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At least 415 records · Page 23Linked to original sources

PubMed2002

The p23 protein of citrus tristeza virus controls asymmetrical RNA accumulation.

Citrus tristeza virus (CTV), a member of the Closteroviridae, has a 19.3-kb positive-stranded RNA genome that is organized into 12 open reading frames (ORFs) with the 10 3' genes expressed via a nested set of nine or ten 3'-coterminal subgenomic mRNAs (sgRNAs). Relatively large amounts of negative-stranded RNAs complementary to both genomic and sgRNAs accumulate in infected cells. As is characteristic of RNA viruses, wild-type CTV produced more positive than negative strands, with the plus-to-minus ratios of genomic and sgRNAs estimated at 10 to 20:1 and 40 to 50:1, respectively. However, a mutant with all of the 3' genes deleted replicated efficiently, but produced plus to minus strands at a markedly decreased ratio of 1 to 2:1. Deletion analysis of 3'-end genes revealed that the p23 ORF was involved in asymmetric RNA accumulation. A mutation which caused a frameshift after the fifth codon resulted in nearly symmetrical RNA accumulation, suggesting that the p23 protein, not a cis-acting element within the p23 ORF, controls asymmetric accumulation of CTV RNAs. Further in-frame deletion mutations in the p23 ORF suggested that amino acid residues 46 to 180, which contained RNA-binding and zinc finger domains, were indispensable for asymmetrical RNA accumulation, while the N-terminal 5 to 45 and C-terminal 181 to 209 amino acid residues were not absolutely required. Mutation of conserved cysteine residues to alanines in the zinc finger domain resulted in loss of activity of the p23 protein, suggesting involvement of the zinc finger in asymmetric RNA accumulation. The absence of p23 gene function was manifested by substantial increases in accumulation of negative-stranded RNAs and only modest decreases in positive-stranded RNAs. Moreover, the substantial decrease in the accumulation of negative-stranded coat protein (CP) sgRNA in the presence of the functional p23 gene resulted in a 12- to 15-fold increase in the expression of the CP gene. Apparently the excess negative-stranded sgRNA reduces the availability of the corresponding positive-stranded sgRNA as a messenger. Thus, the p23 protein controls asymmetric accumulation of CTV RNAs by downregulating negative-stranded RNA accumulation and indirectly increases expression of 3' genes.

Amino Acid Sequence↗

PubMedDate not supplied

Correlation between p53 gene mutation, p53 protein labeling and PCNA expression in oral squamous cell carcinomas.

BACKGROUND: The prevalence of oral squamous cell carcinoma (OSCC) among the Black community in South Africa is unacceptably high. The association between p53 protein, and PCNA overexpression and the presence of p53 gene mutations was evaluated. MATERIALS AND METHODS: One hundred and ten formalin-fixed, paraffin-embedded blocks of OSCC were selected for immunohistochemical studies for p53 protein and PCNA expression using the DO-7 and PC10 monoclonal antibodies, respectively. DNA was extracted from fifty-five blocks and exons 5 to 9 of the p53 gene were amplified with nested primers, thereafter sequencing was performed to confirm the presence of mutations detected by single stranded conformational polymorphism. RESULTS: Fifty-six cases (51%) showed p53 expression, while fourteen mutations (25%) were detected. A significant difference was found between the PCNA index in p53 positive and p53 negative tumors while the mean PCNA index for the tumors with p53 mutations was not significantly different from the tumors without mutations. CONCLUSIONS: No association between p53 protein overexpression and p53 gene mutations could be demonstrated.

Adult↗

PubMed2001

Sequence analysis of the DRB1 promoter reveals limited polymorphism with no influence on gene expression.

HLA-class II promoters contain a set of conserved regulatory regions necessary for constitutive and induced gene expression. For the HLA-DQB as well as for the DRB1 promoter sequence, polymorphisms with influence on gene expression have been reported. In contrast to these data we could show that there is very limited allele-specific polymorphism among the HLA-DRB1 promoter alleles. In a long range PCR we amplified a DNA sequence containing the promoter and the second exon of the DRB1 gene in one fragment. Nested PCR products of this PCR fragment for the promoter and for the second exon were analysed by DNA sequencing to allow the linkage of a promoter to its DR allele. Most investigated DRB1 alleles exhibited the same promoter consensus sequence except for two point mutations. An A to T transversion (position -70 bp) was closely associated with DRB1*08, whereas a C-deletion (position -30 bp) was most commonly observed together with DRB1*10. Both polymorphisms did not influence promoter activity in luciferase reporter gene assays.

Base Sequence↗

PubMed2000

Determination of human immunodeficiency virus type 1 subtypes in Taiwan by vpu gene analysis.

The genetic diversity of human immunodeficiency virus (HIV) type 1 (HIV-1) has been characterized mainly by analysis of the env and gag genes. Information on the vpu genes in the HIV sequence database is very limited. In the present study, the nucleotide sequences of the vpu genes were analyzed, and the genetic subtypes determined by analysis of the vpu gene were compared with those previously determined by analysis of the gag and env genes. The vpu genes were amplified by nested PCR of proviral DNA extracted from 363 HIV-1-infected individuals and were sequenced directly by use of the PCR products. HIV-1 subtypes were determined by sequence alignment and phylogenetic analysis with reference strains. The strains in all except one of the samples analyzed could be classified as subtype A, B, C, E, or G. The vpu subtype of one strain could not be determined. Of the strains analyzed, genetic subtypes of 247 (68.0%) were also determined by analysis of the env or gag gene. The genetic subtypes determined by vpu gene analysis were, in general, consistent with those determined by gag and/or env gene analysis except for those for two AG recombinant strains. All the strains that clustered with a Thailand subtype E strain in the vpu phylogenetic analyses were subtype E by env gene analysis and subtype A by gag gene analysis. In summary, our genetic typing revealed that subtype B strains, which constituted 73.8% of all strains analyzed, were most prevalent in Taiwan. While subtype E strains constituted about one-quarter of the viruses, they were prevalent at a higher proportion in the group infected by heterosexual transmission. Genetic analysis of vpu may provide an alternate method for determination of HIV-1 subtypes for most of the strains, excluding those in which intersubtype recombination has occurred.

Amino Acid Sequence↗

PubMed2004

Promoter activity and regulation of the corneal CYP4B1 gene by hypoxia.

Hypoxic injury to the ocular surface provokes an inflammatory response that is mediated, in part, by corneal epithelial-derived 12-hydroxyeicosanoids. Recent studies indicate that a cytochrome P450 (CYP) monooxygenase, identified as CYP4B1, is involved in the production of these eicosanoids which exhibit potent inflammatory and angiogenic properties. We have isolated and cloned a corneal epithelial CYP4B1 full-length cDNA and demonstrated that the CYP4B1 mRNA is induced by hypoxia in vitro and in vivo. To further understand the molecular regulation that underlies the synthesis of these potent inflammatory eicosanoids in response to hypoxic injury, we isolated and cloned the CYP4B1 promoter region. GenomeWalker libraries constructed from rabbit corneal epithelial genomic DNA were used as templates for primary and nested PCR amplifications with gene- and adaptor-specific primers. A 3.41-kb DNA fragment of the 5'-flanking region of the CYP4B1 promoter was isolated, cloned, sequenced, and analyzed by computer software for the presence of known cis-acting elements. Analysis of the promoter sequence revealed the presence of consensus DNA binding sequences for factors known to activate gene transcription in response to hypoxia including HIF-1, NFkappaB, and AP-1. Transient transfection of luciferase reporter (pGL3-Basic) vectors containing different lengths of the CYP4B1 promoter fragment demonstrated hypoxia-induced transcription in rabbit corneal epithelial (RCE) cells. Electrophoretic mobility shift assay (EMSA) revealed a marked induction of nuclear binding activity for the labeled HIF-1 probe from the CYP4B1 promoter in nuclear extracts of cells exposed to hypoxia. This binding activity was due to sequence-specific binding to the HIF-1 oligonucleotide probe as shown by competition with excess unlabeled probe for the HIF-1 but not with unlabeled NFkappaB probe. The nuclear binding activity of AP-1 and NFkappaB probes from the CYP4B1 promoter was also enhanced in response to hypoxia suggesting that these transcription factors contribute to the hypoxic induction of CYP4B1 expression. The results of this study provide the first molecular mechanistic explanation for the induction of CYP4B1 and, thereby, the production of inflammatory eicosanoids in response to hypoxic injury. Further studies are needed to fully evaluate the molecular regulation of this gene during inflammation.

Animals↗

PubMed1998

Further complexity of the human SOX gene family revealed by the combined use of highly degenerate primers and nested PCR.

SOX proteins contain a conserved HMG-related DNA-binding domain. They fulfill essential functions during the development of animals. Mutations in several SOX genes have been implicated in human diseases. We present here a new set of PCR primers designed to amplify a broad range of SOX HMG-box sequences. These primers facilitated the cloning of several new SOX HMG boxes from human genomic DNA, revealing unexpected complexity of the SOX gene family.

Amino Acid Sequence↗

PubMed1996

Low-grade gastric B-cell lymphoma of mucosa-associated lymphoid tissue: clinicopathologic analysis of 19 cases.

Low-grade gastric B-cell lymphoma of mucosa-associated lymphoid tissue type (MALToma) is a recently recognized disease entity. We report the clinicopathologic features of 19 patients with MALToma in Taiwan. The 19 patients included eight men and 11 women, ranging in age from 26 to 77 years, with a mean age of 58.8 years. Most complained of abdominal pain or gastrointestinal bleeding. The endoscopic and gross features of the gastric lesions revealed erosion (flat type), ulceration (depressed type), cobblestone appearance or abnormal gastric folds (elevated type), mimicking chronic gastritis, ulcer or early gastric carcinoma. Typical histopathologic features included lymphoepithelial lesion and extensive mucosal infiltration of centrocyte-like cells in all cases. Clonality analysis of the variable-diversity-joining region of the immunoglobulin gene by semi-nested polymerase chain reaction demonstrated monoclonality in 72% of the cases. Helicobacter pylori bacilli (H. pylori) could be identified on histologic sections in 15 cases (78.9%); the serologic test for H. pylori was positive in 12 of 13 patients tested (92%). In six patients receiving triple therapy (amoxicillin, bismuth subcitrate and metronidazole), five showed significant histologic regression with eradication of H. pylori 4 to 6 months after the start of treatment; one patient showed persistent lesions and presence of H. pylori. However, persistence of residual lymphoid cells and monoclonality of the immunoglobulin gene, could still be demonstrated in four cases. Of nine patients treated with surgery or chemotherapy, two died: one due to concomitant gastric carcinoma and the other one due to sudden apnea. No recurrence was observed in the remaining seven patients. The remaining four patients were lost to follow-up. Our experience confirmed that gastric MALToma is a low-grade neoplastic process. The dramatic response of gastric MALToma to anti-H. pylori treatment suggests that H. pylori infection is closely related to the pathogenesis of low-grade gastric MALToma. However, long-term follow-up is mandatory due to the persistence of the monoclonality of the immunoglobulin gene in the residual lymphoid cells after treatment.

Adult↗

PubMed1993

The Drosophila 78C early late puff contains E78, an ecdysone-inducible gene that encodes a novel member of the nuclear hormone receptor superfamily.

We report the molecular definition of an early late puff locus, at position 78C, that is inducible by ecdysone at the onset of Drosophila metamorphosis. This puff contains a single ecdysone-inducible gene consisting of two nested transcription units, E78A and E78B. E78A mRNA is expressed during a brief interval in mid-pupal development and encodes a novel member of the nuclear hormone receptor superfamily. E78B encodes a truncated receptor isoform that lacks the DNA-binding domain and is predominantly expressed at puparium formation and immediately following E78A in pupae. E78B is directly inducible by ecdysone in late third instar larvae and depends on ecdysone-induced protein synthesis for its maximal level of expression. These observations indicate that E78 represents a distinct subset of early ecdysone-inducible regulatory genes.

Amino Acid Sequence↗

PubMed1994

Selective interaction of a subset of interferon-gamma response element-binding proteins with the intercellular adhesion molecule-1 (ICAM-1) gene promoter controls the pattern of expression on epithelial cells.

Intercellular adhesion molecule-1 (ICAM-1) modulates epithelial and endothelial leukocyte adherence, but epithelial cell ICAM-1 levels (unlike endothelial cell levels) are selectively sensitive to interferon-gamma (IFN-gamma). Nuclear run-off assays indicated that IFN-gamma regulation of epithelial ICAM-1 levels occurs at a transcriptional level, so the basis for selective cytokine control of ICAM-1 expression was investigated using the ICAM-1 gene promoter region. A plasmid construct containing 5.0 kilobases of ICAM-1 gene 5'-flanking region fused to a reporter gene was selectively responsive to IFN-gamma in (human tracheal) epithelial cells but not in (human umbilical vein) endothelial cells, indicating that this region is sufficient to mediate proper cell-specific expression. An IFN-gamma response element (IRE) was localized to a DNA segment (nucleotides -130 to -94) in the ICAM-1 gene by comparisons of nested 5'-deletional constructs and by demonstrating that this segment confers IFN-gamma responsiveness on heterologous promoters. This same IRE formed a single major binding complex (IRE-BC) in gel retardation assays with nuclear proteins from IFN-gamma-stimulated but not unstimulated epithelial cells, and mutation of the IRE consensus motif (TTTCCGGGAAA at -116 to -106) resulted in loss of IRE-protein binding and abolished IFN-gamma responsiveness, indicating that this sequence is required for ICAM-1 IRE function. Comparison of the ICAM-1 IRE to DNA elements that confer IFN responsiveness in other human genes indicated similarity only to response regions in the Fc gamma RI and IRF-1 genes. The findings provide evidence for a distinct IRE subset that combines a DNA element common to all IFN-responsive genes (GAAA) with a distinct flanking sequence (the inverted repeat GAAA) in order to fine-tune IFN responses and activate a subset of immune response genes (ICAM-1, Fc gamma RI, and IRF-1).

Base Sequence↗

PubMed1998

Intragenic variability of human cytomegalovirus glycoprotein B in clinical strains.

Human cytomegalovirus (HCMV) strains can be classified into four glycoprotein B (gB) genotypes, and there has been evidence of differences in viral virulence. In this study, intragenic variability of HCMV gB strains was analyzed. The gB gene was amplified by nested polymerase chain reaction using samples from immunosuppressed patients. The genotype of fragments corresponding to the cleavage site of gB was determined by restriction fragment analysis; fragments corresponding to the N- and C-termini (gBn and gBc) were sequenced and compared with published sequences. At the cleavage site, the four known genotypes were found. Typing revealed four major genotypes at the N-terminus and two at the C-terminus. In 22 of 44 strains, the gB type determined at the cleavage site was different from the gBn or gBc type (or either), indicating that intragenic variability within the gB gene occurs frequently.

Base Sequence↗

PubMed2005

[RT-PCR detecting NUP98-HOX fusion gene in leukemia].

To investigate whether there are NUP98-HOXA, NUP98-HOXB, NUP98-HOXC, NUP98-HOXD fusion genes in leukemia patients in Xinjiang, cellular total RNA was extracted from the bone marrow mononuclear cells, the formaldehyde-agarose gel electrophoresis was used to judge whether RNA was intact, the 17 RT-PCR primers were designed to amplify the predicted fusion junctions and 412 bp GAPDH was used as an internal control, NUP98-HOXA fusion genes were amplified by nested-PCR following reverse transcription. One-step PCR was performed to amplify the other predicted fusion genes. The results showed that RNA was proved to be intact and expression of GAPDH was found in every sample. However, no predicted fusion transcripts were detected in leukemia patients. In conclusion, no NUP98-HOX fusion genes were detected in the samples from Xinjiang.

Adult↗

PubMed1989

Intronic positioning maximizes co-expression and co-amplification of nonselectable heterologous genes.

The overproduction of heterologous gene products in mammalian cells is often a prerequisite for studies of protein structure, function, and therapeutic efficacy. We report that recombinant fusion of a nonselectable reporter template into the intronic sequences of an amplifiable minigene gives dramatically enhanced co-expression efficiency in stable, primary transformants. Further incremental selective pressure for marker gene amplification results in the rapid acquisition of very high expression levels from the intronically positioned reporter. Nested within a constitutively expressing gene, these templates can be independently regulated at moderate gene dosage levels. Intronic positioning may therefore be of general utility for a variety of recombinant studies.

Animals↗

PubMed2006

Genetic characterization of GRA6 genes from Toxoplasma gondii from pigs in Okinawa, Japan.

Toxoplasma gondii from pigs in Okinawa Prefecture was characterized by nested PCR-restriction fragment length polymorphism (RFLP) and DNA sequence analysis of the dense granule antigen GRA6 gene. By nested PCR, parasite DNA was detected in 33 out of 91 lymph node samples with lesions similar to those found in toxoplasmosis samples that had been collected from pigs at an abattoir. RFLP analysis with MseI was successfully conducted in 29 of 33 PCR-positive samples to group the isolates into one of the three genotypes of T. gondii. Genotyping of the 29 studied samples rendered the following results: 13 of type I (44.8%), 14 of type II (48.3%), and 2 of type III (6.9%). The GRA6 genes of 12 Okinawa isolates were cloned and sequenced. Nine new nucleotide sequences were found, and nucleotide substitutions specific for the Okinawa isolates were found at 13 positions. Phylogenetic analysis indicated that all GRA6 sequences were divided into one of the 3 main groups, and Okinawa isolates of GRA6 genotypes II and III seemed to be closely related to the Beverley strain and the NED strain, respectively. The results from this study may provide basic and useful information for the analysis of the molecular epidemiology of T. gondii infection within Japan.

Amino Acid Sequence↗

PubMed2003

A simple method for obtaining cell-specific cDNA from small numbers of growing root-hair cells in Arabidopsis thaliana.

A simple and rapid method for cloning specific cDNAs from mRNA populations derived solely from small numbers of root-hair cells is described here. To identify genes expressed during the earliest visible stage of root-hair cell development, cell contents were aspirated from small numbers of Arabidopsis root-hair cells at or just before this stage. This material was used to make reusable solid-phase oligo-dT-primed cDNA libraries. To demonstrate that the libraries contained high quality longer cDNAs, a fragment located 2.7 kb from the 3' end of the cDNA of the single copy root-hair expressed gene RHD3 was cloned using a nested PCR strategy. This technique was also used to obtain novel gene expression information by cloning the full-length 0.85 kb cDNA of the Rop2 GTPase from this library. This approach offers a means of cloning larger cDNAs directly from small numbers of growing root-hair cells and, potentially, other epidermal cell types.

Arabidopsis↗

PubMed2002

High frequency of LOH, MSI and abnormal expression of FHIT in gastric cancer.

The FHIT gene is a putative tumour suppressor gene. In this study, we analysed a set of 50 gastric tumours for alterations of FHIT, and found 38 of 45 tumours (84%) exhibiting loss of heterozygosity (LOH) within the FHIT gene. We used both nested Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) and single step RT-PCR to analyse the FHIT transcripts and found 34 of 39 (87%) tumours and seven of the 11 (64%) corresponding non-cancerous tissues showed low or aberrant expression of FHIT mRNA and the appearance of the aberrant FHIT transcripts depended on the conditions of the RT-PCR. In these aberrant transcripts, frequent deletions and/or insertions were detected by direct sequencing. All breakpoints for deletions and insertions were at splicing sites. All insertions came from the adjacent introns, whose appearance was completely in accordance with the 'GU-AG' rule for pre-mRNA splicing. It may be suggested that an alternative splicing mechanism functions in the formation of these aberrant transcripts. The fragile nature of FRA3B within the FHIT gene could be responsible for the formation of the aberrant mRNA. Negative or reduced Fhit expression was detected in 39 of 50 tumours (78%). Moreover, an association was found between abnormal Fhit expression and positive node status (P=0.012). Thirteen of 48 tumours (27%) displayed microsatellite instability (MSI), among which 10 tumours also showed MSI within the FHIT gene. Furthermore, we detected an association between MSI and negative node status (P=0.02). We conclude that the abnormalities of FHIT, presumably associated with the unstable nature of FRA3B within the FHIT gene, are involved in the carcinogenesis of gastric cancer, and lack of mismatch repair (MMR) could possibly promote its alteration in a subset of gastric tumours.

Acid Anhydride Hydrolases↗

PubMed2005

[Genetic polymorphism of tumor necrosis factor-alpha in patients with chronic benzene poisoning].

OBJECTIVE: To study the relationship between genetic polymorphism of tumor necrosis factor-alpha (TNF-alpha, sites at -238 nt and -308 nt) and susceptibility to chronic benzene poisoning. METHOD: The polymorphism of TNF-alpha gene were detected by nested polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique from 50 benzene poisoning patients and 60 control individuals exposed to benzene. RESULTS: The frequency of the TNF-alpha-238G/G, A/G and A/A in controls (95%, 5% and 0%, respectively), were not significantly different from those in patients (92%, 6% and 2%, respectively, P > 0.05). The frequency of the TNF-alpha-308G/G, A/G and A/A in patients were 76%, 24% and 0% respectively, and that in control individuals were 93%, 7% and 0% respectively. Chi(2) test showed that frequency of TNF-alpha-308A/G in patients was significantly higher than that in controls (chi(2) = 6.22, P = 0.013). Logistic analysis showed that TNF-alpha-308A/G was the independent risk factor of benzene poisoning (OR = 5.3, P < 0.05). CONCLUSION: Individuals with TNF-alpha-308A/G gene polymorphism are susceptible to benzene poisoning.

Adult↗

PubMed1997

[Genetic subtyping of HIV-1 strains by heteroduplex mobility assay].

DNA fragments of HIV-1 env gene were amplified by nested PCR from uncultured peripheral blood mononuclear cells (PBMCs) obtained from 24 HIV-1 infected individuals. The PCR products were separated by melting and annealing with denatured PCR product prepared from reference plasimd of representative subtypes. Heteroduplex were then formed between the single-stranded DNA from the two sources and were analysed on polyacrylamide gels. The results from heteroduplex mobility assay (HMA) were compared with HIV-1 subtype results determined by DNA sequencing. With advantages of high speed, low cost and high specificity, HMA is a reliable screening method for HIV-1 subtyping.

Acquired Immunodeficiency Syndrome↗

PubMed2001

A comparison of ammonia-oxidiser populations in eutrophic and oligotrophic basins of a large freshwater lake.

A combination of PCR amplification and oligonucleotide probing was used to investigate the populations of ammonia-oxidisers of the beta-Proteobacteria in the eutrophic and oligotrophic basins of Lake Windermere, a large temperate lake in the English Lake District. Numbers of ammonia-oxidisers (MPN) in the Windermere lakewater were low (< 100 cells ml(-1)) throughout the year with the exception of peaks in August, which coincided with stratification, and November in the South Basin where overturn may have introduced ammonia-oxidising bacteria into the water column. Sediment samples contained larger populations of ammonia oxidisers, usually ca. 10(4) per g. dry weight, which remained relatively constant throughout the seasonal cycle in both Basins. DNA was recovered from lakewater and sediment samples and Nitrosospira and N. europaea-eutropha lineage 16S rRNA genes amplified in a nested PCR reaction, with confirmation of identity by oligonucleotide hybridisation. Nitrosospira 16S rDNA was readily detected in all samples and therefore found to be ubiquitous. In contrast, nitrosomonad DNA of the N. europaea-eutropha lineage could only be detected in the oligotrophic North Basin. Enrichment cultures of lakewater samples only exhibited nitrification at low (0.67 mM) and medium (5 mM) ammonium concentrations, whilst sediment enrichments nitrified at all concentrations tested including high (12.5 mM) ammonium medium. These data suggest that ammonia-oxidiser populations may be physiologically distinguished between lakewater and sediment, and that species distribution in a single lake is non-uniform.

Ammonia↗