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PubMed2004

Occurrence of genes associated with enterotoxigenic and enterohemorrhagic Escherichia coli in agricultural waste lagoons.

The prevalence among all Escherichia coli bacteria of the LTIIa toxin gene and STII toxin gene, both associated with enterotoxigenic E. coli, and of three genes (stxI, stxII, and eaeA) associated with enterohemorrhagic E. coli was determined in farm waste disposal systems seasonally for 1 year. Single- and nested-PCR results for the number of E. coli isolates carrying each toxin gene trait were compared with a five-replicate most-probable-number (MPN) method. The STII and LTIIa toxin genes were present continuously at all farms and downstream waters that were tested. Nested-MPN-PCR manifested sensitivity increased over that of single-MPN-PCR by a factor of 32 for LTIIa, 10 for STII, and 2 for the stxI, stxII, and eaeA genes. The geometric mean prevalence of each toxin gene within the E. coli community in waste disposal site waters after nested MPN-PCR was 1:8.5 E. coli isolates (1:8.5 E. coli) for the LTIIa toxin gene and 1:4 E. coli for the STII toxin gene. The geometric mean prevalence for the simultaneous occurrence of toxin genes stxI, stxII, and eaeA, was 1:182 E. coli. These findings based on total population analysis suggest that prevalence rates for these genes are higher than previously reported in studies based on surveys of single isolates. With a population-based approach, the frequency of each toxin gene at the corresponding disposal sites and the endemic nature of diseases on farms can be easily assessed, allowing farmers and public health officials to evaluate the risk of infection to animals or humans.

Adhesins, Bacterial↗

PubMed2006

Characterization of bacterial community associated to biofilms of corroded oil pipelines from the southeast of Mexico.

Microbial communities associated to biofilms promote corrosion of oil pipelines. The community structure of bacteria in the biofilm formed in oil pipelines is the basic knowledge to understand the complexity and mechanisms of metal corrosion. To assess bacterial diversity, biofilm samples were obtained from X52 steel coupons corroded after 40 days of exposure to normal operation and flow conditions. The biofilm samples were directly used to extract metagenomic DNA, which was used as template to amplify 16S ribosomal gene by PCR. The PCR products of 16S ribosomal gene were also employed as template for sulfate-reducing bacteria (SRB) specific nested-PCR and both PCR products were utilized for the construction of gene libraries. The V3 region of the 16S rRNA gene was also amplified to analyse the bacterial diversity by analysis of denaturing gradient gel electrophoresis (DGGE). Ribosomal library and DGGE profiles exhibited limited bacterial diversity, basically including Citrobacter spp., Enterobacter spp. and Halanaerobium spp. while Desulfovibrio alaskensis and a novel clade within the genus Desulfonatronovibrio were detected from the nested PCR library. The biofilm samples were also taken for the isolation of SRB. Desulfovibrio alaskensis and Desulfovibrio capillatus, as well as some strains related to Citrobacter were isolated. SRB consists in a very small proportion of the community and Desulfovibrio spp. were the relatively abundant groups among the SRB. This is the first study directly exploring bacterial diversity in corrosive biofilms associated to steel pipelines subjected to normal operation conditions.

Bacteria↗

PubMed1999

[Sequence analysis of human immunodeficiency virus type 1 tat gene among the long-term HIV infected non-progressoris in Yunnan province].

OBJECTIVE: HIV-1 tat gene is one of its regulatory genes necessary for its replication. This study is to explore whether the variation of tat gene influences the AIDS progress of HIV infected individual. METHODS: We carried out investigation on tat gene of HIV among the long term HIV infected non-progressors and the commonly infected individuals. Mononuclear cells of peripheral blood were isolated and cellular DNA was extracted. Nested PCR method was used to amplify tat gene and their sequences were analyzed. RESULTS: Blood were collected from 22 HIV infected individuals, of which 11 cases were infected with B subtype strains based on previous env gene analysis and belonged to long term non-progressors according to clinical features and immunology. The other 11 cases were common HIV infection of which 5 subtype B and 6 subtype C were found. Both long term non-progressor group (subtype B) and the commonly HIV infectedly group (subtype B) had constantly four amino acids different from that of international B subtype consensus sequence The both groups clustered randomly on the phylogenetic tree. In commonly HIV infected subtype C group there were 6 amino acids different from that of international subtype C. The variation inside the tatgene of common subtype C group was small. CONCLUSIONS: There was no regular variation and significant difference between long term HIV infected non-progressive group and commonly HIV infected subtype B group. There is no evidence showing that progressive speed of AIDS correlated with the tat sequence profile of HIV-1.

Amino Acid Sequence↗

PubMed1993

Molecular analysis of the LMP (latent membrane protein) oncogene in Hodgkin's disease.

Molecular analysis of the LMP (latent membrane protein) oncogene was performed in 21 Epstein-Barr virus (EBV) positive cases of Hodgkin's disease (HD) with proven LMP gene expression. In each case, viral DNA of the LMP gene was assessed for polymorphism (deletions, insertions, mutations) by polymerase chain reaction (PCR) amplification with selected primers. Specificity of the amplified targets was proven by internal oligonucleotide hybridisation and nested primer PCR. Homogeneity of the 5' LMP gene region coding for the amino terminal, transmembrane, and short extracytoplasmic domains of the protein was identified in all cases. However, deletions or insertions of small DNA sequences within the coding region for the intracytoplasmic LMP domain were observed in about 20% of cases. In one of them, a 30-base-pair deletion was precisely localized by DNA sequencing. A particularly high frequency of DNA polymorphism (30% of cases) was found in the 3' untranslated LMP region. However, when analysing the LMP gene in seven benign conditions, no DNA polymorphism was found. These data suggest conservation of oncogenic LMP regions coding for the protein domains known to be associated with transforming capacities and immunogenic functions. They also show a considerable genomic heterogeneity of the coding region for the intracytoplasmic domain and the 3' untranslated mRNA region. This LMP DNA polymorphism identified within a localized (Swiss) population suffering from HD is unexpected. Its eventual clinical significance remains to be determined.

Antigens, Viral↗

PubMed2003

Molecular cloning and expression of uroplakins in transitional cell carcinoma.

BACKGROUND: Uroplakins (UPs), urothelium-specific transmembrane proteins, are present only in urothelia and may be good candidates as tumor markers specific for transitional cell carcinomas (TCCs). We investigated the expression of UP genes in the tissues and peripheral blood of patients with TCCs. MATERIALS AND METHODS: We determined the nucleotide sequences of UPs by a polymerase chain reaction (PCR)-based method. We then investigated UP gene expression in tissues from 12 patients with TCC by reverse transcription (RT)-PCR. We also investigated UP gene expression in peripheral blood of 12 other patients with TCC by nested RT-PCR. Polyclonal and monoclonal antibodies against UPs were generated using synthesized polypeptides and recombinant protein, respectively, as immunogens. RESULTS: We determined the nucleotide sequence of human UP-Ib, UP-II, and UP-III cDNAs and produced gene-specific primer pairs for each and for UP-Ia. UP genes were expressed in both cancerous and non-cancerous urothelia taken from all patients examined (as detected by RT-PCR). The detection sensitivity of our assay system was such that 1 cancer cell could be detected in 5 mL of peripheral blood. UP gene-expression was also detected in the peripheral blood of 3 patients with metastatic TCC, but not from 9 patients with non-metastatic TCC or from 3 healthy volunteers. Antibodies against both UP-Ia and UP-Ib reacted with the cell membrane of TCCs. CONCLUSIONS: UPs may be employed as tumor markers for TCCs, because they are highly conserved and well expressed in non-cancerous and cancerous cells. Furthermore, detection of UP gene expression in blood by nested RT-PCR may provide helpful information in the diagnosis and management of TCCs. We are currently expanding an immunohistochemical study by targeting a larger number of patients to examine the clinical usefulness of these antibodies.

Adult↗

PubMed1997

Revertant fibres: a possible genetic therapy for Duchenne muscular dystrophy?

The mdx mouse, an animal model used to study Duchenne muscular dystrophy (DMD), has a nonsense mutation in exon 23 of the dystrophin gene which should result in a truncated protein that cannot be correctly localized at the sarcolemma of the muscle fibres. Immunohistochemical staining with anti-dystrophin antibodies had shown that while most of the muscle tissue was dystrophin-negative, a small percentage of muscle fibres were clearly dystrophin-positive and had somehow by-passed the primary nonsense mutation. A nested PCR-based examination of dystrophin gene transcripts around the mdx mutation revealed several alternatively processed transcripts, of which four mRNA species skipped the mutation in exon 23, were in-frame and could be translated into a shorter, but still functional dystrophin protein. Specific tests for these transcripts demonstrated these were also present in normal adult and embryonic mouse muscle tissue.

Animals↗

PubMed1994

The Arabidopsis phytochrome A gene has multiple transcription start sites and a promoter sequence motif homologous to the repressor element of monocot phytochrome A genes.

We have determined the sequence of the phytochrome A gene (PHYA) and its flanking DNA from Arabidopsis thaliana and have identified transcription start sites for three nested transcripts of increasing length. The overall structure of the gene is similar as regards exon/intron organization to other angiosperm PHY genes characterized. The triple transcription start site arrangement is similar to that of pea PHYA but different from the single start site of oat, rice and maize PHYA genes, indicating a possible monocot-dicot difference. Comparison of the Arabidopsis PHYA promoter sequence with others available indicates that both pea and Arabidopsis promoters contain a DNA element with a core sequence motif identical to one conserved in all existing monocot PHYA sequences and defined by functional assay in the oat PHYA gene as repressor element, RE1, responsible for negative light regulation.

Amino Acid Sequence↗

PubMedDate not supplied

The mouse mammary tumor virus-like env gene sequence is not detectable in breast cancer tissue of Austrian patients.

The mammary mouse tumor virus (MMTV) has been related to human breast cancer in previous studies, but these have yielded contradictory results. An MMTV env gene-like sequence was detectable in a relatively high proportion (38%) of human breast cancer tissues. The aim of this study was to determine the proportion of this 660 bp MMTV env gene-like sequence in a population of Austrian breast cancer patients. We performed PCR, repeat PCR, and nested PCR. We did not find any exogenous MMTV env gene sequences in the 50 DNA samples of human breast cancer tissue nor in 22 breast cancer cell lines including MCF-7, which has previously been described as a positive control.

Austria↗

PubMed1990

Mechanism of polysialic acid chain elongation in Escherichia coli K1.

Understanding the mechanisms of polysialic acid synthesis in Escherichia coli K1 requires a molecular description of the polymerase complex. Since the number of potential models explaining polysialic acid assembly would be constrained if only one sialyltransferase were required for this process, the phenotypes of a sialyltransferase null mutation generated by transposon mutagenesis were investigated. The chromosomal insertion mutation was mapped by Southern hybridization analysis and by complementation with plasmid subclones, demonstrating that sialyltransferase is encoded by neuS, a gene implicated previously as coding for the polymerase (Vimr et al., 1989). As expected, if only one gene encoded sialyltransferase, the null mutant had undetectable polymerase activity when assayed with endogenous or exogenous acceptors, and accumulated sugar nucleotide precursors intracellularly. Nested deletion analysis of neuS ruled out polarity effects of transposon insertion mutation and provided more precise mapping of the sialyltransferase structural gene. Maxicell analysis of the nested deletion set implicated a 34,000 molecular weight polypeptide as the neuS gene product. These results, together with biochemical characterization of sialyltransferase reaction products in the wild type, indicated that CMP-sialic acid is the probable sialosyl donor for polysialic acid elongation and that chain growth is by sequential addition of monomeric units.

Blotting, Southern↗

PubMed2005

Comparative analysis of mycobacterial infections in wild striped bass Morone saxatilis from Chesapeake Bay.

During an ongoing epizootic of mycobacteriosis, wild striped bass Morone saxatilis from Chesapeake Bay were analyzed using 3 methods for detection of either mycobacterial infection or associated granulomatous pathology. The specific detection techniques, which utilized aseptically collected splenic tissue, were histology, quantitative culture and nested PCR. Based on analysis of 118 samples, detection of infection differed significantly between the 3 methods (chi-square, p = 0.0007). Quantitative culture and nested PCR detected similar, higher rates of infection (69 and 75%, respectively) than the histological method (52%). Although primary PCR assays for a 924 to 940 bp segment of the mycobacterial 16S rRNA gene were positive for genomic DNA from mycobacterial cultures, a secondary, nested PCR reaction for an internal 300 bp gene segment was required in order to detect mycobacteria within splenic tissue. A similar rate of mycobacterial infection was present in fish collected from all sites tested. Although all detection methods found that striped bass age 4.0 to 4.9 yr had the highest positive incidence, nested PCR detected a higher frequency of mycobacterial infection in fish > or = 6.0 yr of age than the other 2 methods. Quantitative bacteriology was a more sensitive detection technique when the fish tissue contained < or = 10(3) mycobacteria g(-1).

Age Factors↗

PubMed1999

Detection of genes for periplasmic nitrate reductase in nitrate respiring bacteria and in community DNA.

A nested PCR primed by four degenerate oligonucleotides was developed for the specific amplification of sequences from the napA gene encoding the periplasmic nitrate reductase. This approach was used to amplify fragments of the napA gene from 10 Pseudomonas species and one Moraxella sp., previously shown to be able to express the periplasmic nitrate reductase activity, from Rhodobacter capsulatus and from community DNA extracted from a fresh-water sediment. Amino acid sequences encoded by the napA fragments were compared to one another and to the corresponding regions of related enzymes. This comparison indicates that the amplification protocol is specific for its intended target. The napA sequences amplified from community DNA were tightly clustered, which may indicate a degree of homogeneity in the sediment community. All tested Gram-negative strains capable of aerobic nitrate respiration were found to have periplasmic nitrate reductase genes. However, some strains which have and express the genes are incapable of aerobic nitrate respiration. The PCR primers and amplification protocols described will be useful in future studies of nitrate respiring populations.

Amino Acid Sequence↗

PubMed1999

Isolation of a Kawasaki disease-associated bacterial sequence from peripheral blood leukocytes.

BACKGROUND: The clinical and epidemiologic features of Kawasaki disease (KD) suggest an infectious etiology, but the agent(s) remains unknown. We aimed to isolate the causative bacterial gene from peripheral blood leukocytes of patients with acute KD. METHODS: Nested polymerase chain reaction (PCR) assay was used to amplify the bacterial 16S ribosomal RNA gene (rDNA). The amplified DNA were cloned into a plasmid vector and sequenced. Phylogenetic analysis was performed with clustal W program and the neighbour-joining method. RESULTS: First, the PCR reagents were examined by the PCR assay using conservative primers and we found more than 10 16S rDNA sequences contaminating the reagents. We then examined five KD patients using the PCR assay, excluding the contaminated sequences, and obtained five 16S rDNA sequences as possible KD-associated sequences. The primers specific to each 16S rDNA sequence were synthesized and used for specific PCR assays. Only the PCR assay specific to the 16S rDNA sequence termed 16S71-33 did not show any false positives with the control DNA from non-KD patients. The 16S71-33 sequence was positive in three of 20 patients with acute KD before gamma-globulin therapy, but it became negative after therapy. The phylogenetic analysis showed a new species of the genus Corynebacterium as the origin of the 16S71-33 sequence. CONCLUSIONS: These data show that an infectious KD agent is traced in peripheral leukocytes and that a new Corynebacterium species may be responsible for KD in some cases. The true frequency and the role of the new Corynebacterium in KD would be clarified by measuring specific antibodies to it.

Base Sequence↗

PubMedDate not supplied

Detailed transcript map of a 810-kb region at 11p14 involving identification of 10 novel human 3' exons.

A limited number of genes, including the human brain-derived neutrotrophic factor (BDNF) gene, have been identified in the human chromosome 11p14 region. Since this area is involved in a genetic disorder (WAGR syndrome) and because of interest in studying the regulation of the human BDNF gene, we have established a detailed transcript map of a 810-kb region clone in a yeast artificial chromosome (YAC), corresponding to a portion of this genomic locus. A set of nested deletion mutants has been generated to map genes at a mean resolution of 75kb. Four genic markers from available mapping databases have been mapped on the YAC. Ten potential novel human exons have been isolated by a 3' terminal exon trapping procedure directly applied to purified YAC DNA. Most of these exons display polyadenylation signals and they all yield positive signals in RT-PCR experiments, confirming their status of transcribed sequences. The BDNF gene is now co-localised with three other genes on a 120 kb DNA fragment.

Brain-Derived Neurotrophic Factor↗

PubMed1993

The structural and functional organization of the Autographa californica nuclear polyhedrosis virus genome.

Baculoviruses are used as biological control agents of insect pests in agriculture and forestry. The multiple-nucleocapsid nuclear polyhedrosis virus of Autographa californica (AcMNPV) is the prototype baculovirus. Recently, this virus has become widely used as vector for the high-level expression of foreign genes in insect cells. An updated physical map of restriction sites as well as the location of open reading frames (ORFs) and transcripts are presented. Most characteristic is the dispersal of "early", "late", and "very late" genes over the genome and the presence of nested sets of 3' and 5' coterminal transcripts.

Baculoviridae↗

PubMed2005

Identification and prevalence of Ehrlichia chaffeensis infection in Haemaphysalis longicornis ticks from Korea by PCR, sequencing and phylogenetic analysis based on 16S rRNA gene.

Genomic DNAs extracted from 1,288 Haemaphysalis longicornis ticks collected from grass vegetation and various animals from nine provinces of Korea were subjected to screening by genus-specific (Ehrlichia spp. or Anaplasma spp.) real-time TaqMan PCR and speciesspecific (E. chaffeensis) nested-PCR based on amplification of 16S rRNA gene fragments. In all, 611 (47.4%) ticks tested positive for genus-specific amplification of 116 bp fragment of 16S rRNA of Ehrlichia spp. or Anaplasma spp. Subsequently, 396 bp E. chaffeensis-specific fragment of 16S rRNA was amplified from 4.2% (26/611) tick samples. The comparison of the nucleotide sequence of 16S rRNA gene from one tick (EC-PGHL, GeneBank accession number AY35042) with the sequences of 20 E. chaffeensis strains available in the database showed that EC-PGHL was 100% identical or similar to the Arkansas (AF416764), the Sapulpa (U60476) and the 91HE17 (U23503) strains. The phylogenetic analysis also revealed that the E. chaffeensis EC-PGHL formed a single cluster with the above strains. This is the first study to report molecular detection and phylogenetic analysis of E. chaffeensis from H. longicornis ticks in Korea. The implicit significance of E. chaffeensis infection in H. longicornis ticks in Korea is discussed.

Anaplasma↗

PubMed1995

Sensitive assay for detection of hepatocellular carcinoma associated gene transcription (alpha-fetoprotein mRNA) in blood.

The sensitivity of RT-PCR and nested RT-PCR for detection of circulating hepatocellular carcinoma was assessed by demonstrating the tumor cell-associated gene transcription, alpha-fetoprotein mRNA, in the nuclear cells of peripheral blood. When HepG2 cells were mixed in blood, 100-1000 tumor cells/5ml of blood could be detected by RT-PCR, in contrast to 1-10 tumor cells/5ml of blood by nested RT-PCR. In addition, 2 x 10(4) copies of AFP mRNA were found in one HepG2 cell when analyzed by the quantitative nested RT-PCR assay. Thus, the nested RT-PCR assay could provide a useful tool for detecting a tiny amount of circulating tumor cells in patients with hepatocellular carcinoma presenting extra-hepatic metastasis.

Base Sequence↗

PubMed2006

Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs.

The family of box H/ACA snoRNA is an abundant class of non-protein-coding RNAs, which play important roles in the post-transcriptional modification of rRNAs and snRNAs. Here we report the characterization in the human genome of 202 sequences derived from box H/ACA snoRNAs. Most of them were retrogenes formed using the L1 integration machinery. About 96% of the box H/ACA RNA-related sequences are found in corresponding locations on the chimpanzee and human chromosomes, while the mouse shares approximately 50% of these human sequences, suggesting that some of the H/ACA RNA-related sequences in primate occurred after the rodent/primate divergence. Of the H/ACA RNA-related sequences, 49% are found in intronic regions of protein-coding genes and 64 H/ACA-related sequences can be folded to the typical secondary structure of the box H/ACA snoRNA family, while 30 of them were recognized as functional homologs of their corresponding box H/ACA snoRNAs previously reported. Of the 64 sequences with the typical secondary structure of the box H/ACA RNA family, 11 were found in EST databases and 5 among which were shown to be expressed in more than one human tissue. Notably, U107f is nested in an intron of a protein gene coding for nudix-type motif 13, but expressed from the opposite strand, and the searching of EST databases revealed it can be expressed in liver and spleen, even in melanotic melanoma.

Animals↗

PubMed2005

Novel single-round PCR and cloning of full-length envelope genes of HIV-1 may yield new insight into biomolecular antibacterial drug development.

Nested or semi-nested polymerase chain reaction (PCR) with a 'hot start' is the preferred amplification method for full-length, in-frame envelope genes (gp160) of the human immunodeficiency virus type 1 (HIV-1). This generally follows an extensive screening process. This paper describes an effective single-round PCR method and cloning process for HIV-1 gp160 from clinical samples, and cell and tissue cultures developed during the early stages of construction of a molecular HIV-1 vaccine. The amplification method and cloning process are adaptable to full-length HIV-1, HIV-2, and other viral production processes. Also described within, is one solution to the most-often extensive screening process for inserts containing full-length, in-frame gp160. Of note, was a perceived toxicity of gp160 to bacteria during the culturing and the scaling-up process that created the extensive screening process. The toxicity association was not found with the individual gp160 genes, the gp120 or the gp41 gene, with other viral regions similar or larger in molecular weight to gp160, or with other non-gp160 full-length genes of HIV-1 such as pol and gag genes. The HIV-1 gp160 toxicity issue may provide insight towards the development of the next generation of novel biomolecular drugs against bacterial infections.

AIDS Vaccines↗