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Supplemental Table 1 Phylum % Family % Genus % Bacteroidaceae 28.40% Bacteroides 28.40% Prevotella 9 15.50% Bacteroidetes 63.20% Prevotellaceae 25.80% Unknown Prevotellaceae 8.10% Tannerellaceae 7.50% Parabacteroides 7.50% Megamonas 7.20% Veillonellaceae 9.40% Megasphaera 2.20% Firmicutes 16.70% Acidaminococcaceae 3.80% Phascolarctobacterium 3.80% Lachnospiraceae 1.90% Blautia 1.00% Succinivibrionaceae 9.70% Anaerobiospirillum 9.60% Proteobacteria 13.80% Burkholderiaceae 1.90% Sutterella 1.90% Enterobacteriaceae 1.80% Escherichia-Shigella 1.70% Fusobacteria 4.00% Fusobacteriaceae 4.00% Fusobacterium 4.00% Actinobacteria 1.40% Bifidobacteriaceae 1.00% Bifidobacterium 1.00% Epsilonbacteraeota 0.70% Verrucomicrobia 0.10% Spirochaetes 0.00% Cyanobacteria 0.00% Deferribacteres 0.00% Supplemental Table 2. ANCOM analysis by source in healthy marmosets Phylum Class Order Family Genus W MITNE MITCL MITB MITA MIT Abundance Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Prevotella 9 136 10.64% 33.40% 9.44% 25.17% 15.40% Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Alloprevotella 136 0.00% 2.51% 0.00% 0.00% 0.38% Fusobacteria Fusobacteriia Fusobacteriales Fusobacteriaceae Fusobacterium 136 5.01% 3.96% 1.63% 8.24% 4.13% Proteobacteria Gammaproteobacteria Aeromonadales Succinivibrionaceae Anaerobiospirillum 136 13.77% 1.47% 8.50% 10.17% 9.77% Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Escherichia-Shigella 136 0.13% 3.16% 0.61% 4.92% 1.30% Firmicutes Clostridia Clostridiales Lachnospiraceae Blautia 133 0.80% 0.65% 1.68% 0.43% 1.02% Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Unknown 131 4.78% 6.37% 13.83% 5.84% 8.07% Actinobacteria Actinobacteria Bifidobacteriales Bifidobacteriaceae Bifidobacterium 130 0.53% 0.96% 1.42% 1.19% 0.96% Bacteroidetes Bacteroidia Bacteroidales Tannerellaceae Parabacteroides 126 6.06% 4.71% 9.61% 8.62% 7.30% Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides 126 37.37% 17.44% 29.94% 14.39% 29.27% Firmicutes Negativicutes Selenomonadales Acidaminococcaceae Phascolarctobacterium 125 4.27% 2.76% 3.85% 2.78% 3.73% Firmicutes Negativicutes Selenomonadales Veillonellaceae Megamonas 125 6.21% 9.37% 8.22% 5.62% 7.28% Firmicutes Negativicutes Selenomonadales Veillonellaceae Megasphaera 116 1.04% 2.69% 2.96% 3.96% 2.25% Bacteroidetes Bacteroidia Bacteroidales Barnesiellaceae Coprobacter 136 0.27% 0.00% 0.08% 0.00% 0.14% Bacteroidetes Bacteroidia Bacteroidales Muribaculaceae __ 136 0.15% 0.42% 0.13% 0.05% 0.17% Bacteroidetes Bacteroidia Bacteroidales Muribaculaceae uncultured bacterium 136 0.38% 0.08% 0.82% 0.36% 0.48% Bacteroidetes Bacteroidia Bacteroidales Rikenellaceae Alistipes 136 0.18% 0.08% 0.08% 0.02% 0.11% Firmicutes Clostridia Clostridiales Lachnospiraceae __ 136 0.06% 0.01% 0.11% 0.05% 0.07% Firmicutes Clostridia Clostridiales Lachnospiraceae Lachnoclostridium 136 0.08% 0.00% 0.22% 0.18% 0.13% Firmicutes Clostridia Clostridiales Ruminococcaceae Ruminiclostridium 5 136 0.04% 0.02% 0.01% 0.00% 0.02% Firmicutes Erysipelotrichia Erysipelotrichales Erysipelotrichaceae Asteroleplasma 136 0.20% 0.11% 0.70% 0.40% 0.37% Proteobacteria Deltaproteobacteria Desulfovibrionales Desulfovibrionaceae Bilophila 136 0.01% 0.13% 0.15% 0.16% 0.09% Proteobacteria Gammaproteobacteria __ __ __ 136 0.00% 0.00% 0.00% 0.14% 0.02% Proteobacteria Gammaproteobacteria Aeromonadales Succinivibrionaceae Succinatimonas 136 0.02% 0.13% 0.05% 0.01% 0.05% Bacteroidetes Bacteroidia Bacteroidales Barnesiellaceae Barnesiella 135 0.63% 0.28% 0.06% 0.14% 0.33% Bacteroidetes Bacteroidia Bacteroidales Marinifilaceae Butyricimonas 135 0.28% 0.07% 0.02% 0.03% 0.14% Bacteroidetes Bacteroidia Bacteroidales Marinifilaceae Odoribacter 134 0.12% 0.00% 0.01% 0.00% 0.05% Firmicutes Clostridia Clostridiales Lachnospiraceae [Ruminococcus] gnavus group 134 0.05% 0.21% 0.00% 0.05% 0.06% Firmicutes Clostridia Clostridiales Lachnospiraceae Howardella 134 0.00% 0.00% 0.03% 0.01% 0.01% Firmicutes Clostridia Clostridiales Lachnospiraceae uncultured 134 0.04% 0.12% 0.19% 0.05% 0.10% Proteobacteria Deltaproteobacteria Desulfovibrionales Desulfovibrionaceae Desulfovibrio 134 0.12% 0.00% 0.01% 0.00% 0.05% Actinobacteria Coriobacteriia Coriobacteriales Atopobiaceae Olsenella 133 0.11% 0.05% 0.15% 0.03% 0.10% Firmicutes Clostridia Clostridiales Lachnospiraceae Lachnospiraceae UCG-004 133 0.00% 0.05% 0.00% 0.00% 0.01% Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Proteus 133 0.01% 0.00% 0.00% 0.08% 0.01% Firmicutes Clostridia Clostridiales Peptococcaceae Peptococcus 132 0.08% 0.01% 0.01% 0.01% 0.04% Firmicutes Negativicutes Selenomonadales Veillonellaceae Allisonella 132 0.00% 0.04% 0.01% 0.02% 0.01% Firmicutes Negativicutes Selenomonadales Veillonellaceae Dialister 132 0.00% 0.22% 0.01% 0.00% 0.04% Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Paraprevotella 131 0.87% 0.47% 0.79% 0.65% 0.76% Actinobacteria Coriobacteriia Coriobacteriales Atopobiaceae Libanicoccus 130 0.06% 0.02% 0.10% 0.03% 0.06% Firmicutes Clostridia Clostridiales Lachnospiraceae Oribacterium 128 0.39% 0.81% 0.62% 0.57% 0.55% Spirochaetes Spirochaetia Spirochaetales Spirochaetaceae Sphaerochaeta 127 0.05% 0.00% 0.00% 0.00% 0.02% Bacteroidetes Bacteroidia Bacteroidales Porphyromonadaceae Porphyromonas 126 0.00% 0.02% 0.01% 0.00% 0.01% Firmicutes Clostridia Clostridiales Lachnospiraceae GCA-900066575 126 0.04% 0.00% 0.03% 0.00% 0.02% Firmicutes Clostridia Clostridiales Ruminococcaceae Ruminococcaceae UCG-014 125 0.09% 0.00% 0.00% 0.00% 0.04% Firmicutes Clostridia Clostridiales Lachnospiraceae Lachnospiraceae NK4A136 group 124 0.04% 0.00% 0.00% 0.00% 0.02% Proteobacteria Alphaproteobacteria Rhodospirillales uncultured __ 124 0.09% 0.00% 0.02% 0.00% 0.04% Firmicutes Clostridia Clostridiales Ruminococcaceae Fournierella 123 0.00% 0.01% 0.00% 0.00% 0.00% Firmicutes Clostridia Clostridiales Clostridiaceae 1 Sarcina 122 0.06% 0.03% 0.04% 0.00% 0.04% Firmicutes Clostridia Clostridiales Ruminococcaceae __ 122 0.01% 0.00% 0.00% 0.00% 0.01% Bacteroidetes Bacteroidia Bacteroidales Barnesiellaceae uncultured 121 0.03% 0.00% 0.02% 0.00% 0.02% Firmicutes Clostridia Clostridiales Ruminococcaceae Ruminococcaceae UCG-004 121 0.02% 0.00% 0.00% 0.00% 0.01% Firmicutes Bacilli Lactobacillales Aerococcaceae Aerococcus 120 0.00% 0.00% 0.00% 0.41% 0.05% Firmicutes Clostridia Clostridiales Ruminococcaceae Ruminiclostridium 9 120 0.05% 0.01% 0.02% 0.00% 0.03% Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae __ 120 0.00% 0.00% 0.00% 0.08% 0.01% Actinobacteria Coriobacteriia Coriobacteriales Coriobacteriaceae Collinsella 119 0.24% 0.18% 0.34% 0.09% 0.25% Verrucomicrobia Verrucomicrobiae Verrucomicrobiales Akkermansiaceae Akkermansia 112 0.25% 0.05% 0.00% 0.00% 0.11% Firmicutes Bacilli Lactobacillales Leuconostocaceae Leuconostoc 110 0.00% 0.06% 0.00% 0.00% 0.01% Firmicutes Clostridia Clostridiales Peptostreptococcaceae Peptoclostridium 109 0.00% 0.05% 0.00% 0.00% 0.01% Firmicutes Clostridia Clostridiales Ruminococcaceae Oscillibacter 107 0.01% 0.01% 0.00% 0.00% 0.01% Epsilonbacteraeota Campylobacteria Campylobacterales Helicobacteraceae Helicobacter 104 1.00% 0.20% 0.63% 0.65% 0.72% Firmicutes Clostridia Clostridiales Family XIII Family XIII UCG-001 103 0.00% 0.00% 0.00% 0.00% 0.00% Cyanobacteria Melainabacteria Gastranaerophilales __ __ 102 0.01% 0.00% 0.00% 0.00% 0.00% Firmicutes Clostridia Clostridiales Ruminococcaceae Subdoligranulum 102 0.00% 0.00% 0.00% 0.00% 0.00% Supplemental Table 3. Number of marmosets and associated health status for animals on study Healthy Stricture IBD MITA 8 (73%) 0 (0%) 3 (27%) MITB 27 (75%) 1 (3%) 8 (22%) MITCL 19 (43%) 1 (2%) 24 (55%) MITNE 37 (45%) 21 (26%) 24 (29%) MITALL 91 (53%) 23 (13%) 59 (34%) Supplemental Table 4. Overlap of top 25 ASVs in 4 IBD models ASVs of importance in 3+ models Family Genus ASV219 Burkholderiaceae Sutterella ASV115 Bacteroidaceae Bacteroides ASV207 Burkholderiaceae Sutterella ASV209 Burkholderiaceae Sutterella ASV346 Erysipelotrichaceae Asteroleplasma ASV779 Prevotellaceae Prevotella 9 ASV1044 Veillonellaceae Megamonas ASV1087 Veillonellaceae Megamonas Genera of importance in 3+ models with number of ASVs per model Genus MIT (all) MIT B MIT CL MIT NE Total Bacteroides 8 4 4 4 20 Sutterella 3 3 1 3 10 Megamonas 2 3 3 0 8 Bifidobacterium 1 4 2 0 7 Prevotella 9 2 0 2 3 7 Unknown Prevotellaceae 0 2 2 1 5 Parabacteroides 1 1 0 3 5 Prevotellaceae UCG-001 2 0 1 1 4 Asteroleplasma 1 1 1 0 3 Supplemental Table 5. Differentially expressed genes in the duodenum between stricture and non-stricture Supp. Table 5a. Genes upregulated in Stricture Gene name logFC logCPM F PValue FDR HYDIN -5.57275 8.235763 255.7079 9.64E-09 0.000186 FCN2 -6.2382 5.877223 181.0315 9.24E-08 0.000677 LOC100385035 -4.39198 4.35918 159.023 1.06E-07 0.000677 KIFC3 -3.72529 6.16206 147.199 1.55E-07 0.000745 FRMD1 -4.56494 4.611455 129.1226 2.96E-07 0.001139 GOLT1A -3.66778 5.210277 124.2568 3.57E-07 0.001146 LOC100415170 -4.60077 4.395378 112.2745 6.08E-07 0.001456 LOC100390425 -4.07882 7.969966 112.2804 6.21E-07 0.001456 SLC2A7 -2.82598 6.173383 104.4619 8.31E-07 0.0016 TUBAL3 -3.41415 6.772312 100.0865 1.02E-06 0.001788 LOC103792726 -3.50238 4.766558 92.43918 1.50E-06 0.001872 AQP10 -3.17156 6.834658 90.41122 1.66E-06 0.001872 ESPL1 -2.35296 7.029238 90.60278 1.65E-06 0.001872 CHAD -2.32012 6.502384 94.50606 1.35E-06 0.001872 LOC108590320 -3.69941 3.094203 81.63781 2.70E-06 0.001911 PRAP1 -3.50931 9.558516 86.09876 2.10E-06 0.001911 EPDR1 -3.28843 5.553597 85.40134 2.18E-06 0.001911
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    N-Arachidonoyl Dopamine Modulates Acute Systemic Inflammation via Nonhematopoietic TRPV1 This information is current as Samira K. Lawton, Fengyun Xu, Alphonso Tran, Erika of October 1, 2021. Wong, Arun Prakash, Mark Schumacher, Judith Hellman and Kevin Wilhelmsen J Immunol 2017; 199:1465-1475; Prepublished online 12 July 2017; doi: 10.4049/jimmunol.1602151 http://www.jimmunol.org/content/199/4/1465 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2017/07/12/jimmunol.160215 Material 1.DCSupplemental http://www.jimmunol.org/ References This article cites 69 articles, 11 of which you can access for free at: http://www.jimmunol.org/content/199/4/1465.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on October 1, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Author Choice Freely available online through The Journal of Immunology Author Choice option Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2017 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology N-Arachidonoyl Dopamine Modulates Acute Systemic Inflammation via Nonhematopoietic TRPV1 Samira K.
  • Delineation of Aeromonas Hydrophila Pathotypes by Dectection of Putative Virulence Factors Using Polymerase Chain Reaction and N

    Delineation of Aeromonas Hydrophila Pathotypes by Dectection of Putative Virulence Factors Using Polymerase Chain Reaction and N

    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by DigitalCommons@Kennesaw State University Kennesaw State University DigitalCommons@Kennesaw State University Master of Science in Integrative Biology Theses Biology & Physics Summer 7-20-2015 Delineation of Aeromonas hydrophila Pathotypes by Dectection of Putative Virulence Factors using Polymerase Chain Reaction and Nematode Challenge Assay John Metz Kennesaw State University, [email protected] Follow this and additional works at: http://digitalcommons.kennesaw.edu/integrbiol_etd Part of the Integrative Biology Commons Recommended Citation Metz, John, "Delineation of Aeromonas hydrophila Pathotypes by Dectection of Putative Virulence Factors using Polymerase Chain Reaction and Nematode Challenge Assay" (2015). Master of Science in Integrative Biology Theses. Paper 7. This Thesis is brought to you for free and open access by the Biology & Physics at DigitalCommons@Kennesaw State University. It has been accepted for inclusion in Master of Science in Integrative Biology Theses by an authorized administrator of DigitalCommons@Kennesaw State University. For more information, please contact [email protected]. Delineation of Aeromonas hydrophila Pathotypes by Detection of Putative Virulence Factors using Polymerase Chain Reaction and Nematode Challenge Assay John Michael Metz Submitted in partial fulfillment of the requirements for the Master of Science Degree in Integrative Biology Thesis Advisor: Donald J. McGarey, Ph.D Department of Molecular and Cellular Biology Kennesaw State University ABSTRACT Aeromonas hydrophila is a Gram-negative, bacterial pathogen of humans and other vertebrates. Human diseases caused by A. hydrophila range from mild gastroenteritis to soft tissue infections including cellulitis and acute necrotizing fasciitis. When seen in fish it causes dermal ulcers and fatal septicemia, which are detrimental to aquaculture stocks and has major economic impact to the industry.
  • UNIVERSITY of CALIFORNIA RIVERSIDE Investigations Into The

    UNIVERSITY of CALIFORNIA RIVERSIDE Investigations Into The

    UNIVERSITY OF CALIFORNIA RIVERSIDE Investigations into the Role of TAF1-mediated Phosphorylation in Gene Regulation A Dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Cell, Molecular and Developmental Biology by Brian James Gadd December 2012 Dissertation Committee: Dr. Xuan Liu, Chairperson Dr. Frank Sauer Dr. Frances M. Sladek Copyright by Brian James Gadd 2012 The Dissertation of Brian James Gadd is approved Committee Chairperson University of California, Riverside Acknowledgments I am thankful to Dr. Liu for her patience and support over the last eight years. I am deeply indebted to my committee members, Dr. Frank Sauer and Dr. Frances Sladek for the insightful comments on my research and this dissertation. Thanks goes out to CMDB, especially Dr. Bachant, Dr. Springer and Kathy Redd for their support. Thanks to all the members of the Liu lab both past and present. A very special thanks to the members of the Sauer lab, including Silvia, Stephane, David, Matt, Stephen, Ninuo, Toby, Josh, Alice, Alex and Flora. You have made all the years here fly by and made them so enjoyable. From the Sladek lab I want to thank Eugene, John, Linh and Karthi. Special thanks go out to all the friends I’ve made over the years here. Chris, Amber, Stephane and David, thank you so much for feeding me, encouraging me and keeping me sane. Thanks to the brothers for all your encouragement and prayers. To any I haven’t mentioned by name, I promise I haven’t forgotten all you’ve done for me during my graduate years.
  • Supplementary File 1

    Supplementary File 1

    Supplementary The Effect of Increasing Inclusion Levels of a Fucoidan Rich Extract Derived from Ascophyllum nodosum on Growth Performance and Aspects of Intestinal Health of Pigs Post-Weaning Ruth Rattigan 1, Stafford Vigors 1, Gaurav Rajauria 1, Torres Sweeney 2, Kevin Thornton 2 and John V O’Doherty 1,* Supplementary document 1. Alpha diversity & gene expression Figure S1. The effect of fucoidan supplementation at 250ppm on Observed, Shannon and Simpson measures of alpha diversity in caecal and colonic digesta. Table DS1. Effect of fucoidan on gene expression in the duodenum (Least-square means with their standard errors) Group Gene Basal Fucoidan SEM P value 250ppm Digestive SI 23195.53 21920.53 3734.92 0.813 enzymes CNDP1 220.76 195.56 57.42 0.761 FABP2 64101.33 63277.94 13214.97 0.966 SLC2A1 340.44 103.05 47.20 0.364 SLC2A2 3501.49 3760.72 603.38 0.766 SLC2A5 979.44 789.62 90.78 0.163 SLC2A7 508.99 496.96 88.62 0.925 SLC2A8 226.76 401.46 66.18 0.083 Nutrient SLC16A1 2246.59 2698.03 218.08 0.165 transporters SLC15A1 3936.03 4139.35 585.09 0.810 SLC5A1 11917.91 11381.36 1652.19 0.822 SLC16A10 649.47 581.32 71.64 0.512 SLC6A19 2623.95 2733.15 213.52 0.723 SLC7A1 157.24 181.69 12.93 0.202 SLC5A8 3214.00 4059.56 199.78 0.010 GLP2R 153.47 163.79 10.00 0.479 Appetite GCG 723.21 264.69 275.57 0.261 regulators CCK 825.90 813.21 98.49 0.929 CLDN3 2284.64 2545.28 135.22 0.194 CLDN5 65.53 55.71 3.18 0.047 Tight junctions OCLN 2290.33 2235.59 148.52 0.798 TJP1 1050.29 1051.15 28.50 0.983 NFKB1 561.69 598.47 16.04 0.127 IFNG 90.61 110.40 16.36