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Transcription Profiling (transcription + profiling)
Selected AbstractsBiomarker as a classifier in pharmacogenomics clinical trials: a tribute to 30th anniversary of PSI,,PHARMACEUTICAL STATISTICS: THE JOURNAL OF APPLIED STATISTICS IN THE PHARMACEUTICAL INDUSTRY, Issue 4 2007Sue-Jane Wang Abstract Pharmacogenetics is one of many evolving sciences that have come to the fore since the formation of the Statisticians in the Pharmaceutical Industry (PSI) 30 years ago. Following the completion of the human genome project and the HapMap in the early 21st century, pharmacogenetics has gradually focused on studies of whole-genome single-nucleotide-polymorphisms screening associating disease pathophysiology with potential therapeutic interventions. Around this time, transcription profiling aiming at similar objectives has also been actively pursued, known as pharmacogenomics. It has become increasingly apparent that treatment effects between different genomic patient subsets can be dissimilar, and the value and need for genomic biomarkers to help predict effects, particularly in cancer clinical studies, have become issues of paramount importance. Pharmacogenomics/pharmaogenetics has thus become intensely focused on the search for genomic biomarkers for use as classifiers to select patients in randomized-controlled trials. We highlight that the predictive utility of a genomic classifier has tremendous clinical appeal and that there will be growing examples in which use of a companion diagnostic will need to be considered and may become an integral part in the utilization of drugs in medical practice. The credible mechanism to test the clinical utility of a genomic classifier is to employ the study results from a prospective trial that recruits all patients. Such investigations, if well designed, will allow analysis of all relevant performance factors in the drug and diagnostic combination including the sensitivity, specificity, positive and negative predictive values of the diagnostic test and the efficacy of the drug. Published in 2007 by John Wiley & Sons, Ltd. [source] Identification and molecular analysis of candidate genes homologous to HcrVf genes for scab resistance in applePLANT BREEDING, Issue 1 2009A. Boudichevskaia Abstract The genetic locus for resistance to apple scab most frequently used in apple breeding is Vf, derived from Malus floribunda 821. For the Vf locus a cluster of four resistance gene paralogs (called as HcrVf genes) encoding receptor-like proteins (RLP) with similarity to the tomato Cf resistance genes is known. Based on published sequences for HcrVf1 and HcrVf2 PCR primers were designed from the domain B and the variable leucine-rich repeat (LRR) C1 subdomain. PCR products with high amino acid identity (85,100%) to HcrVf1 and HcrVf2 were obtained not only from M. floribunda 821 and Vf cultivars but also from other apple scab resistance sources, such as ,Russian Seedling' R12740-7A (Vr resistance) or ,Antonovka polutorafuntovaya' (VA resistance). A series of 13 HcrVf candidate genes have been partly cloned from the PCR fragments spanning N-terminal LRRs 20,30. A considerable number of amino acid exchanges within the solvent-exposed xxLxLxx structural motives were detected among the homologous sequences. Expression analyses and mapping focused on a selected Vf- homologous candidate gene (called Vf2ARD) identified in resistant Malus genotypes known for carrying other scab resistance genes than Vf. RT-PCR experiments showed that Vf2ARD is expressed under pathogen-free conditions. The results of a quantitative PCR-based transcription profiling suggest that this gene is scab-inducible in some resistant cultivars. Vf2ARD has been mapped on linkage group LG 1. It is separated from the Vf gene cluster with a genetic distance of about 2 cM and might be a member of a second Vf - like locus on apple linkage group LG 1. [source] Proteomic and transcriptomic analysis of human CD8+ T lymphocytes over-expressing telomerasePROTEOMICS - CLINICAL APPLICATIONS, Issue 3 2007Lynne Thadikkaran Abstract Human T lymphocytes have a finite life span resulting from progressive telomere shortening that occurs at each cell division, eventually leading to chromosomal instability. It has been shown that ectopic expression of the human telomerase reverse transcriptase (hTERT) gene into various human cells results in the extension of their replicative life span, without inducing changes associated with transformation. However, it is still unclear whether cells that over-express telomerase are physiologically and biochemically indistinguishable from normal cells. To address this question, we compared the proteome of young and aged human CD8+ T lymphocytes with that of T cells transduced with hTERT. Interestingly, we found no global changes in the protein pattern in young T cells, irrespective of telomerase expression. In contrast, several relevant proteins with differential expression patterns were observed in hTERT-transduced T cells with extended life span upon long-term culture. Altogether, our data revealed that T lymphocytes over-expressing telomerase displayed an intermediate protein pattern, sharing a similar protein expression not only with young T cells, but also with aged T cells. Finally, the results obtained from this global proteomic approach are in agreement with the overall gene transcription profiling performed on the same T-cell derived clones. [source] Mapping and transcription profiling of CASP1, 3, 6, 7 and 8 in relation to caspase activity in the bovine cumulus,oocyte complexANIMAL GENETICS, Issue 3 2004Y. Q. Yuan Summary So far 12 caspases have been described in mouse and human while only one (CASP13) is known in cattle. The aim of this study was to (1) search for other bovine caspases by reverse transcription and polymerase chain reaction (RT,PCR) and (2) examine the presence of bovine caspase mRNA and active protein in the cumulus,oocyte complex. Five caspases (1, 3, 6, 7 and 8) were identified, partially cloned and sequenced. Four of them were mapped. Differential transcription of the caspase genes was detected, but no active caspase protein was found in diverse bovine oocytes. Cumulus granulosa cells (CGC) contain CASP1, 6, 7 and 8 mRNA and active caspase protein. The presence of caspase mRNA and active caspase proteins in CGCs suggests the occurrence of apoptosis in cumulus,oocyte complex, while caspase activation is blocked in fresh oocytes and therefore caspase transcription cannot be used to predict the oocyte developmental capacity. [source] | ||||||||||