Analysis of genetic similarities among species of Fragaria, Potentilla, and Duchesnea found in northwest Argentina by using morphological, anatomical, and molecular characters

2000 ◽  
Vol 78 (4) ◽  
pp. 547-556 ◽  
Author(s):  
Marta Ontivero ◽  
Marta Arias ◽  
Juan Diaz Ricci ◽  
Judith Babot ◽  
Patricia Albornoz ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Molecular Techniques ◽  
Dna Polymorphisms ◽  
Randomly Amplified Polymorphic Dna ◽  
Specific Primers ◽  
Northwest Argentina ◽  
Identification Of Species ◽  
Wild Strawberry ◽  
Anatomical Characters ◽  
Molecular Characters

Morphological, anatomical, and molecular techniques were used to characterize wild strawberry and wild strawberry-like species in northwest Argentina. Characteristics of leaves, flowers, runners, achenes, and genomic DNA polymorphisms were used to analyze similarities among Potentilla tucumanensis Castagnaro & Arias, Duchesnea indica (Andr.) Focke, and Fragaria vesca L. Comparison of phenograms obtained by using morphological and anatomical traits or genomic DNA characters revealed similar clustering of the species. Both phenograms suggest that D. indica is more closely related to P. tucumanensis than to F. vesca. Using the randomly amplified polymorphic DNA (RAPD) technique with specific primers, we detected polymorphic bands that permit the identification of P. tucumanensis, D. indica, and F. vesca. In addition, we report new morphological and anatomical characters that can be used as diagnostic traits for better identification of species in reproductive and vegetative states.Key words: Fragaria, Potentilla, Duchesnea, RAPD, DNA fingerprinting, morphological traits, anatomical traits.

scholarly journals Classic and molecular study of Giardia duodenalis in children from a daycare center in the region of Presidente Prudente, São Paulo, Brazil

2009 ◽  
Vol 51 (1) ◽  
pp. 19-24 ◽  
Author(s):  
Nair Toshiko Tashima ◽  
Maria Jacira Silva Simões ◽  
Clarice Queico Fujimura Leite ◽  
Antonio Fluminhan ◽  
Marco Antonio Nogueira ◽  
...  
Keyword(s):  
Molecular Typing ◽  
Genomic Dna ◽  
Giardia Duodenalis ◽  
Molecular Study ◽  
Epidemiological Studies ◽  
Molecular Techniques ◽  
Parasite Transmission ◽  
Randomly Amplified Polymorphic Dna ◽  
Enterobius Vermicularis ◽  
Daycare Center

Epidemiological studies on giardiasis by using molecular techniques such as RAPD (Randomly Amplified Polymorphic DNA) may give information on factors related to the transmission of Giardia duodenalis. The aim of this work was to assess the epidemiology of G. duodenalis in 101 children attended at a daycare center in Presidente Bernardes, SP, Brazil. After parasitological examinations in feces samples, 15 children presented cysts of G. duodenalis. Their respective parents, brothers and pets, besides the daycare center workers, also had their feces submitted to parasitological analysis. Seven mothers and nine brothers also presented G. duodenalis cysts, while fathers, daycare workers and pets (dogs) did not presented the parasite. Besides the 15 cases with G. duodenalis, other 23 children presented other enteroparasites (Entamoeba coli, Endolimax nana, Enterobius vermicularis, Ascaris lumbricoides and Trichuris trichiura). Samples of G. duodenalis cysts from children and their relatives were submitted to molecular typing by RAPD after genomic DNA extraction and amplification of a fragment of the 18S rDNA region by PCR. After examining 31 isolates of G. duodenalis (children and their respective mothers and brothers), it was concluded that the parasite transmission occurred in children, probably during daily cohabitation at the daycare center, but not at home among their relatives or pets.

scholarly journals Genetic Diversity of Salvia Species Assessed by ISSR and RAPD Markers

2016 ◽  
Vol 44 (2) ◽  
pp. 431-436 ◽  
Author(s):  
Masoumeh YOUSEFIAZARKHANIAN ◽  
Ali ASGHARI ◽  
Jafar AHMADI ◽  
Behvar ASGHARI ◽  
Ali Ashraf JAFARI
Keyword(s):  
Genetic Diversity ◽  
Genetic Polymorphisms ◽  
Genomic Dna ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Genetic Variations ◽  
Molecular Techniques ◽  
Wild Populations ◽  
Similarity Coefficients ◽  
The World

The genus Salvia includes an enormous assemblage of nearly 1,000 species dispersed around the world. Due to possible threats to this genus, there is an immediate requirement to evaluate the diversity of its wild populations. ISSR and RAPD molecular techniques were used to evaluate the genetic relationships among twenty-one ecotypes of eight Salvia species. Amplification of genomic DNA using 23 primers (15 RAPD and eight ISSR) produced 280 bands, of which 91% were polymorphic. The results of marker parameters showed no clear difference between two marker systems. It was generally observed that both ISSR and RAPD markers had similar efficiency in detecting genetic polymorphisms with remarkable ability to differentiate the closely related ecotypes of Salvia. Nei’s similarity coefficients for these techniques ranged from 0.48 to 0.98. Based on the results of clustering, PCoA and AMOVA, the genetic diversity between and within species was confirmed. So, conservation and domestication of the genus Salvia must be due to levels of genetic variations.

scholarly journals Identification and Mapping of a 2,009-bp DNA Deletion inSERPING1of a Hereditary Angioedema Patient

2019 ◽  
Vol 2019 ◽  
pp. 1-7 ◽  
Author(s):  
Wai-Yu Wong ◽  
Helen Wong ◽  
Elaine Au ◽  
Eric Chan
Keyword(s):  
Hereditary Angioedema ◽  
Genomic Dna ◽  
Epigastric Pain ◽  
Molecular Techniques ◽  
Type I ◽  
Base Pairs ◽  
Dna Deletion ◽  
Dna Deletions ◽  
Left And Right ◽  
Dependent Probe

We report a heterozygous, 2,009 base pairs (bps) genomic DNA deletion within theSERPING1gene that has not previously been reported in a case of type I hereditary angioedema (HAE). The patient is a 28-year-old Han Chinese female living in Hong Kong who has suffered from recurrent angioedema since adolescence, with increasing attack frequency as she entered adulthood; in the past, episodes occurred annually, but now occur every two to three months. The affected areas are not itchy and include common sites such as the left and right forearms, but without throat involvement. The patient also experiences epigastric pain. The patient’s mother suffers from similar symptoms. A mutation in the serine protease inhibitor, clade G, member 1 (SERPING1) gene is associated with HAE. Patients with HAE type I commonly carry either a small deletion withinSERPING1or a truncated transcript. We performed a multiplex ligation-dependent probe amplification (MLPA) assay on our indexed patient. Our result suggests a 2,009 bps deletion spanning across exons 5 and 6 withinSERPING1. Although earlier literature has described other large DNA deletions encasing exons 5 and 6 inSERPING1, these DNA rearrangements were larger in size between 4 and 6 kbps, and the breakpoint locations were generally not determined due to technical constraints (Pappalardo et al., 2000; Duponchel et al., 2001; Roche et al., 2005; Loules et al., 2018; and Göβwein et al., 2008). Our report describes mapping of this 2,009 bps inSERPING1. Using a combination of molecular techniques, we were able to confirm and locate this large heterozygous genomic DNA deletion that includes both exons 5 and 6 ofSERPING1.

DNA-DNA Hybridization, Phylogenetic Reconstruction and the Fossil Record

1988 ◽  
Vol 1 ◽  
pp. 75-88 ◽  
Author(s):  
Charles R. Marshall
Keyword(s):  
Dna Hybridization ◽  
Nuclear Dna ◽  
Phylogenetic Reconstruction ◽  
Cost Effective ◽  
Single Copy ◽  
Molecular Techniques ◽  
Phylogenetic Information ◽  
Molecular Approaches ◽  
Molecular Characters ◽  
Rates Of Molecular Evolution

In 1962 Zuckerkandl & Pauling suggested that the amino acid sequence of proteins might evolve in a clock-like fashion and thus may be useful for phylogenetic reconstruction. Since then, many different molecular approaches to phylogenetic reconstruction have been proposed (Wilson et al., 1977). Enthusiasm for the clock hypothesis was dampened by the discovery that rates of molecular evolution for many macromolecules have been highly variable through time (Romero-Herrera et al., 1979). However, the contribution of molecular characters to the study of phylogeny is not necessarily dependent on the notion of a molecular clock and molecular approaches continue to be an important source of phylogenetic information. One of the more powerful and cost-effective molecular techniques for phylogenetic purposes is DNA-DNA hybridization, which measures the single-copy nuclear DNA sequence divergences between species.

scholarly journals Development of Catechol 2,3-Dioxygenase-Specific Primers for Monitoring Bioremediation by Competitive Quantitative PCR

2000 ◽  
Vol 66 (2) ◽  
pp. 678-683 ◽  
Author(s):  
Matthew B. Mesarch ◽  
Cindy H. Nakatsu ◽  
Loring Nies
Keyword(s):  
Quantitative Pcr ◽  
Molecular Techniques ◽  
Complex Environments ◽  
Specific Primers ◽  
Field Evidence ◽  
Gene Copies ◽  
Dioxygenase Gene ◽  
Petroleum Contaminated Soil ◽  
Dioxygenase Enzymes ◽  
Dioxygenase Genes

ABSTRACT Benzene, toluene, xylenes, phenol, naphthalene, and biphenyl are among a group of compounds that have at least one reported pathway for biodegradation involving catechol 2,3-dioxygenase enzymes. Thus, detection of the corresponding catechol 2,3-dioxygenase genes can serve as a basis for identifying and quantifying bacteria that have these catabolic abilities. Primers that can successfully amplify a 238-bp catechol 2,3-dioxygenase gene fragment from eight different bacteria are described. The identities of the amplicons were confirmed by hybridization with a 238-bp catechol 2,3-dioxygenase probe. The detection limit was 102 to 103 gene copies, which was lowered to 100 to 101 gene copies by hybridization. Using the dioxygenase-specific primers, an increase in catechol 2,3-dioxygenase genes was detected in petroleum-amended soils. The dioxygenase genes were enumerated by competitive quantitative PCR with a 163-bp competitor that was amplified using the same primers. Target and competitor sequences had identical amplification kinetics. Potential PCR inhibitors that could coextract with DNA, nonamplifying DNA, soil factors (humics), and soil pollutants (toluene) did not impact enumeration. Therefore, this technique can be used to accurately and reproducibly quantify catechol 2,3-dioxygenase genes in complex environments such as petroleum-contaminated soil. Direct, non-cultivation-based molecular techniques for detecting and enumerating microbial pollutant-biodegrading genes in environmental samples are powerful tools for monitoring bioremediation and developing field evidence in support of natural attenuation.

A comparative hybridization analysis of yeast DNA with Paramecium parafusin- and different phosphoglucomutase-specific probes

2000 ◽  
Vol 78 (6) ◽  
pp. 683-690 ◽  
Author(s):  
Elzbieta Wyroba ◽  
Birgit H Satir
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Nucleotide Sequence ◽  
Genomic Dna ◽  
Pcr Amplification ◽  
Molecular Size ◽  
Molecular Probes ◽  
Hybridization Analysis ◽  
Yeast Genome ◽  
Specific Primers ◽  
Genome Database

Molecular probes designed for the parafusin (PFUS), the Paramecium exocytic-sensitive phospho glyco protein, gave distinct hybridization patterns in Saccharomyces cerevisiae genomic DNA when compared with different phosphoglucomutase specific probes. These include two probes identical to segments of yeast phosphoglucomutase (PGM) genes 1 and 2. Neither of the PGM probes revealed the 7.4 and 5.9 kb fragments in Bgl II-cut yeast DNA digest detected with the 1.6 kb cloned PFUS cDNA and oligonucleotide constructed to the PFUS region (insertion 3 – I-3) not found in other species. PCR amplification with PFUS-specific primers generated yeast DNA-species of the predicted molecular size which hybridized to the I-3 probe. A search of the yeast genome database produced an unassigned nucleotide sequence that showed 55% identity to parafusin gene and 37% identity to PGM2 (the major isoform of yeast phosphoglucomutase) within the amplified region.Key words: parafusin, phosphoglucomutase, yeast, hybridization, PCR.

Association of CYP2B6 c.516G>T Polymorphism with Acute Lymphoblastic Leukemia Susceptibility

2014 ◽  
Vol 926-930 ◽  
pp. 1073-1076
Author(s):  
Zhong Hai Yuan ◽  
Yi Ju Hou ◽  
Chen Zhao ◽  
Yan Li
Keyword(s):  
Acute Lymphoblastic Leukemia ◽  
Genomic Dna ◽  
Lymphoblastic Leukemia ◽  
Control Group ◽  
Study Group ◽  
Regression Analyses ◽  
Specific Primers ◽  
Blood Leukocytes ◽  
Chi Square ◽  
Chi Square Test

Abstract:Objective: To investigate whether any association exists between genetic polymorphism in CYP2B6 c.516G>T and individual susceptibility to acute lymphoblastic leukemia (ALL). Methods: Our study group consisted of 96 ALL patients(T-ALL 17 cases, B-ALL 79 cases) and 348 unrelated healthy newborn volunteers as a control group. Genomic DNA was extracted from peripheral blood and cord blood leukocytes. We genotyped CYP2B6 c.516G>T polymorphism by use of PCR with sequence-specific primers (PCR-SSP). The data were analyzed statistically using chi-square and logistic regression analyses. Results: The frequencies of GG genotype were 74.14%, 57.29%, 29.41% and 63.29%, and GT genotype were 23.85%, 37.50%, 64.71% and 31.65%, and TT genotype were 2.01%, 5.21%, 5.88% and 5.06% in control group, ALL, T-ALL, and B-ALL cases, respectively. Chi-square test showed a significant correlation between the CYP2B6 c.516G>T polymorphism GT genotype and ALL patients (OR=2.035, 95%CI=1.249-3.313, P=0.004); and T-ALL patients (OR=6.839, 95%CI=2.309-20.252, P=0.000); whereas and B-ALL patients (OR=1.554, 95%CI=0.906-2.667, P=0.108). Conclusions: This study revealed the CYP2B6 c.516GT genotype may be a risk factor to the development of ALL, especially T-ALL.

Azotobacter chroococcum does not contain sodA or its gene product Mn-superoxide dismutase

2002 ◽  
Vol 48 (2) ◽  
pp. 183-187 ◽  
Author(s):  
Jane M Caldwell ◽  
Hosni M Hassan
Keyword(s):  
Superoxide Dismutase ◽  
Genomic Dna ◽  
Ammonium Acetate ◽  
Azotobacter Vinelandii ◽  
Polymerase Chain Reaction Analysis ◽  
Azotobacter Chroococcum ◽  
Chain Reaction ◽  
Specific Primers ◽  
Its Gene ◽  
Polymerase Chain

Azotobacter chroococcum and Azotobacter vinelandii grown in Burk medium with 1% mannitol (BM) or in BM supplemented with 2.2 mg/mL ammonium acetate (BM+N) were found to have only iron-containing and CuZn-containing superoxide dismutase. Furthermore, genomic DNA from A. chroococcum and A. vinelandii were subjected to polymerase chain reaction analysis using sodA- and sodB-specific primers and yielded only a sodB product. These results dispute the assertion by Buchanan and Lees (Can. J. Microbiol. 26: 441–447, 1980) that A. chroococcum contains Mn-superoxide dismutase.Key words: FeSOD, Cu-ZnSOD, MnSOD, Azotobacter chroococcum, Azotobacter vinelandii.

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