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Identification and characterization of novel variants of the thioredoxin reductase 3 new transcript 1 TXNRD3NT1.

We have identified and characterized a new gene sequence, TXNRD3NT1, whose transcripts, corresponding to the EST AA430236, were found by Affymetrix DNA chip analysis to be significantly down regulated in affected psoriatic tissue. The full-length cDNA of TXNRD3NT1 was isolated and characterized by combining 5'- and 3'-RACE (rapid amplication of cDNA ends) with screening a keratinocyte cDNA library, designing appropriate PCR primers, cloning amplified products, sequencing, and sequence analysis. Because part of this gene overlaps the previously described thioredoxin reductase 3 (TXNRD3) gene, we have named it TXNRD3NT1 (TXNRD3 new transcript 1). The full-length TXNRD3NT1 cDNA has 1133 nucleotides with a 251-bp 3-UTRand 2 poly(A)signal variants and 2 poly (A) sites. The TXNRD3NT1 cDNA ORF encodes for 133 amino acids, with the first four residues coding for a tubulin-beta mRNA autoregulation signal. Mapping the cDNA nucleotide sequence to the human genome sequence revealed that the TXNRD3NT1 gene has 4 exons located on Chromosome 3, at position 3q21. Exons 1 and 2 of the TXNRD3NT1 gene overlap with exons 15 and 16 of the thioredoxin reductase 2 gene which has different ORFs to that of TXNRD3NT1. The translation initiation codon ATG was found in exon 3 of the TXNRD3NT1 gene. RT-PCR showed that the full-length variant of the TXNRD3NT1 gene was expressed in only four issues (pancreas, esophagus, bone marrow, and keratinocytes) of the 30 different tissues tested. In most other tissues, an aberrant and truncated form of the transcript (i.e., missing exon 3 and part of exon 4) was detected. The result of a preliminary association study between psoriasis and single microsatellite marker of the TXNRD3NT1 gene suggests that it may not be a significant genetic determinant of psoriasis. However, we cannot exclude the possibility that other sequence variants may still exist within the TXNRD3NT1 gene. Sequence analysis of the TXNRD3NT1 gene from 8 psoriasis patients and 8 healthy controls revealed a number of synonymous SNPs that may be useful markers for future disease association studies.

Alternative Splicing↗

Site-directed mutagenesis by overlap extension using the polymerase chain reaction.

Overlap extension represents a new approach to genetic engineering. Complementary oligodeoxyribonucleotide (oligo) primers and the polymerase chain reaction are used to generate two DNA fragments having overlapping ends. These fragments are combined in a subsequent 'fusion' reaction in which the overlapping ends anneal, allowing the 3' overlap of each strand to serve as a primer for the 3' extension of the complementary strand. The resulting fusion product is amplified further by PCR. Specific alterations in the nucleotide (nt) sequence can be introduced by incorporating nucleotide changes into the overlapping oligo primers. Using this technique of site-directed mutagenesis, three variants of a mouse major histocompatibility complex class-I gene have been generated, cloned and analyzed. Screening of mutant clones revealed at least a 98% efficiency of mutagenesis. All clones sequenced contained the desired mutations, and a low frequency of random substitution estimated to occur at approx. 1 in 4000 nt was detected. This method represents a significant improvement over standard methods of site-directed mutagenesis because it is much faster, simpler and approaches 100% efficiency in the generation of mutant product.

Amino Acid Sequence↗

Mycobacterium tuberculosis efpA encodes an efflux protein of the QacA transporter family.

The Mycobacterium tuberculosis H37Rv efpA gene encodes a putative efflux protein, EfpA, of 55,670 Da. The deduced EfpA protein was similar in secondary structure to Pur8, MmrA, TcmA, LfrA, EmrB, and other members of the QacA transporter family (QacA TF) which mediate antibiotic and chemical resistance in bacteria and yeast. The predicted EfpA sequence possessed all transporter motifs characteristic of the QacA TF, including those associated with proton-antiport function and the motif considered to be specific to exporters. The 1,590-bp efpA open reading frame was G+C rich (65%), whereas the 40-bp region immediately upstream had an A+T bias (35% G+C). Reverse transcriptase-PCR assays indicated that efpA was expressed in vitro and in situ. Putative promoter sequences were partially overlapped by the A+T-rich region and by a region capable of forming alternative secondary structures indicative of transcriptional regulation in analogous systems. PCR single-stranded conformational polymorphism analysis demonstrated that these upstream flanking sequences and the 231-bp, 5' coding region are highly conserved among both drug-sensitive and multiply-drug-resistant isolates of M. tuberculosis. The efpA gene was present in the slow-growing human pathogens M. tuberculosis, Mycobacterium leprae, and Mycobacterium bovis and in the opportunistic human pathogens Mycobacterium avium and Mycobacterium intracellular. However, efpA was not present in 17 other opportunistically pathogenic or nonpathogenic mycobacterial species.

Amino Acid Sequence↗

p53 in prostate cancer: frequent expressed transition mutations.

BACKGROUND: Carcinoma of the prostate is the second most common cause of cancer deaths in men. Little is known about the pathogenesis of this disease and the molecular genetic events that contribute to its development. Molecular studies have begun to reveal biologic characteristics of this disease, notably, the loss of genetic material as determined by studies of restriction fragment length polymorphism, oncogene activation, and production and response to growth factors. PURPOSE: Our goal was to characterize p53 gene mutations in human carcinoma of the prostate and to analyze base-pair changes within the coding regions of p53 mRNA (exons 4 through 11). METHODS: Forty-four prostate tissue specimens and four metastatic lesions were obtained from 48 prostate carcinoma patients who had surgical resection. RNA was either immediately extracted or the specimens were snap-frozen in liquid N2 and stored at -70 degrees C until used. Total RNA was extracted from tumor specimens. Expression of p53 was analyzed by polymerase chain reaction (PCR) analysis of mRNA (RNA/PCR). Following confirmation of the RNA/PCR products by Southern blotting, quantitation of message levels was performed by laser densitometry. Absolute area integrations of the curves representing each tissue were then compared after adjustment for the housekeeping gene c-N-ras. Two overlapping regions (exons 4-6 and 6-11) were examined by a nonisotopic PCR single-strand conformation polymorphism (SSCP) analysis system. All specimens displaying SSCP abnormalities were sequenced in both directions to confirm the findings. RESULTS: Of the 48 prostate specimens, three (6%) (two primary and one metastatic) displayed nearly undetectable expression of p53 mRNA (samples PS-70, L113, and PS-95) and 17 (35%) of 48 expressed mutant p53 mRNA encoding amino acid substitutions within exons 4-11 (14 of 17) and/or deletions within the p53 transcripts (three of 17). Overall, the frequency of p53 gene abnormalities that would result in altered protein expression was 20 (42%) of 48 in the tissue samples from prostate carcinoma patients. Nucleotide base-pair transitions of A-->G or T-->C were the most frequent. CONCLUSIONS: p53 mutations are common in prostate cancer. The patterns of p53 gene mutations are dramatically different from data obtained on other cancers and indicate the possible involvement of a carcinogenic agent(s). IMPLICATIONS: Further studies are required to determine the biologic role of p53 gene alterations in the development and progression of this disease and to determine whether p53 mutations can be useful as prognostic markers or for the selection of better treatments for prostate cancer patients.

Base Sequence↗

Generation of a human chromosome 18-specific YAC clone collection and mapping of 55 unique YACs by FISH and fingerprinting.

A yeast artificial chromosome (YAC) library was constructed from a somatic cell hybrid line in which the human chromosome content had been reduced by repeated subcloning to one or two copies of chromosome 18. Screening of 4700 primary yeast transformants generated 74 clones containing a YAC with a human DNA insert averaging 190 kb in size. The human YACs were localized to subregions of chromosome 18 by in situ hybridization of biotin-labeled Alu-PCR products obtained using total yeast DNA as a template. Comparisons of interspersed repetitive sequence-PCR and restriction fragment fingerprint patterns identified five sets of identical and three sets of overlapping YACs. Dual-label fluorescence in situ hybridization interphase mapping was used to determine the order of some nonoverlapping YACs. STS (sequence-tagged site) content mapping was carried out with PCR primers for 56 chromosome 18-specific markers. The identification of YACs containing four known genes--encoding the pituitary adenylate cyclase activating polypeptide (PA-CAP), the myelin basic protein (MBP), ferrochelatase (FECH), and SSAV1, an endogenous retroviral element related to the SSAV virus--provides a precise cytological map position for the respective loci. Our final collection of 55 randomly isolated, unique, and regionally localized YACs (D18S107-D18S161) is distributed over the entire chromosome and collectively covers approximately 12 Mb, i.e., 16% of the estimated 77 Mb of DNA in euchromatin of chromosome 18. These YACs provide reagents for the isolation of genes in these regions and represent nucleation points for the generation of STS to increase coverage of the chromosome by YAC contigs.

Adenylyl Cyclases↗

Detection and identification of Leishmania species in field-captured phlebotomine sandflies based on mini-exon gene PCR.

Leishmaniasis is one of the most diverse and complex of all vector-borne diseases. Because it involves several overlapping species and sandfly vectors, the disease has a complex ecology and epidemiology. Adequate therapy and follow-up depend on parasitological diagnosis, but classical methods present several constraints when identifying species. We describe a polymerase chain reaction (PCR) which uses primers designed from mini-exon repetitive sequences that are specific for subgenus LeishmaniaViannia (PV), as well as sequences with specificity for genus (PG) that can distinguish between Leishmania species from other insect flagellates with minor differences in PCR products. For standardization, these PCR were tested in experimentally infected sandflies, and Leishmania infection in these insects was successfully confirmed. This methodology identified a 3.9% infection rate in field-captured phlebotomine sandflies from an endemic region in Brazil. Natural infection by Leishmania species was identified in three samples of Lutzomyia longipalpis, of which two were Leishmania (L.) chagasi and one Leishmania (L.) amazonensis. Irrespective of specific epidemiological conclusions, the method used in this study was able to identify Leishmania infections both in experimentally infected and field-captured phlebotomine sandflies, and could be a useful tool in epidemiological studies and strategic planning for the control of human leishmaniasis.

Animals↗

Quantitative analysis of Cyclin D1 and CD23 expression in mantle cell lymphoma and B-chronic lymphocytic leukemia.

We studied Cyclin D1 (CyD1) and CD23 mRNA expression with real-time quantitative reverse transcription polymerase chain reaction (RQ-PCR) method. CyD1 expression in peripheral blood of seven mantle cell lymphoma (MCL) patients was found to be 1305.4 times higher than in 24 B-chronic lymphocytic leukemia (CLL) patients. CD23 expression in CLL was found to be 54.8 times higher than in MCL. These differences were statistically significant, and no overlap was found in CyD1 expression intensities between MCL and CLL. RQ-PCR allows rapid, simple and accurate quantification of CyD1 and CD23 expression, even from small samples, and is thus useful for the diagnosis of MCL and CLL.

Adult↗

Detection of latency-associated transcripts of equid herpesvirus 1 in equine leukocytes but not in trigeminal ganglia.

Results from Southern hybridization and PCR amplification experiments using a randomly synthesized reverse transcription-PCR product showed that peripheral blood leukocytes from horses showing no clinical signs of disease expressed a putative latency-associated transcript antisense to and overlapping the 3' end of the equid herpesvirus 1 (EHV-1) immediate-early gene (gene 64). A PCR product derived from this transcript has > or =96% identity with the published EHV-1 sequence. In situ hybridization studies of equine bronchial lymph nodes corroborated these findings and are consistent with reactivation data (D. A. Smith, A. Hamblin, and N. Edington, unpublished data), indicating that EHV-1 latency is established predominantly in CD5+/CD8+ leukocytes.

Animals↗

Peptide nucleic acid-mediated PCR clamping as a useful supplement in the determination of microbial diversity.

Peptide nucleic acid (PNA)-mediated PCR clamping (H. Orum, P. E. Nielsen, M. Egholm, R. H. Berg, O. Buchardt, and C. Stanley, Nucleic Acids Res. 21:5332-5336, 1993) was introduced as a novel procedure to selectively amplify ribosomal DNAs (rDNAs) which are not frequently found in clone libraries generated by standard PCR from complex microbial consortia. Three different PNA molecules were used; two of these molecules (PNA-ALF and PNA-EUB353) overlapped with one of the amplification primers, whereas PNA-1114F hybridized to the middle of the amplified region. Thus, PCR clamping was achieved either by competitive binding between the PNA molecules and the forward or reverse primers (competitive clamping) or by hindering polymerase readthrough (elongation arrest). Gene libraries generated from mixed rDNA templates by using PCR clamping are enriched for clones that do not contain sequences homologous to the appropriate PNA oligomer. This effect of PCR clamping was exploited in the following two ways: (i) analysis of gene libraries generated by PCR clamping with PNA-ALF together with standard libraries reduced the number of clones which had to be analyzed to detect all of the different sequences present in an artificial rDNA mixture; and (ii) PCR clamping with PNA-EUB353 and PNA-1114F was used to selectively recover rDNA sequences which represented recently described phylogenetic groups (NKB19, TM6, cluster related to green nonsulfur bacteria) from an anaerobic, dechlorinating consortium described previously. We concluded that PCR clamping might be a useful supplement to standard PCR amplification in rDNA-based studies of microbial diversity and could be used to selectively recover members of undescribed phylogenetic clusters from complex microbial communities.

Bacteria↗

Construction of overlapping oligonucleotide templates for the production of cRNA standards for quantitative reverse transcription polymerase chain reaction.

The reverse transcriptase polymerase chain reaction (PCR) is a technique for the study of gene expression that requires far less RNA for analysis than Northern blots. The inclusion of cRNA standards in the initial reverse transcription step is a way to control for the tube-to-tube variation often inherent in the technique and to permit quantitation of the starting amount of the native mRNA being analyzed. We describe a method using overlapping oligonucleotides to produce templates for the production of cRNA standards for up to three different mRNA species. The first step is the synthesis of a pair of overlapping oligonucleotides each of which encodes, respectively, sequences analogous to either sense or antisense primers for the PCR amplification of up to three different messages. These oligonucleotides are designed to have complementary 3' ends which permit spontaneous annealing and allow subsequent mutually priming extension of the annealed double-stranded portion by T7 DNA polymerase. The T7 and SP6 RNA polymerase promoters are then added to the ends of the template using standard PCR techniques. Once the template is assembled, T7 and SP6 RNA polymerases are used to produce copious quantities of cRNA standards and controls. This technique can be used to construct multiple cRNA standards for essentially any messages of interest. Production of cRNA by a single T7 RNA polymerase reaction yields standards sufficient for several thousand separate reverse transcriptions.

Base Sequence↗

A PCR-based method for site-specific domain replacement that does not require restriction recognition sequences.

We describe a PCR-based method for domain replacement that does not require restriction site sequences. We illustrate the technique in which the first epidermal growth factor (EGF1)-like domain of factor IX (FIX) is replaced by the EGF1-like domain of protein C. The method employs four oligonucleotide primers. Two are external primers (forward primer A and inverse primer B) and contain sequences flanking the FIX cDNA nucleotides. The other two primers (forward primer C and inverse primer D) direct the PCR amplification of the EGF1-like domain of protein C, and they are hybrid primers that contain sequences of protein C gene at the 3' end and of FIX gene at the 5' end. Thus the amplified fragment of EGF1-like domain of protein C (PCEGF1 fragment) is flanked by FIX gene sequences on both ends. When this fragment is mixed with FIX cDNA and subjected to one cycle of PCR, two products are obtained: one containing PCEGF1 fragment linked to FIX cDNA sequence upstream and the other containing PCEGF1 fragment linked to FIX cDNA sequence downstream of its EGF1-like domain. The first product is amplified using primers A and D, and the second product is amplified using primers B and C. Both products contain overlapping sequences, which allow annealing upon mixing. The annealed product is amplified by PCR using primers A and B. The final product contains FIX cDNA in which its EGF1 sequence has been replaced by the PCEGF1 sequence.

Base Sequence↗

Analysis of the co-amplified STR loci D1S1656, D12S391 and D18S51: population data and validation study for a highly discriminating triplex-PCR.

A multiplex-PCR composed of the three highly variable STR loci D1S1656, D12S391 and D18S51 has been established. The non-overlapping fragment sizes allow allele detection using a monochrome automated laser fluorescent sequencer (A.L.F. express, Pharmacia Biotech). The typing results of the triplex-PCR showed no difference to those of singleplex-PCR. Allele frequencies were determined in a Western German population of 228 individuals from Cologne. The heterozygosities and exclusion chances (D1S1656, 0.982; D12S391, 0.979; D18S51, 0.97) are very high compared to other short tandem repeats used for forensic applications. No deviations from the Hardy-Weinberg equilibrium were found. Successful typing of DNA amounts down to 50-100 pg is possible. Mixtures of up to 1:10 can be identified. In conclusion, the high combined exclusion chance due to the well-balanced allelic distribution and its high sensitivity make this triplex-PCR a valuable tool for forensic casework.

Blood Stains↗

Mutations in surface and polymerase gene of chronic hepatitis B patients with coexisting HBsAg and anti-HBs.

AIM: To investigate the clinical significance and presence of mutations in the surface (S) and overlapping polymerase gene of hepatitis B patients with coexisting HBsAg and anti-HBs. METHODS: Twenty-three patients with chronic hepatitis B were studied. Of the 23 patients, 11 were both positive for hepatitis B virus (HBV) surface antigen (HBsAg) and antibody to HBV surface antigen (anti-HBs), 12 were negative for anti-HBs while positive for HBsAg. DNA was extracted from 200 muL serum of the patients. Nucleotide of the surface and overlapping polymerase gene from HBV-infected patients was amplified by PCR, and the PCR products were sequenced. RESULTS: Forty-one mutations were found within the surface gene protein of HBV in 15 patients (10 with coexisting HBsAg and anti-HBs). Six (14.6%) out of 41 mutations were located at "alpha " determinant region in 5 patients (4 positive for HBsAg and anti-HBs). Eleven mutations (26.8%) occurred in the downstream or upstream of "alpha " determinant region. Lamivudine (LMV)-selected mutations were found in three patients who developed anti-HBs, which occurred in amino acid positions (196, 198, 199) of the surface protein and in YMDD motif (M204I/V) of the polymerase protein simultaneously. Presence of these mutations did not relate to changes in ALT and HBV DNA levels. CONCLUSION: Besides mutations in the "alpha " deter-minant region, mutations at downstream or upstream of the "alpha " determinant region may contribute to the development of anti-HBs. These mutations do not block the replicating competency of HBV in the presence of high titer of anti-HBs.

Adult↗

Insulin-receptor cDNA sequence in NIDDM patient homozygous for insulin-receptor gene RFLP.

Resistance to insulin action is a well-established feature of non-insulin-dependent diabetes mellitus (NIDDM) and is believed to contribute to the etiology of this condition. A strong genetic contribution to the etiology of NIDDM exists, and we previously identified an insulin-receptor gene restriction-fragment-length polymorphism (RFLP) associated with the NIDDM phenotype. In an attempt to elucidate whether structural defects in the insulin receptor could be a primary cause of insulin resistance in NIDDM, we analyzed the insulin-receptor cDNA sequence in a subject with NIDDM who is also homozygous for this RFLP. The insulin-receptor cDNA was sequenced with the polymerase chain reaction (PCR). mRNA from transformed lymphocytes was reverse transcribed and amplified with five overlapping sets of primers that span the coding sequence of both alpha- and beta-subunits. No difference was found in the predicted amino acid sequence of the subject's insulin receptor compared with the normal insulin receptor. At nucleotide positions 831 and 2247, the subject is heterozygous for silent nucleotide polymorphisms that do not affect the amino acid sequence. Exon 11 encodes a 12-amino acid insert in the alpha-subunit, which, due to alternate splicing, is not expressed in lymphocyte insulin-receptor mRNA. Consequently, exon 11 was amplified from genomic DNA by PCR; the sequence of exon 11 was found to be normal. In addition, when this patient's transformed lymphocytes were maintained in culture, no abnormalities in insulin binding were observed. We conclude that the insulin resistance seen in this NIDDM subject is not due to a structural alteration in the insulin receptor itself.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

Use of the cross-section technique linked with multivariate calibration methods to resolve complex pesticide mixtures.

The potential of the cross-section (CS) approach in combination with the partial least squares (PLS) and principal component regression (PCR) was assessed in the resolution of a complex pesticide mixture showing twelve overlapped components in High Performance Liquid Chromatography with Diode Array Detection (HPLC-DAD). Careful selection of the CS through the three-dimensional (3D) (A, lambda, t) data matrix gave two-dimensional (2D) signals with the best sensitivity for the determination of each pesticide. In all cases, the application of the PLS method demonstrated a better quantitative prediction ability than that of the PCR method. The CS-PLS approach is a powerful analytical tool. Ten pesticides were well-resolved, while for the other two pesticides of the mixture prediction ability was poor, and they could not be determined, probably due to their low net analytical signal. The CS-PLS model was evaluated by predicting the concentrations of independent test set samples. Finally, the proposed model was successfully applied for the determination of these pesticides in groundwater.

Calibration↗

LD-PCR coupled to long-read direct sequencing: an approach for mutation detection in genes with compact genomic structures.

A number of techniques have been developed as primary screens to scan for DNA sequence variants, including denaturing gradient gel electrophoresis, denaturing high-performance liquid chromatography, single-strand conformation polymorphism and heteroduplex analysis. Variant alleles detected by these assays are subsequently characterised by DNA sequencing. Sequencing itself is rarely used as a primary screen because of labour intensity, cost, and, upon automation, occasional inaccuracy in identifying heterozygous sites. We have previously developed an approach based on coupling long-distance PCR (LD-PCR) to long-read direct sequencing to allow the detection of mutations in the approximately 1.1 kb exon 3 of MECP2. Our use of dye-labelled primers generated high-quality bi-directional sequence runs > 650 bp and allowed easy discrimination of heterozygous bases. We now describe the application of this approach to the detection of mutations in a considerably larger 6.35 kb LD-PCR fragment spanning 10 exons (exons 32-41) of the structurally complex, but genomically compact, TSC2 gene. In a blind analysis, 15/15 previously characterised mutations were successfully identified using seven overlapping bi-directional sequencing reactions. Our approach of long-read sequencing of long-distance PCR products may allow rapid sequencing of multiple exons of compact genes and may be appropriate as a highly sensitive primary screen for mutations.

Base Sequence↗

Partial amplification of the measles virus nucleocapsid gene from stored sera and cerebrospinal fluids for molecular epidemiological studies.

The analysis of stored sera for retrospective molecular epidemiological studies provides a powerful tool to investigate strain variation in measles viruses that had circulated up to 20 years ago. For this purpose, a rapid and simple method for extraction of RNA from stored sera and cerebrospinal fluids (CSF) was developed. When used on sera and CSFs that have been frozen for as long as 20 years, this method proved to be more efficient than established techniques. The extracted RNA was reverse transcribed into cDNA by using random hexamer primers. The PCR amplification of the 3' terminus of the nucleocapsid gene (N) was divided into two overlapping fragments of 375 and 384 bp length, covering the entire region of interest. This region is thought to have the highest variability within the MV genome and has previously been shown to be suitable for strain characterization. The resulting PCR fragments were sequenced manually by using standard methods without the need of further clean-up steps.

Amino Acid Sequence↗

The porcine follitropin receptor: cDNA cloning, functional expression and chromosomal localization of the gene.

The porcine follitropin receptor-encoding cDNA (pFSHR) was cloned using reverse transcription-polymerase chain reaction (RT-PCR). Total RNA from porcine granulosa cells was used as template. Two overlapping cDNA fragments encoding, respectively, aa 1 to 290 and aa 191 to 694 of the pFSHR were obtained. Taken together, the two fragments represented the whole coding sequence, assuming a comparable length for the FSHR from the porcine, rat and human species. Functionality of the cloned receptor was assessed by expression experiments; COS cells transfected with the pFSHR cDNA exhibited high-affinity specific binding for [125I]hFSH and FSH-dependent cAMP production. The primary sequence of the porcine FSHR N-terminal hormone-binding domain showed high percentages of identity with the sequences from ovine, human, and rat origins. A truncated form of the pFSHR cDNA, lacking aa 75 to 124 in the N-terminal domain, was also cloned and sequenced. A PCR-derived cDNA fragment of 1.45 kb was used as gene-specific hybridisation probe to map the pFSHR-encoding gene by radioactive in situ hybridization. This gene was found co-localized (as in human) with the porcine lutropin hormone receptor (pLHR)-encoding gene on the q2.2-q2.3 region of pig chromosome 3.

Amino Acid Sequence↗