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Osek J, Lachtara B, Wieczorek K. Listeria monocytogenes in foods-From culture identification to whole-genome characteristics. Food Sci Nutr 2022; 10:2825-2854. [PMID: 36171778 PMCID: PMC9469866 DOI: 10.1002/fsn3.2910] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/06/2022] [Accepted: 04/19/2022] [Indexed: 12/03/2022] Open
Abstract
Listeria monocytogenes is an important foodborne pathogen, which is able to persist in the food production environments. The presence of these bacteria in different niches makes them a potential threat for public health. In the present review, the current information on the classical and alternative methods used for isolation and identification of L. monocytogenes in food have been described. Although these techniques are usually simple, standardized, inexpensive, and are routinely used in many food testing laboratories, several alternative molecular-based approaches for the bacteria detection in food and food production environments have been developed. They are characterized by the high sample throughput, a short time of analysis, and cost-effectiveness. However, these methods are important for the routine testing toward the presence and number of L. monocytogenes, but are not suitable for characteristics and typing of the bacterial isolates, which are crucial in the study of listeriosis infections. For these purposes, novel approaches, with a high discriminatory power to genetically distinguish the strains during epidemiological studies, have been developed, e.g., whole-genome sequence-based techniques such as NGS which provide an opportunity to perform comparison between strains of the same species. In the present review, we have shown a short description of the principles of microbiological, alternative, and modern methods of detection of L. monocytogenes in foods and characterization of the isolates for epidemiological purposes. According to our knowledge, similar comprehensive papers on such subject have not been recently published, and we hope that the current review may be interesting for research communities.
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Affiliation(s)
- Jacek Osek
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
| | - Beata Lachtara
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
| | - Kinga Wieczorek
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
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Noviana E, Indrayanto G, Rohman A. Advances in Fingerprint Analysis for Standardization and Quality Control of Herbal Medicines. Front Pharmacol 2022; 13:853023. [PMID: 35721184 PMCID: PMC9201489 DOI: 10.3389/fphar.2022.853023] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/26/2022] [Indexed: 01/01/2023] Open
Abstract
Herbal drugs or herbal medicines (HMs) have a long-standing history as natural remedies for preventing and curing diseases. HMs have garnered greater interest during the past decades due to their broad, synergistic actions on the physiological systems and relatively lower incidence of adverse events, compared to synthetic drugs. However, assuring reproducible quality, efficacy, and safety from herbal drugs remains a challenging task. HMs typically consist of many constituents whose presence and quantity may vary among different sources of materials. Fingerprint analysis has emerged as a very useful technique to assess the quality of herbal drug materials and formulations for establishing standardized herbal products. Rather than using a single or two marker(s), fingerprinting techniques take great consideration of the complexity of herbal drugs by evaluating the whole chemical profile and extracting a common pattern to be set as a criterion for assessing the individual material or formulation. In this review, we described and assessed various fingerprinting techniques reported to date, which are applicable to the standardization and quality control of HMs. We also evaluated the application of multivariate data analysis or chemometrics in assisting the analysis of the complex datasets from the determination of HMs. To ensure that these methods yield reliable results, we reviewed the validation status of the methods and provided perspectives on those. Finally, we concluded by highlighting major accomplishments and presenting a gap analysis between the existing techniques and what is needed to continue moving forward.
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Affiliation(s)
- Eka Noviana
- Departement of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Abdul Rohman
- Departement of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Center of Excellence, Institute for Halal Industry and Systems, Universitas Gadjah Mada, Yogyakarta, Indonesia
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PRIMER OPTIMIZATION AS GENETIC MARKER PRIMER BASED ON CYTOCHROME B GENE ON SUMATRAN ELEPHANT (Elephas maximus sumatranus) NON-INVASIVE SAMPLES. BIOVALENTIA: BIOLOGICAL RESEARCH JOURNAL 2022. [DOI: 10.24233/biov.8.1.2022.216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sumatran elephant is declared as critically endangered by IUCN since 2011. In supporting conservation efforts on sumatran elephant in its natural habitat, molecular data collection of their population needs to be done. Genetic source material is mostly obtained in its natural habitat is its dung/feces. Study on cytochrome B gene as genetic marker from sumatran elephant fecal samples can be done to get additional genetic data as a form of conservation effort. Primer optimization as genetic marker based on cytochrome B gene has been carried out as an early study on sumatran elephant genetics. Primer optimization program based on cytochrome B genetic marker from sumatran elephant fecal samples was under Higher Education Applied Research funded by The Ministry of Research, Technology, and Higher Education. DNA was isolated from fecal samples of captive sumatran elephants in Elephant Training Center, Way Kambas National Park. Primer optimization was done via amplification by increasing certain temperature. Specificity test was done to ensure that the primer only recognized sumatran elephant DNA. The best result was obtained with the annealing temperature of 52oC
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Ortiz-Lemus JF, Campoy S, Martín JF. Biological control of mites by xerophile Eurotium species isolated from the surface of dry cured ham and dry beef cecina. J Appl Microbiol 2020; 130:665-676. [PMID: 32869458 DOI: 10.1111/jam.14839] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/28/2020] [Accepted: 08/20/2020] [Indexed: 11/29/2022]
Abstract
Some meat dry products, including dry cured ham and dry beef cecina, are cured in cellars at moderately cold temperature allowing the growth of a lawn of fungi on their surface. During the curing process, frequently these products became contaminated with fungivore mites of the Acaridae family that feed on fungal mycelium and spores. AIMS The aim of this article is to study the possible biological control of mites by fungi that form part of the normal microbiota of these meat products. METHODS AND RESULTS Some yellow/orange pigmented fungi growing on the ham surface decreased the proliferation of mites; therefore, we isolated from ham and cecina xerophilic yellow/orange coloured fungal strains that were identified as members of the genus Eurotium (recently reclassified as Aspergillus section Aspergillus). Using molecular genetic tools, we have identified 158 strains as Eurotium rubrum (Aspergillus ruber), Eurotium repens (Aspergillus pseudoglaucus) and Eurotium chevalieri (Aspergillus chevalieri). Two strains, E. rubrum C47 and E. rubrum C49, showed strong miticidal activity. The toxic compound(s) are associated with the formation of cleistothecia. In synchronized mite development experiments, we observed that all stages of the mite lifecycle were inhibited by the E. rubrum C47 strain. In addition, we searched for miticidal activity in 13 culture collection Eurotium strains isolated from different habitats, and found that only one, Eurotium cristatum NRRL 4222 (Aspergillus cristatus) has a strong miticidal activity. CONCLUSIONS These fungal strains have proliferated on the surface of ham and cecina for decades, and possibly have acquired miticidal activity as a resistance mechanism against fungivores. SIGNIFICANCE AND IMPACT OF THE STUDY Biological control of infecting mites by favouring growth of E. rubrun C47, in place of the normal mixed population of Aspergillus and Penicillium, is an attractive approach to control mite infestations.
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Affiliation(s)
- J F Ortiz-Lemus
- Área de Microbiología, Departmento de Biología Molecular, Universidad de León, León, Spain.,Instituto de Biotecnología de León, INBIOTEC, León, Spain.,Departamento de Microbiología, Universidad de Pamplona, Pamplona, Colombia
| | - S Campoy
- Área de Microbiología, Departmento de Biología Molecular, Universidad de León, León, Spain.,Instituto de Biotecnología de León, INBIOTEC, León, Spain
| | - J F Martín
- Área de Microbiología, Departmento de Biología Molecular, Universidad de León, León, Spain.,Instituto de Biotecnología de León, INBIOTEC, León, Spain
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Singh RB, Mahenderakar MD, Jugran AK, Singh RK, Srivastava RK. Assessing genetic diversity and population structure of sugarcane cultivars, progenitor species and genera using microsatellite (SSR) markers. Gene 2020; 753:144800. [PMID: 32454179 DOI: 10.1016/j.gene.2020.144800] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/13/2020] [Accepted: 05/19/2020] [Indexed: 01/15/2023]
Abstract
Sugarcane is one among the most important commercial crops used to produce sugar, ethanol, and other byproducts, which significantly contributes in the GDP of India and many other countries around the world. Genetic diversity is a platform for any breeding program of a plant species. Estimation of the genetic variability and population structure play a vital role for conservation planning and management of plant genetic resources. Genetic variability serves as a source of noble alleles responsible for key agronomic and quality traits, which ultimately form basis for identification and selection of promising parents for breeding programs. In the present study genetic diversity and population structure of 139 accessions of the genus Saccharum, allied genera of family Poaceae and cultivars were assessed using informative microsatellite (SSR) markers. A sum of 427 alleles was produced using 61 polymorphic primers and number of alleles generated was ranged from 2 to 13 with an average of 7 alleles per locus. PIC values were ranged from 0.35 to 0.90, with a mean value of 0.66 for all the markers evaluated. Cluster analysis based on UPGMA method revealed three major clusters which were further subdivided into nine subclusters. Population structure analysis also established three subpopulations of used accession set, however there were no correlation of sub-groupings with that of place of origin. AMOVA analysis also confirmed that 83% and 17% of total variations were attributed to the within- and between-populations, correspondingly, demonstrating greater exchange of gene pool across places of origin. The principal component analysis (PCA) demonstrated the distribution of accessions in the scatter-plot was substantially dispersed, revealing rich genetic diversity among accessions of different species. The findings from this study will be useful in breeding programs for introgression of noble alleles into modern cultivars by exploiting natural genetic variation existing in sugarcane genetic resources.
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Affiliation(s)
- Ram Baran Singh
- International Crops Research Institute for the Semi-arid Tropics (ICRISAT), Patancheru-503 324, Hyderabad, Telangana State, India; Uttar Pradesh Council of Sugarcane Research (UPCSR), Shahjahanpur-242 001, Uttar Pradesh, India.
| | - Mahesh D Mahenderakar
- International Crops Research Institute for the Semi-arid Tropics (ICRISAT), Patancheru-503 324, Hyderabad, Telangana State, India
| | - Arun K Jugran
- G.B. Pant National Institute of Himalayan Environment & Sustainable Development, Almora 243 643, Uttarakhand, India
| | - Ram Kushal Singh
- Uttar Pradesh Council of Sugarcane Research (UPCSR), Shahjahanpur-242 001, Uttar Pradesh, India
| | - Rakesh K Srivastava
- International Crops Research Institute for the Semi-arid Tropics (ICRISAT), Patancheru-503 324, Hyderabad, Telangana State, India
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Lozano-Villegas K, Rodríguez-Hernández R, Rondón-Barragán I. Effectiveness of six molecular typing methods as epidemiological tools for the study of Salmonella isolates in two Colombian regions. Vet World 2019; 12:1998-2006. [PMID: 32095053 PMCID: PMC6989315 DOI: 10.14202/vetworld.2019.1998-2006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 11/20/2019] [Indexed: 11/23/2022] Open
Abstract
Aim: The aim of this study was the genotypic characterization of the strains of Salmonella spp. isolated from broiler chickens and humans with gastroenteritis from two regions of Colombia, by BOXA1R-polymerase chain reaction (PCR) and random amplification of polymorphic DNA (RAPD)-PCR methods. Materials and Methods: Forty-nine strains of Salmonella were assessed, 15 from poultry farms in Santander region, and 34 from Tolima region isolated from poultry farms (n=24) and the stool samples of people with gastroenteritis (n=10). BOXA1R primers were selected for repetitive element-based PCR (REP-PCR) and five arbitrary primers, namely, GTG 5, OPB 15, OPP 16, OPS 11, and P 1254 were used for RAPD-PCR to generate DNA fingerprints from the isolates. Fingerprint data from each typing method were under composite analysis and the diversity of the data was analyzed by grouping (clustering). The dendrogram was generated by the unweighted group method with analysis of the arithmetic mean based on the Dice similarity coefficient. In addition, Simpson’s index was evaluated to discriminate the power of the methods. Results: OPP 16 primer and composite analysis proved to be superior compared to other REP-PCR typing methods. The best discriminatory index was observed when GTG 5 (0.92) and OPP 16 (0.85) primers were used alone or combined with RAPD-PCR and BOX-PCR (0.99). Conclusion: This study indicated that OPP 16 and GTG 5 primers provide suitable molecular typing results for the discrimination of the genetic relationship among Salmonella spp. isolates and may be useful for epidemiological studies.
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Affiliation(s)
- Kelly Lozano-Villegas
- Research Group in Immunobiology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué 730006299, Colombia
| | - Roy Rodríguez-Hernández
- Poultry Research Group, Faculty of Veterinary Medicine, University of Tolima, Santa Helena Highs, Ibagué 730006299, Colombia
| | - Iang Rondón-Barragán
- Research Group in Immunobiology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué 730006299, Colombia.,Poultry Research Group, Faculty of Veterinary Medicine, University of Tolima, Santa Helena Highs, Ibagué 730006299, Colombia
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Shekhawat SS, Gaurav A, Joseph B, Kumar H, Kumar N. Random amplified polymorphic DNA-based molecular heterogeneity analysis of Salmonella enterica isolates from foods of animal origin. Vet World 2019; 12:146-154. [PMID: 30936669 PMCID: PMC6431806 DOI: 10.14202/vetworld.2019.146-154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/03/2018] [Indexed: 12/31/2022] Open
Abstract
Aim: This study aims to study the significance of random amplified polymorphic DNA (RAPD) typing in heterogeneity analysis of Salmonella serovars, isolated from foods of animal origin. Materials and Methods: Salmonella serovars isolated and identified from different foods of animal origin such as meat, milk, and egg by standard bacteriological methods. DNA isolated from all 10 isolates which are confirmed by biochemical and serotyping methods and then RAPD was performed using the primers OPB 10, primer 1290, NSC I, NSC II, and primer 3. Then, RAPD data were analyzed using the BioNumerics software, Belgium, Germany. Results: RAPD polymerase chain reaction (PCR) using five primers, namely OPB 10, primer 1290, NSC I, NSC II, and primer 3, classified the 10 isolates into 9, 10, 10, 7, and 10 RAPD-PCR types with discriminating powers of 0.1987, 0.423, 0.50889, 0.1842, and 0.2582, respectively. The phylogram constructed with NSC I profile classified isolates based on geographical origin. Primer 1290, NSC II, and primer 3 produced some uniform bands in all isolates indicating their binding ability in conserved genomic region. This study revealed that RAPD profile can be best used for finding out the heterogeneity at molecular level of Salmonella isolates in combination with other molecular and phenotypic typing techniques. Thus, our results support earlier observation of its significance by different workers on different Salmonella serotypes. Conclusion: Repeatability of RAPD-PCR is insufficient to distinguish genetic differences among Salmonella serovars.
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Affiliation(s)
- Surendra Singh Shekhawat
- Department of Veterinary Public Health and Epidemiology, College of Veterinary and Animal Science, Navania, Vallabhnagar, Udaipur, Rajasthan, India
| | - Abhishek Gaurav
- Department of Veterinary Public Health and Epidemiology, College of Veterinary and Animal Science, Navania, Vallabhnagar, Udaipur, Rajasthan, India
| | - Bincy Joseph
- Department of Veterinary Microbiology, College of Veterinary and Animal Science, Navania, Vallabhnagar, Udaipur, Rajasthan, India
| | - Hitesh Kumar
- Department of Veterinary Public Health and Epidemiology, College of Veterinary and Animal Science, Navania, Vallabhnagar, Udaipur, Rajasthan, India
| | - Nirmal Kumar
- Department of Veterinary Public Health and Epidemiology, College of Veterinary and Animal Science, Navania, Vallabhnagar, Udaipur, Rajasthan, India
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Lee J. Development and Evolution of Molecular Markers and Genetic Maps in Capsicum Species. COMPENDIUM OF PLANT GENOMES 2019. [DOI: 10.1007/978-3-319-97217-6_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Ja'afar JN, Bhore SJ, Phua KK. Non-specificity of sequence characterised amplified region as an alternative molecular epidemiology marker for the identification of Salmonella enterica subspecies enterica serovar Typhi. BMC Res Notes 2018; 11:766. [PMID: 30373642 PMCID: PMC6206845 DOI: 10.1186/s13104-018-3870-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/19/2018] [Indexed: 12/30/2022] Open
Abstract
Objective Identification of Salmonella Typhi by conventional culture techniques is labour-intensive, time consuming, and lack sensitivity and specificity unlike high-throughput epidemiological markers that are highly specific but are not affordable for low-resource settings. SCAR, obtained from RAPD technique, is an affordable, reliable and reproducible method for developing genetic markers. Hence, this study investigated the use of SCAR as an alternative molecular epidemiological marker for easy identification of S. Typhi in low-resource settings. Results One hundred and twenty RAPD primers were screened through RAPD-PCR against a panel of common enterobacteriaceae for the best RAPD band pattern discrimination to develop SCAR primers that were used to develop a RAPD-SCAR PCR. Of this number, 10 were selected based on their calculated indices of discrimination. Four RAPD primers, SBSA02, SBSA03, SBSD08 and SBSD11 produced suitable bands ranging from 900 to 2500 bp. However, only SBSD11 was found to be specific for S. Typhi, and was cloned, sequenced and used to design new SCAR primers. The primers were used to amplify a panel of organisms to evaluate its specificity. However, the amplified regions were similar to other non-Typhi genomes denoting a lack of specificity of the primers as a marker for S. Typhi.
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Affiliation(s)
- Ja'afar Nuhu Ja'afar
- Enteric Diseases Research Cluster, Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, USM, George Town, Penang, Malaysia. .,Department of Biotechnology, School of Life Sciences, Modibbo Adama University of Technology (MAUTECH), Yola, PMB 2076, Adamawa State, Nigeria.
| | - Subhash Janardhan Bhore
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, 08100, Bedong, Kedah, Malaysia
| | - Kia Kien Phua
- Enteric Diseases Research Cluster, Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, USM, George Town, Penang, Malaysia.
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Isolation and Molecular Characterization of Some Marine Aeromonas phages: Protective Effects for Nile Tilapia Infected with Aeromonas hydrophila. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.3.17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Abesha E, Caetano-Anollés G, Høiland K. Population genetics and spatial structure of the fairy ring fungusMarasmius oreadesin a Norwegian sand dune ecosystem. Mycologia 2017; 95:1021-31. [DOI: 10.1080/15572536.2004.11833018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Gustavo Caetano-Anollés
- Division of Molecular Biology, Department of Biology, University of Oslo, P.O. Box 1066, Blindern, 0316 Oslo, Norway
| | - Klaus Høiland
- Division of Botany and Plant Physiology, Department of Biology, University of Oslo, P.O. Box 1066, Blindern, 0316 Oslo, Norway
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12
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Some Mixotrophic Flagellate Species Selectively Graze on Archaea. Appl Environ Microbiol 2016; 83:AEM.02317-16. [PMID: 27815273 DOI: 10.1128/aem.02317-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/31/2016] [Indexed: 11/20/2022] Open
Abstract
Many phototrophic flagellates ingest prokaryotes. This mixotrophic trait becomes a critical aspect of the microbial loop in planktonic food webs because of the typical high abundance of these flagellates. Our knowledge of their selective feeding upon different groups of prokaryotes, particularly under field conditions, is still quite limited. In this study, we investigated the feeding behavior of three species (Rhodomonas sp., Cryptomonas ovata, and Dinobryon cylindricum) via their food vacuole content in field populations of a high mountain lake. We used the catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) protocol with probes specific for the domain Archaea and three groups of Eubacteria: Betaproteobacteria, Actinobacteria, and Cytophaga-Flavobacteria of Bacteroidetes Our results provide field evidence that contrasting selective feeding exists between coexisting mixotrophic flagellates under the same environmental conditions and that some prokaryotic groups may be preferentially impacted by phagotrophic pressure in aquatic microbial food webs. In our study, Archaea were the preferred prey, chiefly in the case of Rhodomonas sp., which rarely fed on any other prokaryotic group. In general, prey selection did not relate to prey size among the grazed groups. However, Actinobacteria, which were clearly avoided, mostly showed a size of <0.5 μm, markedly smaller than cells from the other groups. IMPORTANCE That mixotrophic flagellates are not randomly feeding in the main prokaryotic groups under field conditions is a pioneer finding in species-specific behavior that paves the way for future studies according to this new paradigm. The particular case that Archaea were preferentially affected in the situation studied shows that phagotrophic pressure cannot be disregarded when considering the distribution of this group in freshwater oligotrophic systems.
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Giraldo Marroquín N, Bustamante Rodríguez SL, Pinzón Gutiérrez YA, Buitrago Hurtado G. Caracterización molecular de Colletotrichum gloeosporioides aislado de plantas de ñame de la Costa Atlántica Colombiana utilizando la técnica “DNA Amplification Fingerprinting (DAF)”. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2016. [DOI: 10.15446/rev.colomb.biote.v18n1.57720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
<p>La antracnosis en ñame, causada por el hongo Colletotrichum gloeosporioides, es una enfermedad relevante que posee el potencial de destruir el 100% de la cosecha, convirtiéndose en la principal limitante fitosanitaria para el rendimiento del cultivo en el país. Esta es una situación preocupante considerando que aproximadamente 35.000 familias de pequeños y medianos agricultores de la Costa Atlántica Colombiana subsisten de este cultivo; es por esto que el objetivo de este trabajo fue caracterizar molecularmente 42 aislamientos del hongo procedentes de plantas de ñame con síntomas de la enfermedad, utilizando la técnica molecular “DNA Amplification Fingerprinting (DAF)”, caracterizada por su resolución en la determinación de la variabilidad genética de diferentes organismos. Para la determinación de polimorfismos, se amplificaron 16 marcadores DAF implementando iniciadores tipo decámero, los cuales fueron visualizados por electroforesis en microchip con el equipo MCE-202 MultiNA. Se evaluó la reproducibilidad de la técnica DAF. La amplificación arrojó 391 bandas inequívocamente polimórficas en todas las muestras, el coeficiente de Dice identificó cinco grupos con 0.30% de similaridad y el índice de diversidad genética fue de 0.28; datos que reflejan un alto grado de variabilidad en la colección estudiada de C. gloeosporioides. Ésta puede deberse, al intercambio de germoplasma, a su condición heterotálica, a las mutaciones y al alto potencial de dispersión de las conidias que le permiten mantener la viabilidad bajo condiciones adversas. Por último, se encontró que DAF es una técnica reproducible, confirmando que es una metodología fiable para la caracterización molecular de hongos.</p>
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Nachimuthu VV, Muthurajan R, Duraialaguraja S, Sivakami R, Pandian BA, Ponniah G, Gunasekaran K, Swaminathan M, K K S, Sabariappan R. Analysis of Population Structure and Genetic Diversity in Rice Germplasm Using SSR Markers: An Initiative Towards Association Mapping of Agronomic Traits in Oryza Sativa. RICE (NEW YORK, N.Y.) 2015; 8:30. [PMID: 26407693 PMCID: PMC4583558 DOI: 10.1186/s12284-015-0062-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 08/08/2015] [Indexed: 05/05/2023]
Abstract
BACKGROUND Genetic diversity is the main source of variability in any crop improvement program. It serves as a reservoir for identifying superior alleles controlling key agronomic and quality traits through allele mining/association mapping. Association mapping based on LD (Linkage dis-equilibrium), non-random associations between causative loci and phenotype in natural population is highly useful in dissecting out genetic basis of complex traits. For any successful association mapping program, understanding the population structure and assessing the kinship relatedness is essential before making correlation between superior alleles and traits. The present study was aimed at evaluating the genetic variation and population structure in a collection of 192 rice germplasm lines including local landraces, improved varieties and exotic lines from diverse origin. RESULTS A set of 192 diverse rice germplasm lines were genotyped using 61 genome wide SSR markers to assess the molecular genetic diversity and genetic relatedness. Genotyping of 192 rice lines using 61 SSRs produced a total of 205 alleles with the PIC value of 0.756. Population structure analysis using model based and distance based approaches revealed that the germplasm lines were grouped into two distinct subgroups. AMOVA analysis has explained that 14 % of variation was due to difference between with the remaining 86 % variation may be attributed by difference within groups. CONCLUSIONS Based on these above analysis viz., population structure and genetic relatedness, a core collection of 150 rice germplasm lines were assembled as an association mapping panel for establishing marker trait associations.
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Affiliation(s)
- Vishnu Varthini Nachimuthu
- Plant Molecular Biology, Plant Breeding and Genetics Divison, International Rice Research Institute, Manila, Philippines.
| | - Raveendran Muthurajan
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India.
| | - Sudhakar Duraialaguraja
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India.
| | - Rajeswari Sivakami
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India.
| | | | - Govinthraj Ponniah
- International Crops Research Institute for the Semi-Arid-Tropics, Hyderabad, India.
| | - Karthika Gunasekaran
- Crop Physiology laboratory, International Crops Research Institute for the Semi-Arid-Tropics, Hyderabad, India.
| | - Manonmani Swaminathan
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India.
| | - Suji K K
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India.
| | - Robin Sabariappan
- Centre of Excellence in Molecular Breeding, Tamil Nadu Agricultural University, Coimbatore, India.
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Nwabor OF, Dickson ID, Ajibo QC. Epidemiology of <i>Salmonella</i> and <i>Salmonellosis</i>. INTERNATIONAL LETTERS OF NATURAL SCIENCES 2015. [DOI: 10.56431/p-w7t10s] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The prevalence of enteritis and its accompanying diarrheal and other health challenges linked to infections with Salmonella has continuously plagued sub Saharan Africa. In Nigeria, typhoid fever is among the major widespread diseases affecting both young and old as a result of many interrelated factors such as inadequate sanitaion, indiscriminate use of antibiotics and fecal contamination of water sources. Morbidity associated with illness due to Salmonella continues to increase with untold fatal consequences, often resulting in death. An accurate figure of cases is difficult to arrive at because only large outbreaks are mostly investigated whereas sporadic cases are under-reported. A vast majority of rural dwellers in Africa often resort to self-medication or seek no treatment at all, hence serving as carries of this disease. Non typhoidal cases of salmonellosis account for about 1.3 billion cases with 3 million deaths annually. Given the magnitude of the economic losses incurred by African nations in the battle against salmonella and salmonellosis, this article takes a critical look at the genus Salmonella, its morphology, isolation, physiological and biochemical characteristics, typing methods, methods of detection, virulence factor, epidemiology and methods of spread within the environment.
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16
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Samardjieva KG, Marinova E. Microsatellites—A New Approach of Marker- Assisted Selection. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.1995.10818855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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17
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Kuklin A, Weaver K, Cerny T, Conger B. DNA Amplification Fingerprinting of Embryogenic and Nonembryogenic Clones of Orchardgrass (Dactylis Glomerata L.). BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.1994.10818753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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18
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Böhm M, Löw R, Haag-Kerwer A, Lüttge U, Rausch T. Evaluation of Comparative DNA Amplification Fingerprinting for Rapid Species Identification within the GenusClusia. ACTA ACUST UNITED AC 2014. [DOI: 10.1111/j.1438-8677.1993.tb00773.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Nybom H, Weising K, Rotter B. DNA fingerprinting in botany: past, present, future. INVESTIGATIVE GENETICS 2014; 5:1. [PMID: 24386986 PMCID: PMC3880010 DOI: 10.1186/2041-2223-5-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 12/02/2013] [Indexed: 12/20/2022]
Abstract
Almost three decades ago Alec Jeffreys published his seminal Nature papers on the use of minisatellite probes for DNA fingerprinting of humans (Jeffreys and colleagues Nature 1985, 314:67-73 and Nature 1985, 316:76-79). The new technology was soon adopted for many other organisms including plants, and when Hilde Nybom, Kurt Weising and Alec Jeffreys first met at the very First International Conference on DNA Fingerprinting in Berne, Switzerland, in 1990, everybody was enthusiastic about the novel method that allowed us for the first time to discriminate between humans, animals, plants and fungi on the individual level using DNA markers. A newsletter coined "Fingerprint News" was launched, T-shirts were sold, and the proceedings of the Berne conference filled a first book on "DNA fingerprinting: approaches and applications". Four more conferences were about to follow, one on each continent, and Alec Jeffreys of course was invited to all of them. Since these early days, methodologies have undergone a rapid evolution and diversification. A multitude of techniques have been developed, optimized, and eventually abandoned when novel and more efficient and/or more reliable methods appeared. Despite some overlap between the lifetimes of the different technologies, three phases can be defined that coincide with major technological advances. Whereas the first phase of DNA fingerprinting ("the past") was dominated by restriction fragment analysis in conjunction with Southern blot hybridization, the advent of the PCR in the late 1980s gave way to the development of PCR-based single- or multi-locus profiling techniques in the second phase. Given that many routine applications of plant DNA fingerprinting still rely on PCR-based markers, we here refer to these methods as "DNA fingerprinting in the present", and include numerous examples in the present review. The beginning of the third phase actually dates back to 2005, when several novel, highly parallel DNA sequencing strategies were developed that increased the throughput over current Sanger sequencing technology 1000-fold and more. High-speed DNA sequencing was soon also exploited for DNA fingerprinting in plants, either in terms of facilitated marker development, or directly in the sense of "genotyping-by-sequencing". Whereas these novel approaches are applied at an ever increasing rate also in non-model species, they are still far from routine, and we therefore treat them here as "DNA fingerprinting in the future".
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Affiliation(s)
- Hilde Nybom
- Department of Plant Breeding–Balsgård, Swedish University for Agricultural Sciences, Fjälkestadsvägen 459, Kristianstad 29194, Sweden
| | - Kurt Weising
- Plant Molecular Systematics, Institute of Biology, University of Kassel, Kassel 34109, Germany
| | - Björn Rotter
- GenXPro GmbH, Altenhöferallee 3, Frankfurt 60438, Germany
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Babu KN, Rajesh MK, Samsudeen K, Minoo D, Suraby EJ, Anupama K, Ritto P. Randomly amplified polymorphic DNA (RAPD) and derived techniques. Methods Mol Biol 2014; 1115:191-209. [PMID: 24415476 DOI: 10.1007/978-1-62703-767-9_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Understanding biology and genetics at molecular level has become very important for dissection and manipulation of genome architecture for addressing evolutionary and taxonomic questions. Knowledge of genetic variation and genetic relationship among genotypes is an important consideration for classification, utilization of germplasm resources, and breeding. Molecular markers have contributed significantly in this respect and have been widely used in plant science in a number of ways, including genetic fingerprinting, diagnostics, identification of duplicates and selecting core collections, determination of genetic distances, genome analysis, developing molecular maps, and identification of markers associated with desirable breeding traits. The application of molecular markers largely depends on the type of markers employed, distribution of markers in the genome, type of loci they amplify, level of polymorphism, and reproducibility of products. Among many DNA markers available, random amplified polymorphic DNA (RAPD) is the simplest and cost-effective and can be performed in a moderate laboratory for most of its applications. In addition RAPDs can touch much of the genome and has the advantage that no prior knowledge of the genome under research is necessary. The recent improvements in the RAPD technique like AP-PCR, SCAR, DAF, SRAP, CAPS, RAMPO, and RAHM can complement the shortcomings of RAPDs and have enhanced the utility of this simple technique for specific applications. Simple protocols for these techniques are presented.
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21
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Bisht SC, Mishra PK, Joshi GK. Genetic and functional diversity among root-associated psychrotrophic Pseudomonad's isolated from the Himalayan plants. Arch Microbiol 2013; 195:605-15. [PMID: 23861148 DOI: 10.1007/s00203-013-0908-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 05/09/2013] [Accepted: 06/18/2013] [Indexed: 11/25/2022]
Abstract
Out of 534 psychrotrophic bacteria, 12 bacteria were selected on the basis of plant growth promoting activities at 4 °C and identified as Pseudomonas genus. These strains showed high level of genetic polymorphisms based on RAPD and rep-PCR fingerprinting. This genetic variability revealed that isolates belonging to same species were as high as the variability among different species. Further inoculation of these Pseudomonas strains significantly improves root/shoot biomass and nutrients uptake of lentil plant as compared to non-bacterized control after 40 days of seed showing. Agglomerative hierarchical clustering analysis of pot assay results revealed that genetically diverse strains showing the same prototype in functional parameter and representing diverse blueprint of plant growth promoting attributes. Results of present findings explain the huge beneficial microbial resources from root zone of hilly crops of Himalayan region that could be effectively exploited as bio-inoculums for cold climatic condition.
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Affiliation(s)
- Shekhar Chandra Bisht
- Department of Biotechnology, H.N.B Garhwal University, Srinagar, 246174, Uttarakhand, India.
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22
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Kumar A, Misra P, Dube A. Amplified fragment length polymorphism: an adept technique for genome mapping, genetic differentiation, and intraspecific variation in protozoan parasites. Parasitol Res 2012; 112:457-66. [DOI: 10.1007/s00436-012-3238-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 12/06/2012] [Indexed: 10/27/2022]
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Grimont PA, Grimont F. [Contribution of molecular biology to typing: Methodological over view.]. Med Mal Infect 2012; 26 Suppl 3:379-85. [PMID: 17292305 DOI: 10.1016/s0399-077x(96)80178-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Molecular biology yielded universal typing methods. However, different methods have different applications. Multilocus enzyme electrophoresis allows precise population genetics studies. Random amplification is useful for quickly comparing a few strains. Pulse field gel electrophoresis, which is more discriminating than ribotyping, is indicated for the study of epidemics which do not last more than a few months. Ribotyping, which gives most stable types, is indicated for tracing clones world-wide and for many years. Automatization of key experimental steps and computer-aided interpretation are essential for an objective comparison of many strains. Databases of molecular typing patterns are in completion.
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Affiliation(s)
- P A Grimont
- Unité des Entérobactéries, Unité INSERM 389, Institut Pasteur, 75724 Paris Cedex 15, France
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24
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Gatphoh EM, Sharma SK, Rajkumari K, Rama Rao S. Efficacy of random primer-pair arrays in plant genome analysis: a case study of Cucumis (Cucurbitaceae) for identification of wild and cultivated species. GENETICS AND MOLECULAR RESEARCH 2012; 10:1416-26. [PMID: 21823091 DOI: 10.4238/vol10-3gmr1083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The efficacy of random primer-pair arrays compared to conventional RAPD method with a single decamer primer was evaluated using DNA from two species of Cucumis. The banding patterns of amplicons revealed enhanced utility of primer-pair arrays over conventional RAPDs, producing more bands and a higher degree of polymorphism, both at intra- and inter-specific levels. Amplification produced by both methods clearly distinguished a wild from a cultivated species of the genus Cucumis. The main advantage of the primer-pair RAPD over single-primer-based RAPD is the increase in the number of reactions and amplification products in the form of novel/unique bands with a limited number of primers. It also enables the generation of reliable amplicons with a large number of polymorphic bands, which can be linked to gene-governing traits, allowing sequence-characterized partial genome analysis.
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Affiliation(s)
- E M Gatphoh
- Plant Biotechnology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, India
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25
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Barker GLA, Green JC, Hayes PK, Medlin LK. Preliminary results using the rapd analysis to screen bloom populations ofEmiliania huxleyi(Haptophyta). ACTA ACUST UNITED AC 2012. [DOI: 10.1080/00364827.1994.10413562] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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27
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Sarwat M, Nabi G, Das S, Srivastava PS. Molecular markers in medicinal plant biotechnology: past and present. Crit Rev Biotechnol 2011; 32:74-92. [DOI: 10.3109/07388551.2011.551872] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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28
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Fourie G, Steenkamp ET, Ploetz RC, Gordon TR, Viljoen A. Current status of the taxonomic position of Fusarium oxysporum formae specialis cubense within the Fusarium oxysporum complex. INFECTION GENETICS AND EVOLUTION 2011; 11:533-42. [PMID: 21256980 DOI: 10.1016/j.meegid.2011.01.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 01/12/2011] [Accepted: 01/14/2011] [Indexed: 12/24/2022]
Abstract
Fusarium oxysporum is an asexual fungal species that includes human and animal pathogens and a diverse range of nonpathogens. Pathogenic and nonpathogenic strains of this species can be distinguished from each other with pathogenicity tests, but not with morphological analysis or sexual compatibility studies. Substantial genetic diversity among isolates has led to the realization that F. oxysporum represents a complex of cryptic species. F. oxysporum f. sp cubense (Foc), causal agent of Fusarium wilt of banana, is one of the more than 150 plant pathogenic forms of F. oxysporum. Multi-gene phylogenetic studies of Foc revealed at least eight phylogenetic lineages, a finding that was supported by random amplified polymorphic DNAs, restriction fragment length polymorphisms and amplified fragment length polymorphisms. Most of these lineages consist of isolates in closely related vegetative compatibility groups, some of which possess opposite mating type alleles, MAT-1 and MAT-2; thus, the evolutionary history of this fungus may have included recent sexual reproduction. The ability to cause disease on all or some of the current race differential cultivars has evolved convergently in the taxon, as members of some races appear in different phylogenetic lineages. Therefore, various factors including co-evolution the plant host and horizontal gene transfer are thought to have shaped the evolutionary history of Foc. This review discusses the evolution of Foc as a model formae specialis in F. oxysporum in relation to recent research findings involving DNA-based studies.
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Affiliation(s)
- G Fourie
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.
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29
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Xiong F, Zhong R, Han Z, Jiang J, He L, Zhuang W, Tang R. Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated peanut (Arachis hypogaea L.) genotypes. Mol Biol Rep 2010; 38:3487-94. [DOI: 10.1007/s11033-010-0459-6] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2009] [Accepted: 11/09/2010] [Indexed: 10/18/2022]
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30
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Cassan L, Moreau L, Segouin S, Bellamy A, Falque M, Limami AM. Genetic map construction and quantitative trait loci (QTL) mapping for nitrogen use efficiency and its relationship with productivity and quality of the biennial crop Belgian endive (Cichorium intybus L.). JOURNAL OF PLANT PHYSIOLOGY 2010; 167:1253-63. [PMID: 20619484 DOI: 10.1016/j.jplph.2010.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Revised: 04/15/2010] [Accepted: 04/16/2010] [Indexed: 05/29/2023]
Abstract
A genetic study of the biennial crop Belgian endive (Cichorium intybus) was carried out to examine the effect of nitrogen nutrition during the vegetative phase in the control of the productivity and quality of the chicon (etiolated bud), a crop that grows during the second phase of development (forcing process). A population of 302 recombinant inbred lines (RIL) was obtained from the cross between contrasting lines "NS1" and "NR2". A genetic map was constructed and QTLs of several physiological and agronomical traits were mapped under two levels of nitrogen fertilization during the vegetative phase (N- and N+). The agronomical traits showed high broad sense heritability, whereas the physiological traits were characterized by low broad sense heritability. Nitrogen reserves mobilization during the forcing process was negatively correlated with nitrogen reserves content of the tuberized root and common QTLs were detected for these traits. The chicon productivity and quality were not correlated, but showed one common QTL. This study revealed that chicon productivity and quality were genetically associated with nitrogen reserves mobilization that exerts opposite effects on both traits. Chicon productivity was positively correlated with N reserves mobilization under N- and N+ and a common QTL with the same additive effects was detected for both traits. Chicon quality was negatively correlated with N reserves mobilization under N- and N+ and a common QTL with opposite additive effects was detected for both traits. These results lead to the conclusion that N reserves mobilization is a more effective trait than N reserves content in predicting chicon productivity and quality. Finally, this study revealed agronomical and physiological QTLs utilizable by breeders via marker-assisted selection to aid the optimization of chicon quality under adapted N fertilization.
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Affiliation(s)
- Laurent Cassan
- Station Expérimentale de l'Endive, Association des Producteurs d'Endives de France, 2 Rue des Fleurs, 62000 Arras, France
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31
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Thakur R, Sandhu SS. Species confirmation of fungal isolates by molecular analysis. Indian J Microbiol 2010; 50:280-91. [PMID: 23100842 DOI: 10.1007/s12088-010-0062-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Accepted: 10/15/2008] [Indexed: 10/18/2022] Open
Abstract
Traditional taxonomy of hyphomycetes has been based on conidial morphology and development. In order to confirm species level for the detection and identification of the entomopathogenic fungus, we analysed the species-specific fingerprints to investigate molecular characteristics within isolates of six species and to resolve morphologically atypical isolates. The extent of fingerprint profile observed by RAPD was sufficient to confirm the species level of all the isolates. The genetic similarity among morphologically identified isolates of each species was considerably higher, allowing us to conclude that all the isolates are of same species. These results establish a molecular framework for further taxonomic, phylogenetic and comparative biological investigations.
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Affiliation(s)
- Rupesh Thakur
- Biochemical Research Laboratory, Centre for Scientific Research and Development, People's Group, Bhopal, Madhya Pradesh India
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32
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Kalendar R, Flavell AJ, Ellis THN, Sjakste T, Moisy C, Schulman AH. Analysis of plant diversity with retrotransposon-based molecular markers. Heredity (Edinb) 2010; 106:520-30. [PMID: 20683483 DOI: 10.1038/hdy.2010.93] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Retrotransposons are both major generators of genetic diversity and tools for detecting the genomic changes associated with their activity because they create large and stable insertions in the genome. After the demonstration that retrotransposons are ubiquitous, active and abundant in plant genomes, various marker systems were developed to exploit polymorphisms in retrotransposon insertion patterns. These have found applications ranging from the mapping of genes responsible for particular traits and the management of backcrossing programs to analysis of population structure and diversity of wild species. This review provides an insight into the spectrum of retrotransposon-based marker systems developed for plant species and evaluates the contributions of retrotransposon markers to the analysis of population diversity in plants.
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Affiliation(s)
- R Kalendar
- MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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33
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Neilan BA. Identification and phylogenetic analysis of toxigenic cyanobacteria by multiplex randomly amplified polymorphic DNA PCR. Appl Environ Microbiol 2010; 61:2286-91. [PMID: 16535049 PMCID: PMC1388467 DOI: 10.1128/aem.61.6.2286-2291.1995] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Randomly amplified polymorphic DNA PCR was used to generate unique and identifying DNA profiles for members of the cyanobacterial genera Anabaena and Microcystis, which are responsible for much of the production of nuisance blooms in various freshwater systems, including recreational and drinking water supplies. A method based on the combination of two 10-mer oligonucleotides in a single PCR was developed to provide specific and repeatable DNA fingerprints for cyanobacterial isolates. The strain-specific randomly amplified polymorphic DNA profiles made it possible to discriminate among all toxigenic cyanobacteria studied to the three taxonomic levels of genus, species, and strain. Analysis of DNA typing results obtained by the described method clearly distinguishes between the genera Anabaena and Microcystis. The markers produced for each strain were also applied to a phylogenetic analysis to infer genetic relatedness in this group of prokaryotes.
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Crawford BH, Hussain AKMA, Jideama NM. Evidence of a genomic biomarker in normal human epithelial mammary cell line, MCF-10A, that is absent in the human breast cancer cell line, MCF-7. J Biomed Biotechnol 2010; 2006:43181. [PMID: 16883051 PMCID: PMC1510942 DOI: 10.1155/jbb/2006/43181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
This study investigated the use of DNA amplification
fingerprinting (DAF) to identify biomarkers useful in the
elucidating genetic factors that lead to carcinogenesis. The DNA
amplification fingerprinting (DAF) technique was used to generate
fingerprint profiles of a normal human mammary epithelial cell
line (MCF-10A) and a human breast cancer cell line (MCF-7).
When compared with one another, a polymorphic biomarker gene
(262 base pairs (bps)) was identified in MCF-10A but was not
present in MCF-7. This gene was cloned from the genomic DNA of
the MCF-10A cell line, and subjected to Genbank database
analysis. The analysis of the nucleotide sequence polymorphic
marker (Genbank account: AC079630) shows that this biomarker has
100% homology with the nucleotide sequence of human
chromosome 12 BAC RP11-476D10 (bps 19612-19353). The
nucleotide sequence was used for possible protein translation
product and the result obtained indicated that the gene codes for
hypothetical protein XF2620. In order to evaluate the effects
that the 262 bps biomarker would have on the morphology of
MCF-7 cells, it was transfected into MCF-7 cells. There were
observable changes in the morphology of the transfected cells.
These changes included an increase in cell elongation and a
decrease in cell aggregation.
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Affiliation(s)
- Brian H. Crawford
- Department of Biological Sciences, Clark Atlanta University, 223 James P Brawley Drive, Atlanta, GA 30314, USA
| | - AKM A. Hussain
- Department of Biological Sciences, Clark Atlanta University, 223 James P Brawley Drive, Atlanta, GA 30314, USA
| | - Nathan M. Jideama
- Department of Biological Sciences, Clark Atlanta University, 223 James P Brawley Drive, Atlanta, GA 30314, USA
- *Nathan M. Jideama:
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35
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Genetic Relatedness of Pearl Grey Guinea Fowl and Single Comb White Leghorn Chickens. J Poult Sci 2010. [DOI: 10.2141/jpsa.010010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Smith E, Ray S, Bakst M, Teuscher C, Savage T. Simple sequence repeat‐based single primer amplification of genomic DNA in random bred populations of turkeys and chickens. Anim Biotechnol 2009. [DOI: 10.1080/10495399609525847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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37
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Cushwa W, Medrano J. Applications of the random amplified polymorphic DNA (RAPD) assay for genetic analysis of livestock species. Anim Biotechnol 2009. [DOI: 10.1080/10495399609525845] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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38
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Gardner SN, Hiddessen AL, Williams PL, Hara C, Wagner MC, Colston BW. Multiplex primer prediction software for divergent targets. Nucleic Acids Res 2009; 37:6291-304. [PMID: 19759213 PMCID: PMC2770652 DOI: 10.1093/nar/gkp659] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We describe a Multiplex Primer Prediction (MPP) algorithm to build multiplex compatible primer sets to amplify all members of large, diverse and unalignable sets of target sequences. The MPP algorithm is scalable to larger target sets than other available software, and it does not require a multiple sequence alignment. We applied it to questions in viral detection, and demonstrated that there are no universally conserved priming sequences among viruses and that it could require an unfeasibly large number of primers (∼3700 18-mers or ∼2000 10-mers) to generate amplicons from all sequenced viruses. We then designed primer sets separately for each viral family, and for several diverse species such as foot-and-mouth disease virus (FMDV), hemagglutinin (HA) and neuraminidase (NA) segments of influenza A virus, Norwalk virus, and HIV-1. We empirically demonstrated the application of the software with a multiplex set of 16 short (10 nt) primers designed to amplify the Poxviridae family to produce a specific amplicon from vaccinia virus.
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Affiliation(s)
- Shea N Gardner
- Computations/Global Security, Lawrence Livermore National Laboratory and QuantaLife, Inc, Livermore, CA, USA.
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Kumar D, Chaudhary K, Boora KS. Characterization of native Bacillus thuringiensis strains by PCR-RAPD based fingerprinting. Indian J Microbiol 2009; 50:27-32. [PMID: 23100804 DOI: 10.1007/s12088-009-0011-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2007] [Accepted: 02/21/2008] [Indexed: 10/21/2022] Open
Abstract
Seventy isolates of Bacillus thuringiensis were isolated from soil samples collected from cotton fields. These isolates were characterized by randomly amplified poylmorphic DNA (RAPD) markers to determine their genetic diversity pattern based on their source of origin. Different random decamer primers were used for RAPD amplification, which generated a total of 1935 fragments; of these 1865 were polymorphic and 68 monomorphic. The primers OPA03, OPA08, OPD14, OPD19, OPD20, OPE17 and OPD19 produced 100% polymorphic fragments, whereas primers OPC06, OPC20 and OPD17 produced 20, 31 and 17 monomorphic fragments, respectively. When the RAPD banding pattern data was subjected to dendrogram construction, the 70 isolates fell into two separate clusters, cluster I and cluster II, which includes 26 and 44 B. thuringiensis isolates, respectively. These two main clusters were further divided into four subclusters at Eucledian distance of 150 and 80% similarity index. All primers showed amplification and indicated the good diversity of B. thuringiensis isolates. The RAPD pattern showed 4-10 bands per isolate, with MWt in the range of 0.4-3.5 Kb and an average of 193.5 fragments were produced per primer. The primer OPE17 was found to be the most discriminatory as it produced 286 polymorphic bands.
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Affiliation(s)
- Dharmender Kumar
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology, Murthal, Sonepat, 131 039 Haryana India ; Department of Biotechnology and Molecular Biology, College of Basic Sciences and Humanities, CCS Haryana Agricultural University, Hisar, 125 004 Haryana India
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Palacios CARMEN, Kresovich STEPHEN, González-Candelas FERNANDO. A population genetic study of the endangered plant speciesLimonium dufourii(Plumbaginaceae) based on amplified fragment length polymorphism (AFLP). Mol Ecol 2008. [DOI: 10.1046/j.1365-294x.1999.t01-1-00597.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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41
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Zhou YB, Yang MX, Zhao GM, Wei JG, Jiang QW. Oncomelania hupensis (Gastropoda: Rissooidea), Intermediate Host Of Schistosoma japonicum In China: Genetics and Molecular Phylogeny Based On Amplified Fragment Length Polymorphisms. MALACOLOGIA 2007. [DOI: 10.4002/0076-2997-49.2.367] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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42
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43
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Yip PY, Chau CF, Mak CY, Kwan HS. DNA methods for identification of Chinese medicinal materials. Chin Med 2007; 2:9. [PMID: 17803808 PMCID: PMC2042497 DOI: 10.1186/1749-8546-2-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Accepted: 09/05/2007] [Indexed: 11/10/2022] Open
Abstract
As adulterated and substituted Chinese medicinal materials are common in the market, therapeutic effectiveness of such materials cannot be guaranteed. Identification at species-, strain- and locality-levels, therefore, is required for quality assurance/control of Chinese medicine. This review provides an informative introduction to DNA methods for authentication of Chinese medicinal materials. Technical features and examples of the methods based on sequencing, hybridization and polymerase chain reaction (PCR) are described and their suitability for different identification objectives is discussed.
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Affiliation(s)
- Pui Ying Yip
- Department of Biology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chi Fai Chau
- Department of Food Science and Biotechnology, National Chung Hsing University, 250 Kuokuang Road, Taichung 40227, Taiwan
| | - Chun Yin Mak
- Department of Biology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Hoi Shan Kwan
- Department of Biology, The Chinese University of Hong Kong, Shatin, Hong Kong
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44
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Simon MV, Benko-Iseppon AM, Resende LV, Winter P, Kahl G. Genetic diversity and phylogenetic relationships in Vigna Savi germplasm revealed by DNA amplification fingerprinting. Genome 2007; 50:538-47. [PMID: 17632575 DOI: 10.1139/g07-029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The pantropical genus Vigna (Leguminosae) comprises 7 cultivated species that are adapted to a wide range of extreme agroclimatic conditions. Few data are available on the relationships among these cultivated species or on their importance as sources of resistance against biotic and abiotic stresses. Therefore, we optimized DNA amplification fingerprinting (DAF) to estimate the genetic diversity within, and genetic relationships among, a representative core collection of cowpea, as compared with 16 accessions representing cultivars from 6 Vigna species. A set of 26 primers was selected from 262 tested random primers and used for the characterization of 85 Vigna accessions (6 V. angularis , 4 each of V. mungo and V. radiata , 2 V. umbellata , 1 V. aconitifolia , and 68 V. unguiculata ), with Phaseolus vulgaris subsp. vulgaris as outgroup. A total of 212 polymorphic bands were used for maximum parsimony analysis. Our results clearly distinguished Brazilian from African V. unguiculata genotypes. At the species level, V. angularis was the most related and V. radiata the most divergent species relative to V. unguiculata. DAF markers were also informative at the intraspecific level, detecting a large diversity between cowpea cultivars. The implications of the presented results for cowpea breeding programs are discussed.
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Affiliation(s)
- M V Simon
- Universidade Federal de Pernambuco, CCB, Department of Genetics, Av. Prof. Moraes Rego, s/no. 50732-970, Recife, Pernambuco, Brazil
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Kilian M, Frandsen EVG, Haubek D, Poulsen K. The etiology of periodontal disease revisited by population genetic analysis. Periodontol 2000 2006; 42:158-79. [PMID: 16930310 DOI: 10.1111/j.1600-0757.2006.00159.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Mogens Kilian
- Department of Bacteriology, Institute of Medical Microbiology and Immunology, University of Aarhus, Aarhus, Denmark
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Atienzar FA, Jha AN. The random amplified polymorphic DNA (RAPD) assay and related techniques applied to genotoxicity and carcinogenesis studies: a critical review. Mutat Res 2006; 613:76-102. [PMID: 16979375 DOI: 10.1016/j.mrrev.2006.06.001] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2006] [Revised: 06/12/2006] [Accepted: 06/12/2006] [Indexed: 01/01/2023]
Abstract
More than 9000 papers using the random amplified polymorphic DNA (RAPD) or related techniques (e.g. the arbitrarily primed polymerase chain reaction (AP-PCR)) have been published from 1990 to 2005. The RAPD method has been initially used to detect polymorphism in genetic mapping, taxonomy and phylogenetic studies and later in genotoxicity and carcinogenesis studies. Despite their extensive use, these techniques have also attracted some criticisms, mainly for lack of reproducibility. In the light of their widespread applications, the objectives of this review are to (1) identify the potential factors affecting the optimisation of the RAPD and AP-PCR assays, (2) critically describe and analyse these techniques in genotoxicity and carcinogenesis studies, (3) compare the RAPD assay with other well used methodologies, (4) further elucidate the impact of DNA damage and mutations on the RAPD profiles, and finally (5) provide some recommendations/guidelines to further improve the applications of the assays and to help the identification of the factors responsible for the RAPD changes. It is suggested that after proper optimisation, the RAPD is a reliable, sensitive and reproducible assay, has the potential to detect a wide range of DNA damage (e.g. DNA adducts, DNA breakage) as well as mutations (point mutations and large rearrangements) and therefore can be applied to genotoxicity and carcinogenesis studies. Nevertheless, the interpretation of the changes in RAPD profiles is difficult since many factors can affect the generation of RAPD profiles. It is therefore important that these factors are identified and taken into account while using these assays. On the other hand, further analyses of the relevant bands generated in RAPD profile allow not only to identify some of the molecular events implicated in the genomic instability but also to discover genes playing key roles, particularly in the initiation and development of malignancy. Finally, to elucidate the potential genotoxic effects of environmental contaminants, a powerful strategy could be firstly to use the RAPD assay as a screening method and secondly to apply more specific methods measuring for instance DNA adducts, gene mutations or cytogenetic effects. It is also envisaged that these assays (i.e. RAPD and related techniques), which reflect effects at whole genome level, would continue to complement the use of emerging technologies (e.g. microarrays which aim to quantify expression of individual genes).
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Affiliation(s)
- Franck A Atienzar
- School of Biological Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, Devon, UK.
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Abstract
DNA fingerprinting is a powerful technology that has revolutionized forensic science. No two individuals can have an identical DNA pattern except identical twins. Such DNA-based technologies have enormous social implications and can help in the fight against crime. This technology has experienced many changes over time with many advancements occurring. DNA testing is a matter of serious concern as it involves ethical issues. This article describes various trends in DNA fingerprinting and the current technology used in DNA profiling, possible uses and misuses of DNA databanks and ethical issues involved in DNA testing. Limitations and problems prevailing in this field are highlighted.
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Motiwala AS, Li L, Kapur V, Sreevatsan S. Current understanding of the genetic diversity of Mycobacterium avium subsp. paratuberculosis. Microbes Infect 2006; 8:1406-18. [PMID: 16697677 DOI: 10.1016/j.micinf.2005.12.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2005] [Revised: 11/29/2005] [Accepted: 12/02/2005] [Indexed: 11/29/2022]
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the etiological agent of Johne's disease (or paratuberculosis). Paratuberculosis is a chronic gastroenteritis mainly affecting cattle, sheep and other ruminants. MAP is also of concern due to the heretofore unresolved issue of its possible role in Crohn's disease in humans. We present here a review of MAP (i) mobile genetic elements; (ii) repetitive elements; (iii) single nucleotide polymorphisms; and (iv) whole-genome comparisons to study the molecular epidemiology of MAP. A summary of the findings to date is presented, and the discriminatory power, advantage and disadvantages of each of the methods are compared and discussed.
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Affiliation(s)
- Alifiya S Motiwala
- Food Animal Health Research Program, Ohio Agricultural Research Development Center and Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH, USA
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Ambak MA, . AMAB, . PI, . BM. Genetic Variation of Snakehead Fish (Channa striata) Populations Using Random Amplified Polymorphic DNA. ACTA ACUST UNITED AC 2005. [DOI: 10.3923/biotech.2006.104.110] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Abstract
DNA microarrays offer the potential for simultaneous detection of many pathogens that are of interest to homeland security, public health, medicine, and veterinary diagnostics. These tools are best suited for detecting the presence or absence of genetic sequences characteristic of specific pathogens, but microarrays are poorly suited for determining pathogen viability, and current methods provide only limited potential for pathogen enumeration. Two basic strategies have been described for pathogen detection: using enzymatic amplification to generate targets for interrogation with a microarray, or using direct interrogation of DNA or RNA without pre-amplification. Multiplex PCR has the advantage of a high degree of sensitivity and specificity, but associated microarrays are necessarily limited in scope. PCR-independent, whole-genome amplification eliminates biases inherent in PCR amplification and can accommodate more extensive microarrays, but assay sensitivity is compromised and these methods are probably of limited use when testing tissue samples. Direct hybridization of DNA or RNA provides the least bias in gene detection, but also the lowest level of analytic sensitivity. Ultimately, cost and limited sample throughput make it unlikely that planar microarrays will play a significant role in future pathogen detection schemes. Alternative microarray formats such as bead arrays, however, may circumvent the cost and throughput limitations and permit us to apply what we have learned from planar microarrays to develop robust pathogen detection systems. Assay validation and sample preparation will continue to be significant challenges for these detection systems.
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Affiliation(s)
- Douglas R Call
- Department of Veterinary Microbiology and Pathology and Center for Reproductive Biology, Washington State University, Pullman, Washington 99164-7040, USA.
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