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  1. Article ; Online: Analysis of clinical

    Bergin, Sean / Doorley, Laura A / Rybak, Jeffrey M / Wolfe, Kenneth H / Butler, Geraldine / Cuomo, Christina A / Rogers, P David

    Antimicrobial agents and chemotherapy

    2024  , Page(s) e0161923

    Abstract: We used whole-genome sequencing to analyze a collection of 35 fluconazole-resistant and 7 ... ...

    Abstract We used whole-genome sequencing to analyze a collection of 35 fluconazole-resistant and 7 susceptible
    Language English
    Publishing date 2024-05-07
    Publishing country United States
    Document type Journal Article
    ZDB-ID 217602-6
    ISSN 1098-6596 ; 0066-4804
    ISSN (online) 1098-6596
    ISSN 0066-4804
    DOI 10.1128/aac.01619-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 809: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)
    Einzelsignatur: Show issues

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  2. Article ; Online: CRISPR-Cas9 Editing Induces Loss of Heterozygosity in the Pathogenic Yeast Candida parapsilosis.

    Lombardi, Lisa / Bergin, Sean A / Ryan, Adam / Zuniga-Soto, Evelyn / Butler, Geraldine

    mSphere

    2022  , Page(s) e0039322

    Abstract: Genetic manipulation is often used to study gene function. However, unplanned genome changes (including single nucleotide polymorphisms [SNPs], aneuploidy, and loss of heterozygosity [LOH]) can affect the phenotypic traits of the engineered strains. Here, ...

    Abstract Genetic manipulation is often used to study gene function. However, unplanned genome changes (including single nucleotide polymorphisms [SNPs], aneuploidy, and loss of heterozygosity [LOH]) can affect the phenotypic traits of the engineered strains. Here, we compared the effect of classical deletion methods (replacing target alleles with selectable markers by homologous recombination) with CRISPR-Cas9 editing in the diploid human-pathogenic yeast Candida parapsilosis. We sequenced the genomes of 9 isolates that were modified using classic recombination methods and 12 that were edited using CRISPR-Cas9. As a control, the genomes of eight isolates that were transformed with a Cas9-expressing plasmid in the absence of a guide RNA were also sequenced. Following gene manipulation using classic homologous recombination, only one strain exhibited extensive LOH near the targeted gene (8.9 kb), whereas another contained multiple LOH events not associated with the intended modification. In contrast, large regions of LOH (up to >1,100 kb) were observed in most CRISPR-Cas9-edited strains. LOH most commonly occurred adjacent to the Cas9 cut site and extended to the telomere in four isolates. In two isolates, we observed LOH on chromosomes that were not targeted by CRISPR-Cas9. Among the CRISPR-edited isolates, two exhibited cysteine and methionine auxotrophy caused by LOH at a heterozygous site in
    Language English
    Publishing date 2022-11-23
    Publishing country United States
    Document type Journal Article
    ISSN 2379-5042
    ISSN (online) 2379-5042
    DOI 10.1128/msphere.00393-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Analysis of clinical

    Bergin, Sean / Doorley, Laura A / Rybak, Jeffrey M / Wolfe, Kenneth H / Butler, Geraldine / Cuomo, Christina A / Rogers, P David

    bioRxiv : the preprint server for biology

    2023  

    Abstract: We used whole-genome sequencing to analyse a collection of 35 fluconazole resistant and 7 ... ...

    Abstract We used whole-genome sequencing to analyse a collection of 35 fluconazole resistant and 7 susceptible
    Language English
    Publishing date 2023-12-14
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.12.13.571446
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Genome sequences of two isolates of the yeast

    McLaughlin, Richard W / Hession, Conor / Bergin, Sean / Cosgrove, Aoife / Dowd, Andrew / Garvey, Niall / Litovskich, Gabrielle / Osaigbovo, Evita / Popa, Denis / Thuku, Cynthia / Butler, Geraldine / Wolfe, Kenneth H / Byrne, Kevin P

    Microbiology resource announcements

    2024  Volume 13, Issue 3, Page(s) e0108123

    Abstract: We report genome sequences of two new isolates of the budding ... ...

    Abstract We report genome sequences of two new isolates of the budding yeast
    Language English
    Publishing date 2024-02-09
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.01081-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Draft Genome Sequence of the Yeast Torulaspora quercuum Strain UCD657, Isolated from Soil in Ireland.

    Igharo, Blessing / Byrne, Kevin P / Ghnewa, Heytham / Davey, Ryan P / Fubara, Athaliah / Welc, Julia / Oubihi, Shafik / Moore, Luke / Smith, Cian / Ó Cinnéide, Eoin / Bergin, Sean A / Hession, Conor / Wolfe, Kenneth H / Butler, Geraldine

    Microbiology resource announcements

    2022  Volume 11, Issue 11, Page(s) e0095222

    Abstract: Torulaspora quercuum is an ascomycete yeast first isolated in 2009. Here, we present the genome sequence of T. quercuum isolate UCD657, which was isolated from soil in Ireland. This genome is 10.4 Mb and was assembled into 8 chromosome-sized scaffolds of ...

    Abstract Torulaspora quercuum is an ascomycete yeast first isolated in 2009. Here, we present the genome sequence of T. quercuum isolate UCD657, which was isolated from soil in Ireland. This genome is 10.4 Mb and was assembled into 8 chromosome-sized scaffolds of >1 Mb in size, plus a mitochondrial genome scaffold.
    Language English
    Publishing date 2022-10-10
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.00952-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Draft Genome Sequence of the Yeast Blastobotrys aristata Strain UCD613, Isolated from Soil in Ireland.

    Don, Aida / Byrne, Kevin P / Alqaderi, Fouz / Mazhova, Alexandra / O'Leary Chaney, Ben / Redmond, Sarah / Allen, Stephen / Gao, Jiaran / Ó Cinnéide, Eoin / Bergin, Sean A / Hession, Conor / Wolfe, Kenneth H / Butler, Geraldine

    Microbiology resource announcements

    2022  Volume 11, Issue 11, Page(s) e0095722

    Abstract: Blastobotrys aristata is a member of the Trichomonascaceae family in the order Saccharomycetales. Here, we present the genome sequence ... ...

    Abstract Blastobotrys aristata is a member of the Trichomonascaceae family in the order Saccharomycetales. Here, we present the genome sequence of
    Language English
    Publishing date 2022-10-12
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.00957-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Systematic Analysis of Copy Number Variations in the Pathogenic Yeast Candida parapsilosis Identifies a Gene Amplification in

    Bergin, Sean A / Zhao, Fang / Ryan, Adam P / Müller, Carolin A / Nieduszynski, Conrad A / Zhai, Bing / Rolling, Thierry / Hohl, Tobias M / Morio, Florent / Scully, Jillian / Wolfe, Kenneth H / Butler, Geraldine

    mBio

    2022  Volume 13, Issue 5, Page(s) e0177722

    Abstract: We analyzed the genomes of 170 C. parapsilosis isolates and identified multiple copy number variations (CNVs). We identified two genes, ...

    Abstract We analyzed the genomes of 170 C. parapsilosis isolates and identified multiple copy number variations (CNVs). We identified two genes,
    MeSH term(s) Antifungal Agents/pharmacology ; Arsenates ; Candida parapsilosis/drug effects ; Candida parapsilosis/genetics ; DNA Copy Number Variations ; Drug Resistance, Fungal/genetics ; Gene Amplification ; Phosphatidylcholines ; Phylogeny ; Saccharomyces cerevisiae
    Chemical Substances Antifungal Agents ; Arsenates ; miltefosine (53EY29W7EC) ; Phosphatidylcholines
    Language English
    Publishing date 2022-09-19
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; 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.01777-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Identification of European isolates of the lager yeast parent Saccharomyces eubayanus.

    Bergin, Sean A / Allen, Stephen / Hession, Conor / Ó Cinnéide, Eoin / Ryan, Adam / Byrne, Kevin P / Ó Cróinín, Tadhg / Wolfe, Kenneth H / Butler, Geraldine

    FEMS yeast research

    2022  Volume 22, Issue 1

    Abstract: Lager brewing first occurred in Bavaria in the 15th century, associated with restrictions of brewing to colder months. The lager yeast, Saccharomyces pastorianus, is cold tolerant. It is a hybrid between Saccharomyces cerevisiae and Saccharomyces ... ...

    Abstract Lager brewing first occurred in Bavaria in the 15th century, associated with restrictions of brewing to colder months. The lager yeast, Saccharomyces pastorianus, is cold tolerant. It is a hybrid between Saccharomyces cerevisiae and Saccharomyces eubayanus, and has been found only in industrial settings. Natural isolates of S. eubayanus were first discovered in Patagonia 11 years ago. They have since been isolated from China, Tibet, New Zealand, and North America, but not from Europe. Here, we describe the first European strains UCD646 and UCD650, isolated from a wooded area on a university campus in Dublin, Ireland. We generated complete chromosome level assemblies of both genomes using long- and short-read sequencing. The UCD isolates belong to the Holarctic clade. Genome analysis shows that isolates similar to the Irish strains contributed to the S. eubayanus component of S. pastorianus, but isolates from Tibet made a larger contribution.
    MeSH term(s) Humans ; China ; New Zealand ; North America
    Language English
    Publishing date 2022-08-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 2036775-2
    ISSN 1567-1364 ; 1567-1356
    ISSN (online) 1567-1364
    ISSN 1567-1356
    DOI 10.1093/femsyr/foac053
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5454: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  9. Article ; Online: Identification of a novel Candida metapsilosis isolate reveals multiple hybridization events.

    O'Brien, Caoimhe E / Zhai, Bing / Ola, Mihaela / Bergin, Sean A / Ó Cinnéide, Eoin / O'Connor, Ísla / Rolling, Thierry / Miranda, Edwin / Babady, N Esther / Hohl, Tobias M / Butler, Geraldine

    G3 (Bethesda, Md.)

    2021  Volume 12, Issue 1

    Abstract: Candida metapsilosis is a member of the Candida parapsilosis species complex, a group of opportunistic human pathogens. Of all the members of this complex, C. metapsilosis is the least virulent, and accounts for a small proportion of invasive Candida ... ...

    Abstract Candida metapsilosis is a member of the Candida parapsilosis species complex, a group of opportunistic human pathogens. Of all the members of this complex, C. metapsilosis is the least virulent, and accounts for a small proportion of invasive Candida infections. Previous studies established that all C. metapsilosis isolates are hybrids, originating from a single hybridization event between two lineages, parent A and parent B. Here, we use MinION and Illumina sequencing to characterize a C. metapsilosis isolate that originated from a separate hybridization. One of the parents of the new isolate is very closely related to parent A. However, the other parent (parent C) is not the same as parent B. Unlike C. metapsilosis AB isolates, the C. metapsilosis AC isolate has not undergone introgression at the mating type-like locus. In addition, the A and C haplotypes are not fully collinear. The C. metapsilosis AC isolate has undergone loss of heterozygosity with a preference for haplotype A, indicating that this isolate is in the early stages of genome stabilization.
    MeSH term(s) Antifungal Agents ; Candida/genetics ; Candida parapsilosis/genetics ; Candidiasis/genetics ; Genome ; Humans ; Hybridization, Genetic
    Chemical Substances Antifungal Agents
    Language English
    Publishing date 2021-11-17
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2629978-1
    ISSN 2160-1836 ; 2160-1836
    ISSN (online) 2160-1836
    ISSN 2160-1836
    DOI 10.1093/g3journal/jkab367
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Draft Genome Sequence of a Diploid and Hybrid

    Ryan, Adam / Ó Cinnéide, Eoin / Bergin, Sean A / Alhajeri, Ghozlan / Almotawaa, Hawraa / Daly, Isabelle / Heneghan, Sophia / Horan, Kellie / Kavanagh, Roslyn / Keane, Christopher / Martin, Aaron / McDonagh, Ada / O'Leary, Julia / Osborne, Matthieu / Watson, Emma / Byrne, Kevin P / Wolfe, Kenneth H / Butler, Geraldine

    Microbiology resource announcements

    2021  Volume 10, Issue 38, Page(s) e0076121

    Abstract: Candida sanyaensis is a CUG-Ser1 clade yeast that is associated with soil. Assembly of short-read and long-read data shows that C. sanyaensis has a diploid and hybrid genome, with approximately 97% identity between the haplotypes. The haploid genome size ...

    Abstract Candida sanyaensis is a CUG-Ser1 clade yeast that is associated with soil. Assembly of short-read and long-read data shows that C. sanyaensis has a diploid and hybrid genome, with approximately 97% identity between the haplotypes. The haploid genome size is approximately 15.4 Mb.
    Language English
    Publishing date 2021-09-23
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.00761-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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