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PubMed1999

Members of the nuclear factor 1 transcription factor family regulate rat 3alpha-hydroxysteroid/dihydrodiol dehydrogenase (3alpha-HSD/DD AKR1C9) gene expression: a member of the aldo-keto reductase superfamily.

Rat 3alpha-hydroxysteroid/dihydrodiol dehydrogenase (3alpha-HSD/DD; AKR1C9), a member of the aldo-keto reductase (AKR) superfamily, inactivates nearly all steroid hormones by converting 5alpha- and 5beta-dihydrosteroids to their respective 3alpha,5alpha- and 3alpha,5beta-tetrahydrosteroids and protects against circulating steroid hormone excess. It is highly expressed in rat liver comprising 0.5-1.0% of the soluble protein. Previously, we identified a powerful distal enhancer resident at about -4.0 kb to -2.0 kb in the 5'-flanking region of the 3alpha-HSD/DD gene. We now report the functional dissection of this enhancer. Transfection of nested deletions of the 5'-end of the gene promoter linked to chloramphenicol acetyltransferase (CAT) into HepG2 cells located the enhancer activity between (-4673 to -4179 bp). Further internal and 5'-end deletion mutants revealed that a 73-bp fragment (from -4351 to -4279 bp) contained a major enhancer element. This fragment spanned two imperfect direct repeats GTGGAAAAACCCAGGAA and GTGGAAAAAACCCAGGAA and contained three direct repeats of GGAAAAA. This fragment also contained three potential half-nuclear factor 1 (NF1) sites (TGGA-NNNNNGCCA) and a putative CCAAT-enhancer binding protein (C/EBP) binding site. The 73-bp fragment enhanced CAT activity from the basal 3alpha-HSD/DD gene promoter. Recombinant C/EBPalpha and C/EBPbeta did not bind to this fragment. Electrophoretic mobility shift assays showed that HepG2 and rat liver nuclear extracts bound to this 73-bp fragment. The 73-bp protein complex was competed out by a NF1 oligonucleotide and was supershifted by an NF1 antibody. When the 73-bp fragment was fused to an alpha1-globin promoter-CAT construct and cotransfected with CCAAT transcription factor 1 (CTF1)/NF1 into Drosophila Schneider SL2 insect cells (which lack NF1-like proteins) trans-activation of CAT activity was observed. These results indicate that members of the NF1 transcription factor family regulate high constitutive expression of the rat 3alpha-HSD/DD gene that is responsible for steroid hormone inactivation. The potential role of NF1 in regulating other AKR genes that have protective roles is discussed.

Animals↗

PubMed1999

Association of polymorphism at the type I collagen (COL1A1) locus with reduced bone mineral density, increased fracture risk, and increased collagen turnover.

OBJECTIVE: To examine the relationship between a common polymorphism within intron 1 of the COL1A1 gene and osteoporosis in a nested case-control study. METHODS: We studied 185 healthy women (mean +/- SD age 54.3+/-4.6 years). Bone mineral density (BMD) was measured using dual x-ray absorptiometry, and fractures were determined radiographically. The COL1A1 genotype was assessed using the polymerase chain reaction and Bal I endonuclease digestion. RESULTS: Genotype frequencies were similar to those previously observed and in Hardy-Weinberg equilibrium: SS 61.1%, Ss 36.2%, and ss 2.7%. Carriage of at least one copy of the "s" allele was associated with a significant reduction in lumbar spine BMD (P = 0.02) and an increased risk of total fracture (P = 0.04). Urinary pyridinoline levels were significantly elevated in those with the risk allele (P < 0.05). CONCLUSION: These data support the findings that the COL1A1 gene polymorphism is associated with low BMD and fracture risk, and suggest a possible physiologic effect on total body turnover of type I collagen.

Absorptiometry, Photon↗

PubMed1995

Amplification of 16S ribosomal RNA genes of autotrophic ammonia-oxidizing bacteria demonstrates the ubiquity of nitrosospiras in the environment.

Oligonucleotide sequences selected from the 16S rRNA genes of various species of ammonia-oxidizing bacteria were evaluated as specific PCR amplification primers and probes. The specificities of primer pairs for eubacterial, Nitrosospira and Nitrosomonas rRNA genes were established with sequence databases, and the primer pairs were used to amplify DNA from laboratory cultures and environmental samples. Eubacterial rRNA genes amplified from samples of soil and activated sludge hybridized with an oligonucleotide probe specific for Nitrosospira spp., but not with a Nitrosomonas-specific probe. Lakewater and sediment samples were analysed using a nested PCR technique in which eubacterial rRNA genes were subjected to a secondary amplification with Nitrosomonas or Nitrosospira specific primers. Again, the presence of Nitrosospira DNA, but not Nitrosomonas DNA, was detected and this was confirmed by hybridization of the amplified DNA with an internal oligonucleotide probe. Enrichments of lakewater and sediment samples, incubated for two weeks in the presence of ammonium, produced nitrite and were found to contain DNA from both Nitrosospira and Nitrosomonas as determined by nested PCR amplification and probing of 16S rRNA genes. This demonstrates that Nitrosospira spp. are widespread in the environment. The implications of the detection of Nitrosomonas DNA only after enrichment culture are discussed.

Ammonia↗

PubMed1996

A 2.5 kb polypyrimidine tract in the PKD1 gene contains at least 23 H-DNA-forming sequences.

A pyrimidine-rich element (PyRE), present in the 21st intron of the PKD1 gene, posed a significant obstacle in determining the primary structure of the gene. Only cycle sequencing of nested, single-stranded phage templates of the CT-rich strand enabled complete and accurate sequence data. Similar attempts on the GA-rich strand were unsuccessful. The resulting primary structure showed the 3 kb 21st intron to contain a 2.5 kb PyRE, whose sense-strand is 97% C + T. The PKD1 PyRE does not appear to be polymorphic based on RFLP analysis of DNA from 6 unrelated individuals digested with 9 different restriction enzymes. This is the largest pyrimidine tract sequenced to date, being over twice as large as those previously identified and shows little homology to other polypyrimidine tracts. Additional analysis of this PyRE revealed the presence of 23 mirror repeats with stem lengths of at least 10 nucleotides. The 23 H-DNA-forming sequences in the PKD1 PyRE exceed the cumulative total of 22 found in 157 human genes that have been completely sequenced. The mirror repeats confer this region of the PKD1 gene with a strong probability of forming H-DNA or triplex structures under appropriate conditions. Based on studies with PyRE found in other eukaryotic genes, the PKD1 PyRE may play a role in regulating PKD1 expression, and its potential for forming an extended triplex structure may explain some of the observed instability in the PKD1 locus.

Base Sequence↗

PubMed1993

Specificity and sensitivity of polymerase chain reaction (PCR) in comparison with other methods for the detection of mycoplasma contamination in cell lines.

The polymerase chain reaction (PCR) amplification was used for the detection of mycoplasma contamination in 42 continuous cell lines. Using the microbiological cultivation on agar as the reference method, 29 cell lines were regarded as positive and 13 cell lines as negative. The double-step PCR analysis employed nested primers that anneal to gene sequences coding for the evolutionarily conserved 16 S rRNA of some 25 different mycoplasma species (including the ones most commonly found in cell cultures). In terms of the positivity or negativity of mycoplasma infection the results were identical for the agar assay and PCR amplification. All positive cell lines displayed distinct, unequivocal, objectively discernible bands on agarose gels while the non-infected specimens showed no DNA amplification. A simultaneously performed comparison with four other commonly used detection methods (DNA-RNA hybridization in solution, DAPI DNA fluorescence staining, immunostaining with a monoclonal antibody and an ELISA) showed that PCR produced significantly less false-negative or false-positive results than all the other methods. Furthermore, in dilution experiments, PCR correctly detected the infecting mycoplasmas at the lowest level of 1/10(4) whereas the other assays were less sensitive. It is concluded that double-step PCR employing nested primers is superior to other mycoplasma detection methods in many respects: simplicity and speed, high specificity and extreme sensitivity, objectivity and accuracy.

Animals↗

PubMed1994

Sensitive and specific polymerase chain reaction assays for detection of Bordetella pertussis in nasopharyngeal specimens.

Polymerase chain reaction (PCR) assays that amplify segments of a repeated gene element and a toxin promoter gene of Bordetella pertussis were compared with a culture established for the diagnosis of pertussis. Of 44 nasopharyngeal (NP) aspirates collected during a pertussis outbreak, repeated gene element PCR showed a positive result in 21 (48%), including all three patients with positive culture results. Results of toxin promoter gene PCR were positive in eight (18%) cases, and the pathogen was not detected in one patient with a positive culture result. A more sensitive nested PCR assay, based on repeated gene element PCR, was then developed. During a second outbreak two different transportation systems were tested in 146 duplicate NP swabs. Transportation of swabs in empty tubes proved to be better than in transport media for PCR. A total of 190 NP specimens from the two outbreaks were tested, and in 56 the results were shown to be positive by PCR, including all 16 cases confirmed as positive by culture. We conclude that the PCR assay is more sensitive than culture in the diagnosis of pertussis; NP swabbing is a simple, practical, and reliable method of collecting clinical specimens for PCR assays and cultures.

Adult↗

PubMed2004

A proline tRNA(CGG) gene encompassing the attachment site of temperate phage 16-3 is functional and convertible to suppressor tRNA.

Several temperate bacteriophage utilize chromosomal sequences encoding putative tRNA genes for phage attachment. However, whether these sequences belong to genes which are functional as tRNA is generally not known. In this article, we demonstrate that the attachment site of temperate phage 16-3 (attB) nests within an active proline tRNA gene in Rhizobium meliloti 41. A loss-of-function mutation in this tRNA gene leads to significant delay in switching from lag to exponential growth phase. We converted the putative Rhizobium gene to an active amber suppressor gene which suppressed amber mutant alleles of genes of 16-3 phage and of Escherichia coli origin in R. meliloti 41 and in Agrobacterium tumefaciens GV2260. Upon lysogenization of R. meliloti by phage 16-3, the proline tRNA gene retained its structural and functional integrity. Aspects of the co-evolution of a temperate phage and its bacterium host is discussed. The side product of this work, i.e. construction of amber suppressor tRNA genes in Rhizobium and Agrobacterium, for the first time widens the options of genetic study.

Agrobacterium tumefaciens↗

PubMed2004

No association between base excision repair gene polymorphisms and risk of lung cancer.

In a nested case-cohort study, we have investigated the occurrence of lung cancer in relation to polymorphisms in base excision repair genes XRCC1 and OGG1. Among 54,220 members of a Danish prospective cohort study, aged 50-65 years at entry, 265 lung cancer cases were identified and a subcohort comprising 272 individuals was used for comparison. No associations were found between the polymorphisms OGG1 Ser326Cys, XRCC1 Arg280His, and XRCCI Arg399Gln and risk of lung cancer. This is the first study of polymorphisms in base excision repair genes in relation to lung cancer among Danes.

Aged↗

PubMed2005

Study of the occurrence of Vibrio vulnificus in oysters in India by polymerase chain reaction (PCR) and heterogeneity among V. vulnificus by randomly amplified polymorphic DNA PCR and gyrB sequence analysis.

The pathogenic bacterium Vibrio vulnificus is widely distributed in estuarine waters throughout the world. In this study, the presence of V. vulnificus in oysters was studied both by conventional culture and DNA-based molecular technique. Following enrichment in alkaline peptone water (APW), the bacteria were lysed and a nested polymerase chain reaction (PCR) for vvhA gene was performed. The effect of duration of enrichment on the sensitivity of detection by PCR was evaluated. The organism was isolated from 43% of samples after 18 h enrichment in APW by conventional culture method. Nested PCR amplifying a fragment of vvhA gene detected the organism in 11%, 60% and 81% of samples following 0, 6 and 18 h of enrichment. All the biochemically identified V. vulnificus strains possessed vvhA gene and belonged to biotype 1. The genetic relatedness among the strains was studied by randomly amplified polymorphic DNA (RAPD) PCR and gyrB sequence analysis. The results suggest the presence of two distinct clonal groups of V. vulnificus in oysters in India. The study demonstrates, for the first time that gyrB sequence analysis could be used to study the genetic diversity of V. vulnificus.

Amino Acid Sequence↗

PubMed1997

Molecular subtyping of human T-lymphotropic virus type I (HTLV-I) by a nested polymerase chain reaction-restriction fragment length polymorphism analysis of the envelope gene: two distinct lineages of HTLV-I in Taiwan.

The major type of human T-lymphotropic virus type I (HTLV-I), generally referred to as the cosmopolitan type, has been grouped into three subtypes (A, B, and C) by phylogenetic analysis of the long terminal repeat sequences of the viral genome. Twelve subtype-specific nucleotide variations have been deduced by comparison between the envelope (env) sequences of 16 HTLV-I strains with defined subtypes and 9 Taiwanese HTLV-I strains. To gain further insights into the molecular epidemiology of HTLV-I and the origin of this virus in Taiwan, a rapid method of identification for the cosmopolitan subtypes was developed by using a nested polymerase chain reaction (PCR) and subsequent restriction fragment length polymorphism (RFLP) studies using the two subtype B-specific and four subtype C-specific nucleotides located within the positions 5708 to 6320 of the envgene. The nested PCR-RFLP method was used to subtype HTLV-I from four virus-positive cell lines derived from 1 Japanese and 3 North American patients, as well as 41 blood-unrelated Taiwan Chinese. The sequences of PCR products were determined and the six positions of subtype-specific nucleotide variations were examined. The sequence data completely supported the subtyping data via the nested PCR-RFLP method. The results demonstrated that, as is the case in Japan, at least two distinct cosmopolitan subtypes (A and B) of HTLV-I were present in Taiwan, but the more prevalent subtype in Taiwan is A in contrast to subtype B in Japan. Furthermore, rapid subtyping could facilitate molecular epidemiological studies of HTLV-I infection and linkage between HTLV-I subtypes and virus-associated diseases.

Base Sequence↗

PubMed1998

Genetic heterogeneity of env gene of feline immunodeficiency virus obtained from multiple districts in Japan.

Feline immunodeficiency virus (FIV) infection is widespread in many countries. FIV isolates have been classified into five distinct subtypes, A, B, C, D and E based on their env gene sequences. Several reports indicate that most of the FIVs isolated in Japan belong to subtype B which includes the first Japanese isolate, TM2 strain. To examine the distribution of FIV subtypes in Japan, proviral DNA sequences of the env gene were directly amplified by nested PCR from FIV-infected cats that had been kept in multiple districts throughout Japan. Phylogenetic analysis of the 11 strains showed that four FIV subtypes, A, B, C and D, were present in Japan. Among these subtypes, subtypes B and D were the two most common subtypes in Japan, and they were mainly distributed in the eastern and western parts of Japan, respectively. The present study provides information that is fundamental for development of a vaccine to protect against FIV infection in cats.

Amino Acid Sequence↗

PubMed1990

Analysis of sequence elements important for expression and regulation of the adenylate cyclase gene (cya) of Salmonella typhimurium.

We determined the nucleotide sequence of the regulatory region of the cya gene of Salmonella typhimurium. A set of nested BAL-31 deletions originating upstream of the promoter/regulatory region and extending into the cya structural gene was constructed in M13mp::cya phages and was tested for complementation of a chromosomal cya deletion mutation. BAL-31 deletion mutants unable to complement cya localized the major cya promoter. The synthetic tac promoter was inserted upstream of the BAL-31 deletions so that expression of cya was dependent on transcription from tac. Those tac derivative phages unable to complement cya localized the translation initiation region. The cya DNA sequence revealed at least three potential promoters capable of transcribing cya, with a CRP binding site straddling the-10 hexamer of the promoter proximal to the structural gene. The leader RNA sequence initiated at the latter promoter is approximately 140 bases long and includes a region that may form a stable secondary structure (delta G = -23.8 kcal). There exist two possible in-frame translation start points, one of which is TTG and the other of which is ATG. The sequence of the S. typhimurium regulatory region was compared with that reported for Escherichia coli.

Adenylyl Cyclases↗

PubMed2000

The role of methylation in CML.

Methylation of the proximal promoter of the ABL1 oncogene is common epigenetic alteration associated with clinical progression of chronic myeloid leukemia (CML). In presented study we queried whether both the Ph'-associated and normal ABL1 alleles undergo methylation; what may be the proportion of hematopoietic progenitors bearing methylated ABL1 promoters in chronic versus acute phase disease; whether methylation affects the promoter uniformly or in patches with discrete clinical relevance; and, finally whether methylation of ABL1 reflects a generalized process or is gene-specific. To address these issues, the technique of methylation-specific PCR and bisulfite-sequencing was adapted to study the regulatory regions of ABL1 and other genes. In cell lines established from CML blast crisis, which only carry a single ABL1 allele nested within the BCR-ABL fusion gene, ABL1 promoters were universally methylated. In clinical samples from patients at advanced stages of the disease, both methylated and unmethylated promoter alleles were detectable. In colonies derived from single hematopoietic progenitors methylated and unmethylated promoter alleles were revealed as well. ABL1 methylation was was noted in the vast majority of colonies from blast crisis, but not chronic-phase CML. It was shown finally that ABL1 methylation does not reflect a generalized process and may be unique among DNA repair/genotoxic stress response genes. These data suggest that specific methylation of the Ph'-associated ABL1 allele accompanies clonal evolution in CML.

Alleles↗

PubMed1999

DLA-DRB1 histocompatibility genotyping using RT-nested PCR and cycle sequencing.

Class-II histocompatibility genes are associated with predisposition to autoimmune diseases in many mammal species. We have developed a technique using reverse transcriptase and nested-PCR for amplification from blood samples of expressed sequences encoded by canine DLA-DRB1 loci. In the first polymerase chain reaction (PCR), we utilize primers DR-SP and DR-STOP as developed by Sarmiento et al. (1990). In the nested PCR, we utilize two additional primers, namely primer 57 [5'-TCTTGGAGGCTCCTGGATGACAGC-3'] and primer 367 [5'-CACAACTACGGGGTGATTGAGAGC-3'] to produce a 334 bp amplified product. After digestion with restriction endonucleases, some of the alleles can be identified by restriction fragment length polymorphism (RFLP). The increasing information on new DLA-DRB1 alleles over the last two years renders the DLA-DRB1 too diverse for convenient use of RFLP. However, the expressed sequences amplified by our protocol can be conveniently identified by cycle sequencing. This RT n-PCR protocol will suffice for the genotyping of individual dogs at the DLA-DRB1 locus.

Alleles↗

PubMed2005

[Molecular analysis of telomere length in follicular lymphomas. Its participation in tumor progression].

Telomeres are essential for maintaining chromosomal integrity and stability. We studied here telomere length (TL) in bone marrow and/or lymph node from 36 patients: 29 with follicular lymphoma (FL) at diagnosis and 7 with diffuse large B cell lymphoma secondary to FL (S-DLBCL). TL was evaluated using terminal restriction fragments (TRF) assay. BCL-2 gene rearrangement was analyzed by nested and long distance PCR. Mean TRF values showed significant telomere shortening in FL (4.18 +/- 0.18 Kb) and S-DLBCL (3.31 +/- 0.25 Kb) respect to controls (8.50 +/- 0.50 Kb) (p<0.001). Differences between both histological subtypes (p=0.036) were also detected. Moreover, the samples positive for BCL-2 rearrangements showed longer TL (4.25 +/- 0.19 Kb) than the negative ones (3.39 +/- 0.30 Kb) (p=0.023). A trend to telomere shortening was observed when Major Breakpoint Region (MBR-JH), minor cluster region (mcr-JH) and BCL-2 negative patients were compared (4.35 +/- 0.21 Kb; 3.84 +/- 0.45 Kb and 3.39 +/- 0.30 Kb, respectively). Our results show a TL reduction in FL and S-DLBCL, with significant short TRFs in the last group, suggesting the participation of telomere shortening in tumor progression. Furthermore, the differences detected between BCL-2 positive and negative FL support the involvement of diverse pathogenic mechanisms.

Adult↗

PubMed2005

Conservation implications of complex population structure: lessons from the loggerhead turtle (Caretta caretta).

Complex population structure can result from either sex-biased gene flow or population overlap during migrations. Loggerhead turtles (Caretta caretta) have both traits, providing an instructive case history for wildlife management. Based on surveys of maternally inherited mtDNA, pelagic post-hatchlings show no population structure across the northern Atlantic (phi(ST) < 0.001, P = 0.919), subadults in coastal habitat show low structure among locations (phi(ST) = 0.01, P < 0.005), and nesting colonies along the southeastern coast of the United States have strong structure (phi(ST) = 0.42, P < 0.001). Thus the level of population structure increases through progressive life history stages. In contrast, a survey of biparentally inherited microsatellite DNA shows no significant population structure: R(ST) < 0.001; F(ST) = 0.002 (P > 0.05) across the same nesting colonies. These results indicate that loggerhead females home faithfully to their natal nesting colony, but males provide an avenue of gene flow between regional nesting colonies, probably via opportunistic mating in migratory corridors. As a result, all breeding populations in the southeastern United States have similar levels of microsatellite diversity (H(E) = 0.70-0.89), whereas mtDNA haplotype diversity varies dramatically (h = 0.00-0.66). Under a conventional interpretation of the nuclear DNA data, the entire southeastern United States would be regarded as a single management unit, yet the mtDNA data indicate multiple isolated populations. This complex population structure mandates a different management strategy at each life stage. Perturbations to pelagic juveniles will have a diffuse impact on Atlantic nesting colonies, mortality of subadults will have a more focused impact on nearby breeding populations, and disturbances to adults will have pinpoint impact on corresponding breeding populations. These findings demonstrate that surveys of multiple life stages are desirable to resolve management units in migratory marine species.

Analysis of Variance↗

PubMed2006

[Effect of co-expressing M-bcr/abl and m-bcr/abl fusion gene transcripts on the clinical features of patients with chronic myelogenous leukemia at diagnosis].

OBJECTIVE: To study the effect of co-expressing M-bcr/abl and m-bcr/abl fusion gene transcripts on the clinical features of the patients with chronic myelogenous leukemia (CML) at diagnosis. METHODS: m-bcr/abl fusion gene transcripts were detected by nested PCR. RESULTS: The percentage of the CML patients who co-expressed M-bcr/abl and m-bcr/abl was 51.4% at diagnosis. Comparison of the patients who co-expressed and those who expressed M-bcr/abl alone showed there was no difference in their hemoglobin concentrations, WBC counts, neutrophilic alkaline phosphatase (NAP) stains, Ph chromosomes and hepatosplenomegaly; however, significant difference in platelet count was seen. In the patients with b3a2 who co-expressed m-bcr/abl, an increased platelet count was noted, compared with that of patients with M-bcr/abl alone. But in patients with b2a2, the two groups showed no difference in all clinical features. Two patients had priapism, their m-bcr/abl being negative. CONCLUSIONS: CML patients who co-expressed b3a2 and m-bcr/abl showed a tendency to have an increased platelet count at diagnosis. Co-expressing m-bcr/abl has no the effect on the clinical features of CML patients with b2a2.

Adolescent↗

PubMed2000

Identification and characterization of alternative splice products encoded by the human phosphotyrosyl phosphatase activator gene.

The phosphotyrosyl phosphatase activator (PTPA), a protein phosphatase 2A (PP2A) regulatory protein, specifically stimulates the phosphotyrosyl phosphatase activity of PP2A in vitro. Human PTPA is encoded by a single gene, the structure and chromosomal localization of which have been determined in our previous work. In this paper, we report the identification and characterization of six additional splice variants, termed PTPAbeta to PTPAeta, in addition to the originally identified PTPAalpha form. Interestingly, PTPAbeta and PTPAgamma contain a novel exon that had been overlooked in the formerly identified gene structure. As revealed by nested PCR, all these PTPA transcripts are expressed in various human cDNA libraries and cell lines. However, a quantitative approach, using a single PCR reaction followed by detection of the reaction products with a radioactively labeled probe, revealed only PTPAalpha, beta and delta, suggesting that the other transcripts are expressed very poorly. In vitro transcription-translation revealed that only PTPAalpha, beta, delta and epsilon are translated into functional proteins, whereas translation of PTPAgamma, zeta and eta is stopped prematurely due to a frameshift resulting from skipping exon 2, suggesting that the latter isoforms may result from splicing errors. By western analysis of HepG2 and Saos-2 cell extracts, only PTPAalpha and beta were detected. PTPAalpha and beta were expressed as GST fusion proteins in bacteria, and were found to contain the same specific phosphotyrosyl phosphatase stimulatory activity towards PP2A. The identification of this family of PTPA variants adds another level of complexity to the in vivo function(s) of PTPA, opening up the possibility that different isoforms may perform different functions.

Alternative Splicing↗