Systematic Phenotyping of a Large-Scale Candida glabrata Deletion Collection Reveals Novel Antifungal Tolerance Genes
Publication Date
June 19, 2014
Journal
PLoS Pathogens
Authors
Tobias Schwarzmüller, Biao Ma, Ekkehard Hiller, Fabian Istel, et al
Volume
10
Issue
6
Pages
e1004211
DOI
https://dx.plos.org/10.1371/journal.ppat.1004211
Publisher URL
http://journals.plos.org/plospathogens/article?id=10.1371%2Fjournal.ppat.1004211
Web of Science
000338197400044
Scopus
84903457483
Mendeley
http://www.mendeley.com/research/systematic-phenotyping-largescale-candida-glabrata-deletion-collection-reveals-novel-antifungal-tole
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Mendeley | Further Information

{"title"=>"Systematic Phenotyping of a Large-Scale Candida glabrata Deletion Collection Reveals Novel Antifungal Tolerance Genes", "type"=>"journal", "authors"=>[{"first_name"=>"Tobias", "last_name"=>"Schwarzmüller", "scopus_author_id"=>"22036039600"}, {"first_name"=>"Biao", "last_name"=>"Ma", "scopus_author_id"=>"7403300877"}, {"first_name"=>"Ekkehard", "last_name"=>"Hiller", "scopus_author_id"=>"23034171300"}, {"first_name"=>"Fabian", "last_name"=>"Istel", "scopus_author_id"=>"55355254300"}, {"first_name"=>"Michael", "last_name"=>"Tscherner", "scopus_author_id"=>"35081406500"}, {"first_name"=>"Sascha", "last_name"=>"Brunke", "scopus_author_id"=>"12240425000"}, {"first_name"=>"Lauren", "last_name"=>"Ames", "scopus_author_id"=>"55363146600"}, {"first_name"=>"Arnaud", "last_name"=>"Firon", "scopus_author_id"=>"6506585596"}, {"first_name"=>"Brian", "last_name"=>"Green", "scopus_author_id"=>"7401824976"}, {"first_name"=>"Vitor", "last_name"=>"Cabral", "scopus_author_id"=>"55083574600"}, {"first_name"=>"Marina", "last_name"=>"Marcet-Houben", "scopus_author_id"=>"27267797400"}, {"first_name"=>"Ilse D.", "last_name"=>"Jacobsen", "scopus_author_id"=>"8676553500"}, {"first_name"=>"Jessica", "last_name"=>"Quintin", "scopus_author_id"=>"24464688900"}, {"first_name"=>"Katja", "last_name"=>"Seider", "scopus_author_id"=>"34873480700"}, {"first_name"=>"Ingrid", "last_name"=>"Frohner", "scopus_author_id"=>"25622338600"}, {"first_name"=>"Walter", "last_name"=>"Glaser", "scopus_author_id"=>"7006335033"}, {"first_name"=>"Helmut", "last_name"=>"Jungwirth", "scopus_author_id"=>"6603729920"}, {"first_name"=>"Sophie", "last_name"=>"Bachellier-Bassi", "scopus_author_id"=>"23484604000"}, {"first_name"=>"Murielle", "last_name"=>"Chauvel", "scopus_author_id"=>"21533338000"}, {"first_name"=>"Ute", "last_name"=>"Zeidler", "scopus_author_id"=>"25947947400"}, {"first_name"=>"Dominique", "last_name"=>"Ferrandon", "scopus_author_id"=>"6701372660"}, {"first_name"=>"Toni", "last_name"=>"Gabaldón", "scopus_author_id"=>"35229109400"}, {"first_name"=>"Bernhard", "last_name"=>"Hube", "scopus_author_id"=>"7003738705"}, {"first_name"=>"Christophe", "last_name"=>"d'Enfert", "scopus_author_id"=>"57150749600"}, {"first_name"=>"Steffen", "last_name"=>"Rupp", "scopus_author_id"=>"56227854200"}, {"first_name"=>"Brendan", "last_name"=>"Cormack", "scopus_author_id"=>"7004516992"}, {"first_name"=>"Ken", "last_name"=>"Haynes", "scopus_author_id"=>"7101942599"}, {"first_name"=>"Karl", "last_name"=>"Kuchler", "scopus_author_id"=>"7006436989"}], "year"=>2014, "source"=>"PLoS Pathogens", "identifiers"=>{"sgr"=>"84903457483", "pmid"=>"24945925", "pui"=>"373412692", "isbn"=>"10.1371/journal.ppat.1004211", "scopus"=>"2-s2.0-84903457483", "doi"=>"10.1371/journal.ppat.1004211", "issn"=>"15537374"}, "id"=>"79e6cea7-3371-3dd4-a211-f54c9515314c", "abstract"=>"Clinical infections by the yeast-like pathogen Candida glabrata have been ever-increasing over the past years. Importantly, C. glabrata is one of the most prevalent causes of drug-refractory fungal infections in humans. We have generated a novel large-scale collection encompassing 619 bar-coded C. glabrata mutants, each lacking a single gene. Extensive profiling of phenotypes reveals a number of novel genes implicated in tolerance to antifungal drugs that interfere with proper cell wall function, as well as genes affecting fitness of C. glabrata both during normal growth and under environmental stress. 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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1543063"], "description"=>"<p>The set of mutants was screened on plates for hypersensitivity to four distinct stress conditions (CF, CR, CW and 42°C heat stress) using serial dilution assays on agar plates. (A) Two-dimensional hierarchical cluster plot of chemical-genetic profiles. On the horizontal axis genes are listed and stress conditions on the vertical axis. Interactions are shown in yellow depending on the degree of growth sensitivity (yellow = no growth, black = WT growth). Stress conditions and genes are clustered by the similarity of their interactions. (B) The clusters of genes are enlarged to highlight the chemical-genetic interaction profile of Caspofungin (blue bar in ‘a’ labeled ‘b’). (C) A section of the cluster (orange bar labeled ‘C’) involved in heat stress (42°C) is enlarged. (D) Genes implicated in sensitivity to the cell wall-perturbing agents CR and CW (red and green bar labeled ‘D’).</p>", "links"=>[], "tags"=>["Biochemistry", "genetics", "microbiology", "Medical microbiology", "Microbial pathogens", "susceptibility", "deletion"], "article_id"=>1064173, "categories"=>["Biological Sciences"], "users"=>["Tobias Schwarzmüller", "Biao Ma", "Ekkehard Hiller", "Fabian Istel", "Michael Tscherner", "Sascha Brunke", "Lauren Ames", "Arnaud Firon", "Brian Green", "Vitor Cabral", "Marina Marcet-Houben", "Ilse D. Jacobsen", "Jessica Quintin", "Katja Seider", "Ingrid Frohner", "Walter Glaser", "Helmut Jungwirth", "Sophie Bachellier-Bassi", "Murielle Chauvel", "Ute Zeidler", "Dominique Ferrandon", "Toni Gabaldón", "Bernhard Hube", "Christophe d'Enfert", "Steffen Rupp", "Brendan Cormack", "Ken Haynes", "Karl Kuchler"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004211.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clustering_of_susceptibility_data_of_the_C_glabrata_gene_deletion_collection_/1064173", "title"=>"Clustering of susceptibility data of the <i>C. glabrata</i> gene deletion collection.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-19 15:13:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1541538"], "description"=>"<p>The set of mutants was screened on plates for hypersensitivity to four distinct stress conditions (CF, CR, CW and 42°C heat stress) using serial dilution assays on agar plates. (A) Two-dimensional hierarchical cluster plot of chemical-genetic profiles. On the horizontal axis genes are listed and stress conditions on the vertical axis. Interactions are shown in yellow depending on the degree of growth sensitivity (yellow = no growth, black = WT growth). Stress conditions and genes are clustered by the similarity of their interactions. (B) The clusters of genes are enlarged to highlight the chemical-genetic interaction profile of Caspofungin (blue bar in ‘a’ labeled ‘b’). (C) A section of the cluster (orange bar labeled ‘C’) involved in heat stress (42°C) is enlarged. (D) Genes implicated in sensitivity to the cell wall-perturbing agents CR and CW (red and green bar labeled ‘D’).</p>", "links"=>[], "tags"=>["Biochemistry", "genetics", "microbiology", "Medical microbiology", "Microbial pathogens", "susceptibility", "deletion"], "article_id"=>1063006, "categories"=>["Biological Sciences"], "users"=>["Tobias Schwarzmüller", "Biao Ma", "Ekkehard Hiller", "Fabian Istel", "Michael Tscherner", "Sascha Brunke", "Lauren Ames", "Arnaud Firon", "Brian Green", "Vitor Cabral", "Marina Marcet-Houben", "Ilse D. Jacobsen", "Jessica Quintin", "Katja Seider", "Ingrid Frohner", "Walter Glaser", "Helmut Jungwirth", "Sophie Bachellier-Bassi", "Murielle Chauvel", "Ute Zeidler", "Dominique Ferrandon", "Toni Gabaldón", "Bernhard Hube", "Christophe d'Enfert", "Steffen Rupp", "Brendan Cormack", "Ken Haynes", "Karl Kuchler"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004211.g005", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clustering_of_susceptibility_data_of_the_C_glabrata_gene_deletion_collection_/1063006", "title"=>"Clustering of susceptibility data of the <i>C. glabrata</i> gene deletion collection.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-19 03:40:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/1543122", "https://ndownloader.figshare.com/files/1543123", "https://ndownloader.figshare.com/files/1543124", "https://ndownloader.figshare.com/files/1543125", "https://ndownloader.figshare.com/files/1543126", "https://ndownloader.figshare.com/files/1543127", "https://ndownloader.figshare.com/files/1543128", "https://ndownloader.figshare.com/files/1543129", "https://ndownloader.figshare.com/files/1543130", "https://ndownloader.figshare.com/files/1543131", "https://ndownloader.figshare.com/files/1543132", "https://ndownloader.figshare.com/files/1543133", "https://ndownloader.figshare.com/files/1543134", "https://ndownloader.figshare.com/files/1543136", "https://ndownloader.figshare.com/files/1543137", "https://ndownloader.figshare.com/files/1543138", "https://ndownloader.figshare.com/files/1543139", "https://ndownloader.figshare.com/files/1543140", "https://ndownloader.figshare.com/files/1543141", "https://ndownloader.figshare.com/files/1543142", "https://ndownloader.figshare.com/files/1543143"], "description"=>"<div><p>The opportunistic fungal pathogen <i>Candida glabrata</i> is a frequent cause of candidiasis, causing infections ranging from superficial to life-threatening disseminated disease. The inherent tolerance of <i>C. glabrata</i> to azole drugs makes this pathogen a serious clinical threat. To identify novel genes implicated in antifungal drug tolerance, we have constructed a large-scale <i>C. glabrata</i> deletion library consisting of 619 unique, individually bar-coded mutant strains, each lacking one specific gene, all together representing almost 12% of the genome. Functional analysis of this library in a series of phenotypic and fitness assays identified numerous genes required for growth of <i>C. glabrata</i> under normal or specific stress conditions, as well as a number of novel genes involved in tolerance to clinically important antifungal drugs such as azoles and echinocandins. We identified 38 deletion strains displaying strongly increased susceptibility to caspofungin, 28 of which encoding proteins that have not previously been linked to echinocandin tolerance. Our results demonstrate the potential of the <i>C. glabrata</i> mutant collection as a valuable resource in functional genomics studies of this important fungal pathogen of humans, and to facilitate the identification of putative novel antifungal drug target and virulence genes.</p></div>", "links"=>[], "tags"=>["Biochemistry", "genetics", "microbiology", "Medical microbiology", "Microbial pathogens", "systematic", "phenotyping", "large-scale", "deletion", "reveals", "antifungal", "genes"], "article_id"=>1064219, "categories"=>["Biological Sciences"], "users"=>["Tobias Schwarzmüller", "Biao Ma", "Ekkehard Hiller", "Fabian Istel", "Michael Tscherner", "Sascha Brunke", "Lauren Ames", "Arnaud Firon", "Brian Green", "Vitor Cabral", "Marina Marcet-Houben", "Ilse D. Jacobsen", "Jessica Quintin", "Katja Seider", "Ingrid Frohner", "Walter Glaser", "Helmut Jungwirth", "Sophie Bachellier-Bassi", "Murielle Chauvel", "Ute Zeidler", "Dominique Ferrandon", "Toni Gabaldón", "Bernhard Hube", "Christophe d'Enfert", "Steffen Rupp", "Brendan Cormack", "Ken Haynes", "Karl Kuchler"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1004211.s001", "https://dx.doi.org/10.1371/journal.ppat.1004211.s002", "https://dx.doi.org/10.1371/journal.ppat.1004211.s003", "https://dx.doi.org/10.1371/journal.ppat.1004211.s004", "https://dx.doi.org/10.1371/journal.ppat.1004211.s005", "https://dx.doi.org/10.1371/journal.ppat.1004211.s006", "https://dx.doi.org/10.1371/journal.ppat.1004211.s007", "https://dx.doi.org/10.1371/journal.ppat.1004211.s008", "https://dx.doi.org/10.1371/journal.ppat.1004211.s009", "https://dx.doi.org/10.1371/journal.ppat.1004211.s010", "https://dx.doi.org/10.1371/journal.ppat.1004211.s011", "https://dx.doi.org/10.1371/journal.ppat.1004211.s013", "https://dx.doi.org/10.1371/journal.ppat.1004211.s014", "https://dx.doi.org/10.1371/journal.ppat.1004211.s015", "https://dx.doi.org/10.1371/journal.ppat.1004211.s016", "https://dx.doi.org/10.1371/journal.ppat.1004211.s017", "https://dx.doi.org/10.1371/journal.ppat.1004211.s018", "https://dx.doi.org/10.1371/journal.ppat.1004211.s019", "https://dx.doi.org/10.1371/journal.ppat.1004211.s020", "https://dx.doi.org/10.1371/journal.ppat.1004211.s021", "https://dx.doi.org/10.1371/journal.ppat.1004211.s022"], "stats"=>{"downloads"=>28, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Systematic_Phenotyping_of_a_Large_Scale_Candida_glabrata_Deletion_Collection_Reveals_Novel_Antifungal_Tolerance_Genes/1064219", "title"=>"Systematic Phenotyping of a Large-Scale <i>Candida glabrata</i> Deletion Collection Reveals Novel Antifungal Tolerance Genes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-06-19 15:13:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1541534"], "description"=>"<p>(A) Overlap between the chemical-genetic profile of CF (38 genes), CR (12 genes) and CW (6 genes). 28 genes (labeled in bold letters) were novel CF tolerance genes, since they have not been previously associated with echinocandin hypersensitivity in <i>S. cerevisiae</i> or <i>C. albicans</i>. (B) Overlap between the chemical-genetic profile of CF, azoles and AmB. 61 genes displayed an increased sensitivity to CF (38 genes plus 10 genes with weak sensitivity), azoles (14 genes; fluconazole and voriconazole) and AmB (13 genes). The mutant strain collection was screened in a 96 well microplate format using an endpoint assay and medium was supplemented with 5 µg/ml fluconazole, 100 ng/ml voriconazole and 1,5 µg/ml AmB. The OD<sub>600</sub> was determined after 24 and 48 hours of incubation at 30°C. Grey-colored genes only display a weak sensitivity phenotype or were excluded from further analysis due to strong variations in the screening. Nodes represent compounds or genes and edges indicate chemical-genetic interactions. Gene nodes are color-coded according to GO annotation. Venn diagrams summarize distribution of genes affecting resistance to one of the three compounds.</p>", "links"=>[], "tags"=>["Biochemistry", "genetics", "microbiology", "Medical microbiology", "Microbial pathogens", "chemogenetic"], "article_id"=>1063002, "categories"=>["Biological Sciences"], "users"=>["Tobias Schwarzmüller", "Biao Ma", "Ekkehard Hiller", "Fabian Istel", "Michael Tscherner", "Sascha Brunke", "Lauren Ames", "Arnaud Firon", "Brian Green", "Vitor Cabral", "Marina Marcet-Houben", "Ilse D. Jacobsen", "Jessica Quintin", "Katja Seider", "Ingrid Frohner", "Walter Glaser", "Helmut Jungwirth", "Sophie Bachellier-Bassi", "Murielle Chauvel", "Ute Zeidler", "Dominique Ferrandon", "Toni Gabaldón", "Bernhard Hube", "Christophe d'Enfert", "Steffen Rupp", "Brendan Cormack", "Ken Haynes", "Karl Kuchler"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004211.g004", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Classification_of_C_glabrata_chemogenetic_profiles_/1063002", "title"=>"Classification of <i>C. glabrata</i> chemogenetic profiles.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-19 03:40:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/1543052"], "description"=>"<p>Wild type and mutant strains were induced to form biofilms in 96-well polystyrene plates in minimal medium at 37°C and the biofilm biomass was quantified using fluorescein diacetate (FDA). For each strain, a relative biofilm fitness was calculated based on FDA hydrolysis data from at least two independent cultures. Data were obtained for 420 knock-out mutants (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004211#ppat.1004211.s018\" target=\"_blank\">Table S9</a>). Strains that showed strong variations in relative fitness between independent mutants or independent cultures were omitted from further analysis (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004211#ppat.1004211.s017\" target=\"_blank\">Table S8</a>).</p>", "links"=>[], "tags"=>["Biochemistry", "genetics", "microbiology", "Medical microbiology", "Microbial pathogens", "biofilm"], "article_id"=>1064167, "categories"=>["Biological Sciences"], "users"=>["Tobias Schwarzmüller", "Biao Ma", "Ekkehard Hiller", "Fabian Istel", "Michael Tscherner", "Sascha Brunke", "Lauren Ames", "Arnaud Firon", "Brian Green", "Vitor Cabral", "Marina Marcet-Houben", "Ilse D. Jacobsen", "Jessica Quintin", "Katja Seider", "Ingrid Frohner", "Walter Glaser", "Helmut Jungwirth", "Sophie Bachellier-Bassi", "Murielle Chauvel", "Ute Zeidler", "Dominique Ferrandon", "Toni Gabaldón", "Bernhard Hube", "Christophe d'Enfert", "Steffen Rupp", "Brendan Cormack", "Ken Haynes", "Karl Kuchler"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004211.g003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_biofilm_fitness_distribution_/1064167", "title"=>"Relative biofilm fitness distribution.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-19 15:13:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1541528"], "description"=>"<p>(a) Wild type and mutant strains were grown in rich medium at 30°C and doubling times were recorded. The median doubling time of the wild type <i>C. glabrata</i> ATCC2001 strain under these conditions was 63.9 min while the median for mutant strains was 68.1 min. For each strain, the relative fitness was calculated using doubling times from at least two independent cultures of 1–6 independent mutants. Strains that showed strong variations in relative fitness between independent mutants or independent cultures were omitted from further analysis (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004211#ppat.1004211.s014\" target=\"_blank\">Table S5</a>). Data were obtained for 503 knock-out mutants (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004211#ppat.1004211.s015\" target=\"_blank\">Table S6</a>). (b) Colony and cell morphologies of <i>C. glabrata</i> deletion strains. Different types of distinct cell and colony morphologies were found. Cell morphology classes: ellipsoid (a), chains (b, f, g, i, k, l), elongated (c, d), large clumps (d, j, m, n), round (e), large and round (h); colony morphologies: smooth (a, b, c, e, f, g, i), small (h), slightly wrinkled (k, l), wrinkled (d, j, m, n). WT = HTL background strain; white bars correspond to 10 µm.</p>", "links"=>[], "tags"=>["Biochemistry", "genetics", "microbiology", "Medical microbiology", "Microbial pathogens", "morphology", "deletion"], "article_id"=>1062997, "categories"=>["Biological Sciences"], "users"=>["Tobias Schwarzmüller", "Biao Ma", "Ekkehard Hiller", "Fabian Istel", "Michael Tscherner", "Sascha Brunke", "Lauren Ames", "Arnaud Firon", "Brian Green", "Vitor Cabral", "Marina Marcet-Houben", "Ilse D. Jacobsen", "Jessica Quintin", "Katja Seider", "Ingrid Frohner", "Walter Glaser", "Helmut Jungwirth", "Sophie Bachellier-Bassi", "Murielle Chauvel", "Ute Zeidler", "Dominique Ferrandon", "Toni Gabaldón", "Bernhard Hube", "Christophe d'Enfert", "Steffen Rupp", "Brendan Cormack", "Ken Haynes", "Karl Kuchler"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004211.g002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_fitness_distribution_and_morphology_of_C_glabrata_gene_deletion_strains_/1062997", "title"=>"Relative fitness distribution and morphology of <i>C. glabrata</i> gene deletion strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-19 03:40:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/1543051"], "description"=>"<p>(a) Wild type and mutant strains were grown in rich medium at 30°C and doubling times were recorded. The median doubling time of the wild type <i>C. glabrata</i> ATCC2001 strain under these conditions was 63.9 min while the median for mutant strains was 68.1 min. For each strain, the relative fitness was calculated using doubling times from at least two independent cultures of 1–6 independent mutants. Strains that showed strong variations in relative fitness between independent mutants or independent cultures were omitted from further analysis (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004211#ppat.1004211.s014\" target=\"_blank\">Table S5</a>). Data were obtained for 503 knock-out mutants (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004211#ppat.1004211.s015\" target=\"_blank\">Table S6</a>). (b) Colony and cell morphologies of <i>C. glabrata</i> deletion strains. Different types of distinct cell and colony morphologies were found. Cell morphology classes: ellipsoid (a), chains (b, f, g, i, k, l), elongated (c, d), large clumps (d, j, m, n), round (e), large and round (h); colony morphologies: smooth (a, b, c, e, f, g, i), small (h), slightly wrinkled (k, l), wrinkled (d, j, m, n). WT = HTL background strain; white bars correspond to 10 µm.</p>", "links"=>[], "tags"=>["Biochemistry", "genetics", "microbiology", "Medical microbiology", "Microbial pathogens", "morphology", "deletion"], "article_id"=>1064166, "categories"=>["Biological Sciences"], "users"=>["Tobias Schwarzmüller", "Biao Ma", "Ekkehard Hiller", "Fabian Istel", "Michael Tscherner", "Sascha Brunke", "Lauren Ames", "Arnaud Firon", "Brian Green", "Vitor Cabral", "Marina Marcet-Houben", "Ilse D. Jacobsen", "Jessica Quintin", "Katja Seider", "Ingrid Frohner", "Walter Glaser", "Helmut Jungwirth", "Sophie Bachellier-Bassi", "Murielle Chauvel", "Ute Zeidler", "Dominique Ferrandon", "Toni Gabaldón", "Bernhard Hube", "Christophe d'Enfert", "Steffen Rupp", "Brendan Cormack", "Ken Haynes", "Karl Kuchler"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004211.g002", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_fitness_distribution_and_morphology_of_C_glabrata_gene_deletion_strains_/1064166", "title"=>"Relative fitness distribution and morphology of <i>C. glabrata</i> gene deletion strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-19 15:13:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1543047"], "description"=>"<p>(a) Generation of gene deletion constructs by fusion PCR using the dominant selectable marker <i>NAT1</i>. A set of two times 96 unique barcode sequences was integrated in oligonucleotides to amplify the marker fragment and to add overlap sequences. (b) Transformants were verified by colony PCR for correct integration on the 5′ and 3′ junction and checked for absence of the target ORF. (c) Overview of the construction of the gene deletion strain library.</p>", "links"=>[], "tags"=>["Biochemistry", "genetics", "microbiology", "Medical microbiology", "Microbial pathogens", "mutants", "systematic", "phenotypic"], "article_id"=>1064162, "categories"=>["Biological Sciences"], "users"=>["Tobias Schwarzmüller", "Biao Ma", "Ekkehard Hiller", "Fabian Istel", "Michael Tscherner", "Sascha Brunke", "Lauren Ames", "Arnaud Firon", "Brian Green", "Vitor Cabral", "Marina Marcet-Houben", "Ilse D. Jacobsen", "Jessica Quintin", "Katja Seider", "Ingrid Frohner", "Walter Glaser", "Helmut Jungwirth", "Sophie Bachellier-Bassi", "Murielle Chauvel", "Ute Zeidler", "Dominique Ferrandon", "Toni Gabaldón", "Bernhard Hube", "Christophe d'Enfert", "Steffen Rupp", "Brendan Cormack", "Ken Haynes", "Karl Kuchler"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004211.g001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Generation_of_C_glabrata_mutants_and_systematic_phenotypic_analysis_/1064162", "title"=>"Generation of <i>C. glabrata</i> mutants and systematic phenotypic analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-19 15:13:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1541523"], "description"=>"<p>(a) Generation of gene deletion constructs by fusion PCR using the dominant selectable marker <i>NAT1</i>. A set of two times 96 unique barcode sequences was integrated in oligonucleotides to amplify the marker fragment and to add overlap sequences. (b) Transformants were verified by colony PCR for correct integration on the 5′ and 3′ junction and checked for absence of the target ORF. (c) Overview of the construction of the gene deletion strain library.</p>", "links"=>[], "tags"=>["Biochemistry", "genetics", "microbiology", "Medical microbiology", "Microbial pathogens", "mutants", "systematic", "phenotypic"], "article_id"=>1062992, "categories"=>["Biological Sciences"], "users"=>["Tobias Schwarzmüller", "Biao Ma", "Ekkehard Hiller", "Fabian Istel", "Michael Tscherner", "Sascha Brunke", "Lauren Ames", "Arnaud Firon", "Brian Green", "Vitor Cabral", "Marina Marcet-Houben", "Ilse D. Jacobsen", "Jessica Quintin", "Katja Seider", "Ingrid Frohner", "Walter Glaser", "Helmut Jungwirth", "Sophie Bachellier-Bassi", "Murielle Chauvel", "Ute Zeidler", "Dominique Ferrandon", "Toni Gabaldón", "Bernhard Hube", "Christophe d'Enfert", "Steffen Rupp", "Brendan Cormack", "Ken Haynes", "Karl Kuchler"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004211.g001", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Generation_of_C_glabrata_mutants_and_systematic_phenotypic_analysis_/1062992", "title"=>"Generation of <i>C. glabrata</i> mutants and systematic phenotypic analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-19 03:40:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/1541576"], "description"=>"<p>Sensitivities of deletion strains constructed in clinical isolates (KK004, KK006, KK045 and KK047) or in the ATCC2001 strain were tested for caspofungin (CF) susceptibility on plates. Strains were spotted in serial dilutions on synthetic agar medium supplemented with the indicated CF concentrations and growth was monitored for 3 days at 30°C. Screening was performed for (A) <i>CCH1</i>, (B) <i>MID1</i>, (C) <i>DEP1</i>, (D) <i>PMT2</i>, (E) <i>SLA1</i>, (F) <i>MNS1</i>, (G) <i>MNT3</i> and (H) <i>ANP1</i>.</p>", "links"=>[], "tags"=>["Biochemistry", "genetics", "microbiology", "Medical microbiology", "Microbial pathogens", "deletion"], "article_id"=>1063042, "categories"=>["Biological Sciences"], "users"=>["Tobias Schwarzmüller", "Biao Ma", "Ekkehard Hiller", "Fabian Istel", "Michael Tscherner", "Sascha Brunke", "Lauren Ames", "Arnaud Firon", "Brian Green", "Vitor Cabral", "Marina Marcet-Houben", "Ilse D. Jacobsen", "Jessica Quintin", "Katja Seider", "Ingrid Frohner", "Walter Glaser", "Helmut Jungwirth", "Sophie Bachellier-Bassi", "Murielle Chauvel", "Ute Zeidler", "Dominique Ferrandon", "Toni Gabaldón", "Bernhard Hube", "Christophe d'Enfert", "Steffen Rupp", "Brendan Cormack", "Ken Haynes", "Karl Kuchler"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004211.g006", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Caspofungin_sensitivity_of_C_glabrata_clinical_isolate_deletion_strains_/1063042", "title"=>"Caspofungin sensitivity of <i>C. glabrata</i> clinical isolate deletion strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-19 03:40:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/1543060"], "description"=>"<p>(A) Overlap between the chemical-genetic profile of CF (38 genes), CR (12 genes) and CW (6 genes). 28 genes (labeled in bold letters) were novel CF tolerance genes, since they have not been previously associated with echinocandin hypersensitivity in <i>S. cerevisiae</i> or <i>C. albicans</i>. (B) Overlap between the chemical-genetic profile of CF, azoles and AmB. 61 genes displayed an increased sensitivity to CF (38 genes plus 10 genes with weak sensitivity), azoles (14 genes; fluconazole and voriconazole) and AmB (13 genes). The mutant strain collection was screened in a 96 well microplate format using an endpoint assay and medium was supplemented with 5 µg/ml fluconazole, 100 ng/ml voriconazole and 1,5 µg/ml AmB. The OD<sub>600</sub> was determined after 24 and 48 hours of incubation at 30°C. Grey-colored genes only display a weak sensitivity phenotype or were excluded from further analysis due to strong variations in the screening. Nodes represent compounds or genes and edges indicate chemical-genetic interactions. Gene nodes are color-coded according to GO annotation. Venn diagrams summarize distribution of genes affecting resistance to one of the three compounds.</p>", "links"=>[], "tags"=>["Biochemistry", "genetics", "microbiology", "Medical microbiology", "Microbial pathogens", "chemogenetic"], "article_id"=>1064170, "categories"=>["Biological Sciences"], "users"=>["Tobias Schwarzmüller", "Biao Ma", "Ekkehard Hiller", "Fabian Istel", "Michael Tscherner", "Sascha Brunke", "Lauren Ames", "Arnaud Firon", "Brian Green", "Vitor Cabral", "Marina Marcet-Houben", "Ilse D. Jacobsen", "Jessica Quintin", "Katja Seider", "Ingrid Frohner", "Walter Glaser", "Helmut Jungwirth", "Sophie Bachellier-Bassi", "Murielle Chauvel", "Ute Zeidler", "Dominique Ferrandon", "Toni Gabaldón", "Bernhard Hube", "Christophe d'Enfert", "Steffen Rupp", "Brendan Cormack", "Ken Haynes", "Karl Kuchler"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004211.g004", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Classification_of_C_glabrata_chemogenetic_profiles_/1064170", "title"=>"Classification of <i>C. glabrata</i> chemogenetic profiles.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-19 15:13:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1541531"], "description"=>"<p>Wild type and mutant strains were induced to form biofilms in 96-well polystyrene plates in minimal medium at 37°C and the biofilm biomass was quantified using fluorescein diacetate (FDA). For each strain, a relative biofilm fitness was calculated based on FDA hydrolysis data from at least two independent cultures. Data were obtained for 420 knock-out mutants (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004211#ppat.1004211.s018\" target=\"_blank\">Table S9</a>). Strains that showed strong variations in relative fitness between independent mutants or independent cultures were omitted from further analysis (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004211#ppat.1004211.s017\" target=\"_blank\">Table S8</a>).</p>", "links"=>[], "tags"=>["Biochemistry", "genetics", "microbiology", "Medical microbiology", "Microbial pathogens", "biofilm"], "article_id"=>1062999, "categories"=>["Biological Sciences"], "users"=>["Tobias Schwarzmüller", "Biao Ma", "Ekkehard Hiller", "Fabian Istel", "Michael Tscherner", "Sascha Brunke", "Lauren Ames", "Arnaud Firon", "Brian Green", "Vitor Cabral", "Marina Marcet-Houben", "Ilse D. Jacobsen", "Jessica Quintin", "Katja Seider", "Ingrid Frohner", "Walter Glaser", "Helmut Jungwirth", "Sophie Bachellier-Bassi", "Murielle Chauvel", "Ute Zeidler", "Dominique Ferrandon", "Toni Gabaldón", "Bernhard Hube", "Christophe d'Enfert", "Steffen Rupp", "Brendan Cormack", "Ken Haynes", "Karl Kuchler"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004211.g003", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_biofilm_fitness_distribution_/1062999", "title"=>"Relative biofilm fitness distribution.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-19 03:40:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/1541618", "https://ndownloader.figshare.com/files/1541619", "https://ndownloader.figshare.com/files/1541620", "https://ndownloader.figshare.com/files/1541621", "https://ndownloader.figshare.com/files/1541622", "https://ndownloader.figshare.com/files/1541623", "https://ndownloader.figshare.com/files/1541624", "https://ndownloader.figshare.com/files/1541625", "https://ndownloader.figshare.com/files/1541626", "https://ndownloader.figshare.com/files/1541627", "https://ndownloader.figshare.com/files/1541628", "https://ndownloader.figshare.com/files/1541629", "https://ndownloader.figshare.com/files/1541630", "https://ndownloader.figshare.com/files/1541631", "https://ndownloader.figshare.com/files/1541632", "https://ndownloader.figshare.com/files/1541633", "https://ndownloader.figshare.com/files/1541634", "https://ndownloader.figshare.com/files/1541635", "https://ndownloader.figshare.com/files/1541636", "https://ndownloader.figshare.com/files/1541637", "https://ndownloader.figshare.com/files/1541638"], "description"=>"<div><p>The opportunistic fungal pathogen <i>Candida glabrata</i> is a frequent cause of candidiasis, causing infections ranging from superficial to life-threatening disseminated disease. The inherent tolerance of <i>C. glabrata</i> to azole drugs makes this pathogen a serious clinical threat. To identify novel genes implicated in antifungal drug tolerance, we have constructed a large-scale <i>C. glabrata</i> deletion library consisting of 619 unique, individually bar-coded mutant strains, each lacking one specific gene, all together representing almost 12% of the genome. Functional analysis of this library in a series of phenotypic and fitness assays identified numerous genes required for growth of <i>C. glabrata</i> under normal or specific stress conditions, as well as a number of novel genes involved in tolerance to clinically important antifungal drugs such as azoles and echinocandins. We identified 38 deletion strains displaying strongly increased susceptibility to caspofungin, 28 of which encoding proteins that have not previously been linked to echinocandin tolerance. Our results demonstrate the potential of the <i>C. glabrata</i> mutant collection as a valuable resource in functional genomics studies of this important fungal pathogen of humans, and to facilitate the identification of putative novel antifungal drug target and virulence genes.</p></div>", "links"=>[], "tags"=>["Biochemistry", "genetics", "microbiology", "Medical microbiology", "Microbial pathogens", "systematic", "phenotyping", "large-scale", "deletion", "reveals", "antifungal", "genes"], "article_id"=>1063073, "categories"=>["Biological Sciences"], "users"=>["Tobias Schwarzmüller", "Biao Ma", "Ekkehard Hiller", "Fabian Istel", "Michael Tscherner", "Sascha Brunke", "Lauren Ames", "Arnaud Firon", "Brian Green", "Vitor Cabral", "Marina Marcet-Houben", "Ilse D. Jacobsen", "Jessica Quintin", "Katja Seider", "Ingrid Frohner", "Walter Glaser", "Helmut Jungwirth", "Sophie Bachellier-Bassi", "Murielle Chauvel", "Ute Zeidler", "Dominique Ferrandon", "Toni Gabaldón", "Bernhard Hube", "Christophe d'Enfert", "Steffen Rupp", "Brendan Cormack", "Ken Haynes", "Karl Kuchler"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1004211.s001", "https://dx.doi.org/10.1371/journal.ppat.1004211.s002", "https://dx.doi.org/10.1371/journal.ppat.1004211.s003", "https://dx.doi.org/10.1371/journal.ppat.1004211.s004", "https://dx.doi.org/10.1371/journal.ppat.1004211.s005", "https://dx.doi.org/10.1371/journal.ppat.1004211.s006", "https://dx.doi.org/10.1371/journal.ppat.1004211.s007", "https://dx.doi.org/10.1371/journal.ppat.1004211.s008", "https://dx.doi.org/10.1371/journal.ppat.1004211.s009", "https://dx.doi.org/10.1371/journal.ppat.1004211.s010", "https://dx.doi.org/10.1371/journal.ppat.1004211.s011", "https://dx.doi.org/10.1371/journal.ppat.1004211.s013", "https://dx.doi.org/10.1371/journal.ppat.1004211.s014", "https://dx.doi.org/10.1371/journal.ppat.1004211.s015", "https://dx.doi.org/10.1371/journal.ppat.1004211.s016", "https://dx.doi.org/10.1371/journal.ppat.1004211.s017", "https://dx.doi.org/10.1371/journal.ppat.1004211.s018", "https://dx.doi.org/10.1371/journal.ppat.1004211.s019", "https://dx.doi.org/10.1371/journal.ppat.1004211.s020", "https://dx.doi.org/10.1371/journal.ppat.1004211.s021", "https://dx.doi.org/10.1371/journal.ppat.1004211.s022"], "stats"=>{"downloads"=>51, "page_views"=>40, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Systematic_Phenotyping_of_a_Large_Scale_Candida_glabrata_Deletion_Collection_Reveals_Novel_Antifungal_Tolerance_Genes/1063073", "title"=>"Systematic Phenotyping of a Large-Scale <i>Candida glabrata</i> Deletion Collection Reveals Novel Antifungal Tolerance Genes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-06-19 03:40:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/1543080"], "description"=>"<p>Sensitivities of deletion strains constructed in clinical isolates (KK004, KK006, KK045 and KK047) or in the ATCC2001 strain were tested for caspofungin (CF) susceptibility on plates. Strains were spotted in serial dilutions on synthetic agar medium supplemented with the indicated CF concentrations and growth was monitored for 3 days at 30°C. Screening was performed for (A) <i>CCH1</i>, (B) <i>MID1</i>, (C) <i>DEP1</i>, (D) <i>PMT2</i>, (E) <i>SLA1</i>, (F) <i>MNS1</i>, (G) <i>MNT3</i> and (H) <i>ANP1</i>.</p>", "links"=>[], "tags"=>["Biochemistry", "genetics", "microbiology", "Medical microbiology", "Microbial pathogens", "deletion"], "article_id"=>1064191, "categories"=>["Biological Sciences"], "users"=>["Tobias Schwarzmüller", "Biao Ma", "Ekkehard Hiller", "Fabian Istel", "Michael Tscherner", "Sascha Brunke", "Lauren Ames", "Arnaud Firon", "Brian Green", "Vitor Cabral", "Marina Marcet-Houben", "Ilse D. Jacobsen", "Jessica Quintin", "Katja Seider", "Ingrid Frohner", "Walter Glaser", "Helmut Jungwirth", "Sophie Bachellier-Bassi", "Murielle Chauvel", "Ute Zeidler", "Dominique Ferrandon", "Toni Gabaldón", "Bernhard Hube", "Christophe d'Enfert", "Steffen Rupp", "Brendan Cormack", "Ken Haynes", "Karl Kuchler"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004211.g006", "stats"=>{"downloads"=>6, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Caspofungin_sensitivity_of_C_glabrata_clinical_isolate_deletion_strains_/1064191", "title"=>"Caspofungin sensitivity of <i>C. glabrata</i> clinical isolate deletion strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-19 15:13:50"}

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