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  • Online Resource  (8)
  • American Society for Microbiology  (8)
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  • Biodiversity Research  (8)
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  • 1
    Online Resource
    Online Resource
    Prevalence, Distribution, and Diversity of Salmonella enterica in a Major Produce Region of California
    American Society for Microbiology ; 2011
    In:  Applied and Environmental Microbiology Vol. 77, No. 8 ( 2011-04-15), p. 2734-2748
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 77, No. 8 ( 2011-04-15), p. 2734-2748
    Abstract: A survey was initiated to determine the prevalence of Salmonella enterica in the environment in and around Monterey County, CA, a major agriculture region of the United States. Trypticase soy broth enrichment cultures of samples of soil/sediment ( n = 617), water ( n = 252), wildlife ( n = 476), cattle feces ( n = 795), and preharvest lettuce and spinach ( n = 261) tested originally for the presence of pathogenic Escherichia coli were kept in frozen storage and later used to test for the presence of S. enterica . A multipathogen oligonucleotide microarray was employed to identify a subset of samples that might contain Salmonella in order to test various culture methods to survey a larger number of samples. Fifty-five of 2,401 (2.3%) samples yielded Salmonella , representing samples obtained from 20 different locations in Monterey and San Benito Counties. Water had the highest percentage of positives (7.1%) among sample types. Wildlife yielded 20 positive samples, the highest number among sample types, with positive samples from birds ( n = 105), coyotes ( n = 40), deer ( n = 104), elk ( n = 39), wild pig ( n = 41), and skunk ( n = 13). Only 16 (2.6%) of the soil/sediment samples tested positive, and none of the produce samples had detectable Salmonella . Sixteen different serotypes were identified among the isolates, including S. enterica serotypes Give, Typhimurium, Montevideo, and Infantis. Fifty-four strains were sensitive to 12 tested antibiotics; one S. Montevideo strain was resistant to streptomycin and gentamicin. Pulsed-field gel electrophoresis (PFGE) analysis of the isolates revealed over 40 different pulsotypes. Several strains were isolated from water, wildlife, or soil over a period of several months, suggesting that they were persistent in this environment.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.02321-10
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2011
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    detail.hit.zdb_id: 1478346-0
    SSG: 12
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    Online Resource
  • 2
    Online Resource
    Online Resource
    Multitiered Approach Using Quantitative PCR To Track Sources of Fecal Pollution Affecting Santa Monica Bay, California
    American Society for Microbiology ; 2006
    In:  Applied and Environmental Microbiology Vol. 72, No. 2 ( 2006-02), p. 1604-1612
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 72, No. 2 ( 2006-02), p. 1604-1612
    Abstract: The ubiquity of fecal indicator bacteria such as Escherichia coli and Enterococcus spp. in urban environments makes tracking of fecal contamination extremely challenging. A multitiered approach was used to assess sources of fecal pollution in Ballona Creek, an urban watershed that drains to the Santa Monica Bay (SMB) near Los Angeles, Calif. A mass-based design at six main-stem sites and four major tributaries over a 6-h period was used (i) to assess the flux of Enterococcus spp. and E. coli by using culture-based methods (tier 1); (ii) to assess levels of Enterococcus spp. by using quantitative PCR and to detect and/or quantify additional markers of human fecal contamination, including a human-specific Bacteroides sp. marker and enterovirus, using quantitative reverse transcriptase PCR (tier 2); and (iii) to assess the specific types of enterovirus genomes found via sequence analysis (tier 3). Sources of fecal indicator bacteria were ubiquitous, and concentrations were high, throughout Ballona Creek, with no single tributary dominating fecal inputs. The flux of Enterococcus spp. and E. coli averaged 10 9 to 10 10 cells h −1 and was as high at the head of the watershed as at the mouth prior to discharge into the SMB. In addition, a signal for the human-specific Bacteroides marker was consistently detected: 86% of the samples taken over the extent during the study period tested positive. Enteroviruses were quantifiable in 14 of 36 samples (39%), with the highest concentrations at the site furthest upstream (Cochran). These results indicated the power of using multiple approaches to assess and quantify fecal contamination in freshwater conduits to high-use, high-priority recreational swimming areas.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.72.2.1604-1612.2006
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2006
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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    Online Resource
  • 3
    Online Resource
    Online Resource
    Rapid Detection of Enteroviruses in Small Volumes of Natural Waters by Real-Time Quantitative Reverse Transcriptase PCR
    American Society for Microbiology ; 2005
    In:  Applied and Environmental Microbiology Vol. 71, No. 8 ( 2005-08), p. 4523-4530
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 71, No. 8 ( 2005-08), p. 4523-4530
    Abstract: Despite viral contamination of recreational waters, only bacterial, not viral, indicators are monitored routinely, due to a lack of rapid and cost-effective assays. We used negatively charged filters to capture enteroviruses from seawater and freshwater. Viral RNA was extracted using a commercial kit, and the viruses were quantified by real-time quantitative reverse transcriptase PCR (qRT-PCR). Poliovirus (6.6 to 330,000 virus particles/ml) was added to samples from watersheds in Los Angeles, California, and analysis showed that with 50-ml samples, a cellulose acetate/nitrate (HA) filter yielded final recovery of 51% ( r 2 = 0.99) in fresh water and 23% ( r 2 = 0.90) in seawater. However, for additions of low levels of virus (more likely to represent field samples; 〈 10 4 enterovirus particles/ml), the recovery was lower and more variable, with HA being best in freshwater (17%, r 2 = 0.97) and the type GF/F glass filter having higher average recovery in seawater (GF/F, 17%; r 2 = 0.93; HA 12%, r 2 = 0.87). The optimized method was used with 1-liter field samples from two very different freshwater “creeks” that drain into Santa Monica Bay, California: Topanga Creek (TC), a relatively pristine mountain creek, and Ballona Creek (BC), a concrete-lined urban storm drain. One TC site out of 10 and 2 BC sites out of 7 tested significantly positive for enteroviruses, with higher enterovirus concentrations in BC than in TC (ca. 10 to 25 versus 1 equivalent enterovirus particle/ml). The presented filtration-qRT-PCR approach is fast ( 〈 8 h from sampling to results), sensitive, and cost efficient and is promising for monitoring viral contamination in environmental water samples.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.71.8.4523-4530.2005
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2005
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Proteomic Profiling and Identification of Immunodominant Spore Antigens of Bacillus anthracis , Bacillus cereus , and Bacillus thuringiensis
    American Society for Microbiology ; 2006
    In:  Applied and Environmental Microbiology Vol. 72, No. 9 ( 2006-09), p. 6355-6363
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 72, No. 9 ( 2006-09), p. 6355-6363
    Abstract: Differentially expressed and immunogenic spore proteins of the Bacillus cereus group of bacteria, which includes Bacillus anthracis , Bacillus cereus , and Bacillus thuringiensis , were identified. Comparative proteomic profiling of their spore proteins distinguished the three species from each other as well as the virulent from the avirulent strains. A total of 458 proteins encoded by 232 open reading frames were identified by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry analysis for all the species. A number of highly expressed proteins, including elongation factor Tu (EF-Tu), elongation factor G, 60-kDa chaperonin, enolase, pyruvate dehydrogenase complex, and others exist as charge variants on two-dimensional gels. These charge variants have similar masses but different isoelectric points. The majority of identified proteins have cellular roles associated with energy production, carbohydrate transport and metabolism, amino acid transport and metabolism, posttranslational modifications, and translation. Novel vaccine candidate proteins were identified using B. anthracis polyclonal antisera from humans postinfected with cutaneous anthrax. Fifteen immunoreactive proteins were identified in B. anthracis spores, whereas 7, 14, and 7 immunoreactive proteins were identified for B. cereus and in the virulent and avirulent strains of B. thuringiensis spores, respectively. Some of the immunodominant antigens include charge variants of EF-Tu, glyceraldehyde-3-phosphate dehydrogenase, dihydrolipoamide acetyltransferase, Δ-1-pyrroline-5-carboxylate dehydrogenase, and a dihydrolipoamide dehydrogenase. Alanine racemase and neutral protease were uniquely immunogenic to B. anthracis . Comparative analysis of the spore immunome will be of significance for further nucleic acid- and immuno-based detection systems as well as next-generation vaccine development.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.00455-06
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2006
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Short-Term Metabolome Dynamics and Carbon, Electron, and ATP Balances in Chemostat-Grown Saccharomyces cerevisiae CEN.PK 113-7D following a Glucose Pulse
    American Society for Microbiology ; 2006
    In:  Applied and Environmental Microbiology Vol. 72, No. 5 ( 2006-05), p. 3566-3577
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 72, No. 5 ( 2006-05), p. 3566-3577
    Abstract: The in vivo kinetics in Saccharomyces cerevisiae CEN.PK 113-7D was evaluated during a 300-second transient period after applying a glucose pulse to an aerobic, carbon-limited chemostat culture. We quantified the responses of extracellular metabolites, intracellular intermediates in primary metabolism, intracellular free amino acids, and in vivo rates of O 2 uptake and CO 2 evolution. With these measurements, dynamic carbon, electron, and ATP balances were set up to identify major carbon, electron, and energy sinks during the postpulse period. There were three distinct metabolic phases during this time. In phase I (0 to 50 seconds after the pulse), the carbon/electron balances closed up to 85%. The accumulation of glycolytic and storage compounds accounted for 60% of the consumed glucose, caused an energy depletion, and may have led to a temporary decrease in the anabolic flux. In phase II (50 to 150 seconds), the fermentative metabolism gradually became the most important carbon/electron sink. In phase III (150 to 300 seconds), 29% of the carbon uptake was not identified in the measurements, and the ATP balance had a large surplus. These results indicate an increase in the anabolic flux, which is consistent with macroscopic balances of extracellular fluxes and the observed increase in CO 2 evolution associated with nonfermentative metabolism. The identified metabolic processes involving major carbon, electron, and energy sinks must be taken into account in in vivo kinetic models based on short-term dynamic metabolome responses.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.72.5.3566-3577.2006
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2006
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    The Fibronectin Type 3-Like Repeat from the Clostridium thermocellum Cellobiohydrolase CbhA Promotes Hydrolysis of Cellulose by Modifying Its Surface
    American Society for Microbiology ; 2002
    In:  Applied and Environmental Microbiology Vol. 68, No. 9 ( 2002-09), p. 4292-4300
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 68, No. 9 ( 2002-09), p. 4292-4300
    Abstract: Fibronectin type 3 homology domains (Fn3) as found in the cellobiohydrolase CbhA of Clostridium thermocellum are common among bacterial extracellular glycohydrolases. The function of these domains is not clear. CbhA is modular and composed of an N-terminal family IV carbohydrate-binding domain (CBDIV), an immunoglobulin-like domain, a family 9 glycosyl hydrolase catalytic domain (Gh9), two Fn3-like domains (Fn3 1,2 ), a family III carbohydrate-binding domain (CBDIII), and a dockerin domain. Efficiency of cellulose hydrolysis by truncated forms of CbhA increased in the following order: Gh9 (lowest efficiency), Gh9-Fn3 1,2 (more efficient), and Gh9-Fn3 1,2 -CBDIII (greatest efficiency). Thermostability of the above constructs decreased in the following order: Gh9 (most stable), Gh9-Fn3 1,2 , and then Gh9-Fn3 1,2 -CBDIII (least stable). Mixing of Orpinomyces endoglucanase CelE with Fn3 1,2, or Fn3 1,2 -CBDIII increased efficiency of hydrolysis of acid-swollen cellulose (ASC) and filter paper. Scanning electron microscopic studies of filter paper treated with Fn3 1,2 , Fn3 1,2 -CBDIII, or CBDIII showed that the surface of the cellulose fibers had been loosened up and crenellated by Fn3 1,2 and Fn3 1,2 -CBDIII and to a lesser extent by CBDIII. X-ray diffraction analysis did not reveal changes in the crystallinity of the filter paper. CBDIII bound to ASC and filter paper with capacities of 2.45 and 0.73 μmoles g −1 and relative affinities ( K r ) of 1.12 and 2.13 liters g −1 , respectively. Fn3 1,2 bound weakly to both celluloses. Fn3 1,2 -CBD bound to ASC and filter paper with capacities of 3.22 and 0.81 μmoles g −1 and K r s of 1.14 and 1.98 liters g −1 , respectively. Fn3 1,2 and CBDIII contained 2 and 1 mol of calcium per mol, respectively. The results suggest that Fn3 1,2 aids the hydrolysis of cellulose by modifying its surface. This effect is enhanced by the presence of CBDIII, which increases the concentration of Fn3 1,2 on the cellulose surface.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.68.9.4292-4300.2002
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2002
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 7
    Online Resource
    Online Resource
    Contribution of Complex I NADH Dehydrogenase to Respiratory Energy Coupling in Glucose-Grown Cultures of Ogataea parapolymorpha
    American Society for Microbiology ; 2020
    In:  Applied and Environmental Microbiology Vol. 86, No. 15 ( 2020-07-20)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 86, No. 15 ( 2020-07-20)
    Abstract: The thermotolerant yeast Ogataea parapolymorpha (formerly Hansenula polymorpha ) is an industrially relevant production host that exhibits a fully respiratory sugar metabolism in aerobic batch cultures. NADH-derived electrons can enter its mitochondrial respiratory chain either via a proton-translocating complex I NADH-dehydrogenase or via three putative alternative NADH dehydrogenases. This respiratory entry point affects the amount of ATP produced per NADH/O 2 consumed and therefore impacts the maximum yield of biomass and/or cellular products from a given amount of substrate. To investigate the physiological importance of complex I, a wild-type O. parapolymorpha strain and a congenic complex I-deficient mutant were grown on glucose in aerobic batch, chemostat, and retentostat cultures in bioreactors. In batch cultures, the two strains exhibited a fully respiratory metabolism and showed the same growth rates and biomass yields, indicating that, under these conditions, the contribution of NADH oxidation via complex I was negligible. Both strains also exhibited a respiratory metabolism in glucose-limited chemostat cultures, but the complex I-deficient mutant showed considerably reduced biomass yields on substrate and oxygen, consistent with a lower efficiency of respiratory energy coupling. In glucose-limited retentostat cultures at specific growth rates down to ∼0.001 h −1 , both O. parapolymorpha strains showed high viability. Maintenance energy requirements at these extremely low growth rates were approximately 3-fold lower than estimated from faster-growing chemostat cultures, indicating a stringent-response-like behavior. Quantitative transcriptome and proteome analyses indicated condition-dependent expression patterns of complex I subunits and of alternative NADH dehydrogenases that were consistent with physiological observations. IMPORTANCE Since popular microbial cell factories have typically not been selected for efficient respiratory energy coupling, their ATP yields from sugar catabolism are often suboptimal. In aerobic industrial processes, suboptimal energy coupling results in reduced product yields on sugar, increased process costs for oxygen transfer, and volumetric productivity limitations due to limitations in gas transfer and cooling. This study provides insights into the contribution of mechanisms of respiratory energy coupling in the yeast cell factory Ogataea parapolymorpha under different growth conditions and provides a basis for rational improvement of energy coupling in yeast cell factories. Analysis of energy metabolism of O. parapolymorpha at extremely low specific growth rates indicated that this yeast reduces its energy requirements for cellular maintenance under extreme energy limitation. Exploration of the mechanisms for this increased energetic efficiency may contribute to an optimization of the performance of industrial processes with slow-growing eukaryotic cell factories.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.00678-20
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2020
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Analysis of mechanisms regulating expression of the ver-1 gene, involved in aflatoxin biosynthesis
    American Society for Microbiology ; 1997
    In:  Applied and Environmental Microbiology Vol. 63, No. 3 ( 1997-03), p. 1058-1065
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 63, No. 3 ( 1997-03), p. 1058-1065
    Abstract: Previous studies have shown that ver-1A encodes an enzyme which is directly involved in the conversion of versicolorin A to demethylsterigmatocystin during aflatoxin B1 (AFB1) biosynthesis in the filamentous fungus Aspergillus parasiticus. In this study, two different tools were utilized to study the regulation of ver-1A expression at the level of transcription and protein accumulation. First, a ver-1A cDNA was expressed in Escherichia coli with the vector pMAL-c2. The resulting maltose-binding protein-Ver-1A fusion protein was purified and used to generate polyclonal antibodies. Western blot analyses showed that these antibodies specifically recognized the Ver-1 protein (approximately 28 kDa) in cell extracts of Aspergillus parasiticus SU1. Second, a GUS (uidA; encodes beta-glucuronidase) reporter system was developed by fusing the ver-1A promoter and transcription terminator to the GUS gene. Reporter constructs were transformed into A. parasiticus, resulting in a single copy of the ver-1A-GUS reporter integrated adjacent to the wild-type ver-1A gene (3' end) in the chromosome. Western blot analysis, Northern hybridization analysis, and a GUS activity assay were used to analyze transformants. The timing of appearance and pattern of accumulation of GUS transcript and GUS protein in transformants were consistent with the timing of appearance and pattern of accumulation of ver-1 transcript and Ver-1 protein. These data suggested that the GUS gene was under the same regulatory control as the wild-type ver-1 gene and confirmed that transcriptional regulation plays an important role in ver-1A expression. Integration of the ver-1A-GUS reporter construct at the niaD locus resulted in 500-fold-lower GUS activity, but the temporal pattern of accumulation of GUS activity was not affected. Therefore, chromosomal location can play a role in determining the level of gene expression in A. parasiticus and should be an important consideration when analyzing promoter function in this organism.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/aem.63.3.1058-1065.1997
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 1997
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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