scholarly journals Characterization of genetic diversity of animal and human Mycobacterium avium strains by IS1245-IS1311 spacer typing

2012 ◽  
Vol 50 (No. 4) ◽  
pp. 175-180 ◽  
Author(s):  
M. Pate ◽  
M. Ocepek ◽  
M. Zolnir-Dovc ◽  
B. Krt
Keyword(s):  
Genetic Diversity ◽  
Mycobacterium Avium ◽  
Pcr Method ◽  
High Degree ◽  
Positive Results ◽  
Degree Of Heterogeneity

A PCR method previously developed for typing Mycobacterium avium was used to characterize the genetic diversity of M. avium strains isolated from swine (n = 90) and humans (n = 24). The strains were identified with IS901 PCR and IS1245 PCR: 38 strains were of IS901+ and IS1245+ genotype (M. avium subsp. avium) and 76 strains were of IS901– and IS1245+ genotype (M. avium subsp. hominissuis). All human isolates were IS901 negative. IS1245-IS1311 spacer typing was successfully accomplished for 59 isolates while 55 isolates gave no amplification signal. The isolates with negative typing results were additionally tested for the presence of IS1311 and all with the exception of one gave positive results. IS1245-IS1311 spacer typing failed in all IS901+ isolates as they yielded no bands. A high degree of heterogeneity among isolates was observed: 59 isolates demonstrated 43 different patterns comprising up to 6 bands.

scholarly journals Characterization of Indian Mustard Germplasm on the Basis of Morphological Traits and SSR Markers

2020 ◽  
pp. 300-311
Author(s):  
Narendra Singh Rajpoot ◽  
M. K. Tripathi ◽  
Sushma Tiwari ◽  
R. S. Tomar ◽  
V. S. Kandalkar
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Morphological Traits ◽  
Indian Mustard ◽  
Morphological Characters ◽  
High Genetic Diversity ◽  
Average Value ◽  
Seed Crops ◽  
High Degree

The genus Brassica is one of the most important oil seed crops in India with high degree of genetic diversity. In present study, genetic diversity was studied in forty germplasm lines and eight cultivars of Indian mustard using morphological traits and SSR markers. Morphological characters were taken for days to 50% flowering, days to maturity, plant height (cm), length of main raceme (cm), number of primary branches/plant, number of secondary branches/plant, number of silique per plant, number of seeds per silique, 1000 seed weight (g) and seed yield per plant (g). Total 50 SSR markers were used for characterization of these lines, out of which 7 SSR markers were highly polymorphic between all the germplasms of mustard. An UPGMA phonogram was constructed for all 48 Germplasms and the similarity coefficient ranged from 0.00 to 0.91. Number of alleles ranged from 3 to 4, genetic diversity ranged from 71% to 65% with average value of 67%, heterozygosity raged from 20 to 10% with average of 12% and PIC value for markers ranged from 0.65 to 0.59 with mean PIC value 0.61. All seven SSR primers showed PIC value above 0.5 (50%) indicating high genetic diversity in the studied plant material.

scholarly journals Characterization of Environmentally Persistent Escherichia coli Isolates Leached from an Irish Soil

2010 ◽  
Vol 76 (7) ◽  
pp. 2175-2180 ◽  
Author(s):  
Fiona P. Brennan ◽  
Florence Abram ◽  
Fabio A. Chinalia ◽  
Karl G. Richards ◽  
Vincent O'Flaherty
Keyword(s):  
Escherichia Coli ◽  
Genetic Diversity ◽  
Soil Conditions ◽  
E Coli ◽  
Metabolic Capability ◽  
Genotypic Analysis ◽  
Pcr Method ◽  
Favorable Conditions ◽  
Environmental Fitness

ABSTRACT Soils are typically considered to be suboptimal environments for enteric organisms, but there is increasing evidence that Escherichia coli populations can become resident in soil under favorable conditions. Previous work reported the growth of autochthonous E. coli in a maritime temperate Luvic Stagnosol soil, and this study aimed to characterize, by molecular and physiological means, the genetic diversity and physiology of environmentally persistent E. coli isolates leached from the soil. Molecular analysis (16S rRNA sequencing, enterobacterial repetitive intergenic consensus PCR, pulsed-field gel electrophoresis, and a multiplex PCR method) established the genetic diversity of the isolates (n = 7), while physiological methods determined the metabolic capability and environmental fitness of the isolates, relative to those of laboratory strains, under the conditions tested. Genotypic analysis indicated that the leached isolates do not form a single genetic grouping but that multiple genotypic groups are capable of surviving and proliferating in this environment. In physiological studies, environmental isolates grew well across a broad range of temperatures and media, in comparison with the growth of laboratory strains. These findings suggest that certain E. coli strains may have the ability to colonize and adapt to soil conditions. The resulting lack of fecal specificity has implications for the use of E. coli as an indicator of fecal pollution in the environment.

scholarly journals Characteristics of own collection of Pseudomonas aeruginosa clinical strains, hosts of bacteriophages

2018 ◽  
pp. 115-127
Author(s):  
Monika Brzychczy-Włoch ◽  
Dorota Ochońska ◽  
Anna Dobrut ◽  
Ewa Olchawa ◽  
Małgorzata Bulanda
Keyword(s):  
Genetic Diversity ◽  
The Other ◽  
Molecular Characteristics ◽  
Phenotypic Characteristics ◽  
Arginine Dihydrolase ◽  
Wide Range ◽  
Biochemical Fingerprinting ◽  
Pcr Method ◽  
Spot Tests ◽  
High Degree

Introduction: The paper presents the phenotypic and molecular characteristics of the collection of 18 P. aeruginosa clinical isolates used as host indicators to study the lytic range of 12 phages against P. aeruginosa. Methods: The phages host ranges were assayed by spot tests. Phenotypic characteristics of strains was investigated by the API 20NE biochemical fingerprinting, oxidase tests, the production of pyocyanin, fluorescein and L-arginine dihydrolase. Resistance profiles were analyzed. The PCR method and sequencing were used to study the distribution the genes of alkaline protease (aprA), exotoxin A (exoA), elastase B (lasB), exotoxins (exoS/T/U/Y), phenazine modyfing genes (phzM, phzS) and to identify selected β-lactamases (blaGES, blaIMP, blaKPC, blaOXA-2, blaOXA-10, blaPER, blaSPM-1, blaSHV, blaTEM, blaVIM). Additionaly, the genetic diversity was investigated by PFGE.116 M. Brzychczy-Włoch i inni Nr 2-4 Results: Twenteen newly isolated P. aeruginosa phages were found to lyse 100% of the analyzed strains. Phages PAR_3 and PAR_10 exhibited the highest lytic activity against isolates, lysing, 77,8% strains tested. The other phages, PAR_9 and PAR_12, presented generally weaker activity against bacteria, lysing respectively, 50% and 44,4% of tested strains. AprA, exoA, phzM, phzS were presented in all strains; lasB in 77,8%. The most frequentlycombination of egzoenzyme genes S+/T+/U-/Y+ in 78% isolates was remarked. In collection, 18 different resistance profiles were observed and 44% isolates were classified as MDR. The blaGES was the most prevalent gene (44%), followed by blaSPM-1 and blaTEM detected in 17% and 11,1% isolates, respectively. BlaOXA-2 was detected in only 5,5% of all isolates. In PFGE method, 18 singletons (A-S) were identified. No relationship between resistance, virulence and PFGE groups was found. Conclusion: In summarize, all phages infect multiple host species and showed a broad lytic spectrum. All bacteria tested were infected by multiple phages and displayed a wide range of susceptibility. In general, we observed a high degree of genetic diversity and individuality of the studied P. aeruginosa collection, bacteriophage hosts.

Morphological and molecular characterization of underutilized medicinal wild ginger (Zingiber barbatum Wall.) from Myanmar

2011 ◽  
Vol 9 (4) ◽  
pp. 531-542 ◽  
Author(s):  
Noladhi Wicaksana ◽  
Syed Abdullah Gilani ◽  
Dawood Ahmad ◽  
Akira Kikuchi ◽  
Kazuo N. Watanabe
Keyword(s):  
Genetic Diversity ◽  
Growth Habit ◽  
Crop Improvement ◽  
Morphological Characters ◽  
Molecular Characteristics ◽  
Medicinal Species ◽  
Primer Sets ◽  
High Degree ◽  
Morphological And Molecular Characterization

Zingiber barbatum Wall. (family Zingiberaceae), is an underutilized medicinal plant and commonly known as ‘Meik tha-lin’ in Myanmar where it is used in the indigenous system of medicine. In the present study, 19 accessions of Z. barbatum from five provinces in Myanmar have been utilized to characterize and assess genetic diversity. Twenty-nine morphological characters were noted, including growth habit, leaf, pseudo-stem and rhizome characters. Fifteen primer sets of P450-based analogue (PBA) markers were used to reveal molecular characteristics. Of the 29 morphological characters, 22 showed a high degree of variation within wild ginger accessions, whereas 20 of these characters contributed significantly to morphological variation. Eleven amplified primer sets gave a total of 175 bands and exhibited 92.15% polymorphism across Z. barbatum accessions. Based on morphological characters and PBA markers, 19 accessions can be divided into two morphotype groups with comparatively higher genetic diversity. This information can be applied in future crop improvement, proper conservation and better use of this underutilized medicinal species.

scholarly journals Avian Bornaviruses in Wild Aquatic Birds of the Anseriformes Order in Poland

Pathogens ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 98
Author(s):  
Edyta Świętoń ◽  
Kamila Dziadek ◽  
Krzysztof Śmietanka
Keyword(s):  
Genetic Diversity ◽  
Aquatic Bird ◽  
Rt Pcr ◽  
Aquatic Birds ◽  
Genetic Characteristics ◽  
Low Genetic Diversity ◽  
Pcr Method ◽  
Single Cluster ◽  
Positive Results ◽  
Wild Waterfowl

Bornaviruses are a diverse family of viruses infecting various hosts, including birds. Aquatic bird bornavirus 1 (ABBV-1) and aquatic bird bornavirus 2 (ABBV-2) have been found in wild waterfowl but data on their prevalence are scarce. To gain knowledge on the occurrence of ABBVs in Poland, samples originating from dead birds of the Anseriformes order collected in 2016–2021 were tested with a real time RT-PCR method targeting the ABBVs genome. A total of 514 birds were examined, including 401 swans, 96 ducks and 17 geese. The presence of ABBV-1 RNA was detected in 52 swans (10.1% of all tested birds) from 40 different locations. No positive results were obtained for ducks and geese. Sequences of about 2300 bases were generated for 18 viruses and phylogenetic analysis was performed. A relatively low genetic diversity of the examined ABBV-1 strains was observed as all were gathered in a single cluster in the phylogenetic tree and the minimum nucleotide identity was 99.14%. The Polish strains were closely related to ABBV-1 identified previously in Denmark and Germany, but a limited number of sequences from Europe hinders the drawing of conclusions about interconnections between Polish and other European ABBVs. The results of the present study provide new insights into the distribution and genetic characteristics of ABBVs in wild birds in Europe.

scholarly journals Development and characterization of EST-SSRs for Muscidae (Diptera) and their cross-genera transferability

2019 ◽  
Vol 28 (3) ◽  
pp. 148-156
Author(s):  
Dan-Dan Wang ◽  
Dong-Xia Yang
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Expressed Sequence Tag ◽  
Species Assemblages ◽  
High Genetic Diversity ◽  
Low Genetic Diversity ◽  
High Degree ◽  
Expressed Sequence ◽  
Simple Sequence

EST-SSR (Expressed Sequence Tag-Simple Sequence Repeat)markers were developed and used to examine genetic diversity of species assemblages of ten genera of Muscidae (Diptera), and specifically the genetic diversity of Phaonia Robineau species, from ten regions in China. 18 EST-SSR markers with high polymorphism and clear bands were screened out from 216 tested markers, with 219 alleles in total (95–280 bp) with an average of 6.1 alleles per locus. In various regions in China such as Tibet, Sichuan, and Yunnan, Muscidae species assemblages exhibited rich genetic diversity, with the polymorphism information content (PIC) values ranging from 0.831 to 0.934, while Hainan region showed a relatively low genetic diversity (PIC = 0.511). Low gene flow (Nm = 0.842) was found among the regions, and the average genetic differentiation coefficient (Fst) was 0.238, indicating a high degree of genetic differentiation among the ten surveyed assemblages. Accordingly, the ten genera of Muscidae exhibited high genetic diversity and genetic differentiation.

scholarly journals Genetic Diversity of O-Antigen Biosynthesis Regions inVibrio cholerae

2011 ◽  
Vol 77 (7) ◽  
pp. 2247-2253 ◽  
Author(s):  
Antonina Aydanian ◽  
Li Tang ◽  
J. Glenn Morris ◽  
Judith A. Johnson ◽  
O. Colin Stine
Keyword(s):  
Genetic Diversity ◽  
Vibrio Cholerae ◽  
Gene Order ◽  
Gene Content ◽  
Polysaccharide Biosynthesis ◽  
O Antigen ◽  
Genetic Pool ◽  
High Degree ◽  
Degree Of Heterogeneity

ABSTRACTO-antigen biosynthetic (wbf) regions forVibrio choleraeserogroups O5, O8, and O108 were isolated and sequenced. Sequences were compared to those of other publishedV. choleraeO-antigen regions. Thesewbfregions showed a high degree of heterogeneity both in gene content and in gene order. Genes identified frequently showed greater similarities to polysaccharide biosynthesis genes from species other thanV. cholerae. Our results demonstrate the plasticity of O-antigen genes inV. cholerae, the diversity of the genetic pool from which they are drawn, and the likelihood that new pandemic serogroups will emerge.

scholarly journals Characterization of genetic diversity of wild pomegranate collected from Himachal Pradesh, India.

2018 ◽  
Vol 7 (2) ◽  
pp. 2042 ◽  
Author(s):  
Ritu Mahajan ◽  
Azhar Javed ◽  
Nisha Kapoor
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Himachal Pradesh ◽  
Genomic Information ◽  
Dissimilarity Index ◽  
High Genetic Diversity ◽  
Breeding Programs ◽  
Genetic Dissimilarity ◽  
High Degree

Wild pomegranate is distributed in three states of India. However, genomic information is rare in this plant. In this paper we studied the genetic diversity of wild pomegranate collected from different places of Himachal Pradesh using RAPD primers. A high degree of polymorphism of 80.7% was observed. Cluster analysis demarcated the accessions into two distinct groups. The genetic dissimilarity index calculated varied from 0.16 to 0.68 for twenty-one wild pomegranate genotypes. The presence of high genetic diversity can be useful for understanding the process of domestication and cultivated pomegranate breeding programs.

Characterization of RF Sputtered ZnO Piezoelectric Films Using Transmission Electron Microscope

1975 ◽  
Vol 33 ◽  
pp. 86-87
Author(s):  
Kemining W. Yeh ◽  
Richard S. Muller ◽  
Wei-Kuo Wu ◽  
Jack Washburn
Keyword(s):  
Integrated Circuit ◽  
Acoustic Waves ◽  
New Technology ◽  
Surface Acoustic Waves ◽  
Electromechanical Properties ◽  
Leading Role ◽  
Saw Devices ◽  
Transmission Electron ◽  
High Degree

Considerable and continuing interest has been shown in the thin film transducer fabrication for surface acoustic waves (SAW) in the past few years. Due to the high degree of miniaturization, compatibility with silicon integrated circuit technology, simplicity and ease of design, this new technology has played an important role in the design of new devices for communications and signal processing. Among the commonly used piezoelectric thin films, ZnO generally yields superior electromechanical properties and is expected to play a leading role in the development of SAW devices.

Diagnosis of helicobacter pylori infection: problems and prospects

2020 ◽  
pp. 54-59
Author(s):  
A. S. Molostova ◽  
N. S. Gladyshev ◽  
A. V. Svarval ◽  
R. S. Ferman ◽  
A. B. Karasyova ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Urease Activity ◽  
Diagnostic Methods ◽  
Study Group ◽  
Biochemical Method ◽  
Antimicrobial Drugs ◽  
Non Invasive ◽  
Number Of Patients ◽  
Pcr Method ◽  
Positive Results

(HP) infection was performed using invasive and non-invasive methods. The study group consisted of 95 patients with dyspepsia. HP infection was detected in 47 patients (49.4 %). The expediency of using a set of diagnostic methods for detecting HP (PCR, immunochromatographic, bacteriological and method for determining urease activity) is proved. Most often (100 %) in patients HP infection was detected in biopsies using the PCR method. Somewhat less frequently it was detected when examining biopsies with an invasive biochemical method (AMA RUT Reader) (82 %) and fecal immunochromatographic method (83 %). Despite the fact that helicobacteriosis was detected bacteriologically in a small number of patients (24 %), this method is of particular value, since it allows you to assess the sensitivity to antimicrobial drugs and probiotics, and does not give false positive results.

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