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Composition,function,and timing:exploring the early‑life gut microbiota in piglets for probiotic interventions

Journal of Animal Science and Biotechnology 2024年第2期15卷 659-678页

作者： Jianping Quan Cineng Xu Donglin Ruan Yong Ye Yibin Qiu Jie Wu Shenping Zhou Menghao Luan Xiang Zhao Yue Chen Danyang Lin Ying Sun Jifei Yang Enqin Zheng Gengyuan Cai Zhenfang Wu Jie Yang College of Animal Science and National Engineering Research Center for Breeding Swine Industry South China Agricultural UniversityGuangzhouGuangdongPeople’s Republic of China guangdong Provincial Key laboratory of Agro‑Animal Genomics and Molecular Breeding South China Agricultural UniversityGuangzhouGuangdongChina yunfu subcenter of guangdong laboratory for lingnan modern agriculture YunfuGuangdongChina National Engineering Research Center for Breeding Swine Industry Wens Foodstuff Group Co.Ltd.YunfuGuangdongPeople’s Republic of China

Background The establishment of a robust gut microbiota in piglets during their early developmental stage holds the potential for long-term advantageous ***,the optimal timeframe for introducing probiotics to achieve this outcome remains *** In the context of this investigation,we conducted a longitudinal assessment of the fecal microbiota of 63 piglets at three distinct pre-weaning time ***,we gathered vaginal and fecal samples from 23 *** 16S rRNA gene and metagenomic sequencing methodologies,we conducted a comprehensive analysis of the fluctuation patterns in microbial composition,functional capacity,interaction networks,and colonization resistance within the gut microbiota of *** the piglets progressed in age,discernible modifications in intestinal microbial diversity,composition,and function were observed.A source-tracking analysis unveiled the pivotal role of fecal and vaginal microbiota derived from sows in populating the gut microbiota of neonatal *** D21,the microbial interaction network displayed a more concise and efficient configuration,accompanied by enhanced colonization resistance relative to the other two time ***,we identified three strains of Ruminococcus *** D10 as potential candidates for improving piglets’weight gain during the weaning *** The findings of this study propose that D10 represents the most opportune juncture for the introduction of external probiotic interventions during the early stages of piglet *** investigation augments our comprehension of the microbiota dynamics in early-life of piglets and offers valuable insights for guiding forthcoming probiotic interventions.

关键词： Colonization resistance Intestinal microbiota Piglet Weaning Weight gain

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Dynamic intrauterine crosstalk promotes porcine embryo implantation during early pregnancy

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Science China(Life Sciences) 2024年第8期67卷 1676-1696页

作者： Xupeng Zang Shengchen Gu Wenjing Wang Junsong Shi Jianyu Gan Qun Hu Chen Zhou Yue Ding Yanjuan He Lei Jiang Ting Gu Zheng Xu Sixiu Huang Huaqiang Yang Fanming Meng Zicong Li Gengyuan Cai Linjun Hong Zhenfang Wu State Key laboratory of Swine and Poultry Breeding Industry National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou 510642China guangdong Provincial Key laboratory of Agro-Animal Genomics and Molecular Breeding South China Agricultural UniversityGuangzhou 510642China yunfu subcenter of guangdong laboratory for lingnan modern agriculture Yunfu 527300China guangdong Key laboratory of Animal Breeding and Nutrition Institute of Animal ScienceGuangdong Academy of Agricultural SciencesGuangzhou 510640China Key laboratory of South China modern Biological Seed Industry Ministry of Agriculture and Rural AffairsGuangzhou 510520China

Dynamic crosstalk between the embryo and mother is crucial during ***,we comprehensively profile the single-cell transcriptome of pig peri-implantation embryos and corresponding maternal endometrium,identifying 4 different lineages in embryos and 13 cell types in the ***-specific gene expression characterizes 4 distinct trophectoderm subpopulations,showing development from undifferentiated trophectoderm to polar and mural *** expression of genes in different types of endometrial cells illustrates their molecular response to embryos during ***,we developed a novel tool,ExtraCellTalk,generating an overall dynamic map of maternal-foetal crosstalk using uterine luminal proteins as *** cross-species comparisons,we identified a conserved RBP4/STRA6 pathway in which embryonic-derived RBP4 could target the STRA6 receptor on stromal cells to regulate the interaction with other endometrial *** results provide insight into the maternal-foetal crosstalk during embryo implantation and represent a valuable resource for further studies to improve embryo implantation.

关键词： endometrial remodeling ExtraCellTalk implantation maternal-foetal crosstalk trophoblast

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Porcine enteric alphacoronavirus infection increases lipid droplet accumulation to facilitate the virus replication

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Journal of Integrative agriculture 2024年第3期23卷 988-1005页

作者： Qi Gao Yongzhi Feng Ting Gong Dongdong Wu Xiaoyu Zheng Yizhuo Luo Yunlong Yang Zebu Song Lang Gong Guihong Zhang guangdong Provincial Key laboratory of Zoonosis Prevention and Control College of Veterinary MedicineSouth China Agricultural UniversityGuangzhou 510642China Maoming Branch Guangdong Laboratory for Lingnan Modern AgricultureMaoming 525000China Key laboratory of Animal Vaccine Development Ministry of Agriculture and Rural AffairsGuangzhou 510000China guangdong laboratory for lingnan modern agriculture Guangzhou 510642China

Coronaviruses are widely transmissible between humans and animals, causing diseases of varying severity. Porcine enteric alphacoronavirus(PEAV) is a newly-discovered pathogenic porcine enteric coronavirus in recent years, which causes watery diarrhea in newborn piglets. The host inflammatory responses to PEAV and its metabolic regulation mechanisms remain unclear, and no antiviral studies have been reported. Therefore, we investigated the pathogenic mechanism and antiviral drugs of PEAV. The transcriptomic analysis of PEAV-infected host cells revealed that PEAV could upregulate lipid metabolism pathways. In lipid metabolism, steady-state energy processes, which can be mediated by lipid droplets(LDs), are the main functions of organelles. LDs are also important in viral infection and inflammation. In infected cells, PEAV increased LD accumulation, upregulated NF-κB signaling, promoted the production of the inflammatory cytokines IL-1β and IL-8, and induced cell death. Inhibiting LD accumulation with a DGAT-1 inhibitor significantly inhibited PEAV replication, downregulated the NF-κB signaling pathway, reduced the production of IL-1β and IL-8, and inhibited cell death. The NF-κB signaling pathway inhibitor BAY11-7082 significantly inhibited LD accumulation and PEAV replication. Metformin hydrochloride also exerted anti-PEAV effects and significantly inhibited LD accumulation, downregulated the NF-κB signaling pathway, reduced the production of IL-1β and IL-8, and inhibited cell death. LD accumulation in the lipid metabolism pathway therefore plays an important role in the replication and pathogenesis of PEAV, and metformin hydrochloride inhibits LD accumulation and the inflammatory response to exert anti-PEAV activity and reducing pathological injury. These findings contribute new targets for developing treatments for PEAV infections.

关键词： porcine enteric alphacoronavirus NF-κB inflammatory pathway lipid droplet metformin hydrochloride

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Analysis of RNA Recognition and Binding Characteristics of OsCPPR1 Protein in Rice

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Rice science 2024年第2期31卷 215-225,I0032-I0035页

作者： ZHENG Shaoyan CHEN Junyu LI Huatian LIU Zhenlan LI Jing ZHUANG Chuxiong State Key laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/guangdong laboratory for lingnan modern agriculture/College of Life Sciences South China Agricultural UniversityGuangzhou 510642China

Pentatricopeptide repeat(PPR)proteins represent one of the largest protein families in plants and typically localize to organelles like mitochondria and *** contrast,CYTOPLASMLOCALIZED PPR1(OsCPPR1)is a cytoplasm-localized PPR protein that can degrade OsGOLDENLIKE1(OsGLK1)mRNA in the tapetum of rice ***,the mechanism,by which OsCPPR1 recognizes and binds to OsGLK1 transcripts,remains *** protein structure prediction and macromolecular docking experiments,we observed that distinct PPR motif structures of OsCPPR1 exhibited varying binding efficiencies to OsGLK1 ***,RNA-electrophoretic mobility shift assay experiment demonstrated that the recombinant OsCPPR1 can directly recognize and bind to OsGLK1 mRNA in *** further confirmed that the mutations in the conserved amino acids in each PPR motif resulted in loss of activity,while truncation of OsCPPR1 decreased its binding *** findings collectively suggest that it may require some co-factors to assist in cleavage,a facet that warrants further exploration in subsequent studies.

关键词： OsCPPR1 RNA recognition and binding pentatricopeptide repeat rice

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Improving error-correcting capability in DNA digital storage via soft-decision decoding

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National Science Review 2024年第2期11卷 135-144页

作者：丁璐璐伍世刚候志浩李阿伦许亚苹冯虎潘玮华阮珏 Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural Sciences guangdong Provincial Key laboratory of Plant Molecular Breeding State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesSouth China Agricultural University

Error-correcting codes(ECCs) employed in the state-of-the-art DNA digital storage(DDS) systems suffer from a trade-off between error-correcting capability and the proportion of redundancy. To address this issue, in this study, we introduce soft-decision decoding approach into DDS by proposing a DNA-specific error prediction model and a series of novel strategies. We demonstrate the effectiveness of our approach through a proof-of-concept DDS system based on Reed-Solomon(RS) code, named as Derrick. Derrick shows significant improvement in error-correcting capability without involving additional redundancy in both in vitro and in silico experiments, using various sequencing technologies such as Illumina, Pac Bio and Oxford Nanopore Technology(ONT). Notably, in vitro experiments using ONT sequencing at a depth of 7× reveal that Derrick, compared with the traditional hard-decision decoding strategy, doubles the error-correcting capability of RS code, decreases the proportion of matrices with decoding-failure by 229-fold, and amplifies the potential maximum storage volume by impressive 32 388-fold. Also, Derrick surpasses ‘state-of-the-art' DDS systems by comprehensively considering the information density and the minimum sequencing depth required for complete information recovery. Crucially, the soft-decision decoding strategy and key steps of Derrick are generalizable to other ECCs' decoding algorithms.

关键词： DNA digital storage (DDS) error-correcting code (ECC) soft-decision decoding error-correcting capability storage volume

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Role of feline ANP32 proteins in regulating polymerase activity of influenza A virus

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Journal of Integrative agriculture 2024年第9期23卷 3145-3158页

作者： Gang Lu Feiyan Zheng Yuqing Xiao Ran Shao Jiajun Ou Xin Yin Shoujun Li Guihong Zhang College of Veterinary Medicine South China Agricultural UniversityGuangzhou 510642China State Key laboratory for Animal Disease Control and Prevention Harbin Veterinary Research InstituteChinese Academy of Agricultural SciencesHarbin 150000China Maoming Branch Guangdong Laboratory for Lingnan Modern AgricultureMaoming 525000China guangdong laboratory for lingnan modern agriculture Guangzhou 510642China

Recently,increasing natural infection cases and experimental animal challenge studies demonstrated domestic cats are susceptible to multiple subtypes influenza A virus(IAV)***,some subtype IAV strains could circulate in domestic cats after cross-species transmission and even infected humans,posing a threat to public *** factors related to viral polymerase activity could determine host range of IAV and acidic nuclear phosphoprotein 32(ANP32)is the most important one among ***,role of cat-derived ANP32 on viral polymerase activity and host range of IAV is still *** the present study,a total of 10 feline ANP32(feANP32)splice variants(including 5 feANP32A,3 feANP32B,and 2 feANP32E)were obtained from domestic cats by *** alignment results demonstrated amino acid deletions and/or insertions occurred among feANP32 variants,but all feANP32 proteins were primarily localized to cell *** replication systems for several representative IAV strains were established and the support ability of feANP32 on IAV polymerase activity was *** results indicated that most feANP32A and feANP32B splice variants were able to support all the tested IAV strains,though the support activity of a single feANP32 protein on polymerase activity varied among different IAV *** addition,the role of feANP32 in supporting H3N2 canine influenza virus was determined by investigating viral replication in ***,our study systematically investigated the support activity of feANP32 on IAV,providing a clue for further exploring the mechanism of susceptibility of cats to IAV.

关键词： ANP32 influenza A virus feline cross-species transmission

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Integrated multi-omics analysis reveals liver metabolic reprogramming by fish iridovirus and antiviral function of alpha-linolenic acid

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Zoological Research 2024年第3期45卷 520-534页

作者： Lin Liu Ya Zhang Meng-Di Yuan Dong-Miao Xiao Wei-Hua Xu Qi Zheng Qi-Wei Qin You-Hua Huang Xiao-Hong Huang College of Marine Sciences South China Agricultural UniversityGuangdong Laboratory for Lingnan Modern AgricultureGuangzhouGuangdong 510642China Nansha-South China Agricultural University Fishery Research Institute GuangzhouGuangdong 511464China Southern Marine Science and Engineering guangdong laboratory ZhuhaiGuangdong 519082China

Iridovirus poses a substantial threat to global aquaculture due to its high mortality rate;however,the molecular mechanisms underpinning its pathogenesis are not well ***,a multi-omics approach was applied to groupers infected with Singapore grouper iridovirus(SGIV),focusing on the roles of key *** showed that SGIV induced obvious histopathological damage and changes in metabolic enzymes within the ***,SGIV significantly reduced the contents of lipid droplets,triglycerides,cholesterol,and *** analysis indicated that the altered metabolites were enriched in 19 pathways,with a notable down-regulation of lipid metabolites such as glycerophosphates and alpha-linolenic acid(ALA),consistent with disturbed lipid homeostasis in the *** of transcriptomic and metabolomic data revealed that the top enriched pathways were related to cell growth and death and nucleotide,carbohydrate,amino acid,and lipid metabolism,supporting the conclusion that SGIV infection induced liver metabolic *** integrative transcriptomic and proteomic analysis indicated that SGIV infection activated crucial molecular events in a phagosome-immune depression-metabolism dysregulation-necrosis signaling *** note,integrative multi-omics analysis demonstrated the consumption of ALA and linoleic acid(LA)metabolites,and the accumulation of L-glutamic acid(GA),accompanied by alterations in immune,inflammation,and cell death-related *** experimental data showed that ALA,but not GA,suppressed SGIV replication by activating antioxidant and anti-inflammatory responses in the ***,these findings provide a comprehensive resource for understanding host response dynamics during fish iridovirus infection and highlight the antiviral potential of ALA in the prevention and treatment of iridoviral diseases.

关键词： Iridovirus Liver damage Metabolic reprogramming SGIV Alpha-linolenic acid Antiinflammatory

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Arbuscular mycorrhizal fungi inoculation and exogenous indole-3-acetic acid application induce antioxidant defense response to alleviate cadmium toxicity in Broussonetia papyrifera

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Pedosphere 2024年第2期34卷 447-459页

作者： Xue LI Jingwei LIANG Hongjian WEI Yuxuan KUANG Hui CHEN Ming TANG Wentao HU State Key laboratory of Conservation and Utilization of Subtropical Agro-Bioresources Guangdong Laboratory for Lingnan Modern AgricultureGuangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmCollege of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhou 510642China

Cadmium(Cd)contamination in soil poses a huge threat to plants even at low concentrations;Broussonetia papyrifera has great potential in remediation of soil heavy metal ***,whether exogenous indole-3-acetic acid(IAA)application and arbuscular mycorrhizal fungi(AMF)have synergistic effects on Cd tolerance of *** remains *** investigate the effects of AMF inoculation and IAA application on the tolerance of *** to Cd stress,two experiments were conducted:the first to investigate the effect of AMF(Rhizophagus irregularis)inoculation on the tolerance of *** to Cd stress and the second to investigate the combined effects of AMF inoculation and IAA application on the tolerance of *** to Cd *** including endogenous hormone concentration,antioxidant defense response,malondialdehyde(MDA)content,and gene expression related to antioxidant enzyme system and hormone were *** results indicated that AMF alleviated Cd toxicity of *** by reducing MDA content and improving antioxidant enzyme activities and Cd absorption ***,the combination of AMF inoculation and IAA application had a synergetic effect on the tolerance of *** to Cd stress through upregulating BpAUX1 and BpAUX2,which might contribute to root growth and root xylem synthesis,and by upregulating BpSOD2 and BpPOD34 to enhance the antioxidant enzyme *** work provides a new insight into the application of IAA in the remediation of soil Cd pollution by mycorrhizal plants.

关键词： enzyme activity geneexpression heavy metal phytoremediation remediation Rhizophagus irregularis soil cadmium pollution stress tolerance

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Path planning for agricultural robots in wild livestock farm environments

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International Journal of Agricultural and Biological Engineering 2024年第4期17卷 207-216页

作者： Haixia Qi Jinzhuo Jiang Chaohai Wang College of Engineering South China Agricultural UniversityGuangzhou 510642China guangdong laboratory for lingnan modern agriculture GuangzhouGuangdong 510642China

Path planning for field agricultural robots must satisfy several criteria:establishing feeding routes,maintaining gentle slopes,approaching multiple livestock observation points,ensuring timely environmental monitoring,and achieving high *** complex terrain of outdoor farming areas poses a *** A*algorithms,which generate only the shortest path,fail to meet these requirements and often produce paths that lack ***,identifying the most suitable path,rather than merely the shortest one,is *** study introduced a path-planning algorithm tailored to field-based livestock farming environments,building upon the traditional A**** constructed a digital elevation model,integrated an artificial potential field for evaluating multiple target points,calculated terrain slope,optimized the search neighborhood based on robot traversability,and employed Bézier curve segmentation for path *** method segmented the path into multiple curves by evaluating the slopes of the lines connecting adjacent nodes,ensuring a smoother and more efficient *** experimental results demonstrate its superiority to traditional A^(*),ensuring paths near multiple target points,significantly reducing the search space,and resulting in over 69.4%faster search speeds.Bézier curve segmentation delivers smoother paths conforming to robot trajectories.

关键词： field-based livestock farming agricultural robots path planning A*algorithm artificial potential field Bézier curve segmentation

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Divergent responses of growth rate and antioxidative system of ten Bacillus strains to acid stresses

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Soil Ecology Letters 2024年第1期6卷 107-118页

作者： Xiaoran Shan Jiayi Chen Jiaen Zhang Ziqiang Liu Shufang Chen Hui Wei Key laboratory of Agro-Environment in the Tropics of Ministry of agriculture and Rural Affairs Guangdong Laboratory for Lingnan Modern AgricultureCollege of Natural Resources and EnvironmentSouth China Agricultural UniversityGuangzhou 510642China guangdong Engineering Research Center for modern Eco-agriculture and Circular agriculture South China Agricultural UniversityGuangzhou 510642China

Response of growth rate and antioxidative system of ten Bacillus strains to acid stresses was *** acid treatment significantly decreased the growth rate of the *** stresses increased the GPX activity and GSSG content of the tested *** changes occurred in ROS and antioxidative system(SOD,CAT,GR,MDA and GSH).Environmental changes including soil acidification exert obvi-ous stresses on soil ecosystems and influence soil *** this study,ten microbial strains were incubated under different acid treatments to investigate responses of microbial growth and antioxidative system to acid *** the strains belong to Bacillus genus,but exhibit distinct ecological *** observed that these microbial strains had obviously different pH tolerance threshold,in spite of the close phylogenetic classification among *** stresses exerted significant effects on microbial antiox-idative system,including superoxide dismutase(SOD),cata-lase(CAT)and glutathione transferring enzymes(GPX and GR)and reactants(GSH and GSSH),but the effects were strain ***,we found acid stress effects on total variances of the investigated microbial antioxidative system along the first two principal components(PCs).Activities of CAT and SOD contributed substantially to PC1 that reflected obvious acid effects on NC7 and ZC4,and closely related to intracellular malondialdehyde *** GSSG activities and GSH/GSSG contributed greatly to PC2 that unveiled acid stress effects on most of the microbial *** results highlight substantially heterogeneous responses of microbial strains to acid stress and support that phylogenetic closeness does not imply functional similarity of soil microorganisms under environmental changes.

关键词： soil acidification microbial strain acid tolerance capacity microbial growth oxidative stress antioxidative system

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