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Multi‑omics integration identifies regulatory factors underlying bovine subclinical mastitis

Journal of Animal Science and Biotechnology 2024年第3期15卷 987-1007页

作者： Mengqi Wang Naisu Yang Mario Laterriere David Gagne Faith Omonijo Eveline M.Ibeagha‑Awemu agriculture and agri‑food canada Sherbrooke Research and Development CentreSherbrookeQCCanada Department of Animal Science Universite LavalQuebec CityQCCanada Quebec Research and Development Centre Agriculture and Agri-Food CanadaQuebec CityQCCanada

Background Mastitis caused by multiple factors remains one of the most common and costly disease of the dairy industry.Multi-omics approaches enable the comprehensive investigation of the complex interactions between mul-tiple layers of information to provide a more holistic view of disease pathogenesis.Therefore,this study investigated the genomic and epigenomic signatures and the possible regulatory mechanisms underlying subclinical mastitis by integrating RNA sequencing data(mRNA and lncRNA),small RNA sequencing data(miRNA)and DNA methylation sequencing data of milk somatic cells from 10 healthy cows and 20 cows with naturally occurring subclinical mastitis caused by Staphylococcus aureus or Staphylococcus chromogenes.Results Functional investigation of the data sets through gene set analysis uncovered 3458 biological process GO terms and 170 KEGG pathways with altered activities during subclinical mastitis,provided further insights into subclin-ical mastitis and revealed the involvement of multi-omics signatures in the altered immune responses and impaired mammary gland productivity during subclinical mastitis.The abundant genomic and epigenomic signatures with sig-nificant alterations related to subclinical mastitis were observed,including 30,846,2552,1276 and 57 differential methylation haplotype blocks(dMHBs),differentially expressed genes(DEGs),lncRNAs(DELs)and miRNAs(DEMs),respectively.Next,5 factors presenting the principal variation of differential multi-omics signatures were identified.The important roles of Factor 1(DEG,DEM and DEL)and Factor 2(dMHB and DEM),in the regulation of immune defense and impaired mammary gland functions during subclinical mastitis were revealed.Each of the omics within Factors 1 and 2 explained about 20%of the source of variation in subclinical mastitis.Also,networks of impor-tant functional gene sets with the involvement of multi-omics signatures were demonstrated,which contributed to a comprehensive view of the possible regulatory mechanisms underlying subclinical mastiti

关键词： Candidate discriminant multi-omics signature Gene Long non-coding RNA Methylation haplotype block MicroRNA Multi-omics integration Natural killer cell mediated cytotoxicity pathway Staphylococcus aureus infection pathway

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Transcriptomics integrated with metabolomics reveals the mechanism of CaCl_(2)-HCl electrolyzed water-induced glucosinolate biosynthesis in broccoli sprouts

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food Science and Human Wellness 2024年第2期13卷 801-812页

作者： Cui Li Shuhui Song Yanan He Haijie Liu College of food Science and Nutritional Engineering China Agricultural UniversityBeijing 100083China Institute of agri-food Processing and Nutrition Beijing Academy of Agriculture and Forestry SciencesBeijing 100097China

Glucosinolates are important phytochemicals in Brassicaceae.We investigated the effect of CaCl_(2)-HCl electrolyzed water(CHEW)on glucosinolates biosynthesis in broccoli sprouts.The results showed that CHEW treatment significantly decreased reactive oxygen species(ROS)and malondialdeh yde(MDA)contents in broccoli sprouts.On the the 8^(th)day,compared to tap water treatment,the the total glucosinolate content of broccoli sprouts with CHEW treatment increased by 10.6%and calcium content was dramatically enhanced from 14.4 mg/g DW to 22.7 mg/g DW.Comparative transcriptome and metabolome analyses revealed that CHEW treatment activated ROS and calcium signaling transduction pathways in broccoli sprouts and they interacted through MAPK cascades.Besides,CHEW treatment not only promoted the biosynthesis of amino acids,but also enhanced the expression of structural genes in glucosinolate synthesis through transcription factors(MYBs,bHLHs,WRKYs,etc.).The results of this study provided new insights into the regulatory network of glucosinolates biosynthesis in broccoli sprouts under CHEW treatment.

关键词： Broccoli sprouts CaCl_(2)-HCl electrolyzed water Glucosinolates Transcriptomics Metabolomics

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Upland rice and lowland rice exhibited different P/P expression under water deficit and ABA treatment

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Cell Research 2006年第7期 651-660页

作者： David Lane agriculture and agri-food canada Pacific agri-food Research Centre Summerland B.C. V0H-1Z0.canada

Aquaporins play a significant role in plant water relations.To further understand the aquaporin function in plants underwater stress,the expression of a subgroup of aquaporins,plasma membrane intrinsic proteins(PIPs),was studied at boththe protein and mRNA level in upland rice(Oryza sativa L.cv.Zhonghan 3)and lowland rice(Oryza sativa L.cv.Xiushui63)when they were water stressed by treatment with 20% polyethylene glycol(PEG).Plants responded differently to20% PEG treatment.Leaf water content of upland rice leaves was reduced rapidly.PIP protein level increased markedlyin roots of both types,but only in leaves of upland rice after 10h of PEG treatment.At the mRNA level,OsPIP1;2,Os-PIP1;3,OsPIP2;1 and OsPIP2;5 in roots as well as OsPIP1;2 and OsPIP1;3 in leaves were significantly up-regulatedin upland rice,whereas the corresponding genes remained unchanged or down-regulated in lowland rice.Meanwhile,weobserved a significant increase in the endogenous abscisic acid(ABA)level in upland rice but not in lowland rice underwater deficit.Treatment with 60μM ABA enhanced the expression of OsPIP1;2,OsPIP2;5 and OsPIP2;6 in roots andOsPIP1;2,OsPIP2;4 and OsPIP2;6 in leaves of upland rice.The responsiveness of PIP genes to water stress and ABAwere different,implying that the regulation of PIP genes involves both ABA-dependent and ABA-independent signalingpathways during water deficit.

关键词： aquaporin gene expression PIP rice water deficit

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Effect of L-theanine combined with geniposide on depression-like behavior induced by the chronic unpredictable mild stress(CUMS) in mice

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food Science and Human Wellness 2024年

作者： Qi-Ming Yu Yan Zhu Tao Jiang Ying Gao Nan Ling Na Wang John Shi Wei-Chun Pan Qi-Zhen Du Jun-Feng Yin Tea Research Institute Chinese Academy of agricultural Sciences Key Laboratory of Tea Biology and Resources Utilization Ministry of agriculture College of food and Health Sciences Zhejiang A & F University Zhejiang Gongshang University Guelph food Research Center agriculture and agri-food canada College of Public Health Guilin Medical University

Depression is a prevalent mental disorder with limited effective treatments， posing a significant global issue. This study explored L-theanine and geniposide， key components in "food-medicine homology" materials， to determine if their combination (TG) could alleviate depression-like behaviors and hippocampal neuronal damage in a chronic unpredictable mild stress (CUMS) mouse model. Male C57BL/6J mice were divided into control， CUMS model， and CUMS+TG groups with varying doses. The CUMS group displayed depression-like behaviors， including reduced activity and sucrose preference. TG treatment partially reversed these changes， significantly increasing antioxidant enzyme activities， decreasing pro-inflammatory cytokine levels， and improving neuromodulator levels. RNA-seq analysis identified the transthyretin (TTR) gene， upregulated in the model group but downregulated after TG treatment. TG treatment modulated intestinal microbiota composition compared to the CUMS group， including increased Firmicutes， reduced Bacteroidetes and Prevotella， and variable changes in Bifidobacterium abundance. In conclusion， our study indicates that CUMS exposure upregulates stress hormones and TTR expression， associated with neuroinflammation， oxidative stress， monoamine depletion， depression-like behaviors， and intestinal microbiota dysbiosis. TG treatment alleviates these effects and modulates intestinal microbiota， suggesting L-theanine and geniposide’s potential as a novel depression therapy.

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Phosphorylation of PB2 at serine 181 restricts viral replication and virulence of the highly pathogenic H5N1 avian influenza virus in mice

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Virologica Sinica 2024年第1期39卷 97-112页

作者： Jiao Hu Zixiong Zeng Xia Chen Manyu Zhang Zenglei Hu Min Gu Xiaoquan Wang Ruyi Gao Shunlin Hu Yu Chen Xiaowen Liu Daxin Peng Xiufan Liu Animal Infectious Disease Laboratory School of Veterinary MedicineYangzhou UniversityYangzhou225009China Joint International Research Laboratory of agriculture and agri-Product Safety The Ministry of Education of ChinaYangzhou University225009China Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis Yangzhou UniversityYangzhou225009China Key Laboratory of Prevention and Control of Biological Hazard Factors(Animal Origin)for agri-food Safety and Quality Ministry of Agriculture of China(26116120)Yangzhou UniversityYangzhou225009China

Influenza A virus(IAV)continues to pose a pandemic threat to public health,resulting a high mortality rate annually and during pandemic years.Posttranslational modification of viral protein plays a substantial role in regulating IAV infection.Here,based on immunoprecipitation(IP)-based mass spectrometry(MS)and purified virus-coupled MS,a total of 89 phosphorylation sites distributed among 10 encoded viral proteins of IAV were identified,including 60 novel phosphorylation sites.Additionally,for the first time,we provide evidence that PB2 can also be acetylated at site K187.Notably,the PB2 S181 phosphorylation site was consistently identified in both IP-based MS and purified virus-based MS.Both S181 and K187 are exposed on the surface of the PB2 protein and are highly conserved in various IAV strains,suggesting their fundamental importance in the IAV life cycle.Bioinformatic analysis results demonstrated that S181E/A and K187Q/R mimic mutations do not significantly alter the PB2 protein structure.While continuous phosphorylation mimicked by the PB2 S181E mutation substantially decreases viral fitness in mice,PB2 K187Q mimetic acetylation slightly enhances viral virulence in mice.Mechanistically,PB2 S181E substantially impairs viral polymerase activity and viral replication,remarkably dampens protein stability and nuclear accumulation of PB2,and significantly weakens IAV-induced inflammatory responses.Therefore,our study further enriches the database of phosphorylation and acetylation sites of influenza viral proteins,laying a foundation for subsequent mechanistic studies.Meanwhile,the unraveled antiviral effect of PB2 S181E mimetic phosphorylation may provide a new target for the subsequent study of antiviral drugs.

关键词： H5N1 influenza virus PB2 Phosphorylation Acetylation Viral fitness Mice

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Antibacterial mechanism of kojic acid and tea polyphenols against Escherichia coli O157:H7 through transcriptomic analysis

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food Science and Human Wellness 2024年第2期13卷 736-747页

作者： Yilin Lin Ruifei Wang Xiaoqing Li Keren Agyekumwaa Addo Meimei Fang Yehui Zhang Yigang Yu School of food Sciences and Engineering South China University of TechnologyGuangzhou 510640China Sericulture&agri-food Research Institute Guangdong Academy of agricultural Sciences Key Laboratory of Functional FoodsMinistry of Agriculture and Rural AffairsGuangdong Key Laboratory of Agricultural Products ProcessingGuangzhou 510610China Research Center of food Safety and Detection College of Food Science and EngineeringSouth China University of TechnologyGuangzhou 510640China

Escherichia coli O157:H7 is one of the major foodborne pathogenic bacterial that cause infectious diseases in humans.The previous found that a combination of kojic acid and tea polyphenols exhibited better activity against E.coli O157:H7 than using either alone.This study aimed to explore responses underlying the antibacterial mechanisms of kojic acid and tea polyphenols from the gene level.The functional enrichment analysis by comparing kojic acid and tea polyphenols individually or synergistically against E.coli O157:H7 found that acid resistance systems in kojic acid were activated,and the cell membrane and genomic DNA were destructed in the cells,resulting in“oxygen starvation”.The oxidative stress response triggered by tea polyphenols inhibited both sulfur uptake and the synthesis of ATP,which affected the bacteria's life metabolic process.Interestingly,we found that kojic acid combined with tea polyphenols hindered the uptake of iron that played an essential role in the synthesis of DNA,respiration,tricarboxylic acid cycle.The results suggested that the iron uptake pathways may represent a novel approach for kojic acid and tea polyphenols synergistically against E.coli O157:H7 and provided a theoretical basis for bacterial pathogen control in the food industry.

关键词： Kojic acid Tea polyphenols Antibacterial mechanism Escherichia coli O157:H7 RNA-seq

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Stress responsive gene CIPK14 is involved in phytochrome A-mediated far-red light inhibition of greening in Arabidopsis

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Science China(Life Sciences) 2010年第11期53卷 1307-1314页

作者： QIN YuZhi2,3, GUO Ming1, LI Xu1, XIONG XingYao2,3, HE ChangZheng2,3, NIE XianZhou4 & LIU XuanMing1 1College of Life Science and Biotechnology, Hunan University, Changsha 410082, China 2College of Horticulture and Landscape, Hunan agricultural University, Changsha 410128, China 3Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan agricultural University, Changsha 410128, China 4Potato Research Centre, agriculture and agri-food canada, Fredericton, New Brunswick E3B 4Z7, canada College of Horticulture and Landscape Hunan Agricultural University Changsha China Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization Hunan Agricultural University Changsha China College of Life Science and Biotechnology Hunan University Changsha China Potato Research Centre Agriculture and Agri-Food Canada Fredericton Canada

In this study, we show that CIPK14,a stress responsive CBL-interacting protein kinase gene,is involved in phytochrome A-mediated far-red light inhibition of greening in Arabidopsis seedlings. The CIPK14-impairment mutant cipk14 grown in continuous far-red (FR) light did not show greening when exposed to white light illumination for 15 h. By contrast, the FR-grown phytochrome A null mutant phyA greened within 0.5 h of exposure to white light. Although greening of Col-4 (wild-type) was not completely abolished by FR, it exhibited a significantly decreased greening capacity compared with that of phyA. Further analyses demonstrated that the expression of protochlorophyllide reductase (POR) genes was correlated with the greening ability of the genotypes. In addition, CIPK14 appeared to be regulated by both the circadian clock and PhyA. Taken together, these results suggest that CIPK14 plays a role in PhyA-mediated FR inhibition of seedling greening, and that a Ca-related kinase may be involved in a previously undefined branch point in the phytochrome A signaling pathway.

关键词： chlorophyll CIPK14 far-red light inhibition of greening POR phytochrome A

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Structural elucidation of mulberry leaf oligosaccharide and its selective promotion of gut microbiota to alleviate type 2 diabetes mellitus

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food Science and Human Wellness 2024年第4期13卷 2161-2173页

作者： Tenggen Hu Yuanshan Yu Jijun Wu Yujuan Xu Gengsheng Xiao Kejing An Erna Li Sentai Liao Yuxiao Zou Sericultural&agri-food Research Institute Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional FoodsMinistry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products ProcessingGuangzhou 510610China Huagongliya(Foshan)Technology Industry Co. Ltd.Foshan 528313China Heyuan Branch Guangdong Laboratory for Lingnan Modern AgricultureHeyuan 517001China Zhongkai University of agriculture and Engineering Guangzhou 510225China

Two oligosaccharide fractions(MLO 2-1 and 2-2)were purified from enzymatic hydrolysate of mulberry leaf polysaccharide.The results of simulated digestion showed that MLO 2-2 was a digestible oligosaccharide,which could be degraded by human digestive juice;while MLO 2-1 possessed the non-digestible property in the upper gastrointestinal tract and performed the function by regulating the gut microbiota.Hence,MLO 2-1 was selected for the further analysis.The structure of MLO 2-1 was elucidated as follow:α-T-Glcp-(1→3)-β-Glcp-(1→5)-α-Araf-(1→5)-α-Araf-1→5)-α-Araf-(1→3)-α-(2-OAc)-Glcp-1.The in vitro fecal fermentation results showed that MLO 2-1 could modulate the composition of gut microbiota.Meanwhile,MLO 2-1 was effectively metabolized by fecal bacteria to produce lactate and short chain fatty acids,especially acetate and butyrate.The specific metabolic pathways of MLO 2-1 by gut microbiota were further illuminated.Gut microbiota analysis revealed that MLO 2-1 selectively promoted the growth of Ligilactobacillus murinus,a commensal bacterium presented a reduced level in T2DM mice.Animal experiments indicated that MLO 2-1 and L.murinus exhibited hypoglycemic activities.These results demonstrated that MLO 2-1 might alleviate T2DM by selectively accelerating the proliferation of L.murinus.

关键词： Mulberry leaf oligosaccharide Characterization Gut microbiota Lactobacillus murinus Hypoglycemic activity

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A likely paleo-autotetraploidization event shaped the high conservation of Nyssaceae genome

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Horticultural Plant Journal 2024年第3期10卷 911-930页

作者： Yishan Feng Zhenyi Wang Qimeng Xiao Jia Teng Jianyu Wang Zijian Yu Jiaqi Wang Qiang Xu Yan Zhang Shaoqi Shen Shoutong Bao Yu Li Zimo Yan Yue Ding Zihan Liu Yuxian Li Tianyu Lei Min Yuan Xiu-Qing Li Jinpeng Wang Department of Bioinformatics School of Life SciencesNorth China University of Science and TechnologyTangshanHebei 063000China Fredericton Research and Development Centre Agriculture and Agri-Food CanadaFrederictonNew Brunswick E3B 4Z7Canada State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of ScienceBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China

Scientific knowledge about the ancestral genome of core eudicot plant kingdom can potentially have profound impacts on both basic and applied research,including evolution,genetics,genomics,ecology,agriculture,forestry,and global climate.To investigate which plant conserves best the core eudicots common ancestor genome,we compared Arcto-Tertiary relict Nyssaceae and 30 other eudicot plant families.The genomes of Davidia involucrata(a known living fossil),Camptotheca acuminata and Nyssa sinensis,one per existent genus of Nyssaceae,were performed comparative genomic analysis.We found that Nyssaceae originated from a single Nyssaceae common tetraploidization event(NCT)-autotetraploidization 28-31 Mya after the core eudicot common hexaploidization(ECH).We identified Nyssaceae orthologous and paralogous genes,determined its chromosomal evolutionary trajectory,and reconstructed the Nyssaceae most recent ancestor genome.D.involucrata genome contained the entire seven paleochromosomes and 17 ECH-generated eudicot common ancestor chromosomes and was the slowest in mutation among the analyzed 42 species of 31 plant families.Combing both its high retention of paleochromosomes and its low mutation rate,D.involucrata provides the best case in conservation of the core eudicot paleogenome.

关键词： Nyssaceae Polyploidization Multigenome alignment Evolutionary rate Autotetraploidization Karyotype evolution

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Short-term Effects of Tillage Practices on Organic Carbon in Clay Loam Soil of Northeast China

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Pedosphere 2007年第5期17卷 619-623页

作者： LIANG Ai-Zhen ZHANG Xiao-Ping FANG Hua-Jun YANG Xue-Ming C. F. Drury Northeast Institute of Geography and Agroecology Chinese Academy ofSciences Changchun 130012 （China） Graduate School of the Chinese Academy of Sciences Beijing 100049 （China） Greenhouse ＆ Processing Crops Research Centre Agriculture ＆ Agri-Food Canada Harrow Ontario NOR 1GO （Canada）

一个耕种实验，由犁板组成犁( MP )，山脉耕种( RT )，和没有耕种( NT )，与四在一个使随机化的完全的块图案被执行复制在东北中国在粘壤土土壤的表面层( 30 厘米)在 SOC 内容和它的分发上学习3年的耕种管理的效果。NT 没与 MP 和 RT ... 详细信息

一个耕种实验，由犁板组成犁( MP )，山脉耕种( RT )，和没有耕种( NT )，与四在一个使随机化的完全的块图案被执行复制在东北中国在粘壤土土壤的表面层( 30 厘米)在 SOC 内容和它的分发上学习3年的耕种管理的效果。NT 没与 MP 和 RT 相比在表层土(0 5 厘米) 导致 SOC 的重要增加；然而，在 NT 土壤的 SOC 内容显著地在 5 20 厘米的深度被减少。因此，短期(3 年) NT 管理趋于成层 SOC 集中，然而并非必然增加它在为土壤的犁层的存储。

关键词：中国东北地区粘壤土土壤有机碳耕种模式短期效应

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