scholarly journals Genome characteristic of Bordetella parapertussis isolated from Iran

2022 ◽  
Author(s):  
Azadeh Safarchi ◽  
Samaneh Saedi ◽  
Chin Yen Tay ◽  
Binit Lamichhan ◽  
Masoumeh Nakhost Lotfi ◽  
...  
Keyword(s):  
Whooping Cough ◽  
Clinical Syndrome ◽  
Reference Laboratory ◽  
Nucleotide Polymorphisms ◽  
Biochemical Tests ◽  
Single Nucleotide ◽  
Bordetella Parapertussis ◽  
Evolutionary Changes ◽  
Nasal Swabs ◽  
Relationship Of

Pertussis also known as whooping cough is a respiratory infection in humans particularly in infants and usually caused by Bordetella pertussis. However, Bordetella parapertussis can also cause a similar clinical syndrome. During 2012 to 2015, from nasal swabs sent from different provinces to the pertussis reference laboratory of Pasture Institute of Iran for pertussis confirmation, seven B. parapertussis isolates were identified by bacterial culture, biochemical tests, and the presence of IS1001 insertion in the genome by real-time PCR. Furthermore, the expression of pertactin (Prn) as one the major virulence factor for bacterial adhesion was investigated using western blot. Moreover, the genomic characteristic of one recently collected isolate, IRBP134, from a seven-month infant was investigated using Illumina NextSeq sequencing protocol. The results revealed the genome with G+C content 65% and genome size 4.7 Mbp. A total of 81 single nucleotide polymorphisms (SNPs) and 13 short insertion and deletions were found in the genome compared to the B. parapertussis 12822 as a reference genome showing ongoing evolutionary changes in our isolate. A phylogeny relationship of IRBP134 was also investigated using global B. parapertussis available genomes.

scholarly journals IL-1R2 Polymorphisms and its Interaction Associates With Osteoporosis Susceptibility in Chinese Han Population

2020 ◽  
Author(s):  
Kai Rong ◽  
Zhiquan Liang ◽  
Wenyuan Xiang ◽  
Zhan Wang ◽  
Fengli Wen ◽  
...  
Keyword(s):  
Negative Regulator ◽  
Chinese Han Population ◽  
Nucleotide Polymorphisms ◽  
Chinese Han ◽  
Single Nucleotide ◽  
Han Population ◽  
Testing Accuracy ◽  
Relationship Of ◽  
The Relationship ◽  
Osteoporosis Risk

Abstract Background: IL-1R2, serves as a negative regulator of IL-1 signaling, is involved in the pathogenesis of osteoporosis. This study aimed to determine the correlation between IL-1R2 polymorphism and osteoporosis susceptibility among the Chinese Han population.Methods: We recruited 594 osteoporosis patients and 599 healthy controls. Six single nucleotide polymorphisms (SNPs) in IL-1R2 were selected for genotyping using Agena MassARRAY platform. Odds ratio (OR) and 95% confidence interval (CI) was calculated through logistic regression analysis with adjustment for age and sex. Linkage disequilibrium analysis was plotted by Haploview v4.2. Multifactor dimension reduction (MDR) was performed to estimate the SNP-SNP interaction of IL-1R2 variants.Results: Our result revealed that rs11674595 (OR = 1.86, p = 0.020), rs2072472 (OR = 1.26, p = 0.019) and rs4851527 (OR = 0.78, p = 0.007) were related to the risk of osteoporosis. Moreover, the contribution of IL-1R2 polymorphisms to osteoporosis risk presented age, sex and BMI difference. We found the relationship of Trs11674595Ars4851527 (OR = 0.80, p = 0.015), Crs11674595Grs4851527 (OR = 1.22, p = 0.043) and Ars3218977Grs2072472 (OR = 1.25, p = 0.022) haplotypes to osteoporosis occurrence, and a potential accumulated effect of IL-1R2 SNPs (testing accuracy = 0.5783 and CVC = 10/10) on osteoporosis susceptibility.Conclusion: IL-1R2 polymorphisms (rs11674595, rs4851527, rs2072472 and rs3218977) might contribute to osteoporosis risk among the Chinese Han population. Our finding may increase our understanding of the effects of IL-1R2 polymorphisms on the predisposition of osteoporosis.

scholarly journals Large Sequence Polymorphisms Unveil the Phylogenetic Relationship of Environmental and Pathogenic Mycobacteria Related to Mycobacterium ulcerans

2009 ◽  
Vol 75 (17) ◽  
pp. 5667-5675 ◽  
Author(s):  
Michael K�ser ◽  
Julia Hauser ◽  
Pamela Small ◽  
Gerd Pluschke
Keyword(s):  
Buruli Ulcer ◽  
Etiologic Agent ◽  
Mycobacterium Ulcerans ◽  
Nucleotide Polymorphisms ◽  
Differentiation Markers ◽  
Single Nucleotide ◽  
Virulence Plasmids ◽  
Sequence Polymorphisms ◽  
Genetic Features ◽  
Relationship Of

ABSTRACT Mycolactone is an immunosuppressive cytotoxin responsible for the clinical manifestation of Buruli ulcer in humans. It was believed to be confined to its etiologic agent, Mycobacterium ulcerans. However, the identification of other mycolactone-producing mycobacteria (MPMs) in other species, including Mycobacterium marinum, indicated a more complex taxonomic relationship. This highlighted the need for research on the biology, evolution, and distribution of such emerging and potentially infectious strains. The reliable genetic fingerprinting analyses presented here aim at both the unraveling of phylogenetic relatedness and of dispersal between environmental and pathogenic mycolactone producers and the identification of genetic prerequisites that enable lateral gene transfer of such plasmids. This will allow for the identification of environmental reservoirs of virulence plasmids that encode enzymes required for the synthesis of mycolactone. Based on dynamic chromosomal loci identified earlier in M. ulcerans, we characterized large sequence polymorphisms for the phylogenetic analysis of MPMs. Here, we identify new insertional-deletional events and single-nucleotide polymorphisms that confirm and redefine earlier strain differentiation markers. These results support other data showing that all MPMs share a common ancestry. In addition, we found unique genetic features specific for M. marinum strain M, the genome sequence strain which is used widely in research.

scholarly journals <i>SIRT1</i> gene polymorphisms associated with carcass traits in Luxi cattle

2017 ◽  
Vol 60 (1) ◽  
pp. 27-32 ◽  
Author(s):  
Guifen Liu ◽  
Hongbo Zhao ◽  
Xiuwen Tan ◽  
Haijian Cheng ◽  
Wei You ◽  
...  
Keyword(s):  
Promoter Region ◽  
Muscle Development ◽  
Direct Sequencing ◽  
Carcass Traits ◽  
Sirtuin 1 ◽  
Nucleotide Polymorphisms ◽  
Class Iii ◽  
Single Nucleotide ◽  
Relationship Of ◽  
The Relationship

Abstract. SIRT1 is the gene that codes for Sirtuin 1, an NAD (nicotinamide adenine dinucleotide)-dependent class III histone deacetylase. This gene plays a key role in adipose tissue and muscle development in animals. Chinese Luxi cattle (n  =  169) were selected to identify SIRT1 SNPs (single nucleotide polymorphisms) and investigate the relationship of these SNPs with carcass traits. Five SNPs (g.-382G  >  A, g.-274C  >  G, g.17324T  >  C, g.17379A  >  G, and g.17491G  >  A) were identified by direct sequencing. SNPs g.-382G  >  A and g.-274C  >  G were located within the promoter region of this gene. SNP g.-382G  >  A was significantly associated with dressing percentage, meat percentage, and striploin and ribeye weights, and the g.-274C  >  G polymorphism had a strong effect on carcass, tenderloin, and high rib weights in Luxi cattle. These findings will provide possible clues for the biological roles of SIRT1 underlying beef cattle carcass traits.

scholarly journals Relationship of FTO gene variations with NAFLD risk in Chinese men

2020 ◽  
Vol 15 (1) ◽  
pp. 860-867
Author(s):  
Xuefen Chen ◽  
Yong Gao ◽  
Xiaobo Yang ◽  
Haiying Zhang ◽  
Zengnan Mo ◽  
...  
Keyword(s):  
Susceptibility Gene ◽  
Nucleotide Polymorphisms ◽  
Male Population ◽  
Single Nucleotide ◽  
Unadjusted Odds Ratio ◽  
Nonalcoholic Fatty Liver ◽  
Obesity Susceptibility ◽  
Matched Case ◽  
Relationship Of ◽  
Chinese Male

AbstractBackgroundFat mass and obesity-associated (FTO) gene is an obesity susceptibility gene and its relationship with the nonalcoholic fatty liver disease (NAFLD) remains unclear. This study aims to investigate the relationships of FTO gene variations with NAFLD risk in a Chinese male population.MethodsA 1:2 matched case–control study was performed on 275 cases of NAFLD and 550 controls matched for age. Nine of the FTO gene single nucleotide polymorphisms (SNPs) were genotyped.ResultsLogistic regression analysis found that FTO rs1477196 was significantly associated with the susceptibility to NAFLD in recessive genetic models [unadjusted odds ratio (OR) = 2.52, 95% confidence interval (CI): 1.22–5.19, P = 0.012] and the relativity weakened after further adjustment for body mass index (BMI), uric acid, metabolic syndrome, smoking, and drinking (adjusted OR = 2.18, 95% CI: 0.96–4.99, P = 0.06). In the obese group, the AA + AG genotypes of rs1121980 and rs9940128 were associated with a decreased risk of NAFLD, when compared with the GG genotype, respectively (rs1121980: adjusted OR = 0.62, 95% CI = 0.39–0.99, P = 0.044; rs9940128: adjusted OR = 0.61, 95% CI = 0.38–0.97, P = 0.038). Furthermore, rs1477196 was associated with the severity of NAFLD (OR = 2.95, 95% CI = 1.09–7.94, P = 0.034).ConclusionsOur results demonstrated that the FTO gene was related to the presence and severity of NAFLD in a Chinese male population, and the relationships of the tested SNPs with NAFLD are most probably mediated by BMI.

The Relationship of Single Nucleotide Polymorphisms in the TRPV1 Gene with Lipid Profile, Glucose, and Blood Pressure in Mexican Population

2020 ◽  
Vol 24 (7) ◽  
pp. 420-424
Author(s):  
Anahí González-Mercado ◽  
María Teresa Magaña-Torres ◽  
Josefina Yoaly Sánchez-López ◽  
Mónica Ríos-Silva ◽  
Bertha Ibarra-Cortés ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Single Nucleotide Polymorphisms ◽  
Lipid Profile ◽  
Mexican Population ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Relationship Of ◽  
The Relationship

scholarly journals Molecular red cell genotyping of rare blood donors in South Africa to enhance rare donor-patient blood matching

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Lavendri Govender ◽  
Rosaley D. Prakashchandra ◽  
Pavitra Pillay ◽  
Ute Jentsch
Keyword(s):  
South African ◽  
Reference Laboratory ◽  
Red Cell ◽  
Nucleotide Polymorphisms ◽  
Haemolytic Disease ◽  
Single Nucleotide ◽  
Blood Types ◽  
Targeted Screening ◽  
And Gender ◽  
Transfusion Reactions

Background: Molecular red cell genotyping is devoid of serology limitations such as the scarcity of rare antisera and the possibility of inconclusive results due to biological interferences. Blood incompatibility can result in immune transfusion reactions such as haemolytic transfusion reactions or haemolytic disease of the foetus and newborn.Objective: The study aimed to use molecular red cell genotyping to identify rare blood group donors among South African blood donors.Methods: Red cell genotyping data were extracted retrospectively from the BIDS XT genotyping software in the Immunohaematology Reference Laboratory from January 2015 to August 2016. The ID CORE XT genotyping assay was used to identify the single nucleotide polymorphisms of 10 blood groups system alleles in 150 donors. Associations between the resultant genotypes and predicted phenotypes, ABO group, RhD type, race group and gender were studied.Results: Significant red cell genetic variability was noted among the numerous South African donor genotypes identified in this study. Genotyping further confirmed the presence of at least one of the 16 rare genotypes in 50 donors. Group O Black donors were associated with two rare blood types, while several other rare blood types were found only in White donors, supporting an association between ABO/Rh subtype, race group and rare blood types.Conclusion: Targeted screening of donors for antigen-negative rare blood units for patients should be done to reduce the risk of haemolytic transfusion reactions and haemolytic disease of the foetus and newborn.

PSV-6 Single nucleotide polymorphisms associated with advanced skeletal maturity in finished beef heifers

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 308-309
Author(s):  
Katie A Walker-Shira ◽  
Brenda M Murdoch ◽  
Antonetta M Colacchio ◽  
Kimberly M Davenport ◽  
Michael J Colle ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Bone Mineralization ◽  
Skeletal Maturity ◽  
Strong Relationship ◽  
Nucleotide Polymorphisms ◽  
Beef Heifers ◽  
Allelic Discrimination ◽  
Single Nucleotide ◽  
Relationship Of ◽  
The Impact

Abstract Accelerated skeletal maturity is prevalent in modern commercial heifers harvested under 30 months of age. It is hypothesized that selection for increased growth and earlier reproductive maturity over several decades, unintentionally co-selected for precocious skeletal ossification in heifers. This study examines the relationship of single nucleotide polymorphisms (SNPs) in beef heifers with developmental maturity (A-, B-, C- Maturity) assessed at harvest, and evaluates specific genotype and production implant potency interactions. Two SNPs within Estrogen Receptor 1 (ESR1) and one SNP within Alkaline Phosphatase (ALPL) genes that have been previously associated with carcass skeletal maturity were examined. USDA inspected beef heifer carcasses (&lt; 30 months) that were A- (n = 318), B- (n = 296), or C- (n = 251) skeletal maturity were sampled. DNA was extracted and SNP genotypes were ascertained using custom designed allelic discrimination assays (Taqman® Custom SNP Assays). Dominant and basic association tests were performed, and the impact of implants were evaluated as co-variates against genotypes using a linear regression model in the SNP and Variation Suite (SVS) software (Golden Helix, Inc.). A significant association with skeletal maturity was detected with ESR1 SNP 1 (P &lt; 0.05) and a trend observed with ALPL (P &lt; 0.1), but there was no significance identified in ESR1 SNP 2. A highly significant interaction with genotype and incidence of skeletal maturity was identified for ESR1 SNP 1 (P &lt; 0.01) and ALPL (P &lt; 0.01) when estrogenic implant concentration was included. There exists a strong relationship for these genotypes and advanced skeletal maturity in commercial heifers which is influenced by estrogenic potency of the commercial implant used. This study confirms the association of previously identified genotypes with advanced skeletal maturity and provides evidence that genetic variations in ESR1 play an important role in the regulation of bone mineralization in heifers.

The Relationship of TLR2 Polymorphisms with Infectious Diseases

2021 ◽  
pp. 57-73
Author(s):  
Marcos Jessé Abrahão Silva ◽  
Marceli Batista Martins Lima ◽  
Karla Valéria Batista Lima ◽  
Luana Nepomuceno Gondim Costa Lima
Keyword(s):  
Immune Response ◽  
Infectious Diseases ◽  
Cochrane Collaboration ◽  
Nucleotide Polymorphisms ◽  
Proinflammatory Response ◽  
Single Nucleotide ◽  
The Usa ◽  
The Individual ◽  
Relationship Of ◽  
The Relationship

The proinflammatory response induced by Toll-Like receptors (TLR) is considered the host's first defense line. Single nucleotide polymorphisms (SNPs) correspond to the most frequent type of variation in the human genome, and due to the importance of TLR2 in the immune response, SNPs in the TLR gene are related to susceptibility or resistance to various diseases. Thus, the objective of the present study was to identify the polymorphisms existing in the TLR2 gene that may cause susceptibility or protection against infectious diseases. We conducted a systematic review of the literature in the databases Science Direct, National Library of Medicine National Institutes of Health of the USA (PUBMED), Cochrane Collaboration and Medical Literature Analysis and Retrieval System Online (MEDLINE) between 2000 to 2020. The search resulted in 32 articles, all of which in English. Thus, it was demonstrated that the related polymorphisms are extremely important for the identification of related pathologies, whether for the susceptibility or protection of the individual to the diseases, also being essential for the mechanisms of signal generation and immune responses, and finally indicating that a balance between activation and inactivating these receptors to prevent an excessive inflammatory or immune response.

SARS-CoV-2: Evaluation and Evolution

Coronaviruses ◽  
2021 ◽  
Vol 02 ◽  
Author(s):  
Loay Bedda ◽  
Fayrouz Mahmoud ◽  
Radwa Elkhateib ◽  
Alyaa Dawoud ◽  
Hassan Gamal ◽  
...  
Keyword(s):  
Life Cycle ◽  
Genetic Recombination ◽  
Virus Evolution ◽  
High Morbidity ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
S Protein ◽  
Viral Genomes ◽  
Relationship Of ◽  
The Relationship

: The emerging new COVID 2019 pandemic, which started in 2019 in China (Wuhan) and is caused by SARS-CoV-2, raises critical concerns due to high morbidity and mortality. Given a large number of infected individuals and the fact that the number continues to rise, it's possible that the virus has multiple variants, some of which are more pathogenic than others.Besides, the virus is suspected of various evolutionary pathways since SARS-CoV-2 belongs to the RNA viruses’ family, which is characterized by a high mutation rate. Additionally, it is crucial to understand the life cycle of the virus to be able to urge antiviral studies. Genotyping studies about viruses are also important in order to understand the transmission and evolution of the virus. The genome of SARS-CoV-2 has a furin-like cleavage site in its S protein that may affect its pathogenicity. It was found that insertions and deletions in S protein have an impact on the transmission and fusion of the virus. The single nucleotide polymorphisms (SNP) genotypes are used to track the relationship of virus isolates. Sequence alignment revealed the presence of hundreds of inter-host mutations during person-to-person transmission. Furthermore, genetic recombination provided a second mechanism for virus evolution. In this review, we highlight the life cycle of the virus and methods of virus evolution caused by mutations or recombination of viral genomes.

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