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Weight, habitual fibre intake, and microbiome composition predict tolerance to fructan supplementation

Journal of Plant Foods 2024年第6期75卷

作者： Jeffrey Letourneau Benjamin C. Neubert Diana Dayal Verónica M. Carrion Heather K. Durand Eric P. Dallow Sharon Jiang Michelle Kirtley Geoffrey S. Ginsburg P. Murali Doraiswamy Lawrence A. David a Department of Molecular Genetics and Microbiology Duke University School of Medicine Durham NC USA b Program in Computational Biology and Bioinformatics Duke University School of Medicine Durham NC USA c School of Medicine University of North Carolina Chapel Hill NC USA d Duke Office of Clinical Research Duke University Durham NC USA e Duke Center for Applied Genomics and Precision Medicine Duke University Health System Durham NC USAf Department of Medicine Duke University School of Medicine Durham NC USA e Duke Center for Applied Genomics and Precision Medicine Duke University Health System Durham NC USAf Department of Medicine Duke University School of Medicine Durham NC USAg Department of Psychiatry Duke University School of Medicine Durham NC USAh Duke Microbiome Center Duke University School of Medicine Durham NC USA a Department of Molecular Genetics and Microbiology Duke University School of Medicine Durham NC USAb Program in Computational Biology and Bioinformatics Duke University School of Medicine Durham NC USAh Duke Microbiome Center Duke University School of Medicine Durham NC USA

Fructans are commonly used as dietary fibre supplements for their ability to promote the growth of beneficial gut microbes. However, fructan consumption has been associated with various dosage-dependent side effects. We characterised side effects in an exploratory analysis of a randomised trial in healthy adults (n= 40) who consumed 18 g/day inulin or placebo. We found that individuals weighing more or habitually consuming higher fibre exhibited the best tolerance. Furthermore, we identified associations between gut microbiome composition and host tolerance. Specifically, higher levels ofChristensenellaceae R-7 groupwere associated with gastrointestinal discomfort, and a machine-learning-based approach successfully predicted high levels of flatulence, with[Ruminococcus] torques groupand (Oscillospiraceae)UCG-002 *** as key predictive taxa. These data reveal trends that can help guide personalised recommendations for initial inulin dosage. Our results support prior ecological findings indicating that fibre supplementation has the greatest impact on individuals whose baseline fibre intake is lowest.

关键词： Microbiome inulin dietary fibre gastroenterology bioinformatics

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Cover Image, Volume 20, Issue 9

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Diabetes, Obesity and Metabolism 2018年第9期20卷 i-i页

作者： Ji H. Han PhD Hanho Shin Jun G. Rho Jung-Eun Kim Dong H. Son Juhwan Yoon Yong J. Lee PhD Jung-Hyuck Park Byung J. Song PhD Chang-Sik Choi Seul G. Yoon Il Y. Kim PhD Eun K. Lee PhD Je K. Seong DVM Ki W. Kim PhD Wook Kim PhD Department of Molecular Science & Technology Ajou University Suwon South Korea Department of Oral Biology BK21 PLUS Yonsei University College of Dentistry Seoul South Korea Department of Pharmacology CKD Research Institute Yongin South Korea JW Pharmaceutical Seoul South Korea Laboratory of Developmental Biology and Genomics Research Institute for Veterinary Science and BK21 PLUS Program for Creative Veterinary Science Research College of Veterinary Medicine Seoul National University Seoul South Korea Korea Mouse Phenotyping Center (KMPC) Seoul National University Seoul South Korea Department of Biochemistry College of Medicine The Catholic University of Korea Seoul South Korea Interdisciplinary Program for Bioinformatics Program for Cancer Biology and BIO-MAX/N-Bio Institute Seoul National University Seoul South Korea

The cover image, by Ji H. Han et al., is based on the Original Article Peripheral cannabinoid 1 receptor blockade mitigates adipose tissue inflammation via NLRP3 inflammasome in mouse models of obesity , DOI: 10.1111/...

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An integrative approach to investigate the respective roles of single-nucleotide variants and copy-number variants in Attention-Deficit/Hyperactivity Disorder (vol 6, 22851, 2016)

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SCIENTIFIC REPORTS 2016年第1期6卷 22851-22851页

作者： Lima, Leandro de Araujo Feio-dos-Santos, Ana Cecilia Belangero, Sintia Iole Gadelha, Ary Bressan, Rodrigo Affonseca Salum, Giovanni Abrahao Pan, Pedro Mario Moriyama, Tais Silveira Graeff-Martins, Ana Soledade Tamanaha, Ana Carina Alvarenga, Pedro Krieger, Fernanda Valle Fleitlich-Bilyk, Bacy Jackowski, Andrea Parolin Brietzke, Elisa Sato, Joao Ricardo Polanczyk, Guilherme Vanoni Mari, Jair de Jesus Manfro, Gisele Gus do Rosario, Maria Conceiao Miguel, Euripedes Constantino Puga, Renato David Tahira, Ana Carolina Souza, Viviane Neri Chile, Thais Gouveia, Gisele Rodrigues Simoes, Sergio Nery Chang, Xiao Pellegrino, Renata Tian, Lifeng Glessner, Joseph T. Hashimoto, Ronaldo Fumio Rohde, Luis Augusto Sleiman, Patrick M. A. Hakonarson, Hakon Brentani, Helena Inter-institutional Grad Program on Bioinformatics University of São Paulo São Paulo SP Brazil Center for Applied Genomics The Children’s Hospital of Philadelphia Philadelphia PA USA Department & Institute of Psychiatry University of São Paulo Medical School São Paulo SP Brazil National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq) São Paulo SP Brazil Department of Psychiatry Federal University of São Paulo São Paulo SP Brazil National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq) São Paulo SP Brazil Department of Psychiatry Federal University of São Paulo São Paulo SP Brazil National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq) São Paulo SP Brazil Department of Psychiatry Federal University of São Paulo São Paulo SP Brazil National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq) São Paulo SP Brazil Department of Psychiatry Hospital de Clínicas de Porto Alegre Federal University of Rio Grande do Sul Porto Alegre RS Brazil National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq) São Paulo SP Brazil Department of Psychiatry Federal University of São Paulo São Paulo SP Brazil Department & Institute of Psychiatry University of São Paulo Medical School São Paulo SP Brazil National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq) São Paulo SP Brazil Department of Psychiatry Federal University of São Paulo São Paulo SP Brazil Department & Institute of Psychiatry University of São Paulo Medical School São Paulo SP Brazil National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq) São Paulo SP Brazil National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq) São Paulo SP Brazil Department of Psychiatry Federal University of São Paulo São Paulo SP Brazil Department & Institute of Psychiatry University of S

Many studies have attempted to investigate the genetic susceptibility of Attention-Deficit/Hyperactivity Disorder (ADHD), but without much success. The present study aimed to analyze both single-nucleotide and copy-number variants contributing to the genetic architecture of ADHD. We generated exome data from 30 Brazilian trios with sporadic ADHD. We also analyzed a Brazilian sample of 503 children/adolescent controls from a High Risk Cohort Study for the Development of Childhood Psychiatric Disorders, and also previously published results of five CNV studies and one GWAS meta-analysis of ADHD involving children/adolescents. The results from the Brazilian trios showed that cases with de novo SNVs tend not to have de novo CNVs and vice-versa. Although the sample size is small, we could also see that various comorbidities are more frequent in cases with only inherited variants. Moreover, using only genes expressed in brain, we constructed two “in silico” protein-protein interaction networks, one with genes from any analysis, and other with genes with hits in two analyses. Topological and functional analyses of genes in this network uncovered genes related to synapse, cell adhesion, glutamatergic and serotoninergic pathways, both confirming findings of previous studies and capturing new genes and genetic variants in these pathways.

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The Association Between Levels of Plasma Biomarkers and Cognitive Performance in the Oldest Old

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Alzheimer's & Dementia 2023年第S14期19卷

作者： Linda M.C. Lorenz Meng Zhang Niccoló Tesi Sven J van der Lee Marc Hulsman Mariam Gouda Sietske A.M. Sikkes Charlotte E. Teunissen Henne Holstege Genomics of Neurodegenerative Diseases and Aging Human Genetics Vrije Universiteit Amsterdam Amsterdam UMC location VUmc Amsterdam The Netherlands Amsterdam Netherlands Alzheimer Center Amsterdam Department of Neurology Amsterdam Neuroscience Vrije Universiteit Amsterdam Amsterdam UMC Amsterdam Netherlands Amsterdam Neuroscience Neurodegeneration Amsterdam The Netherlands Amsterdam Netherlands Correspondece Delft Bioinformatics Lab Delft Technical University Delft Netherlands Delft University of Technology Delft Netherlands Genomics of Neurodegenerative Diseases and Aging Human Genetics Vrije Universiteit Amsterdam Amsterdam UMC location VUmc Amsterdam Netherlands Alzheimer Center Amsterdam Neurology Vrije Universiteit Amsterdam Amsterdam UMC location VUmc Amsterdam Netherlands Amsterdam Neuroscience Neurodegeneration Amsterdam Netherlands Genomics of Neurodegenerative Diseases and Aging Human Genetics Vrije Universiteit Amsterdam Amsterdam UMC location VUmc Amsterdam Amsterdam Netherlands Alzheimer Centre Department of Neurology Amsterdam Neuroscience Vrije Universiteit Amsterdam Amsterdam UMC Amsterdam The Netherlands Amsterdam Netherlands 3. Delft Bioinformatics Lab Delft University of Technology Delft The Netherlands Delft Netherlands Neurochemistry Laboratory Department of Clinical Chemistry Amsterdam Neuroscience Vrije Universiteit Amsterdam Amsterdam UMC Amsterdam Netherlands Amsterdam UMC location VUmc Amsterdam Netherlands Faculty of Behavioural and Movement Sciences Clinical Developmental Psychology & Clinical Neuropsychology Vrije Universiteit Amsterdam Amsterdam Netherlands Department of Epidemiology and Biostatistics VU University Medical Center Amsterdam Netherlands Neurochemistry Laboratory Department of Clinical Chemistry Amsterdam Neuroscience Program Neurodegeneration Amsterdam UMC Vrije Universiteit Amsterdam Amsterdam The Netherlands Amsterdam Netherlands Genomics of Neurodegenerative Diseases and Aging Human Gene

Background Lower cognitive performance in Alzheimer’s Disease (AD) patients has been correlated with changes in blood-based biomarkers Amyloid-βeta-40 (Aβ 40 ) , Amyloid-βeta-42 (Aβ 42 ), phosphorylated Tau (pTau), neurofilament light (NfL) and glial fibrillary acidic protein (GFAP). However, it is still unclear whether there is an association between cognitive performance and plasma biomarkers in the oldest old. Here we investigate I) The association of plasma biomarkers with age across a wide age-continuum until extreme age (≥100 years); II) To what extent plasma biomarkers associate with cognitive performance ≥100 years. Method The Dutch 100-plus study cohort comprises of self-reported cognitively healthy centenarians. Biomarkers were measured in 202 centenarians (137 females) on the Simoa platform. We also included centenarian siblings, offspring and their respective partners (N = 318), who were cognitively healthy. I) To investigate the relationship between age and biomarkers, we standardized all biomarkers and performed linear regression analyses. II) Cognitive performance in centenarians was determined using a comprehensive neuropsychological test battery assessing several cognitive domains. Biomarker concentrations were divided into tertiles. Cognitive performance was assessed adjusting for age, sex and education. Result I) We observed an age-related increase Aβ 40 (r s = 0.70; range 46.5-286.5 pg/mL) , Aβ 42 (r s = 0.53; range 1.4-17.7 pg/mL), pTau-181(r s = 0.68; range 0.5-12.8 pg/mL), NfL (r s = 0.81; range 4.5-378.7 pg/mL) and GFAP (r s = 0.76; range 24.4-1085.1 pg/mL), or decrease in Aβ 42/40 (r s = -0.43; range 0.01–0.10 pg/mL; P <0.001 for all biomarkers, Figure 1). II) Lower Aβ 42/40 was associated with lower cognitive performance on global cognition (based on composite z -score of all tests) β(95%CI) 0.26(0.00–0.51), P = 0.002) and domain executive functioning β(95%CI) 0.16(-0.07–0.40), P = 0.039), but not with the Mini-Mental State Examination (MMS

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Correction to: Comparative genome analyses of four rice-infecting Rhizoctonia solani isolates reveal extensive enrichment of homogalacturonan modification genes

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BMC genomics 2021年第1期22卷 306页

作者： Da-Young Lee Jongbum Jeon Ki-Tae Kim Kyeongchae Cheong Hyeunjeong Song Gobong Choi Jaeho Ko Stephen O Opiyo James C Correll Shimin Zuo Sheshu Madhav Guo-Liang Wang Yong-Hwan Lee Department of Plant Pathology The Ohio State University Columbus OH 43210 USA. Fungal Bioinformatics Laboratory Seoul National University Seoul 08826 South Korea. Interdisciplinary Program in Agricultural Genomics Seoul National University Seoul 08826 South Korea. Department of Agricultural Life Science Sunchon National University Suncheon 57922 South Korea. Department of Agricultural Biotechnology Seoul National University Seoul 08826 South Korea. Ohio Agricultural Research and Development Center (OARDC) Molecular & Cellular Imaging Center (MCIC)-Columbus The Ohio State University Columbus OH 43210 USA. Department of Entomology & Plant Pathology University of Arkansas Fayetteville AK 72701 USA. Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding Agricultural College of Yangzhou University Yangzhou China. Indian Council of Agricultural Research-Indian Institute of Rice Research (ICAR-IIRR) Hyderabad Telangana 500030 India. Department of Plant Pathology The Ohio State University Columbus OH 43210 USA. wang.620@osu.edu. Fungal Bioinformatics Laboratory Seoul National University Seoul 08826 South Korea. yonglee@snu.ac.kr. Interdisciplinary Program in Agricultural Genomics Seoul National University Seoul 08826 South Korea. yonglee@snu.ac.kr. Department of Agricultural Biotechnology Seoul National University Seoul 08826 South Korea. yonglee@snu.ac.kr. Center for Fungal Genetic Resources Plant Immunity Research Center Plant Genomics and Breeding Institute and Research Institute of Agriculture and Life Sciences Seoul National University Seoul 08826 South Korea. yonglee@snu.ac.kr.

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Identification of Genetic Variants and Serum Metabolites Associated with Blood-derived Mitochondrial DNA Copy Number

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Alzheimer's & Dementia 2022年第S6期18卷

作者： Tong Tong John Farrell Congcong Zhu Zainab Khurshid Eden R. Martin William S. Bush Margaret A. Pericak-Vance Li-San Wang Gerard D. Schellenberg Jonathan L. Haines Kathryn L. Lunetta Lindsay A. Farrer Xiaoling Zhang Disease Sequencing Project Boston University School of Medicine Boston MA USA Boston University Bioinformatics Program Boston MA USA John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA Case Western Reserve University School of Medicine Cleveland OH USA John P. Hussman Institute for Human Genomics Miller School of Medicine University of Miami Miami FL USA University of Pennsylvania Perelman School of Medicine Philadelphia PA USA University of Pennsylvania Perelman School of Medicine Path & Lab Med Stellar Chance Philadelphia PA USA Case Western Reserve University School of Medicine Department of Population & Quantitative Health Sciences Cleveland Institute for Computational Biology Cleveland OH USA Boston University School of Public Health Boston MA USA

Background Mitochondrial DNA Copy Number (mtDNA-CN) can be used to estimate mitochondrial function and it varies across tissues and cell types. Blood-derived mtDNA-CN has been studied in aging-related diseases including Alzheimer’s Disease (AD). However, little is known about the genetic contribution to variation of blood-derived mtDNA-CN and how this variation affects the level of serum metabolites. Method We developed a fast computational pipeline to accurately estimate mtDNA-CN using whole genome sequence data from blood samples from European ancestry (EA, 2,885 AD cases and 2,777 controls), African American (AA, 1,118 AD cases and 1,725 controls), and Caribbean Hispanic (CH, 1,022 AD cases and 1,949 controls) participants of the Alzheimer’s Disease Sequencing Project (ADSP). In the combined sample and within each population group. We tested association of blood-derived mtDNA-CN with 17,569,705 variants (minor allele count≥20) genome-wide using a linear mixed effect model including covariates for age, sex, sequencing center, PCR, AD status, polygenic risk score of blood cell count, and principal components of ancestry. We also tested the associations of mtDNA-CN and levels of 175 serum metabolites in 1,521 subjects from Alzheimer’s Disease Neuroimaging Initiative. Result In the total sample, we identified genome-wide significant (GWS) associations with variants from 24 independent loci. The top-ranked SNP (rs1455130415 in NDUFS8 , (p=3.25x10 -42 ) was also GWS in EAs (p=3.96x10 -28 ) and AAs (p=2.20x10 -27 ). SNP rs997412864 (p=5.13x10 -9 ) in GCAT was found associated with mtDNA-CN in EAs, but not in other groups. Association of SNP rs1237233197 (p=1.40x10 -8 ) in NDUFS7 was specific to AAs. Measurements of two long-chain acylcarnitine, C14:2-OH (p=4.91x10 -7 ) and C18:2 (p=1.81x10 -5 ), were negatively associated with mtDNA-CN after Bonferroni correction (P<2.9x10 -4 ). Ornithine, a non-proteinogenic amino acid, was also negatively associated with mtDNA-CN (p=2

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Author Correction: Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis

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Nature genetics 2024年第6期56卷 1319页

作者： Sneha Mitra Rohan Malik Wilfred Wong Afsana Rahman Alexander J Hartemink Yuri Pritykin Kushal K Dey Christina S Leslie Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York City NY USA. Rye Country Day School Rye NY USA. Tri-Institutional Training Program in Computational Biology and Medicine New York City NY USA. Hunter College City University of New York New York City NY USA. Department of Computer Science Duke University Durham NC USA. Program in Computational Biology and Bioinformatics Duke University Durham NC USA. Center for Genomic and Computational Biology Duke University Durham NC USA. Department of Computer Science Princeton University Princeton NJ USA. Lewis-Sigler Institute for Integrative Genomics Princeton University Princeton NJ USA. Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York City NY USA. deyk@***. Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York City NY USA. lesliec@***.

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Expression of concern: Microchip-based structure determination of low-molecular weight proteins using cryo-electron microscopy

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Nanoscale 2024年第9期16卷 4919页

作者： Michael A Casasanta G M Jonaid Liam Kaylor William Y Luqiu Maria J Solares Mariah L Schroen William J Dearnaley Jarad Wilson Madeline J Dukes Deborah F Kelly Department of Biomedical Engineering Pennsylvania State University University Park PA 16802 USA. Debkelly@psu.edu. Materials Research Institute Pennsylvania State University University Park PA 16802 USA. Bioinformatics and Genomics Graduate Program Huck Institutes of the Life Sciences Pennsylvania State University University Park PA 16802 USA. Molecular Cellular and Integrative Biosciences Graduate Program Huck Institutes of the Life Sciences Pennsylvania State University University Park PA 16802 USA. Department of Electrical and Computer Engineering Duke University Durham NC 27708 USA. RayBiotech Life Peachtree Corners GA 30092 USA. Applications Science Protochips Inc. Morrisville NC 27560 USA.

Expression of concern for 'Microchip-based structure determination of low-molecular weight proteins using cryo-electron microscopy' by Michael A. Casasanta , , 2021, , 7285-7293, https://***/10.1039/D1NR00388G.

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High-Resolution Imaging of Human Viruses in Liquid Droplets

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Advanced materials (Deerfield Beach, Fla.) 2021年第37期33卷 e2103221页

作者： G M Jonaid William J Dearnaley Michael A Casasanta Liam Kaylor Samantha Berry Madeline J Dukes Michael S Spilman Jennifer L Gray Deborah F Kelly Bioinformatics and Genomics Graduate Program Huck Institutes of the Life Sciences Pennsylvania State University University Park PA 16802 USA. Department of Biomedical Engineering Pennsylvania State University University Park PA 16802 USA. Materials Research Institute Pennsylvania State University University Park PA 16802 USA. Center for Structural Oncology Pennsylvania State University University Park PA 16802 USA. Molecular Cellular and Integrative Biosciences Graduate Program Huck Institutes of the Life Sciences Pennsylvania State University University Park PA 16802 USA. Protochips Inc. Morrisville NC 27560 USA. Direct Electron LP. San Diego CA 92128 USA.

Liquid-phase electron microscopy (LP-EM) is an exciting new area in the materials imaging field, providing unprecedented views of molecular processes. Time-resolved insights from LP-EM studies are a strong complement to the remarkable results achievable with other high-resolution techniques. Here, the opportunities to expand LP-EM technology beyond 2D temporal assessments and into the 3D regime are described. The results show new structures and dynamic insights of human viruses contained in minute volumes of liquid while acquired in a rapid timeframe. To develop this strategy, adeno-associated virus (AAV) is used as a model system. AAV is a well-known gene therapy vehicle with current applications involving drug delivery and vaccine development for COVID-19. Improving the understanding of the physical properties of biological entities in a liquid state, as maintained in the human body, has broad societal implications for human health and disease.

关键词： COVID-19 SARS-CoV-2 adeno-associated virus direct electron detector liquid-phase electron microscopy silicon nitride

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Erratum to: Identifying candidate positive selection genes in Korean imported pig breeds

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Genes & genomics 2017年第6期39卷 687-687页

作者： Wonseok Lee Mengistie Taye Taehyung Kwon Joon Yoon Dongsung Jang Shunsuke Suzuki Heebal Kim Department of Agricultural Biotechnology Animal Biotechnology and Research Institute of Agriculture and Life Sciences Seoul National University Seoul Republic of Korea Bahir Dar University College of Agriculture and Environmental Sciences Bahir Dar Ethiopia Department of Natural Science Interdisciplinary Program in Bioinformatics Seoul National University Seoul Republic of Korea Interdisciplinary Program in Agricultural Genomics Seoul National University Seoul Republic of Korea Epigenomics Division Frontier Agriscience and Technology Center Faculty of Agriculture Shinshu University Kami‑Ina Japan Department of Interdisciplinary Genome Sciences and Cell Metabolism Institute for Biomedical Sciences Interdisciplinary Cluster for Cutting Edge Research Shinshu University Kami‑Ina Japan Institute for Biomedical Sciences Shinshu University Kami‑Ina Japan

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