pair of miRNA and disease automatically. A final label is given by a convolutional neural network taking the reduced feature representation as input. The evaluation results showed that the proposed framework outperformed some state-of-the-art approaches in a large margin on both tasks of miRNA-disease associations prediction and miRNA-phenotype associations prediction.\n\nAvailabilityThe software will be available after the manuscript is accepted.\n\nContactjiajiepeng@nwpu.edu.cn;zywei@fudan.edu.cn;shang@nwpu.edu.cn\n\nSupplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2018

An epigenetic biomarker of aging for lifespan and healthspan

Identifying reliable biomarkers of aging is a major goal in geroscience. While the first generation of epigenetic biomarkers of aging were developed using chronological age as a surrogate for biological age, we hypothesized that incorporation of composite clinical measures of phenotypic age that capture differences in lifespan and healthspan may identify novel CpGs and facilitate the development of a more powerful epigenetic biomarker of aging. Using a innovative two-step process, we develop a new epigenetic biomarker of aging, DNAm PhenoAge, that strongly outperforms previous measures in regards to predictions for a variety of aging outcomes, including all-cause mortality, cancers, healthspan, physical functioning, and Alzheimers disease. While this biomarker was developed using data from whole blood, it correlates strongly with age in every tissue and cell tested. Based on an in-depth transcriptional analysis in sorted cells, we find that increased epigenetic, relative to chronological age, is associated increased activation of pro-inflammatory and interferon pathways, and decreased activation of transcriptional/translational machinery, DNA damage response, and mitochondrial signatures. Overall, this single epigenetic biomarker of aging is able to capture risks for an array of diverse outcomes across multiple tissues and cells, and provide insight into important pathways in aging.

epidemiology↗

bioRxiv2018

A catalog of microbial genes from the bovine rumen reveals the determinants of herbivory

BackgroundThe rumen microbiota provides essential services to its host and, through its role in ruminant production, contributes to human nutrition and food security. A thorough knowledge of the genetic potential of rumen microbes will provide opportunities for improving the sustainability of ruminant production systems. The availability of gene reference catalogs from gut microbiomes has advanced the understanding of the role of the microbiota in health and disease in humans and other mammals. In this work, we established a catalog of reference prokaryote genes from the bovine rumen.\n\nResultsUsing deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen. Compared to human, pig and mouse gut metagenome catalogs, the rumen is larger and richer in functions and microbial species associated with the degradation of plant cell wall material and production of methane. Genes encoding enzymes catalyzing the breakdown of plant polysaccharides showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. The catalog expands by several folds the dataset of carbohydrate-degrading enzymes described in the rumen. Using an independent dataset from a group of 77 cattle fed 4 common dietary regimes, we found that only <0.1% of genes were shared by all animals, which contrast with a large overlap for functions, i.e. 63% for KEGG functions. Different diets induced differences in the relative abundance rather than the presence or absence of genes explaining the great adaptability of cattle to rapidly adjust to dietary changes.\n\nConclusionsThese data bring new insights into functions, carbohydrate-degrading enzymes and microbes of the rumen that is complementing the available information on microbial genomes. The catalog is a significant biological resource enabling deeper understanding of phenotypes and biological processes and will be expanded as new data is made available.

microbiology↗

bioRxiv2017

Melanism patches up the defective cuticular morphological traits through promoting the up-regulation of cuticular protein-coding genes in Bombyx mori

Melanin and cuticular proteins are important cuticle components in insect. Cuticle defects caused by mutations in cuticular protein-encoding genes can hinder melanin deposition. However, the effects of melanin variation on cuticular protein-encoding genes and the corresponding morphological traits associated with these genes are remain largely unknown. Using Bombyx mori as a model, we showed that the melanism levels during larval cuticle pigmentation correlated positively with the expression of cuticular protein-encoding genes. This correlation stemmed from the simultaneous induction of these genes by the melanin precursors. More importantly, the effect of the melanism background on the cuticles induced the up-regulation of other functionally redundant cuticular protein-encoding genes to rescue the morphological and adaptive defects caused by the dysfunction of some mutated cuticular proteins, and the restorative ability increased with increasing melanism levels, which gives a novel evidence that melanism enhances insect adaptability. These findings deepen our understanding of the interactions among cuticle components, as well as their importance in the stabilizing of the normal morphology and function of the cuticle.

genetics↗

bioRxiv2017

A correlation analysis framework for localization-based super-resolution microscopy

Super-resolution images reconstructed from single-molecule localizations can reveal cellular structures close to the macromolecular scale and are now being used routinely in many biomedical research applications. However, because of their coordinate-based representation, a widely applicable and unified analysis platform that can extract a quantitative description and biophysical parameters from these images is yet to be established. Here, we propose a conceptual framework for correlation analysis of coordinate-based super-resolution images using distance histograms. We demonstrate the application of this concept in multiple scenarios including image alignment, tracking of diffusing molecules, as well as for quantification of colocalization.\n\nSignificance statementCorrelation analysis is one of the most widely used image processing method. In the quantitative analysis of localization-based super-resolution images, there still lacks a generalized coordinate-based correlation analysis framework to take fully advantage of the super-resolution information. We show a coordinate-based correlation analysis framework for localization-based super-resolution microscopy. This framework is highly general and flexible in that it can be easily extended to model the effect of localization uncertainty, to the time domain and other distance definitions, enabling it to be adapted for a wide range of applications. Our work will greatly benefit the quantitative interpretation of super-resolution images and thus the biological application of super-resolution microscopy.

bioengineering↗

bioRxiv2017

wingless is a positive regulator of eyespot color patterns in Bicyclus anynana butterflies

Eyespot patterns of nymphalid butterflies are an example of a novel trait yet, the developmental origin of eyespots is still not well understood. Several genes have been associated with eyespot development but few have been tested for function. One of these genes is the signaling ligand, wingless, which is expressed in the eyespot centers during early pupation and may function in eyespot signaling and color ring differentiation. Here we tested the function of wingless in wing and eyespot development by down-regulating it in transgenic Bicyclus anynana butterflies via RNAi driven by an inducible heat-shock promoter. Heat-shocks applied during larval and early pupal development led to significant decreases in wingless mRNA levels and to decreases in eyespot size and wing size in adult butterflies. We conclude that wingless is a positive regulator of eyespot and wing development in B. anynana butterflies.

developmental biology↗

bioRxiv2017

LncRNA-TUG1/EZH2 Axis Promotes Cell Proliferation, Migration And The EMT Phenotype Formation Through Sponging miR-382

Pancreatic carcinoma (PC) is the one of the most common and malignant cancer in the world. Despite many effort have been made in recent years, the survival rate of PC still remains unsatisfied. Therefore, investigating the mechanisms underlying the progression of PC might facilitate the development of novel treatments that improve patient prognosis. LncRNA Taurine Up-regulated Gene 1 (TUG1) was initially identified as a transcript up - regulated by taurine, siRNA - based depletion of TUG1 suppresses mouse retinal development, and the abnormal expression of TUG1 has been reported in many cancers. However, the biological role and molecular mechanism of TUG1 in pancreatic carcinoma (PC) still needs to be further investigated. In the current study, the expression of TUG1 in the PC cell lines and tissues was measured by quantitative real-time PCR (qRT-PCR), and loss-of-function and gain-of-function approaches were applied to investigate the function of TUG1 in PC cell. Online database analysis tools showed that miR-382 could interact with TUG1 and we found an inverse correlation between TUG1 and miR-382 in PC specimens. Moreover, dual luciferase reporter assay, RNA-binding protein immunoprecipitation (RIP) and applied biotin-avidin pulldown system further provide evidence that TUG1 directly targeted miR-382 by binding with microRNA binding site harboring in the TUG1 sequence. Furthermore, gene expression array analysis using clinical samples and RT-qPCR proposed that EZH2 was a target of miR-382 in PC. Collectively, these findings revealed that TUG1 functions as an oncogenic lncRNA that promotes tumor progression at least partially through function as an endogenous sponge by competing for miR-382 binding to regulate the miRNA target EZH2.

cancer biology↗