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NCBI Database (ncbi + database)
Selected AbstractsSingle nucleotide polymorphisms in succinate dehydrogenase subunits and citrate synthase genes: association results for impaired spermatogenesisINTERNATIONAL JOURNAL OF ANDROLOGY, Issue 3 2007Sandra Bonache Abstract Evaluation of the possible implication of the SDHA, SDHB, SDHC, SDHD and CS genes in non-obstructive male infertility was performed on the basis that sperm concentration in the ejaculate has been previously correlated with nuclear-encoded mitochondrial enzyme activities (the four subunits of succinate dehydrogenase/complex II of the respiratory chain and citrate synthase). We performed an exhaustive analysis of the five genes for the presence of sequence variants that could be associated with impairment of sperm production. blastn searches in the genomic sequence NCBI database evidenced the presence of highly homologous sequences elsewhere on the genome that can interfere with polymerase chain reaction experiments. Therefore, a careful design of the analytical strategy to search for sequence variants was performed. In this report, we provide primer sequences that allowed selective amplification of coding and immediate flanking regions of the five genes. Fifty-five sequence variations in the five genes were identified in infertile and normozoospermic fertile individuals as controls and only one of them (SDHA c.456+32G>A) showed significant genotype association with impairment of sperm production. Moreover, new single nucleotide polymorphisms identified should be useful in future association studies for other human diseases related to nuclear-encoded genes, leading to mitochondrial respiratory chain activity impairment revealing the physiological role of these genes. [source] Accumulation of Defence Response-related and Unique Expressed Sequence Tags during the Incompatible Interaction in the Oryza sativa,Magnaporthe oryzae PathosystemJOURNAL OF PHYTOPATHOLOGY, Issue 7-8 2009Rekha Dixit Abstract Resistance gene-dependent accumulation of expressed sequence tags (ESTs) was studied in a blast resistant, Oryza sativa ssp. indica cv. Tetep after challenge inoculation with an incompatible race of Magnaporthe oryzae. The nucleotide sequence of 287 randomly selected cDNA clones from the rice cDNA library constructed from the RNA isolated after challenge inoculation of the host was obtained and submitted in NCBI Genbank (Accession Nos. DN475717,DN475431). Of these, 184 (63%) ESTs were highly representative of the rice transcriptomes. A set of 178 unique transcripts was identified after assembly of 287 ESTs into unigenes. These unigenes were categorized into 17 functional groups. Analysis of this EST library illustrated a broad functional representation. Twenty-one unigenes were identified as putative homologues of the genes that were up regulated during host,pathogen interaction. Similarity search of 178 unigenes with NCBI database of 14 plants unigenes showed similarity ranging from 29,100%. The unigenes obtained in this study were physically located on the pseudomolecules of rice genome. This information can be used for determining the arrays of genes being expressed during Oryza sativa,M. oryzae interactions, which will be helpful in understanding the molecular basis of disease resistance. [source] Determination of self-incompatible genotypes in sweet cherry (Prunus avium L.) accessions and cultivars of the German Fruit Gene Bank and from private collectionsPLANT BREEDING, Issue 5 2007M. Schuster Abstract Sweet cherries are self-incompatible because of a gametophytic self-incompatibility system. S alleles in the style and pollen determine the crossing relationships. Knowledge of the S allele constitution of cultivars is very important for cherry growers and breeders, and recently, molecular methods have been developed to distinguish the S alleles in sweet cherries. The S allele genotypes of 149 sweet cherry cultivars and clones, including 126 not previously genotyped, were determined by using PCR analysis. Thirteen different S alleles in 40 combinations were distinguished and nine new incompatibility groups were documented. Two new S alleles were identified in five local sweet cherry processing cultivars from southwestern Germany using the second intron primers. The sequence of these alleles was determined and compared to all known sequences available in the NCBI database. The sequences obtained showed high similarities to the alleles S19 and S22, previously described only in wild cherries, Prunus avium L. [source] Proteome analysis of human monocytic THP-1 cells primed with oxidized low-density lipoproteinsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 4 2006Jeong Han Kang Abstract Native low-density lipoprotein (LDL) and oxidized LDL (oxLDL) possess a wide variety of biological properties, and play a central role in atherogenesis. In this study, we used a proteomic analysis of human monocyte THP-1 cells induced with oxLDL or with LDL, to identify proteins potentially involved in atherosclerotic processes. Of the 2500,proteins detected, 93,were differentially expressed as a result of priming with LDL or oxLDL. The proteins were unambiguously identified by comparing the masses of their tryptic peptides with those of all known proteins using MALDI,TOF,MS and the NCBI database. The largest differences in expression were observed for vimentin (94-fold increase), meningioma-expressed antigen,6 (48-fold increase), serine/threonine protein phosphatase,2A (40-fold increase), and beta-1,3-galactosyltransferase (15-fold increase). In contrast, the abundance of an unnamed protein product and phosphogluconate dehydrogenase decreased 30-fold and 25-fold, respectively. The expression of some selected proteins was confirmed by Western blot and RT-PCR analyses. The proteins identified in this study are attractive candidates for further biomarker research. This description of the altered protein profiles induced by oxLDL in human monocytes will support functional studies of the macrophage-derived foam cells involved in the pathogenesis of atherosclerosis. [source] Development of microsatellite DNA markers and their chromosome assignment in the common marmosetAMERICAN JOURNAL OF PRIMATOLOGY, Issue 11 2009Hideki Katoh Abstract This study was performed to develop microsatellite DNA markers, which are useful for linkage analyses, gene mapping and blood chimera analyses in the common marmoset (Callithrix jacchus). We searched 153 of 295 bacterial artificial clone DNA sequences of the common marmoset that were archived in the NCBI database in 2004. On the basis of the search, we designed 186 PCR primer sets. When tested using 5 unrelated individuals, we successfully detected 154 markers with PCR products, of which 80 (52%) were polymorphic and 74 (48%) were monomorphic. We assigned each of the 154 markers to a human chromosome based on BLAST searches, which was achieved by searching the entire human genome sequences using an ,3,kb section of each forward primer sequence, including ,1.5,kb of the upstream and ,1.5,kb of the downstream sequences. Combining our assignment data and the chromosome painting-assisted karyotype of the common marmoset [Sherlock et al., Genomics 33:214,219, 1996], we prepared a list of 154 microsatellite DNA markers that were assigned to human chromosomes, except for the Y chromosome, which is equivalent to a chromosome map. Using five microsatellite DNA markers, we have established a fragment analysis method with a sequencer, which can be routinely used for blood chimera analysis, parentage diagnosis and individual identification. Am. J. Primatol. 71:912,918, 2009. © 2009 Wiley-Liss, Inc. [source] | ||||||||||