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1.
Journal of Experimental Hematology ; (6): 1034-1038, 2021.
Article in Chinese | WPRIM | ID: wpr-888515

ABSTRACT

OBJECTIVE@#To study the effects of FLT3-ITD length on 32D cell proliferation, apoptosis and sensitivity to FLT3 inhibitor, so as to provide references for stepwise therapy of FLT3-ITD mutated acute myeloid leukemia patients.@*METHODS@#Three different FLT3-ITD mutants with same or adjacent insert sites were selected and constructed in an eukaryotic expression vector. FLT3-ITD mutants stably expressed 32D cell strains were selected with the help of lentivirus system and IL3 free cell culture medium. The proliferation and apoptosis of 32D cell strains after AC220 treatment were detected.@*RESULTS@#FLT3-ITD mutants (ITD1, ITD2 and ITD3) stably expressed 32D cell strains were constructed successfully. In the absence of IL3 factor, the proliferation number of ITD1, ITD2 and ITD3 cell strains were mounted up to 2.3 folds, 3.7 folds, and 4.3 folds after 48 hours, respectively. Under the exposure of FLT3 inhibitor AC220, the IC@*CONCLUSION@#FLT3-ITD mutant expressed cell strains with longer ITD show higher capacity of proliferation and higher tolerance to AC220 treatment.


Subject(s)
Apoptosis , Cell Proliferation , Humans , Leukemia, Myeloid, Acute/genetics , Mutation , Protein Kinase Inhibitors , Tandem Repeat Sequences , fms-Like Tyrosine Kinase 3/genetics
3.
Article in Korean | WPRIM | ID: wpr-816605

ABSTRACT

BACKGROUND: Rapid and accurate detection of Mycobacterium tuberculosis (MTB) is of primary importance for infection control and selection of anti-tuberculosis drugs. However, most clinical laboratories report MTB complex (MTC) without reporting MTB because MTC comprising MTB, Mycobacterium bovis, Mycobacterium africanum, Mycobacterium microti, Mycobacterium caprae and Mycobacterium pinnipedii have 99.9% similarity at the nucleotide level and identical 16S rRNA sequences. This study was conducted to analyze the species frequency of MTC isolates obtained from clinical specimen.METHODS: Of 310 MTC isolates obtained from clinical samples in a tertiary care hospital from February 2017 to August 2018, MolecuTech Real TB-Taq (YD Diagnostics, Korea) real-time PCR was performed, specifically to detect MTB. For DNA showing MTB negative results by MTB-specific real-time PCR or pyrazinamide-resistant strains, PCR-based MTC typing, spoligotyping, and exact tandem repeat D gene sequencing were performed.RESULTS: All the 310 MTC isolates were identified to be MTB. Two MTB strains of East-African-Indian 4-Vietnam genotype, which have not been reported in Korea, were also found.CONCLUSION: There was no zoonotic tuberculosis in this study. Since we investigated only 310 MTC isolates detected in only one medical institution, multi-center study is needed to accurately know the prevalence of zoonotic tuberculosis in Korea.


Subject(s)
DNA , Genotype , Goats , Infection Control , Korea , Mycobacterium bovis , Mycobacterium tuberculosis , Mycobacterium , Prevalence , Real-Time Polymerase Chain Reaction , Sequence Analysis , Tandem Repeat Sequences , Tertiary Healthcare , Tuberculosis
4.
Gac. méd. Méx ; 155(5): 463-470, Sep.-Oct. 2019. tab, graf
Article in English | LILACS | ID: biblio-1286544

ABSTRACT

The first draft of the human genome sequencing published in 2001 reported a large number of single nucleotide polymorphisms (SNPs). Given that these polymorphisms could practically represent all the variability involved in the susceptibility, protection, severity, among other aspects, of various common diseases, as well as in their response to medications, it was thought that they might be “the biomarkers of choice” in personalized genomic medicine. With the new information obtained from the sequencing of a larger number of genomes, we have understood that SNPs are only an important part of the genetic markers involved in these traits. In addition to SNPs, other variants have been identified, such as insertions/deletions (INDELs) and copy number variants (CNVs), which – in addition to classic variable number tandem repeats (VNTRs) and short tandem repeats (STRs) – originate or contribute to the development of diseases. The use of these markers has served to identify regions of the genome involved in Mendelian diseases (one gene-one disease) or genes directly associated with multifactorial diseases. This review has the purpose to describe the role of STRs, VNTRs, SNPs, CNVs and INDELs in linkage and association studies and their role in Mendelian and multifactorial diseases.


Subject(s)
Humans , Genetic Variation/physiology , Disease/genetics , Polymorphism, Single Nucleotide , Genetic Markers , Genome, Human , Mutagenesis, Insertional , Gene Deletion , Tandem Repeat Sequences , Lod Score , Mutation
5.
Article in English | WPRIM | ID: wpr-758883

ABSTRACT

Anthrax, caused by Bacillus anthracis, is a non-contagious infectious disease that affects a wide range of animal species (primarily ruminants) including humans. Due to the often-fatal outcome in humans, quick administration of definitely effective antimicrobials is crucial either as prophylaxis or as a clinical case therapy. In this study, 110 B. anthracis strains, temporally, geographically, and genetically different, isolated during anthrax outbreaks in Italy from 1984 to 2017, were screened using a broth microdilution method to determine their susceptibility to 16 clinically relevant antimicrobial agents. The strains were isolated from various matrices (human, animal, and environmental samples) and were representative of thirty distinct genotypes previously identified by 15-loci multiple-locus variable-number of tandem repeats analysis. The antimicrobials tested were gentamicin, ceftriaxone, streptomycin, penicillin G, clindamycin, chloramphenicol, vancomycin, linezolid, cefotaxime, tetracycline, erythromycin, rifampin, amoxicillin, ciprofloxacin, doxycycline, and trimethoprim. All isolates were susceptible to most of the tested antimicrobials, with the exception of trimethoprim for which all of them showed high minimal inhibitory concentration values. An intermediate level of susceptibility was recorded for ceftriaxone and cefotaxime. Although the Centers for Disease Control and Prevention recommend the use of doxycycline, ciprofloxacin, penicillin G, and amoxicillin for treatment of human cases and for post-exposure prophylaxis to anthrax spores, this study shows a high degree of in vitro susceptibility of B. anthracis to many other antimicrobials, suggesting the possibility of an alternative choice for prophylaxis and therapy.


Subject(s)
Amoxicillin , Animals , Anthrax , Anti-Infective Agents , Bacillus anthracis , Bacillus , Cefotaxime , Ceftriaxone , Chloramphenicol , Ciprofloxacin , Clindamycin , Communicable Diseases , Disease Outbreaks , Doxycycline , Erythromycin , Genotype , Gentamicins , Humans , In Vitro Techniques , Italy , Linezolid , Methods , Microbial Sensitivity Tests , Penicillin G , Post-Exposure Prophylaxis , Rifampin , Spores , Streptomycin , Tandem Repeat Sequences , Tetracycline , Trimethoprim , Vancomycin
6.
Article in English | WPRIM | ID: wpr-715066

ABSTRACT

OBJECTIVES: Chronic otitis media (COM) is followed by irreversible tissue damage and destruction of the middle ear structures, with the possibility of complications under the maintenance of inflammation. Inflammatory mediators such as cytokines play a crucial role in the initial stage of inflammation. The aim of this study was to evaluate the association of the polymorphisms in two innate immunity/inflammation cascade genes from interleukin-1 (IL-1) gene cluster with COM with regard to cholesteatoma. METHODS: In the cross-sectional case-control study, DNA samples were collected from 189 patients with COM and 119 controls from a population of Serbia. The +3953 C/T (rs1143634), TaqI polymorphism in interleukin-1 beta (IL-1β) gene and 86 bp variable number tandem repeat (VNTR, rs2234663) polymorphism in the IL-1 receptor antagonist (IL-1RA) gene were analyzed by polymerase chain reaction. RESULTS: The IL-1β TaqI polymorphism was not significantly different in patients compared with the control group. The significant difference between patients and controls was observed for both, genotype and allele frequencies of IL-1RA VNTR polymorphism (chi-square P < 0.01). We found that carriers of IL-1RA allele 2 (odds ratio, 0.47; 95% confidence interval, 0.29 to 0.76; P=0.004) have a favorable association with COM, using multivariate logistic analysis that included both polymorphisms, age and sex. The IL-1RA allele frequency distribution was significantly different with regard to cholesteatoma. CONCLUSION: The carriers of allele 2 of VNTR IL-1RA polymorphism had a decreased odds ratio for COM, which is in agreement with findings in other inflammatory disease and its previous association with higher IL-1RA levels. Possible down-regulation of IL-1 mediated proinflammatory signaling pathways via IL-1RA in COM as well as results of our study should be further investigated and replicated.


Subject(s)
Alleles , Case-Control Studies , Cholesteatoma , Cytokines , DNA , Down-Regulation , Ear, Middle , Gene Frequency , Genotype , Humans , Inflammation , Interleukin 1 Receptor Antagonist Protein , Interleukin-1 , Interleukin-1beta , Multigene Family , Odds Ratio , Otitis Media , Otitis , Polymerase Chain Reaction , Polymorphism, Genetic , Serbia , Tandem Repeat Sequences
7.
Article in Korean | WPRIM | ID: wpr-725229

ABSTRACT

OBJECTIVES: Psychological resilience is the ability to cope with stress. The genetic background behind psychological resilience is not much known. The serotonin transporter and dopamine transporter are implicated in stress related psychology and emotional processing. The aim of this study is to investigate a possible genetic role of functional polymorphisms of serotonin and dopamine transporters for psychological resilience. METHODS: A total of 951 healthy adult subjects were included. Psychological resilience was measured using Connor-Davidson Resilience Scale (CD-RISC). Genotyping was performed for serotonin transporter gene (SERT) promoter variable number tandem repeat (VNTR) and dopamine transporter gene (DAT1) 3'-untranslated region (UTR) VNTR. Genetic association analysis was conducted between genotypes and the CD-RISC score. RESULTS: No genetic association was observed for SERT promoter VNTR or DAT1 3'-UTR VNTR with CD-RISC score. No genetic interaction between SERT promoter VNTR and DAT1 3'-UTR VNTR with CD-RISC score was detected. CONCLUSIONS: Either serotonin or dopamine transporter did not seem to play a significant role for psychological resilience in this sample.


Subject(s)
Adult , Dopamine Plasma Membrane Transport Proteins , Dopamine , Genetic Background , Genotype , Humans , Psychology , Resilience, Psychological , Serotonin Plasma Membrane Transport Proteins , Serotonin , Tandem Repeat Sequences
8.
Article in English | WPRIM | ID: wpr-758851

ABSTRACT

The aim of this study was to describe the genetic diversity of Mycobacterium avium subsp. paratuberculosis (MAP) obtained from individual cows in Korea. Twelve MAP-positive fecal DNA samples and 19 MAP isolates were obtained from 10 cattle herds located in 5 provinces in Korea. In addition, 5 MAP isolates obtained from the Czech Republic and Slovakia and 3 isolates from Australia were genotyped for comparison with the domestic isolates. The most prevalent strains in Korea were of the “bison-type” genotype (23 of 31 fecal DNA/isolates) and were distributed nationwide. The remaining MAP isolates (8) and all of the foreign isolates were identified as “cattle-type”. The bison-type strains which were discriminated only as INMV 68 in variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR) typing. Multilocus short sequence repeat (MLSSR) typing differentiated the bison-type strains into 3 different subtypes. The cattle-type strains were divided into 3 subtypes by MIRU-VNTR and 8 subtypes by MLSSR. The allelic diversities in the MIRU-VNTR and MLSSR results were calculated as 0.567 and 0.866, respectively. These results suggest that MIRU-VNTR typing cannot provide a sufficient description of the epidemiological situation of MAP. Therefore, an alternative method, such as MLSSR, is needed for typing of MAP strains to elucidate the molecular epidemiology of MAP infections. Overall, this study is the first epidemiological survey report in Korea using both MIRU-VNTR and MLSSR typing methods, and it has provided basic data necessary to elucidate the characteristics of MAP infections in Korea.


Subject(s)
Animals , Australia , Cattle , Czech Republic , DNA , Genetic Variation , Genotype , Korea , Methods , Molecular Epidemiology , Mycobacterium avium , Mycobacterium , Paratuberculosis , Slovakia , Tandem Repeat Sequences
9.
Article in English | WPRIM | ID: wpr-758780

ABSTRACT

Bovine tuberculosis is a chronic contagious disease responsible for major agricultural economic losses. Abattoir monitoring and trace-back systems are an appropriate method to control bovine tuberculosis, particularly in beef cattle. In the present study, a trace-back system was applied to bovine tuberculosis cases in Korean native Hanwoo beef cattle. Bovine tuberculosis was detected in three index beef cattle during abattoir monitoring in Jeonbuk Province, Korea, and the original herds were traced back from each index cow. All cattle in each original herd were subjected to tuberculin skin test. The positive rates in the tuberculin skin test were 64.6% (62 of 96), 4.8% (2 of 42), and 8.1% (3 of 37) at farms A, B, and C, respectively. On post-mortem examination of 56 tuberculin-positive cattle, 62% had granulomatous lesions, and Mycobacterium bovis was cultured from 40 (71.4%) of the cattle. Molecular typing by spoligotyping and the mycobacterial interspersed repetitive unit-variable-number tandem repeat assay revealed the genotype of the M. bovis strains from the index cattle were same as the M. bovis genotype in each original herd. The results suggest that tracing back from index cattle to the original herd is an effective method to control bovine tuberculosis in beef cattle.


Subject(s)
Abattoirs , Agriculture , Animals , Autopsy , Cattle , Disease Outbreaks , Genotype , Korea , Methods , Molecular Typing , Mycobacterium bovis , Red Meat , Skin Tests , Tandem Repeat Sequences , Tuberculin , Tuberculosis, Bovine
10.
Article in Chinese | WPRIM | ID: wpr-690984

ABSTRACT

<p><b>OBJECTIVE</b>To investigate the clinical characteristics of acute myeloid leukemia(AML) patients with FLT3-ITD(Fms-like tyrosine kinase3, intenal tandem duplication) mutation and their response to treatment.</p><p><b>METHODS</b>Retrospective analysis of 128 newly diagnosed AML (except type M3) patients was performed between January 2014 and July 2017. Patients were divided into FLT3-ITD mutated group and non-mutated group. Mutation detection was carried out by using polymerase chain reaction(PCR) and gene sequencing analysis. Standard 3 + 7 or CAG regimen were taken as the first induction chemotherapy, 4 cases received sorafenib, overall survival (OS) was calculated by Kaplan-Meier.</p><p><b>RESULTS</b>Ninety-seven patients can be evaluable for clinical data available; 4 patients were FLT3-TKD mutated, which accounted for 4.1%; 19 patients were FLT3-ITD mutated, which accounted for 19.59%(19/97). Median white blood cell count (WBC), percentage of peripheral blasts and LDH value were significantly higher in FLT3-ITD group than those in non-mutated group [64.65(1.07-587.92)×10/L vs 39.68 (0.45-203.81) ×10/L](P<0.01), [69.62(16-99)% vs 36.35(0-92) %](P<0.01 ) and [LDH 526(124-2 729)U/L vs 265(20-1977)U/L](P<0.05), respectively. The frequency of coexisting NPM1 mutation was higher in FLT3-ITD group than that in non-mutated group [36.8(7/19)% vs 6.8 (5/74) %](P<0.01). The CR+PR was lower in FLT3-ITD group than that in non-mutated group [31.6(6/19)% vs 64.9 (48/74)%](P<0.05). OS in FLT3-ITD group was significantly shorter than that in non-mutated group (5 vs 18 months)(P<0.05). There is no significant difference in OS between FLT3-ITD concomitant with and without NPM1 mutation groups(5 vs 5 months)(P>0.05). The median OS was 13 months for the FLT3-ITD patients taking sorafenib.</p><p><b>CONCLUSION</b>The FLT3-ITD is a common mutation in AML, FLT3-ITD mutated AML is more likely concomitant with NPM1 mutation with higher number of WBC, percentage of peripheral blasts and LDH value, thus CR is low after the 1st treatment and survival is poor.</p>


Subject(s)
Humans , Leukemia, Myeloid, Acute , Mutation , Prognosis , Retrospective Studies , Tandem Repeat Sequences , fms-Like Tyrosine Kinase 3
11.
Biol. Res ; 50: 3, 2017. tab, graf
Article in English | LILACS | ID: biblio-838974

ABSTRACT

Direct tests of the random or non-random distribution of nucleotides on genomes have been devised to test the hypothesis of neutral, nearly-neutral or selective evolution. These tests are based on the direct base distribution and are independent of the functional (coding or non-coding) or structural (repeated or unique sequences) properties of the DNA. The first approach described the longitudinal distribution of bases in tandem repeats under the Bose-Einstein statistics. A huge deviation from randomness was found. A second approach was the study of the base distribution within dinucleotides whose bases were separated by 0, 1, 2... K nucleotides. Again an enormous difference from the random distribution was found with significances out of tables and programs. These test values were periodical and included the 16 dinucleotides. For example a high ¨positive¨ (more observed than expected dinucleotides) value, found in dinucleotides whose bases were separated by (3K + 2) sites, was preceded by two smaller ¨negative¨ (less observed than expected dinucleotides) values, whose bases were separated by (3K) or (3K + 1) sites. We examined mtDNAs, prokaryote genomes and some eukaryote chromosomes and found that the significant non-random interactions and periodicities were present up to 1000 or more sites of base separation and in human chromosome 21 until separations of more than 10 millions sites. Each nucleotide has its own significant value of its distance to neutrality; this yields 16 hierarchical significances. A three dimensional table with the number of sites of separation between the bases and the 16 significances (the third dimension is the dinucleotide, individual or taxon involved) gives directly an evolutionary state of the analyzed genome that can be used to obtain phylogenies. An example is provided.


Subject(s)
Humans , Animals , Phylogeny , Base Sequence/genetics , Genome , Sequence Analysis, DNA/methods , Nucleotides/genetics , Periodicity , Prokaryotic Cells/chemistry , Reference Values , Algorithms , DNA, Mitochondrial/genetics , Chi-Square Distribution , Collagen/genetics , HIV-1/genetics , Evolution, Molecular , Tandem Repeat Sequences , Chromosome Structures , Genetic Drift , Drosophila melanogaster/genetics , Epistasis, Genetic/genetics , Nucleotides/chemistry
12.
Article in English | WPRIM | ID: wpr-115774

ABSTRACT

The aim of this study was to investigate the molecular characteristics and to conduct a comparative genomic analysis of Mycobacterium (M.) bovis strain 1595 isolated from a native Korean cow. Molecular typing showed that M. bovis 1595 has spoligotype SB0140 with mycobacterial interspersed repetitive units-variable number of tandem repeats typing of 4-2-5-3-2-7-5-5-4-3-4-3-4-3, representing the most common type of M. bovis in Korea. The complete genome sequence of strain 1595 was determined by single-molecule real-time technology, which showed a genome of 4351712 bp in size with a 65.64% G + C content and 4358 protein-coding genes. Comparative genomic analysis with the genomes of Mycobacterium tuberculosis complex strains revealed that all genomes are similar in size and G + C content. Phylogenetic analysis revealed all strains were within a 0.1% average nucleotide identity value, and MUMmer analysis illustrated that all genomes showed positive collinearity with strain 1595. A sequence comparison based on BLASTP analysis showed that M. bovis AF2122/97 was the strain with the greatest number of completely matched proteins to M. bovis 1595. This genome sequence analysis will serve as a valuable reference for improving understanding of the virulence and epidemiologic traits among M. bovis isolates in Korea.


Subject(s)
Animals , Cattle , Genome , Genomics , Korea , Molecular Typing , Mycobacterium bovis , Mycobacterium tuberculosis , Mycobacterium , Sequence Analysis , Tandem Repeat Sequences , Virulence
13.
Chinese Medical Journal ; (24): 665-668, 2017.
Article in English | WPRIM | ID: wpr-266929

ABSTRACT

<p><b>BACKGROUND</b>During the past decades, the incidence of invasive aspergillosis (IA) caused by Aspergillus fumigatus has increased dramatically. The aims of this study were to investigate the susceptibility of clinical isolates of A. fumigatus to triazole and the underlying cyp51A mutations in triazole-resistant A. fumigatus.</p><p><b>METHODS</b>A total of 126 A. fumigatus clinical isolates from 126 patients with proven or probable IA were obtained from four large tertiary hospitals in Nanjing, China, between August 2012 and July 2015. The determination of minimal inhibitory concentrations (MICs) for itraconazole, voriconazole, and posaconazole was performed by broth microdilution according to the European Committee on Antimicrobial Susceptibility Testing reference method.</p><p><b>RESULTS</b>A total of 4 A. fumigatus isolates (3.17%) were confirmed to be itraconazole resistant, with MICs of ≥8 mg/L, and one isolate (0.8%) was confirmed to be voriconazole resistant and posaconazole resistant, with MICs of 4 mg/L and 0.5 mg/L, respectively. We found that two of the 4 isolates of triazole-resistant A. fumigatus had the L98H amino acid substitution in combination with a 34-base pair tandem repeat in the promoter region, one isolate had an M220I mutation, and another itraconazole-resistant isolate did not have a substitution in the cyp51A gene.</p><p><b>CONCLUSIONS</b>This study shows that triazole-resistant A. fumigatus clinical isolates are present in Nanjing, China, which is a new challenge to the clinical management of IA.</p>


Subject(s)
Antifungal Agents , Pharmacology , Aspergillus fumigatus , Genetics , China , Drug Resistance, Fungal , Itraconazole , Pharmacology , Microbial Sensitivity Tests , Promoter Regions, Genetic , Genetics , Tandem Repeat Sequences , Genetics , Triazoles , Pharmacology , Voriconazole , Pharmacology
14.
Rev. bras. psiquiatr ; 38(1): 17-23, Jan.-Mar. 2016. tab
Article in English | LILACS | ID: lil-776495

ABSTRACT

Objective: In obsessive-compulsive disorder (OCD), symmetry-related symptoms may be important. Although clinical correlates of symmetry-related symptoms have been identified in OCD, few data exist on genetic associations. Animal studies indicate involvement of dopamine in symmetry-related behavior, suggesting this may be relevant to analogous symptoms in OCD. Alterations in dopamine may also reflect environmental influences. However, the association of symmetry-related symptomatology, early adversity, and polymorphisms in dopaminergic genes has not been investigated in OCD. Methods: Clinical information and polymorphisms in key dopaminergic genes were compared between OCD patients with primary symmetry symptoms and those without. Results: OCD patients with primary symmetry symptoms comprised 46.6% (n=210) of the sample (n=451), and were older (p < 0.01), had longer illness duration (p < 0.01), higher OCD severity scores (p = 0.01), and greater comorbidity (p < 0.01) than those without. In Caucasians (n=343), genotype frequency differed significantly between groups for ANKK1 rs1800497, with more OCD patients with symmetry symptoms being homozygous for the A2 (CC) genotype (χ2 = 7.296; p = 0.026). Conclusion: Symmetry symptoms have some distinct clinical features and may represent a marker of severity in OCD. However, clinical associations, in combination with the association found with the ANKK1 rs1800497 A2 variant, suggest that primary symmetry symptoms may represent a distinctive clinical and psychobiological profile.


Subject(s)
Humans , Male , Female , Adolescent , Adult , Young Adult , Dopamine/genetics , Obsessive-Compulsive Disorder/diagnosis , Obsessive-Compulsive Disorder/genetics , Polymorphism, Genetic/genetics , Stress Disorders, Post-Traumatic/complications , Severity of Illness Index , Protein Serine-Threonine Kinases/genetics , Tandem Repeat Sequences/genetics , Depressive Disorder, Major/complications , Perfectionism , Genotype , Middle Aged , Obsessive-Compulsive Disorder/complications
15.
International Journal of Mycobacteriology. 2016; 5 (1): 74-79
in English | IMEMR | ID: emr-177665

ABSTRACT

In this study, we analyzed Mycobacterium tuberculosis complex [MTC] genetic diversity in Anambra State, Nigeria based on spoligotyping followed by 5-loci exact tandem repeats [ETRs]. Spoligotyping of 180 MTC strains isolated in 2009-2011 from pulmonary tuberculosis [TB] patients led to a total of 31 distinct patterns. A comparison with the SITVIT2 international database showed that all the 31 patterns could be classified as Shared-types [SITs] in this database; briefly, 26/31 SITs [n = 174 isolates] matched a preexisting shared-type in the database, whereas 5/31 SITs [n = 6 isolates] were newly created due to 2 or more strains belonging to an identical new pattern within this study [S1T3396] or after a match with an orphan in the database [S1T3397, S1T3398, S1T3399 and S1T3400]. A total of 18/31 SITs containing 167 or 92.8% isolates were clustered within this study [2-89 isolates per cluster] while 13/31 SITs contained unique strains. Using VNTR typing, a total of 36 distinct patterns were identified; 27 patterns [n = 157 isolates] matched a pattern already reported in the SITVIT2 database. Combination of both the methods generated 47 combined patterns for the 180 strains: 17 belonged to clustered isolates [n = 127 isolates or 70.5%] while 30 corresponded to as many unique strains [note 23 strains could not be typed using 5-loci ETRs]. No correlation was found between the spoligotyping pattern and the HIV status of the patient or drug sensitivity of the strain. This study showed that the LAM10-CAM prototype SIT61 accounted for highest number of isolates [n = 89] in Anambra State, showing its relative contribution to the TB burden in the study


Subject(s)
Humans , Male , Female , Mycobacterium tuberculosis , Genetic Variation , Tandem Repeat Sequences
16.
Article in English | WPRIM | ID: wpr-80080

ABSTRACT

Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, remains one of the most serious global health problems. Molecular typing of M. tuberculosis has been used for various epidemiologic purposes as well as for clinical management. Currently, many techniques are available to type M. tuberculosis. Choosing the most appropriate technique in accordance with the existing laboratory conditions and the specific features of the geographic region is important. Insertion sequence IS6110-based restriction fragment length polymorphism (RFLP) analysis is considered the gold standard for the molecular epidemiologic investigations of tuberculosis. However, other polymerase chain reaction-based methods such as spacer oligonucleotide typing (spoligotyping), which detects 43 spacer sequence-interspersing direct repeats (DRs) in the genomic DR region; mycobacterial interspersed repetitive units–variable number tandem repeats, (MIRU-VNTR), which determines the number and size of tandem repetitive DNA sequences; repetitive-sequence-based PCR (rep-PCR), which provides high-throughput genotypic fingerprinting of multiple Mycobacterium species; and the recently developed genome-based whole genome sequencing methods demonstrate similar discriminatory power and greater convenience. This review focuses on techniques frequently used for the molecular typing of M. tuberculosis and discusses their general aspects and applications.


Subject(s)
Base Sequence , Dermatoglyphics , Genome , Global Health , Methods , Molecular Typing , Mycobacterium tuberculosis , Mycobacterium , Polymerase Chain Reaction , Polymorphism, Restriction Fragment Length , Repetitive Sequences, Nucleic Acid , Tandem Repeat Sequences , Tuberculosis
17.
Article in Chinese | WPRIM | ID: wpr-360081

ABSTRACT

<p><b>UNLABELLED</b>OBJECTICE: To evaluate the application of high-throughput sequencing to sequence the FMS-like Tyrosine Kinase 3 internal tandem duplication (FLT3-ITD) in de novo acute myeloid leukemia (AML) patients with lower allelic ratio FLT3-ITD mutation or more than one ITD, and to analyze the feature of ITD.</p><p><b>METHODS</b>The genomic DNA of 23 AML patients with positive FLT3-ITD was amplified by PCR, capillary electrophoresis was used to detect the ITD mutation. Then, the FLT3 gene was amplified using primer with different barcode, and the product was analyzed by illumina Miseq, and the results were compared with UCSC database.</p><p><b>RESULTS</b>Out of 23 AML patients, 17 had a single ITD, and 3 had 2 ITDs, and the remaining 3 had 3 ITD detected by capillary electrophoresis. The high-throughput sequencing showed that 17 ITD were the complate duplications of wild-type FLT3, and the remaining 16 ITD were partial duplications in the all 33 ITDs. The same length ITD mutation contained 2 different ITD sequences in one patient with more than one ITD, and the other patient with 2 ITD had the same ITD insertion position. The ITD occurred in the regions from p. Y572 to p. L602 of the FLT3 protein, and all the patient ITD covered one or more amino acid between p. V592 and p. E598.</p><p><b>CONCLUSION</b>Illumina Miseq can analyze the sequence of ITDs precisely and accurately. ITD mutation varies widely, but the hotspots are concentrated.</p>


Subject(s)
Alleles , DNA Mutational Analysis , Genotype , High-Throughput Nucleotide Sequencing , Humans , Leukemia, Myeloid, Acute , Genetics , Mutation , Polymerase Chain Reaction , Tandem Repeat Sequences , fms-Like Tyrosine Kinase 3 , Genetics
18.
Infection and Chemotherapy ; : 285-293, 2016.
Article in English | WPRIM | ID: wpr-26690

ABSTRACT

BACKGROUND: Stenotrophomonas maltophilia is one of several opportunistic pathogens of growing significance. Several studies on the molecular epidemiology of S. maltophilia have shown clinical isolates to be genetically diverse. MATERIALS AND METHODS: A total of 121 clinical isolates tentatively identified as S. malophilia from seven tertiary-care hospitals in Korea from 2007 to 2011 were included. Species and groups were identified using partial gyrB gene sequences and antimicrobial susceptibility testing was performed using a broth microdilution method. Multi locus variable number of tandem repeat analysis (MLVA) surveys are used for subtyping. RESULTS: Based on partial gyrB gene sequences, 118 isolates were identified as belonging to the S. maltophilia complex. For all S. maltophilia isolates, the resistance rates to trimethoprime-sulfamethoxazole (TMP/SMX) and levofloxacin were the highest (both, 30.5%). Resistance rate to ceftazidime was 28.0%. 11.0% and 11.9% of 118 S. maltophilia isolates displayed resistance to piperacillin/tazobactam and tigecycline, respectively. Clade 1 and Clade 2 were definitely distinguished from the data of MLVA with amplification of loci. All 118 isolates were classified into several clusters as its identification. CONCLUSION: Because of high resistance rates to TMP/SMX and levofloxacin, the clinical laboratory department should consider providing the data about other antimicrobial agents and treatment of S. maltophilia infections with a combination of antimicrobials can be considered in the current practice. The MLVA evaluated in this study provides a fast, portable, relatively low cost genotyping method that can be employed in genotypic linkage or transmission networks comparing to analysis of the gyrB gene.


Subject(s)
Anti-Infective Agents , Ceftazidime , Korea , Levofloxacin , Methods , Molecular Epidemiology , Stenotrophomonas maltophilia , Stenotrophomonas , Tandem Repeat Sequences
19.
Arq. bras. med. vet. zootec ; 67(5): 1461-1464, mapas
Article in English | LILACS, VETINDEX | ID: biblio-1095985

ABSTRACT

Diversidade genética de Mycoplasma hyopneumoniae tem sido relatada em análise múltipla de repetições em tandem em número variável (MLVA). O objetivo deste estudo foi descrever a distribuição espacial e a heterogeneidade genética de tipos de M. hyopneumoniae no Brasil, bem como investigar a correlação entre regiões de repetição 1 (RR1) e 3 (RR3) de duas adesinas importantes (P97 e P146). Foram identificados 39 tipos de MLVA baseados no número de repetições em tandem em P97 RR1 e RR3 P146. A correlação negativa significativa (Spearman's rho = -0,26; P = 0,022) entre P97 RR1 e RR3 P146 foi observada, o que sugere um possível mecanismo compensatório que permitiria a bactéria manter a sua capacidade de adesão. Os resultados contribuem para compreender a epidemiologia das M. hyopneumoniae no quarto maior país produtor de suínos do mundo.(AU)


Subject(s)
Adhesins, Bacterial , Tandem Repeat Sequences , Mycoplasma hyopneumoniae/genetics , Pneumonia of Swine, Mycoplasmal/genetics , Swine/microbiology
20.
Int. arch. otorhinolaryngol. (Impr.) ; 19(2): 116-120, Apr-Jun/2015. tab
Article in English | LILACS | ID: lil-747152

ABSTRACT

Introduction Thyroid cancer incidence has increased in the previous 2 decades. Preoperative identification of lymph node metastasis is a suggested risk factor associated with recurrence following thyroidectomy. Objectives We aimed to evaluate the accuracy of preoperative radiologic investigations of nodal status in determining the postoperative risk of regional nodal recurrence in cases of well-differentiated thyroid cancer. Methods This is a case series. We retrospectively reviewed data, including preoperative ultrasonography and/or computed tomography results, on patients who underwent total thyroidectomy for thyroid cancer at our hospital between 2006 and 2012. Prognostic factors for predicting recurrence, including age, sex, tumor diameter, and nodal diameter, were evaluated. Results Total thyroidectomy was performed on 24 male and 74 female patients (median age, 43 years). The median follow-up time was 21 months. Sixty-eight patients had papillary thyroid cancer, and 30 had follicular cancer. Nodal recurrence was evident in 30% of patients, and 4% of patients died. Identification of lymph node involvement during preoperative radiologic investigations was strongly prognostic for recurrence: 35.3% of patients with positive preoperative ultrasonography findings and 62.5% of those with positive preoperative computed tomography findings had recurrence (p = 0.01). Conclusions Preoperative identification of lymph node metastasis on radiologic studies was correlated with an increased risk of regional nodal recurrence in well-differentiated thyroid cancer. Computed tomography was superior to ultrasonography in detecting metastatic nodal involvement preoperatively and is therefore recommended for preoperative assessment and postoperative follow-up. .


Subject(s)
Animals , Humans , Hematopoiesis/genetics , Leukemia, Myeloid, Acute/genetics , Zebrafish Proteins/physiology , Zebrafish/physiology , /physiology , Amino Acid Sequence , Animals, Genetically Modified , Conserved Sequence , Embryo, Nonmammalian , Molecular Sequence Data , Protein Structure, Tertiary/genetics , Sequence Homology, Amino Acid , Tandem Repeat Sequences , Transcriptome , Zebrafish Proteins/chemistry , Zebrafish/embryology , /chemistry
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