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Molecular bases of morphologically diffused tumors across multiple cancer types

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National Science Review 2022年第11期9卷 65-67页

作者： Dingyun Liu Feiyang Xing Yueying Wang Jun Xiao Zheng An Ying Xu College of Computer Science and Technology Jilin University Center for Cancer systems biology China-Japan Union Hospital of Jilin University school of Life Sciences Jilin University China Computational systems biology Lab Department of Biochemistry and Molecular Biology and Institute of BioinformaticsUniversity of Georgia

Diffuse gastric cancer (DGC) and intestinal gastric cancer (IGC) are the two main gastric cancer subtypes [1]. Morphologically, DGC consists of numerous disjoint tiny tumors while IGC forms one or a few solid tumors (Supplementary Supplementary Fig. S1)[1,2]. In-depth studies have discovered that DGCs generally have an ill-defined or missing glandular structure and reduced cell–cell adhesion,

关键词： identification enantioselective semisynthesis (−)-anisomelic acid oral agent anti-SARS-CoV-2

Modification of tubular chitosan-based peripheral nerve implants: applications for simple or more complex approaches

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Neural Regeneration Research 2020年第8期15卷 1421-1431页

作者： Nina Dietzmeyer Maria F?rthmann Claudia Grothe Kirsten Haastert-Talini Institute of Neuroanatomy and Cell biology Hannover Medical School Center for Systems Neuroscience (ZSN) Hannover

Surgical treatment of peripheral nerve injuries is still a major challenge in human clinic.Up to now,none of the well-developed microsurgical treatment options is able to guarantee a complete restoration of nerve function.This restriction is also effective for novel clinically approved artificial nerve guides.In this review,we compare surgical repair techniques primarily for digital nerve injuries reported with relatively high prevalence to be valuable attempts in clinical digital nerve repair and point out their advantages and shortcomings.We furthermore discuss the use of artificial nerve grafts with a focus on chitosan-based nerve guides,for which our own studies contributed to their approval for clinical use.In the second part of this review,very recent future perspectives for the enhancement of tubular(commonly hollow)nerve guides are discussed in terms of their clinical translatability and ability to form three-dimensional constructs that biomimick the natural nerve structure.This includes materials that have already shown their beneficial potential in in vivo studies like fibrous intraluminal guidance structures,hydrogels,growth factors,and approaches of cell transplantation.Additionally,we highlight upcoming future perspectives comprising co-application of stem cell secretome.From our overview,we conclude that already simple attempts are highly effective to increase the regeneration supporting properties of nerve guides in experimental studies.But for bringing nerve repair with bioartificial nerve grafts to the next level,e.***.repair of defects>3 cm in human patients,more complex intraluminal guidance structures such as innovatively manufactured hydrogels and likely supplementation of stem cells or their secretome for therapeutic purposes may represent promising future perspectives.

关键词： bioartificial nerve graft biological nerve graft cell transplantation cellular products luminal structures peripheral nerve repair

Metabolic reprogramming in cancer: the bridge that connects intracellular stresses and cancer behaviors

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National Science Review 2020年第8期7卷 1270-1273页

作者： Yi Zhou Huiyan Sun Ying Xu Cancer systems biology Center The China-Japan Union Hospital Department of Biochemistry and Molecular biology University of Georgia school of Artificial Intelligence Jilin University

Extensive changes in cellular metabolisms have been observed in cancer. They are probably induced by the same intracellular stressor, persistent off-balance in intracellular p H across possibly all adult cancers. It is these altered metabolisms that gives rise to a variety of cancerous behaviors such as continuous cell division, metastasis and drug resistance.

关键词： IRON

systems perspectives on mRNA processing

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Cell Research 2007年第7期17卷 581-590页

作者： Adrienne E McKee Pamela A Silver USA Department of systems biology Harvard Medical school Boston Department of systems biology Harvard Medical school Boston MA 02115

The application of genomic technologies to the study of mRNA processing is increasingly conducted in metazoanorganisms in order to understand the complex events that occur during and after transcription. Large-scale systemsanalyses of mRNA-protein interactions and mRNA dynamics have revealed specificity in mRNA transcription, splicing,transport, translation, and turnover, and have begun to make connections between the different layers of mRNA process-ing. Here, we review global studies of post-transcriptional processes and discuss the challenges facing our understandingof mRNA regulation in metazoan organisms. In parallel, we examine genome-scale investigations that have expandedour knowledge of RNA-binding proteins and the networks of mRNAs that they regulate.

关键词： RNA-binding protein post-transcriptional regulation systems biology functional genomics

Arabidopsis co-chaperonin CPN20 antagonizes Mg-chelatase H subunit to derepress ABA-responsive WRKY40 transcription repressor

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Science China(Life Sciences) 2014年第1期57卷 11-21页

作者： ZHANG XiaoFeng JIANG Tao YU YongTao WU Zhen JIANG ShangChuan LU Kai FENG XiuJing LIANG Shan LU YanFen WANG XiaoFang ZHANG DaPeng MOE systems biology and Bioinformatics Laboratory School of Life Sciences Tsinghua University

Our previous study demonstrated that a chloroplast co-chaperonin 20(CPN20),one of the interaction partners of the magnesium-protoporphyrin IX chelatase H subunit(CHLH/ABAR),negatively regulates ABA signaling at the same node with ABAR but upstream of WRKY40 transcription repressor in Arabidopsis thaliana.In the present experiment,we showed that ABA directly inhibits the ABAR-CPN20 interaction,and also represses expression of CPN20,which depends on ABAR.CPN20 inhibits ABAR-WRKY40 interaction by competitively binding to ABAR.ABAR downregulates,but CPN20 upregulates,WRKY40 expression.The cpn20-1 mutation induces downregulation of WRKY40,and suppresses the upregulated level of WRKY40 due to the cch mutation in the ABAR gene.ABA-induced repressive effect of the WRKY40 gene is strengthened by downregulation of CPN20 but reduced by upregulation of CPN20.Together with our previously reported genetic data,we provide evidence that CPN20 functions through antagonizing the ABAR-WRKY40 coupled pathway,and ABA relieves this pathway of repression by inhibiting the ABAR-CPN20 interaction to activate ABAR-WRKY40 interaction.

关键词： ABA诱导分子伴侣 H亚基拟南芥抑制因子合酶拮抗转录

Directed yeast genome evolution by controlled introduction of trans-chromosomic structural variations

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Science China(Life Sciences) 2022年第9期65卷 1703-1717页

作者： Bin Jia Jin Jin Mingzhe Han Bingzhi Li Yingjin Yuan Frontier Science Center for Synthetic biology and Key Laboratory of systems Bioengineering(Ministry of Education) School of Chemical Engineering and TechnologyTianjin UniversityTianjin 300072China

Naturally occurring structural variations(SVs)are a considerable source of genomic variation that can reshape the 3D architecture of chromosomes.Controllable methods aimed at introducing the complex SVs and their related molecular mechanisms have remained farfetched.In this study,an SV-prone yeast strain was developed using Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution(SCRaMbLE)technology with two synthetic chromosomes,namely synV and synX.The biosynthesis of astaxanthin is used as a readout and a proof of concept for the application of SVs in industries.Our findings showed that complex SVs,including a pericentric inversion and a trans-chromosome translocation between synV and synX,resulted in two neo-chromosomes and a 2.7-fold yield of astaxanthin.Also,genetic targets were mapped,which resulted in a higher astaxanthin yield,thus demonstrating the SVs’ability to reorganize genetic information along the chromosomes.The rational design of trans-chromosome translocation and pericentric inversion enabled precise induction of these phenomena.Collectively,this study provides an effective tool to not only accelerate the directed genome evolution but also to reveal the mechanistic insight of complex SVs for altering phenotypes.

关键词： directed genome evolution structural variations SCRaMbLE synthetic genome synthetic biology

Current advances of biocontainment strategy in synthetic biology

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Chinese Journal of Chemical Engineering 2023年第4期56卷 141-151页

作者： Xueying Zhu Zhaoyang Zhang Bin Jia Yingjin Yuan Frontier Science Center for Synthetic biology and Key Laboratory of systems Bioengineering(Ministry of Education) School of Chemical Engineering and TechnologyTianjin UniversityTianjin 300072China

Synthetic biotechnology has led to the widespread application of genetically modified organisms(GMOs)in biochemistry, bioenergy, and therapy. However, the uncontrolled spread of GMOs may lead to genetic contamination by horizontal gene transfer, resulting in unpredictable biosafety risks. To deal with these challenges, many effective methods have been developed for biocontainment. In this article, we summarize and discuss recent advances in biocontainment strategies from three aspects: DNA replication, transcriptional regulation, and protein translation. We also briefly introduce the efforts in the biocontainment convention, such as the recent publication of the Tianjin Biosecurity Guidelines for the Code of Conduct for Scientists.

关键词： Genetically modified organisms(GMOs) Biocontainment Biosecurity Synthetic biology Molecular biology Biotechnology

Cancer bioinformatics:detection of chromatin states, SNP-containing motifs, and functional enrichment modules

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Chinese Journal of Cancer 2013年第4期32卷 153-154页

作者： Xiaobo Zhou Center for Bioinformatics and systems biology Wake Forest University-School of Medicine

In this editorial preface, I briefly r eview cancer bioinformatics and introduce the four articles in this special issue highlighting important applications of the field: detection of chromatin states; detection of SNP- containing motifs and association with transcription factor-binding sites; improvements in functional enrichment modules; and gene association studies on aging and cancer. We expect this issue to provide bioinformatics scientists, cancer biologists, and clinical doctors with a better understanding of how cancer bioinformatics can be used to identify candidate biomarkers and targets and to conduct functional analysis.

关键词： Chromatin sates, SNP-containing motifs, functional enrichment analysis, gene association

Self-assembly of artificial architectures in living cells-design and applications

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Science China Chemistry 2022年第1期65卷 31-47页

作者： Xiaolei Sun Yuhang Dong Yujie Liu Nachuan Song Feng Li Dayong Yang Frontiers Science Center for Synthetic biology Key Laboratory of Systems Bioengineering(Ministry of Eeducation)School of Chemical Engineering and TechnologyTianjin UniversityTianjin 300350China

Self-assembly exists widely in natural living system and artificial synthetic material system.Administration of self-assemblies of artificial architectures in living cells can be used to explore the molecular physicochemical fundamentals and operating mechanisms of living system,and consequently promote the development of biomedicine.In order to mimic naturally occurring self-assemblies and realize controllable functions,great efforts have been devoted to constructing dynamic assembly of artificial architectures in living cells by responding to intracellular specific stimuli,which can be used to regulate morphology,behaviors and fate of living cells.This review highlights the recent progress on artificial self-assembly in living cells.The molecular fundamentals and characteristics of intracellular environment that can induce the self-assembly of artificial architectures are introduced,and the representative work on dynamic artificial self-assembly in living cells is sketched chronologically.Moreover,intracellular stimuli-mediated pathways of artificial assembly in living cells are categorized,biological effects caused by intracellular self-assembly are summarized,and biomedical applications focusing on therapy and imaging are described.In the end,the perspective and challenges of artificial self-assembly in living cells are fully discussed.It is believed that the grand advances on artificial self-assembly in living cells will contribute to elaborating the molecular mechanisms in cells,and further promoting the biologically and medically-related applications in the future.

关键词： self-assembly stimulus responsiveness biomaterials biomedicine