Reproducible DNA fingerprinting with the random amplified polymorphic DNA (RAPD) method

Micheli, Maria Rita; Bova, Rodolfo; Pascale, Esterina; D’Ambrosio, Ettoré

doi:10.1093/nar/22.10.1921

Cited by 156 publications

(74 citation statements)

References 2 publications

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“…Several studies have shown that the number of loci amplified with RAPD primers depends on factors such as reagents and reaction conditions, sample conditions, and DNA quality and extraction methods (Williams et al 1990;Black 1993;Ellsworth et al 1993;Kernodle et al 1993;MacPherson et al 1993;Meunier and Grimont 1993;Micheli et al 1994;Gallego and Martinez 1997;Khandka et al 1997). Variations were minimized and amplifications of artifacts in the RAPD profiles were prevented by using heads and legs of individual frozen flies, by using similar amounts of template DNA for PCR runs, by running a negative control in each reaction, and by using 2 batches of each potential primer and AmpliTaq® DNA Polymerase Stoffel Fragment during the replication process.…”

Section: Discussionmentioning

confidence: 99%

Genetic Relationships Among <I>Aedes aegypti</I> (Diptera: Culicidae) Populations from Argentina Using Random Amplified Polymorphic DNA Polymerase Chain Reaction Markers

Sousa

Blanco

Gardenal

2001

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Section: Discussionmentioning

confidence: 99%

Genetic Relationships Among <I>Aedes aegypti</I> (Diptera: Culicidae) Populations from Argentina Using Random Amplified Polymorphic DNA Polymerase Chain Reaction Markers

Sousa

Blanco

Gardenal

2001

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“…Random amplified polymorphic DNA (RAPD) oligonucleotide primers were synthesized and PCR was carried out by using 10 ng genomic DNA as template. 11 …”

Section: Treatment Of Lung Cancer Cell Lines With Differentiation Indmentioning

confidence: 99%

Homeobox gene HOP has a potential tumor suppressive activity in human lung cancer

Chen

Pacyna-Gengelbach

Deutschmann

et al. 2007

Intl Journal of Cancer

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The homeobox containing gene HOP (Homeodomain Only Protein) was identified in the developing heart and lung where it functions downstream of Nkx2.5 and Nkx2.1 to modulate cardiac and lung gene expression. Previously, we found that HOP was downregulated in lung cancer. In this study, we constructed an expression vector containing the full-length cDNA of HOP and transfected it into a lung cancer cell line H2170. Stable transfection led to an increased expression of HOP confirmed by Northern blot analysis. HOP positive transfectants remarkably reduced the growth rate and the ability of anchorage-independent growth in soft agar, and moreover suppressed the tumor formation in nude mice compared to controls. Transient transfection of Nkx2.1 into H2170 resulted in the overexpression of HOP, and correspondingly, siRNA silencing of Nkx2.1 reduced the expression of HOP in lung cancer cells. Treatment with a differentiation modulating agent 5-bromodeoxyuridine (BrdU) led to restoration of HOP expression in a small cell lung cancer cell line H526. In 29 paired primary lung tumor samples, loss of heterozygosity (LOH) analysis was performed by using the 3 microsatellite markers D4S189, D4S231 and D4S392 around the region of chromosome 4q12 where HOP locates. LOH was only found in 4 out 23 cases (17.4%) indicating that allelic loss is a rare genetic event not responsible for the downregulation of HOP in lung cancer. Taken together, our data suggest that HOP is a potential tumor suppressor possibly involved in lung cancer differentiation, and functions downstream of Nkx2.1. ' 2007 Wiley-Liss, Inc.Key words: HOP; lung cancer; stable transfection; tumor suppressor; RNA interference; differentiation Lung cancer is a predominant cause of cancer death in both men and women. 1 Although current therapies for patients with lung cancer include surgical resection and/or radiotherapy or chemotherapy, the outcome is poor with an overall 5-year survival rate of 15%. New molecular targets for the diagnosis and therapy are therefore required to improve the prognosis for lung cancer patients.In a previous study, we performed suppression subtractive hybridization (SSH) to reveal lung cancer associated genes by comparing the gene expression between normal human bronchial epithelial cells (HBEC) and lung squamous carcinoma cells of H2170. 2 Two cDNA libraries representing mainly the genes that are over-expressed and under-expressed in HBEC and tumor cell line were cloned. The homeobox gene LAGY (Lung Cancer Associated Gene Y; Genbank Accession Nr. AF454763) was identified to be downregulated in lung cancer cell lines compared to HBEC, and a decreased gene expression was also observed in primary lung tumors. 3 LAGY, also called HOP (Homeodomain Only Protein), Cameo (Cardiac homeodomain) and NECC1 (Not Expressed in Choriocarcinoma Clone 1), was initially identified in the embryonic heart and it acts at multiple steps in the pathway for heart development. 4,5 Later, reports about the involvement of this gene in carcinogenesis emerged. For example, t...

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“…Among these RAPD analysis is cheap and easy to apply, although its repeatability is not perfect with respect to amplification products profile. Careful optimization of the RAPD protocol has been shown to increase the reproducibility of the RAPD data (Micheli et al, 1994). This marker system has been extensively used for variability study in various crops.…”

Section: Discussionmentioning

confidence: 99%

Use of RAPD Markers in Comparison with Agro-morphological Traits for Estimation of Diversity among Chickpea Genotypes

Bakhsh¹,

Iqbal²,

Rahman³

et al. 2017

IJAB

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To cite this paper: Bakhsh, A., S.M. Iqbal, M.U. Rahman and A. Javaid, 2017. Use of RAPD markers in comparison with agro-morphological traits for estimation of diversity among chickpea genotypes. AbstractGenetic diversity was assessed among 38 chickpea (Cicer arietinum L.) genotypes on the basis of random amplified polymorphic DNA (RAPD) in comparison with agro-morphological traits. Evaluation of agro-morphological traits revealed highly significant differences among genotypes. Days to 50% flowering ranged from 92-118, plant height 54.16-87 cm, number of fruit bearing branches 4-17.25, number of pods per plant 7.6-27.4, and grain yield per plant 3.5-9.8 g. Ascochyta blight (caused by Ascochyta rabiei) score of these genotypes was recorded on 1-9 rating scale that varied from 3-9. Cluster analysis showing relationship based on morphological traits (scale: Euclidean distance) placed 35 genotypes into five distinct groups, while three genotypes namely Noor-91, Local Mankera and BR4 did not include in any cluster. RAPD analysis showed that 35 RAPD primers amplified a total of 212 fragments out of which 45 were polymorphic. Polymorphic bands were generated by 21 primers whereas 14 primers were monomorphic. Genetic similarity matrix based on Nei and Li's index revealed similarity coefficients ranging from 92-97% indicating lower level of genetic polymorphism revealed by RAPD primers. Dandrogram constructed on the basis of these coefficients grouped all the genotypes into 2 major and 3 small clusters at 92% similarity level. Two decamers, OPC5 and OPC14 distinguished between three Desi and two Kabuli genotypes. This study showed that the level of genetic variability observed in chickpea for agro-morphological traits was not reflected in DNA polymorphism obtained by RAPD analysis.

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Reproducible DNA fingerprinting with the random amplified polymorphic DNA (RAPD) method

Abstract: Much interest has recently arisen in methods for DNA fingerprinting based on the polymerase chain reaction (PCR).

Cited by 156 publications

References 2 publications

Genetic Relationships Among <I>Aedes aegypti</I> (Diptera: Culicidae) Populations from Argentina Using Random Amplified Polymorphic DNA Polymerase Chain Reaction Markers

Genetic Relationships Among <I>Aedes aegypti</I> (Diptera: Culicidae) Populations from Argentina Using Random Amplified Polymorphic DNA Polymerase Chain Reaction Markers

Homeobox gene HOP has a potential tumor suppressive activity in human lung cancer

Use of RAPD Markers in Comparison with Agro-morphological Traits for Estimation of Diversity among Chickpea Genotypes

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