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Used PCR (used + pcr)

Distribution by Scientific Domains

Medical Sciences	75%

Selected Abstracts

Inter- alu PCR detects high frequency of genetic alterations in glioma cells exposed to sub-lethal cisplatin

INTERNATIONAL JOURNAL OF CANCER, Issue 4 2005
Tapasya Srivastava
Abstract Increased genomic instability contributes to higher frequency of secondary drug resistance and neoplastic progression in tumors as well as in cells exposed to sub-lethal concentrations of chemotherapeutic agents. We have used PCR based DNA fingerprinting techniques of randomly amplified polymorphic DNA (RAPD) and inter- alu PCR to study this phenomenon in the tumor genome. The choice of the primer, either random (for RAPD) or specific (inter- alu PCR) can determine the nature of alterations being assessed. We have compared the inter- alu PCR and RAPD profiles of U87MG glioblastoma cells exposed to sequentially increasing low doses of cisplatin for 24 passages to that of untreated controls. Inter- alu PCR, with 2 primers, demonstrated a number of alterations in the treated cells, in the form of loss / gain and changes in the intensity of bands. No changes were observed by RAPD analysis with 5 primers, however, indicating a preferential increase in the alu mediated recombination frequency in the treated cells (p = 1.866 × 10,4). The number of changes observed with respect to the corresponding leucocyte DNA in the inter- alu PCR profile of 26 primary tumors (Grade II = 13; Grade IV = 13), resected before chemotherapy, for the 2 inter- alu primers was very small. We present a novel application of the inter- alu PCR in detecting alterations in long term cultured cells at low dose exposure to a chemotherapeutic agent. Our results suggest that alu mediated recombination may be important in cells exposed to sub-lethal doses of cisplatin but not in the genesis of primary glioma. © 2005 Wiley-Liss, Inc. [source]

The mitochondrial genome sequence and molecular phylogeny of the turkey, Meleagris gallopavo

ANIMAL GENETICS, Issue 2 2009
X. Guan
Summary The mitochondrial genome (mtGenome) has been little studied in the turkey (Meleagris gallopavo), a species for which there is no publicly available mtGenome sequence. Here, we used PCR-based methods with 19 pairs of primers designed from the chicken and other species to develop a complete turkey mtGenome sequence. The entire sequence (16 717 bp) of the turkey mtGenome was obtained, and it exhibited 85% similarity to the chicken mtGenome sequence. Thirteen genes and 24 RNAs (22 tRNAs and 2 rRNAs) were annotated. An mtGenome-based phylogenetic analysis indicated that the turkey is most closely related to the chicken, Gallus gallus, and quail, Corturnix japonica. Given the importance of the mtGenome, the present work adds to the growing genomic resources needed to define the genetic mechanisms that underlie some economically significant traits in the turkey. [source]

Virulence genes in verocytotoxigenic Escherichia coli strains isolated from humans and cattle,

APMIS, Issue 9 2005
C. WELINDER-OLSSON
Verocytotoxigenic Escherichia coli (VTEC) causing diarrhoea, haemorrhagic colitis and haemolytic-uremic syndrome usually have additional traits such as the adhesin intimin and a large plasmid that seems to increase virulence. There are, however, isolates of VTEC causing serious symptoms that do not harbour these traits. In the present study we have used PCR with primers detecting adhesin genes other than eaeA, namely fimA, papC, sfaD/sfaE and daaE. We have also used PCR to detect the genes hlyA and iutA that besides the plasmid-borne gene E-hly possibly support the bacterial access to iron. The aim of the study was to identify and compare the presence of virulence genes in VTEC isolates of human and cattle origin. The main finding was that the absence of E-hly might be compensated for by the gene iutA coding for aerobactin or hlyA coding for ,-haemolysin as 94% of the human VTEC isolates had at least one of these genes. Interestingly, only 45% of VTEC isolated from cattle had any of these genes. We propose that this might be the reason for the relatively low incidence of symptomatic VTEC infections among humans in relation to the high number of VTEC among cattle. [source]

16 Kallikrein 15 (KLK15) in prostate cancer: in silico analysis and single nucleotide polymorphism verification

BJU INTERNATIONAL, Issue 2006
M.A. KEDDA
Introduction:, Prostate cancer is the most common cancer in Caucasian men and there is strong evidence that kallikreins are part of an enzymatic cascade pathway activated in this disease. Altered KLK15 expression has been associated with cancer progression and grade and we postulate that single nucleotide polymorphisms (SNPs) in the KLK15 gene, will alter gene expression and will be associated with prostate cancer susceptibility and prognosis. Materials and Methods:, We have used in silico prediction of function of wildtype and variant promoter sequences through assessment of hormone receptor elements and transcription factor binding sites; as well as prediction of likely splice variants through genomic, splicing and EST databases and web sites, and multiple sequence alignment packages. We have also used PCR and sequence analysis to further characterise the promoter region of the gene. Results:,In silico analysis of the KLK15 gene has identified the following: two putative promoter regions, two putative androgen response elements (AREs) and four putative estrogen response elements (EREs); two clusters of cis elements; and 109 SNPs. Forty-seven SNPs alter transcription factor sites (22 gain sites), 20 gain/increase probability of an ERE and three alter nuclear hormone receptor binding sites. Three new EST clones have been identified by analysis of gene expression in CGAP databases and suggest a new KLK15 splice variant, with a different start site. Conclusion:, We have identified a number of new SNPs in the KLK15 gene, which may be functionally important and, in collaboration with the Queensland Cancer Fund (ProsCan Study), we will further investigate the association of these SNPs with prostate cancer risk and prognosis. [source]