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RT-PCR Products (rt-pcr + products)
Selected AbstractsSemiquantitative determination of Alicyclobacillus acidoterrestris in orange juice by reverse- transcriptase polymerase chain reaction and capillary electrophoresis , laser induced fluorescence using microchip technologyELECTROPHORESIS, Issue 21-22 2004Maribel Funes-Huacca Abstract The semiquantitative detection of Alicyclobacillus acidoterrrestris in orange juice by reverse-transcriptase polymerase chain reaction (RT-PCR) with a linear dynamic range of 2×105, 2 colony forming units (CFU)/mL in terms of cell count is described. Separation, detection, and quantification of the RT-PCR products were accomplished using the Agilent 2100 bioanalyzer in conjunction with the DNA 1000 LabChip kit. After 0 and 12 h of enrichment, it was possible to generate a linear standard curve between the amount of cells and amplicon concentration of RT-PCR and PCR products. Using this method, cell diminution was verified in samples of orange juice treated with a natural inhibitor (Sapindus saponaria), determining the persistence of viable cells. Semiquantitative RT-PCR using the Agilent 2100 bioanalyzer is a potentially useful approach for rapid in vitro determination of A. acidoterrestris and monitoring of inhibitor susceptibility for the orange juice-producing industry. [source] Using a minigene approach to characterize a novel splice site mutation in human F7 gene causing inherited factor VII deficiency in a Chinese pedigreeHAEMOPHILIA, Issue 6 2009T. YU Summary., Factor VII deficiency which transmitted as an autosomal recessive disorder is a rare haemorrhagic condition. The aim of this study was to identify the molecular genetic defect and determine its functional consequences in a Chinese pedigree with FVII deficiency. The proband was diagnosed as inherited coagulation FVII deficiency by reduced plasma levels of FVII activity (4.4%) and antigen (38.5%). All nine exons and their flanking sequence of F7 gene were amplified by polymerase chain reaction (PCR) for the proband and the PCR products were directly sequenced. The compound heterozygous mutations of F7 (NM_000131.3) c.572-1G>A and F7 (NM_000131.3) c.1165T>G; p.Cys389Gly were identified in the proband's F7 gene. To investigate the splicing patterns associated with F7 c.572-1G>A, ectopic transcripts in leucocytes of the proband were analyzed. F7 minigenes, spanning from intron 4 to intron 7 and carrying either an A or a G at position -1 of intron 5, were constructed and transiently transfected into human embryonic kidney (HEK) 293T cells, followed by RT-PCR analysis. The aberrant transcripts from the F7 c.572-1G>A mutant allele were not detected by ectopic transcription study. Sequencing of the RT-PCR products from the mutant transfectant demonstrated the production of an erroneously spliced mRNA with exon 6 skipping, whereas a normal splicing occurred in the wide type transfectant. The aberrant mRNA produced from the F7 c.572-1G>A mutant allele is responsible for the factor VII deficiency in this pedigree. [source] Macrobrachium rosenbergii nodavirus infection in M. rosenbergii (de Man) with white tail disease cultured in TaiwanJOURNAL OF FISH DISEASES, Issue 6 2008C S Wang Abstract White tail disease (WTD) is a serious problem in Macrobrachium rosenbergii hatcheries and nursery ponds in Asia. The causative agents have been identified as M. rosenbergii nodavirus (MrNV) and its associated extra small virus. This is the first report demonstrating MrNV virus in M. rosenbergii displaying WTD signs in Taiwan by reverse transcriptase-polymerase chain reaction (RT-PCR). Amplified fragments of 850 and 425 bp for RNA-1 and RNA-2 of MrNV, respectively, were obtained by RT-PCR. RT-PCR products of about 850 and 1121 bp for RNA-1 and RNA-2 of MrNV were also obtained using different primer pairs. The amplicons were individually cloned into pGEM-T vector and sequenced. Using this recombinant plasmid of MrNV RNA-2 as DNA template, the non-radioactive DNA probes were prepared by PCR amplification with DIG,11-dUTP. The probes were used to successfully detect MrNV infection in the striated muscle tissues of WTD-diseased prawns using in situ hybridization. The 1121 bp genomic fragment of RNA-2 of MrNV consisted of a unique open reading frame with 1116 nucleotides, and it encoded a structural protein with 371 amino acids. The nucleotide sequence of the partial genome of MrNV RNA-2 revealed a 97% identity with an Indian isolate. A phylogenetic tree constructed using the nucleotide sequence of the viral capsid gene from insect and fish nodaviruses revealed that the MrNV Taiwan isolate could be interpreted as a new genus within the family Nodaviridae. However, its position showed more affinity with Alphanodavirus than with Betanodavirus. The study confirmed the presence of MrNV infection in freshwater prawns cultured in Taiwan suffering from WTD. [source] Malonyl CoA decarboxylase deficiency: C to T transition in intron 2 of the MCD geneJOURNAL OF NEUROSCIENCE RESEARCH, Issue 6 2001Sankar Surendran Abstract Malonyl CoA decarboxylase (MCD) is an enzyme involved in the metabolism of fatty acids synthesis. Based on reports of MCD deficiency, this enzyme is particular important in muscle and brain metabolism. Mutations in the MCD gene result in a deficiency of MCD activity, that lead to psychomotor retardation, cardiomyopathy and neonatal death. To date however, only a few patients have been reported with defects in MCD. We report here studies of a patient with MCD deficiency, who presented with hypotonia, cardiomyopathy and psychomotor retardation. DNA sequencing of MCD revealed a homozygous intronic mutation, specifically a ,5 C to T transition near the acceptor site for exon 3. RT-PCR amplification of exons 2 and 3 revealed that although mRNA from a normal control sample yielded one major DNA band, the mutant mRNA sample resulted in two distinct DNA fragments. Sequencing of the patient's two RT-PCR products revealed that the larger molecular weight fragments contained exons 2 and 3 as well as the intervening intronic sequence. The smaller size band from the patient contained the properly spliced exons, similar to the normal control. Western blotting analysis of the expressed protein showed only a faint band in the patient sample in contrast to a robust band in the control. In addition, the enzyme activity of the mutant protein was lower than that of the control protein. The data indicate that homozygous mutation in intron 2 disrupt normal splicing of the gene, leading to lower expression of the MCD protein and MCD deficiency. J. Neurosci. Res. 65:591,594, 2001. © 2001 Wiley-Liss, Inc. [source] Altered Cbfal expression and biomineralization in an osteosarcoma cell lineJOURNAL OF ORTHOPAEDIC RESEARCH, Issue 2 2004H. Perinpanayagam Abstract Osteoblast differentiation and expression are regulated by Cbfal transcription factors. Recent evidence suggests that Cbfal may also regulate bone mineralization. The purpose of this study was to characterize Cbfal expression in relation to mineralization in rat UMR106-01 osteoblastic cell cultures. UMR106-01 BSP cultures consistently form bone-like mineral, whereas the UI subclone mineralize gradually. BSP and UI cultures were grown for 48 h and then treated with ,-glycerophosphate. BSP cultures had alizarin red stained calcifications and mineral-like deposits within 24 h of phosphate. Atomic absorption spectroscopy measured significantly (P < 0.0001) more calcium in the phosphate-treated BSP cultures than in the UI. Cbfal message was detected in the BSP and UI cultures, but the Cbfal N-terminal isoform was deficient in UI and appeared to be up-regulated in the phosphate-treated BSP cultures. Cbfal protein levels were also reduced in the UI. DNA sequence from the RT-PCR products was utilized to design Taqman Real-time RT-PCR reagents. Quantitative Real-time RT-PCR analysis showed that Cbfal mRNA levels relative to endogenous 18 s rRNA were lower in the slower mineralizing UI cultures. Furthermore, the Cbfal N-terminal isoform mRNA levels were significantly (P < 0.001) lower in the slower mineralizing cultures. Transfection with Cbfal or isoform antisense caused a significant (P < 0.001) reduction in mineralization. Therefore, Cbfal expression may be associated with bone-like mineral formation in rat UMR106-01 osteoblastic cell cultures. © 2003 Orthopaedic Research Society. Published by Elsevier Ltd. All rights reserved. [source] Study of mRNA Expression by Real Time PCR of Cpkk1, Cpkk2 and Cpkk3, three MEKs of Cryphonectria parasitica, in Virus-free and Virus-infected Isogenic IsolatesJOURNAL OF PHYTOPATHOLOGY, Issue 6 2010Laura Rostagno Abstract Cpkk1 and Cpkk2 are two previously characterized Mitogen-activated protein kinase kinases (MEK) from Cryphonectria parasitica. For the characterization of the third MEK, primers designed to a conserved region of the known fungal MEK sequences were used in a PCR reaction to amplify genomic DNA from C. parasitica. The sequence of the resulting amplicon was compared to known sequences in the database using a Blast search. Results of the sequence comparison indicated that the initial fragment obtained encoded for a new MEK from C. parasitica, that had highest homology to Pbs2 from Saccharomyces cerevisiae. By inverse PCR we obtained a genomic fragment spanning the entire coding sequence of this MEK, which was named Cpkk3. The cDNA of Cpkk3 was obtained by compiling the sequences of RT-PCR products resulting from the amplification of purified mRNA. TaqMan® Probes were designed to analyse the expression of Cpkk1, Cpkk2 and Cpkk3 mRNA through RT-Real Time PCR. This protocol allowed the expression of Cpkk3 to be successfully compared to the expression of Cpkk1 and Cpkk2, two previously cloned C. parasitica MEKs. No variation in expression was associated with the presence of a virus after 2 days of growth in standard conditions whereas an increase in the expression level of all the three MEKs was shown after 4 days of growth. [source] Oligophrenin-1, a Rho GTPase-activating protein (RhoGAP) involved in X-linked mental retardation, is expressed in the enteric nervous systemTHE ANATOMICAL RECORD : ADVANCES IN INTEGRATIVE ANATOMY AND EVOLUTIONARY BIOLOGY, Issue 2 2003Junhua Xiao Abstract Oligophrenin-1 is a RhoGTPase-activating protein (RhoGAP) that is involved in the regulation of shape changes in dendritic spines, and outgrowth of axons and dendrites in the brain. These changes in neuronal morphology are central to the mechanisms of plasticity, learning, and memory. Although the enteric nervous system also exhibits long-term changes in neuronal function, the expression and involvement of oligophrenin-1 has not previously been investigated. We show by RT-PCR analysis that oligophrenin-1 mRNA is expressed in the myenteric plexus (MP) of the guinea pig ileum. Sequencing of RT-PCR products showed that guinea pig oligophrenin-1 mRNA is 98% and 87% homologous to human and mouse oligophrenin-1, respectively, except that a 42 bp sequence is absent from the guinea pig mRNA. This 42 bp sequence codes for a sequence of 14 amino acids located near the carboxy-terminal end of the RhoGAP domain in the human sequence. An antibody that recognizes human oligophrenin-1 identified a 91 kDa protein band in rat and mouse brain lysates and in guinea pig sciatic nerve, and a 36 kDa protein band in both purified enteric ganglion cell and brain lysate from guinea pig. Oligophrenin-1 is localized specifically to neurons and varicose axons in the MPs and submucosal plexuses (SMPs) of the guinea pig and rat, but is not detectable in glial cells, smooth muscle, or other cell types. These findings indicate that oligophrenin-1 is expressed in the enteric nervous system, where it may regulate morphological changes in axons and dendrites, and thus modulate neuronal connectivity. Anat Rec Part A 273A:671,676, 2003. © 2003 Wiley-Liss, Inc. [source] Changes in estrogen receptor alpha expression in the bursa of Fabricius during chick embryonic developmentANIMAL SCIENCE JOURNAL, Issue 1 2008Young-Ha SHIN ABSTRACT Sex steroid hormones have been reported to be modulators that augment or suppress immune functions. Applying estrogen to chick embryos has been reported to influence antibody production after hatching, suggesting that estrogen acts on B cell differentiation and proliferation in the bursa of chick embryos. We previously reported the presence of estrogen receptor , (ER,) in the bursa during the late period of embryogenesis. In the present study we examined the time course of ER, expression in the bursa of chick embryos at the late period of embryogenesis by ER,-messenger RNA (mRNA) expression analysis by reverse-transcription-polymerase chain reaction (RT-PCR) using primers for chicken ER,, and immunohistochemistry using an anti-ER antibody. The quantity of ER,-mRNA expressed, estimated from the relative densities of the ER, RT-PCR products to those of ,-actin, changed with time during the late period of embryogenesis (day 10 to day 21). ER,-mRNA expression was observed at all ages examined in the present experiment. The expression increased between day 10 and day 15 of embryogenesis and then the value was decreased between day 15 and day 21 of embryogenesis. The numbers of ER-positive cells in the bursa also changed with time during the late period of embryogenesis (day 14 to day 18). ER-positive cells showed the highest level on day 14 of embryogenesis, and then the value declined. ER-positive cells were observed in lymphoid follicular cells, stromal cells and epithelial cells, and the density of ER-positive cells was highest in epithelial cells among the three cell components of the bursa. The high level of ER expression in the bursa of Fabricius (BF) of chick embryos at the late period of embryogenesis suggests that this stage of embryogenesis is critical in B cell differentiation in the bursa in connection with estrogen effects on antibody production after hatching. [source] Molecular diagnosis of lyssaviruses and sequence comparison of Australian bat lyssavirus samplesAUSTRALIAN VETERINARY JOURNAL, Issue 7 2006AJ FOORD Objective To evaluate and implement molecular diagnostic tests for the detection of lyssaviruses in Australia. Design A published hemi-nested reverse transcriptase polymerase chain reaction (RT-PCR) for the detection of all lyssavirus genotypes was modified to a fully nested RT-PCR format and compared with the original assay. TaqMan assays for the detection of Australian bat lyssavirus (ABLV) were compared with both the nested and hemi-nested RT-PCR assays. The sequences of RT-PCR products were determined to assess sequence variations of the target region (nucleocapsid gene) in samples of ABLV originating from different regions. Results The nested RT-PCR assay was highly analytically specific, and at least as analytically sensitive as the hemi-nested assay. The TaqMan assays were highly analytically specific and more analytically sensitive than either RT-PCR assay, with a detection level of approximately 10 genome equivalents per µl. Sequence of the first 544 nucleotides of the nucleocapsid protein coding sequence was obtained from all samples of ABLV received at Australian Animal Health Laboratory during the study period. Conclusion The nested RT-PCR provided a means for molecular diagnosis of all tested genotypes of lyssavirus including classical rabies virus and Australian bat lyssavirus. The published TaqMan assay proved to be superior to the RT-PCR assays for the detection of ABLV in terms of analytical sensitivity. The TaqMan assay would also be faster and cross contamination is less likely. Nucleotide sequence analyses of samples of ABLV from a wide geographical range in Australia demonstrated the conserved nature of this region of the genome and therefore the suitability of this region for molecular diagnosis. [source] | |||||||||||||