Secreted protein gene derived-single nucleotide polymorphisms (SP-SNPs) reveal population diversity and differentiation of Puccinia striiformis f. sp. tritici in the United States

We validated 2 multiplex real-time PCR (rtPCR) assays based on single nucleotide polymorphisms (SNPs) of the hemagglutinin-1 ( HA1) gene of H3N8 equine influenza A virus (EIV) to determine clade affiliation of prototype and field isolates. Initial validation of the 2 multiplex rtPCR assays (SNP1 and SNP2) was performed using nucleic acid from 14 EIV Florida sublineage clade 1 and 2 prototype strains. We included in our study previously banked EIV rtPCR-positive nasal secretions from 341 horses collected across the United States in 2012–2017 to determine their clade affiliation. All 14 EIV prototype strains were identified correctly as either Florida sublineage clade 1 or clade 2 using the 2 SNP target positions. Of 341 EIV rtPCR-positive samples, 337 (98.8%) and 4 (1.2%) isolates were classified as belonging to clade 1 and 2 Florida sublineage EIV, respectively. All clade 1 Florida sublineage EIV strains were detected in domestic horses, three clade 2 Florida sublineage EIV strains originated from horses recently imported into the United States, and one clade 2 Florida sublineage EIV strain originated from a healthy horse recently vaccinated with a modified-live intranasal EIV vaccine containing the American lineage strain A/eq/Kentucky/1991. EIV Florida sublineage clade differentiation using a fast and reliable multiplex rtPCR platform will help monitor the introduction of clade 2 Florida sublineage EIV strains into North America via international transportation.

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Chromosomal localization, structure, single-nucleotide polymorphisms, and expression of the human H-protein gene of the glycine cleavage system (GCSH), a candidate gene for nonketotic hyperglycinemia

Journal of Human Genetics ◽

10.1007/s100380170057 ◽

2001 ◽

Vol 46 (7) ◽

pp. 378-384 ◽

Cited By ~ 20

Author(s):

S. Kure ◽

K. Kojima ◽

T. Kudo ◽

K. Kanno ◽

Y. Aoki ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Candidate Gene ◽

Protein Gene ◽

Chromosomal Localization ◽

Nucleotide Polymorphisms ◽

Glycine Cleavage System ◽

Single Nucleotide ◽

Glycine Cleavage ◽

Nonketotic Hyperglycinemia ◽

H Protein

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Genome-Wide Analysis of Synonymous Single Nucleotide Polymorphisms in Mycobacterium tuberculosis Complex Organisms: Resolution of Genetic Relationships Among Closely Related Microbial Strains

Genetics ◽

10.1093/genetics/162.4.1533 ◽

2002 ◽

Vol 162 (4) ◽

pp. 1533-1543

Author(s):

Michaela M Gutacker ◽

James C Smoot ◽

Cristi A Lux Migliaccio ◽

Stacy M Ricklefs ◽

Su Hua ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Single Nucleotide Polymorphisms ◽

Allelic Variation ◽

Genetic Relationships ◽

The United States ◽

Sensu Stricto ◽

Phylogenetic Position ◽

Nucleotide Polymorphisms ◽

Tuberculosis Complex ◽

Single Nucleotide

Abstract Several human pathogens (e.g., Bacillus anthracis, Yersinia pestis, Bordetella pertussis, Plasmodium falciparum, and Mycobacterium tuberculosis) have very restricted unselected allelic variation in structural genes, which hinders study of the genetic relationships among strains and strain-trait correlations. To address this problem in a representative pathogen, 432 M. tuberculosis complex strains from global sources were genotyped on the basis of 230 synonymous (silent) single nucleotide polymorphisms (sSNPs) identified by comparison of four genome sequences. Eight major clusters of related genotypes were identified in M. tuberculosis sensu stricto, including a single cluster representing organisms responsible for several large outbreaks in the United States and Asia. All M. tuberculosis sensu stricto isolates of previously unknown phylogenetic position could be rapidly and unambiguously assigned to one of the eight major clusters, thus providing a facile strategy for identifying organisms that are clonally related by descent. Common clones of M. tuberculosis sensu stricto and M. bovis are distinct, deeply branching genotypic complexes whose extant members did not emerge directly from one another in the recent past. sSNP genotyping rapidly delineates relationships among closely related strains of pathogenic microbes and allows construction of genetic frameworks for examining the distribution of biomedically relevant traits such as virulence, transmissibility, and host range.

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What are the Prevalence and Risk Factors of Alzheimer’s Disease in China and the United States?

E3S Web of Conferences ◽

10.1051/e3sconf/202018503031 ◽

2020 ◽

Vol 185 ◽

pp. 03031

Author(s):

Yiyang Xu

Keyword(s):

United States ◽

Risk Factors ◽

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Brain Activity ◽

Disease Onset ◽

The United States ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Desk Research

Dementia, especially Alzheimer’s dementia, which occupies more than 60% of total dementia cases, has become one of the most significant health problems in the world due to its increasing global prevalence, irreversible pathology, and rising social and economic costs. In this research, the author compared Alzheimer’s disease (AD) prevalence in China and the United States and found the common pattern of its epidemiology. Apart from the quantitative analysis, this research also identifies the pathophysiological, socioenvironmental, and other risk factors of Alzheimer’s disease by qualitative desk research. It was found that the risk factors related to or controlled by genes such as Single Nucleotide Polymorphisms (SNPs) have more influential effects on Alzheimer’s disease onset than the socio-environmental factors. Some socioenvironmental factors such as level of education reflecting the brain activity of a person are also correlated with Alzheimer’s disease prevalence. This disease is caused by an interplay of numerous factors, so there needs to be further investigations into its mechanisms as well as the combination therapy.

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Identification of single nucleotide polymorphisms in the prion protein gene in Santa Ines and Dorset sheep

Pesquisa Veterinária Brasileira ◽

10.1590/1678-5150-pvb-5365 ◽

2018 ◽

Vol 38 (4) ◽

pp. 624-628

Author(s):

Caroline P. Andrade ◽

José D. Barbosa Neto ◽

David Driemeier

Keyword(s):

Single Nucleotide Polymorphisms ◽

Prion Protein ◽

Protein Gene ◽

Risk Group ◽

Prion Protein Gene ◽

Nucleotide Polymorphisms ◽

Moderate Risk ◽

Single Nucleotide ◽

Group 3 ◽

Santa Inês

ABSTRACT: Scrapie is a transmissible spongiform encephalopathy (TSE) that affects sheep and goats and results from accumulation of the abnormal isoform of a prion protein in the central nervous system. Resistance or susceptibility to the disease is dependent on several factors, including the strain of infecting agent, the degree of exposure, and the presence of single nucleotide polymorphisms (SNPs) in the prion protein gene. The most important polymorphisms are present in codons 136, 154, and 171. SNPs have also been identified in other codons, such as 118, 127, 141, 142, and 143. The objective of this study was to investigate the genotypic profile of Santa Ines (n=94) and Dorset (n=69) sheep and identify polymorphisms in the prion protein gene using real-time PCR techniques and sequencing. We analyzed SNPs in 10 different codons (127, 136, 138, 140, 141, 142, 143, 154, 171, and 172) in Santa Ines sheep. Classification of the flock into risk groups associated with scrapie revealed that approximately 68% of the Santa Ines herd was considered at moderate risk (group 3), and the most frequent haplotype was ARQ/ARQ (47.8%). For Dorset sheep, 42% of the herd was considered at moderate risk (group 3), 40% at low risk (group 2), and 12% at very low risk (group 1). These findings improve our understanding of the genotype breed and further highlight the importance of genotyping and identification of polymorphisms in Brazilian herds to assess their effects on potential infections upon exposure to the sheep prion.

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