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Jones, Chris J.; Edwards, K. J.; Castaglione, S.; Winfield, Mark; Sala, F.; Wiel, C.C.M. van de; Bredemeijer, G. M. M.; Vosman, Ben; Matthes, Michaela C.; Daly, Allan; Brettschneider, Reinhold; Bettini, P.; Buiatti, M.; Maestri, Elena; Malcevschi, Alessio; Marmiroli, Nelson; Aert, Rita; Volckaert, Guido; Rueda, Julia; Linacero, Rosario; Vázquez, Ana María; Karp, A.

doi:10.1023/a:1009612517139

Cited by 622 publications

(55 citation statements)

References 25 publications

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“…For these eight genera, encompassing both gram-positive and gram-negative bacteria, it was found after extensive investigation of different primer combinations that a dual restriction digest with EcoRI and MseI followed by MseI plus CT and EcoRI plus 0 as a common primer combination was an excellent approach for generating information-rich FAFLP patterns from all of these bacterial isolates. Moreover, all FAFLP reactions were run in triplicate over a period of 4 months, and the same FAFLP profiles for each set of replicates were observed; this highlights the excellent reproducibility of FAFLP, a phenomenon observed by other workers, who showed the robustness of AFLP between different laboratories (18).…”

Section: Resultssupporting

confidence: 63%

Fluorescent Amplified Fragment Length Polymorphism Probabilistic Database for Identification of Bacterial Isolates from Urinary Tract Infections

2002

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The ability of the fluorescent amplified fragment length polymorphism (FAFLP) technique to identify bacterial isolates from urinary tract infections (UTIs) was investigated. FAFLP was carried out using the single primer combination MseI plus CT and EcoRI plus 0, and information-rich FAFLP profiles were generated from all 69 UTI isolates studied, which comprised both gram-negative and gram-positive bacteria encompassing eight genera. The genetic relatedness of these 69 bacteria was determined by cluster analysis, and this revealed eight main groups corresponding to the eight bacterial genera. Finer discrimination on the same dendrogram showed species and subspecies differentiations, thus demonstrating the potential of FAFLP for describing a wide diversity range within microbial populations. The interpretation of FAFLP profiles is often complicated because it relies upon the investigator interpreting dendrograms; this process may be subjective if the tree is complicated, particularly if it includes polytomies (unresolved nodes). Therefore, we have developed a method based on Bayes' theorem for the identification of bacteria against an FAFLP probabilistic identification matrix. Thus, FAFLP is suitable for the objective identification of causal agents of UTI, and the procedure offers great potential in the clinical laboratory.Urinary tract infections (UTIs) are of significant clinical concern worldwide. For example, the annual incidence in England and Wales is about 2.5 million, with the family doctor consultation rate for women with UTI being 63.5 consultations/1,000 women/year (37). The fact that UTIs mainly afflict women is mirrored in the United States, where 11.3 million women had at least one presumed UTI treated with antibiotics in 1995 (10). Nosocomial UTI is also common (3), as is incidence in the elderly and children, with 2% of boys and 8% of girls showing clinical symptoms by the age of 7 (6). The bacteria typically associated with UTI are members of the family Enterobacteriaceae, predominantly Escherichia coli (the causative organism of Ͼ50% of all cases) and Klebsiella spp., while gram-positive bacteria, in particular enterococci, are also a significant problem (29).Despite such clinical importance, there are considerable variations in the approaches of laboratories and physicians towards UTIs. Routine diagnosis includes a quantitative microbial count of urine. Counts of Ͼ10 5 organisms/ml are regarded as showing significant bacteriuria (25). Diagnosis is followed by characterization of the causal agent and sometimes antibiotic sensitivity tests to determine appropriate courses of treatment, because the empirical choice of an effective treatment is becoming more difficult as urinary pathogens become increasingly resistant to commonly used antibiotics (15).Further identification of the isolates may not be undertaken except in complex and acute cases (27), because conventional methods are expensive, time-consuming, and labor-intensive (11). However, recurrent infections are common, particularly in childr...

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Section: Resultssupporting

confidence: 63%

Fluorescent Amplified Fragment Length Polymorphism Probabilistic Database for Identification of Bacterial Isolates from Urinary Tract Infections

2002

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“…RAPD markers have been a commonly used method for hybrid identification; however, they are difficult to reproduce, and are sensitive to minor changes in reaction conditions (JONES et al, 1997;MC GREGOR et al, 2000). The reliability of fragments screening was improved by developing candidate RAPD fragments into SCAR markers.…”

Section: Discussionmentioning

confidence: 99%

Diagnosis of interspecific hybrids between Acacia mangium and A. auriculiformis using single nucleotide polymorphism (SNP) markers

et al. 2011

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This paper describes a diagnostic system to verify interspecific hybrids between Acacia mangium and A. auriculiformis using single nucleotide polymorphism (SNP) markers. Forty-eight DNA fragments were selected based on random amplified polymorphic DNAs (RAPD) amplified across 48 individuals from each parental species, and were transformed into 44 sequence-characterized amplified region (SCAR) markers. Five SNP markers that generated species-specific alleles for each species were selected from the 28 sequenced SCARs. A multiplex single nucleotide primer extension (SNuPE) analyses of the five SNPs using 40 A. mangium, 40 A. auriculiformis and 16 Acacia hybrids showed high discrimination power. This diagnostic system, with high discriminatory ability, provides a highly reliable and fast method for identifying interspecific hybrids of A. mangium and A. auriculiformis.

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“…Its simplicity and low cost are reasons for its wide application. However, the RAPD technique is highly sensitive to the reaction conditions, hence reproducibility between different laboratories is low [15].…”

Section: Random Amplified Polymorphic Dnas (Rapds)mentioning

confidence: 99%

Molecular Markers for Genetic Diversity Studies in African Leafy Vegetables

Omondi¹,

Debener²,

Linde³

et al. 2016

ABB

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African leafy vegetables are becoming important crops in tackling nutrition and food security in many parts of sub-Saharan Africa, since they provide important micronutrients and vitamins, and help resource-poor farm families bridge lean periods of food shortage. Genetic diversity studies are essential for crop improvement programmes as well as germplasm conservation efforts, and research on genetic diversity of these vegetables using molecular markers has been increasing over time. Diversity studies have evolved from the use of morphological and biochemical markers to molecular markers. Molecular markers provide valuable data, since they detect mostly selectively neutral variations at the DNA level. They are well established and their strengths and limitations have been described. New marker types are being developed from a combination of the strengths of the basic techniques to improve sensitivity, reproducibility, polymorphic information content, speed and cost. This review discusses the principles of some of the established molecular markers and their application to genetic diversity studies of African leafy vegetables with a main focus on the most common Solanum, Amaranthus, Cleome and Vigna species.

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Cited by 622 publications

References 25 publications

Fluorescent Amplified Fragment Length Polymorphism Probabilistic Database for Identification of Bacterial Isolates from Urinary Tract Infections

Fluorescent Amplified Fragment Length Polymorphism Probabilistic Database for Identification of Bacterial Isolates from Urinary Tract Infections

Diagnosis of interspecific hybrids between Acacia mangium and A. auriculiformis using single nucleotide polymorphism (SNP) markers

Molecular Markers for Genetic Diversity Studies in African Leafy Vegetables

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