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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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Studies on the temporal, structural, and interacting features of the clubroot resistance gene Rcr1 using CRISPR/Cas9-based systems

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Horticultural Plant Journal 2024年第4期10卷 1035-1048页

作者： Hao Hu Fengqun Yu agriculture and agri-food Canada Saskatoon Research and Development Centre107 Science Place

Clubroot disease is a severe threat to Brassica crops globally, particularly in western Canada. Genetic resistance, achieved through pyramiding clubroot resistance(CR) genes with different modes of action, is the most important strategy for managing the disease. However,studies on the CR gene functions are quite limited. In this study, we have conducted investigations into the temporal, structural, and interacting features of a newly cloned CR gene, Rcr1, using CRISPR/Cas9 technology. For temporal functionality, we developed a novel CRISPR/Cas9-based binary vector, pHHIGR-Hsp18.2, to deliver Rcr1 into a susceptible canola line(DH12075) and observed that early expression of Rcr1 is critical for conferring resistance. For structural functionality, several independent mutations in specific domains of Rcr1 resulted in loss-offunction, highlighting their importance for CR phenotype. In the study of the interacting features of Rcr1, a cysteine protease gene and its homologous allele in canola were successfully disrupted via CRISPR/Cas9 as an interacting component with Rcr1 protein, resulting in the conversion from clubroot resistant to susceptible in plants carrying intact Rcr1. These results indicated an indispensable role of these two cysteine proteases in Rcr1-mediated resistance response. This study, the first of its kind, provides valuable insights into the functionality of Rcr1. Further, the new vector p HHIGR-Hsp18.2 demonstrated an inducible feature on the removal of add-on traits, which should be useful for functional genomics and other similar research in brassica crops.

关键词： Clubroot resistance Brassica crops Canola Rcr1 CRISPR/Cas9 system Gene knock-out Timing control Non-synonymous mutation Protein–protein interaction

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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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Results Involving Partial Differential Equations and Their Solution by Certain Integral Transform

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Computer Modeling in Engineering & Sciences 2024年第2期138卷 1593-1616页

作者： Rania Saadah Mohammed Amleh Ahmad Qazza Shrideh Al-Omari Ahmet Ocak Akdemir department of Mathematics Faculty of ScienceZarqa UniversityZarqa13110Jordan department of Mathematics Faculty of ScienceAl-Balqa Applied UniversityAmman11134Jordan department of Mathematics Faculty of Science and LettersAgri Ibrahim莈鏴n UniversityAgri04100Turkey

In this study,we aimto investigate certain triple integral transformand its application to a class of partial differentialequations.We discuss various properties of the new transformincluding inversion, linearity, existence, scaling andshifting, etc. Then,we derive several results enfolding partial derivatives and establish amulti-convolution theorem.Further, we apply the aforementioned transform to some classical functions and many types of partial differentialequations involving heat equations,wave equations, Laplace equations, and Poisson equations aswell.Moreover,wedraw some figures to illustrate 3-D contour plots for exact solutions of some selected examples involving differentvalues in their variables.

关键词： ARA transform double ARA transform triple ARA transform partial differential equations integral transform

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Polyphenol components in black chokeberry(Aronia melanocarpa)as clinically proven diseases control factors——an overview

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food Science and Human Wellness 2024年第3期13卷 1152-1167页

作者： Ningxuan Gao Chi Shu Yuehua Wang Jinlong Tian Yuxi Lang Chenyu Jin Xingyue Cui Hanqian Jiang Shi’an Liu Zhiying Li Wei Chen Hao Xu Bin Li department of food Science College of FoodShenyang Agricultural UniversityShenyang 110161China department of food Science and Nutrition College of Biosystems Engineering and Food ScienceZhejiang UniversityHangzhou 310058China Chaoyang Beihe food Co. Ltd.Chaoyang 122100China

The black chokeberry is rich in polyphenols,including flavonoids with anthocyanins,flavanols and lavonols as the main components and a variety of phenolic acids represented by chlorogenic acid.Because of these polyphenols,black chokeberry has the effect of preventing and adjuvant therapy diseases.This study summarized the current research results on the types and contents of functional components in black chokeberry,and analyzed their digestion,absorption and metabolism in human body.On this basis,the disease control functions that have been proved effective in clinical research were reviewed and analyzed.These studies showed that black chokeberry have good prevention and adjuvant therapy effects on hyperlipidemia,hypertension,diabetes and inflammation.Because there are different functional components in black chokeberry,its prevention and treatment of the same disease can come from multiple pathways,which provides a more reliable effectiveness for the disease control of different populations.

关键词： Black chokeberry Hyperlipidemia Hypertension Diabetes Inflammation

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Two intestinal microbiota-derived metabolites, deoxycholic acid and butyrate, synergize to enhance host defense peptide synthesis and alleviate necrotic enteritis

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Journal of Animal Science and Biotechnology 2024年第3期15卷 1158-1172页

作者： Dohyung M.Kim Jing Liu Melanie A.Whitmore Isabel Tobin Zijun Zhao Guolong Zhang department of Animal and food Sciences Oklahoma State UniversityStillwaterOKUSA

Background Necrotic enteritis(NE)is a major enteric disease in poultry,yet effective mitigation strategies remain elusive.Deoxycholic acid(DCA)and butyrate,two major metabolites derived from the intestinal microbiota,have independently been shown to induce host defense peptide(HDP)synthesis.However,the potential synergy between these two compounds remains unexplored.Methods To investigate the possible synergistic effect between DCA and butyrate in regulating HDP synthesis and barrier function,we treated chicken HD11 macrophage cells and jejunal explants with DCA and sodium butyrate(NaB),either individually or in combination,for 24 h.Subsequently,we performed RNA isolation and reverse transcrip-tion-quantitative PCR to analyze HDP genes as well as the major genes associated with barrier function.To further determine the synergy between DCA and NaB in enhancing NE resistance,we conducted two independent trials with Cobb broiler chicks.In each trial,the diet was supplemented with DCA or NaB on the day-of-hatch,followed by NE induction through sequential challenges with Eimeria maxima and Clostridium perfringens on d 10 and 14,respectively.We recorded animal mortality after infection and assessed intestinal lesions on d 17.The impact of DCA and NaB on the microbiota in the ileum and cecum was evaluated through bacterial 16S rRNA gene sequencing.Results We found that the combination of DCA and NaB synergistically induced multiple HDP genes in both chicken HD11 cells and jejunal explants.Additionally,the gene for claudin-1,a major tight junction protein,also exhibited synergistic induction in response to DCA and NaB.Furthermore,dietary supplementation with a combination of 0.75 g/kg DCA and 1 g/kg NaB led to a significant improvement in animal survival and a reduction in intestinal lesions compared to either compound alone in a chicken model of NE.Notably,the cecal microbiota of NE-infected chickens showed a marked decrease in SCFA-producing bacteria such as Bacteroides,Faecalibacterium,and Cuneatibacter,with lactobaci

关键词： Bile acids Host defense peptides Metabolites Microbiome Necrotic enteritis Short-chain fatty acids

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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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Fractal image analysis and bruise damage evaluation of impact damage in guava

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Information Processing in agriculture 2024年第2期11卷 217-227页

作者： Than Htike Rattapon Saengrayap Hiroaki Kitazawa Saowapa Chaiwong School of Agro-Industry Mae Fah Luang UniversityChiang Rai 57100Thailand department of agriculture Ministry of AgricultureLivestock and Irrigation 11181Myanmar Integrated agri-Tech Ecosystem Research Group Mae Fah Luang UniversityChiang Rai 57100Thailand Institute of food Research National Agriculture and Food Research OrganizationIbaraki 305-8642Japan

Impact bruise damage and quality of‘Gim Ju’guava were investigated for different drop heights and number of drops using fractal image analysis.For the impact test,a stainless-steel metal ball(250 g)was dropped on fruit from three drop heights(0,0.3,0.6 m)either once or five times.Fruit quality was evaluated for impact energy,bruise area(BA),bruise volume(BV),bruise susceptibility,bruise score and pulp color(L*,a*,b*and C values).The fractal dimension(FD)value using fractal image analysis was analyzed at the bruise region.Results showed that five drops(0.3 m)with a high impact energy(3678.75 J)and a single drop(0.6 m)with a low impact energy(1471.50 J)exhibited no significant in BA,BV,bruise score as well as all color values(L*,a*,b*and C).While the FD value of a single drop from 0.6 m had a higher FD value than that of five drops from 0.3 m.It is indicated that FD exhibited a better performance to classify impact bruising level of guava than BA,BV and color parameters.The FD value gradually decreased with increase of storage time and bruise severity.The correlation coefficient(r)values of FD(r=−0.794 and−0.745)between BA and BV were more significant than those L*(r=−0.660 and−0.615)and a*(r=0.579 and 0.473).The coefficient of determination(R^(2))of the polynomial equation in bruised fruit(R^(2)=0.85 to 0.99)was greater than the control(no bruise)(R^(2)=0.80).A higher R^(2)val(0.88 and 0.92)was exhibited at five drops.Interestingly,FD analysis showed greater potential than color measurement to assess bruise impact damage in guava.

关键词： Bruise susceptibility Impact bruise Mechanical injury Transportation

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The modulatory effect of oolong tea polyphenols on intestinal flora and hypothalamus gene expression in a circadian rhythm disturbance mouse model

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food Science and Human Wellness 2024年第2期13卷 748-764页

作者： Ruonan Yan Chi-Tang Ho Yanan Liu Shengnan Zhan Zufang Wu Xin Zhang department of food Science and Engineering Ningbo UniversityNingbo 315211China department of food Science Rutgers UniversityNew BrunswickNew Jersey 08901USA

The interaction between host circadian rhythm and gut microbes through the gut-brain axis provides new clues for tea polyphenols to improve host health.Our present research showed that oolong tea polyphenols(OTP)improved the structural disorder of the intestinal flora caused by continuous darkness,thereby modulating the production of metabolites related to pyruvate metabolism,glycolysis/gluconeogenesis,and tryptophan metabolism to alleviate the steady-state imbalance.After fecal microbiota transplantation from the OTP group,the single-cell transcriptomic analysis revealed that OTP significantly increased the number of hypothalamus cell clusters,up-regulated the number of astrocytes and fibroblasts,and enhanced the expression of circadian rhythm genes Cry2,Per3,Bhlhe41,Nr1d1,Nr1d2,Dbp and Rorb in hypothalamic cells.Our results confirmed that OTP can actively improve the intestinal environmental state as well as internal/peripheral circadian rhythm disorders and cognitive impairment,with potential prebiotic functional characteristics to notably contribute to host health.

关键词： Gut microbiota Circadian rhythm Oolong tea polyphenols Single-cell sequencing Metabolism

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Changes in milk fat globule membrane proteins along lactation stage of Laoshan dairy goat

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Journal of Integrative agriculture 2024年第5期23卷 1737-1748页

作者： Chuozi Liang Zhongna Yu Guangming Zhu Yixuan Li Xueheng Sun Hongning Jiang Qijing Du Rongbo Fan Jun Wang Yongxin Yang Rongwei Han College of food Science and Engineering Qingdao Agricultural UniversityQingdao 266109China Bathurst Future agri-Tech Institute Qingdao Agricultural UniversityQingdao 266109China Haidu Cllege Qingdao Agricultural UniversityQingdao 266109China

The milk fat globule membrane(MFGM)is a complex structure with numerous functions,and its composition is affected by many factors.There have been few systematic investigations on goat MFGM proteome profiling during lactation.Individual milk samples from 15 healthy dairy goats were obtained at six lactation time points for investigation of the MFGM proteome using both data-independent acquisition(DIA)and data-dependent acquisition(DDA)proteomics techniques combined with multivariate statistical analysis.Using the DIA method,890 variably abundant MFGM proteins were discovered throughout the lactation cycle.From 1 to 240 d,butyrophilin subfamily 1 member A1,lipoprotein lipase,perilipin-2,and adipose triglyceride lipase were upregulated,while APOE,complement C3,clusterin,and IgG were downregulated.Furthermore,from 1 to 90 d,annexin A1,annexin A2,and antithrombin-ll were downregulated,then upregulated by d 240.Albumin had a high degree of connectedness,indicating that it was a key protein,according to protein-protein interaction research.Overall,our findings gave new insights into the biological features of MFGM protein in goat milk throughout lactation,which may aid in the creation of specialized MFGM products and infant formula.

关键词： goat milk fat globule membrane protein data-independent acquisition(DIA) data-dependent acquisition(DDA) lactation proteomics

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