The Experts below are selected from a list of 31620 Experts worldwide ranked by ideXlab platform
Tom Edlind - One of the best experts on this subject based on the ideXlab platform.
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listeria environmental sampling tests are compatible with Polymorphic Locus sequence typing
Journal of Food Science, 2021Co-Authors: Tom Edlind, Yanhong LiuAbstract:Food processors invest significant resources into environmental sampling to detect contamination with potential pathogens, particularly Listeria monocytogenes. To facilitate these efforts, multiple environmental sampling tests (ESTs) have been developed and commercialized that minimize workload, turnaround time, and cost while providing convenient colorimetric detection. For presumptive-positive ESTs, we hypothesized that a relatively minor additional investment could provide, in addition to species confirmation, valuable strain typing data for tracking pathogen spread through a facility, identifying harborage sites, and distinguishing sporadic from persistent or resident contaminants. This hypothesis is based on the demonstrated compatibility of Polymorphic Locus sequence typing (PLST) with crude samples including food enrichments. Five Listeria ESTs were tested here: broth-based InSite (Hygiena), Path-Chek (Mericon), and Pathfinder (Hardy Diagnositics); and gel-based Petrifilm (3M) and HardyChrom (Hardy Diagnostics). ESTs were inoculated with strains representing two common L. monocytogenes serotypes and nonpathogenic Listeria innocua. Following incubation, broths or suspended colonies were heat treated to inactivate bacteria. Lysates or purified DNAs were prepared and used as templates in PCRs targeting the previously described PLST loci LmiMT1 and LisMT2. Single clear products were obtained from all inoculated ESTs; uninoculated controls were negative. PCR products were subjected to Sanger sequencing, yielding high-quality chromatograms. Phylogenetic analysis confirmed identities to previously determined sequences and revealed relatedness to serotype-matched strains represented in GenBank databases. PRACTICAL APPLICATION: Multiple environmental sampling tests have been commercialized in recent years to facilitate the proactive detection of pathogens, particularly Listeria monocytogenes, within food processing facilities. Coupling a positive detection test with strain typing would enhance its value by providing data that can be used to track pathogen spread through a facility, identify harborage sites, and distinguish sporadic from resident contamination.
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development and evaluation of Polymorphic Locus sequence typing for epidemiological tracking of vibrio parahaemolyticus
Foodborne Pathogens and Disease, 2019Co-Authors: Tom Edlind, Gary P RichardsAbstract:Vibrio parahaemolyticus is a common inhabitant of coastal estuaries, and can accumulate to high levels in the shellfish that populate those waters. Human gastrointestinal infection occasionally follows ingestion of raw oysters, and it can lead to extended closures of implicated oyster beds with serious economic consequences. To track down the source of human infection, and to monitor strain variation in the environment, a user-friendly and affordable typing method that provides sufficient resolution for epidemiological analysis is needed. Polymorphic Locus sequence typing (PLST) is based on conventional PCR and dideoxynucleotide sequencing of the one or two most phylogenetically informative genomic loci. Bioinformatic analyses of GenBank databases identified the V. parahaemolyticus Polymorphic tandem repeat-containing loci VpMT1 and VpMT2 on chromosomes 1 and 2, respectively, as promising PLST targets, yielding diversity indexes of 0.99. Phylogenetic analysis identified multiple clusters representing strains known or likely to be epidemiologically related. Correlations with serotype and multiLocus sequence type were strong but resolution was higher; for example, North American ST36 strains yielded 16 VpMT1 alleles. In the laboratory, VpMT1 and VpMT2 were robust, resolving 16 of 17 strains following PCR and sequencing directly from heat-killed colonies. Finally, 4 of 13 retail oyster enrichments yielded VpMT sequences that were unique but closely related to previously characterized clinical or environmental V. parahaemolyticus isolates.
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evaluation of Polymorphic Locus sequence typing for candida glabrata epidemiology
Journal of Clinical Microbiology, 2016Co-Authors: Santosh K Katiyar, Eric Shiffrin, Celeste Shelton, Kelley R Healey, Johnpaul Vermitsky, Tom EdlindAbstract:The opportunistic yeast Candida glabratais increasingly refractory to antifungal treatment or prophylaxis and relatedly is increasingly implicated in health care-associated infections. To elucidate the epidemiology of these infections, strain typing is required. Sequence-based typing provides multiple advantages over length-based methods, such as pulsed-field gel electrophoresis (PFGE); however, conventional multiLocus sequence typing (targeting 6 conserved loci) and whole-genome sequencing are impractical for routine use. A commercial sequence-based typing service for C. glabratathat targets Polymorphic tandem repeat-containing loci has recently been developed. These CgMT-J and CgMT-M services were evaluated with 56 epidemiologically unrelated isolates, 4 to 7 fluconazole-susceptible or fluconazole-resistant isolates from each of 5 center A patients, 5 matched pairs of fluconazole-susceptible/resistant isolates from center B patients, and 7 isolates from a center C patient who responded to then failed caspofungin therapy. CgMT-J and CgMT-M generated congruent results, resolving isolates into 24 and 20 alleles, respectively. Isolates from all but one of the center A patients shared the same otherwise rare alleles, suggesting nosocomial transmission. Unexpectedly, Pdr1 sequencing showed that resistance arose independently in each patient. Similarly, most isolates from center B also clustered together; however, this may reflect a dominant clone since their alleles were shared by multiple unrelated isolates. Although distinguishable by their echinocandin susceptibilities, all isolates from the center C patient shared alleles, in agreement with the previously reported relatedness of these isolates based on PFGE. Finally, we show how phylogenetic clusters can be used to provide surrogate parents to analyze the mutational basis for antifungal resistance.
Jiale Li - One of the best experts on this subject based on the ideXlab platform.
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Polymorphic microsatellite loci for population studies of the razor clam sinonovacula constricta
Conservation Genetics, 2008Co-Authors: Jiale LiAbstract:The razor clam (Sinonovacula constricta) is an important aquacultured bivalve in China. The natural populations of this species are decreasing quickly. To facilitate studies on genetic diversity and population structure of wild populations, microsatellites were isolated from a CA enriched genomic library. Eight microsatellite loci were Polymorphic in 30 individuals from Chongming in Shanghai, China. The number of alleles per Polymorphic Locus varied from 6 to 13 and the values of observed heterozygosity and expected heterozygosity ranged from 0.350 to 1.000 and from 0.602 to 0.902, respectively. These microsatellites are being used in studying population differentiation and genetic diversity for effective conservation and management genetic resources of S. constricta.
Lingfeng Kong - One of the best experts on this subject based on the ideXlab platform.
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development and characterization of 14 Polymorphic microsatellite loci in the razor clam sinonovacula constricta
Conservation Genetics Resources, 2010Co-Authors: Qun Jiang, Qi Li, Yang Yuan, Lingfeng KongAbstract:The razor clam, Sinonovacula constricta is an important fishery resource with high nutritive and economic value. To investigate its genetic diversity and population structure, 14 Polymorphic microsatellite loci were developed and characterized. The number of alleles per Polymorphic Locus ranged from 8 to 29, and the observed and expected heterozygosities varied from 0.200 to 1.000 and from 0.792 to 0.973, respectively. These markers will be used in future studies of population structure of this species.
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isolation and characterization of 14 Polymorphic microsatellite loci in the ark shell scapharca subcrenata bivalvia arcidae
Conservation Genetics, 2009Co-Authors: Yanwei Feng, Qi Li, Lingfeng KongAbstract:The ark shell Scapharca subcrenata is an important fishery resource, but has been suffering from severe population decline due to the deterioration of the coastal environment and over-exploitation. To investigate the genetic variation and structure among populations of S. subcrenata, 14 Polymorphic microsatellite loci were developed. The number of alleles per Polymorphic Locus ranged from 11 to 29 and the observed and expected heterozygosity varied from 0.400 to 0.923 and from 0.705 to 0.965, respectively. These microsatellites will help advance the investigation of the genetic population structure and genetic diversity in this species.
Miki Nakajima - One of the best experts on this subject based on the ideXlab platform.
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genetic polymorphism in the 5 flanking region of human cyp1a2 gene effect on the cyp1a2 inducibility in humans
Journal of Biochemistry, 1999Co-Authors: Miki Nakajima, Tsuyoshi Yokoi, Mayumi Mizutani, Moritoshi Kinoshita, Masato Funayama, Tetsuya KamatakiAbstract:A genetic polymorphism was identified in the 5'-flanking region of human CYP1A2 gene, and its effect on the transcriptional activation of the CYP1A2 gene was investigated. Nucleotide sequence analysis revealed the existence of a point mutation from guanine (wild type) to adenine (mutated type) at position -2964 in the gene. This point mutation was detected by a polymerase chain reaction-restriction fragment length polymorphism method using DdeI or BslI restriction enzyme, and was proven to be genetically inherited. Allele frequency in 116 Japanese subjects showed 0.77 and 0.23 for the wild and mutated types of allele, respectively. The point mutation caused a significant decrease of CYP1A2 activity measured by the rate of caffeine 3-demethylation in Japanese smokers (p<0.05). Gel retardation analysis showed the existence of protein bound to the Polymorphic Locus. These results suggest that this polymorphism is a causal factor of decreased CYP1A2 inducibility.
T Yoshimi - One of the best experts on this subject based on the ideXlab platform.
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a population association study of four candidate genes hexokinase ii glucagon like peptide 1 receptor fatty acid binding protein 2 and apolipoprotein c ii with type 2 diabetes and impaired glucose tolerance in japanese subjects
Diabetic Medicine, 1996Co-Authors: T Yagi, S Nishi, S Hinata, M Murakami, T YoshimiAbstract:In order to define the major genetic factor(s) for the development of Type 2 (non-insulin-dependent) diabetes mellitus in Japanese subjects, a population association study of candidate genes involved in either glucose or lipid metabolism was carried out using microsatellite DNA polymorphisms. Each Polymorphic Locus near the four candidate genes, hexokinase II (HKII), glucagon-like peptide-1 receptor (GLP1R), fatty acid binding protein-2 (FABP-2), and apolipoprotein C-II (apoC-II) genes, were amplified by polymerase chain reaction (PCR) using 32P-labelled primers and each subject was genotyped for the association study. The HKII, GLP1R, FABP-2, and apoC-II polymorphisms exhibited 18, 10, 7, and 10 alleles, respectively. While polymorphism information contents (PICs) of these polymorphisms were relatively high, allele frequencies in these polymorphisms did not differ among subjects with Type 2 diabetes, impaired glucose tolerance (IGT) and non-diabetic controls. These results suggest that the HKII, GLP1R, FABP-2, and apoC-II genes are not the major inherited factors for the development of Type 2 diabetes or IGT in Japanese subjects, although minor contributions cannot be ruled out.
