Genetic diversity of theMycobacterium tuberculosisBeijing family based on multiple genotyping profiles

2015 ◽  
Vol 144 (8) ◽  
pp. 1728-1735 ◽  
Author(s):  
Y. LIU ◽  
S. WANG ◽  
H. LU ◽  
W. CHEN ◽  
W. WANG
Keyword(s):  
Genetic Diversity ◽  
Tandem Repeats ◽  
Cross Sectional Study ◽  
Variable Number ◽  
Beijing Genotype ◽  
Nucleotide Polymorphisms ◽  
Beijing Family ◽  
Cross Sectional ◽  
Discriminatory Ability ◽  
Family Based

SUMMARYAmong the most prevalentMycobacterium tuberculosis(Mtb) strains worldwide is the Beijing genotype, which has caused large outbreaks of tuberculosis (TB). Characteristics facilitating the dissemination of Beijing family strains remain unknown, but they are presumed to have been acquired through evolution of the lineage. To explore the genetic diversity of the Beijing family Mtb and explore the discriminatory ability of mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) loci in several regions of East Asia, a cross-sectional study was conducted with a total of 163 Beijing strains collected from registered TB patients between 1 June 2009 and 31 November 2010 in Funing County, China. The isolated strains were analysed by 15-MIRU-VNTR loci typing and compared with published MIRU-VNTR profiles of Beijing strains. Synonymous single nucleotide polymorphisms at 10 chromosomal positions were also analysed. The combination of SNP and MIRU-VNTR typing may be used to assess Mtb genotypes in areas dominated by Beijing strains. The modern subfamily in Shanghai overlapped with strains from other countries, whereas the ancient subfamily was genetically differentiated across several countries. Modern subfamilies, especially ST10, were prevalent. Qub11b and four other loci (MIRU 26, Mtub21, Qub26, Mtub04) could be used to discriminate Beijing strains.

scholarly journals Genetic Variants in Smoking-Related Genes in Two Smoking Cessation Programs: A Cross-Sectional Study

2021 ◽  
Vol 18 (12) ◽  
pp. 6597
Author(s):  
Gloria Pérez-Rubio ◽  
Luis Alberto López-Flores ◽  
Ana Paula Cupertino ◽  
Francisco Cartujano-Barrera ◽  
Luz Myriam Reynales-Shigematsu ◽  
...  
Keyword(s):  
Smoking Cessation ◽  
Cross Sectional Study ◽  
Nucleotide Polymorphisms ◽  
Sectional Study ◽  
Cross Sectional ◽  
Single Nucleotide ◽  
Genotype Frequencies ◽  
Quitting Smoking ◽  
Genes Encoding ◽  
Genomic Regions

Previous studies have identified variants in genes encoding proteins associated with the degree of addiction, smoking onset, and cessation. We aimed to describe thirty-one single nucleotide polymorphisms (SNPs) in seven candidate genomic regions spanning six genes associated with tobacco-smoking in a cross-sectional study from two different interventions for quitting smoking: (1) thirty-eight smokers were recruited via multimedia to participate in e-Decídete! program (e-Dec) and (2) ninety-four attended an institutional smoking cessation program on-site. SNPs genotyping was done by real-time PCR using TaqMan probes. The analysis of alleles and genotypes was carried out using the EpiInfo v7. on-site subjects had more years smoking and tobacco index than e-Dec smokers (p < 0.05, both); in CYP2A6 we found differences in the rs28399433 (p < 0.01), the e-Dec group had a higher frequency of TT genotype (0.78 vs. 0.35), and TG genotype frequency was higher in the on-site group (0.63 vs. 0.18), same as GG genotype (0.03 vs. 0.02). Moreover, three SNPs in NRXN1, two in CHRNA3, and two in CHRNA5 had differences in genotype frequencies (p < 0.01). Cigarettes per day were different (p < 0.05) in the metabolizer classification by CYP2A6 alleles. In conclusion, subjects attending a mobile smoking cessation intervention smoked fewer cigarettes per day, by fewer years, and by fewer cumulative pack-years. There were differences in the genotype frequencies of SNPs in genes related to nicotine metabolism and nicotine dependence. Slow metabolizers smoked more cigarettes per day than intermediate and normal metabolizers.

scholarly journals Evaluation and comparison of pain questionnaires for clinical screening of osteoarthritis in cats

2019 ◽  
Vol 185 (24) ◽  
pp. 757-757 ◽  
Author(s):  
Sarah Stadig ◽  
B Duncan X Lascelles ◽  
Gorel Nyman ◽  
Anna Bergh
Keyword(s):  
Physical Examination ◽  
Home Environment ◽  
Internal Consistency ◽  
Internal Consistency Reliability ◽  
Cross Sectional Study ◽  
Behavioural Response ◽  
Lifestyle Changes ◽  
Cross Sectional ◽  
Discriminatory Ability ◽  
Physical Dysfunction

BackgroundFeline osteoarthritis (OA) is a common cause of long-standing pain and physical dysfunction. Performing a physical examination of a cat is often challenging. There is a need for disease-specific questionnaires or the so-called clinical metrology instruments (CMIs) to facilitate diagnosis and evaluation of treatment of feline OA. The CMI provides the owners an assessment of the cat’s behavioural and lifestyle changes in the home environment. The purpose of the study was to evaluate readability, internal consistency, reliability and discriminatory ability of four CMIs.MethodsThis is a prospective, cross-sectional study with 142 client-owned cats. Feline OA was diagnosed based on medical history, orthopaedic examination and radiography.ResultsThe results indicate that all four instruments have sound readability, internal consistency, are reliable over time and have good discriminatory ability. Preliminary cut-off values with optimal sensitivity and specificity were suggested for each instrument. The osteoarthritic cats showed significant changes in behavioural response to pain during orthopaedic examination, compared with sound cats.ConclusionThe results indicate that all four questionnaires make an important contribution in a clinical setting, and that the cat’s behavioural response to pain during physical examination should be a parameter to take into account as a possible indication of chronic pain.

scholarly journals Impact of the Neuregulin rs35753505 C/T Polymorphisms on Neuregulin 1 Levels in Preterm Infants

2019 ◽  
Vol 7 (12) ◽  
pp. 1931-1934
Author(s):  
Bugis Mardina Lubis ◽  
Sjarif Hidajat Effendi ◽  
Ratna Akbari Ganie ◽  
Oke Rina Ramayani
Keyword(s):  
Preterm Infants ◽  
Cross Sectional Study ◽  
Enzyme Linked Immunosorbent Assay ◽  
P Value ◽  
Nucleotide Polymorphisms ◽  
Gene Encoding ◽  
Cross Sectional ◽  
Neuregulin 1 ◽  
Organ Systems ◽  
The Impact

BACKGROUND: Neuregulin (NRG) 1 plays an important role in the development of various organ systems in human. Single nucleotide polymorphisms rs35753505 C/Tof the gene encoding NRG1 evident as allele C and T with genotypes of CT, CC, and TT are believed to have an impact on NRG1 levels.AIM: To determine the impact of the NRGrs35753505 C/T polymorphisms on NRG1 levels in preterm infants.METHODS: A cross-sectional study was conducted from February to December 2018, whereas 48 eligible preterm infants with a gestational age of 32- < 37 weeks were enrolled. An umbilical cord blood specimen was collected for determination of NRG1 levels with enzyme-linked immunosorbent assay (ELISA) and NRG1 polymorphisms with polymerase chain reaction (PCR). Statistical analysis was performed with 95%CI and P value of < 0.05 was considered statistically significant.RESULTS: Median value of NRG1 levels (174.4 pg/ml) served as a cut off value. NRG 1 polymorphisms composed distribution of CC (31%), CT (42%), TT (27%) genotypes and distribution of C and T alleles were 52% and 48%. The median NRG1 levels in CC and CT genotypes were significantly lower compared to TT genotype (151.1 pg/ml vs 407.2 pg/ml, P = 0.005 and 159.1 pg/ml vs 407.2 pg/ml, P = 0.009). Subjects with C allele had significantly lower median NRG1 levels than T allele (151.1 pg/ml vs 407.2 pg/ml, P = 0.002). Subjects with CC and CT genotypes had higher risk to develop lower NRG1 levels compared to TT genotype (OR = 8.25, P = 0.016 and OR = 10.74, P = 0.005, respectively).CONCLUSION: Allele C is associated with lower NRG1 levels. Preterm infants with CC and CT genotypes pose a higher risk to have lower NRG1 levels.

scholarly journals Genetic diversity ofPneumocystis jiroveciifrom a cluster of cases of pneumonia in renal transplant patients: Cross-sectional study

Mycoses ◽  
2018 ◽  
Vol 61 (11) ◽  
pp. 845-852 ◽  
Author(s):  
Giannina Ricci ◽  
Daniel Wagner Santos ◽  
Joseph A. Kovacs ◽  
Angela Satie Nishikaku ◽  
Taina Veras de Sandes-Freitas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Renal Transplant ◽  
Cross Sectional Study ◽  
Sectional Study ◽  
Cross Sectional ◽  
Transplant Patients ◽  
Renal Transplant Patients

scholarly journals How does the UK childcare energy-balance environment influence anthropometry of children aged 3–4 years? A cross-sectional exploration

BMJ Open ◽  
2018 ◽  
Vol 8 (7) ◽  
pp. e021520 ◽  
Author(s):  
Kathryn R Hesketh ◽  
Sara E Benjamin-Neelon ◽  
Esther M F van Sluijs
Keyword(s):  
Physical Activity ◽  
Energy Balance ◽  
Skinfold Thickness ◽  
Cross Sectional Study ◽  
Hierarchical Regression ◽  
Cross Sectional ◽  
Early Childhood Obesity ◽  
Family Based ◽  
The Uk ◽  
Objectively Measured

ObjectivesTo assess the association between time spent in care, the childcare energy-balance environment, and preschool-aged children’s body mass index z-score (z-BMI), waist-to-height ratio (WHR) and sum of skinfold thickness (SST).DesignCross-sectional study.Setting and participantsChildren aged 3–4 years were recruited from 30 childcare centres in Cambridgeshire (UK) in 2013.Main outcome measuresObjectively measured height and weight was used to calculate z-BMI; waist circumference and height were used to generate WHR; subscapular and tricep skinfolds were used to calculate SST. Associations between childcare attendance, the nutrition, physical activity, and overall childcare environment, and three anthropometric outcomes were explored using two-level hierarchical regression models, adjusting for demographic and family based confounders.ResultsValid data were available for 196 children (49% female). Time spent in care, the nutrition, physical activity and overall childcare environment were not associated with children’s z-BMI, WHR and SST.ConclusionsChildcare environment and level of attendance were not associated with UK preschool-aged children’s anthropometry. The childcare environment has been central to intervention efforts to prevent/reduce early childhood obesity, yet other factors, including child-level, family level, wider environmental and policy-level factors warrant substantial attention when considering obesity prevention strategies for young children.

The Prevalence of Ultrarapid Metabolizers of Codeine in a Diverse Urban Population

2018 ◽  
Vol 160 (3) ◽  
pp. 420-425
Author(s):  
Jordan Virbalas ◽  
Bernice E. Morrow ◽  
David Reynolds ◽  
John P. Bent ◽  
Thomas J. Ow
Keyword(s):  
New York ◽  
Census Data ◽  
Tertiary Care ◽  
Copy Number Variants ◽  
Ethnically Diverse ◽  
Cross Sectional Study ◽  
Nucleotide Polymorphisms ◽  
Cross Sectional ◽  
Ultrarapid Metabolizers ◽  
Clinically Significant

Objective To examine the prevalence of ultrarapid metabolizers of codeine among children in an ethnically diverse urban community. Study Design Cross-sectional study. Setting A tertiary care academic children’s hospital in the Bronx, New York. Subjects and Methods In total, 256 children with nonsyndromic congenital sensorineural hearing loss were analyzed. DNA was assessed for 63 previously described single-nucleotide polymorphisms (SNPs) and copy number variants (CNVs) known to alter the function and expression of the CYP2D6 gene primarily responsible for codeine metabolism. The rate of CYP2D6 metabolism was predicted based on participants’ haplotype. Results Ethnic distribution in the study subjects paralleled recent local census data, with the largest portion (115 children, 45.8%) identified as Hispanic or Latino. A total of 154 children (80.6%) had a haplotype that corresponds to extensive codeine metabolism, 18 children (9.42%) were identified as ultrarapid metabolizers (UMs), and 16 children (8.37%) were intermediate metabolizers. Only 3 children in our cohort (1.57%) were poor metabolizers. Patients identifying as Caucasian or Hispanic had an elevated incidence of UMs (11.3% and 11.2%, respectively) with extensive variability within subpopulations. Conclusions The clinically significant rate of ultrarapid metabolizers reinforces safety concerns regarding the use of codeine and related opiates. A patient-targeted approach using pharmacogenomics may mitigate adverse effects by individualizing the selection and dosing of these analgesics.

scholarly journals First Description of Macrolide-Resistant Mycoplasma pneumoniae in Adults with Community-Acquired Pneumonia in Italy

2019 ◽  
Vol 2019 ◽  
pp. 1-5 ◽  
Author(s):  
Daniela Loconsole ◽  
Anna Lisa De Robertis ◽  
Rosanna Mallamaci ◽  
Anna Sallustio ◽  
Anna Morea ◽  
...  
Keyword(s):  
Mycoplasma Pneumoniae ◽  
Variable Number Tandem Repeat ◽  
Point Mutations ◽  
Cross Sectional Study ◽  
Variable Number ◽  
Community Acquired Pneumonia ◽  
23S Rrna ◽  
Cross Sectional ◽  
South Italy ◽  
Multiple Loci

Background. Mycoplasma pneumoniae is a common cause of community-acquired pneumonia (CAP). This cross-sectional study aimed to determine the prevalence of macrolide-resistant M. pneumoniae strains in a convenience series of 234 adult hospitalised and nonhospitalised subjects with a diagnosis of CAP in January 2013 to April 2015 in South Italy. Methods. Respiratory samples were subjected to real-time PCR. In M. pneumoniae-positive samples, domain V of 23S rRNA was sequenced to detect resistance-conferring point mutations. P1 major adhesion protein typing and multiple loci variable-number tandem repeat analysis (MLVA) were also performed. Results. Of the 234 samples, 15 (6.4%) were positive for M. pneumoniae. Three of these had a macrolide-resistant genotype: two and one had A2063G and A2064G mutations, respectively. Fourteen of the 15 strains were subtyped: half had subtype 1 and half had subtype 2. Eight strains underwent MLVA profiling: one each had the J, A, and Z type. The remainder was unclassifiable. Conclusions. This novel discovery of macrolide-resistant M. pneumoniae strains in adults with CAP in Italy suggests that there may be increasing circulation of these strains in the population. To facilitate rapid optimization of the antibiotic strategy in Italy, macrolide resistance should be monitored by a surveillance system that is based on molecular methods.

scholarly journals Evaluation of variable numbers of tandem repeat as molecular epidemiological markers of Mycobacterium tuberculosis in Japan

2007 ◽  
Vol 56 (8) ◽  
pp. 1052-1057 ◽  
Author(s):  
Takayuki Wada ◽  
Shinji Maeda ◽  
Atsushi Hase ◽  
Kazuo Kobayashi
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Tandem Repeat ◽  
Tandem Repeats ◽  
Allelic Diversity ◽  
Rflp Analysis ◽  
Strain Typing ◽  
Beijing Family ◽  
Discrimination Power ◽  
Family Based ◽  
Vntr Analysis

Using 243 Mycobacterium tuberculosis isolates obtained in 2001 in Osaka City, Japan, the discriminatory power of variable numbers of tandem repeats (VNTRs) of 12 standard mycobacterial interspersed repetitive units (MIRUs) was assessed. The biggest cluster defined by MIRU-VNTRs consisted of 57 (23.5 %) isolates and they belonged to the Beijing family based on spoligotyping. When additional VNTR loci were included in the MIRU-VNTR analysis, the 57 originally clustered strains were further differentiated by the addition of Queen's University Belfast (QUB)-VNTRs, but not exact tandem repeat-VNTR. The allelic diversity of additional VNTR loci such as VNTR 3232 (QUB-3232), VNTR 2163a (QUB-11a), VNTR 2163b (QUB-11b) and VNTR 1982 (QUB-18) was high in the 57 strains. When the 243 M. tuberculosis isolates were analysed using 16-locus VNTR (the 12 standard MIRUs and the 4 QUB loci) and IS6110 RFLP, the respective Hunter–Gaston discriminatory indexes were 0.9966 and 0.9971. The discrimination power of 16-locus VNTR was equal to that of IS6110 RFLP analysis. If appropriate loci are added to the standard MIRU analysis, VNTR genotyping could be a valuable tool for strain typing and epidemiological research of M. tuberculosis in Japan.

The Pharmacogenetics and Inhibitor Risk (PIR) Study: Establishing the Spectrum of Factor (F)VIII Gene (F8) Mutations in African-American Hemophilia A Patients.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 3207-3207
Author(s):  
Tom E. Howard ◽  
Deepa K. Machiah ◽  
Kevin R. Viel ◽  
Cynthia Channel ◽  
Afshin Ameri ◽  
...  
Keyword(s):  
African American ◽  
Neutralizing Antibodies ◽  
Hemophilia A ◽  
Alternative Hypothesis ◽  
Cross Sectional Study ◽  
Causative Mutation ◽  
Nucleotide Polymorphisms ◽  
Cross Sectional ◽  
Molecular Abnormalities ◽  
Ethnic Subgroups

Abstract The development of neutralizing antibodies against plasma-derived or recombinant (r) molecules of wildtype (wt) factor (F)VIII protein is the most serious complication of replacement therapy for hemophilia A (hA) patients. Although the pathogenesis of these antibodies, termed inhibitors, is complex and poorly understood, ethnicity, a recently established risk determinant, is clearly involved since African-American (AA) patients experience this complication ~2-fold more often than Caucasians. In a previous study -- in which the FVIII genes (F8) from 137 unrelated healthy people, representing 7 ethnic groups, were resequenced -- we identified 4 common nonsynonymous single nucleotide polymorphisms (nsSNPs) and thereby demonstrated that FVIII is not a monomorphic protein in non-hemophiliacs. Interestingly, 5 of the 6 distinct wt proteins encoded by the allelic combinations or haplotypes (H) of these nsSNPs, designated H1, H2, ..., H5, are expressed by AA’s compared to only 2 in Caucasians (H1 and H2). Because H3, H4 and H5 are 1) partially defined by AA-restricted minor alleles of R484H and M2238V, 2 nsSNPs that substitute amino acids in the A2 and C2 major B-cell inhibitor epitopes, 2) represent the wt FVIII protein in ~27% of AA’s, and 3) differ from the rFVIII proteins used clinically, we designed the PIR study -- the 1st cross-sectional study of AA hA patients -- to determine if pharmacogenetic factors contribute to their greater inhibitor risk. Because the strongest known risk factor for inhibitors is the F8 mutation type, we are resequencing the known functional regions of F8 in the 1st 50 enrolled PIR subjects, out of the 223 total AA hA patients treated at the six participating Region IV South hemophilia treatment centers, to test the plausible alternative hypothesis that the higher inhibitor incidence is due to a different spectrum of molecular abnormalities than has been found in other ethnic subgroups of patients already examined at the DNA sequence level. We have 1) determined the plasma FVIII-activity and -antigen levels, 2) identified the causative mutation in 18 patients, several of which are novel, and 3) are currently performing RT-PCR analyses for detecting the common inversions in introns 1 and 22. Once completed, we will statistically compare the prevalence of AA F8 mutation subtypes to that in hA patients from other ethnic subgroups (detailed in the HAMSTeRS database), and the proportion of AA FVIII deficiencies that are 1) severe, moderate and mild, and 2) CRM-positive and -negative.

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