DOCSLIB.ORG

Abstract Book

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Abstract Book PSB 2012 Abstract Book PACIFIC SYMPOSIUM ON BIOCOMPUTING 2012 ABSTRACT BOOK Papers are organized by session then last name of first author. Presenting authors’ names are underlined. 1 PSB 2012 Abstract Book ACCEPTED PROCEEDINGS PAPERS WITH ORAL PRESENTATIONS .................................... 10 IDENTIFICATION OF ABERRANT PATHWAY AND NETWORK ACTIVITY FROM HIGH- THROUGHPUT DATA ......................................................................................................................... 11 SSLPRED: PREDICTING SYNTHETIC SICKNESS LETHALITY ................................................. 12 NirmAlyA BandyopAdHyAy, SanJay RanKa and Tamer KAHveci Predicting tHe Effects of Copy-Number Variation in Double and Triple Mutant Combinations ...................................................................................................................................... 13 Gregory W. CArter, MicHelle HAys, Song Li, TimotHy GAlitsKi INTEGRATIVE NETWORK ANALYSIS TO IDENTIFY ABERRANT PATHWAY NETWORKS IN OVARIAN CANCER ......................................................................................................................... 14 Li CHen, JiAnHuA XuAn, JingHua Gu, Yue Wang, ZHen ZHang, TiAn-Li Wang, Ie-Ming SHiH Role of SyntHetic Genetic InterActions in UnderstAnding FunctionAl InterActions Among PAtHwAys ................................................................................................................................ 15 ShAHin MoHammadi, Giorgos KolliAs, And Ananth GrAmA Discovery of MutAted SubnetworKs AssociAted witH ClinicAl DAtA in CAncer ............... 16 Fabio Vandin, PAtricK ClAy, Eli Upfal, Benjamin J. Raphael INTRINSICALLY DISORDERED PROTEINS: ANALYSIS, PREDICTION AND SIMULATION .................................................................................................................................................................. 17 QuAsi-AnHArmonic AnAlysis reveAls intermediAte stAtes in tHe nucleAr co-activator receptor binding domAin ensemble ............................................................................................ 18 VirginiA M. Burger, Arvind RamAnAtHAn, AndreJ J. SAvol, CHristopHer B. StAnley, PrAtul K. AgArwal and ChakrA S. ChennubhotlA EFFICIENT CONSTRUCTION OF DISORDERED PROTEIN ENSEMBLES IN A BAYESIAN FRAMEWORK WITH OPTIMAL SELECTION OF CONFORMATIONS ..................................... 19 Charles K. Fisher, Orly UllmAn, Collin M. Stultz INTRINSIC PROTEIN DISORDER AND PROTEIN-PROTEIN INTERACTIONS ..................... 20 Wei-Lun Hsu, CHristopHer Oldfield, Jingwei Meng, Fei HuAng, Bin Xue#, VlAdimir N. UversKy, Pedro Romero, And A. KeitH Dunker SUBCLASSIFYING DISORDERED PROTEINS BY THE CH-CDF PLOT METHOD ................. 21 Fei Huang, CHristopHer Oldfield, Jingwei Meng, Wei-Lun Hsu, Bin Xue, Vladimir N. UversKy, Pedro Romero And A. KeitH DunKer FUNCTIONAL ANNOTATION OF INTRINSICALLY DISORDERED DOMAINS BY THEIR AMINO ACID CONTENT USING IDD NAVIGATOR ...................................................................... 22 AsHwini PAtil, SHunsuKe TerAgucHi, Huy DinH, KentA NAKAi, Daron M StAndley MODULATING PROTEIN–DNA INTERACTIONS BY POST-TRANSLATIONAL MODIFICATIONS AT DISORDERED REGIONS ............................................................................ 23 DanA VuzmAn, Yonit HoffmAn, YaAKov Levy MICROBIOME STUDIES: ANALYTICAL TOOLS AND TECHNIQUES ...................................... 24 EstimAting populAtion diversity witH unreliAble low frequency counts ........................ 25 JoHn Bunge, DAnKmAr BoHning, HeAtHer K. Allen, JAmes A. Foster 2 PSB 2012 Abstract Book COMPARISONS OF DISTANCE METHODS FOR COMBINING COVARIATES AND ABUNDANCES IN MICROBIOME STUDIES ................................................................................... 26 Julia FuKuyAmA, PAul J. McMurdie, Les DetHlefsen, DAvid A. RelmAn, SusAn Holmes SEPP: SATe ́ -EnAbled PHylogenetic PlAcement ........................................................................ 27 S. Mirarab, N. Nguyen, T. WArnow ARTIFICIAL FUNCTIONAL DIFFERENCE BETWEEN MICROBIAL COMMUNITIES CAUSED BY LENGTH DIFFERENCE OF SEQUENCING READS .................................................................. 28 QuAn ZHAng, THomAs G. DoAK, YuzHen Ye MetaDomain: a profile HMM-bAsed protein domAin clAssificAtion tool for short sequences ............................................................................................................................................. 29 YuAn ZHAng, Yanni Sun MODELING HOST-PATHOGEN INTERACTIONS ......................................................................... 30 STRUCTURAL MODELS FOR HOST-PATHOGEN PROTEIN-PROTEIN INTERACTIONS: ASSESSING COVERAGE AND BIAS .................................................................................................. 31 Eric A. FranzosA, Yu XiA IDENTIFICATION OF CELL CYCLE-REGULATED, PUTATIVE HYPHAL GENES IN CANDIDA ALBICANS .......................................................................................................................... 32 RalucA GordAn, SAumyAdiptA Pyne, MArtHA L. BulyK Determining confidence of predicted interActions between HIV-1 and human proteins using conformAl metHod ................................................................................................ 33 Ilia Nouretdinov, Alex GAmmermAn, YAnjun Qi, JuditH Klein-SeetHaraman PERSONALIZED MEDICINE .............................................................................................................. 34 Interpretome: A Freely AvAilAble, ModulAr, And Secure PersonAl Genome InterpretAtion Engine ....................................................................................................................... 35 KonrAd J. KarczewsKi, Robert P. Tirrell, PAblo Cordero, NicHolAs P. TAtonetti, Joel T. Dudley, KeyAn SAlAri, MicHAel Snyder, Russ B. AltmAn, StuArt K. Kim A KinAse inHibition mAp ApproAcH for tumor sensitivity prediction And combinAtion tHerApy design for tArgeted drugs ............................................................................................... 36 RanAdip PAl and NoAH Berlow MIXTURE MODEL FOR SUB-PHENOTYPING IN GWAS ............................................................ 37 David WArde-Farley, MichAel Brudno, QuAid Morris, AnnA Goldenberg TEXT AND KNOWLEDGE MINING FOR PHARMACOGENOMICS ............................................ 38 THe ExtrAction of PHArmAcogenetic And PHArmAcogenomic RelAtions – A CAse Study Using PHArmGKB ................................................................................................................................ 39 Ekaterina BuyKo, Elena Beisswanger and Udo Hahn LINKING PHARMGKB TO PHENOTYPE STUDIES AND ANIMAL MODELS OF DISEASE FOR DRUG REPURPOSING ............................................................................................................... 40 Robert HoeHndorf, AniKA OellricH, DietricH RebHolz-ScHuHmann, Paul N. Schofield, Georgios V. Gkoutos IntegrAting VA’s NDF-RT drug terminology witH PHArmGKB: PreliminAry Results .... 41 JyotisHmAn PAtHAK, LAurA C. Weiss, MAttHew J. DursKi, QiAn ZHu, Robert R. FreimutH, Christopher G. Chute 3 PSB 2012 Abstract Book Discovery And ExplAnAtion of Drug-Drug InterActions viA Text Mining ......................... 42 BetHAny PercHA, YAel GArten, Russ B. AltmAn RANKING GENE-DRUG RELATIONSHIPS IN BIOMEDICAL LITERATURE USING LATENT DIRICHLET ALLOCATION ................................................................................................................. 43 YongHui Wu, Mei Liu, W. Jim ZHeng, ZHongming ZHAo, HuA Xu ACCEPTED PROCEEDINGS PAPERS WITH POSTER PRESENTATIONS ............................... 44 INTRINSICALLY DISORDERED PROTEINS: ANALYSIS, PREDICTION AND SIMULATION .................................................................................................................................................................. 45 CORRELATION BETWEEN POSTTRANSLATIONAL MODIFICATION AND INTRINSIC DISORDER IN PROTEIN .................................................................................................................... 46 Jianjiong GAo and Dong Xu Intrinsic disorder witHin And flAnKing tHe DNA-binding domAins of HumAn trAnscription fActors ......................................................................................................................... 47 Xin Guo, MArtHA L. BulyK, and Alexander J. HarteminK Coevolved residues And tHe functionAl AssociAtion for intrinsicAlly disordered proteins ................................................................................................................................................. 48 Chan-SeoK Jeong and Dongsup Kim CRYPTIC DISORDER: AN ORDER-DISORDER TRANSFORMATION REGULATES THE FUNCTION OF NUCLEOPHOSMIN ................................................................................................... 49 DiAnA M MitreA And RicHArd W KriwAcKi ON THE COMPLEMENTARITY OF THE CONSENSUS-BASED DISORDER PREDICTION .. 50 Zhenling Peng and LuKasz Kurgan MICROBIOME STUDIES: ANALYTICAL TOOLS AND TECHNIQUES ...................................... 51 PROTEOTYPING OF MICROBIAL COMMUNITIES BY OPTIMIZATION OF TANDEM MASS SPECTROMETRY DATA INTERPRETATION ................................................................................ 52 Alys Hugo, DouglAs J. BAxter, WilliAm R. CAnnon, AnAntH KAlyAnArAmAn, GAurAv KulKArni, StepHen J. Callister pHyloseq: A Bioconductor pAcKAge for HAndling And AnAlysis of High-tHroughput pHylogenetic sequence dAtA ..........................................................................................................
Load more

Recommended publications
  • Phylogenetic Analysis of the Gut Bacterial Microflora of the Fungus-Growing Termite Macrotermes Barneyi
    African Journal of Microbiology Research Vol. 6(9), pp. 2071-2078, 9 March, 2012 Available online at http://www.academicjournals.org/AJMR DOI: 10.5897/AJMR11.1345 ISSN 1996-0808 ©2012 Academic Journals Full Length Research Paper Phylogenetic analysis of the gut bacterial microflora of the fungus-growing termite Macrotermes barneyi Yunhua Zhu1,2,3, Jian Li1,2, Huhu Liu1,2, Hui Yang1,2, Sheng Xin1,2, Fei Zhao1,2, Xuejia Zhang1,2, Yun Tian1,2* and Xiangyang Lu1,2* 1College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China. 2Hunan Agricultural Bioengineering Research Institute, Changsha 410128, China. 3College of Pharmacy and Life Science, Nanhua University, Hengyang 421001, China. Accepted 29 December, 2011 Termites are an extremely successful group of wood-degrading organisms and are therefore important both for their roles in carbon turnover in the environment and as potential sources of biochemical catalysts for efforts aimed at converting wood into biofuels. To contribute to the evolutional study of termite digestive symbiosis, a bacterial 16S rRNA gene clone library from the gut microbial community of the fungus-growing termite Macrotermes barneyi was constructed. After screening by restriction fragment length polymorphism (RFLP) analysis, 25 out of 105 clones with unique RFLP patters were sequenced and phylogenetically analyzed. Many of the clones (95%) were derived from three phyla within the domain bacteria: Bacteroidetes, Firmicutes and Proteobacteria. In addition, a few clones derived from Deferribacteres, Actinobacteria and Planctomycetes were also found. No one clone affiliated with the phylum Spirochaetes was identified, in contrast to the case of wood-feeding termites. The phylogenetic analysis revealed that nearly half of the representative clones (11 phylotypes) formed monophyletic clusters with clones obtained from other termite species, especially with the sequences retrieved from fungus-growing termites.
    [Show full text]
  • Inhibition of Tumor Growth by Dietary Indole-3-Carbinol in a Prostate Cancer Xenograft Model May Be Associated with Disrupted Gut Microbial Interactions
    nutrients Article Inhibition of Tumor Growth by Dietary Indole-3-Carbinol in a Prostate Cancer Xenograft Model May Be Associated with Disrupted Gut Microbial Interactions Yanbei Wu 1,2,3, Robert W. Li 4, Haiqiu Huang 3 , Arnetta Fletcher 2,5, Lu Yu 2, Quynhchi Pham 3, Liangli Yu 2, Qiang He 1,* and Thomas T. Y. Wang 3,* 1 College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu 610065, China; [email protected] 2 Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA; afl[email protected] (A.F.); [email protected] (L.Y.); [email protected] (L.Y.) 3 Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, USDA-ARS, Beltsville, MD 20705, USA; [email protected] (H.H.); [email protected] (Q.P.) 4 Animal Parasitic Diseases Laboratory, USDA-ARS, Beltsville, MD 20705, USA; [email protected] 5 Department of Family and Consumer Sciences, Shepherd University, Shepherdstown, WV 25443, USA * Correspondence: [email protected] (Q.H.); [email protected] (T.T.Y.W.); Tel.: +86-28-85468323 (Q.H.); +(301)-504-8459 (T.T.Y.W.) Received: 2 January 2019; Accepted: 19 February 2019; Published: 22 February 2019 Abstract: Accumulated evidence suggests that the cruciferous vegetables-derived compound indole-3-carbinol (I3C) may protect against prostate cancer, but the precise mechanisms underlying its action remain unclear. This study aimed to verify the hypothesis that the beneficial effect of dietary I3C may be due to its modulatory effect on the gut microbiome of mice. Athymic nude mice (5–7 weeks old, male, Balb c/c nu/nu) with established tumor xenografts were fed a basal diet (AIN-93) with or without 1 µmoles I3C/g for 9 weeks.
    [Show full text]
  • Exploring the Role of Mucispirillum Schaedleri in Enteric Salmonella Enterica Serovar Typhimurium Infection
    Aus dem Max von Pettenkofer-Institut Lehrstuhl für Medizinische Mikrobiologie und Krankenhaushygiene der Ludwig-Maximilians-Universität München Vorstand: Prof. Dr. med. Sebastian Suerbaum Exploring the role of Mucispirillum schaedleri in enteric Salmonella enterica serovar Typhimurium infection Dissertation zum Erwerb des Doktorgrades der Naturwissenschaften an der Medizinischen Fakultät der Ludwig-Maximilians-Universität München vorgelegt von Simone Herp aus Offenburg 2018 Gedruckt mit Genehmigung der Medizinischen Fakultät der Ludwig-Maximilians-Universität München Betreuerin: Prof. Dr. Barbara Stecher-Letsch Zweitgutachterin: Prof. Dr. Gabriele Rieder Dekan: Prof. Dr. med. dent. Reinhard Hickel Tag der mündlichen Prüfung: 19.02.2019 i Eidesstattliche Erklärung Ich, Simone Herp, erkläre hiermit an Eides statt, dass ich die vorliegende Dissertation mit dem Thema: Exploring the role of Mucispirillum schaedleri in enteric Salmonella enterica serovar Typhimurium infection selbständig verfasst, mich außer der angegebenen keiner weiteren Hilfsmittel bedient und alle Erkenntnisse, die aus dem Schrifttum ganz oder annähernd übernommen sind, als solche kenntlich gemacht und nach ihrer Herkunft unter Bezeichnung der Fundstelle einzeln nachgewiesen habe. Ich erkläre des Weiteren, dass die hier vorgelegte Dissertation nicht in gleicher oder in ähnlicher Form bei einer anderen Stelle zur Erlangung eines akademischen Grades eingereicht wurde. München, den 07.03.2019 Simone Herp ii Table of Contents Table of Contents Table of Contents .......................................................................................................................
    [Show full text]
  • Comparison of Gut Microbiota of 96 Healthy Dogs by Individual Traits: Breed, Age, and Body Condition Score
    animals Article Comparison of Gut Microbiota of 96 Healthy Dogs by Individual Traits: Breed, Age, and Body Condition Score Inhwan You 1,2 and Min Jung Kim 1,2,* 1 Department of Research and Development, Mjbiogen Corp., 144 Gwangnaru-ro, Seongdong-gu, Seoul 14788, Korea; [email protected] 2 College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea * Correspondence: [email protected] Simple Summary: The gut microbial ecosystem is affected by various factors such as lifestyle, environment, and disease. Although gut microbiota is closely related to host health, an understanding of the gut microbiota of dogs is still lacking. Therefore, we investigated gut microbial composition in healthy dogs and divided them into groups according to their breed, age, or body condition score. From our results, age is the most crucial factor driving the gut microbial community of dogs compared to breed and body condition score (especially Fusobacterium perfoetens, which was much more abundant in the older group). We have revealed that even in healthy dogs without any diseases, there are differences in gut microbiota depending on individual traits. These results can be used as a basis for improving the quality of life by managing dogs’ gut microbiota. Abstract: Since dogs are part of many peoples’ lives, research and industry related to their health and longevity are becoming a rising topic. Although gut microbiota (GM) is a key contributor to Citation: You, I.; Kim, M.J. host health, limited information is available for canines. Therefore, this study characterized GM Comparison of Gut Microbiota of 96 according to individual signatures (e.g., breed, age, and body condition score—BCS) of dogs living Healthy Dogs by Individual Traits: in the same environment.
    [Show full text]
  • Dietary Energy Level Affects the Composition of Cecal Microbiota of Starter Pekin Ducklings
    Original Paper Czech J. Anim. Sci., 63, 2018 (1): 24–31 doi: 10.17221/53/2017-CJAS Dietary Energy Level Affects the Composition of Cecal Microbiota of Starter Pekin Ducklings Jun-Qiang Liu1, Yan-Hong Wang1, Xing-Tang Fang1, Ming Xie3, Yun-Sheng Zhang3, Shui-Sheng Hou3, Hong Chen1, Guo-Hong Chen2, Chun-Lei Zhang1,2* 1Institute of Cellular and Molecular Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, P.R. China 2College of Animal Science and Technology, Yangzhou University, Yangzhou, P.R. China 3Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China *Corresponding author: [email protected] ABSTRACT Liu J.-Q., Wang Y.-H., Fang X.-T., Xie M., Zhang Y.-S., Hou S.-S., Chen H., Chen G.-H., Zhang C.-L. (2018): Dietary energy level affects the composition of cecal microbiota of starter Pekin ducklings. Czech J. Anim. Sci., 63, 24–31. In this study, we evaluated the phylogenetic diversity of the cecal microbiota of 3-week-old ducklings fed three diets differing in metabolizable energy. The contents of the ceca were collected from ducklings of different groups. The ceca bacterial DNA was isolated and the V3 to V4 regions of 16S rRNA genes were amplified. The amplicons were subjected to high-throughput sequencing to analyze the bacterial diversity of different groups. The predominant bacterial phyla were Bacteroidetes (~65.67%), Firmicutes (~17.46%), and Proteobacteria (~10.73%). The abundance of Bacteroidetes increased and that of Firmicutes decreased with increasing dietary energy level. The diversity decreased (Simpson diversity index and Shannon diversity index) with the increase in dietary energy level, but the richness remained constant.
    [Show full text]
  • Distinct Microbial Communities in the Murine Gut Are Revealed by Taxonomy- 2 Independent Phylogenetic Random Forests 3 Gurdeep Singh1, Andrew Brass2, Sheena M
    bioRxiv preprint doi: https://doi.org/10.1101/790923; this version posted October 2, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Distinct microbial communities in the murine gut are revealed by taxonomy- 2 independent phylogenetic random forests 3 Gurdeep Singh1, Andrew Brass2, Sheena M. Cruickshank1, and Christopher G. Knight3. 4 5 1 Faculty of Biology, Medicine and Health, Lydia Becker Institute of Immunology and 6 Inflammation, Manchester Academic Health Science Centre, A.V. Hill Building, The 7 University of Manchester, Oxford Road, Manchester, M13 9PT, United Kingdom. 8 [email protected], [email protected] 9 10 2 Faculty of Biology, Medicine and Health, Division of Informatics, Imaging and Data 11 Sciences, Stopford Building, The University of Manchester, Oxford Road, Manchester, M13 12 9PT, United Kingdom. [email protected] 13 14 3 Faculty of Science and Engineering, School of Earth and Environmental Sciences, Michael 15 Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PT, United 16 Kingdom. [email protected] 17 Corresponding author: Sheena M. Cruickshank A.V. Hill Building The University of Manchester Oxford Road Manchester M13 9PT [email protected] Phone +44 (0) 161 275 1582 18 19 Running title: Phylogenetic mouse gut microbiomes 20 21 1 bioRxiv preprint doi: https://doi.org/10.1101/790923; this version posted October 2, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.
    [Show full text]
  • Longitudinal Analysis of the Faecal Microbiome in Pigs Fed Cyberlindnera Jadinii Yeast As a Protein Source During the Weanling P
    bioRxiv preprint doi: https://doi.org/10.1101/2021.02.11.430725; this version posted February 11, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Longitudinal analysis of the faecal microbiome in pigs fed Cyberlindnera jadinii yeast as a protein source during the weanling period followed by a rapeseed- and faba bean-based grower-finisher diet Iakhno, S.1,*, Delogu, F.2, Umu, O.C.O.¨ 1, Kjos, N.P.3, H˚aken˚asen,I.M.3, Mydland, L.T.3, Øverland, M.3 and Sørum, H.1 1 Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway 2 Luxembourg Centre for Systems Biomedicine, Universit´edu Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg 3 Faculty of Biosciences, Norwegian University of Life Sciences, As,˚ Norway * [email protected] Abstract The porcine gut microbiome is closely connected to diet and is central to animal health and growth. The gut microbiota composition in relation to Cyberlindnera jadinii yeast as a protein source in a weanling diet was studied previously. Also, there is a mounting body of knowledge regarding the porcine gut microbiome composition in response to the use of rapeseed (Brassica napus subsp. napus) meal, and faba beans (Vicia faba) as protein sources during the growing/finishing period. However, there is limited data on how the porcine gut microbiome respond to a combination of C.
    [Show full text]
  • Investigation of Microbiota in Health and Disease of Poultry
    University of Arkansas, Fayetteville ScholarWorks@UARK Theses and Dissertations 8-2019 Investigation of Microbiota in Health and Disease of Poultry Bishnu Adhikari University of Arkansas, Fayetteville Follow this and additional works at: https://scholarworks.uark.edu/etd Part of the Animal Diseases Commons, Bacteriology Commons, Microbial Physiology Commons, Molecular Biology Commons, and the Poultry or Avian Science Commons Recommended Citation Adhikari, Bishnu, "Investigation of Microbiota in Health and Disease of Poultry" (2019). Theses and Dissertations. 3371. https://scholarworks.uark.edu/etd/3371 This Dissertation is brought to you for free and open access by ScholarWorks@UARK. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of ScholarWorks@UARK. For more information, please contact [email protected]. Investigation of Microbiota in Health and Disease of Poultry A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Poultry Science by Bishnu Adhikari Tribhuvan University Bachelor of Veterinary Science & Animal Husbandry, 2010 Aarhus University Master of Science in Sustainable Animal Nutrition and Feeding, 2015 University of Debrecen Master of Science in Sustainable Animal Nutrition Agricultural Engineer, 2015 August 2019 University of Arkansas The dissertation is approved for recommendation to the Graduate Council. Young Min Kwon, Ph.D. Dissertation Director Billy M. Hargis, Ph.D. Jiangchao Zhao, Ph.D. Committee Member Committee Member Guillermo Tellez-Isaias, Ph.D. Committee Member ABSTRACT The microbiotas play vital roles in health and diseases of both humans and animals. 16S rRNA genes sequence analysis is one of the most popular and commonly used methods in the analysis of microbiotas associated with hosts.
    [Show full text]
  • Dietary Cholesterol Drives Fatty Liver-Associated Liver Cancer By
    Hepatology ORIGINAL RESEARCH Dietary cholesterol drives fatty liver- associated liver Gut: first published as 10.1136/gutjnl-2019-319664 on 21 July 2020. Downloaded from cancer by modulating gut microbiota and metabolites Xiang Zhang,1 Olabisi Oluwabukola Coker,1 Eagle SH Chu,1 Kaili Fu,1 Harry C H Lau ,1 Yi- Xiang Wang,2 Anthony W H Chan,3 Hong Wei,4,5 Xiaoyong Yang,6 Joseph J Y Sung,1 Jun Yu 1 ► Additional material is ABSTRACT Significance of this study published online only. To view Objective Non- alcoholic fatty liver disease (NAFLD)- please visit the journal online associated hepatocellular carcinoma (HCC) is an (http:// dx. doi. org/ 10. 1136/ What is already known on this subject? gutjnl- 2019- 319664). increasing healthcare burden worldwide. We examined the role of dietary cholesterol in driving NAFLD–HCC ► Non- alcoholic fatty liver disease (NAFLD)- For numbered affiliations see associated hepatocellular carcinoma (HCC) is end of article. through modulating gut microbiota and its metabolites. Design High-fat/high- cholesterol (HFHC), high- fat/ an increasing healthcare burden worldwide. ► Cholesterol is a major lipotoxic molecule. Correspondence to low- cholesterol or normal chow diet was fed to C57BL/6 Jun Yu, Institute of Digestive male littermates for 14 months. Cholesterol-lowering What are the new findings? Disease and The Department drug atorvastatin was administered to HFHC- fed mice. ► High- fat high- cholesterol diet (HFHC) of Medicine and Therapeutics, Germ-free mice were transplanted with stools from Chinese University of Hong spontaneously and sequentially induced fatty Kong, New Territories, Hong mice fed different diets to determine the direct role liver, steatohepatitis, fibrosis and NAFLD–HCC Kong; junyu@ cuhk.
    [Show full text]
  • Exploring the Ecology of Complex Microbial Communities Through
    EXPLORING THE ECOLOGY OF COMPLEX MICROBIAL COMMUNITIES THROUGH THE COCKROACH GUT MICROBIOME by KARA ANN TINKER (Under the Direction of Elizabeth A. Ottesen) ABSTRACT Microbes represent the majority of biomass and diversity found on planet earth and are essential to the maintenance of global biochemical processes. However, there is still much that is unknown about what drives the formation and maintenance of complex microbial communities. Here, we explore the ecology of complex microbial communities through an examination of the cockroach gut microbiome. The cockroach gut microbiota is highly complex and is analogous to the human gut microbiome in structure, function, and overall diversity. Insects in the superorder Dictyoptera include: carnivorous praying mantids, omnivorous cockroaches, and herbivorous termites. We use 16S rRNA amplicon sequencing to survey the structure and diversity across of gut microbiota 237 cockroaches in the Blattodea order. Results show that host species plays a key role in the gut microbiota of cockroaches. This suggests that cockroach host-microbe coevolution preceded the emergence and possibly facilitated the dietary specialization of termites. Previous work suggests that diet is plays an important role in shaping the Blattodea gut microbiome. We conducted a series of dietary perturbations to determine the effect of diet on the structure of the cockroach gut microbiome. We found the cockroach hosts a taxonomically stable gut microbiome, which may aid the host in survival during low-food and/or starvation events. This stability is highly unusual and has not been found in any other animal that hosts a complex gut microbial community. This suggests that cockroaches have evolved unique mechanisms for establishing and maintaining a diverse and stable core microbiome.
    [Show full text]
  • Disentangling the Relative Roles of Vertical Transmission, Subsequent
    bioRxiv preprint doi: https://doi.org/10.1101/2020.07.01.183558; this version posted July 3, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Disentangling the relative roles of vertical transmission, subsequent 2 colonizations and diet on cockroach microbiome assembly 3 4 Kristjan Germer1*, Justinn Renelies-Hamilton1*, David Sillam-Dussès2, Kasun H. Bodawatta3 5 and Michael Poulsen1 6 7 8 Running title: Gut microbial community assembly in cockroaches 9 10 11 1Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 12 Copenhagen, Denmark 13 14 2Université Sorbonne Paris Nord, Laboratoire d'Ethologie Expérimentale et Comparée 15 UR4443, Villetaneuse, France. 16 17 3Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark 18 19 *Contributed equally to this work 20 21 22 Corresponding author: Michael Poulsen: [email protected], +45 35330377 23 24 25 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.01.183558; this version posted July 3, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 26 Abstract 27 A multitude of factors affect the assemblies of complex microbial communities associated 28 with animal hosts, with implications for community flexibility, resilience and long-term 29 stability; however, their relative effects have rarely been deduced. Here, we use a tractable 30 lab model to quantify the relative and combined effects of parental transmission (egg case 31 microbiome present/reduced), gut inocula (cockroach vs.
    [Show full text]
  • An Ensemble Approach to the Taxonomic Classification of Metatranscriptomic Sequence Data
    bioRxiv preprint doi: https://doi.org/10.1101/081026; this version posted October 28, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Gist – an ensemble approach to the taxonomic classification of metatranscriptomic sequence data. Samantha Halliday1,2 and John Parkinson1,3,4,* 1 Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, M5G 1L7, Canada 2 Department of Computer Science, University of Toronto, Toronto, Ontario, M5S 1A8, Canada 3 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada 4 Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada * To whom correspondence should be addressed: [email protected] Running Title: Taxonomic classification of metatranscriptomic data Keywords: metatranscriptomics, taxonomic classification, 1 bioRxiv preprint doi: https://doi.org/10.1101/081026; this version posted October 28, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. ABSTRACT The study of whole microbial communities through RNA-seq, or metatranscriptomics, offers a unique view of the relative levels of activity for different genes across a large number of species simultaneously. To make sense of these sequencing data, it is necessary to be able to as- sign both taxonomic and functional identities to each sequenced read. High-quality identifica- tions are important not only for community profiling, but to also ensure that functional assign- ments of sequence reads are correctly attributed to their source taxa.
    [Show full text]