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1دورية أكاديمية
المؤلفون: Bae, Dam, Dasari, Surendra, Dennis, Courtney, Evans, Charles R, Gaul, David A, Ilkayeva, Olga, Ivanova, Anna A, Kachman, Maureen T, Keshishian, Hasmik, Lanza, Ian R, Lira, Ana C, Muehlbauer, Michael J, Nair, Venugopalan D, Piehowski, Paul D, Rooney, Jessica L, Smith, Kevin S, Stowe, Cynthia L, Zhao, Bingqing, Clark, Natalie M, Jimenez-Morales, David, Lindholm, Malene E, Many, Gina M, Sanford, James A, Smith, Gregory R, Vetr, Nikolai G, Zhang, Tiantian, Almagro Armenteros, Jose J, Avila-Pacheco, Julian, Bararpour, Nasim, Ge, Yongchao, Hou, Zhenxin, Marwaha, Shruti, Presby, David M, Natarajan Raja, Archana, Savage, Evan M, Steep, Alec, Sun, Yifei, Wu, Si, Zhen, Jimmy, Bodine, Sue C, Esser, Karyn A, Goodyear, Laurie J, Schenk, Simon, Montgomery, Stephen B, Fernández, Facundo M, Sealfon, Stuart C, Snyder, Michael P, Adkins, Joshua N, Ashley, Euan, Burant, Charles F, Carr, Steven A, Clish, Clary B, Cutter, Gary, Gerszten, Robert E, Kraus, William E, Li, Jun Z, Miller, Michael E, Nair, K Sreekumaran, Newgard, Christopher, Ortlund, Eric A, Qian, Wei-Jun, Tracy, Russell, Walsh, Martin J, Wheeler, Matthew T, Dalton, Karen P, Hastie, Trevor, Hershman, Steven G, Samdarshi, Mihir, Teng, Christopher, Tibshirani, Rob, Cornell, Elaine, Gagne, Nicole, May, Sandy, Bouverat, Brian, Leeuwenburgh, Christiaan, Lu, Ching-ju, Pahor, Marco, Hsu, Fang-Chi, Rushing, Scott, Walkup, Michael P, Nicklas, Barbara, Rejeski, W Jack, Williams, John P, Xia, Ashley, Albertson, Brent G, Barton, Elisabeth R, Booth, Frank W, Caputo, Tiziana, Cicha, Michael, De Sousa, Luis Gustavo Oliveira, Farrar, Roger, Hevener, Andrea L, Hirshman, Michael F, Jackson, Bailey E, Ke, Benjamin G, Kramer, Kyle S, Lessard, Sarah J, Makarewicz, Nathan S, Marshall, Andrea G, Nigro, Pasquale
المصدر: Nature. 629(8010)
مصطلحات موضوعية: Health Sciences, Sports Science and Exercise, Prevention, Genetics, Human Genome, Physical Activity, Behavioral and Social Science, Cardiovascular, Aetiology, 1.1 Normal biological development and functioning, Underpinning research, 2.1 Biological and endogenous factors, Inflammatory and immune system, Generic health relevance, Good Health and Well Being, Animals, Female, Humans, Male, Rats, Acetylation, Blood, Cardiovascular Diseases, Databases, Factual, Endurance Training, Epigenome, Inflammatory Bowel Diseases, Internet, Lipidomics, Metabolome, Mitochondria, Multiomics, Non-alcoholic Fatty Liver Disease, Organ Specificity, Phosphorylation, Physical Conditioning, Animal, Physical Endurance, Proteome, Proteomics, Time Factors, Transcriptome, Ubiquitination, Wounds and Injuries, MoTrPAC Study Group, Lead Analysts, MoTrPAC Study Group, General Science & Technology
وصف الملف: application/pdf
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2دورية أكاديمية
المؤلفون: Gentry, Emily C, Collins, Stephanie L, Panitchpakdi, Morgan, Belda-Ferre, Pedro, Stewart, Allison K, Carrillo Terrazas, Marvic, Lu, Hsueh-han, Zuffa, Simone, Yan, Tingting, Avila-Pacheco, Julian, Plichta, Damian R, Aron, Allegra T, Wang, Mingxun, Jarmusch, Alan K, Hao, Fuhua, Syrkin-Nikolau, Mashette, Vlamakis, Hera, Ananthakrishnan, Ashwin N, Boland, Brigid S, Hemperly, Amy, Vande Casteele, Niels, Gonzalez, Frank J, Clish, Clary B, Xavier, Ramnik J, Chu, Hiutung, Baker, Erin S, Patterson, Andrew D, Knight, Rob, Siegel, Dionicio, Dorrestein, Pieter C
المصدر: Nature. 626(7998)
مصطلحات موضوعية: Medical Biochemistry and Metabolomics, Analytical Chemistry, Biomedical and Clinical Sciences, Chemical Sciences, Inflammatory Bowel Disease, Digestive Diseases, Crohn's Disease, Prevention, Animals, Humans, Bifidobacterium, Bile Acids and Salts, CD4-Positive T-Lymphocytes, Clostridium, Cohort Studies, Crohn Disease, Enterococcus, Esters, Fatty Acids, Inflammatory Bowel Diseases, Metabolomics, Phenotype, Pregnane X Receptor, Reproducibility of Results, Tandem Mass Spectrometry, Amides, General Science & Technology
وصف الملف: application/pdf
الوصول الحر: https://escholarship.org/uc/item/9tp855xwTest
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3دورية أكاديمية
المؤلفون: Paik, Donggi, Yao, Lina, Zhang, Yancong, Bae, Sena, D’Agostino, Gabriel D, Zhang, Minghao, Kim, Eunha, Franzosa, Eric A, Avila-Pacheco, Julian, Bisanz, Jordan E, Rakowski, Christopher K, Vlamakis, Hera, Xavier, Ramnik J, Turnbaugh, Peter J, Longman, Randy S, Krout, Michael R, Clish, Clary B, Rastinejad, Fraydoon, Huttenhower, Curtis, Huh, Jun R, Devlin, A Sloan
المصدر: Nature. 603(7903)
مصطلحات موضوعية: Inflammatory Bowel Disease, Digestive Diseases, 2.1 Biological and endogenous factors, Aetiology, Underpinning research, 1.1 Normal biological development and functioning, Oral and gastrointestinal, Inflammatory and immune system, Bacteria, Bile Acids and Salts, Cell Differentiation, Gastrointestinal Tract, Humans, Inflammatory Bowel Diseases, Interleukin-17, Lithocholic Acid, Th17 Cells, General Science & Technology
وصف الملف: application/pdf
الوصول الحر: https://escholarship.org/uc/item/3h0402bcTest
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4دورية أكاديميةA distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning
المؤلفون: Vatanen, Tommi, Ang, Qi Yan, Siegwald, Léa, Sarker, Shafiqul Alam, Le Roy, Caroline I., Duboux, Stéphane, Delannoy-Bruno, Omar, Ngom-Bru, Catherine, Boulangé, Claire L., Stražar, Martin, Avila-Pacheco, Julian, Deik, Amy, Pierce, Kerry, Bullock, Kevin, Dennis, Courtney, Sultana, Shamima, Sayed, Sharika, Rahman, Mahbubar, Ahmed, Tahmeed, Modesto, Monica, Mattarelli, Paola, Clish, Clary B., Vlamakis, Hera, Plichta, Damian R., Sakwinska, Olga, Xavier, Ramnik J.
المساهمون: CAMM - Research Program for Clinical and Molecular Metabolism, University of Helsinki, Faculty Common Matters (Faculty of Medicine)
مصطلحات موضوعية: bifidobacteria, Bifidobacterium longum, breastfeeding, diarrhea, gut metabolome, infant growth, infant gut, microbiome, weaning, 3111 Biomedicine, 1182 Biochemistry, cell and molecular biology
وصف الملف: application/pdf
العلاقة: Finally, B. longum subsp. infantis and its associated metabolites, such as indolelactate, were positively correlated with two measures of growth (WFL and WFA) in our cohort, thus adding to a growing body of evidence supporting the importance of B. longum subsp. infantis and its metabolites for infant development (Barratt et al., 2022). We found N-acetylglutamate levels in the stool, as well as two microbial pathways involving N-acetylglutamate, to be positively associated with all tested growth measures including LFA. This observation is notable since bacterially produced N-acetyl amino acids enhanced growth in a Drosophila model (Gallo et al., 2021; Martino et al., 2018). A more recent study provided mechanistic insights on how a related compound, N-acetylglutamine, promoted growth in a Drosophila model via down-regulation of a peptidoglycan recognition protein and immune effectors against beneficial microbes, thus providing an intriguing example of host-microbe symbiosis wherein bacterial metabolic products mediate host immune regulation and growth (Gallo et al., 2021; Martino et al., 2018).We would like to thank participants and their families for their involvement in the study. We thank Tiffany Poon, Luke Besse, and Sara Garamszegi for project management of sample processing and data handling. We thank Florence Rochat, Nadine Porta, Anne Bruttin and Solenn Pruvost for technical assistance in obtaining and sequencing bacterial isolates. We also thank the Broad Institute Genomics Platform and Microbial ‘Omics Core for help with sequencing data generation and sample processing. We are grateful to Heather Kang for editorial assistance. Generation of metagenomics and metabolomics data was supported by a grant from Nestle to the Broad Institute (H.V.). Principal investigators, T.V. O.S. H.V. and R.J.X.; metagenomic data analysis, T.V. Q.Y.A. L.S. and D.R.P.; metabolomic data analysis, T.V. Q.Y.A. M.S. A.D. K.P. K.B. C.D. J.A.-P. and C.B.C.; bacterial isolation and genome sequencing and annotation, L.S. S.D. C.N.-B. and O.S.; phylogenetic and functional genomic analyses: T.V. L.S. S.D. C.N.-B. and O.D.-B.; study design, S.A.S. and T.A.; collection of samples and health information, S.A.S. S.Sayed, S.Sultana, and M.R.; manuscript drafting: T.V. Q.Y.A. L.S. C.I.L.R. C.L.B. D.R.P. S.D. O.D.-B. O.S. and R.J.X. All authors discussed the results, critically reviewed the text, and approved the final manuscript. L.S. C.L.B. C.I.L.R. S.D. O.D-B. C.N-B. and O.S. are employees of Société des Produits Nestlé (SPN). R.J.X. is a member of the Scientific Advisory Board at Nestlé, founder of Jnana and Celsius Therapeutics and board member of MoonLake Immunotherapeutics. We filed a patent related to findings described in this study. R.J.X. H.V. T.V. O.S. L.S. S.D. and C.N.-B. are listed as inventors (Bifidobacterium Longum Transitional Microorganisms, Compositions and Uses Thereof, PCT/US2022/035,310). We would like to thank participants and their families for their involvement in the study. We thank Tiffany Poon, Luke Besse, and Sara Garamszegi for project management of sample processing and data handling. We thank Florence Rochat, Nadine Porta, Anne Bruttin and Solenn Pruvost for technical assistance in obtaining and sequencing bacterial isolates. We also thank the Broad Institute Genomics Platform and Microbial ‘Omics Core for help with sequencing data generation and sample processing. We are grateful to Heather Kang for editorial assistance. Generation of metagenomics and metabolomics data was supported by a grant from Nestle to the Broad Institute (H.V.).; Vatanen , T , Ang , Q Y , Siegwald , L , Sarker , S A , Le Roy , C I , Duboux , S , Delannoy-Bruno , O , Ngom-Bru , C , Boulangé , C L , Stražar , M , Avila-Pacheco , J , Deik , A , Pierce , K , Bullock , K , Dennis , C , Sultana , S , Sayed , S , Rahman , M , Ahmed , T , Modesto , M , Mattarelli , P , Clish , C B , Vlamakis , H , Plichta , D R , Sakwinska , O & Xavier , R J 2022 , ' A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning ' , Cell , vol. 185 , no. 23 , pp. 4280-4297.e12 . https://doi.org/10.1016/j.cell.2022.10.011Test; ORCID: /0000-0003-0949-1291/work/128033163; http://hdl.handle.net/10138/573344Test; 51bb33c1-fd6c-48ca-bf9d-c4596edd9d6e; 85141522383; 000908351600006
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5دورية أكاديمية
المؤلفون: Vatanen, Tommi, Jabbar, Karolina S., Ruohtula, Terhi, Honkanen, Jarno, Avila-Pacheco, Julian, Siljander, Heli, Stražar, Martin, Oikarinen, Sami, Hyöty, Heikki, Ilonen, Jorma, Mitchell, Caroline M., Yassour, Moran, Virtanen, Suvi M., Clish, Clary B., Plichta, Damian R., Vlamakis, Hera, Knip, Mikael, Xavier, Ramnik J.
المساهمون: CAMM - Research Program for Clinical and Molecular Metabolism, Faculty Common Matters (Faculty of Medicine), University of Helsinki, Children's Hospital, Helsinki University Hospital Area, HUS Children and Adolescents, Clinicum
مصطلحات موضوعية: gut metabolome, horizontal gene transfer, infant gut microbiome, mother-to-infant microbiome transmission, 3111 Biomedicine, 1182 Biochemistry, cell and molecular biology
وصف الملف: application/pdf
العلاقة: We thank Tiffany Poon, Luke Besse, and Timothy Arthur for sample and data management and Theresa Reimels for editorial assistance and figure preparation. This work was funded by the National Institutes of Health ( P30 DK043351 to R.J.X.), Juvenile Diabetes Research Foundation ( 2-SRA-2016-247-S-B ), Center for Microbiome Informatics and Therapeutics, and Wallenberg Foundations (to K.S.J.). M.Y. is the Rosalind, Paul and Robin Berlin Faculty Development Chair in Perinatal Research. We thank Tiffany Poon, Luke Besse, and Timothy Arthur for sample and data management and Theresa Reimels for editorial assistance and figure preparation. This work was funded by the National Institutes of Health (P30 DK043351 to R.J.X.), Juvenile Diabetes Research Foundation (2-SRA-2016-247-S-B), Center for Microbiome Informatics and Therapeutics, and Wallenberg Foundations (to K.S.J.). M.Y. is the Rosalind, Paul and Robin Berlin Faculty Development Chair in Perinatal Research. T.V. H.V. M.K. and R.J.X. served as principal investigators. T.V. and K.S.J. analyzed metagenomic data. T.V. K.S.J. J.A.-P. M.S. C.B.C. and D.R.P. analyzed metabolomic data. T.R. analyzed intestinal biomarkers. J.H. analyzed cytokines. T.R. J.H. H.S. S.O. H.H. J.I. S.M.V. and M.K. contributed to collection of stool and blood samples and patient information. M.Y. and C.M.M. collected breast milk samples. T.V. K.S.J. D.R.P. H.V. and R.J.X. drafted the manuscript. All authors discussed the results, critically reviewed the text, and approved the final manuscript. R.J.X. is co-founder of Jnana Therapeutics and Celsius Therapeutics, board director at MoonLake Immunotherapeutics, and consultant to Nestlé; these organizations had no role in the study.; Vatanen , T , Jabbar , K S , Ruohtula , T , Honkanen , J , Avila-Pacheco , J , Siljander , H , Stražar , M , Oikarinen , S , Hyöty , H , Ilonen , J , Mitchell , C M , Yassour , M , Virtanen , S M , Clish , C B , Plichta , D R , Vlamakis , H , Knip , M & Xavier , R J 2022 , ' Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism ' , Cell , vol. 185 , no. 26 , pp. 4921-4936.e15 . https://doi.org/10.1016/j.cell.2022.11.023Test , https://doi.org/10.1016/j.cell.2022.11.023Test; ORCID: /0000-0002-2779-3384/work/128032679; ORCID: /0000-0003-0949-1291/work/128033162; 85144246023; b361273f-28e6-4eab-a116-e5c6f415caea; http://hdl.handle.net/10138/569828Test; 000910695500001
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6دورية أكاديمية
المؤلفون: Bhosle, Amrisha, Bae, Sena, Zhang, Yancong, Chun, Eunyoung, Avila-Pacheco, Julian, Geistlinger, Ludwig, Pishchany, Gleb, Glickman, Jonathan N, Michaud, Monia, Waldron, Levi, Clish, Clary B, Xavier, Ramnik J, Vlamakis, Hera, Franzosa, Eric A, Garrett, Wendy S, Huttenhower, Curtis
المصدر: EMBO Press
مصطلحات موضوعية: Applied Mathematics, Computational Theory and Mathematics, General Agricultural and Biological Sciences, General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, Information Systems
وصف الملف: application/pdf
العلاقة: Molecular Systems Biology; https://hdl.handle.net/1721.1/153816Test; Bhosle, Amrisha, Bae, Sena, Zhang, Yancong, Chun, Eunyoung, Avila-Pacheco, Julian et al. 2024. "Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease." Molecular Systems Biology.
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7دورية أكاديمية
المؤلفون: Ambrosio, Laura Fernanda, Volpini, Ximena, Quiroz, Juan Nahuel, Brugo, María Belén, Knubel, Carolina Paola, Herrera, Melisa Rocío, Fozzatti, Laura, Avila Pacheco, Julián, Clish, Clary B., Takenaka, Maisa C., Beloscar, Juan, Theumer, Martín Gustavo, Quintana, Francisco Javier, Perez, Ana Rosa, Motrán, Claudia Cristina
المصدر: Frontiers in Immunology ; volume 14 ; ISSN 1664-3224
مصطلحات موضوعية: Immunology, Immunology and Allergy
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8دورية أكاديمية
المؤلفون: Schirmer, Melanie, Stražar, Martin, Avila-Pacheco, Julian, Rojas-Tapias, Daniel F., Brown, Eric M., Temple, Emily, Deik, Amy, Bullock, Kevin, Jeanfavre, Sarah, Pierce, Kerry, Jin, Shen, Invernizzi, Rachele, Pust, Marie-Madlen, Costliow, Zach, Mack, David R., Griffiths, Anne M., Walters, Thomas, Boyle, Brendan M., Kugathasan, Subra, Vlamakis, Hera, Hyams, Jeffrey, Denson, Lee, Clish, Clary B., Xavier, Ramnik J.
المصدر: Cell Host & Microbe ; volume 32, issue 2, page 209-226.e7 ; ISSN 1931-3128
مصطلحات موضوعية: Virology, Microbiology, Parasitology
الإتاحة: https://doi.org/10.1016/j.chom.2023.12.013Test
https://api.elsevier.com/content/article/PII:S1931312823005085?httpAccept=text/xmlTest
https://api.elsevier.com/content/article/PII:S1931312823005085?httpAccept=text/plainTest -
9دورية أكاديمية
المؤلفون: Sturm, Alexander, Sun, Penny, Avila-Pacheco, Julian, Clatworthy, Anne E., Bloom-Ackermann, Zohar, Wuo, Michael G., Gomez, James E., Jin, Soomin, Clish, Clary B., Kiessling, Laura L., Hung, Deborah T.
المساهمون: Philips, Jennifer, Broad Institute TB Gift Donors
المصدر: mBio ; volume 15, issue 2 ; ISSN 2150-7511
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10دورية أكاديمية
المؤلفون: Wagner, Allon, Wang, Chao, Fessler, Johannes, DeTomaso, David, Avila-Pacheco, Julian, Kaminski, James, Zaghouani, Sarah, Christian, Elena, Thakore, Pratiksha, Schellhaass, Brandon, Akama-Garren, Elliot, Pierce, Kerry, Singh, Vasundhara, Ron-Harel, Noga, Douglas, Vivian Paraskevi, Bod, Lloyd, Schnell, Alexandra, Puleston, Daniel, Sobel, Raymond A, Haigis, Marcia, Pearce, Erika L, Soleimani, Manoocher, Clish, Clary, Regev, Aviv, Kuchroo, Vijay K, Yosef, Nir
المصدر: Cell. 184(16)
مصطلحات موضوعية: Brain Disorders, Autoimmune Disease, Genetics, 2.1 Biological and endogenous factors, Aetiology, Inflammatory and immune system, Acetyltransferases, Adenosine Triphosphate, Aerobiosis, Algorithms, Animals, Autoimmunity, Chromatin, Citric Acid Cycle, Cytokines, Eflornithine, Encephalomyelitis, Autoimmune, Experimental, Epigenome, Fatty Acids, Glycolysis, Jumonji Domain-Containing Histone Demethylases, Mice, Inbred C57BL, Mitochondrial Membrane Transport Proteins, Models, Biological, Oxidation-Reduction, Putrescine, Single-Cell Analysis, T-Lymphocytes, Regulatory, Th17 Cells, Transcriptome, DFMO, T helper 17 cell, experimental autoimmune encephalomyelitis, immunometabolism, in silico metabolic modeling, multiple sclerosis, polyamines, putrescine, single cell transcriptomics, spermidine, Biological Sciences, Medical and Health Sciences, Developmental Biology
وصف الملف: application/pdf
الوصول الحر: https://escholarship.org/uc/item/5mk3b7x2Test