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Journal of Genetics and Genomics 2024年第9期51卷 947-956页

作者： Zhan Liu Hui Zeng Huimin Xiang Shanjun Deng Xionglei He state key laboratory of biocontrol School of Life SciencesSun Yat-Sen UniversityGuangzhouGuangdong 510275China

Unraveling the lineage relationships of all descendants from a zygote is fundamental to advancing our understanding of developmental and stem cell ***,existing cell barcoding technologies in zebrafish lack the resolution to capture the majority of cell divisions during embryogenesis.A recently developed method,a substitution mutation-aided lineage-tracing system(SMALT),successfully reconstructed high-resolution cell phylogenetic trees for Drosophila ***,we implement the SMALT system in zebrafish,recording a median of 14 substitution mutations on a one-kilobase-pair barcoding sequence for one-day post-fertilization *** this system,we reconstruct four cell lineage trees for zebrafish fin cells,encompassing both original and regenerated *** tree consists of hundreds of internal nodes with a median bootstrap support of 99%.Analysis of the obtained cell lineage trees reveals that regenerated fin cells mainly originate from cells in the same part of the *** multiple times sampling germ cells from the same individual,we show the stability of the germ cell pool and the early separation of germ cell and somatic cell *** system offers the potential for reconstructing high-quality cell phylogenies across diverse tissues,providing valuable insights into development and disease in zebrafish.

关键词： Lineage tracing Cellular barcoding Zebrafishcell phylogeny Fin regeneration Germcell lineage

A dual-function selection system enables positive selection of multigene CRISPR mutants and negative selection of Cas9-free progeny in Arabidopsis

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aBIOTECH 2024年第2期5卷 140-150页

作者： Feng-Zhu Wang Ying Bao Zhenxiang Li Xiangyu Xiong Jian-Feng Li state key laboratory of biocontrol Guangdong Provincial Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat-sen UniversityGuangzhou 510275China

The CRISPR/Cas9 technology revolutionizes targeted gene knockout in diverse organisms including ***,screening edited alleles,particularly those with multiplex editing,from herbicide-or antibiotic-resistant transgenic plants and segregating out the Cas9 transgene represent two laborious *** solutions to facilitate these processes rely on different selection ***,by taking advantage of the opposite functions of a D-amino acid oxidase(DAO)in detoxifying D-serine and in metabolizing non-toxic D-valine to a cytotoxic product,we develop a DAO-based selection system that simultaneously enables the enrichment of multigene edited alleles and elimination of Cas9-containing progeny in Arabidopsis *** five DAOs tested in Escherichia coli,the one encoded by Trigonopsis variabilis(TvDAO)could confer slightly stronger D-serine resistance than other *** expression of TvDAO in Arabidopsis allowed a clear distinction between transgenic and nontransgenic plants in both D-serine-conditioned positive selection and D-valine-conditioned negative *** a proof of concept,we combined CRISPR-induced single-strand annealing repair of a dead TvDAO with D-serine-based positive selection to help identify transgenic plants with multiplex editing,where D-serine-resistant plants exhibited considerably higher co-editing frequencies at three endogenous target genes than those selected by ***,D-valine-based negative selection successfully removed Cas9 and TvDAO transgenes from the survival offspring carrying inherited ***,this work provides a novel strategy to ease CRISPR mutant identification and Cas9 transgene elimination using a single selection marker,which promises more efficient and simplified multiplex CRISPR editing in plants.

关键词： CRISPR Genome editing D-amino acid oxidase Cas9-free Selection marker

CRISPR/Cas9-mediated NlInR2 mutants:Analyses of residual mRNA and truncated proteins

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Journal of Integrative Agriculture 2024年第6期23卷 2006-2017页

作者： Jun Lü Jingxiang Chen Yutao Hu Lin Chen Shihui Li Yibing Zhang Wenqing Zhang state key laboratory of biocontrol/school of life sciences Sun Yat-sen UniversityGuangzhou 510275China Development of Food Science and Engineering Moutai InstituteRenhuai 564507China

CRISPR/Cas9 technology is a powerful genome manipulation tool in ***,little is known about whether mRNA and protein of a target gene are completely cleared in homozygous *** study generated homozygous mutants of the insulin receptor gene 2(NlInR2)in the brown planthopper(Nilaparvata lugens)using CRISPR/Cas9 genome *** frameshift mutants,E5_D17 and E6_I7,differentiated towards long wings,but there were differences in wing morphology,with E5_D17 showing wing *** investigations revealed the presence of residual expression of NlInR2 mRNA in both mutants,as well as the occurrence of spliceosomes featuring exon skipping splicing in E5_***,the E5_D17 exhibited the detection of N-terminally truncated NlInR2 *** interference experiments indicated that the knockdown of NlInR2 expression in the E5_D17 mutant line increased the proportion of wing deformities from 11.1 to 65.6%,suggesting that the residual NlInR2 mRNA of the E5_D17 mutant might have retained some genetic *** results imply that systematic characterization of residual protein expression or function in CRISPR/Cas9-generated mutant lines is necessary for phenotypic interpretation.

关键词： CRISPR/Cas9 Nilaparvata lugens residual mRNA skipping exon truncated protein

Implications of mosquito metabolism on vector competence

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Insect Science 2024年第3期31卷 674-682页

作者： Li Gao Wenxu Yang Jingwen Wang state key laboratory of Genetic Engineering School of Life SciencesFudan UniversityShanghaiChina Ministry of Education key laboratory of Contemporary Anthropology School of Life SciencesFudan UniversityShanghaiChina

Mosquito-borne diseases(MBDs)annually kill nearly half a million *** to the lack of effective vaccines and drugs on most MBDs,disease prevention relies primarily on controlling *** huge efforts having been put into mosquito control,eco-friendly and sustainable mosquito-control strategies are still lacking and urgently *** mosquito-transmitted pathogens have lost the capacity of de novo nutrition biosynthesis,and rely on their vertebrate and invertebrate hosts for sustenance during the long-term obligate parasitism ***,a better understanding of the metabolic interactions between mosquitoes and pathogens will contribute to the discovery of novel metabolic targets or regulators that lead to reduced mosquito populations or vector *** review summarizes the current knowledge about the effects of mosquito metabolism on the transmission of multiple *** also discuss that research in this area remains to be explored to develop multiple biological prevention and control strategies for MBDs.

关键词： flaviviruses mosquito metabolism Plasmodium vector competence

Genomic analysis of Nypa fruticans elucidates its intertidal adaptations and early palm evolution

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Journal of Integrative Plant Biology 2024年第4期66卷 824-843页

作者： Weihong Wu Xiao Feng Nan Wang Shao Shao Min Liu Fa Si Linhao Chen Chuanfeng Jin Shaohua Xu Zixiao Guo Cairong Zhong Suhua Shi Ziwen He state key laboratory of biocontrol and Guangdong Provincial key laboratory of Plant Resources School of Life SciencesSun Yat-sen UniversityGuangzhou 510275China Greater Bay Area Institute of Precision Medicine School of Life SciencesFudan UniversityGuangzhou 511462China Hainan Academy of Forestry(Hainan Academy of Mangrove) Haikou 571100China

Nypa fruticans(Wurmb),a mangrove palm species with origins dating back to the Late Cretaceous period,is a unique species for investigating long-term adaptation strategies to intertidal environments and the early evolution of ***,we present a chromosome-level genome sequence and assembly for *** integrated the genomes of *** and other palm family members for a comparative genomic analysis,which confirmed that the common ancestor of all palms experienced a whole-genome duplication event around 89 million years ago,shaping the distinctive characteristics observed in this *** also inferred a low mutation rate for the *** genome,which underwent strong purifying selection and evolved slowly,thus contributing to its stability over a long evolutionary ***,ancient duplicates were preferentially retained,with critical genes having experienced positive selection,enhancing waterlogging tolerance in ***,we discovered that the pseudogenization of Early Methionine-labelled 1(EM1)and EM6 in *** underly its crypto-vivipary characteristics,reflecting its intertidal *** study provides valuable genomic insights into the evolutionary history,genome stability,and adaptive evolution of the mangrove *** results also shed light on the long-term adaptation of this species and contribute to our understanding of the evolutionary dynamics in the palm family.

关键词： crypto-vivipary genome stability long-term adaptation mangrove Nypa fruticans palm

A perspective on greenhouse gas emission studies integrating arbuscular mycorrhiza

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Pedosphere 2024年第3期34卷 525-529页

作者： Stavros D.VERESOGLOU Junjiang CHEN state key laboratory of biocontrol School of EcologySun Yat-sen UniversityShenzhen 518107(China)

Climate change is a global *** is only possible to pace down global change through addressing the triggers of it,greenhouse gas *** commendable progress,we think that there is plenty of room to further make the studies addressing global change realistic,through integrating into them biotic *** make a case for this statement through a bibliometrics analysis on agricultural studies exploring greenhouse gas emissions that consider arbuscular *** show that even though mycorrhizal studies account right now for a small fraction of the agricultural literature,they get cited more *** further demonstrate that mycorrhizal studies are typically more descriptive in their nature,which we support through comparing the keywords they *** subsequently use the opportunity to identify shortcomings and opportunities to further integrate mycorrhiza into agricultural studies assaying greenhouse gas *** finally make a call to better integrate arbuscular mycorrhiza into global change studies.

关键词： bibliometric analysis biochemical models global change biology Glomeromycota sustainable agricultural intensification

A twist in the tale:global insights into archaeal box C/D RNA-guided 2′-O-methylation

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Science China(life sciences) 2024年第4期67卷 849-850页

作者： Bin Li Jianhua Yang MOE key laboratory of Gene Function and Regulation State Key Laboratory of BiocontrolSchool of Life SciencesSun Yat-sen UniversityGuangzhou 510275China The Fifth Affiliated Hospital Sun Yat-sen UniversityZhuhai 519000China

The 2′-O-methylation of RNA stands as a dynamic and multifaceted modification,wielding significant influence over the regulation of RNA function,stability,and interactions within the cellular context(Sun et al.,2023)... 详细信息

关键词： twist insight

Tributyltin causes generational neurodevelopmental toxicity and the protective effect of folic acid in zebrafish

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Journal of Environmental sciences 2024年第3期137卷 615-625页

作者： Haoxing Cai Naying Zheng Chen Tang Yuxuan Zhang Zhenghong Zuo Chengyong He state key laboratory of Cellular Stress Biology School of Life SciencesFaculty of Medicine and Life SciencesXiang’an Hospital of Xiamen UniversityXiamen UniversityXiamen 361005China

Tributyltin(TBT),a common organotin environmental pollutant,may pose a threat to human development during critical early-life *** aimed to assess the neurodevelopmental intergenerational toxicity of early-life exposure to TBT and the protective effect of DNA methyl donor folic acid(FA).Specifically,after early-life exposure(1–21 days postfertilization,dpf)to TBT(0,1,10 and 100 ng/L),zebrafish(Danio rerio)were cultured in clean medium until sexual *** exposed females were mated with unexposed males to produce embryos(F1).The F1 generation were cultured(4–120 hours post-fertilization,hpf)with and without 1 mmol/L *** neurotoxic effects of early-life TBT exposure for zebrafish and their offspring(F1)were significantly enhanced anxiety and reduced aggression,decreased gene expression of DNA methyltransferase in the brain and increased serotonin levels in the ***,the intergenerational neurodevelopmental toxicity,as manifested in the F1 generation,was attenuated by FA *** summary,early-life TBT exposure led to intergenerational neurodevelopmental deficits in zebrafish,and DNA methyl donors had a protective effect on F1 neurodevelopment,which can inform the prevention and treatment of intergenerational neurotoxicity due to organotin pollutants.

关键词： Tributyltin Neurodevelopment Intergeneration DNA methylation Folic acid Zebrafish

Biosensor-assisted CRISPRi high-throughput screening to identify genetic targets in Zymomonas mobilis for high d-lactate production

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Synthetic and Systems Biotechnology 2024年第2期9卷 242-249页

作者： Qiqun Peng Weiwei Bao Binan Geng Shihui Yang state key laboratory of Biocatalysis and Enzyme Engineering and School of Life SciencesHubei UniversityWuhan430062China

Lactate is an important monomer for the synthesis of poly-lactate(PLA),which is a substitute for the petrochemical *** achieve the goal of high lactate titer,rate,and yield for commercial production,efficient lactate production pathway is needed as well as genetic targets that affect high lactate production and *** this study,an LldR-based d-lactate biosensor with a broad dynamic range was first applied into Zymomonas mobilis to select mutant strains with strong GFP fluorescence,which could be the mutant strains with increased d-lactate ***,LldR-based d-lactate biosensor was combined with a genome-wide CRISPR interference(CRISPRi)library targeting the entire genome to generate thousands of mutants with gRNA targeting different genetic targets across the whole ***,two mutant libraries were selected containing 105 and 104 mutants with different interference sites from two rounds of fluorescence-activated cell sorting(FACS),*** genetic targets of ZMO1323 and ZMO1530 were characterized and confirmed to be associated with the increased d-lactate production,further knockout of ZMO1323 and ZMO1530 resulted in a 15%and 21%increase of d-lactate production,*** work thus not only established a high-throughput approach that combines genome-scale CRISPRi and biosensor-assisted screening to identify genetic targets associated with d-lactate production in ***,but also provided a feasible high-throughput screening approach for rapid identification of genetic targets associated with strain performance for other industrial microorganisms.

关键词： D-lactate Biosensor LldR Genome-wide CRISPRi FACS Zymomonas mobilis

Metabolic engineering of an industrial bacterium Zymomonas mobilis for anaerobic l-serine production

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Synthetic and Systems Biotechnology 2024年第2期9卷 349-358页

作者： Zhen Wang Xia Wang Xiongying Yan Haixia Yi Shuche He Haoyu Zhang Xinli Zhou Qiaoning He Shihui Yang state key laboratory of Biocatalysis and Enzyme Engineering and school of life sciences Hubei UniversityWuhan430062China

Due to the complicated metabolic and regulatory networks of l-serine biosynthesis and degradation,microbial cell factories for l-serine production using non-model microorganisms have not been *** this study,a combination of synthetic biology and process optimization were applied in an ethanologenic bacterium Zymomonas mobilis for l-serine *** blocking the degradation pathway while introducing an exporter EceamA from ***,l-serine titer in recombinant *** was increased from 15.30 mg/L to 62.67 mg/*** was further increased to 260.33 mg/L after enhancing the l-serine biosynthesis ***,536.70 mg/L l-serine was achieved by removing feedback inhibition with a SerA mutant,and an elevated titer of 687.67 mg/L was further obtained through increasing serB copies while enhancing the ***,855.66 mg/L l-serine can be accumulated with the supplementation of the glutamate *** work thus not only constructed an l-serine producer to help understand the bottlenecks limiting l-serine production in *** for further improvement,but also provides guidance on engineering non-model microbes to produce biochemicals with complicated pathways such as amino acids or terpenoids.

关键词： Zymomonas mobilis Metabolic engineering l-serine Feedback inhibition Anaerobic fermentation