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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

Curation,nomenclature,and topological classification of receptor-like kinases from 528 plant species for novel domain discovery and functional inference

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Molecular Plant 2024年第4期17卷 658-671页

作者： Qian Liu Qiong Fu Yujie Yan Qian Jiang Longfei Mao Long Wang Feng Yu Heping Zheng State Key Laboratory of Chemo/Biosensing and Chemometrics Hunan University College of BiologyChangshaHunan 410082China bioinformatics center Hunan University College of BiologyChangshaHunan 410082China

Receptor-like kinases(RLKs)are the most numerous signal transduction components in plants and play important roles in determining how different plants adapt to their ecological *** on RLKs has focused mainly on a small number of typical RLK members in a few model *** is an urgent need to study the composition,distribution,and evolution of RLKs at the holistic level to increase our understanding of how RLKs assist in the ecological adaptations of different plant *** this study,we collected the genome assemblies of 528 plant species and constructed an RLK *** this dataset,we identified and characterized 524948 RLK family *** member underwent systematic topological classification and was assigned a gene ID based on a unified nomenclature ***,we identified two novel extracellular domains in some RLKs,designated Xiao and *** analysis of the RLK family revealed that the RLCK-XVII and RLCK-XII-2 classes were present exclusively in dicots,suggesting that diversification of RLKs between monocots and dicots may have led to differences in downstream cytoplasmic *** also used an interaction proteome to help empower data mining for inference of new RLK functions from a global perspective,with the ultimate goal of understanding how RLKs shape the adaptation of different plants to the environments/*** assembled RLK dataset,together with annotations and analytical tools,forms an integrated foundation of multiomics data that is publicly accessible via the metaRLK web portal(http://***).

关键词： RLK RLCK domain signaling pathway receptor-protein interactions

Refining biome labeling for large-scale microbial community samples:Leveraging neural networks and transfer learning

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Environmental Science and Ecotechnology 2024年第1期17卷 128-137页

作者： Nan Wang Teng Wang Kang Ning Key Laboratory of Molecular Biophysics of the Ministry of Education Hubei Key Laboratory of Bioinformatics and Molecular-imagingCenter of AI BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan430074HubeiChina

Microbiome research has generated an extensive amount of data,resulting in a wealth of publicly accessible *** annotation of these samples is crucial for effectively utilizing microbiome data across scientific ***,a notable challenge arises from the lack of essential annotations,particularly regarding collection location and sample biome information,which significantly hinders environmental microbiome *** this study,we introduce Meta-Sorter,a novel approach utilizing neural networks and transfer learning,to enhance biome labeling for thousands of microbiome samples in the MGnify database that have incomplete *** findings demonstrate that Meta-Sorter achieved a remarkable accuracy rate of 96.7%in classifying samples among the 16,507 lacking detailed biome ***,Meta-Sorter provides precise classifications for representative environmental samples that were previously ambiguously labeled as“Marine”in MGnify,thereby elucidating their specific origins in benthic and water column ***,Meta-Sorter effectively distinguishes samples derived from human-environment interactions,enabling clear differentiation between environmental and human-related *** improving the completeness of biome label information for numerous microbial community samples,our research facilitates more accurate knowledge discovery across diverse disciplines,with particular implications for environmental research.

关键词： Microbial community Transfer learning Sample classification Environmental scientific research Novel knowledge discovery

Interplant communication:an emerging battlefield in plant-aphid-virus interactions

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Science China(Life Sciences) 2024年第5期67卷 1069-1071页

作者： Yunjing Wang Qian Gong Yule Liu MOE Key Laboratory of bioinformatics and center for Plant biology School of Life SciencesTsinghua UniversityBeijing 100084China Tsinghua-Peking center for Life Sciences Beijing 100084China

Plants constantly face threats from various organisms,including pathogens and *** the pathogens,plant viruses are obligate intracellular parasites that infect plants and cause serious crop yield losses.

关键词： plant Plants communication

scEpiTools: a database to comprehensively interrogate analytic tools for single-cell epigenomic data

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Journal of Genetics and Genomics 2024年第4期51卷 462-465页

作者： Zijing Gao Xiaoyang Chen Zhen Li Xuejian Cui Qun Jiang Keyi Li Shengquan Chen Rui Jiang Ministry of Education Key Laboratory of bioinformatics Bioinformatics Division at the Beijing National Research Center for Information Science and TechnologyCenter for Synthetic and Systems BiologyDepartment of AutomationTsinghua UniversityBeijing 100084China School of Mathematical Sciences and LPMC Nankai UniversityTianjin 300071China

Recent advances in single-cell sequencing technologies provide significant implications for understanding cellular heterogeneity,developmental biology,and disease *** fully exploit the potential of these data,numerous tools have been proposed for upstream and downstream *** the the single-cell RNA sequencing(scRNA-seq)community,scRNA-tools(Zappia et al.,2018)was proposed to help researchers navigate the plethora of tools by *** its inception,scRNA-tools has been widely used and its updated version further reveals trends in the field with over 1000 collected tools(Zappia and Theis,2021),providing a valuable guidance in selecting tools for analyses.

关键词： analytic selecting Tools

Alternaria TeA toxin activates a chloroplast retrograde signaling pathway to facilitate JAdependent pathogenicity

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Plant Communications 2024年第3期5卷 123-140页

作者： Jiale Shi He Wang Mengping Li Liru Mi Yazhi Gao Sheng Qiang Yu Zhang Dan Chen Xinbin Dai Hongyu Ma Huan Lu Chanhong Kim Shiguo Chen Weed Research Laboratory Nanjing Agricultural UniversityNanjing 210095China Shanghai center for Plant Stress biology Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China bioinformatics and Computational biology Laboratory Noble Research Institute2510 Sam Noble ParkwayArdmoreOK 73401USA College of Plant Protection Nanjing Agricultural UniversityNanjing 210095China Department of Botany and Plant biology University of GenevaGenevaSwitzerland

The chloroplast is a critical battleground in the arms race between plants and *** microbe-secreted mycotoxins,tenuazonic acid(TeA),produced by the genus Alternaria and other phytopathogenic fungi,inhibits photosynthesis,leading to a burst of photosynthetic singlet oxygen(1O2)that is implicated in damage and chloroplast-to-nucleus retrograde *** the signicant crop damage caused by Alternaria pathogens,our understanding of the molecular mechanism by which TeA promotes pathoge-nicity and cognate plant defense responses remains *** now reveal that *** induces necrotrophic foliar lesions by harnessing EXECUTER1(EX1)/EX2-mediated chloroplast-to-nucleus retro-grade signaling activated by TeA toxin–derived photosynthetic 1O2 in Arabidopsis *** of the 1O2-sensitive EX1-W643 residue or complete deletion of the EX1 singlet oxygen sensor domain compro-mises expression of 1O2-responsive nuclear genes and foliar *** also found that TeA toxin rapidly induces nuclear genes implicated in jasmonic acid(JA)synthesis and signaling,and EX1-mediated retro-grade signaling appears to be critical for establishing a signaling cascade from 1O2 to *** present study sheds new light on the foliar pathogenicity of ***,during which EX1-dependent 1O2 signaling in-duces JA-dependent foliar cell death.

关键词： TeA mycotoxin Alternaria pathogen chloroplast singlet oxygen retrograde signaling jasmonic acid

Characterization of the infectivity of an Indonesian Zika virus strain in mammalian cell lines

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Asian Pacific Journal of Tropical Biomedicine 2024年第5期14卷 215-224页

作者： Justus Thomas Obiajulu Sievers Anom Bowolaksono R.Tedjo Sasmono Graduate School of biology Department of BiologyFaculty of Mathematics and Natural SciencesUniversitas IndonesiaDepok 16424Indonesia Eijkman Research center for Molecular biology National Research and Innovation AgencyCibinong 16911Indonesia Cellular and Molecular Mechanisms in Biological system Research Group Department of BiologyFaculty of Mathematics and Natural SciencesUniversitas IndonesiaDepok 16424Indonesia

Objective:To characterize the infection patterns and growth characteristics of the Zika virus(ZIKV)strain JMB-185 from Indonesia in various mammalian cell ***:ZIKV was grown in human(A549,HEK293,HepG2,Huh7,Jurkat,and THP-1)and non-human mammalian(RAW264.7,Vero,and Vero76)cell *** replication kinetics were measured using plaque assay,while intra-and extracellular viral RNA concentrations were assessed using *** cytometry was used to quantify the infected cells and cell viability was measured using an MTT *** ability of ZIKV to infect cell lines was visualized using a fluorescence immunostaining ***:This ZIKV strain preferentially infected the lung,kidney,and liver cell lines A549,HEK293,Huh7,Vero,and Vero76,but not the immune cells Jurkat,RAW264.7,and *** contrast,the ZIKV showed no sign of infection in HepG2 cells,while maintaining viral titer over 3 days post-infection,with no infection recorded in immunostaining,no increase in viral RNA,and no indication of cell ***:The Indonesian ZIKV strain has a similar infection profile as other strains,except for its poor infectivity on HepG2 *** on the growth characteristics of Indonesia ZIKV will help expand our understanding of the biology of ZIKV which will be useful for various applications including antiviral discovery.

关键词： Zika virus Infectivity Replication Cell lines In vitro

Finding my way: The role of dirigent proteins in lignin assembly

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Molecular Plant 2024年第2期17卷 230-232页

作者： Dyoni M.Oliveira Igor Cesarino Department of Plant Biotechnology and bioinformatics Ghent University9052 GhentBelgium VIB center for Plant systems biology 9052 GhentBelgium Departamento de Botanica Instituto de BiocienciasUniversidade de Sao PauloRua do Matao277Sao Paulo 05508-090Brazil Synthetic and systems biology center InovaUSPAvenida Professor Lucio Martins Rodrigues370SaoPaulo 05508-020Brazil

Lignin emerged around 450 million years ago in early tracheophytes and played a pivotal role in the colonization of terrestrial ecosystems by *** aromatic biopolymer provides mechanical strength to supportive tissues and hydrophobicity to water-transporting vasculature and acts as a physical barrier against herbivores and pathogens(Renault et al.,2019).The deposition of lignin in cell walls for proper cellular functionalization involves several molecular steps,including the tight regulation of tissue-or cell-type-specific expression of lignin biosynthetic genes,the biosynthesis of distinct lignin monomers and their transportation to the apoplast,and the polymerization of monomer radicals to produce tissue-or cell-type-dependent polymers with distinct physico-chemical properties.

关键词： properties. lignin walls

Novel concept of nano-additive design:PTFE@silica Janus nanoparticles for water lubrication

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Friction 2024年第2期12卷 258-270页

作者： Yanfei LIU Hailing HE Meng YANG Ruize ZHANG Shengtao YU Tiantian YANG Wenzhong WANG Fuxin LIANG School of Mechanical Engineering Beijing Institute of TechnologyBeijing 100081China Institute of Polymer Science&Engineering Department of Chemical EngineeringTsinghua UniversityBeijing 100084China MOE Key Laboratory of bioinformatics Center for Plant BiologySchool of Life SciencesTsinghua UniversityBeijing 100084China Tsinghua-Peking center for Life Sciences Beijing 100084China College of Biological Sciences China Agricultural UniversityBeijing 100193China

Polytetrafluoroethylene(PTFE)has been widely used as a lubrication additive for reducing friction and wear;however,the hydrophobic nature of PTFE restricts its application in eco-friendly water-based lubrication *** this study,for the first time,we designed novel PTFE@silica Janus nanoparticles(JNs)to meet the requirement for additives in water-based lubricants,which have excellent dispersion stability in water attributed to the unique amphiphilic *** introducing the lubrication of the aqueous dispersion of the JNs with a concentration of 0.5 wt%,the coefficient of friction(COF)and wear volume were reduced by 63.8%and 94.2%,respectively,comparing to those with the lubrication of pure ***,the JNs suspension also exhibits better lubrication and wear-resistance performances comparing to commercial silica and PTFE *** excellent tribological behaviors of PTFE@silica JNs as nano-additives could be attributed to the synergetic effect of the two components,where the PTFE provided lubrication through the formed tribofilms on the friction pairs,and the rigid silica further enhanced the wear-resistance *** importantly,the unique structure of JNs makes it possible to use PTFE as an additive in water-lubrication *** study shed light on the design and application of novel JNs nanomaterials as additives to meet the requirements of future industrial applications.

关键词： Janus nanoparticles(JNs) polytetrafluoroethylene(PTFE) nano-additives friction lubrication