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The system capacity view of aging and longevity

Frontiers of Electrical and Electronic Engineering in China 2017年第3期5卷 251-259页

作者： Jing-Dong J. Han Lei Hou Na Sun Chi Xu Joseph McDermott Dan Wang Key Laboratory of computational biology CAS Center for Excellence in Molecular Cell Science Collaborative Innovation Center for Genetics and Developmental Biology Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China

Background： Aging is a complex systems level problem that needs a systems level solution. However, system models of aging and longevity, although urgently needed, are still lacking, largely due to the paucity of conceptual frameworks for modeling such a complex process. Results： We propose that aging can be viewed as a decline in system capacity, defined as the maximum level of output that a system produces to fulfill demands. Classical aging hallmarks and anti-aging strategies can be well-aligned to system capacity. Genetic variants responsible for lifespan variation across individuals or species can also be explained by their roles in system capacity. We further propose promising directions to develop systems approaches to modulate system capacity and thus extend both healthspan and lifespan. Conclusions： The system capacity model of aging provides an opportunity to examine aging at the systems level. This model predicts that the extent to which aging can be modulated is normally limited by the upper bound of the system capacity of a species. Within such a boundary, aging can be delayed by moderately increasing an individual＇s system capacity. Beyond such a boundary, increasing the upper bound is required, which is not unrealistic given the unlimited potential of regenerative medicine in the future, but it requires increasing the capacity of the whole system instead of only part of it.

关键词： systems system capacity aging longevity

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An introduction to computational tools for differential binding analysis with ChlP-seq data

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Frontiers of Electrical and Electronic Engineering in China 2017年第3期5卷 226-235页

作者： Shiqi Tu Zhen Shao CAS Key Laboratory of computational biology Collaborative Innovation Center for Genetics and Developmental Biology CAS- Max Planck Society Partner Institute for Computational Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China. Graduate university of chinese academy of sciences Beijing 100049 China

Background： Gene transcription in eukaryotie cells is collectively controlled by a large panel of ehromatin associated proteins and ChIP-seq is now widely used to locate their binding sites along the whole genome. Inferring the differential binding sites of these proteins between biological conditions by comparing the corresponding ChIP-seq samples is of general interest, yet it is still a computationally challenging task. Results： Here, we briefly review the computationhl tools developed in recent years for differential binding analysis with ChIP-seq data. The methods are extensively classified by their strategy of statistical modeling and s＇cope of application. Finally, a decision tree is presented for choosing proper tools based on the specific dataset. Conclusions： computational tools for differential binding analysis with ChIP-seq data vary significantly with respect to their applicability and performance. This review can serve as a practical guide for readers to select appropriate tools for their own datasets.

关键词： ChIP-seq peak calling differential binding analysis computational tools

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C4 Rice-an Ideal Arena for Systems biology Research

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Journal of Integrative Plant biology 2010年第8期52卷 762-770页

作者： Xin-Guang Zhu Lanlan Shan Yu Wang William Paul Quick Key Laboratory of computational biology CAS-MPG Partner Institute for Computational Biology Shanghai Institutes for Biologica Sciences Chinese Academy of Sciences Shanghai 200031 China The International Rice Research institute Los Banos Philippines

Engineering the C4 photosynthetic pathway into C3 crops has the potential to dramatically increase the yields of major C3 crops. The genetic control of features involved in C4 photosynthesis are still far from being understood; which partially explains why we have gained little success in C4 engineering thus far. Next generation sequencing techniques and other high throughput technologies are offering an unprecedented opportunity to elucidate the developmental and evolutionary processes of C4 photosynthesis. Two contrasting hypotheses about the evolution of C4 photosynthesis exist, i.e. the master switch hypothesis and the incremental gain hypothesis. These two hypotheses demand two different research strategies to proceed in parallel to maximize the success of C4 engineering. In either case, systems biology research will play pivotal roles in identifying key regulatory elements controlling development of C4 features, identifying essential biochemical and anatomical features required to achieve high photosynthetic efficiency, elucidating genetic mechanisms underlining C4 differentiation and ultimately identifying viable routes to engineer C4 rice. As a highly interdisciplinary project, the C4 rice project will have far-reaching impacts on both basic and applied research related to agriculture in the 21st century.

关键词： Engineering Engines Engineers Viverridae Genetics Crops Oesophagus Forecasting Rice Technology

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Regulators of alternative polyadenylation operate at the transition from mitosis to meiosis

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Journal of Genetics and Genomics 2017年第2期44卷 95-106页

作者： Lingjuan Shan Chan Wu Di Chen Lei Hou Xin Li Lixia Wang Xiao Chu Yifeng Hou Zhaohui Wang State Key Laboratory of Molecular Developmental biology Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100102China The University of chinese academy of sciences Beijing 100049China Key Laboratory of computational biology Chinese Academy of Sciences-Man Planck Partner Institute for Computational BiologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai 200031China State Key Laboratory of Plant Genomics and National Center for Plant Gene Research Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Key Laboratory of Cenetic Network biology Collaborative Innovation Center of Genetics and DevelopmentInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China

In the sexually reproductive organisms, gametes are produced by meiosis following a limited mitotic amplification. However, the intrinsic program switching cells from mitotic to meiotic cycle is *** polyadenylation（APA） is a highly conserved means of gene regulation and is achieved by the RNA 30-processing machinery to generate diverse 30 UTR profiles. In Drosophila spermatogenesis, we observed distinct profiles of transcriptome-wide 30 UTR between mitotic and meiotic cells. In mutant germ cells stuck in mitosis, 30 UTRs of hundreds of genes were consistently shifted. Remarkably, altering the levels of multiple 30-processing factors disrupted germline＇s progression to meiosis, indicative of APA＇s active role in this transition. An RNA-binding protein（RBP） Tut could directly bind 30 UTRs of 30-processing factors whose expressions were repressed in the presence of Tut-containing complex. Further,we demonstrated that this RBP complex could execute the repression post-transcriptionally by recruiting CCR4/Twin of deadenylation complex. Thus, we propose that an RBP complex regulates the dynamic APA profile to promote the mitosis-to-meiosis transition.

关键词： Germ cell Mitosis to meiosis Alternative polyadenylation RNA-binding protein 3'UTR

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CXXC5 suppresses hepatocellular carcinoma by promoting TGF-β-induced cell cycle arrest and apoptosis

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Journal of Molecular Cell biology 2018年第1期10卷 48-59页

作者： Xiaohua Yan Jingyi Wu Quanlong Jiang Hao Cheng Jing-Dong J. Han Ye-Guang Chen The State Key Laboratory of Membrane biology Tsinghua-Peking Center for Life Sciences School of Life Sciences Tsinghua University Beijing 100084 China Department of Biochemistry and Molecular biology School of Basic Medical Sciences Nanchang University Nanchang 330006 China chinese academy of sciences-max planck partner institute for computational biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China

Evading TGF-β-mediated growth inhibition is often associated with tumorigenesis in liver, including hepatocellular carcinoma （HCC）. To better understand the functions and the underlying molecular mechanisms of TGF-β in HCC initiation and progression, we carried out transcriptome sequencing （RNA-Seq） to identify the target genes of TGF-β. CXXCS, a member of the CXXC-type zinc finger domain-containing protein family, was identified as a novel TGF-β target gene in Hep3B HCC cells. Knockdown of CXXC5 attenuated the expression of a substantial portion of TGF-p target genes and ameliorated TGF-13-induced growth inhibition or apoptosis of Hep3B cells, suggesting that CXXC5 is required for TGF-p-mediated inhibition of HCC progression. Analysis of the TCGA database indicated that CXXC5 expression is reduced in the majority of HCC tissue samples in comparison to that in normal tissues. Furthermore, CXXC5 associates with the histone deacetylase HDAC1 and competes its interaction with Smad2/3, thereby abolishing the inhibitory effect of HDAC1 on TGF-β signaling. These observations together suggest that CXXC5 may act as a tumor suppressor by promoting TGF-β signaling via a positive feedback loop, and reveal a strategy for HCC to bypass TGF-β-mediated cytostasis by disrupting the positive feedback regulation. Our findings shed new light on TGF-β signaling regulation and demon- strate the function of CXXC5 in HCC development.

关键词： hepatocellular carcinoma (HCC) TGF-β CXXC5 HDAC signaling regulation

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The Precursor of GRB211211A:A Tide-induced Giant Quake?

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Research in Astronomy and Astrophysics 2024年第2期24卷 206-215页

作者： Enping Zhou Yong Gao Yurui Zhou Xiaoyu Lai Lijing Shao Weiyang Wang Shaolin Xiong Renxin Xu Shuxu Yi Garvin Yim Han Yue Zhen Zhang School of Physics Huazhong University of Science and TechnologyWuhan 430074China Kavli institute for Astronomy and Astrophysics Peking UniversityBeijing 100871China School of Physics Peking UniversityBeijing 100871China Research Center for Astronomy Hubei University of EducationWuhan 430205China University of chinese academy of sciences Beijing 100049China Key Laboratory of Particle Astrophysics Institute of High Energy PhysicsChinese Academy of SciencesBeijing 100049China School of Earth and Space sciences Peking UniversityBeijing 100871China

The equilibrium configuration of a solid strange star in the final inspiral phase with another compact object is generally discussed,and the starquake-related issue is revisited,for a special purpose to understand the precursor emission of binary compact star merger events(e.g.,that of GRB211211A).As the binary system inspirals inward due to gravitational wave radiation,the ellipticity of the solid strangeon star increases due to the growing tidal field of its compact *** energy is hence accumulated during the inspiral stage which might trigger a starquake before the merger when the energy exceeds a critical *** energy released during such starquakes is calculated and compared to the precursor observation of GRB211211 *** result shows that the energy might be insufficient for binary strangeon-star case unless the entire solid strangeon star shatters,and hence favors a black hole-strangeon star scenario for *** timescale of the precursor as well as the frequency of the observed quasi-periodic-oscillation have also been discussed in the starquake model.

关键词： stars neutron-(stars:)gamma-ray burst general-black hole physics

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AncestryPainter:A Graphic Program for Displaying Ancestry Composition of Populations and Individuals

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Genomics, Proteomics & Bioinformatics 2018年第5期16卷 382-385页

作者： Qidi Feng Dongsheng Lu Shuhua Xu CAS Key Laboratory of computational biology Max Planck Independent Research Group on Population GenomicsCAS-MPG Partner Institute for Computational BiologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai 200031China University of chinese academy of sciences Beijing 100049China School of Life Science and Technology ShanghaiTech UniversityShanghai 201210China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China Collaborative Innovation Center of Genetics and Development Shanghai 200438China Human Phenome institute Fudan UniversityShanghai 201203China

Ancestry composition of populations and individuals has been extensively investigated in recent years due to advances in the genotyping and sequencing technologies. As the number of populations and individuals used for ancestry inference increases remarkably, say more than 100 populations or 1000 individuals, it is usually challenging to present the ancestry composition in a traditional way using a rectangular graph. To address this issue, we developed a program,AncestryPainter, which can illustrate the ancestry composition of populations and individuals with a rounded and nice-looking graph to save space. Individuals are depicted as length-fixed bars partitioned into colored segments representing different ancestries, and the population of interest can be highlighted as a pie chart in the center of the circle plot. In addition, AncestryPainter can also be applied to display personal ancestry in a way similar to that for displaying population *** is publicly available at http://***/PGG/***.

关键词： Graphic program Admixed populations Ancestry composition AncestryPainter Admixture proportions

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Development of plant communities after restoration of the Antaibao mining site, China

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Frontiers in biology 2009年第2期4卷 222-227页

作者： Xiaoyu GUO Guilian ZHANG Huili GONG Kaiyun WANG Jintun ZHANG Key Laboratory of Resource Environment and Geography Information System College of ResourceEnvironment and TourismCapital Normal UniversityBeijing 100037China chinese academy of Science-max planck Society partner institute for computational biology Shanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai 200031China College of Life sciences Beijing Normal UniversityBeijing 100875China

To investigate the dynamic changes in the artificial vegetation in an abandoned mining site,we analyzed the re lationships among community types,environmental variables and community structure in the process of vegetation restoration in the Antaibao mining site,China by survey of the communities and use of biological dating *** means of the quantitative classification method(two-way indicator-species analysis,TWINSPAN)and the ordination technique(de-trended correspondence analysis,DCA;and de-trended canonical correspondence analysis,DCCA),the plant communities were classified into seven groups:community I,Robinia pseudoacacia+Pimus tabulaeformis-Caragana kor-shinskii-Agropyron cristatum;community II,Robinia pseudoacacia-Hippophae rhamnoides-Artemisia capil-laries;community II,Ulmus pumila-Elaeagmus angu-stifolia-Artemisia capillaries;community IV,Caragana korshinskii-Agropyron cristatum+Artemisia capillaries;community V,Hippophae rhamnoides-Elymus dahur-icus;community VI,Elaeagnus angustifolia+Hippophae rhamnoides-Brassica jucea;community VII,Hippophae rhammoides+Elaeagnus angustifolia-Salsola *** conclude that the community types and diversity are mainly influenced by the succession time and the soil organic matter *** forest community is more adaptable to the special inhabitation than the shrub community.

关键词： mining site plant community succession recovery of vegetation restoration ecology species diversity Shanxi

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Inferring epigenetic and transcriptional regulatory Networks

Inferring epigenetic and transcriptional regulatory Networks

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者：韩敬东 chinese academy of sciences-max planck partner institute for computational biology Shanghai Institutes for Biological SciencesChinese Academy of Sciences

Microarrays and deep sequencing technologies have provided unprecedented opportunities for mapping mutations,transcripts,transcription factor binding and histone modifications at high resolution and at genome-wide *** has revolutionized the way transcriptome,regulatory network and epigenetic regulations are studies and generated a large amount of heterogeneous data, which is begging to be unbiasedly and efficiently *** to integrate these data still remains a big *** have explored various bioinformatics approaches,ranging from flow optimization to Bayesian network inference to reconstruct or reverse engineer regulatory networks based on genomic,epigenomic and transcriptomic *** do so,we have developed novel methods to extend the existing *** find that innovative integrations of the data from different layers can lead to identification of not only global regulation patterns,but also detailed biological insights regarding complex biological processes,such as development of complex phenotypes and diseases.

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Differentiation of embryonic stem cells in adult bone marrow

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Journal of Genetics and Genomics 2010年第7期37卷 431-439页

作者： Yueying Li Jing He Fengchao Wang Zhenyu Ju Sheng Liu Yu Zhang Zhaohui Kou Yanfeng Liu Tao Cheng Shaorong Gao State Key Laboratory of Experimental Hematology Institute of Hematology and Blood Diseases Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Tianjin 300020 China National institute of Biological sciences Beijing 102206 China max-planck-partner Group on Stem Cell Aging Institute of Laboratory Animal Science Chinese Academy of Medical Sciences Beijing 100021 China Center for Stem Cell Medicine Chinese Academy of Medical Sciences Beijing 100730 China.

Embryonic stem cells （ESCs） are a potential source of generating transplantable hematopoietic stem and progenitor cells,which in turn can serve as ＂seed＂ cells for hematopoietic *** this study,we aimed to gauge the ability of mouse ESCs directly differentiating into hematopoietic cells in adult bone marrow （BM）.To this end,we first derived a new mouse ESC line that constitutively expressed the green fluorescent protein （GFP） and then injected the ESCs into syngeneic BM via *** progeny of the transplanted ESCs were then analyzed at different time points after ***,however,most injected ESCs differentiated into non-hematopoietic cells in the BM whereas only a minority of the cells acquired hematopoietic cell surface *** study provides a strategy for evaluating the differentiation potential of ESCs in the BM micro-environment,thereby having important implications for the physiological maintenance and potential therapeutic applications of ESCs.

关键词： embryonic stem cells differentiation bone marrow transplantation

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