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  1. Book ; Online: The Pangenome

    Tettelin, Hervé / Medini, Duccio

    Diversity, Dynamics and Evolution of Genomes

    2020  

    Author's details edited by Hervé Tettelin, Duccio Medini
    Keywords Microbial genetics ; Microbial genomics ; Evolutionary biology ; Biomathematics ; Microbial ecology ; Human genetics ; Genetics
    Subject code 579.135
    Language English
    Size 1 Online-Ressource (XIV, 309 p. 43 illus., 41 illus. in color)
    Edition 1st ed. 2020
    Publisher Springer International Publishing ; Imprint: Springer
    Publishing place Cham
    Document type Book ; Online
    HBZ-ID HT020443980
    ISBN 978-3-030-38281-0 ; 9783030382803 ; 9783030382827 ; 9783030382834 ; 3-030-38281-8 ; 303038280X ; 3030382826 ; 3030382834
    DOI 10.1007/978-3-030-38281-0
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Book ; Online: The Pangenome

    Tettelin, Hervé / Medini, Duccio

    2020  

    Abstract: This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of ...

    Abstract This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book's respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics
    Keywords Biology (General) ; Mathematics ; Ecology ; Medicine (General)
    Size 1 electronic resource (307 pages)
    Publisher Springer Nature
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT020481425
    ISBN 9783030382810 ; 3030382818
    DOI 10.1007/978-3-030-38281-0
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  3. Article ; Online: Identification of Virulence-Associated Properties by Comparative Genome Analysis of Streptococcus pneumoniae, S. pseudopneumoniae, S. mitis, Three S. oralis Subspecies, and

    Kilian, Mogens / Tettelin, Hervé

    mBio

    2019  Volume 10, Issue 5

    Abstract: From a common ancestor, ...

    Abstract From a common ancestor,
    MeSH term(s) Biological Evolution ; Comparative Genomic Hybridization ; Endocarditis/microbiology ; Genes, Bacterial/genetics ; Genome, Bacterial/genetics ; Humans ; Streptococcus/classification ; Streptococcus/genetics ; Streptococcus/physiology ; Streptococcus mitis/genetics ; Streptococcus oralis/genetics ; Streptococcus pneumoniae/genetics ; Symbiosis ; Virulence/genetics ; Virulence Factors/genetics ; Virulence Factors/isolation & purification
    Chemical Substances Virulence Factors
    Language English
    Publishing date 2019-09-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mBio.01985-19
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Erratum for Kilian and Tettelin, "Identification of Virulence-Associated Properties by Comparative Genome Analysis of Streptococcus pneumoniae,

    Kilian, Mogens / Tettelin, Hervé

    mBio

    2019  Volume 10, Issue 5

    Language English
    Publishing date 2019-10-15
    Publishing country United States
    Document type Journal Article ; Published Erratum
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mBio.02520-19
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Adaptation of Nontypeable

    Murphy, Timothy F / Kirkham, Charmaine / D'Mello, Adonis / Sethi, Sanjay / Pettigrew, Melinda M / Tettelin, Hervé

    mBio

    2023  Volume 14, Issue 2, Page(s) e0014023

    Abstract: Chronic obstructive pulmonary disease (COPD) is a common debilitating disorder that is the third most common cause of death globally. Chronic lower airway infection by nontypeable Haemophilus influenzae (NTHi) in adults with COPD increases airway ... ...

    Abstract Chronic obstructive pulmonary disease (COPD) is a common debilitating disorder that is the third most common cause of death globally. Chronic lower airway infection by nontypeable Haemophilus influenzae (NTHi) in adults with COPD increases airway inflammation, causes increased symptoms, and accelerates progressive loss of lung function. Little is known about the mechanisms by which NTHi survives in COPD airways. To explore this question, the present study analyzes, in detail, 14 prospectively collected, serial isolates of a strain that persisted for 543 days in a patient with COPD, including analysis of four gap-free complete genomes. The NTHi genome underwent inversion of a ~400-kb segment three times during persistence. This inversion event resulted in switching of expression of the HMW1A and HMW2A adhesins as the inversion sites are in the promoter regions of HMW1 and HMW2. Regulation of the level of expression of HMW 1 and HMW2 in the human airways was controlled by the ~400-kb inversion and by 7-bp repeats in the HMW promoters. Analysis of knockout mutants of the persistent strain demonstrated that HMW1 and HMW2 proteins both function in the adherence of NTHi to human respiratory epithelial cells during persistence and that HMW1 also facilitates invasion of epithelial cells. An inverse relationship between biofilm formation and HMW1 expression was observed during persistence. This work advances understanding of the mechanisms of persistence of NTHi in COPD airways, which can inform the development of novel interventions to treat and prevent chronic NTHi infection in COPD.
    MeSH term(s) Adult ; Humans ; Haemophilus influenzae/genetics ; Respiratory System ; Adhesins, Bacterial/genetics ; Pulmonary Disease, Chronic Obstructive/complications ; Pulmonary Disease, Chronic Obstructive/genetics ; Inflammation ; Haemophilus Infections
    Chemical Substances Adhesins, Bacterial
    Language English
    Publishing date 2023-03-16
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mbio.00140-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Sugar-Coated Killer: Serotype 3 Pneumococcal Disease.

    Luck, Jennifer N / Tettelin, Hervé / Orihuela, Carlos J

    Frontiers in cellular and infection microbiology

    2020  Volume 10, Page(s) 613287

    Abstract: Capsular polysaccharide (CPS), which surrounds the bacteria, is one of the most significant and multifaceted contributors ... ...

    Abstract Capsular polysaccharide (CPS), which surrounds the bacteria, is one of the most significant and multifaceted contributors to
    MeSH term(s) Humans ; Pneumococcal Infections/prevention & control ; Pneumococcal Vaccines ; Serogroup ; Streptococcus pneumoniae ; Sugars
    Chemical Substances Pneumococcal Vaccines ; Sugars
    Language English
    Publishing date 2020-12-23
    Publishing country Switzerland
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 2619676-1
    ISSN 2235-2988 ; 2235-2988
    ISSN (online) 2235-2988
    ISSN 2235-2988
    DOI 10.3389/fcimb.2020.613287
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Book ; Online: The Pangenome

    Tettelin, Hervé / Medini, Duccio

    2020  

    Abstract: This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of ...

    Abstract This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book’s respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.
    Keywords Microbial Genetics and Genomics ; Evolutionary Biology ; Genetics and Population Dynamics ; Microbial Ecology ; Human Genetics ; Genetics and Genomics ; Comparative genomics ; Metagenomics ; Microbial Population Analysis ; Pangenome Profile ; Supra-Genome Analysis ; Adaptive Evolution ; Computational Tools ; Bioinformatic Genomics ; Core Dispensable Genome ; Selection ; Recombination ; Composition ; Acquired Resistance ; Bacterial Species Concept ; Genomic Diversity ; Bacterial Ecology ; Microevolution ; Open Access ; Pan-metagenomics ; Pan-microbiomics ; Pan-epigenome ; Gene Transfer ; Pan-phenomes ; Microbiology (non-medical) ; Genetics (non-medical) ; Evolution ; Applied mathematics ; Ecological science ; the Biosphere ; Medical genetics
    Language English
    Publisher Springer Nature
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  8. Article ; Online: COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning.

    Huffman, Anthony / Ong, Edison / Hur, Junguk / D'Mello, Adonis / Tettelin, Hervé / He, Yongqun

    Briefings in bioinformatics

    2022  Volume 23, Issue 4

    Abstract: Rational vaccine design, especially vaccine antigen identification and optimization, is critical to successful and efficient vaccine development against various infectious diseases including coronavirus disease 2019 (COVID-19). In general, computational ... ...

    Abstract Rational vaccine design, especially vaccine antigen identification and optimization, is critical to successful and efficient vaccine development against various infectious diseases including coronavirus disease 2019 (COVID-19). In general, computational vaccine design includes three major stages: (i) identification and annotation of experimentally verified gold standard protective antigens through literature mining, (ii) rational vaccine design using reverse vaccinology (RV) and structural vaccinology (SV) and (iii) post-licensure vaccine success and adverse event surveillance and its usage for vaccine design. Protegen is a database of experimentally verified protective antigens, which can be used as gold standard data for rational vaccine design. RV predicts protective antigen targets primarily from genome sequence analysis. SV refines antigens through structural engineering. Recently, RV and SV approaches, with the support of various machine learning methods, have been applied to COVID-19 vaccine design. The analysis of post-licensure vaccine adverse event report data also provides valuable results in terms of vaccine safety and how vaccines should be used or paused. Ontology standardizes and incorporates heterogeneous data and knowledge in a human- and computer-interpretable manner, further supporting machine learning and vaccine design. Future directions on rational vaccine design are discussed.
    MeSH term(s) COVID-19/prevention & control ; COVID-19 Vaccines ; Data Mining ; Humans ; Machine Learning ; Vaccines/chemistry ; Vaccines/genetics ; Vaccinology/methods
    Chemical Substances COVID-19 Vaccines ; Vaccines
    Language English
    Publishing date 2022-06-01
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2068142-2
    ISSN 1477-4054 ; 1467-5463
    ISSN (online) 1477-4054
    ISSN 1467-5463
    DOI 10.1093/bib/bbac190
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6262: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  9. Article: Group B

    Gopalakrishna, Kathyayini P / Hillebrand, Gideon H / Bhavana, Venkata H / Elder, Jordan L / D'Mello, Adonis / Tettelin, Hervé / Hooven, Thomas A

    bioRxiv : the preprint server for biology

    2023  

    Abstract: ... Group ... ...

    Abstract Group B
    Language English
    Publishing date 2023-05-24
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.05.24.542094
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Group B Streptococcus Cas9 variants provide insight into programmable gene repression and CRISPR-Cas transcriptional effects.

    Gopalakrishna, Kathyayini P / Hillebrand, Gideon H / Bhavana, Venkata H / Elder, Jordan L / D'Mello, Adonis / Tettelin, Hervé / Hooven, Thomas A

    Communications biology

    2023  Volume 6, Issue 1, Page(s) 620

    Abstract: Group B Streptococcus (GBS; S. agalactiae) causes chorioamnionitis, neonatal sepsis, and can also cause disease in healthy or immunocompromised adults. GBS possesses a type II-A CRISPR-Cas9 system, which defends against foreign DNA within the bacterial ... ...

    Abstract Group B Streptococcus (GBS; S. agalactiae) causes chorioamnionitis, neonatal sepsis, and can also cause disease in healthy or immunocompromised adults. GBS possesses a type II-A CRISPR-Cas9 system, which defends against foreign DNA within the bacterial cell. Several recent publications have shown that GBS Cas9 influences genome-wide transcription through a mechanism uncoupled from its function as a specific, RNA-programmable endonuclease. We examine GBS Cas9 effects on genome-wide transcription through generation of several isogenic variants with specific functional defects. We compare whole-genome RNA-seq from Δcas9 GBS with a full-length Cas9 gene deletion; dcas9 defective in its ability to cleave DNA but still able to bind to frequently occurring protospacer adjacent motifs; and scas9 that retains its catalytic domains but is unable to bind protospacer adjacent motifs. Comparing scas9 GBS to the other variants, we identify nonspecific protospacer adjacent motif binding as a driver of genome-wide, Cas9 transcriptional effects in GBS. We also show that Cas9 transcriptional effects from nonspecific scanning tend to influence genes involved in bacterial defense and nucleotide or carbohydrate transport and metabolism. While genome-wide transcription effects are detectable by analysis of next-generation sequencing, they do not result in virulence changes in a mouse model of sepsis. We also demonstrate that catalytically inactive dCas9 expressed from the GBS chromosome can be used with a straightforward, plasmid-based, single guide RNA expression system to suppress transcription of specific GBS genes without potentially confounding off-target effects. We anticipate that this system will be useful for study of nonessential and essential gene roles in GBS physiology and pathogenesis.
    MeSH term(s) Animals ; Mice ; CRISPR-Cas Systems ; RNA/metabolism ; Bacteria/genetics ; DNA/genetics ; Streptococcus/genetics
    Chemical Substances RNA (63231-63-0) ; DNA (9007-49-2)
    Language English
    Publishing date 2023-06-09
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-023-04994-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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