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

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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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 elucidated.Here,a multi-omics approach was applied to groupers infected with Singapore grouper iridovirus(SGIV),focusing on the roles of key metabolites.Results showed that SGIV induced obvious histopathological damage and changes in metabolic enzymes within the liver.Furthermore,SGIV significantly reduced the contents of lipid droplets,triglycerides,cholesterol,and lipoproteins.Metabolomic 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 liver.Integration 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 reprogramming.Further integrative transcriptomic and proteomic analysis indicated that SGIV infection activated crucial molecular events in a phagosome-immune depression-metabolism dysregulation-necrosis signaling cascade.Of 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 genes.Further experimental data showed that ALA,but not GA,suppressed SGIV replication by activating antioxidant and anti-inflammatory responses in the host.Collectively,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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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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ORPA:a fast and efficient phylogenetic analysis method for constructing genome-wide alignments of organelle genomes

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Journal of Genetics and Genomics 2024年第3期51卷 352-358页

作者： Guiqi Bi Xinxin Luan Jianbin Yan Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Synthetic BiologyMinistry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518124China Zhengzhou Research Base State Key Laboratory of Cotton BiologySchool of Agricultural SciencesZhengzhou UniversityZhengzhouHenan 450001China

Creating a multi-gene alignment matrix for phylogenetic analysis using organelle genomes involves aligning single-gene datasets manually,a process that can be time-consuming and prone to errors.The HomBlocks pipeline has been created to eliminate the inaccuracies arising from manual operations.The processing of a large number of sequences,however,remains a time-consuming task.To conquer this challenge,we develop a speedy and efficient method called Organelle Genomes for Phylogenetic Analysis(ORPA).ORPA can quickly generate multiple sequence alignments for whole-genome comparisons by parsing the result files of NCBI BLAST,completing the task just in 1 min.With increasing data volume,the efficiency of ORPA is even more pronounced,over 300 times faster than HomBlocks in aligning 60 high-plant chloroplast genomes.The phylogenetic tree outputs from ORPA are equivalent to HomBlocks,indicating its outstanding efficiency.Due to its speed and accuracy,ORPA can identify species-level evolutionary conflicts,providing valuable insights into evolutionary cognition.

关键词： Ultrafast alignment Organelle phylogenomics Phylogenomic conflict Efficient pipeline Multiple sequence alignment pipeline

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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 chloroplasts.By contrast,CYTOPLASMLOCALIZED PPR1(OsCPPR1)is a cytoplasm-localized PPR protein that can degrade OsGOLDENLIKE1(OsGLK1)mRNA in the tapetum of rice anther.However,the mechanism,by which OsCPPR1 recognizes and binds to OsGLK1 transcripts,remains unknown.Through protein structure prediction and macromolecular docking experiments,we observed that distinct PPR motif structures of OsCPPR1 exhibited varying binding efficiencies to OsGLK1 RNA.Moreover,RNA-electrophoretic mobility shift assay experiment demonstrated that the recombinant OsCPPR1 can directly recognize and bind to OsGLK1 mRNA in vitro.This 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 efficiency.These 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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Strigolactone regulates nitrogen-phosphorus balance in rice

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Science China(Life Sciences) 2024年第2期67卷 428-430页

作者： Huwei Sun Hanyun Wang Chengcai Chu guangdong Provincial Key laboratory of Plant Molecular Breeding College of AgricultureSouth China Agricultural UniversityGuangzhou 510642China Key laboratory for Enhancing Resource Use Efficiency of Crops in South China Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhou 510642China guangdong laboratory for lingnan modern Agriculture Guangzhou 510642

Phosphorus(P) is one of the essential elements for growth and development of crops.modern agriculture depends heavily on the application of large amounts of fertilizers,including P fertilizers.Excessive application of P fertilizers causes severe environmental pollution.Additionally,phosphate(Pi) mining is a non-renewable resource(Raghothama,1999).

关键词： pollution phosphorus fertilizers

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Dietary supplementation of benzoic acid and essential oils combination enhances intestinal resilience against LPS stimulation in weaned piglets

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Journal of Animal Science and Biotechnology 2024年第2期15卷 878-897页

作者： Chang Cui Yulong Wei Yibo Wang Wen Ma Xiaoyu Zheng Jun Wang Ziwei Ma Caichi Wu Licui Chu Shihai Zhang Wutai Guan Fang Chen guangdong Provincial Key laboratory of Animal Nutrition Control College of Animal ScienceSouth China Agricultural UniversityGuangzhou 510642China College of Animal Science and National Engineering Research Center for Breeding Swine Industry South China Agricultural UniversityGuangzhou 510642China guangdong laboratory for lingnan modern Agriculture South China Agricultural UniversityGuangzhou 510642China

Background The benefits of combining benzoic acid and essential oils(BAO)to mitigate intestinal impairment during the weaning process have been well established,while the detailed underlying mechanism has not been fully elucidated.Previous research has primarily focused on the reparative effects of BAO on intestinal injury,while neglecting its potential in enhancing intestinal stress resistance.Methods In this study,we investigated the pre-protective effect of BAO against LPS-induced stress using a modified experimental procedure.Piglets were pre-supplemented with BAO for 14 d,followed by a challenge with LPS or saline to collect blood and intestinal samples.Results Our findings demonstrated that BAO supplementation led to significant improvements in piglets’final weight,average daily gain,and feed intake/body gain ratio.Additionally,BAO supplementation positively influenced the composition of intestinal microbiota,increasing beneficial Actinobacteriota and Alloprevotella while reducing harmful Desulfobacterota,Prevotella and Oscillospira.Furthermore,BAO supplementation effectively mitigated oxidative disturbances and inflammatory responses induced by acute LPS challenge.This was evidenced by elevated levels of T-AOC,SOD,and GSH,as well as decreased levels of MDA,TNF-α,and IL-6 in the plasma.Moreover,piglets subjected to LPS challenge and pre-supplemented with BAO exhibited significant improvements in intestinal morphological structure and enhanced integrity,as indicated by restored expression levels of Occludin and Claudin-1 compared to the non-supplemented counterparts.Further analysis revealed that BAO supplementation enhanced the jejunal antioxidative capacity by increasing GSH-Px levels and decreasing MDA levels under the LPS challenge and stimulated the activation of the Nrf2 signaling pathway.Additionally,the reduction of TLR4/NF-κB/MAPK signaling pathways activation and proinflammatory factor were also observed in the jejunal of those piglets fed with BAO.Conclusions In summary,our study demonstrates that

关键词： Anti-stress Benzoic acid Essential oils Intestine LPS Weaned piglets

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miR-378a-3p responds to physical activity by modulating insulin-mediated glucose uptake and tricarboxylic acid cycle in skeletal muscle

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Genes & Diseases 2024年第3期11卷 98-101页

作者： Zishuai Wang Yilong Yao Xinhua Hou Danyang Fan Yanwen Liu Adeyinka Abiola Adetula Yalan Yang kui Li Zhonglin Tang Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong518000China Kunpeng Institute of modern Agriculiture at Foshan Chinese Academy of Agricultural SciencesFoshanGuangdong528226China GuangXi Engineering Centre for Resource Development of Bama Xiang Pig BamaGuangxi 547500China Institute of Animal Science Chinese Academy of Agricultural SciencesBeijing100193China

Aerobic exercise training alters gene expression in skeletal muscle,and miRNAs significantly contribute to motion response.However,the molecular mechanisms by which miRNAs regulate the response to exercise training are not well understood.Here,we found that the abundance of miR-378a-3p in skeletal muscle significantly decreased after exercise training.miR-378a-3p knockout mice showed increased insulin sensitivity,insulin-mediated glucose uptake.

关键词： skeletal miR uptake

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Uncovering key salt-tolerant regulators through a combined eQTL and GWAS analysis using the super pan-genome in rice

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National Science Review 2024年第4期11卷 55-69页

作者： Hua Wei Xianmeng Wang Zhipeng Zhang Longbo Yang Qianqian Zhang Yilin Li Huiying He Dandan Chen Bin Zhang Chongke Zheng Yue Leng Xinglan Cao Yan Cui Chuanlin Shi Yifan Liu Yang Lv Jie Ma Wenchuang He Xiangpei Liu Qiang Xu Qiaoling Yuan Xiaoman Yu Tianyi Wang Hongge Qian Xiaoxia Li Bintao Zhang Hong Zhang Wu Chen Mingliang Guo Xiaofan Dai Yuexing Wang Xiaoming Zheng Longbiao Guo Xianzhi Xie Qian Qian Lianguang Shang 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 Institute of Wetland Agriculture and Ecology Shandong Academy of Agricultural Sciences State Key laboratory of Rice Biology China National Rice Research Institute National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Science Chinese Academy of Agricultural Sciences Yazhouwan National laboratory

For sessile plants, gene expression plays a pivotal role in responding to salinity stress by activating or suppressing specific genes. However, our knowledge of genetic variations governing gene expression in response to salt stress remains limited in natural germplasm. Through transcriptome analysis of the Global Mini-Core Rice Collection consisting of a panel of 202 accessions, we identified 22 345 and 27 610expression quantitative trait loci associated with the expression of 7787 and 9361 e Genes under normal and salt-stress conditions, respectively, leveraging the super pan-genome map. Notably, combined with genome-wide association studies, we swiftly pinpointed the potential candidate gene STG5—a major salt-tolerant locus known as q STS5. Intriguingly, STG5 is required for maintaining Na+/K+homeostasis by directly regulating the transcription of multiple members of the Os HKT gene family. Our study sheds light on how genetic variants influence the dynamic changes in gene expression responding to salinity stress and provides a valuable resource for the mining of salt-tolerant genes in the future.

关键词： super pan-genome expression quantitative trait loci GWAS salt tolerance rice

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Accurate models and nutritional strategies for specific oxidative stress factors: Does the dose matter in swine production?

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Journal of Animal Science and Biotechnology 2024年第2期15卷 519-534页

作者： Changming Hong Yujian Huang Shuting Cao Li Wang Xuefen Yang Shenglan Hu Kaiguo Gao Zongyong Jiang Hao Xiao State Key laboratory of Swine and Poultry Breeding Industry Ministry of Agriculture Key Laboratory of Animal Nutrition and Feed Science in South ChinaGuangdong Public Laboratory of Animal Breeding and NutritionGuangdong Provincial Key Laboratory of Animal Breeding and NutritionMaoming BranchGuangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina Institute of Animal Science Guangdong Academy of Agricultural Sciences1 Dafeng 1st StreetGuangzhou 510640China

Oxidative stress has been associated with a number of physiological problems in swine,including reduced production efficiency.Recently,although there has been increased research into regulatory mechanisms and antioxidant strategies in relation to oxidative stress-induced pig production,it remains so far largely unsuccessful to develop accurate models and nutritional strategies for specific oxidative stress factors.Here,we discuss the dose and dose intensity of the causes of oxidative stress involving physiological,environmental and dietary factors,recent research models and the antioxidant strategies to provide theoretical guidance for future oxidative stress research in swine.

关键词： Accurate models Dose Nutritional strategies Oxidative stress Swine

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