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Stereotypes About Enterotype: the Old and New Ideas

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Genomics, Proteomics & bioinformatics 2019年第1期17卷 4-12页

作者： Mingyue Cheng Kang Ning Key Laboratory of Molecular Biophysics of the Ministry of Education Hubei Key Laboratory of Bioinformatics and Molecular-imaging Department of Bioinformatics and Systems Biology College of Life Science and TechnologyHuazhong University of Science and Technology

In 2011, the term ‘‘enterotype" first appeared to the general public in Nature, which refers to stratification of human gut microbiota. However, with more studies on enterotypes conducted nowadays, doubts about the existence and robustness of enterotypes have also emerged. Here we reviewed current opinions about enterotypes from both conceptual and analytical points of *** firstly illustrated the definition of the enterotype and various factors influencing enterotypes,such as diet, administration of antibiotics, and age. Then we summarized lines of evidence that pose the concept against the enterotype, and described the current methods for enterotype ***, we showed that the concept of enterotype has been extended to other ecological *** on current studies on enterotypes, it has been clear that more studies with larger sample sizes are needed to characterize the enterotypes. Improved computational methods are also required to build sophisticated models, reflecting the dynamics and resilience of enterotypes.

关键词： Enterotype Gut microbiome Biomarker Continuity computational methods

DIProT:A deep learning based interactive toolkit for efficient and effective Protein design

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Synthetic and Systems Biotechnology 2024年第2期9卷 217-222页

作者： Jieling He Wenxu Wu Xiaowo Wang Ministry of Education Key Laboratory of bioinformatics Center for Synthetic and Systems BiologyBioinformatics DivisionBeijing National Research Center for Information Science and TechnologyDepartment of AutomationTsinghua UniversityBeijingChina

The protein inverse folding problem,designing amino acid sequences that fold into desired protein structures,is a critical challenge in biological *** numerous data-driven and knowledge-driven methods,there remains a need for a user-friendly toolkit that effectively integrates these approaches for in-silico protein *** this paper,we present DIProT,an interactive protein design *** leverages a non-autoregressive deep generative model to solve the inverse folding problem,combined with a protein structure prediction *** integration allows users to incorporate prior knowledge into the design process,evaluate designs in silico,and form a virtual design loop with human *** inverse folding model demonstrates competitive performance in terms of effectiveness and efficiency on TS50 and CATH4.2 datasets,with promising sequence recovery and inference *** studies further illustrate how DIProT can facilitate user-guided protein design.

关键词： computational Protein design Interactive design toolkit Protein inverse folding Non-autoregressive decoding

Understanding super-enhancers

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Science China(Life Sciences) 2016年第3期59卷 277-280页

作者： Hao Cheng Xiaoyang Dou Jing-Dong J.Han 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

Super-enhancers are defined as cluster of enhancers with dense TF binding, which can activate proximal cell-identity gene expression. Here we review the identification, func- tional significance of super-enhancers, and their relation- ships with cancer. With the current intense interests in su- per-enhancers, more super-enhancers will be defined and studied in different cell types and tissues and in different developmental and biological contexts to reveal molecular mechanisms of their functions.

关键词：超促进剂基因表达分子机制生物环境定义细胞激活

The secondary metabolite bioinformatics portal: computational tools to facilitate synthetic biology of secondary metabolite production

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Synthetic and Systems Biotechnology 2016年第2期1卷 69-79页

作者： Tilmann Weber Hyun Uk Kim The Novo Nordisk Foundation Center for Biosustainability Technical University of DenmarkKogle Alle 62970 HosholmDenmark bioinformatics Research Center Korea Advanced Institute of Science and Technology(KAIST)Daejeon 34141Republic of Korea

Natural products are among the most important sources of lead molecules for drug *** the development of affordable whole-genome sequencing technologies and other‘omics tools,the field of natural products research is currently undergoing a shift in ***,for decades,mainly analytical and chemical methods gave access to this group of compounds,nowadays genomics-based methods offer complementary approaches to find,identify and characterize such *** paradigm shift also resulted in a high demand for computational tools to assist researchers in their daily *** this context,this review gives a summary of tools and databases that currently are available to mine,identify and characterize natural product biosynthesis pathways and their producers based on‘omics data.A web portal called Secondary Metabolite bioinformatics Portal(SMBP at http://***)is introduced to provide a one-stop catalog and links to these bioinformatics *** addition,an outlook is presented how the existing tools and those to be developed will influence synthetic biology approaches in the natural products field.

关键词： Antibiotics Biosynthesis bioinformatics NRPS PKS Natural product

An inducible CRISPR-ON system for controllable gene activation in human pluripotent stem cells

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Protein & Cell 2017年第5期8卷 379-393页

作者： Jianying Guo Dacheng Ma Rujin Huang Jia Ming Min Ye Kehkooi Kee Zhen Xie Jie Na Department of Basic Medical Sciences School of Medicine Center for Stem Cell Biology Tsinghua University Beijing 100084 China MOE Key Laboratory of bioinformatics and bioinformatics Division Center for Synthetic and System Biology TNLIST/ Department of Automation Tsinghua University Beijing 100084 China

Human pluripotent stem cells （hPSCs） are an important system to study early human development, model human diseases, and develop cell replacement therapies. However, genetic manipulation of hPSCs is challenging and a method to simultaneously activate multiple genomic sites in a controllable manner is sorely needed. Here, we constructed a *** system to efficiently upregulate endogenous genes in hPSCs. A doxycycline （Dox） inducible dCasg-VP64-p65-Rta （dCas9-VPR） transcription activator and a reverse Tet transactivator （rtTA） expression cassette were knocked into the two alleles of the AAVS1 locus to generate an iVPR hESC line. We showed that the dCas9-VPR level could be precisely and reversibly controlled by the addition and withdrawal of Dox. Upon transfection of multiplexed gRNA plasmid targeting the NANOG pro- moter and Dox induction, we were able to control NANOG gene expression from its endogenous locus. Interestingly, an elevated NANOG level promoted naive pluripotsnt gene expression, enhanced cell survival and clonogenicity, and enabled hESCs to integrate with the inner cell mass （ICM） of mouse blastocysts in vitro. Thus, iVPR cells provide a convenient platform for gene function studies as well as high-throughput screens in hPSCs.

关键词： CRISPR transcription activation humanpluripotent stem cells NANOG pluripotency

Active catalytic species generated in situ in zirconia incorporated hydrogen storage material magnesium hydride

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Journal of Magnesium and Alloys 2022年第3期10卷 852-861页

作者： D.Pukazhselvan K.S.Sandhya Devaraj Ramasamy Aliaksandr Shaula Igor Bdikin Duncan Paul Fagg Department of Mechanical Engineering Nanoengineering Research GroupCentre for Mechanical Technology and Automation(TEMA)University of AveiroAveiro 3810-193Portugal Department of Chemistry Malankara Catholic CollegeKaliyakkavilaiTamil Nadu 629153India Department of computational biology and bioinformatics University of KeralaThiruvananthapuramKerala 695581India UIDM ESTGPolytechnic Institute of Viana do CasteloViana do Castelo 4900Portugal

This study explores how zirconia additive interacts with MgH_(2)to improve its hydrogen storage *** it is confirmed that the zirconia added MgH_(2)powder releases hydrogen at a temperature of about 50℃below that of the additive free MgH_(2).Subsequent tests by X ray diffraction(XRD)and infrared(IR)spectroscopy techniques reveal that the ZrO_(2) mixed MgH_(2)powder contains ZrHx(21.5)and MgO secondary *** observation is supported by the negative Gibbs free energy values obtained for the formation of ZrH_(2)/MgO from ZrO_(2)/MgH_(2)powder *** X ray photoelectron spectroscopy(XPS)study reveals that apart from Zr^(4+)cations,Zr^(2+) and zero valent Zr exist in the *** force microscopy(AFM)study reveals that the average grain size is 20 nm and the elemental line scan profiles further proves the existence of oxygen deficient Zr bearing phase(s).This study strengthens the belief that functional metal oxide additives in fact chemically interact with MgH_(2)to make active in-situ catalysts in the MgH_(2)system.

关键词： Hydrogen storage Binary hydrides Metal oxides Additives Nanocatalysis.

computational Assessment of Protein–protein Binding Affinity by Reversely Engineering the Energetics in Protein Complexes

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Genomics, Proteomics & bioinformatics 2021年第6期19卷 1012-1022页

作者： Bo Wang Zhaoqian Su Yinghao Wu Department of Systems and computational biology Albert Einstein College of MedicineBronxNY 10461USA

The cellular functions of proteins are maintained by forming diverse *** stability of these com-plexes is quantified by the measurement of binding affinity,and mutations that alter the binding affinity can cause various diseases such as cancer and *** a result,accurate estimation of the binding stability and the effects of mutations on changes of binding affinity is a crucial step to understanding the biological functions of proteins and their dysfunctional *** has been hypothesized that the stability of a protein complex is dependent not only on the residues at its binding interface by pairwise interactions but also on all other remaining residues that do not appear at the binding ***,we computationally reconstruct the binding affinity by decomposing it into the contributions of interfacial residues and other non-interfacial residues in a protein *** further assume that the contributions of both interfacial and non-interfacial residues to the binding affinity depend on their local structural environments such as solvent-accessible surfaces and secondary structural *** weights of all corresponding parameters are optimized by Monte-Carlo *** cross-validation against a large-scale dataset,we show that the model not only shows a strong correlation between the absolute values of the experimental and calculated binding affinities,but can also be an effective approach to predict the relative changes of binding affinity from ***,we have found that the optimized weights of many parameters can capture the first-principle chemical and physical features of molecular recognition,therefore re-versely engineering the energetics of protein *** results suggest that our method can serve as a useful addition to current computational approaches for predicting binding affinity and understanding the molecular mechanism of protein–protein interactions.

关键词： Protein-protein interaction Binding affinity Non-interfacial residue Knowledge-based potential Monte-Carlo simulation

Dormancy heterogeneity among Arabidopsis thaliana seeds is linked to individual seed size

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Plant Communications 2024年第2期5卷 215-227页

作者： Michal Krzyszton Sebastian P.Sacharowski Veena Halale Manjunath Katarzyna Muter Grzegorz Bokota Ce Wang Dariusz Plewczynski Tereza Dobisova Szymon Swiezewski Laboratory of Seeds Molecular biology Institute of Biochemistry and BiophysicsPAS02-106 WarsawPoland Laboratory of Functional and Structural Genomics Centre of New TechnologiesUniversity of WarsawWarsawPoland Laboratory of bioinformatics and computational Genomics Faculty of Mathematics and Information ScienceWarsaw University of TechnologyWarsawPoland Labdeers Ltd. 680-01 BoskoviceCzech Republic

Production of morphologically and physiologically variable seeds is an important strategy that helps plants to survive in unpredictable natural ***,the model plant Arabidopsis thaliana and most agronomically essential crops produce visually homogenous *** automated phenotype analysis,we observed that small seeds in Arabidopsis tend to have higher primary and secondary dormancy levels than large *** analysis revealed distinct gene expression profiles between large and small *** seeds have higher expression of translation-related genes implicated in germination *** contrast,small seeds have elevated expression of many positive regulators of dormancy,including a key regulator of this process,the DOG1 *** in DOG1 expression are associated with differential production of its alternative cleavage and polyadenylation isoforms;in small seeds,the proximal poly(A)site is selected,resulting in a short mRNA ***,single-seed RNA sequencing analysis demonstrated that large seeds resemble DOG1 knockout mutant ***,on the single-seed level,expression of genes affected by seed size is correlated with expression of genes that position seeds on the path toward *** results demonstrate an unexpected link between seed size and dormancy phenotypes in a species that produces highly homogenous seed pools,suggesting that the correlation between seed morphology and physiology is more widespread than initially assumed.

关键词： seed size dormancy DOG1 Arabidopsis

MINI-EX:Integrative inference of single-cell gene regulatory networks in plants

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Molecular Plant 2022年第11期15卷 1807-1824页

作者： Camilla Ferrari Nicolás Manosalva Pérez Klaas Vandepoele Department of Plant Biotechnology and bioinformatics Ghent University9052 GhentBelgium Center for Plant Systems biology VIB9052 GhentBelgium bioinformatics Institute Ghent Ghent University9052 GhentBelgium

Multicellular organisms,such as plants,are characterized by highly specialized and tightly regulated cell populations,establishing specific morphological structures and executing distinct *** regulatory networks(GRNs)describe condition-specific interactions of transcription factors(TFs)regulating the expression of target genes,underpinning these specific *** efficient and validated methods to identify cell-type-specific GRNs from single-cell data in plants are lacking,limiting our understanding of the organization of specific cell types in both model species and crops,we developed MINI-EX(Motif-Informed Network Inference based on single-cell EXpression data),an integrative approach to infer cell-type-specific networks in ***-EX uses single-cell transcriptomic data to define expression-based networks and integrates TF motif information to filter the inferred regulons,resulting in networks with increased ***,regulons are assigned to different cell types,leveraging cell-specific expression,and candidate regulators are prioritized using network centrality measures,functional annotations,and expression *** embedded prioritization strategy offers a unique and efficient means to unravel signaling cascades in specific cell types controlling a biological process of *** demonstrate the stability of MINI-EX toward input data sets with low number of cells and its robustness toward missing data,and show that it infers state-of-the-art networks with a better performance compared with other related single-cell network ***-EX successfully identifies key regulators controlling root development in Arabidopsis and rice,leaf development in Arabidopsis,and ear development in maize,enhancing our understanding of cell-type-specific regulation and unraveling the roles of different regulators controlling the development of specific cell types in plants.

关键词： single-cell RNA-seq gene regulatory network transcription factors systems biology