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Innovations in functional genomics and molecular breeding of pea:exploring advances and opportunities

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aBIOTECH 2024年第1期5卷 71-93页

作者： Baizhi Chen Yan Shi Yuchen Sun Lu Lu Luyao Wang Zijian Liu Shifeng Cheng Agricultural genomics institute at Shenzhen(AGIS) Chinese Academy of Agricultural Sciences(CAAS)ShenzhenChina

The garden pea(Pisum sativum L.)is a significant cool-season legume,serving as crucial food sources,animal feed,and industrial raw *** advancement of functional genomics over the past two decades has provided substantial theoretical foundations and progress to pea ***,the release of the pea reference genome has enhanced our understanding of plant architecture,symbiotic nitrogen fixation(SNF),flowering time,floral organ development,seed development,and stress ***,a considerable gap remains between pea functional genomics and molecular *** review summarizes the current advancements in pea functional genomics and breeding while highlighting the future challenges in pea molecular breeding.

关键词： Pea Genome study Agronomic traits Breeding

Plant genomic resources at National genomics Data Center:assisting in data-driven breeding applications

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aBIOTECH 2024年第1期5卷 94-106页

作者： Dongmei Tian Tianyi Xu Hailong Kang Hong Luo Yanqing Wang Meili Chen Rujiao Li Lina Ma Zhonghuang Wang Lili Hao Bixia Tang Dong Zou Jingfa Xiao Wenming Zhao Yiming Bao Zhang Zhang Shuhui Song National genomics Data Center Beijing Institute of GenomicsChinese Academy of Sciences&China National Center for BioinformationBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences&China National Center for BioinformationBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Genomic data serve as an invaluable resource for unraveling the intricacies of the higher plant systems,including the constituent elements within and among *** various efforts in genomic data archiving,integrative analysis and value-added curation,the National genomics Data Center(NGDC),which is a part of the China National Center for Bioinformation(CNCB),has successfully established and currently maintains a vast amount of database *** dedicated initiative of the NGDC facilitates a data-rich ecosystem that greatly strengthens and supports genomic research ***,we present a comprehensive overview of central repositories dedicated to archiving,presenting,and sharing plant omics data,introduce knowledgebases focused on variants or gene-based functional insights,highlight species-specific multiple omics database resources,and briefly review the online application *** intend that this review can be used as a guide map for plant researchers wishing to select effective data resources from the NGDC for their specific areas of study.

关键词： Plant-omics data Data repositories Data integration Knowledgebase Plant genomics

Making topological protein links using enzymatic reactions

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National Science Review 2024年第3期11卷 50-51页

作者： Roger Castells-Graells Todd O.Yeates Department of Chemistry and Biochemistry University of California UCLA-DOE institute for genomics and Proteomics

Proteins are exceedingly complex molecules though, at their heart, they are essentially linear polymers. Pull at their ends and one obtains an extended backbone. While that is true in most cases, some natural proteins... 详细信息

关键词： DESIGN

Exposure to sublethal concentration of flupyradifurone alters sexual behavior and cuticular hydrocarbon profile in Heriades truncorum,an oligolectic solitary bee

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Insect Science 2024年第3期31卷 859-869页

作者： Samuel Boff Manfred Ayasse institute of Evolutionary Ecology and Conservation genomics Ulm UniversityUlmGermany

The aboveground oligolectic bee,Heriades truncorum,is a particularly good model for studying the impact of pesticides on sexual communication,since some aspects of its mating behavior have previously been *** have tested(1)the interference of the pesticide flupyradifurone on male precopulatory behavior and male mating partner preferences,(2)the way that the pesticide interferes in male quality assessment by the female,and(3)the effects of the pesticide on the chemical compounds in the female *** exposed bees of both sexes to a sublethal concentration of *** behaviors were registered in a mating arena with two females(one unexposed and one exposed)and one male(either unexposed or exposed).Unexposed males were quicker to attempt to *** also impacted precopulatory behavior and male quality assessment by *** approached unexposed females more quickly than insecticideexposed *** exposed to insecticide produced lower amounts of some cuticular hydrocarbons(sex pheromone candidates)and appeared less choosy than unexposed *** findings suggest that insecticide exposure affects sexual communication,playing a role both in male preference and in male quality assessment by the female.

关键词： courtship display female choice flupyradifurone male partner preference sex communication sublethal effects

Odorant receptor orthologues from moths display conserved responses to cis-jasmone

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Insect Science 2024年第4期31卷 1107-1120页

作者： Xiao-Qing Hou Zhongqiang Jia Dan-Dan Zhang Guirong Wang Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureSynthetic Biology Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong ProvinceChina State Key Laboratory for biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina Department of biology Lund UniversityLundSweden

In insects,the odorant receptor(OR)multigene family evolves by the birth-and-death evolutionary model,according to which the OR repertoire of each species has undergone specific gene gains and losses depending on their chemical environment,resulting in taxon-specific OR lineage radiations with different sizes in the phylogenetic *** the general divergence in the gene family across different insect orders,the ORs in moths seem to be genetically conserved across species,clustered into 23 major clades containing multiple orthologous groups with single-copy gene from each *** hypothesized that ORs in these orthologous groups are tuned to ecologically important compounds and functionally ***-Jasmone is one of the compounds that not only primes the plant defense of neighboring receiver plants,but also functions as a behavior regulator to various *** test our hypothesis,using Xenopus oocyte recordings,we functionally assayed the orthologues of BmorOR56,which has been characterized as a specific receptor for *** results showed highly conserved response specificity of the BmorOR56 orthologues,with all receptors within this group exclusively responding to *** is supported by the dN/dS analysis,showing that strong purifying selection is acting on this ***,molecular docking showed that the ligand binding pockets of BmorOR56 orthologues to cis-jasmone are *** together,our results suggest the high conservation of OR for ecologically important compounds across Heterocera.

关键词： cis-jasmone evolutionary conservation functional characterization molec-ular docking moths purifying selection

Applications of genetic code expansion technology in eukaryotes

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Protein & Cell 2024年第5期15卷 331-363页

作者： Qiao-ru Guo Yu J.Cao State Key Laboratory of Chemical Oncogenomic Guangdong Provincial Key Laboratory of Chemical GenomicsPeking University Shenzhen Graduate SchoolShenzhen 518055China institute of Chemical biology Shenzhen Bay LaboratoryShenzhen 518132China

Unnatural amino acids(UAAs)have gained significant attention in protein engineering and drug development owing to their ability to introduce new chemical functionalities to *** eukaryotes,genetic code expansion(GCE)enables the incorporation of UAAs and facilitates posttranscriptional modification(PTM),which is not feasible in prokaryotic *** is also a powerful tool for cell or animal imaging,the monitoring of protein interactions in target cells,drug development,and switch ***,there is keen interest in utilizing GCE in eukaryotic *** review provides an overview of the application of GCE in eukaryotic systems and discusses current challenges that need to be addressed.

关键词： genetic code expansion unnatural amino acid eukaryotes basic research therapeutic applications

Identification of druggable host dependency factors shared by multiple SARS-CoV-2 variants of concern

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Journal of Molecular Cell biology 2024年第3期16卷 9-23页

作者： Ilaria Frasson Linda Diamante Manuela Zangrossi Elena Carbognin Anna Dalla Pietà Alessandro Penna Antonio Rosato Ranieri Verin Filippo Torrigiani Cristiano Salata Marìa Paula Dizanzo Lorenzo Vaccaro Davide Cacchiarelli Sara N.Richter Marco Montagner Graziano Martello Department of Molecular Medicine University of PaduaPadua 35121Italy Department of biology Armenise/Harvard Pluripotent Stem Cell Biology LaboratoryUniversity of PaduaPadua 35131Italy Department of Surgery Oncology and GastroenterologyUniversity of PaduaPadua 35128Italy Veneto institute of Oncology IOV-IRCCS Padua 35128Italy Department of Comparative Biomedicine and Food Science University of PaduaPadua 35020Italy Telethon institute of Genetics and Medicine(TIGEM) Armenise/Harvard Laboratory of Integrative GenomicsPozzuoli 80078Italy Department of Translational Medicine University of Naples Federico IINaples 80138Italy School for Advanced Studies Genomics and Experimental Medicine ProgramUniversity of Naples Federico IINaples 80138Italy Microbiology and Virology Unit Padua University HospitalPadua 35128Italy

The high mutation rate of SARS-CoV-2 leads to the emergence of multiple variants,some of which are resistant to vaccines and drugs targeting viral *** host dependency factors,*** proteins required for viral replication,would help prevent the development of ***,it remains unclear whether different SARS-CoV-2 variants induce conserved cellular responses and exploit the same core host *** this end,we compared three variants of concern and found that the host transcriptional response was conserved,differing only in kinetics and *** regularly interspaced short palindromic repeats screening identified host genes required for each variant during *** of the genes were shared by multiple *** validated our hits with small molecules and repurposed the US Food and Drug Administration-approved *** the drugs were highly active against all the tested variants,including new variants that emerged during the study(Delta and Omicron).Mechanistically,we identified reactive oxygen species production as a key step in early viral *** such as N-acetyl cysteine(NAC)were effective against all the variants in both human lung cells and a humanized mouse *** study supports the use of available antioxidant drugs,such as NAC,as a general and effective anti-COVID-19 approach.

关键词： SARS-CoV-2 variants of concern host dependency factors antivirals N-acetyl cysteine

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

Insufficient TRPM5 Mediates Lipotoxicity-induced Pancreaticβ-cell Dysfunction

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Current Medical Science 2024年第2期44卷 346-354页

作者： Kai-yuan WANG Shi-mei WU Zheng-jian YAO Yun-xia ZHU Xiao HAN Key Laboratory of Human Functional genomics of Jiangsu Province Department of Biochemistry and Molecular BiologyNanjing Medical UniversityNanjing 211166China

Objective:While the reduction of transient receptor potential channel subfamily M member 5(TRPM5)has been reported in islet cells from type 2 diabetic(T2D)mouse models,its role in lipotoxicity-induced pancreaticβ-cell dysfunction remains *** study aims to study its ***:Pancreas slices were prepared from mice subjected to a high-fat-diet(HFD)at different time points,and TRPM5 expression in the pancreaticβcells was examined using immunofluorescence ***-stimulated insulin secretion(GSIS)defects caused by lipotoxicity were mimicked by saturated fatty acid palmitate(Palm).Primary mouse islets and mouse insulinoma MIN6 cells were treated with Palm,and the TRPM5 expression was detected using qRT-PCR and Western ***-induced GSIS defects were measured following siRNA-based Trpm5 *** detrimental effects of Palm on primary mouse islets were also assessed after overexpressing Trpm5 via an adenovirus-derived Trpm5(Ad-Trpm5).Results:HFD feeding decreased the mRNA levels and protein expression of TRPM5 in mouse pancreatic *** reduced TRPM5 protein expression in a time-and dose-dependent manner in MIN6 *** also inhibited TRPM5 expression in primary mouse *** of Trpm5 inhibited insulin secretion upon high glucose stimulation but had little effect on insulin *** of Trpm5 reversed Palm-induced GSIS defects and the production of functional maturation molecules unique toβ***:Our findings suggest that lipotoxicity inhibits TRPM5 expression in pancreaticβcells both in vivo and in vitro and,in turn,drivesβ-cell dysfunction.

关键词： type 2 diabetes β-cell dysfunction lipotoxicity TRPM5