Towards a Functional Hypothesis Relating Anti-Islet Cell Autoimmunity
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
University of Cincinnati
UNIVERSITY OF CINCINNATI Date: February 22, 2007 I, _ Samuel Lee Hayes________________________________________, hereby submit this work as part of the requirements for the degree of: Doctor of Philosophy in: Biological Sciences It is entitled: Response of Mammalian Models to Exposure of Bacteria from the Genus Aeromonas Evaluated using Transcriptional Analysis and Conjectures on Disease Mechanisms This work and its defense approved by: Chair: _Brian K. Kinkle _Dennis W. Grogan _Richard D. Karp _Mario Medvedovic _Stephen J. Vesper Response of Mammalian Models to Exposure of Bacteria from the Genus Aeromonas Evaluated using Transcriptional Analysis and Conjectures on Disease Mechanisms A dissertation submitted to the Division of Graduate Studies and Research of the University of Cincinnati in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in the Department of Biological Sciences of the College of Arts and Sciences 2007 by Samuel Lee Hayes B.S. Ohio University, 1978 M.S. University of Cincinnati, 1986 Committee Chair: Dr. Brian K. Kinkle Abstract The genus Aeromonas contains virulent bacteria implicated in waterborne disease, as well as avirulent strains. One of my research objectives was to identify and characterize host- pathogen relationships specific to Aeromonas spp. Aeromonas virulence was assessed using changes in host mRNA expression after infecting cell cultures and live animals. Messenger RNA extracts were hybridized to murine genomic microarrays. Initially, these model systems were infected with two virulent A. hydrophila strains, causing up-regulation of over 200 and 50 genes in animal and cell culture tissues, respectively. Twenty-six genes were common between the two model systems. The live animal model was used to define virulence for many Aeromonas spp. -
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. -
Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg -
Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae -
Pdf 279.64 K
Int. J. Environ. Res., 8(3):813-818,Summer 2014 ISSN: 1735-6865 Persian Gulf is a Bioresource of Potent L-Asparaginase Producing Bacteria: Isolation & Molecular Differentiating Izadpanah Qeshmi, F.1,2 , Javadpour, S. 2, Malekzadeh, K. 2 * ,Tamadoni Jahromi, S.3 and Rahimzadeh, M.2 1Department of Miocrobiology; Jahrom Branch; Islamic Azad University; Jahrom; Iran 2Molecular Medicine Research Center (MMRC); Hormozgan University of Medical Science (HUMS); Bandar Abbas; Iran 3Persian Gulf and Oman Sea Ecological Research Institute; Bandar Abbas; Iran Received 3 Nov. 2013; Revised 24 Dec. 2013; Accepted 5 Jan. 2014 ABSTRACT: L-asparaginase is a candidate enzyme for anti-neoplastic agent againstacute lymphoblastic leukemia and also extensively use in the food industry for prevention of acrylamide formation. L-asparaginase is widely distributed among microorganisms. In this study, marine bacteria were isolated from Persian Gulf and screened for L-asparaginase activity. Production of L-asparaginase was carried out by using M9 medium. Among L-asparaginase producing strains, 12 potent strains were differentiated based on nucleotide sequences of 16S rDNA. 12 potent strains included 2 strains of Pseudomonas spp., 8 strains of Bacillus spp, one strain of Zobellella spp. and one strain of Oceanimonas spp. identified and consequently the sequences published in the NCBI databases under the specific accession numbers. This is the first report on L-asparaginase activity of Zobellella spp. from this region. The highest (1.6 IU/ mL) and also the lowest (0.20 IU/ mL) productivity of L-asparaginase enzyme were recorded for Pseudomonas sp. PG_01 and Bacillus sp. PG_13 respectively. This study revealed marine bacteria are potential source of L-asparaginase enzyme .Pseudomonas sp.PG_01 with high productivity can be used for production of L-asparaginase. -
An Update on the Genus Aeromonas: Taxonomy, Epidemiology, and Pathogenicity
microorganisms Review An Update on the Genus Aeromonas: Taxonomy, Epidemiology, and Pathogenicity Ana Fernández-Bravo and Maria José Figueras * Unit of Microbiology, Department of Basic Health Sciences, Faculty of Medicine and Health Sciences, IISPV, University Rovira i Virgili, 43201 Reus, Spain; [email protected] * Correspondence: mariajose.fi[email protected]; Tel.: +34-97-775-9321; Fax: +34-97-775-9322 Received: 31 October 2019; Accepted: 14 January 2020; Published: 17 January 2020 Abstract: The genus Aeromonas belongs to the Aeromonadaceae family and comprises a group of Gram-negative bacteria widely distributed in aquatic environments, with some species able to cause disease in humans, fish, and other aquatic animals. However, bacteria of this genus are isolated from many other habitats, environments, and food products. The taxonomy of this genus is complex when phenotypic identification methods are used because such methods might not correctly identify all the species. On the other hand, molecular methods have proven very reliable, such as using the sequences of concatenated housekeeping genes like gyrB and rpoD or comparing the genomes with the type strains using a genomic index, such as the average nucleotide identity (ANI) or in silico DNA–DNA hybridization (isDDH). So far, 36 species have been described in the genus Aeromonas of which at least 19 are considered emerging pathogens to humans, causing a broad spectrum of infections. Having said that, when classifying 1852 strains that have been reported in various recent clinical cases, 95.4% were identified as only four species: Aeromonas caviae (37.26%), Aeromonas dhakensis (23.49%), Aeromonas veronii (21.54%), and Aeromonas hydrophila (13.07%). -
A Noval Investigation of Microbiome from Vermicomposting Liquid Produced by Thai Earthworm, Perionyx Sp
International Journal of Agricultural Technology 2021Vol. 17(4):1363-1372 Available online http://www.ijat-aatsea.com ISSN 2630-0192 (Online) A novel investigation of microbiome from vermicomposting liquid produced by Thai earthworm, Perionyx sp. 1 Kraisittipanit, R.1,2, Tancho, A.2,3, Aumtong, S.3 and Charerntantanakul, W.1* 1Program of Biotechnology, Faculty of Science, Maejo University, Chiang Mai, Thailand; 2Natural Farming Research and Development Center, Maejo University, Chiang Mai, Thailand; 3Faculty of Agricultural Production, Maejo University, Thailand. Kraisittipanit, R., Tancho, A., Aumtong, S. and Charerntantanakul, W. (2021). A noval investigation of microbiome from vermicomposting liquid produced by Thai earthworm, Perionyx sp. 1. International Journal of Agricultural Technology 17(4):1363-1372. Abstract The whole microbiota structure in vermicomposting liquid derived from Thai earthworm, Perionyx sp. 1 was estimated. It showed high richness microbial species and belongs to 127 species, separated in 3 fungal phyla (Ascomycota, Basidiomycota, Mucoromycota), 1 Actinomycetes and 16 bacterial phyla (Acidobacteria, Armatimonadetes, Bacteroidetes, Balneolaeota, Candidatus, Chloroflexi, Deinococcus, Fibrobacteres, Firmicutes, Gemmatimonadates, Ignavibacteriae, Nitrospirae, Planctomycetes, Proteobacteria, Tenericutes and Verrucomicrobia). The OTUs data analysis revealed the highest taxonomic abundant ratio in bacteria and fungi belong to Proteobacteria (70.20 %) and Ascomycota (5.96 %). The result confirmed that Perionyx sp. 1 -
Gut Microbiota Signature of Pathogen-Dependent Dysbiosis in Viral Gastroenteritis
www.nature.com/scientificreports OPEN Gut microbiota signature of pathogen‑dependent dysbiosis in viral gastroenteritis Taketoshi Mizutani1*, Samuel Yaw Aboagye2, Aya Ishizaka1, Theophillus Afum2, Gloria Ivy Mensah2, Adwoa Asante‑Poku2, Diana Asema Asandem2, Prince Kof Parbie2,3,4, Christopher Zaab‑Yen Abana2, Dennis Kushitor2, Evelyn Yayra Bonney2, Motoi Adachi5, Hiroki Hori5, Koichi Ishikawa4, Tetsuro Matano1,3,4, Kiyosu Taniguchi6, David Opare7, Doris Arhin7, Franklin Asiedu‑Bekoe7, William Kwabena Ampofo2, Dorothy Yeboah‑Manu2, Kwadwo Ansah Koram2, Abraham Kwabena Anang2 & Hiroshi Kiyono1,8,9 Acute gastroenteritis associated with diarrhea is considered a serious disease in Africa and South Asia. In this study, we examined the trends in the causative pathogens of diarrhea and the corresponding gut microbiota in Ghana using microbiome analysis performed on diarrheic stools via 16S rRNA sequencing. In total, 80 patients with diarrhea and 34 healthy adults as controls, from 2017 to 2018, were enrolled in the study. Among the patients with diarrhea, 39 were norovirus‑positive and 18 were rotavirus‑positive. The analysis of species richness (Chao1) was lower in patients with diarrhea than that in controls. Beta‑diversity analysis revealed signifcant diferences between the two groups. Several diarrhea‑related pathogens (e.g., Escherichia‑Shigella, Klebsiella and Campylobacter) were detected in patients with diarrhea. Furthermore, co‑infection with these pathogens and enteroviruses (e.g., norovirus and rotavirus) was observed in several cases. Levels of both Erysipelotrichaceae and Staphylococcaceae family markedly difered between norovirus‑positive and ‑negative diarrheic stools, and the 10 predicted metabolic pathways, including the carbohydrate metabolism pathway, showed signifcant diferences between rotavirus‑positive patients with diarrhea and controls. -
Microbiome Disturbance and Resilience Dynamics of the Upper Respiratory Tract During Influenza a Virus Infection
ARTICLE https://doi.org/10.1038/s41467-020-16429-9 OPEN Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection Drishti Kaul1,12, Raveen Rathnasinghe2,12, Marcela Ferres2, Gene S. Tan1,3, Aldo Barrera2,4, Brett E. Pickett5,6, Barbara A. Methe5,7, Suman Das5, Isolda Budnik2, Rebecca A. Halpin5, David Wentworth5,10, Mirco Schmolke 8,11, Ignacio Mena 8, Randy A. Albrecht 8, Indresh Singh5, Karen E. Nelson5, ✉ ✉ Adolfo García-Sastre 8,9, Chris L. Dupont 1 & Rafael A. Medina 2,4,8 1234567890():,; Infection with influenza can be aggravated by bacterial co-infections, which often results in disease exacerbation. The effects of influenza infection on the upper respiratory tract (URT) microbiome are largely unknown. Here, we report a longitudinal study to assess the temporal dynamics of the URT microbiomes of uninfected and influenza virus-infected humans and ferrets. Uninfected human patients and ferret URT microbiomes have stable healthy ecostate communities both within and between individuals. In contrast, infected patients and ferrets exhibit large changes in bacterial community composition over time and between individuals. The unhealthy ecostates of infected individuals progress towards the healthy ecostate, coinciding with viral clearance and recovery. Pseudomonadales associate statistically with the disturbed microbiomes of infected individuals. The dynamic and resilient microbiome during influenza virus infection in multiple hosts provides a compelling rationale for the maintenance of the microbiome homeostasis as a potential therapeutic target to prevent IAV associated bacterial co-infections. 1 J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA. 2 Departmento de Enfermedades Infecciosas e Inmunología Pediátrica, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile. -
Intestinal Virome Changes Precede Autoimmunity in Type I Diabetes-Susceptible Children,” by Guoyan Zhao, Tommi Vatanen, Lindsay Droit, Arnold Park, Aleksandar D
Correction MEDICAL SCIENCES Correction for “Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children,” by Guoyan Zhao, Tommi Vatanen, Lindsay Droit, Arnold Park, Aleksandar D. Kostic, Tiffany W. Poon, Hera Vlamakis, Heli Siljander, Taina Härkönen, Anu-Maaria Hämäläinen, Aleksandr Peet, Vallo Tillmann, Jorma Ilonen, David Wang, Mikael Knip, Ramnik J. Xavier, and Herbert W. Virgin, which was first published July 10, 2017; 10.1073/pnas.1706359114 (Proc Natl Acad Sci USA 114: E6166–E6175). The authors wish to note the following: “After publication, we discovered that certain patient-related information in the spreadsheets placed online had information that could conceiv- ably be used to identify, or at least narrow down, the identity of children whose fecal samples were studied. The article has been updated online to remove these potential privacy concerns. These changes do not alter the conclusions of the paper.” Published under the PNAS license. Published online November 19, 2018. www.pnas.org/cgi/doi/10.1073/pnas.1817913115 E11426 | PNAS | November 27, 2018 | vol. 115 | no. 48 www.pnas.org Downloaded by guest on September 26, 2021 Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children Guoyan Zhaoa,1, Tommi Vatanenb,c, Lindsay Droita, Arnold Parka, Aleksandar D. Kosticb,2, Tiffany W. Poonb, Hera Vlamakisb, Heli Siljanderd,e, Taina Härkönend,e, Anu-Maaria Hämäläinenf, Aleksandr Peetg,h, Vallo Tillmanng,h, Jorma Iloneni, David Wanga,j, Mikael Knipd,e,k,l, Ramnik J. Xavierb,m, and -
The Impact of Sequence Database Choice on Metaproteomic Results in Gut Microbiota Studies
Tanca et al. Microbiome (2016) 4:51 DOI 10.1186/s40168-016-0196-8 RESEARCH Open Access The impact of sequence database choice on metaproteomic results in gut microbiota studies Alessandro Tanca1, Antonio Palomba1, Cristina Fraumene1, Daniela Pagnozzi1, Valeria Manghina2, Massimo Deligios2, Thilo Muth3,4, Erdmann Rapp3, Lennart Martens5,6,7, Maria Filippa Addis1 and Sergio Uzzau1,2* Abstract Background: Elucidating the role of gut microbiota in physiological and pathological processes has recently emerged as a key research aim in life sciences. In this respect, metaproteomics, the study of the whole protein complement of a microbial community, can provide a unique contribution by revealing which functions are actually being expressed by specific microbial taxa. However, its wide application to gut microbiota research has been hindered by challenges in data analysis, especially related to the choice of the proper sequence databases for protein identification. Results: Here, we present a systematic investigation of variables concerning database construction and annotation and evaluate their impact on human and mouse gut metaproteomic results. We found that both publicly available and experimental metagenomic databases lead to the identification of unique peptide assortments, suggesting parallel database searches as a mean to gain more complete information. In particular, the contribution of experimental metagenomic databases was revealed to be mandatory when dealing with mouse samples. Moreover, the use of a “merged” database, containing all metagenomic sequences from the population under study, was found to be generally preferable over the use of sample-matched databases. We also observed that taxonomic and functional results are strongly database-dependent, in particular when analyzing the mouse gut microbiota. -
Taxonomic Hierarchy of the Phylum Proteobacteria and Korean Indigenous Novel Proteobacteria Species
Journal of Species Research 8(2):197-214, 2019 Taxonomic hierarchy of the phylum Proteobacteria and Korean indigenous novel Proteobacteria species Chi Nam Seong1,*, Mi Sun Kim1, Joo Won Kang1 and Hee-Moon Park2 1Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea 2Department of Microbiology & Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea *Correspondent: [email protected] The taxonomic hierarchy of the phylum Proteobacteria was assessed, after which the isolation and classification state of Proteobacteria species with valid names for Korean indigenous isolates were studied. The hierarchical taxonomic system of the phylum Proteobacteria began in 1809 when the genus Polyangium was first reported and has been generally adopted from 2001 based on the road map of Bergey’s Manual of Systematic Bacteriology. Until February 2018, the phylum Proteobacteria consisted of eight classes, 44 orders, 120 families, and more than 1,000 genera. Proteobacteria species isolated from various environments in Korea have been reported since 1999, and 644 species have been approved as of February 2018. In this study, all novel Proteobacteria species from Korean environments were affiliated with four classes, 25 orders, 65 families, and 261 genera. A total of 304 species belonged to the class Alphaproteobacteria, 257 species to the class Gammaproteobacteria, 82 species to the class Betaproteobacteria, and one species to the class Epsilonproteobacteria. The predominant orders were Rhodobacterales, Sphingomonadales, Burkholderiales, Lysobacterales and Alteromonadales. The most diverse and greatest number of novel Proteobacteria species were isolated from marine environments. Proteobacteria species were isolated from the whole territory of Korea, with especially large numbers from the regions of Chungnam/Daejeon, Gyeonggi/Seoul/Incheon, and Jeonnam/Gwangju.