Differentiation of Vibrio alginolyticus Strains Isolated from Sardinian Waters by Ribotyping and a New Rapid PCR Fingerprinting Method

1999 ◽  
Vol 65 (5) ◽  
pp. 1871-1875 ◽  
Author(s):  
Stefania Zanetti ◽  
Antonella Deriu ◽  
Ilaria Duprè ◽  
Maurizio Sanguinetti ◽  
Giovanni Fadda ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Restriction Enzymes ◽  
Epidemiological Studies ◽  
Vibrio Alginolyticus ◽  
Discriminative Power ◽  
Pcr Fingerprinting ◽  
Rapid Pcr ◽  
Specific Amplification ◽  
Genomic Regions ◽  
Potential Use

ABSTRACT We investigated the usefulness of a novel PCR fingerprinting technique, based on the specific amplification of genomic regions, to differentiate 30 Vibrio alginolyticus strains isolated in Sardinian waters. The different profiles obtained were scanned and analyzed by a computer program in order to determine genetic relationships. The results were then compared with the patterns obtained by ribotyping with HindIII, KpnI, andXbaI restriction enzymes. PCR fingerprinting could differentiate the strains analyzed into 12 different patterns, whereas ribotyping with XbaI, which produced the highest number of patterns, generated only 7 different profiles. This study revealed the superior discriminative power of the proposed technique for the differentiation of related V. alginolyticus strains and the potential use of PCR fingerprinting in epidemiological studies.

Mitochondrial and nuclear DNA variation, genotype fingerprinting and genetic relationships in lentil (Lens culinaris Medik.)

1997 ◽  
Vol 77 (4) ◽  
pp. 515-521 ◽  
Author(s):  
Om P. Rajora ◽  
John D. Mahon
Keyword(s):  
Mitochondrial Dna ◽  
Restriction Fragment ◽  
Lens Culinaris ◽  
Nuclear Dna ◽  
Genetic Relationships ◽  
Restriction Enzymes ◽  
Dna Variation ◽  
Apocytochrome B ◽  
Nuclear Dna Variation ◽  
Mean Similarity

Mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) variations were examined in six cultivars of Lens culinaris ssp. culinaris and two (mtDNA) or one (nuDNA) accession(s) of L. culinaris ssp. orientalis. Total leaf DNA was digested with up to 15 restriction endonucleases, separated by agarose gel electrophoresis and trasferred to nylon membranes. To examine mtDNA variation, blots were probed with mtDNA coding for cytochrome c oxidase I (coxI) and ATPase 6 (atp6) of both wheat and maize as well as apocytochrome b (cob) and Orf25 (orf25) of wheat. Sixteen combinations of mtDNA probes and restriction enzymes revealed 34 fragments that discriminated between at least two lentil accessions. For nuDNA analysis, probes from cDNA and genomic DNA clones of lentil were used to probe the same blots, and identified 46 diagnostic fragments from 19 probe/enzyme combinations. Each lentil accession could be unequivocably distinguished from all others on the basis of both mitochondrial and nuclear DNA fragment patterns. The mitochondrial restriction fragment similarities ranged from 0.944 to 0.989, with a mean of 0.970 but nuclear restriction fragment similarities varied from 0.582 to 0.987, with a mean of 0.743. The apparent genetic relationships among accessions differed according to the source of DNA examined, although the commercial varieties Laird, Brewer and Redchief showed similarly high levels of mean similarity with both nuclear (0.982) and mitochondrial DNA (0.983). Key words: Lens culinaris Medik., genetic variation, mitochondrial, nuclear, DNA, lentil

PCR fingerprinting for epidemiological studies of Staphylococcus aureus

1994 ◽  
Vol 20 (4) ◽  
pp. 235-247 ◽  
Author(s):  
Alex van Belkum ◽  
René Bax ◽  
Piet J.C. van der Straaten ◽  
Wim G.V. Quint ◽  
Etel Veringa
Keyword(s):  
Staphylococcus Aureus ◽  
Epidemiological Studies ◽  
Pcr Fingerprinting

CLASSIFICATION AND IDENTIFICATION OF FUNGAL SEQUENCES USING CHARACTERISTIC RESTRICTION ENDONUCLEASE CUT ORDER

2010 ◽  
Vol 08 (02) ◽  
pp. 181-198 ◽  
Author(s):  
RAJIB SENGUPTA ◽  
DHUNDY R. BASTOLA ◽  
HESHAM H. ALI
Keyword(s):  
Dna Sequences ◽  
Restriction Enzymes ◽  
Epidemiological Studies ◽  
Global Alignment ◽  
Target Sequence ◽  
Alignment Algorithm ◽  
Molecular Fingerprinting ◽  
Data Set ◽  
Alignment Free ◽  
Wet Lab

Restriction Fragment Length Polymorphism (RFLP) is a powerful molecular tool that is extensively used in the molecular fingerprinting and epidemiological studies of microorganisms. In a wet-lab setting, the DNA is cut with one or more restriction enzymes and subjected to gel electrophoresis to obtain signature fragment patterns, which is utilized in the classification and identification of organisms. This wet-lab approach may not be practical when the experimental data set includes a large number of genetic sequences and a wide pool of restriction enzymes to choose from. In this study, we introduce a novel concept of Enzyme Cut Order — a biological property-based characteristic of DNA sequences which can be defined and analyzed computationally without any alignment algorithm. In this alignment-free approach, a similarity matrix is developed based on the pairwise Longest Common Subsequences (LCS) of the Enzyme Cut Orders. The choice of an ideal set of restriction enzymes used for analysis is augmented by using genetic algorithms. The results obtained from this approach using internal transcribed spacer regions of rDNA from fungi as the target sequence show that the phylogenetically-related organisms form a single cluster and successful grouping of phylogenetically close or distant organisms is dependent on the choice of restriction enzymes used in the analysis. Additionally, comparison of trees obtained with this alignment-free and the legacy method revealed highly similar tree topologies. This novel alignment-free method, which utilizes the Enzyme Cut Order and restriction enzyme profile, is a reliable alternative to local or global alignment-based classification and identification of organisms.

Analysis of the molecular mechanisms by flavonoids with potential use for osteoporosis prevention or therapy

2021 ◽  
Vol 28 ◽  
Author(s):  
Valeria Rodríguez ◽  
María Rivoira ◽  
Gabriela Picotto ◽  
Gabriela Díaz de Barboza ◽  
Alejandro Collin ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Osteoporosis Treatment ◽  
Epidemiological Studies ◽  
Common Mechanism ◽  
Osteoporotic Bone ◽  
Osteoporosis Prevention ◽  
Mineral Density ◽  
Pubmed Database ◽  
Molecular Aspects ◽  
Potential Use

Background: Osteoporosis is the most common skeletal disorder worldwide. Flavonoids have the potential to alleviate bone alterations in osteoporotic patients with the advantage of being safer and less expensive than the conventional therapies. Objective: The main objective is to analyze the molecular mechanisms triggered in bone by different subclasses of flavonoids. In addition, this review provides an up-to-date overview on the cellular and molecular aspects of osteoporotic bones versus healthy bones, and a brief description of some epidemiological studies indicating that flavonoids could be useful for osteoporosis treatment. Methods: The PubMed database was searched in the range of years 2001- 2021 using the keywords osteoporosis, flavonoids, and their subclasses such as flavones, flavonols, flavanols, isoflavones, flavanones and anthocyanins, focusing the data on the molecular mechanisms triggered in bone. Results: Although flavonoids comprise many compounds that differ in structure, their effects on bone loss in postmenopausal women or in ovariectomized-induced osteoporotic animals are quite similar. Most of them increase bone mineral density and bone strength, which occur through enhancement of osteoblastogenesis and osteoclast apoptosis, decrease in osteoclastogenesis as well as increase in neovascularization on the site of the osteoporotic fracture. Conclusion: Several molecules of signaling pathways are involved in the effect of flavonoids on osteoporotic bone. Whether all flavonoids have a common mechanism or they act as ligands of estrogen receptors remain to be established. More clinical trials are necessary to know better their safety, efficacy, delivery and bioavailability in humans, as well as comparative studies with conventional therapies.

Haplotype diversity of preharvest sprouting QTLs in wheat

Genome ◽  
2007 ◽  
Vol 50 (2) ◽  
pp. 107-118 ◽  
Author(s):  
Francis C. Ogbonnaya ◽  
Muhammad Imtiaz ◽  
Ron M. DePauw
Keyword(s):  
Genetic Similarity ◽  
Genetic Relationships ◽  
Aegilops Tauschii ◽  
Haplotype Diversity ◽  
Preharvest Sprouting ◽  
Principal Coordinates Analysis ◽  
Factors Affecting ◽  
Type Allele ◽  
Principal Coordinates ◽  
Genomic Regions

Preharvest sprouting (PHS) is one of the most important factors affecting wheat production worldwide in environments characterized by rainfall and high humidity at harvest. In such environments, the incorporation of seed dormancy of a limited duration is required to minimize losses associated with PHS. A global collection of 28 PHS-resistant and -susceptible wheat germplasm was characterized with microsatellite markers flanking the genomic regions associated with PHS-resistance quantitative trait loci (QTLs), particularly on chromosomes 3D and 4A. The genetic diversity analysis revealed 380 alleles at 54 microsatellite loci, with an average of 7.0 alleles per locus, among the 28 wheat genotypes. Gower’s genetic similarity values among all possible pairs of genotypes varied from 0.44 to 0.97, indicating that there is considerable diversity in the PHS germplasm evaluated. Cluster and principal coordinates analysis of genetic similarity estimates differentiated the genotypes into groups, according to their source of PHS resistance. Three major SSR haplotypes were observed on chromosome 4AL, designated RL4137-type allele, Aus1408-type allele, and synthetic-hexaploid-type allele. The RL4137-type allele was prevalent in Canadian cultivars, mostly in cluster 6, followed by the Aus1408-type and its derivatives in clusters 4 and 5. The Syn36 and Syn37 alleles on chromosome 4AL were rare. On chromosome 3DL, the SSRs haplotypes derived from Syn36 and Syn37 were also rare, and proved unique to the Aegilops tauschii - derived synthetic hexaploids. They are therefore likely carrying resistance genes different from those previously reported. Based on genetic relationships, PHS resistance might be improved by selecting parental genotypes from different clusters.

scholarly journals Kohdista: an efficient method to index and query possible Rmap alignments

2019 ◽  
Vol 14 (1) ◽  
Author(s):  
Martin D. Muggli ◽  
Simon J. Puglisi ◽  
Christina Boucher
Keyword(s):  
Single Molecule ◽  
Restriction Enzymes ◽  
Consensus Approach ◽  
E Coli ◽  
Genome Wide ◽  
Alignment Problem ◽  
Optical Map ◽  
Optical Maps ◽  
Map Data ◽  
Genomic Regions

Abstract Background Genome-wide optical maps are ordered high-resolution restriction maps that give the position of occurrence of restriction cut sites corresponding to one or more restriction enzymes. These genome-wide optical maps are assembled using an overlap-layout-consensus approach using raw optical map data, which are referred to as Rmaps. Due to the high error-rate of Rmap data, finding the overlap between Rmaps remains challenging. Results We present Kohdista, which is an index-based algorithm for finding pairwise alignments between single molecule maps (Rmaps). The novelty of our approach is the formulation of the alignment problem as automaton path matching, and the application of modern index-based data structures. In particular, we combine the use of the Generalized Compressed Suffix Array (GCSA) index with the wavelet tree in order to build Kohdista. We validate Kohdista on simulated E. coli data, showing the approach successfully finds alignments between Rmaps simulated from overlapping genomic regions. Conclusion we demonstrate Kohdista is the only method that is capable of finding a significant number of high quality pairwise Rmap alignments for large eukaryote organisms in reasonable time.

Isolating promoters of multigene family members from the polyploid sugarcane genome by PCR-based walking in BAC DNA

Genome ◽  
2010 ◽  
Vol 53 (10) ◽  
pp. 840-847 ◽  
Author(s):  
Mona B. Damaj ◽  
Phillip D. Beremand ◽  
Marco T. Buenrostro-Nava ◽  
John Ivy ◽  
Siva P. Kumpatla ◽  
...  
Keyword(s):  
Multigene Family ◽  
Family Members ◽  
Genome Walking ◽  
Cdna Sequences ◽  
Regulated Expression ◽  
Specific Amplification ◽  
Polyploid Genome ◽  
Polymerase Chain ◽  
Genomic Regions ◽  
Target Promoter

The availability of a wider range of promoters for regulated expression in valuable transgenic crops would benefit functional genomics studies and current biotechnology programs aimed at improved productivity. Polymerase chain reaction (PCR)-based genome walking techniques are commonly used to isolate promoters or 5′ flanking genomic regions adjacent to known cDNA sequences in genomes that are not yet completely sequenced. However, these techniques are problematic when applied directly to DNA isolated from crops with highly complex and large genomes. An adaptor ligation-mediated PCR-based BAC genome walking method is described here for the efficient isolation of promoters of multigene family members, such as the putative defense and fiber biosynthesis DIRIGENT genes that are abundant in the stem of sugarcane, a species with a highly polyploid genome. The advantage of this method is the efficient and specific amplification of the target promoter using BAC genomic DNA as template for the adaptor ligation-mediated PCR walking.

scholarly journals Evidence of Recombination among Enteroviruses

1999 ◽  
Vol 73 (10) ◽  
pp. 8741-8749 ◽  
Author(s):  
Juhana Santti ◽  
Timo Hyypiä ◽  
Leena Kinnunen ◽  
Mika Salminen
Keyword(s):  
Genetic Relationships ◽  
Detailed Comparison ◽  
Evolutionary Divergence ◽  
Coding Region ◽  
Evolutionary Mechanisms ◽  
Bootstrap Analysis ◽  
Protein Coding ◽  
Wide Range ◽  
Genetic Clusters ◽  
Genomic Regions

ABSTRACT Human enteroviruses consist of more than 60 serotypes, reflecting a wide range of evolutionary divergence. They have been genetically classified into four clusters on the basis of sequence homology in the coding region of the single-stranded RNA genome. To explore further the genetic relationships between human enteroviruses and to characterize the evolutionary mechanisms responsible for variation, previously sequenced genomes were subjected to detailed comparison. Bootstrap and genetic similarity analyses were used to systematically scan the alignments of complete genomic sequences. Bootstrap analysis provided evidence from an early recombination event at the junction of the 5′ noncoding and coding regions of the progenitors of the current clusters. Analysis within the genetic clusters indicated that enterovirus prototype strains include intraspecies recombinants. Recombination breakpoints were detected in all genomic regions except the capsid protein coding region. Our results suggest that recombination is a significant and relatively frequent mechanism in the evolution of enterovirus genomes.

scholarly journals Identification and Reproducibility of Plasma Metabolomic Biomarkers of Habitual Food Intake in a US Diet Validation Study

Metabolites ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 382
Author(s):  
Ying Wang ◽  
Rebecca A. Hodge ◽  
Victoria L. Stevens ◽  
Terryl J. Hartman ◽  
Marjorie L. McCullough
Keyword(s):  
Validation Study ◽  
Intraclass Correlation ◽  
Correlation Coefficients ◽  
Ethnically Diverse ◽  
Epidemiological Studies ◽  
Food Groups ◽  
Intraclass Correlation Coefficients ◽  
Bonferroni Adjustment ◽  
Absolute Correlation ◽  
Potential Use

Previous metabolomic studies have identified putative blood biomarkers of dietary intake. These biomarkers need to be replicated in other populations and tested for reproducibility over time for the potential use in future epidemiological studies. We conducted a metabolomics analysis among 671 racially/ethnically diverse men and women included in a diet validation study to examine the correlation between >100 food groups/items (101 by a food frequency questionnaire (FFQ), 105 by 24-h diet recalls (24HRs)) with 1141 metabolites measured in fasting plasma sample replicates, six months apart. Diet–metabolite associations were examined by Pearson’s partial correlation analysis. Biomarker reproducibility was assessed using intraclass correlation coefficients (ICCs). A total of 677 diet–metabolite associations were identified after Bonferroni adjustment for multiple comparisons and restricting absolute correlation coefficients to greater than 0.2 (601 associations using the FFQ and 395 using 24HRs). The median ICCs of the 238 putative biomarkers was 0.56 (interquartile range 0.46–0.68). In this study, with repeated FFQs, 24HRs and plasma metabolic profiles, we identified several potentially novel food biomarkers and replicated others found in our previous study. Our findings contribute to the growing literature on food-based biomarkers and provide important information on biomarker reproducibility which could facilitate their utilization in future nutritional epidemiological studies.

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