Transcriptomic profiles of the ruminal wall in Italian Mediterranean dairy buffaloes fed green forage

[1]  C. Giallongo,et al.  IGFBP-6: At the Crossroads of Immunity, Tissue Repair and Fibrosis , 2022, International journal of molecular sciences.

[2]  J. Gross.  BOARD INVITED REVIEW: Limiting Factors for Milk Production in Dairy Cows: Perspectives from Physiology and Nutrition. , 2022, Journal of animal science.

[3]  F. Gu,et al.  Cross-tissue single-cell transcriptomic landscape reveals the key cell subtypes and their potential roles in the nutrient absorption and metabolism in dairy cattle , 2021, Journal of advanced research.

[4]  T. Iwakuma,et al.  Regulation of p53 and Cancer Signaling by Heat Shock Protein 40/J-Domain Protein Family Members , 2021, International journal of molecular sciences.

[5]  D. Bu,et al.  Oxidative Stress in Dairy Cows: Insights into the Mechanistic Mode of Actions and Mitigating Strategies , 2021, Antioxidants.

[6]  M. Salto‐Tellez,et al.  Robustness of differential gene expression analysis of RNA-seq , 2021, Computational and structural biotechnology journal.

[7]  T. Low,et al.  More Than Meets the Eye: Revisiting the Roles of Heat Shock Factor 4 in Health and Diseases , 2021, Biomolecules.

[8]  J. Vencovský,et al.  S100A11 (calgizzarin) is released via NETosis in rheumatoid arthritis (RA) and stimulates IL-6 and TNF secretion by neutrophils , 2021, Scientific Reports.

[9]  Huijiang Gao,et al.  Transcriptome profiling analysis of muscle tissue reveals potential candidate genes affecting water holding capacity in Chinese Simmental beef cattle , 2021, Scientific Reports.

[10]  A. Limone,et al.  Green feed increases antioxidant and antineoplastic activity of buffalo milk: A globally significant livestock. , 2020, Food chemistry.

[11]  Diego Alonso-López,et al.  Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysis , 2020, Scientific Reports.

[12]  Z. Fu,et al.  Transcriptomic Analyses Reveal the Protective Immune Regulation of Conjugated Linoleic Acids in Sheep Ruminal Epithelial Cells , 2020, Frontiers in Physiology.

[13]  Xiao Qiu,et al.  Multiple omics analysis reveals that high fiber diets promote gluconeogenesis and inhibit glycolysis in muscle , 2020, BMC genomics.

[14]  Tiziano Mazza,et al.  Carnitine Traffic in Cells. Link With Cancer , 2020, Frontiers in Cell and Developmental Biology.

[15]  Adam Hage,et al.  TRIM Proteins in Host Defense and Viral Pathogenesis , 2020, Current Clinical Microbiology Reports.

[16]  G. Gäbel,et al.  Ruminal epithelium: a checkpoint for cattle health , 2020, Journal of Dairy Research.

[17]  Shigeru Sato,et al.  Long-term high-grain diet alters ruminal pH, fermentation, and epithelial transcriptomes, leading to restored mitochondrial oxidative phosphorylation in Japanese Black cattle , 2020, Scientific Reports.

[18]  Hui-Zeng Sun,et al.  Multi-omics reveals functional genomic and metabolic mechanisms of milk production and quality in dairy cows , 2019, Bioinform..

[19]  Neng Zhu,et al.  Wnt5a/Ror2 pathway contributes to the regulation of cholesterol homeostasis and inflammatory response in atherosclerosis. , 2020, Biochimica et biophysica acta. Molecular and cell biology of lipids.

[20]  P. Olinga,et al.  Vanin 1: Its Physiological Function and Role in Diseases , 2019, International journal of molecular sciences.

[21]  A. Limone,et al.  Short communication: Space allocation in intensive Mediterranean buffalo production influences the profile of functional biomolecules in milk and dairy products. , 2019, Journal of dairy science.

[22]  Y. Guan,et al.  Role of HSD17B13 in the liver physiology and pathophysiology , 2019, Molecular and Cellular Endocrinology.

[23]  C. Cajarville,et al.  Productive performance and digestive response of dairy cows fed different diets combining a total mixed ration and fresh forage. , 2019, Journal of dairy science.

[24]  Upasna Sharma,et al.  Buffalo milk transcriptome: A comparative analysis of early, mid and late lactation , 2019, Scientific Reports.

[25]  Xiaoya Ma,et al.  Integrative Analysis of Transcriptome and GWAS Data to Identify the Hub Genes Associated With Milk Yield Trait in Buffalo , 2019, Front. Genet..

[26]  Q. Zebeli,et al.  Symposium review: The importance of the ruminal epithelial barrier for a healthy and productive cow. , 2019, Journal of dairy science.

[27]  Yun Yuting,et al.  Secreted modular calcium-binding protein 2 promotes high fat diet (HFD)-induced hepatic steatosis through enhancing lipid deposition, fibrosis and inflammation via targeting TGF-β1. , 2019, Biochemical and biophysical research communications.

[28]  C. Ao,et al.  Effects of isonitrogenous and isocaloric total mixed ration composed of forages with different quality on milk fatty acid composition and gene expression of mammary lipogenic enzymes in mid-lactating dairy cows. , 2018, Animal science journal = Nihon chikusan Gakkaiho.

[29]  A. Giovane,et al.  Ruminant meat and milk contain δ-valerobetaine, another precursor of trimethylamine N-oxide (TMAO) like γ-butyrobetaine. , 2018, Food chemistry.

[30]  L. Servillo,et al.  Carnitine Precursors and Short-Chain Acylcarnitines in Water Buffalo Milk. , 2018, Journal of agricultural and food chemistry.

[31]  Dongning Pan,et al.  Ifi27 is indispensable for mitochondrial function and browning in adipocytes. , 2018, Biochemical and biophysical research communications.

[32]  Tiangang Li,et al.  Bile acids regulate cysteine catabolism and glutathione regeneration to modulate hepatic sensitivity to oxidative injury. , 2018, JCI insight.

[33]  A. Xiang,et al.  ISL1 overexpression enhances the survival of transplanted human mesenchymal stem cells in a murine myocardial infarction model , 2018, Stem Cell Research & Therapy.

[34]  P. Aranda,et al.  Conjugated linoleic acid content and fatty acids profile of milk from grazing dairy cows in southern Chile fed varying amounts of concentrate , 2018 .

[35]  Peng Bin,et al.  Oxidation Resistance of the Sulfur Amino Acids: Methionine and Cysteine , 2017, BioMed research international.

[36]  L. Guan,et al.  Transcriptome analysis of ruminal epithelia revealed potential regulatory mechanisms involved in host adaptation to gradual high fermentable dietary transition in beef cattle , 2017, BMC Genomics.

[37]  H. Omran,et al.  Mutations in SELENBP1, encoding a novel human methanethiol oxidase, cause extra-oral halitosis , 2017, Nature Genetics.

[38]  Enni Markkanen.  Not breathing is not an option: How to deal with oxidative DNA damage. , 2017, DNA repair.

[39]  Jiusheng Wu,et al.  Effects of dietary physical or nutritional factors on morphology of rumen papillae and transcriptome changes in lactating dairy cows based on three different forage-based diets , 2017, BMC Genomics.

[40]  Zhou Du,et al.  agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update , 2017, Nucleic Acids Res..

[41]  J. Loor,et al.  Effects of dietary neutral detergent fiber and starch ratio on rumen epithelial cell morphological structure and gene expression in dairy cows. , 2017, Journal of dairy science.

[42]  Jianxin Liu,et al.  The Use of “Omics” in Lactation Research in Dairy Cows , 2017, International journal of molecular sciences.

[43]  S. Schiavon,et al.  Factors affecting variations in the detailed fatty acid profile of Mediterranean buffalo milk determined by 2-dimensional gas chromatography. , 2017, Journal of dairy science.

[44]  L. Heilbronn,et al.  Skeletal muscle extracellular matrix remodeling after short-term overfeeding in healthy humans. , 2017, Metabolism: clinical and experimental.

[45]  Z. Shen,et al.  Maintaining stability of the rumen ecosystem is associated with changes of microbial composition and epithelial TLR signaling , 2017, MicrobiologyOpen.

[46]  R. P. Ross,et al.  Effect of pasture versus indoor feeding systems on raw milk composition and quality over an entire lactation. , 2016, Journal of dairy science.

[47]  S. Kushibiki,et al.  Effects of dietary forage and calf starter on ruminal pH and transcriptomic adaptation of the rumen epithelium in Holstein calves during the weaning transition. , 2016, Physiological genomics.

[48]  H. Wiendl,et al.  The potassium channels TASK2 and TREK1 regulate functional differentiation of murine skeletal muscle cells. , 2016, American journal of physiology. Cell physiology.

[49]  G. Barton,et al.  How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? , 2015, RNA.

[50]  A. Theocharis,et al.  Extracellular matrix structure. , 2016, Advanced drug delivery reviews.

[51]  C. Indiveri,et al.  The mitochondrial carnitine/acylcarnitine carrier is regulated by hydrogen sulfide via interaction with C136 and C155. , 2016, Biochimica et biophysica acta.

[52]  J. Loor,et al.  Abundance of ruminal bacteria, epithelial gene expression, and systemic biomarkers of metabolism and inflammation are altered during the peripartal period in dairy cows. , 2015, Journal of dairy science.

[53]  A. Conesa,et al.  Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package , 2015, Nucleic acids research.

[54]  Jiuzhou Z. Song,et al.  Ruminal Transcriptomic Analysis of Grass-Fed and Grain-Fed Angus Beef Cattle , 2015, PloS one.

[55]  W. Hong,et al.  Increased biogenesis of glucagon-containing secretory granules and glucagon secretion in BIG3-knockout mice , 2015, Molecular metabolism.

[56]  M. Stipanuk,et al.  Insights into Taurine Synthesis and Function Based on Studies with Cysteine Dioxygenase (CDO1) Knockout Mice. , 2015, Advances in experimental medicine and biology.

[57]  A. Lizaso,et al.  SIM2 maintains innate host defense of the small intestine. , 2014, American journal of physiology. Gastrointestinal and liver physiology.

[58]  P. Jansen,et al.  Chemical biology tools to study pantetheinases of the vanin family. , 2014, Biochemical Society transactions.

[59]  W. Hong,et al.  BIG3 inhibits insulin granule biogenesis and insulin secretion , 2014, EMBO reports.

[60]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[61]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[62]  S. K. Jensen,et al.  Fatty acids, α-tocopherol, β-carotene, and lutein contents in forage legumes, forbs, and a grass-clover mixture. , 2013, Journal of agricultural and food chemistry.

[63]  Gilles Celeux,et al.  Data-based filtering for replicated high-throughput transcriptome sequencing experiments , 2013, Bioinform..

[64]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[65]  O. Alzahal,et al.  Adaptation to High Grain Diets Proceeds Through Minimal Immune System Stimulation and Differences in Extracellular Matrix Protein Expression in A Model of Subacute Ruminal Acidosis in Non-lactating Dairy Cows , 2012 .

[66]  Richard W. Hanson,et al.  Resurgence of Serine: An Often Neglected but Indispensable Amino Acid* , 2012, The Journal of Biological Chemistry.

[67]  M. Veiga-da-Cunha,et al.  Molecular Identification of Hydroxylysine Kinase and of Ammoniophospholyases Acting on 5-Phosphohydroxy-l-lysine and Phosphoethanolamine* , 2012, The Journal of Biological Chemistry.

[68]  M. Fraga,et al.  Epigenetics and the environment: emerging patterns and implications , 2012, Nature Reviews Genetics.

[69]  K. Yudoh,et al.  Overexpression of SPACIA1/SAAL1, a newly identified gene that is involved in synoviocyte proliferation, accelerates the progression of synovitis in mice and humans. , 2011, Arthritis and rheumatism.

[70]  P. Neufer,et al.  Diet-Induced Muscle Insulin Resistance Is Associated With Extracellular Matrix Remodeling and Interaction With Integrin α2β1 in Mice , 2011, Diabetes.

[71]  E. Borden,et al.  Emerging roles of FAM14 family members (G1P3/ISG 6-16 and ISG12/IFI27) in innate immunity and cancer. , 2011, Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research.

[72]  K. Kavanagh,et al.  UDP-glucose dehydrogenase: structure and function of a potential drug target. , 2010, Biochemical Society transactions.

[73]  R. Baldwin,et al.  Gene expression in the digestive tissues of ruminants and their relationships with feeding and digestive processes. , 2010, Animal : an international journal of animal bioscience.

[74]  I. Cuthill,et al.  Reporting : The ARRIVE Guidelines for Reporting Animal Research , 2010 .

[75]  A. Soldado,et al.  Improving the fatty acid profile of dairy cow milk by combining grazing with feeding of total mixed ration , 2010, Journal of Dairy Research.

[76]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[77]  M. Stipanuk,et al.  Dealing with methionine/homocysteine sulfur: cysteine metabolism to taurine and inorganic sulfur , 2011, Journal of Inherited Metabolic Disease.

[78]  M. Robinson,et al.  A scaling normalization method for differential expression analysis of RNA-seq data , 2010, Genome Biology.

[79]  A. Chaudhry.  Forage based animal production systems and sustainability, an invited keynote , 2008 .

[80]  E. Bayer,et al.  Plant Cell Wall Breakdown by Anaerobic Microorganisms from the Mammalian Digestive Tract , 2008, Annals of the New York Academy of Sciences.

[81]  T. Leto,et al.  Oxidative innate immune defenses by Nox/Duox family NADPH oxidases. , 2008, Contributions to microbiology.

[82]  L. Sistonen,et al.  Heat Shock Factors at a Crossroad between Stress and Development , 2007, Annals of the New York Academy of Sciences.

[83]  Z. Sellers,et al.  Calcium channel γ subunits: a functionally diverse protein family , 2007, Cell Biochemistry and Biophysics.

[84]  Z. Sellers,et al.  Calcium channel gamma subunits: a functionally diverse protein family. , 2007, Cell biochemistry and biophysics.

[85]  T. Kita,et al.  Type IV Collagen Is Transcriptionally Regulated by Smad1 under Advanced Glycation End Product (AGE) Stimulation* , 2004, Journal of Biological Chemistry.

[86]  M. Brosnan,et al.  Plasma Homocysteine Is Regulated by Phospholipid Methylation* , 2003, The Journal of Biological Chemistry.

[87]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[88]  M. Bronner‐Fraser,et al.  Identification and characterization of a calcium channel gamma subunit expressed in differentiating neurons and myoblasts. , 2002, Developmental biology.

[89]  J. Santos.  FEEDING FOR MILK COMPOSITION , 2002 .

[90]  Y. Benjamini,et al.  Controlling the false discovery rate in behavior genetics research , 2001, Behavioural Brain Research.

[91]  G. Lobley.  Control of the metabolic fate of amino acids in ruminants: a review. , 1992, Journal of animal science.

[92]  J. Sutton.  Altering Milk Composition by Feeding , 1989 .

[93]  Robert C. Wolpert,et al.  A Review of the , 1985 .