scholarly journals Molecular Characterization of Phomopsis vexans Isolates of Eggplant of Bangladesh

2013 ◽  
Vol 8 (1-2) ◽  
pp. 131-140 ◽  
Author(s):  
MM Islam ◽  
M Asaduzzaman ◽  
MB Meah
Keyword(s):  
Genomic Dna ◽  
Tandem Repeats ◽  
Variable Number ◽  
Banding Patterns ◽  
Taq Polymerase ◽  
Growing Seasons ◽  
Polymerase Chain ◽  
Phomopsis Vexans ◽  
Template Dna

Forty-four isolates of Phomopsis vexans were collected from eggplant producing areas of Bangladesh during the 2008-2009 growing seasons. The polymerase chain reaction (PCR) -variable number of tandem repeats (VNTR) technique was used to develop molecular markers. The MR-20 primer amplified template DNA for all isolates studied and resulted in distinct bands. The banding patterns of P. vexans isolates were separated into five groups after results with Taq polymerase. The highest genomic DNA concentration 50 ng/?l was found in the isolates of 8, 14, 26, 27 and 38, and the lowest concentration of genomic DNA was found 12.5 ng/?l in the isolates of 1, 2, 5, 15, 17, 22, 30, 31, 33, 34, 36, 40, 41, 42 and 43. Based on the fingerprinting the 44 isolates of Phomopsis vexans were categorized into five different groups. DOI: http://dx.doi.org/10.3329/jsf.v8i1-2.14636 J. Sci. Foundation, 8(1&2): 131-140, June-December 2010

scholarly journals Direct Molecular Characterization of Acid-Fast Bacilli Smear of Nontuberculosis Mycobacterium Species Causing Pulmonary Tuberculosis in Guna Yala Region, Panama

2021 ◽  
Author(s):  
Arístides López ◽  
Fermin Acosta ◽  
Dilcia Sambrano ◽  
Musharaf Tarajia ◽  
Sophia Navajas ◽  
...  
Keyword(s):  
Pulmonary Tuberculosis ◽  
Tandem Repeats ◽  
Nontuberculous Mycobacteria ◽  
Restriction Analysis ◽  
Clinical Signs ◽  
Variable Number ◽  
Remote Areas ◽  
Laboratory Capacity ◽  
Polymerase Chain

Mycobacterium tuberculosis (MTB) stands out as the main causative agent of pulmonary tuberculosis (TB). However, nontuberculous mycobacteria (NTM) species also have the potential to infect and cause TB in susceptible individuals. The objective of this study was to identify NTM species that cause public health problems in remote areas. The study was carried out using 105 sputum smears obtained from patients from the Guna Yala Region of Panama with clinical signs suggestive of TB. DNA was extracted from sputum smears. Nontuberculous mycobacteria and MTB were characterized using polymerase chain reaction restriction analysis (hsp65, rpob) and an evaluation of 24-mycobacterial interspersed repetitive units–variable number of tandem repeats loci. Twenty-six Mycobacterium species were characterized; 19 (18%) were identified as MTB, and 7 (6.7%) were identified as NTM (four M. avium complex, two M. haemophilum, one M. tusciae). These results suggest that at least one in five cases of pulmonary TB among this population is caused by an NTM. Thus, identifying the bacteria causing pulmonary disease is key even in remote regions of the world where standard diagnosis and culture are not available. Strengthening the laboratory capacity within the Guna Yala Region is needed to identify NTM infections promptly.

scholarly journals Sex Determination During Inflorescence Bud Differentiation in Monoecious Pistacia chinensis Bunge

Forests ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 202 ◽  
Author(s):  
Qian Bai ◽  
Chenyi Zhu ◽  
Xia Lei ◽  
Tao Cao ◽  
Shuchai Su ◽  
...  
Keyword(s):  
Sex Determination ◽  
Early Stage ◽  
Sex Differentiation ◽  
Banding Patterns ◽  
Vegetative Period ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Sex Determination Mechanisms

Pistacia chinensis Bunge is widely acknowledged to be dioecious, but rare monoecious individuals have been found. However, the origin of monoecism and the sex differentiation of different sex types remain intriguing questions. Here, sex expressions were explored by identification of sex-associated DNA markers, determination of the sex stability after grafting, and histological characterization of inflorescence bud development using anatomical analysis. The results showed that (1) although polymorphisms among individuals existed, the banding patterns of Polymerase Chain Reaction (PCR) products for different sex types on the same monoecious tree were consistent; (2) the sex expressions of grafted trees were not consistent with those of scions, indicating that monoecism probably did not originate from a stable bud mutation; and (3) both males and females underwent a bisexual period, then the stamen primordia in female buds degenerated into the second round tepals, while the pistil primordia in male buds gradually disappeared. During the sex differentiation phase, female buds were spindle-shaped, while the male buds were full teardrop-shaped, and male buds were bigger than female buds. Taken together, no sex-associated DNA marker was found, sex expressions were unstable after grafting, and the alternative sex organs appeared in the early stage of sex differentiation, suggesting that sex determination occurred during floral development instead of the early vegetative period. These results indicated that the sex expressions may be affected by environmental factors, increasing the understanding of sex determination mechanisms in P. chinensis and other species.

scholarly journals Development of a Variable Number of Tandem Repeats Typing Scheme for the Bacterial Rice Pathogen Xanthomonas oryzae pv. oryzicola

2012 ◽  
Vol 102 (10) ◽  
pp. 948-956 ◽  
Author(s):  
Shuai Zhao ◽  
Lucie Poulin ◽  
Luis M. Rodriguez-R ◽  
Natalia Forero Serna ◽  
Shu-Yan Liu ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Bacterial Pathogen ◽  
Pcr Amplification ◽  
Cost Effective ◽  
Variable Number ◽  
Xanthomonas Oryzae ◽  
Chinese Strain ◽  
Epidemiological Monitoring ◽  
Population Structures ◽  
Polymerase Chain

Xanthomonas oryzae pv. oryzicola is an important bacterial pathogen responsible for outbreaks of bacterial leaf streak (BLS) on rice, mostly occurring in Asia and parts of Africa. To better monitor epidemics and assess population structures, efficient tools that allow the precise identification and diagnosis of pathogenic populations are needed. In this study, we explored variable numbers of tandem repeats (VNTR) as a fast, reliable, and cost-effective molecular typing tool. Screening of three X. oryzae pv. oryzicola genome sequences (Philippine strain BLS256, Chinese strain GX01, and Malian strain MAI10) predicted 28 candidate VNTR loci. Primer pairs for polymerase chain reaction (PCR) amplification of all 28 loci were designed and applied to a panel of 20 X. oryzae pv. oryzicola strains originating from Asia and Africa. Sequencing of PCR amplicons revealed 25 robust and polymorphic VNTR loci that are shared among Asian and African X. oryzae pv. oryzicola strains. A dendrogram constructed from 25 VNTR loci indicated that most Asian strains are clearly discriminated from African strains. However, in agreement with previous reports, one strain from Mali is related to Asian strains, pointing to a possible introduction of Asian strains to the African continent. The new VNTR-based tool described here is useful for studies of population structures and epidemiological monitoring of X. oryzae pv. oryzicola.

Association Between the Aggrecan Gene and Rheumatoid Arthritis

2008 ◽  
Vol 35 (12) ◽  
pp. 2325-2328 ◽  
Author(s):  
THAIS B. de SOUZA ◽  
ELISA F. MENTZ ◽  
CLAITON V. BRENOL ◽  
RICARDO M. XAVIER ◽  
JOÃO C.T. BRENOL ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Blood Donors ◽  
Tandem Repeats ◽  
Dna Amplification ◽  
Variable Number ◽  
Control Group ◽  
Vntr Polymorphism ◽  
Study Population ◽  
Polymerase Chain ◽  
Genetic And Environmental Factors

ObjectiveGenetic and environmental factors seem to be involved in the onset of rheumatoid arthritis (RA). We analyzed whether a variable number of tandem repeats (VNTR) polymorphism in the aggrecan gene was associated to RA.MethodsThe study population comprised 170 European-derived Brazilian patients with diagnosis of RA. The control group comprised 148 European-derived Brazilian healthy blood donors. The aggrecan VNTR polymorphism was genotyped by DNA amplification by polymerase chain reaction, followed by electrophoresis in polyacrylamide gel.ResultsThere was a statistically significant higher frequency of alleles of shorter length in the patient group compared to controls (p = 0.001), suggesting that individuals carrying short alleles are more likely to develop RA. There was no association between short alleles and clinical characteristics of RA.ConclusionOur results provide evidence of an association between the aggrecan gene VNTR polymorphism and RA.

scholarly journals Characterization of the Hyphal Swelling Group of Pythium: DNA Polymorphisms and Cultural and Morphological Characteristics

Plant Disease ◽  
1998 ◽  
Vol 82 (2) ◽  
pp. 218-222 ◽  
Author(s):  
K. Kageyama ◽  
H. Uchino ◽  
M. Hyakumachi
Keyword(s):  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Morphological Characteristics ◽  
Its Region ◽  
Restriction Enzymes ◽  
Dna Polymorphisms ◽  
Banding Patterns ◽  
Length Polymorphisms ◽  
Polymerase Chain

The hyphal swelling (HS) group of Pythium species and P. ultimum were studied for cultural and morphological characteristics, restriction fragment length polymorphisms of the amplified internal transcribed spacer (ITS) region in nuclear rDNA, and random amplified polymorphic DNA (RAPD) analysis of genome DNA. The shape of sporangia was spherical to subspherical or lemoniform and averaged 18.1–23.0 μm. All isolates could grow at 5 to 35°C, and the rate at the optimal temperature, 30°C, was 29–34 mm/24 h. The size of the ITS region amplified by polymerase chain reaction and the banding patterns after digestion with the restriction enzymes showed no variation between the HS group and P. ultimum. No difference in banding patterns was shown between the HS group and P. ultimum by RAPD analysis with each of three primers. Isolates examined were from Japan, and results should be confirmed from other regions.

scholarly journals Identification of a Variable Number of Tandem Repeats Polymorphism and Characterization of LEF-1 Response Elements in the Promoter of the IDO1 Gene

PLoS ONE ◽  
2011 ◽  
Vol 6 (9) ◽  
pp. e25470 ◽  
Author(s):  
Marion Soichot ◽  
Benjamin Hennart ◽  
Alaa Al Saabi ◽  
Audrey Leloire ◽  
Philippe Froguel ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Variable Number ◽  
Response Elements
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