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PubMed1998

Differential mucin MUC7 gene expression in invasive bladder carcinoma in contrast to uniform MUC1 and MUC2 gene expression in both normal urothelium and bladder carcinoma.

Mucins (MUCs) are high molecular weight membrane glycoproteins. The gene expression of MUCs (MUC1-MUC8) may change characteristically during malignant transformation of epithelial tissues. Total RNA was isolated from the four bladder cancer cell lines RT4, 647V, HT1376, and 486P (pathological gradings between G1 and G4) and 17 samples of transitional cell carcinomas, as well as 16 samples of normal human urothelium of the bladder from surgically removed specimens. The RNA samples were studied with MUC1-, MUC2- and MUC7-specific nested reverse transcription-PCRs. Gene expression of MUC1 and MUC2 was found positive in all normal, as well as in malignant, tissue samples and in the tumor cell lines. In contrast, gene expression of MUC7 was only detected in bladder cancer cell lines and samples of invasive transitional cell carcinomas, but neither in superficial, noninvasive bladder tumors nor normal bladder urothelium. Only one of the samples of normal urothelium obtained from 16 different tumor-bearing bladders was positive for MUC7 gene expression. These results suggest a differential MUC7 gene expression with the onset of malignant transformation of the bladder urothelium.

Carcinoma, Transitional Cell↗

PubMed1998

Whole cell protein and partial 16S rRNA gene sequence analysis suggest the existence of a second Rothia species.

OBJECTIVE: To subject ten clinical isolates grouped together based on their biochemical and microbiological profile to further investigations aimed at correct species identification. METHODS: The 16S rRNA gene was partially sequenced using nested amplification. Whole cell protein analysis (SDS-PAGE) and cluster analysis were performed on the 10 strains and also for comparison on 31 reference strains. The API Coryne biochemical kit as well as API 20 Strep were used for analysis of the phenotypic diversity of the strains by use of computerized numerical identification procedures. Antibiotic susceptibility testing was performed using a standardized disk diffusion test. RESULTS: The 265--556-bp-long 16S rRNA gene sequences of all 10 strains showed highest similarity to Rothia dentocariosa. Three strains showed complete identity between the sequences obtained and the sequence of the type strain of Rothia dentocariosa 16S rRNA gene (M59055), and the other seven ranged between 99.7% and 98.3% similarity. Detailed analysis of the sequences revealed a clustering of the strains into two groups. One group consisted of four isolates with the highest degrees of similarity with the reference strain (type I), while the members of another group (type II) showed differences in their nucleotide sequence at four distinct positions in the variable V7 region. T was replaced by C at position 597, C by T at position 608, T by C at position 610, and G by A at position 684 (position numbers according to reference sequence M59055, EMBL/GenBank). Whole cell protein analysis (SDS-PAGE) and cluster analysis also segregated the 10 Rothia dentocariosa strains into two different clusters, with one cluster containing all four strains belonging to 16S rRNA gene type I, and a second cluster containing all six strains belonging to 16S rRNA gene type II. CONCLUSIONS: Partial sequence data of the 16S rRNA gene as well as whole cell protein analysis showed a subdivision of the Rothia species into two groups, genomovar I (Rothia dentocariosa sensu stricto) and genomovar II, a possible new Rothia species.

Journal Article↗

PubMed2001

Non-detection of Chlamydia species in carotid atheroma using generic primers by nested PCR in a population with a high prevalence of Chlamydia pneumoniae antibody.

BACKGROUND: The association of Chlamydia pneumoniae with atherosclerosis is controversial. We investigated the presence of C. pneumoniae and other Chlamydia spp. in atheromatous carotid artery tissue. METHODS: Forty elective carotid endarterectomy patients were recruited (27 males, mean age 65 and 13 females mean age 68), 4 had bilateral carotid endarterectomies (n= 44 endarterectomy specimens). Control specimens were taken from macroscopically normal carotid artery adjacent to the atheromatous lesions (internal controls), except in 8 cases where normal carotid arteries from post mortem (external controls) were used. Three case-control pairs were excluded when the HLA DRB gene failed to amplify from the DNA. Genus specific primers to the major outer membrane protein (MOMP) gene were used in a nested polymerase chain reaction (nPCR) in 41 atheromatous carotid specimens and paired controls. PCR inhibition was monitored by spiking with target C. trachomatis. Atheroma severity was graded histologically. Plasma samples were tested by microimmunofluorescence (MIF) for antibodies to C. pneumoniae, C. trachomatis and C. psittaci and the corresponding white cells were tested for Chlamydia spp. by nPCR. RESULTS: C. pneumoniae was not detected in any carotid specimen. Twenty-five of 38 (66%) plasma specimens were positive for C. pneumoniae IgG, 2/38 (5%) for C. trachomatis IgG and 1/38 (3%) for C. psittaci IgG. CONCLUSIONS: We were unable to show an association between the presence of Chlamydia spp. and atheroma in carotid arteries in the presence of a high seroprevalence of C. pneumoniae antibodies in Northern Ireland.

Adult↗

PubMed2005

Phylogeography and population genetics of the endangered Amazonian manatee, Trichechus inunguis Natterer, 1883 (Mammalia, Sirenia).

We used mitochondrial DNA control region sequences to examine phylogeography and population differentiation of the endangered Amazonian manatee Trichechus inunguis. We observe lack of molecular differentiation among localities and we find weak association between geographical and genetic distances. However, nested clade analysis supports restricted gene flow and/or dispersal with some long-distance dispersal. Although this species has a history of extensive hunting, genetic diversity and effective population sizes are relatively high when compared to the West Indian manatee Trichechus manatus. Patterns of mtDNA haplotype diversity in T. inunguis suggest a genetic disequilibrium most likely explained by demographic expansion resulting from secession of hunting and enforcement of conservation and protective measures. Phylogenetic analysis of T. manatus and T. inunguis haplotypes suggests that T. inunguis is nested within T. manatus, effectively making T. manatus a paraphyletic entity. Paraphyly of T. manatus and recent divergence times of T. inunguis and the three main T. manatus lineages suggest a possible need for a taxonomic re-evaluation of the western Atlantic Trichechus.

Animals↗

PubMed2005

Porcine small intestine submucosa (SIS) is not an acellular collagenous matrix and contains porcine DNA: possible implications in human implantation.

Porcine small intestinal submucosa (SIS) has been recommended as a cell-free, biocompatible biomaterial for the repair of rotator cuff tendon tear. However, we have observed noninfectious edema and severe pain in patients who have undergone SIS implantation for tendon repair. The aim of this study was to conduct an independent assessment of the safety and efficacy of Restore SIS membrane. The Restore orthobiologic implant was examined by histology and the nested PCR technique using porcine immunoreceptor DAP12 gene to examine if SIS membrane contained porcine cells or DNA, respectively. The material was also implanted into mice and rabbits for the evaluation of biological reaction and inflammatory response. Restore SIS was found to contain multiple layers of porcine cells. Chloroacetate esterase staining showed that some of these cells were mast cells. Nested PCR of the DAP12 gene demonstrated that Restore SIS contained porcine DNA material. Subcutaneous implantation of Restore SIS membrane in mice, and in rabbits for rotator cuff tendon repair, showed that the membrane caused an inflammatory reaction characterized by massive lymphocyte infiltration. In conclusion, Restore SIS is not an acellular collagenous matrix, and contains porcine DNA. Our results contradict the current view that Restore SIS is a cell-free biomaterial, and that no inflammatory response is elicited by its implantation. We suggest that further studies should be conducted to evaluate the clinical safety and efficacy of SIS implant biomaterials.

Adaptor Proteins, Signal Transducing↗

PubMed1994

Positive and negative regulatory elements are involved in transcriptional control of the rat glucokinase gene in the insulin producing cell line HIT M2.2.2.

Nested deletion mutants of the 5' flanking region of the beta-cell transcription unit of the rat glucokinase gene (r beta GK) were fused to the CAT-reporter gene. Transient expression studies in HIT M2.2.2 and BHK21 cells revealed a distal (upstream of -359) and a proximal promoter region (between -278/-49) harbouring positive and negative regulatory elements. DNaseI footprinting revealed three protected areas between nucleotides -190 and -60. DNA-elements playing a crucial role in transcriptional control of the insulin genes (IEB- and CT-motifs) have been detected within the proximal promoter region and contribute to beta-cell specific gene regulation. 3' deletion analysis revealed that DNA-elements located downstream from transcription initiation sites (up to +123) contribute to transcriptional regulation.

Animals↗

PubMed1994

Rapid detection and identification of Candida albicans and Torulopsis (Candida) glabrata in clinical specimens by species-specific nested PCR amplification of a cytochrome P-450 lanosterol-alpha-demethylase (L1A1) gene fragment.

PCR of a Candida albicans cytochrome P-450 lanosterol-alpha-demethylase (P450-L1A1) gene segment is a rapid and sensitive method of detection in clinical specimens. This enzyme is a target for azole antifungal action. In order to directly detect and identify the clinically most important species of Candida, we cloned and sequenced 1.3-kbp fragments of the cytochrome P450-L1A1 genes from Torulopsis (Candida) glabrata and from Candida krusei. These segments were compared with the published sequences from C. albicans and Candida tropicalis. Amplimers for gene sequences highly conserved throughout the fungal kingdom were first used; positive PCR results were obtained for C. albicans, T. glabrata, C. krusei, Candida parapsilosis, C. tropicalis, Cryptococcus neoformans, and Trichosporon beigelii DNA extracts. Primers were then selected for a highly variable region of the gene, allowing the species-specific detection from purified DNA of C. albicans, T. glabrata, C. krusei, and C. tropicalis. The assay sensitivity as tested for C. albicans in seeded clinical specimens such as blood, peritoneal fluid, or urine was 10 to 20 cells per 0.1 ml. Compared with results obtained by culture, the sensitivity, specificity, and efficiency of the species-specific nested PCR tested with 80 clinical specimens were 71, 95, and 83% for C. albicans and 100, 97, and 98% for T. glabrata, respectively.

Amino Acid Sequence↗

PubMed1996

The mode of expression and promoter analysis of the arcA gene, an auxin-regulated gene in tobacco BY-2 cells.

The arcA, a member of the G protein beta-subunit family, was isolated from tobacco BY-2 cells as an auxin-responsive gene. Characterization of arcA, which should help to elucidate the function of the gene product in the plant cells, was performed with emphasis on the mode of expression and the analysis of its promoter. Accumulation of the arcA message was detected only after treatments with auxins and not after treatments with other phytohormones or CdCl2, implying that responsiveness of arcA was exclusive to auxin. The putative arcA promoter region was fused to a reporter gene for beta-glucuronidase (GUS), and transient expression was analyzed in tobacco BY-2 cells. Two series of arcA promoter/GUS chimeric genes were constructed. One consisted of a set of 5' nested deletions of the arcA promoter connected to the gene for GUS and the other consisted of a variety of the arcA promoter fragments fused to a minimal promoter-GUS construct. The results indicated that the promoter sequence covering four sets of direct repeats (-562 to -167) was necessary for the sufficient response of arcA promoter to auxin in BY-2 cells. Moreover, irrespective of auxin treatment, elevated activity of GUS driven by this promoter fragment was detected, a result that implies that this region behaves an enhancer in BY-2 cells.

Base Sequence↗

PubMed2006

Immunoglobulin heavy chain locus events and expression of activation-induced cytidine deaminase in epithelial breast cancer cell lines.

When cells transform, phenotypic and genetic profiles can be dramatically altered. Nevertheless, a recent report identifying IgG in breast cancer cells was unexpected, revealing differentiation features normally associated with B lymphocytes. To extend these findings, we focused on immunoglobulin variable (V) region gene analysis using well-defined breast cancer cell lines expressing the epithelial marker, epithelial cell adhesion molecule (EpCAM). V(H) gene transcripts were identifiable by nested reverse transcription-PCR either as single or dual V, diversity (D), and joining (J) rearrangements in four of six lines, most being potentially functional. V(D)J transcripts were observed in sequential cultures, indicating stable expression. To exclude coexisting lymphocytes, each cell line was shown to be EBV negative, with CD19/CD20 and cytoplasmic/surface immunoglobulin also absent by flow cytometry. Identified V(H) transcripts were then sought in individual tumor cells, isolated as EpCAM+ single cells by flow cytometry. Importantly, in three of three selected cell lines, V(H) genes were identifiable in a significant fraction (approximately 32%) of single cells. In five of six identified V(H) genes, somatic mutations were apparent with no intraclonal variation, indicating cessation of mutational activity. V(H) transcripts were pre- and post-isotype switch, with activation of switch events evident from expressed germ-line switch transcripts in two of six lines. Strikingly, six of six cell lines expressed activation-induced cytidine deaminase (AID) essential for mutational and switch activity. These data suggest either a de novo rearrangement and modification of V(H) genes in epithelial tumor cells or assimilation of lymphocyte-derived chromatin. Constitutive AID activation in malignant epithelial cells further raises a potential for inducing aberrant mutational activity.

Amino Acid Sequence↗

PubMed2000

Nested cladistic analysis indicates population fragmentation shapes genetic diversity in a freshwater mussel.

Recently developed phylogeographic analyses that incorporate genealogical relationships of alleles offer the exciting prospect of disentangling historical from contemporary events. However, the relative advantages and shortfalls of this approach remain to be studied. We compared the nested cladistic method to the more traditional analysis of variance approach in a study of intraspecific genetic variation in the freshwater mussel, Lampsilis hydiana. We surveyed 257 specimens for nucleotide sequence level variation in a fragment of the mitochondrial 16S rRNA gene. When compared side by side, nested cladistic analysis and analysis of molecular variance (AMOVA) identified fragmentation of Arkansas river populations from remaining populations to the southwest. Nested cladistic analysis identified a second, more recent separation of Ouachita and Upper Saline river populations that was not detected by AMOVA. Differences among analytical methods probably arise from treatment of spatial hierarchical information: hierarchical groups emerge via a parsimony criterion in nested cladistic analysis but must be specified a priori in AMOVA. Both methods identified significant genetic structure among localities within hierarchical groups. Results from AMOVA suggested little gene flow among local populations with an island model. However, inferences about process that gave rise to patterns at this level were not possible in nested cladistic analysis, because an ancestral (interior) haplotype was not observed for a key one-step clade in the parsimony network. Our results suggest that, under some circumstances, nested cladistic analysis has lower power than more traditional analysis of variance to infer processes at the local population level.

Analysis of Variance↗

PubMed2001

Granulomatous skin lesions in moray eels caused by a novel Mycobacterium species related to Mycobacterium triplex.

An outbreak of granulomatous dermatitis was investigated in a captive population of moray eels. The affected eels had florid skin nodules concentrated around the head and trunk. Histopathological examination revealed extensive granulomatous inflammation within the dermis and subcutaneous fascial plane between the fat and axial musculature. Acid-fast rods were detected within the smallest lesions, which were presumably the ones that had developed earliest. Eventually, after several months of incubation at room temperature, a very slowly growing acid-fast organism was isolated. Sequencing of the 16S rRNA gene identified it as a Mycobacterium species closely related (0.59% divergence) to M. triplex, an SAV mycobacterium. Intradermal inoculation of healthy green moray eels with this organism reliably reproduced the lesion. Experimentally induced granulomatous dermatitis appeared within 2 weeks of inoculation and slowly but progressively expanded during the 2 months of the experiment. Live organisms were recovered from these lesions at all time points, fulfilling Koch's postulates for this bacterium. In a retrospective study of tissues collected between 1993 and 1999 from five spontaneous disease cases, acid-fast rods were consistently found within lesions, and a nested PCR for the rRNA gene also demonstrated the presence of mycobacteria within affected tissues.

Animals↗

PubMed2005

Multilocus sequence typing scheme that provides both species and strain differentiation for the Burkholderia cepacia complex.

A single multilocus sequence typing (MLST) scheme was developed for precise characterization of the opportunistic pathogens of Burkholderia cepacia complex (BCC), a group composed of at least nine closely related species. Seven conserved housekeeping genes were selected after a comparison of five Burkholderia species, and a collection of strains was subjected to nucleotide sequence analysis using a nested PCR amplification approach for each gene. MLST differentiated all nine current BCC species and identified 114 sequence types within a collection of 119 strains. No differentiation was found between strains recovered from environmental or clinical sources. The improved resolution in strain identification offered by MLST was able to identify previously characterized epidemic strain lineages and also demonstrated the presence of four novel potential species groups within the complex. There was also evidence for recombination having an important role in the recent evolution of individual BCC species. This highly transferable, validated, MLST scheme provides a new means to assist in species identification as well as unambiguous strain discrimination of the BCC by a single approach. It is also the first MLST scheme designed at the outset to incorporate multiple species and should facilitate global epidemiological investigations of the BCC.

Alleles↗

PubMed2000

Aberrant transcripts of FHIT, TSG101 and PTEN/MMAC1 genes in normal peripheral mononuclear cells.

Aberrant transcripts of FHIT and TSG101 using nested RT-PCR were reported in many human tumours. The role of these aberrant transcripts in tumourigenesis is not clear. We, therefore, analyzed the aberrant transcripts of FHIT, TSG101 and PTEN/MMAC1 in peripheral mononuclear cells of normal individuals using nested RT-PCR to explore the role of these genes in cancer development. The results showed that there are at least five types of aberrant transcripts: type I is the deletion at junction located in-between normal exon and intron; type II has deletion of some bases and subsequent insertion of several bases in the deletion area; type III accommodates splicing donor or acceptor site-like sequence; type IV has homologous sequences near the deleted junction; and type V comprises the homologous sequences at the deletion junction. A normal healthy person can have more than one aberrant transcripts of FHIT, TSG101 and PTEN/MMAC1 genes. The size and the number of the transcripts vary and the diversity is unconstrained. It is not depended on the time, condition of the reaction, or the isolation method. From these results, we suggested that the aberrant transcripts of FHIT, TSG101 and PTEN/MMAC1 genes may be the imperfect products of splicesome which occur one in every thousands, ten thousands or more. As a result, these data implied no direct association between the aberrant transcripts and tumourigenesis.

Acid Anhydride Hydrolases↗

PubMed2002

Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes.

Orthologous regions in barley, rice, sorghum, and wheat were studied by bacterial artificial chromosome sequence analysis. General microcolinearity was observed for the four shared genes in this region. However, three genic rearrangements were observed. First, the rice region contains a cluster of 48 predicted small nucleolar RNA genes, but the comparable region from sorghum contains no homologous loci. Second, gene 2 was inverted in the barley lineage by an apparent unequal recombination after the ancestors of barley and wheat diverged, 11-15 million years ago (mya). Third, gene 4 underwent direct tandem duplication in a common ancestor of barley and wheat 29-41 mya. All four of the shared genes show the same synonymous substitution rate, but nonsynonymous substitution rates show significant variations between genes 4a and 4b, suggesting that gene 4b was largely released from the strong purifying selection that acts on gene 4a in both barley and wheat. Intergenic retrotransposon blocks, many of them organized as nested insertions, mostly account for the lower gene density of the barley and wheat regions. All but two of the retrotransposons were found in the regions between genes, while all but 2 of the 51 inverted repeat transposable elements were found as insertions in genic regions and outside the retrotransposon blocks.

Biological Evolution↗

PubMed1996

An efficient method for the rescue and analysis of functional HIV-1 env genes: evidence for recombination in the vicinity of the tat/rev splice site.

OBJECTIVE: To establish a robust procedure for the isolation and characterization of full-length expression-competent HIV-1 env genes directly from patient samples. DESIGN: HIV exists as a quasispecies which can be disturbed by in vitro culture, in which numerous members of the population are likely to be defective due to the high error rate of the viral reverse transcriptase. Defective viruses are unlikely to play a dominant role in disease progression. Since env gene translation products play major roles in the initiation and spread of infection we need to study genes with open reading frames. METHODS: A nested polymerase chain reaction (PCR) approach has been used to rescue intact (2.6 kb) env genes, which are cloned into a T7-promoter-containing vector. Expression of gp160 in CV-1 cells is detected by Western blot. Expression-competent clones are sequenced and resulting sequences used for phylogenetic studies. Translation products are analysed in relation to the known immunogenic structure of gp160. RESULTS: From random patient samples collected in London clinics, only HIV-1 subtype B was found. Two of the samples contained viruses with an additional pair of cysteine residues in their V1 regions. For samples collected in Uganda, HIV-1 subtypes A, D and an A/D recombinant were recovered. CONCLUSION: An effective procedure is described for the isolation of HIV-1 env genes directly from patient samples, which has worked for A, B and D subtypes to date. The PCR primers can be utilized with other subtypes with the possible exception of subtype O viruses. Phylogenetic analyses revealed the potential importance of a G/C-rich region near the tat/rev splice site as a site of recombination. The sequences and translation products generated may be more relevant to disease progression in vivo and vaccine formulations than those obtained from viruses selected in long-term culture.

Base Sequence↗

PubMed2003

Rapid hybridization at high salt concentration and detection of bacterial DNA using fluorescence polarization.

The effects of NaCl concentration and temperature on the rate of hybridization of complementary single-stranded DNA (24-mers) were investigated. The single label of fluorescein was used for the probe DNA. The time courses of fluorescence polarization for the probe DNA were monitored. It was shown that detection of a specific DNA sequence (24-mer) was possible in less than 10 min using fluorescence polarization under the optimized conditions of 0.8 M NaCl at 46 degrees C in TE buffer. The effects of base-pair mismatches on DNA hybridization in the presence of NaCl or MgCl(2) were also investigated, and the specificity was considered by comparing the hybridization rate of the fluorescein-labeled probe. Determination of a specific DNA sequence was also possible in TE buffer containing 0.2 M MgCl(2). Moreover, in the presence of 0.2 M MgCl(2), there were no undesirable effects on hybridization and the presence of a single base pair mismatch could be identified. Rapid and specific determination of the DNA of enterohemorrhagic Escherichia coli, methicillin resistant Staphylococcus aureus and Legionella pneumophila, which had been multiplied by the asymmetric PCR, was performed under the optimized conditions for hybridization. It was confirmed that the conditions were also applicable to the hybridization between the probes and the amplified products of the actual bacterial genes. The combination of fluorescence polarization with the asymmetric PCR was quite effective. Moreover, the nested and asymmetric PCR product of bacterial gene could be detected effectively. The DNA detection method could also be used even if the specificity of the DNA amplification was not perfect and some unexpected bands were mixed with the target band during electrophoresis.

DNA Probes↗

PubMed1993

Insect immunity. Two 17 bp repeats nesting a kappa B-related sequence confer inducibility to the diptericin gene and bind a polypeptide in bacteria-challenged Drosophila.

The Drosophila diptericin gene codes for a 9 kDa antibacterial peptide and is rapidly and transiently expressed in larvae and adults after bacterial challenge. It is also induced in a tumorous Drosophila blood cell line by the addition of lipopolysaccharide (LPS). The promoter of this gene contains two 17 bp repeats located closely upstream of the TATA-box and harbouring a decameric kappa B-related sequence. This study reports that the replacement of the two 17 bp repeats by random sequences abolishes bacteria inducibility in transgenic fly lines. In transfected tumorous blood cells, the replacement of both or either of the 17 bp motifs reduces dramatically LPS inducibility, whereas multiple copies significantly increase the level of transcriptional activation by LPS challenge. A specific DNA-protein binding activity is evidenced in cytoplasmic and nuclear extracts of induced blood cells and fat body. It is absent in controls. It is proposed that induction of the diptericin gene mediated by the two 17 bp repeats occurs via a mechanism similar to that of mammalian NF-kappa B.

Animals↗

PubMed1994

Detection and nucleotide sequence analysis of the speC gene in Swedish clinical group A streptococcal isolates.

The production of pyrogenic exotoxins SpeA, SpeB, and SpeC by group A streptococci has been associated with streptococcal toxic shock syndrome. Several epidemiological studies using DNA hybridization and PCR analysis have been performed in attempts to correlate one or several of the toxins with streptococcal toxic shock syndrome. The results reveal great variation in the occurrence of the speA and speC genes among clinical isolates. In this study, we show that the speC gene could be detected by nested PCR in five Swedish T1M1 strains isolated from patients infected with group A streptococci as well as in three Norwegian T1M1 isolates, previously reported to lack speC as determined by dot blot hybridization. To verify the identities of the amplified products, the nucleotide sequences of the PCR fragments from one Swedish T1M1 strain and from the toxin reference strain NY5 were determined. The nucleotide sequences showed that the amplified products were speC and of allele type C2, on the basis of the nucleotides in positions 438 and 456. However, one additional base pair substitution was found in NY5 at position 147 and in the Swedish isolate at position 157, which resulted in nonsynonymous amino acid changes. Thus, these speC genes represent two new allelic variants.

Bacterial Proteins↗