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Methylome and transcriptome data integration reveals potential roles of DNA methylation and candidate biomarkers of cow Streptococcus uberis subclinical mastitis

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Journal of Animal Science and Biotechnology 2023年第2期14卷 593-613页

作者： Mengqi Wang Nathalie Bissonnette Mario Laterriere Pier‑Luc Dudemaine David Gagne Jean‑Philippe Roy Xin Zhao Marc‑Andre Sirard Eveline M.Ibeagha‑Awemu Sherbrooke Research and Development centre Agriculture and Agri-Food CanadaSherbrookeQuebecCanada Department of Animal Science Laval UniversityQuebecQuebecCanada quebec Research and Development centre Agriculture and Agri-Food CanadaQuebecQuebecCanada Department of Clinical Sciences Universite de MontrealSt‑HyacintheQuebecCanada Department of Animal Science McGill UniversitySte‑Anne‑De‑BellevueQuebecCanada.

Background:Mastitis caused by different pathogens including Streptococcus uberis(***)is responsible for huge economic losses to the dairy *** order to investigate the potential genetic and epigenetic regulatory mecha‑nisms of subclinical mastitis due to ***,the DNA methylome(whole genome DNA methylation sequencing)and transcriptome(RNA sequencing)of milk somatic cells from cows with naturally occurring *** subclinical mastitis and healthy control cows(n=3/group)were ***:Globally,the DNA methylation levels of CpG sites were low in the promoters and first exons but high in inner exons and *** DNA methylation levels at the promoter,first exon and first intron regions were nega‑tively correlated with the expression level of genes at a whole‑genome‑wide *** general,DNA methylation level was lower in ***‑positive group(SUG)than in the control group(CTG).A total of 174,342 differentially methylated cytosines(DMCs)(FDR<0.05)were identified between SUG and CTG,including 132,237,7412 and 34,693 DMCs in the context of CpG,CHG and CHH(H=A or T or C),***,101,612 methylation haplotype blocks(MHBs)were identified,including 451 MHBs that were significantly different(dMHB)between the two groups.A total of 2130 differentially expressed(DE)genes(1378 with up‑regulated and 752 with down‑regulated expression)were found in *** of methylome and transcriptome data with MethGET program revealed 1623 genes with signifi‑cant changes in their methylation levels and/or gene expression changes(MetGDE genes,MethGET P‑value<0.001).Functional enrichment of genes harboring≥15 DMCs,DE genes and MetGDE genes suggest significant involvement of DNA methylation changes in the regulation of the host immune response to *** infection,especially cytokine ***,discriminant correlation analysis with DIABLO method identified 26 candidate biomarkers,including 6 DE genes,15 CpG‑DMCs and 5 dMHBs that discrimina

关键词： Discriminant biomarkers Gene expression genome‑wide DNA methylation pattern Immune processes and pathways Methylation haplotype block Milk somatic cell Streptococcus uberis Subclinical mastitis

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Asthma-associated polymorphisms in 17q12-21 locus modulate methylation and gene expression of GSDMA in naive CD4^+ T cells

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Journal of Genetics and Genomics 2020年第3期47卷 171-174页

作者： Anne-Marie Madore Lucile Pain Anne-Marie Boucher-Lafleur Andréanne Morin Jolyane Meloche Marie-Michelle Simon Bing Ge Tony Kwan Warren A.Cheung Tomi Pastinen Catherine Laprise Departement des sciences fondamentales Universite du Quebec a ChicoutimiSaguenayQuebecG7H 2B1Canada Department of Human Genetics McGill UniversityMontrealQuebecH3A 0C7Canada Department of Human Genetics University of ChicagoIL60637USA mcgill university and genome quebec innovation centre MontrealQuebecH3A 0G1Canada Center for Pediatric Genomic Medicine Kansas CityMO64108USA centre intersectoriel en sante durable Universite du Quebec a ChicoutimiSaguenayQuebecG7H 2B1Canada

The 17q12-21 locus harboring ORMDL sphingolipid biosynthesis regulator 3(ORMDL3)and Gasdermin B(GSDMB)genes exhibits one of the most significant and replicated associations with asthma[MIM:600807](Stein et al.,2018).Several studies explored the complex interactions between SNPs,gene expression and epigenetic modifications at this locus,primarily focusing on the levels of expressed ORMDL3 and GSDMB(Stein et al.,2018).Given that DNA methylation and gene expression signals are cell-type specific(Reinius et al.,2012),isolated materials such as lymphocytes from blood and,to a lesser extent,bronchial epithelial cells from biopsies of bronchi or bronchoalveolar lavages have been used in a number of studies to investigate such interactions(Stein et al.,2018).

关键词： FDR T cells Asthma-associated polymorphisms gene expression of GSDMA

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On Inventing Cross-Dehydrogenative Coupling(CDC):Forming C-C Bond from Two Different C-H Bonds

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Chinese Journal of Chemistry 2022年第7期40卷 838-845页

作者： Chao-Jun Li Department of Chemistry FQRNT Centre for Green Chemistry and CatalysisMcGill University801 Sherbrooke Street W.MontrealQuebecH3A0B8 Canada

Constructing C-C bonds is central to the synthesis of all chemical *** conventional C-C bond formation methods always require one or two functional groups,20 years ago,our establishment of the concept of Cross-Dehydrogenative Coupling(CDC),wherein C-C bonds are directly formed from two different C-H bonds via the"formal"removal of two H atoms,has revolutionized chemical synthesis and has become one of the most active research subjects in *** perspective article will provide an insight of the origin of this concept and its early development in our laboratory.

关键词： Cross-Dehydrogenative Coupling(CDC) C-H activation Cross-coupling C-C bond formation Green chemistry

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Cognition and the brain of brood parasitic cowbirds

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Integrative Zoology 2019年第2期14卷 145-157页

作者： David F.SHERRY Mélanie F.GUIGUENO Department of Psychology Western University LondonOntario Department of Natural Resource Sciences McGill UniversityMontrealQuebecCanada

Cowbirds are brood *** lay their eggs in the nests of other species,which then incubate the cowbird eggs and raise the young *** and returning to heterospecific nests presents cowbirds with several cognitive *** some species,such as brown-headed cowbirds(Molothrus ater),females but not males search for and remember the locations of potential host *** describe recent research on sex differences in cognition and the hippocampus associated with this sex difference in search for host *** brown-headed cowbirds perform better than males on some,but not all,tests of spatial memory and females show a pattern of adult hippocampal neurogenesis not found in males or in closely related non-parasitic *** of the apparent specialization of the hippocampus,brown-headed cowbirds may be a good model in which to examine spatial information processing in the avian hippocampus and we also describe recent research on the spatial response properties of brown-headed cowbird hippocampal neurons.

关键词： adult neurogenesis brood parasites cowbirds hippocampus sex differences spatial memory

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Cleavage/cross-coupling strategy for converting β-O-4 linkage lignin model compounds into high valued benzyl amines via dual C–O bond cleavage

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Chinese Chemical Letters 2022年第3期33卷 1519-1523页

作者： Le Jia Chao-Jun Li Huiying Zeng The State Key Laboratory of Applied Organic Chemistry Lanzhou UniversityLanzhou 730000China Department of Chemistry FQRNT Centre for Green Chemistry and CatalysisMcGill UniversityMontrealQuebec H3A 0B8Canada

Lignin is the most recalcitrant of the three components of lignocellulosic biomass. The strength and stability of the linkages have long been a great challenge for the degradation and valorization of lignin biomass to obtain bio-fuels and commercial chemicals. Up to now, the selective cleavage of C–O linkages of lignin to afford chemicals contains only C, H and O atoms. Our group has developed a cleavage/crosscoupling strategy for converting 4-O-5 linkage lignin model compounds into high value-added compounds. Herein, we present a palladium-catalyzed cleavage/cross-coupling of the β-O-4 lignin model compounds with amines via dual C–O bond cleavage for the preparation of benzyl amine compounds and phenols.

关键词： β-O-4 Linkage Lignin C-O bond cleavage Cross-coupling reaction Palladium-catalyzed

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DNA Methylation,Behavior and Early Life Adversity

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Journal of Genetics and Genomics 2013年第7期40卷 331-338页

作者： Moshe Szyf Department of Pharmacology and Therapeutics McGill University3655 Sir William Osler PromenadeMontrealQuebec H3G 1Y6Canada

The impact of early physical and social environments on life-long phenotypes is well known. Moreover, we have documented evidence for gene-environment interactions where identical gene variants are associated with different phenotypes that are dependent on early life adversity. What are the mechanisms that embed these early life experiences in the genome？ DNA methylation is an enzymatically- catalyzed modification of DNA that serves as a mechanism by which similar sequences acquire cell type identity during cellular differentiation and embryogenesis in the same individual. The hypothesis that will be discussed here proposes that the same mechanism confers environmental-exposure specific identity upon DNA providing a mechanism for embedding environmental experiences in the genome, thus affecting long-term phenotypes. Particularly important is the environment early in life including both the prenatal and postnatal social environments.

关键词： DNA methylation Epigenetics Demethylase Stress Glucocorticoids Maternal care Early life adversity Socioeconomic status

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Effect of genome-Wide Genotyping and Reference Panels on Rare Variants Imputation

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Journal of Genetics and Genomics 2012年第10期39卷 545-550页

作者： Hou-Feng Zheng Martin Ladouceur Celia M.T. Greenwood J. Brent Richards Department of Medicine Human Genetics McGill University Montreal Quebec H3T 1E2 Canada Department of Epidemiology and Biostatistics Lady Davis Institute for Medical Research Jewish General Hospital Montreal Quebec H3T 1E2 Canada Research Center of Montreal Heart Institute Montreal Quebec HIT 1C8 Canada Department of Oncology McGill University Montreal Quebec H3T IE2 Canada Twin Research and Genetic Epidemiology King's College London London SE1 7EH United Kingdom

Common variants explain little of the variance of most common disease, prompting large-scale sequencing studies to understand the contribution of rare variants to these diseases. Imputation of rare variants from genome-wide genotypic arrays offers a cost-efficient strategy to achieve necessary sample sizes required for adequate statistical power. To estimate the performance of imputation of rare variants, we imputed 153 individuals, each of whom was genotyped on 3 different genotype arrays including 317k, 610k and 1 million single nucleotide polymorphisms （SNPs）, to two different reference panels： HapMap2 and 1000 genomes pilot March 2010 release （1KGpilot） by using IMPUTE version 2. We found that more than 94% and 84% of all SNPs yield acceptable accuracy （info 〉 0.4） in HapMap2 and 1KGpilot-based imputation, respectively. For rare variants （minor allele frequency （MAF）〈5%）, the proportion of well- imputed SNPs increased as the MAF increased from 0.3% to 5% across all 3 genome-wide association study （GWAS） datasets. The proportion of well-imputed SNPs was 69%, 60% and 49% for SNPs with a MAF from 0.3% to 5% for 1M, 610k and 317k, respectively. None of the very rare variants （MAF 〈 0.3%） were well imputed. We conclude that the imputation accuracy of rare variants increases with higher density of genome-wide genotyping arrays when the size of the reference panel is small. Variants with lower MAF are more difficult to impute. These findings have important implications in the design and replication of large-scale sequencing studies.

关键词： Genotype imputation genome-wide association study 1000 genome Project HapMap Rare variant Common disease

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Quantifying out-of-station waiting time in oversaturated urban metro systems

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Communications in Transportation Research 2022年第1期2卷 13-23页

作者： Kangli Zhu Zhanhong Cheng Jianjun Wu Fuya Yuan Lijun Sun Department of Civil Engineering McGill UniversityMontrealQuebecH3A 0C3Canada State Key Laboratory of Rail Traffic Control and Safety Beijing Jiaotong UniversityBeijing100044China

Metro systems in megacities such as Beijing,Shenzhen,and Guangzhou are under great passenger demand *** peak hours,it is common to see oversaturated conditions(i.e.,passenger demand exceeds network capacity)and a popular control intervention is to restrict the entering rate by setting up out-of-station queueing with crowd control *** out-of-station waiting can make up a substantial proportion of total travel time but is often ignored in the *** out-of-station waiting is important to evaluating the social benefit and cost of metro services;however,out-of-station waiting is difficult to estimate because it leaves no trace in smart card transactions of *** this study,we estimate the out-of-station waiting time by leveraging the information from a small group of transfer passengers—those who transfer from nearby bus routes to the metro *** on the transfer interval of this small group,we infer the out-of-station waiting time for all passengers by a Gaussian Process regression and then use the estimated out-of-station waiting time to build queueing *** apply our method to the Tiantongyuan North station of Beijing metro;results show that the maximum out-of-station waiting time can reach 15 min,and the maximum queue length can be over 3000 *** find out-of-station waiting can cause significant travel costs and thus should be considered in analyzing transit performance,mode choice,and social *** the best of our knowledge,this paper is the first quantitative study for out-of-station waiting time.

关键词： Metro waiting time Smart card data Public transport Crowd management Gaussian processes

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Effect of sonication-cooking on the immunoreactivity of soy slurry from germinated soybeans

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Food innovation and Advances 2023年第2期2卷 60-68页

作者： Akshaya Ravindran Hosahalli S Ramaswamy Department of Food Science McGill UniversityMacdonald Campus21111 Lakeshore RoadSte Anne de BellevueQuebec H9X 3V9Canada

Soy proteins are globular in nature and are resistant to denaturation with lower intensity thermal treatments like ***,germination can also alter the protein structure through the activity of various enzymes and sonication can disrupt the molecular structure through cavitation and other ultrasound effects,and contribute to some reduction in immunoreactivity(IR)of *** study evaluated the effects of germination and sonication pretreatment in combination with common cooking on lowering the soy allergen *** was carried out for up to 120 h and ultrasound sonication treatments were given for 20,40 and 60 min at room *** at 100 oC was carried out for 10 to 60 *** soy allergen IR was evaluated using a commercial sandwich ELISA *** combined action of germination,sonication and cooking helped to reduce the soy allergen IR to single digit mg/L levels from the nearly 400 mg/L initial level in the 5%soy slurry(>99%reduction).These levels are lower than the reported threshold values of soy allergens in *** addition,the germination and ultrasound process was shown to reduce the anti-nutritional properties and enhance the phenolic and radical scavenging activity by over 50%.

关键词： cooking soybean treatment

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Allergen degradation of bee pollen by lactic acid bacteria fermentation and its alleviatory effects on allergic reactions in BALB/c mice

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Food Science and Human Wellness 2024年第1期13卷 349-359页

作者： Shuting Yin Qiangqiang Li Yuxiao Tao Enning Zhou Kun Wang Wanwen Chen Xiangxin Li Liming Wu Institute of Apicultural Research Chinese Academy of Agricultural SciencesBeijing 100093China Department of Animal Science McGill UniversityQuebec H9X 3V9Canada State Key Laboratory of Food Science and Technology School of Food Science and TechnologyJiangnan UniversityWuxi 214122China

Food allergy as a global health problem threatens food *** pollen(BP)is a typical food with allergenic potentials,although it performs various nutritional/pharmacological functions to *** this study,lactic acid bacteria(LAB)were used to ferment Brassica napus BP for alleviating its *** novel allergens(glutaredoxin,oleosin-B2,catalase and lipase)were identified with significant decreases in LAB-fermented BP(FBP)than natural BP by ***,metabolomics analysis showed significant increases of 28 characteristic oligopeptides and amino acids in FBP versus BP,indicating the degradation of LAB on ***,FBP showed alleviatory effects in BALB/c mice,which relieved pathological symptoms and lowered production of allergic *** high-throughput sequencing analysis showed that FBP could regulate gut microbiota and metabolism to strengthen immunity,which were closely correlated with the alleviation of allergic *** findings could contribute to the development and utilization of hypoallergenic BP products.

关键词： Alleviatory effects Lactic acid bacteria fermentation Bee pollen allergen Gut microbiota Host metabolism

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