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Peak identification for ChIP-seq data with no controls

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Zoological Research 2012年第S03期33卷 121-128页

作者： Yanfeng ZHANG bing su State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoologythe Chinese Academy of SciencesKunming 650223China

Chromatin immunoprecipitation followed by sequencing(ChIP-seq)is increasingly being used for genome-wide profiling of transcriptional regulation,as this technique enables dissection of the gene regulatory *** input as control,a variety of statistical methods have been proposed for identifying the enriched regions in the genome,i.e.,the transcriptional factor binding sites and chromatin ***,when there are no controls,whether peak calling is still reliable awaits systematic *** address this question,we used a Bayesian framework approach to show the effectiveness of peak calling without controls(PCWC).Using several different types of ChIP-seq data,we demonstrated the relatively high accuracy of PCWC with less than a 5%false discovery rate(FDR).Compared with previously published methods,e.g.,the model-based analysis of ChIP-seq(MACS),PCWC is reliable with lower ***,to interpret the biological significance of the called peaks,in combination with microarray gene expression data,gene ontology annotation and subsequent motif discovery,our results indicate PCWC possesses a high ***,using in silico data,only a small number of peaks were identified,suggesting the significantly low FDR for PCWC.

关键词： ChIP-seq Bayesian Peak calling Gene regulation

Perspectives on the role of mTORC2 in B lymphocyte development,immunity and tumorigenesis

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Protein & Cell 2011年第7期2卷 523-530页

作者： Adam S.Lazorchak bing su Department of Immunobiology and the Vascular Biology and Therapeutic Program Yale School of MedicineNew HavenCT 06519USA

Mammalian target of rapamycin complex 2(mTORC2)is a key downstream mediator of phosphoinositol-3-kinase(PI3K)dependent growth factor *** lymphocytes,mTORC2 has emerged as an important regulator of cell development,homeostasis and immune ***,our current understanding of mTORC2 functions and the molecular mechanisms regulating mTORC2 signaling in B and T cells are still largely *** studies have begun to shed light on this important *** have previously reported that mTORC2 mediates growth factor dependent phosphorylation of Akt and facilitates Akt dependent phosphorylation and inactivation of transcription factors FoxO1 and *** have recently explored the functions of mTORC2 in B cells and show that mTORC2 plays a key role in regulating survival and immunoglobulin(Ig)gene recombination of bone marrow B cells through an Akt2-FoxO1 dependent *** recombination is suppressed in proliferating B cells to ensure that DNA double strand breaks are not generated in actively dividing *** results raise the possibility that genetic or pharmacologic inhibition of mTORC2 may promote B cell tumor development as a result of inefficient suppression of Ig recombination in dividing B *** also propose a novel strategy to treat cancers based on our recent discovery that mTORC2 regulates Akt protein stability.

关键词： mTOR lymphocyte B cell cancer mTORC2 FoxO Akt Sin1

An Overview of Epigenetics in Chinese Medicine Researches

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Chinese Journal of Integrative Medicine 2017年第9期23卷 714-720页

作者： HU Xue-qing su Shi-bing Research Center for Traditional Chinese Medicine Complexity System Shanghai University of Traditional Chinese MedicineShanghai201203China

Chinese medicine（CM） has contributed to human health care for several thousand years and is still popular in Asian countries. But the mechanisms underlying CM remain obscure, and need to be clarified by modern biological subjects and methods. Recently, CM researches on epigenetics have gained obvious improvement following rapidly developed molecular technologies. In this review, we revealed mutual characteristics of epigenetics and CM, such as holism, yin-yang dynamic nature, reversibility and balance, and visceral manifestation. Moreover, epigenetic modifications, including DNA methylation, histone post-transcriptional modifications, micro RNA interference, etc. may help explore the molecular basis of CM syndrome classification, and mechanisms of Chinese herbal medicine（CHM）, CHM compounds and Chinese herbal formulae activities. Meanwhile, CM and epigenetics might promote each other and jointly develop following the continuous progress of epigenetics in CM researches.

关键词： Chinese medicine epigenetics methylation histone modification Chinese herbal medicine,Chinese herbal formula Chinese medicine syndrome

Regulation of T cell immunity by cellular metabolism

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Frontiers of Medicine 2018年第4期12卷 463-472页

作者： Zhilin Hu Qiang Zou bing su Shanghai Institute of Immunology Department of Immunology and Microbiology Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education Shanghai Jiao Tong University School of Medicine Shanghai 200025 China

T cells are an important adaptive immune response arm that mediates cell-mediated immunity. T cell metabolism plays a central role in T cell activation, proliferation, differentiation, and effector function. Specific metabolic programs are tightly controlled to mediate T cell immune responses, and alterations in T cell metabolism may result in many immunological disorders. In this review, we will summarize the main T cell metabolic pathways and the important factors participating in T cell metabolic programming during T cell homeostasis, differentiation, and function.

关键词： T cell immunity metabolic pathways nutrient uptake metabolic checkpoints

Bayesian Estimation and Model Selection for the Spatiotemporal Autoregressive Model with Autoregressive Conditional Heteroscedasticity Errors

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Acta Mathematicae Applicatae Sinica 2023年第4期39卷 972-989页

作者： bing su Fu-kang ZHU Ju HUANG Department of Statistics&Actuarial Science University of Hong KongHong Kong 999077China School of Mathematics Jilin UniversityChangchun 130012China National Energy Administration Information Center Beijing 100045China

The spatial and spatiotemporal autoregressive conditional heteroscedasticity(STARCH) models receive increasing attention. In this paper, we introduce a spatiotemporal autoregressive(STAR) model with STARCH errors, which can capture the spatiotemporal dependence in mean and variance simultaneously. The Bayesian estimation and model selection are considered for our model. By Monte Carlo simulations, it is shown that the Bayesian estimator performs better than the corresponding maximum-likelihood estimator, and the Bayesian model selection can select out the true model in most times. Finally, two empirical examples are given to illustrate the superiority of our models in fitting those data.

关键词： autoregressive conditional heteroscedasticity model Bayesian estimation model selection spatial ARCH model spatial panel model spatiotemporal model

Sol-gel derived bioactive hydroxyapatite/titania composite films on Ti6Al4V

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Journal of University of Science and Technology Beijing 2006年第5期13卷 469-475页

作者： bing su Guoqing Zhang Xudong Yu Chengtao Wang School of Mechanical and Power Energy Engineering Shanghai Jiaotong University Shanghai 200030 China Military Engineering Department Artillery Academy Hefei 230031 China

The composite films consisting of the titania gel impregnated with hydroxyapatite （HAP） submicron particles were prepared on commercial Ti6A14V plates processed by a sol-gel route. HAP powders were synthesized based on wet chemical precipitation method with Ca（NO3）2.4H2O and （NH4）2HPO4 as starting reagents. After being calcined at 900℃, HAP powders were ultrasonically scattered in ethanol to produce HAP sol. The titania sol was prepared using titanium （IV） isopropoxide {Ti[OCH（CH3）2]4} as precursor. Both the titania sol and the HAP/titania mixture were sequentially spin-coated on the substrates and calcined at various temperatures. The characteristics and mechanical adhesion of the composite films were investigated. The results show that the as-prepared films are dense, homogeneous, well-crystallized, and there is a good interfacial adhesion between the film and the substrate. The in vitro bioactivities of these films were discussed based on the analysis of the variations of Ca and P concentrations in the simulated body fluid and their surface morphologies against immersion time.

关键词： titania hydroxyapatite composite film sol-gel route

A transgenic monkey model for the study of human brain evolution

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Zoological Research 2019年第3期40卷 236-238页

作者： Lei Shi bing su State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China Primate Research Center Kunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming Yunnan 650223China

Why humans have large brains with higher cognitive abilities is a question long asked by ***,much remains unknown,especially the underlying genetic *** the use of a transgenic mon key model,we showed that human-specific sequenee changes of a key brain development gene(Primary microcephaly 1,MCPH7)could result in detectable molecularand cognitive changes resembling human neoteny,a no table characteristic developed during human *** study was published in National Science Review(Shi et al.,2019).

关键词： human brain evolution key model

Origin of modern humans in East Asia:clues from the Y chromosome

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Frontiers in Biology 2009年第3期4卷 241-247页

作者： Hong SHI bing su State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology and Kunming Primate Research CentreChinese Academy of SciencesKunming 650223China

East Asia is one of the most important regions for studying modern human origin and evolution.A lot of efforts have been made to detect the genetic diversity and to reconstruct the evolutionary history of East Asians,especially using Y chromosome genetic data,in recent *** Y chromosome data supports the African origin of modern humans in East Asia and the later migration to East Asia through the southern tropic coastline route,and then the northward migration occurred,leading to peopling of the main *** genetic data of the Y chromosome reflects a clear prehistoric evolution and migration course of East *** well,the Y chromosome data of East Asians provides clues to elucidate modern human origins and evolution in the neighboring regions,***,Oceania and the Pacific Islands.

关键词： Y chromosome East Asia modern human origin prehistoric migration

Development of Laser-HVEM and Its Application on In-situ Observation on Lattice Defects Behavior

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Chinese Journal of Structural Chemistry 2020年第4期39卷 623-629页

作者： YANG Zhan-bing YANG su-bing QU Xiao-Jian SHIBAYAMA Tamaki WATANABE Seiichi School of Metallurgical and Ecological Engineering University of Science and Technology BeijingBeijing 100083China Graduate School of Engineering Hokkaido UniversitySapporoHokkaido 060-8628Japan Centre for Advanced Research of Energy and Materials Faculty of EngineeringHokkaido UniversitySapporoHokkaido 060-8628Japan

A nanosecond pulse laser source head(Nd:YAG laser,Inlite Ⅱ-20,Continuum)was equipped to a high-voltage electron microscope(HVEM,Hitachi,H-1300)to develop a laser-HVEM system at Hokkaido *** the laser-HVEM,new methods for in-situ observation on the formation process of laser-induced lattice point defects at the internal of crystalline solid are achieved;some striking phenomena and potential mechanisms are *** the present paper,we review our progresses on in-situ experiments of lattice defects behavior in metal using the *** progresses are expected to provide insight for a broader application of laser-HVEM in scientific research.

关键词： Laser high-voltage electron microscope Dual-beam irradiation in-situ observation Lattice defect