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Matt Nolan - One of the best experts on this subject based on the ideXlab platform.

  • Standards in Genomic Sciences (2010) 2:9-18 DOI:10.4056/sigs.591104 The Genomic Standards Consortium Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IAT)
    2014
    Co-Authors: Konstantinos Mavromatis, Johannes Sikorski, Alla Lapidus, Hope Tice, Jan-fang Cheng, Susan Lucas, Feng Chen, Tijana Glavina, Del Rio, Matt Nolan
    Abstract:

    encodes flagellar genes, GEBA Alicyclobacillus acidocaldarius (Darland and Brock 1971) is the type species of the larger of the two genera in the bacillal family ‘Alicyclobacillaceae’. A. acidocaldarius is a free-living and non-Pathogenic Organism, but may also be associated with food and fruit spoilage. Due to its acidophilic nature, several enzymes from this species have since long been subjected to detailed molecular and biochemical studies. Here we describe the features of this Organism, together with the complete genome sequence and annotation. This is the first completed ge-nome sequence of the family ‘Alicyclobacillaceae’. The 3,205,686 bp long genome (chromo-some and three plasmids) with its 3,153 protein-coding and 82 RNA genes is part of the Ge

  • complete genome sequence of alicyclobacillus acidocaldarius type strain 104 iat
    Standards in Genomic Sciences, 2010
    Co-Authors: Konstantinos Mavromatis, Johannes Sikorski, Alla Lapidus, Alex Copeland, Hope Tice, Jan-fang Cheng, Susan Lucas, Feng Chen, Tijana Glavina Del Rio, Matt Nolan
    Abstract:

    Alicyclobacillus acidocaldarius (Darland and Brock 1971) is the type species of the larger of the two genera in the bacillal family ‘Alicyclobacillaceae’. A. acidocaldarius is a free-living and non-Pathogenic Organism, but may also be associated with food and fruit spoilage. Due to its acidophilic nature, several enzymes from this species have since long been subjected to detailed molecular and biochemical studies. Here we describe the features of this Organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family ‘Alicyclobacillaceae’. The 3,205,686 bp long genome (chromosome and three plasmids) with its 3,153 protein-coding and 82 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  • Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA^T)
    Standards in Genomic Sciences, 2010
    Co-Authors: Konstantinos Mavromatis, Johannes Sikorski, Alla Lapidus, Tijana Glavina Del Rio, Alex Copeland, Hope Tice, Jan-fang Cheng, Susan Lucas, Feng Chen, Matt Nolan
    Abstract:

    Alicyclobacillus acidocaldarius (Darland and Brock 1971) is the type species of the larger of the two genera in the bacillal family ‘ Alicyclobacillaceae ’. A. acidocaldarius is a free-living and non-Pathogenic Organism, but may also be associated with food and fruit spoilage. Due to its acidophilic nature, several enzymes from this species have since long been subjected to detailed molecular and biochemical studies. Here we describe the features of this Organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family ‘ Alicyclobacillaceae ’. The 3,205,686 bp long genome (chromosome and three plasmids) with its 3,153 protein-coding and 82 RNA genes is part of the G enomic E ncyclopedia of B acteria and A rchaea project.

Christine D Smart - One of the best experts on this subject based on the ideXlab platform.

  • temporal genetic dynamics of an experimental biparental field population of phytophthora capsici
    Frontiers in Genetics, 2017
    Co-Authors: Maryn O Carlson, Elodie Gazave, Michael A Gore, Christine D Smart
    Abstract:

    Defining the contributions of dispersal, reproductive mode, and mating system to the population structure of a Pathogenic Organism is essential to estimating its evolutionary potential. After introduction of the devastating plant pathogen, Phytophthora capsici, into a grower's field, a lack of aerial spore dispersal restricts migration. Once established, coexistence of both mating types results in formation of overwintering recombinant oospores, engendering persistent pathogen populations. To mimic these conditions, in 2008, we inoculated a field with two P. capsici isolates of opposite mating type. We analyzed Pathogenic isolates collected in 2009-13 from this experimental population, using genome-wide single-nucleotide polymorphism markers. By tracking heterozygosity across years, we show that the population underwent a generational shift; transitioning from exclusively F1 in 2009-10; multi-generational in 2011; and ultimately all inbred in 2012-13. Survival of F1 oospores, characterized by heterozygosity excess, coupled with a low rate of selfing, delayed declines in heterozygosity due to inbreeding and attainment of equilibrium genotypic frequencies. Large allele and haplotype frequency changes in specific genomic regions accompanied the generational shift, representing putative signatures of selection. Finally, we identified an approximately 1.6 Mb region associated with mating type determination, constituting the first detailed genomic analysis of a mating type region (MTR) in Phytophthora. Segregation patterns in the MTR exhibited tropes of sex-linkage, where maintenance of allele frequency differences between isolates of opposite mating type was associated with elevated heterozygosity despite inbreeding. Characterizing the trajectory of this experimental system provides key insights into the processes driving persistent, sexual pathogen populations.

  • temporal genetic dynamics of an experimental biparental field population of phytophthora capsici
    bioRxiv, 2016
    Co-Authors: Maryn O Carlson, Elodie Gazave, Michael A Gore, Christine D Smart
    Abstract:

    Defining the contributions of dispersal, reproductive mode, and mating system to the population structure of a Pathogenic Organism is essential to estimating its evolutionary potential. After introduction of the devastating plant pathogen, Phytophthora capsici, into a grower9s field, a lack of aerial spore dispersal restricts migration. Once established, coexistence of both mating types results in formation of overwintering recombinant oospores, engendering persistent pathogen populations. To mimic these conditions, in 2008, we inoculated a field with two P. capsici isolates of opposite mating type. We analyzed Pathogenic isolates collected in 2009-13 from this experimental population, using genome-wide single-nucleotide polymorphism markers. By tracking heterozygosity across years, we show that the population underwent a generational shift; transitioning from exclusively F1 in 2009-10; mixed generational in 2011; and ultimately all inbred in 2012-13. Survival of F1 oospores, characterized by heterozygosity excess, coupled with a low rate of selfing, delayed declines in heterozygosity due to inbreeding and attainment of equilibrium genotypic frequencies. Large allele and haplotype frequency changes in specific genomic regions accompanied the generational shift, representing putative signatures of selection. Finally, we identified an approximately 1.6 Mb region associated with mating type determination, constituting the first detailed genomic analysis of a mating type region (MTR) in Phytophthora. Segregation patterns in the MTR exhibited tropes of sex-linkage, where maintenance of allele frequency differences between isolates of opposite mating type was associated with elevated heterozygosity despite inbreeding. Characterizing the trajectory of this experimental system provides key insights into the processes driving persistent, sexual pathogen populations.

Tara L Greenhow - One of the best experts on this subject based on the ideXlab platform.

  • diagnostic accuracy of the urinalysis for urinary tract infection in infants 3 months of age
    Pediatrics, 2015
    Co-Authors: Alan R Schroeder, Pearl W Chang, Mark W Shen, Eric A Biondi, Tara L Greenhow
    Abstract:

    BACKGROUND: The 2011 American Academy of Pediatrics urinary tract infection (UTI) guideline suggests incorporation of a positive urinalysis (UA) into the definition of UTI. However, concerns linger over UA sensitivity in young infants. Infants with the same Pathogenic Organism in the blood and urine (bacteremic UTI) have true infections and represent a desirable population for examination of UA sensitivity. METHODS: We collected UA results on a cross-sectional sample of 276 infants RESULTS: The final sample included 245 infants with bacteremic UTI and 115 infants with negative urine cultures. The sensitivity of leukocyte esterase was 97.6% (95% confidence interval [CI] 94.5%–99.2%) and of pyuria (>3 white blood cells/high-power field) was 96% (95% CI 92.5%–98.1%). Only 1 infant with bacteremic UTI (Group B Streptococcus ) and a complete UA had an entirely negative UA. In infants with negative urine cultures, leukocyte esterase specificity was 93.9% (95% CI 87.9 – 97.5) and of pyuria was 91.3% (84.6%–95.6%). CONCLUSIONS: In young infants with bacteremic UTI, UA sensitivity is higher than previous reports in infants with UTI in general. This finding can be explained by spectrum bias or by inclusion of faulty gold standards (contaminants or asymptomatic bacteriuria) in previous studies.

  • diagnostic accuracy of the urinalysis for urinary tract infection in infants 3 months of age
    Pediatrics, 2015
    Co-Authors: Alan R Schroeder, Pearl W Chang, Mark W Shen, Eric A Biondi, Tara L Greenhow
    Abstract:

    BACKGROUND: The 2011 American Academy of Pediatrics urinary tract infection (UTI) guideline suggests incorporation of a positive urinalysis (UA) into the definition of UTI. However, concerns linger over UA sensitivity in young infants. Infants with the same Pathogenic Organism in the blood and urine (bacteremic UTI) have true infections and represent a desirable population for examination of UA sensitivity. METHODS: We collected UA results on a cross-sectional sample of 276 infants RESULTS: The final sample included 245 infants with bacteremic UTI and 115 infants with negative urine cultures. The sensitivity of leukocyte esterase was 97.6% (95% confidence interval [CI] 94.5%–99.2%) and of pyuria (>3 white blood cells/high-power field) was 96% (95% CI 92.5%–98.1%). Only 1 infant with bacteremic UTI (Group B Streptococcus ) and a complete UA had an entirely negative UA. In infants with negative urine cultures, leukocyte esterase specificity was 93.9% (95% CI 87.9 – 97.5) and of pyuria was 91.3% (84.6%–95.6%). CONCLUSIONS: In young infants with bacteremic UTI, UA sensitivity is higher than previous reports in infants with UTI in general. This finding can be explained by spectrum bias or by inclusion of faulty gold standards (contaminants or asymptomatic bacteriuria) in previous studies.

Konstantinos Mavromatis - One of the best experts on this subject based on the ideXlab platform.

  • Standards in Genomic Sciences (2010) 2:9-18 DOI:10.4056/sigs.591104 The Genomic Standards Consortium Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IAT)
    2014
    Co-Authors: Konstantinos Mavromatis, Johannes Sikorski, Alla Lapidus, Hope Tice, Jan-fang Cheng, Susan Lucas, Feng Chen, Tijana Glavina, Del Rio, Matt Nolan
    Abstract:

    encodes flagellar genes, GEBA Alicyclobacillus acidocaldarius (Darland and Brock 1971) is the type species of the larger of the two genera in the bacillal family ‘Alicyclobacillaceae’. A. acidocaldarius is a free-living and non-Pathogenic Organism, but may also be associated with food and fruit spoilage. Due to its acidophilic nature, several enzymes from this species have since long been subjected to detailed molecular and biochemical studies. Here we describe the features of this Organism, together with the complete genome sequence and annotation. This is the first completed ge-nome sequence of the family ‘Alicyclobacillaceae’. The 3,205,686 bp long genome (chromo-some and three plasmids) with its 3,153 protein-coding and 82 RNA genes is part of the Ge

  • complete genome sequence of alicyclobacillus acidocaldarius type strain 104 iat
    Standards in Genomic Sciences, 2010
    Co-Authors: Konstantinos Mavromatis, Johannes Sikorski, Alla Lapidus, Alex Copeland, Hope Tice, Jan-fang Cheng, Susan Lucas, Feng Chen, Tijana Glavina Del Rio, Matt Nolan
    Abstract:

    Alicyclobacillus acidocaldarius (Darland and Brock 1971) is the type species of the larger of the two genera in the bacillal family ‘Alicyclobacillaceae’. A. acidocaldarius is a free-living and non-Pathogenic Organism, but may also be associated with food and fruit spoilage. Due to its acidophilic nature, several enzymes from this species have since long been subjected to detailed molecular and biochemical studies. Here we describe the features of this Organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family ‘Alicyclobacillaceae’. The 3,205,686 bp long genome (chromosome and three plasmids) with its 3,153 protein-coding and 82 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  • Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA^T)
    Standards in Genomic Sciences, 2010
    Co-Authors: Konstantinos Mavromatis, Johannes Sikorski, Alla Lapidus, Tijana Glavina Del Rio, Alex Copeland, Hope Tice, Jan-fang Cheng, Susan Lucas, Feng Chen, Matt Nolan
    Abstract:

    Alicyclobacillus acidocaldarius (Darland and Brock 1971) is the type species of the larger of the two genera in the bacillal family ‘ Alicyclobacillaceae ’. A. acidocaldarius is a free-living and non-Pathogenic Organism, but may also be associated with food and fruit spoilage. Due to its acidophilic nature, several enzymes from this species have since long been subjected to detailed molecular and biochemical studies. Here we describe the features of this Organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family ‘ Alicyclobacillaceae ’. The 3,205,686 bp long genome (chromosome and three plasmids) with its 3,153 protein-coding and 82 RNA genes is part of the G enomic E ncyclopedia of B acteria and A rchaea project.

Maryn O Carlson - One of the best experts on this subject based on the ideXlab platform.

  • temporal genetic dynamics of an experimental biparental field population of phytophthora capsici
    Frontiers in Genetics, 2017
    Co-Authors: Maryn O Carlson, Elodie Gazave, Michael A Gore, Christine D Smart
    Abstract:

    Defining the contributions of dispersal, reproductive mode, and mating system to the population structure of a Pathogenic Organism is essential to estimating its evolutionary potential. After introduction of the devastating plant pathogen, Phytophthora capsici, into a grower's field, a lack of aerial spore dispersal restricts migration. Once established, coexistence of both mating types results in formation of overwintering recombinant oospores, engendering persistent pathogen populations. To mimic these conditions, in 2008, we inoculated a field with two P. capsici isolates of opposite mating type. We analyzed Pathogenic isolates collected in 2009-13 from this experimental population, using genome-wide single-nucleotide polymorphism markers. By tracking heterozygosity across years, we show that the population underwent a generational shift; transitioning from exclusively F1 in 2009-10; multi-generational in 2011; and ultimately all inbred in 2012-13. Survival of F1 oospores, characterized by heterozygosity excess, coupled with a low rate of selfing, delayed declines in heterozygosity due to inbreeding and attainment of equilibrium genotypic frequencies. Large allele and haplotype frequency changes in specific genomic regions accompanied the generational shift, representing putative signatures of selection. Finally, we identified an approximately 1.6 Mb region associated with mating type determination, constituting the first detailed genomic analysis of a mating type region (MTR) in Phytophthora. Segregation patterns in the MTR exhibited tropes of sex-linkage, where maintenance of allele frequency differences between isolates of opposite mating type was associated with elevated heterozygosity despite inbreeding. Characterizing the trajectory of this experimental system provides key insights into the processes driving persistent, sexual pathogen populations.

  • temporal genetic dynamics of an experimental biparental field population of phytophthora capsici
    bioRxiv, 2016
    Co-Authors: Maryn O Carlson, Elodie Gazave, Michael A Gore, Christine D Smart
    Abstract:

    Defining the contributions of dispersal, reproductive mode, and mating system to the population structure of a Pathogenic Organism is essential to estimating its evolutionary potential. After introduction of the devastating plant pathogen, Phytophthora capsici, into a grower9s field, a lack of aerial spore dispersal restricts migration. Once established, coexistence of both mating types results in formation of overwintering recombinant oospores, engendering persistent pathogen populations. To mimic these conditions, in 2008, we inoculated a field with two P. capsici isolates of opposite mating type. We analyzed Pathogenic isolates collected in 2009-13 from this experimental population, using genome-wide single-nucleotide polymorphism markers. By tracking heterozygosity across years, we show that the population underwent a generational shift; transitioning from exclusively F1 in 2009-10; mixed generational in 2011; and ultimately all inbred in 2012-13. Survival of F1 oospores, characterized by heterozygosity excess, coupled with a low rate of selfing, delayed declines in heterozygosity due to inbreeding and attainment of equilibrium genotypic frequencies. Large allele and haplotype frequency changes in specific genomic regions accompanied the generational shift, representing putative signatures of selection. Finally, we identified an approximately 1.6 Mb region associated with mating type determination, constituting the first detailed genomic analysis of a mating type region (MTR) in Phytophthora. Segregation patterns in the MTR exhibited tropes of sex-linkage, where maintenance of allele frequency differences between isolates of opposite mating type was associated with elevated heterozygosity despite inbreeding. Characterizing the trajectory of this experimental system provides key insights into the processes driving persistent, sexual pathogen populations.