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Functional Partition of Cpn60α and Cpn60β Subunits in Substrate Recognition and Cooperation with Co-chaperonins

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Molecular Plant 2016年第8期9卷 1210-1213页

作者： Shijia Zhang Huan Zhou Feng Yu Feng Gao Jianhua He Cuimin Liu center for Molecular systems biology Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China

Dear editor A multitude of proteins in cells are assisted in their folding by cylindrical double-ring chaperonin complexes. Group I chapero- nin, such as prokaryotic GroEL, mitochondrial Hsp60, and chloroplastic Cpn60, consists of 14 subunits that are organized into two rings stacked back to back, with each ring possessing an internal central cavity to allow the protein to fold inside （Hartl et al., 2011）. Each chaperonin subunit comprises three domains： an equatorial domain, an apical domain,

关键词： MOLECULAR chaperones PROTEINS

Metabolic reprogramming in tumors:Contributions of the tumor microenvironment

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Genes & Diseases 2020年第2期7卷 185-198页

作者： Andrew N.Lane Richard M.Higashi Teresa W-M.Fan center for Environmental and systems Biochemistry Markey Cancer CenterDepartment of Toxicology and Cancer BiologyUniversity of KentuckyUSA

The genetic alterations associated with cell transformation are in large measure expressed in the metabolic phenotype as cancer cells proliferate and change their local environment,and prepare for ***,the fundamental biochemistry of cancer cells is generally the same as in the untransformed cells,but the cancer cells produce a local environment,the TME,that is hostile to the stromal cells,and compete for *** order to proliferate,cells need sufficient nutrients,either those that cannot be made by the cells themselves,or must be made from simpler ***,in solid tumors,the nutrient supply is often limiting given the potential for rapid proliferation,and the poor quality of the ***,cancer cells may employ a variety of strategies to obtain nutrients for survival,growth and *** much has been learned using established cell lines in standard culture conditions,it is becoming clear from in vivo metabolic studies that this can also be misleading,and which nutrients are used for energy production versus building blocks for synthesis of macromolecules can vary greatly from tumor to tumor,and even within the same *** we review the operation of metabolic networks,and how recent understanding of nutrient supply in the TME and utilization are being revealed using stable isotope tracers in vivo as well as in vitro.

关键词： Cancer metabolism Nutrient supply Stable isotope resolved metabolomics Tumor microenvironment Metabolic flux

Computational Challenges in Deciphering Genomic Structures of Bacteria

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Journal of Computer Science & Technology 2010年第1期25卷 53-70页

作者：徐鹰 Computational systems biology Laboratory Department of Biochemistry and Molecular Biology and Institute of Bioinformatics The University of Georgia BESC BioEnergy Science center College of Computer Science and Technology Jilin University

This article addresses how the functionalities of the cellular machinery of a bacterium might have constrained the genomic arrangement of its genes during evolution and how we can study such problems using computational approaches, taking full advantage of the rapidly increasing pool of the sequenced bacterial genomes, potentially leading to a much improved understanding of why a bacterial genome is organized in the way it is. This article discusses a number of challenging computational problems in elucidating the genomic structures at multiple levels and the information that is encoded through these genomic structures, gearing towards the ultimate understanding of the governing rules of bacterial genome organization.

关键词： bioinformatics microbial genomics genome structure comparative genome analysis biological pathways

RNA Regulations and Functions Decoded by Transcriptome-wide RNA Structure Probing

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Genomics, Proteomics & Bioinformatics 2017年第5期15卷 267-278页

作者： meiling piao lei sun qiangfeng cliff zhang moe key laboratory of bioinformatics beijing advanced innovation center for structural biologycenter for synthetic and systems biologytsinghua-peking joint center for life sciencesschool of life sciencestsinghua universityBeijing 100084China

RNA folds into intricate structures that are crucial for its functions and regulations. To date, a multitude of approaches for probing structures of the whole transcriptome, i.e., RNA struc- turomes, have been developed. Applications of these approaches to different cell lines and tissues have generated a rich resource for the study of RNA structure-function relationships at a systems biology level. In this review, we first introduce the designs of these methods and their applications to study different RNA structuromes. We emphasize their technological differences especially their unique advantages and caveats. We then summarize the structural insights in RNA functions and regulations obtained from the studies of RNA structuromes. And finally, we propose potential directions for future improvements and studies.

关键词： RNA structure probing RNA structurome RNA secondary structure Structure-function relation-ship RNA regulation

The Role of Dopamine in Associative Learning in Drosophila: An Updated Unified Model

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Neuroscience Bulletin 2021年第6期37卷 831-852页

作者： Mohamed Adel Leslie C.Griffith Department of biology Volen National Center for Complex Systems and National Center for Behavioral GenomicsBrandeis UniversityWalthamMA 02454-9110USA

Learning to associate a positive or negative experience with an unrelated cue after the presentation of a reward or a punishment defines associative *** ability to form associative memories has been reported in animal species as complex as humans and as simple as insects and sea *** memory has even been reported in tardigrades[1],species that diverged from other animal phyla 500 million years *** the mechanisms of memory formation is a fundamental goal of neuroscience *** this article,we work on resolving the current contradictions between different Drosophila associative memory circuit models and propose an updated version of the circuit model that predicts known memory behaviors that current models do ***,we propose a model for how dopamine may function as a reward prediction error signal in Drosophila,a dopamine function that is well-established in mammals but not in insects[2,3].

关键词： associative contradiction function

Preparation of biomimetic gene hydrogel via polymerase chain reaction for cell-free protein expression

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Science China Chemistry 2020年第1期63卷 99-106页

作者： Feng Li Wenting Yu Xue Zhang Xiaocui Guo Xihan Xu Xiaolei Sun Dayong Yang Frontier Science center for Synthetic biology Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology Tianjin University

Deoxyribonucleic acid(DNA)hydrogels,a three-dimensional(3 D)network made from DNA chains,have attracted great attention because of its molecular programmability,excellent biocompatibility and wide biomedical *** of hydrogel incorporating genetic function is still a challenge because of the limitations in available preparation ***,we develop a polymerase chain reaction(PCR)based strategy to construct gene integrated hydrogel to mimic the biofunction of nucleus *** primers were chemically modified by methacrylamide,which were used as modular primers in PCR to hybridize with template plasmid DNA,yielding methacrylamide functionalized gene(Acry-gene).Afterwards,Acry-gene was chemically cross-linked and compressed via free radical polymerization of terminal group methacrylamide to form a threedimensional gene network,namely gene *** gene hydrogel retained the genetic function and expressed protein successfully in a cell free protein expression *** work provides a general approach for the construction of biofunctional gene hydrogel which mimics bioprocesses,showing great potential in biomedicine and biomimetic fields.

关键词： hydrogel DNA polymerase chain reaction free radical polymerization biomimetic materials

Factors That Affect the Centrality Controllability of Scale-Free Networks

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Chinese Physics Letters 2015年第12期32卷 174-177页

作者：胡栋孙先李平陈雁张捷 center for Intelligent and Networked Systemest School of Computer Science Southwest Petroleum University Chengdu 610500 center for Computational systems biology Fudan University Shanghai 200433

The influence of a node in a network can be characterized by its macroscopic properties such as eigenvector centrality. An issue of significant theoretical and practical interest is to modify the influence or roles of the nodes in a network, and recent advances indicate that this can be achieved by just controlling a subset of nodes： the socalled controllers. However, the relationship between the structural properties of a network and its controllability, e.g., the control of node importance, is still not well understood. Here we systematically＂ explore this relationship by constructing scale-free networks with a fixed degree sequence and tunable network characteristics. We calculate the relative size （nc＊） of the minimai controlling set required to controi the importance of each individual node in a network. It is found that while clustering has no significant impact on nc＊, changes in degree-degree correlations, heterogeneity and the average degree of networks demonstrate a discernible impact on its controllability.

关键词： net Factors That Affect the Centrality Controllability of Scale-Free Networks

Decline and fall of aging astrocytes:the human perspective

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Neural Regeneration Research 2025年第6期20卷 1713-1714页

作者： Alexei Verkhratsky Alexey Semyanov Faculty of biology Medicine and HealthThe University of ManchesterManchesterUK Department of Neurosciences University of the Basque Country UPV/EHU and CIBERNEDLeioaSpain Department of Forensic Analytical Toxicology School of Forensic MedicineChina Medical UniversityShenyangLiaoning ProvinceChina Department of Stem Cell biology State Research Institute Centre for Innovative MedicineVilniusLithuania International Collaborative center on Big Science Plan for Purinergic Signalling Chengdu University of Traditional Chinese MedicineChengduSichuan ProvinceChina Department of Physiology Jiaxing University College of MedicineJiaxingZhejiang ProvinceChina

“Last scene of all that ends this strange,eventful history,is second childishness and mere oblivion.I am sans teeth,sans eyes,sans taste,sans everything.”William Shakespeare‘As You Like It'Act 2,Sc.7,l.139Aging of the human brain is characterized by a progressive decline of its functional capacity;this decline however varies widely,and cognitive longevity differs substantially between individuals.

关键词： aging teeth progressive

Promote Connections of Young Computational Biologists in China

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Genomics, Proteomics & Bioinformatics 2013年第4期11卷 253-256页

作者： Shihua Zhang Xiu-Jie Wang National center for Mathematics and Interdisciplinary Sciences Academy of Mathematics and Systems ScienceChinese Academy of Sciences center for Molecular systems biology Institute of Genetics and Developmental BiologyChinese Academy of Sciences

The first Youth Investigator Forum on Interdisciplinary Re- search of Mathematics, Computer Science and Biological Sci- ence （YMCB） took place on May 18-19, 2013 in Beijing, China. The conference was hosted by the National center for Mathematics and Interdisciplinary Sciences （NCMIS）, Chi- nese Academy of Sciences （CAS）, and was initiated by Dr. Xiu-Jie Wang （Institute of Genetics and Developmental Biol- ogy, CAS） and Dr. Shihua Zhang （Academy of Mathematics and systems Science, CAS）. This conference was launched to nurture the next generation of computational biologists in Chi- na. More than 300 people from all over the country attended this conference and 21 talks and 40 posters were presented at this meeting. The topics covered next-generation sequencing data analysis, transcription and mRNA regulation, microR- NA and lncRNA regulation, network biology, cancer genom- ics, epigenetics and personalized medicine. The conference was opened by Prof.

关键词： Promote Connections of Young Computational Biologists in China CTCF gene DNA