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Combining genome-wide association study and transcriptome analysis to identify molecular markers and genetic basis of population-asynchronous ovarian development in Coilia nasus

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Zoological Research 2024年第3期45卷 491-505页

作者： Yue Yu Shi-Ming Wan Cheng-You Huang Shuang-Meng Zhang Ai-Li Sun Jun-Qi Liu Shun-Yao Li Yong-Fu Zhu Shu-Xin Gu Ze-Xia Gao College of Fisheries Hubei Hongshan Laboratory/Key Lab of Freshwater Animal BreedingMinistry of Agriculture and Rural Affairs/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationHuazhong Agricultural UniversityWuhanHubei 430070China lab.ratory for marine Biology and biotechnology Qingdao Marine Science and Technology CenterQingdaoShandong 266237China Wuhan Hengyuxin Technology Breeding Professional Cooperative WuhanHubei 430117China Hubei Provincial Aquatic Science Research Institute WuhanHubei 430208China Zhenjiang Jiangzhiyuan Fishery Technology Co. Ltd.ZhenjiangJiangsu 212213China

Coilia nasus,a migratory fish species found in the middle and lower reaches of the Yangtze River and along offshore areas of China,possesses considerable aquacultural and economic ***,the species faces challenges due to significant variation in the gonadal development rate among females,resulting in inconsistent ovarian maturation times at the population level,an extended reproductive period,and limitations on fish growth rate due to ovarian *** the present study,we combined genome-wide association study(GWAS)and comparative transcriptome analysis to investigate the potential single nucleotide polymorphisms(SNPs)and candidate genes associated with population-asynchronous ovarian development in *** of the female population based on whole-genome resequencing yielded 2120695 high-quality SNPs,39 of which were suggestively associated with ovarian *** note,a significant SNP peak on LG21 containing 30 suggestively associated SNPs was identified,with cpne5a determined as the causal gene of the ***,single-marker and haplotype association analyses were performed on cpne5a,revealing four genetic markers(P0.9)significantly associated with the *** transcriptome analysis of precociously and normally maturing individuals screened out 29 and 426 overlapping differentially expressed genes in the brain and ovary,respectively,between individuals of different body *** the GWAS and transcriptome analysis results,this study identified genes and pathways related to hypothalamic-pituitary-gonadal axis hormone secretion,extracellular matrix,angiogenesis,and gap junctions involved in population-asynchronous ovarian *** insights gained from this study provide a basis for a deeper understanding of the molecular mechanisms underlying ovarian development in fish and may facilitate the genetic breeding of *** strains exhibiting population-synchronous ovarian

关键词： Coilia nasus GWAS Transcriptome Ovarian development SNP

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A growth-regulating factor 7(GRF7)-mediated gene regulatory network promotes leaf growth and expansion in sugarcane

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The Crop Journal 2024年第2期12卷 422-431页

作者： Qiaoyu Wang Yihan Li Dadong Lin Xiaoxi Feng Yongjun Wang Tianyou Wang Hongyan Ding Jisen Zhang State Key lab.for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key lab.for Saccharum Biology Guangxi UniversityNanning 530005GuangxiChina Center for Genomics and biotechnology/Fujian Provincial Key lab.ratory of Haixia Applied Plant Systems Biology/Key lab.ratory of Saccharum Biology and Genetic Breeding/National Engineering Research Center for Saccharum Fujian Agriculture and Forestry UniversityFuzhou 350002FujianChina

Knowledge of the function of growth-regulating factors(GRFs)in sugarcane(Saccharum officinarum and ***)growth and development could assist breeders in selecting desirable plant ***,limited information about GRFs is availab.e in Saccharum due to their *** this study,22 GRFs were identified in the two species and their conserved domains,gene structures,chromosome location,and synteny were ***7 expression varied among tissues and responded to diurnal ***7-YFP was localized preferentially in the nucleus and appears to act as a transcriptional ***7 positively regulated the size and length of rice leaves,possibly by regulating cell size and plant *** seven potential transcription factors binding to the SsGRF7 promoter in ***,four showed positive expression patterns,and two showed negative expression patterns relative to SsGRF7.

关键词： Expression analysis Growth-regulating factor Leaf development Sugarcane Transcription factors

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Two H3K36 methyltransferases differentially associate with transcriptional activity and enrichment of facultative heterochromatin in rice blast fungus

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aBIOTECH 2024年第1期5卷 1-16页

作者： Mengting Xu Ziyue Sun Huanbin Shi Jiangnan Yue Xiaohui Xiong Zhongling Wu Yanjun Kou Zeng Tao Ministry of Agriculture Key lab.ratory of Molecular Biology of Crop Pathogens and Insects Institute of BiotechnologyZhejiang UniversityHangzhou 310058China State Key lab.of Rice Biology and Breeding China National Rice Research InstituteHangzhou 310021China

Di-and tri-methylation of lysine 36 on histone H3(H3K36me2/3)is catalysed by histone methyltransferase Set2,which plays an essential role in transcriptional *** there is a single H3K36 methyltransferase in yeast and higher eukaryotes,two H3K36 methyltransferases,Ash1 and Set2,were present in many filamentous ***,their roles in H3K36 methylation and transcriptional regulation remained *** with methods of RNA-seq and ChIP-seq,we revealed that both Ash1 and Set2 are redundantly required for the full H3K36me2/3 activity in Magnaporthe oryzae,which causes the devastating worldwide rice blast ***1 and Set2 distinguish genomic H3K36me2/3-marked regions and are differentially associated with repressed and activated transcription,***,Ash1-catalysed H3K36me2 was co-localized with H3K27me3 at the chromatin,and Ash1 was required for the enrichment and transcriptional silencing of H3K27me3-occupied *** the different roles of Ash1 and Set2,in H3K36me2/3 enrichment and transcriptional regulation on the stress-responsive genes,they differentially respond to various stresses in ***,we reveal a novel mechanism by which two H3K36 methyltransferases catalyze H3K36me2/3 that differentially associate with transcriptional activities and contribute to enrichment of facultative heterochromatin in eukaryotes.

关键词： Ash1 Facultative heterochromatin H3K36me2/3 Magnaporthe oryzae Set2 Transcriptional regulation

A causal multiomics study discriminates the early immune features of Ad5-vectored Ebola vaccine recipients

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The Innovation 2024年第3期5卷 77-87页

作者： Zhe Zhang Wenjing Yang Zhengshan Chen Haoang Chi Shipo Wu Wanru Zheng Ruochun Jin Busen Wang Yudong Wang Nan Huo Jinlong Zhang Xiaohong Song Liyang Xu Jun Zhang Lihua Hou Wei Chen Institute of biotechnology Academy of Military Medical SciencesBeijing 100071China Department of Intelligent Data Science College of Computer Science and TechnologyNational University of Defense TechnologyChangsha 410073China Intelligent Game and Decision lab Academy of Military ScienceBeijing 100091China

The vaccine-induced innate immune response is essential for the generation of an antibody *** date,how Ad5-vectored vaccines are influenced by preexisting anti-Ad5 antibodies during activation of the early immune response remains ***,we investigated the specific alterations in GP1,2-specific IgG-related elements of the early immune response at the genetic,molecular,and cellular levels on days 0,1,3,and 7 after Ad5-EBOV *** a causal multiomics analysis,distinct early immune responses associated with GP1,2-specific IgG were observed in Ad5-EBOV recipients with a low level of preexisting anti-Ad5 *** study revealed the correlates of the Ad5-EBOV-induced IgG response and provided mechanistic evidence for overcoming preexisting Ad5 immunity during the administration of Ad5-vectored vaccines.

关键词： vaccine immunity alterations

Construction of a bivalent vaccine candidate against HAdV4/HAdV7 based on capsid-display strategy via Red-homologous recombination and counter-selection methodology

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Biosafety and Health 2024年第2期6卷 70-79页

作者： Peng Wang Yunting Shao Xichun Yang Wenning Zhang Jianguang Zhou Fang Huang Shuang Liu Jiping Zheng Chengjun Wu Shanhu Li Department of Cell Engineering Beijing Institute of BiotechnologyBeijing 100850China School of Basic Medical Sciences Faculty of MedicineDalian University of TechnologyDalian 116024China lab.of Microbiological Engineering School of Life and Health SciencesHainan UniversityHaikou 570228China

Human adenoviruses(HAdvs)are major respiratory ***,human adenovirus type 4(HAdV4)and human adenovirus type 7(HAdV7)are known for causing fever and pneumonia,with docu-mented cases of fatalities among the *** recent years,HAdV4/HAdv7 has been implicated in caus-ing substantial outbreaks,leading to increased morbidity in multiple *** HAdV4 and HAdV7 infections have been reported in North America,Asia,Europe,Africa,South America,Oceania,and the Middle *** fatalities occurred in North America(the United States)and Asia(China and Singapore).Engineered recombinant adenoviruses have played a crucial role as vaccine *** this study,we con-structed a recombinant adenovirus,Ad4ITRmut-Ad7E3,and evaluated it in vitro and in *** observed that the replication rate of Ad4ITRmut-Ad7E3 was lower than that of the RI-67 strain,indicating that the mutation of inverted terminal repeats(ITRs)weakened the replication ability of *** of BALB/c mice with the bivalent Ad4ITRmut-Ad7E3 vaccine strain,administered by intraperitoneal injection and oral gavage,resulted in the elicitation of neutralizing antibodies targeting HAdV4 and *** finding not only pro-vides a novel method and technique for the efficient construction of a polyvalent recombinant adenovirus vac-cine candidate against HAdV4 and HAdv7 but also against other prevalent adenovirus serotypes such as HAdV3,HAdV11,HAdV14,and HAdv55,from various regions.

关键词： Bivalent adenovirus vaccine Capsid-display strategy ITRs modification Hexon epitope replacement

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Platelet-based bioactive systems guided precision targeting and immune regulation for cancer therapy

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Nano Research 2024年第9期17卷 8269-8284页

作者： Xinyi Cai Long Qiu Zhenying Diao Lintao Cai Ting Yin Hong Pan Guangdong Key lab.ratory of Nanomedicine CAS-HK Joint Lab of BiomaterialsCAS Key Laboratory of Biomedical Imaging Science and SystemInstitute of Biomedicine and BiotechnologyShenzhen Institute of Advanced Technology(SIAT)Chinese Academy of SciencesShenzhen 518055China School of pharmacy Guangdong Medical UniversityDongguan 523808China Sino-Euro Center of Biomedicine and Health Shenzhen 518024China

The antitumor effects of conventional drug carriers are often attenuated and limited in application by biological barriers associated with tumor heterogeneity and resistance brought about by low tumor *** the rapid development of nanotechnology,naturally derived bioactive materials,and live cell carriers,a promising strategy emerges for targeting the tumor microenvironment(TME)for precision cancer *** unique injury-targeting properties of platelets can significantly extend functional activity,which cannot be achieved with conventional *** this review,three strategies based on platelet-engineered materials are systematically described,namely nanoparticles for platelet membrane camouflage,engineered activated platelets,and targeted-platelets ***-based nanomaterials can effectively coordinate local and distant tumor-host crosstalk with controlled active tumor site recognition and killing effects due to the presence of specific membrane proteins on the surface and the self-secretion of a large number of *** advances in platelets for effectively overcoming biological barriers and reducing immune resistance in cancer immunotherapy applications will be discussed in future clinical *** review provides an overview of recent research advances in platelet-based bioactive material-directed immunotherapy and chemotherapy to inform future antitumor combination therapies.

关键词： platelets bionic targeting immune modulation precision therapy deep penetration

Foeniculum vulgare *** lipopolysaccharide-induced microglia activation and ameliorates neuroinflammation-mediated behavioral deficits in mice

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Asian Pacific Journal of Tropical Biomedicine 2024年第1期14卷 28-39页

作者： Sushruta Koppula Ramesh Alluri Spandana Rajendra Kopalli College of Biomedical and Health Sciences Konkuk UniversityChungju-SiChungcheongbuk Do27478Republic of Korea Cognitive Science Research Initiative lab Department of PharmacologyVishnu Institute of Pharmaceutical Education and ResearchNarsapurTelangana502313India Department of Bioscience and biotechnology Sejong UniversityGwangjin-guSeoul 05006Republic of Korea

Objective:To investigate the effect of Foeniculum vulgare extract against lipopolysaccharide(LPS)-induced microglial activation in vitro as well as cognitive behavioral deficits in ***:LPS-activated BV-2 cell viability was measured using MTT assay and reactive oxygen species(ROS)was studied using DCF-DA *** antioxidative enzymes and pro-inflammatory mediators were analyzed using respective ELISA kits and Western *** in vivo testing,LPS(1 mg/kg,i.p.)was given daily for five days in male Swiss albino mice to produce chronic *** and behavioral tests were performed using open-field,passive avoidance,and rotarod experiments in LPS-induced ***:Foeniculum vulgare extract(25,50 and 100μg/mL)significantly attenuated the LPS-activated increase in nitric oxide(NO),ROS,cyclooxygenase-2,inducible NO synthase,IL-6,and TNF-alpha(P<0.05).Moreover,LPS-induced oxidative stress and reduced antioxidative enzyme levels were significantly improved by Foeniculum vulgare extract(P<0.05).The extract also regulated the NF-κB/MAPK signaling in BV-2 *** an in vivo study,Foeniculum vulgare extract(50,100,and 200 mg/kg)markedly mitigated the LPS-induced cognitive and locomotor impairments in *** fingerprinting analysis showed distinctive peaks with rutin,kaempferol-3-O-glucoside,and anethole as identifiable ***:Foeniculum vulgare extract can ameliorate LPS-stimulated neuroinflammatory responses in BV-2 microglial cells and improve cognitive and locomotor performance in LPS-administered mice.

关键词： Foeniculum vulgare Microglia Lipopolysaccharide Antioxidant Neuroinflammation MAPK signaling Cognition

Large-Scale CRISPR Screen of LDLR Pathogenic Variants

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Research 2024年第2期2023卷 213-225页

作者： Mengjing Li Lerong Ma Yiwu Chen Jianing Li Yanbing Wang Wenni You Hongming Yuan Xiaochun Tang Hongsheng Ouyang Daxin Pang Key lab.for Zoonoses Research Ministry of EducationAnimal Genome Editing Technology Innovation CenterCollege of Animal SciencesJilin UniversityChangchunJilin Province 130062China The Institute of Translational Medicine Tianjin Union Medical Center of Nankai UniversityTianjin 300071China Chongqing ResearchInstitute Jilin UniversityChongqing 401123China Chongqing Jitang biotechnology Research Institute Co.Ltd. ChongqingChina

Familial hypercholesterolemia(FH)is a frequently occurring genetic disorder that is linked to early-onset cardiovascular *** left untreated,patients with this condition can develop severe cardiovascular ***,many patients remain undiagnosed,and even when diagnosed,the treatment is often not *** mutations in the LDLR gene are the primary cause of FH,predicting whether novel variants are pathogenic is not a straightforward *** the functionality of LDLR variants is crucial in uncovering the genetic basis of *** study utilized CRISPR/Cas9 cytosine base editors in pooled screens to establish a novel approach for functionally assessing tens of thousands of LDLR variants on a large scale.A total of more than 100 single guide RNAs(sgRNAs)targeting LDLR pathogenic mutations were successfully screened with relatively high *** of these,5 sgRNAs were further subjected to functional verification studies,including 1 in the promoter,1 in the antisense RNA,1 in the exon,and 2 in the *** for the variant caused by the sgRNA located at intron 16,the functionalities of the other LDLR variants were all *** high similarity of LDLR intron sequences may lead to some false ***,these results confirm the reliability of the large-scale screening strategy for functional analysis of LDLR variants,and the screened candidate pathogenic mutations could be used as an auxiliary means of clinical gene detection to prevent FH-induced heart disease.

关键词： LDLR Screen straight

Molecular mechanism of exopolysaccharide biosynthesis regulated by wze and wzd genes on the immunomodulatory effects of probiotic Lacticaseibacillus paracasei S-NB

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Food Science and Human Wellness 2024年

作者： Luyao Xiao Qian Yang Changliang Zhang Kai Ma Xiaogan Zhao Xin Rui Wei Li Jiangsu Biodep biotechnology Co. Ltd. Jiangsu New-Bio biotechnology Co. Ltd. Sanya Institute of Nanjing Agricultural University College of Food Science and Technology Nanjing Agricultural University

The surface macromolecules of probiotic bacteria play crucial roles in modulating immune responses in the host. Exopolysaccharide (EPS) from lactic acid bacteria (lab. have been widely reported to exhibit immunomodulatory activity. In this study， the EPS biosynthesis gene cluster of Lacticaseibacillus paracasei S-NB was analyzed and a deletion mutant S-NB△7576 (two genes S-NB＿2175/wze and S-NB＿2176/wzd were responsible for the chain length determination and export of EPS) was successfully constructed， resulting a 40.02% decrease in the production of EPS. The deletion of wze and wzd had little effect on the monosaccharide composition and major groups of the two EPS fractions (BEPS1 and BEPS2). Both BEPS1 and BEPS2 could inhibit the transcriptional level of tumor necrosis factor-α (TNF-α)， interleukin-1β (IL-1β)， inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) mRNA in RAW 264.7 cells induced by lipopolysaccharide (LPS)， and enhance host immune tolerance via suppressing NF-κB and MAPK signaling. Notably， the S-NB△7576 mutant supplied with the BEPS1/BEPS2 exhibited more significant inhibition of cytokines production and the phosphorylation of p65 and c-Jun N-terminal kinase (JNK) in LPS-stimulated cells compared with the S-NB△7576 mutant alone. Our study provided the immunomodulatory effect of BEPS1 and BEPS2 from L. paracasei S-NB， in which the wze and wzd genes associated with EPS biosynthesis may play an important role.

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