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Results for “Nested Genes”

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At least 541 records · Page 30Linked to original sources

PubMed2003

Legionella pneumophila mip gene sequencing to investigate a cluster of pneumonia cases.

AIMS: To use fluorescent antibody (FA) and PCR studies on fixed lung tissue to investigate whether Legionella pneumophila was the cause of pneumonia in a cluster of three haematology patients. METHODS: Cut sections of paraffin blocks of lung tissue were examined by direct FA (DFA) using fluorescently labelled antibody to serogroup 1 and Pontiac strains of L. pneumophila. In addition, a single tube 'hanging drop' nested PCR targeting the mip gene of Legionella was performed on DNA extracted from the lung sections. Products were sequenced using dye terminator chemistry. RESULTS: Numerous fluorescing bacteria were seen on staining with both antibodies in lung tissue from two of the patients. Identical L. pneumophila mip gene sequences were amplified from both DFA-positive lung sections. Two differing L. pneumophila mip sequences were obtained on three separate occasions from the tissue sections from the third patient negative by DFA. These sequences differed slightly from those obtained from the two DFA positive lung tissues. CONCLUSIONS: There is good epidemiological evidence to link the first two cases who had been treated in the same ward prior to development of fever within two days of each other. The significance of results is controversial for the third patient.

Bacterial Proteins↗

PubMed2005

Transcription regulatory complex including YB-1 controls expression of mouse matrix metalloproteinase-2 gene in NIH3T3 cells.

Matrix metalloproteinase 2 (MMP-2) is a metalloproteinase belonging to a family of structurally related zinc-dependent endopeptidases capable of degrading extracellular matrix components. To elucidate the functional promoter of the mouse MMP-2 gene, systematic transient expression analysis of the 5'-flanking region of the MMP-2 gene was performed using serially nested deletions. The deletion analysis indicated that the proximal 327-bp sequence from nucleotide positions -313 to +14 relative to the transcription start site is essential for minimal promoter activity and that a 10-bp sequence of the promoter at positions -939 to -930 is required for high expression level of the MMP-2 gene. The 10-bp fragment functioned as a potent stimulator of heterologous SV40 promoter activity. This element is identical to the YB-1 binding motif (Y-box) present within the responsive element-1 (RE-1), which has been shown to act as a potent cis-activator of transcription of the rat MMP-2 gene. The binding of a nuclear factor(s) to the 10-bp fragment was also revealed by electrophoretic mobility shift assays (EMSAs). Antibody-supershift EMSAs of nuclear extracts from NIH 3T3 cells demonstrated YB-1 binding to the RE-1 sequence. It was concluded that the RE-1 is the conserved element for potent expression of MMP-2 gene among rodents.

3T3 Cells↗

PubMed1997

[Subtype and sequence analysis of the C2-V3 region of gp120 genes among human immunodeficiency virus infected IDUs in Ruili epidemic area of Yunnan Province of China].

DNA fragments of HIV-1 env gene were amplified by nested-PCR from 17 uncultured peripheral blood mononuclear cells (PBMCs) obtained from HIV-1 seropositive intravenous drug users (IDUs) in Ruili city of Yunnan Province. The C2-V3 region (about 450 bp) of them were sequenced. Sequence analysis showed that there exists two HIV-1 subtypes, B and C, with 5.8% and 2.2% gene divergence inside each subtype. The 12 subtype B strains, were closely related to those found in Thailand, Myanma and Ruili city of Yunnan, and the nucleotide sequence divergence between them ranged from 4.4% to 4.9%; meanwhile, the 5 subtype C strains were most close to those found in India as well as Ruili city, all with a genetic distance of 1.9%. The small divergence among Ruili HIV-1 subtype C strains suggests a recent epidemic. The analysis of V3 loop amino sequence of 12 subtype B HIV-1 reveals that V3-tip motif of 6 samples (50%) is GPGQ and that of 3 samples (25%) is GPGR. In addition, the codon of arginine (R) of all the strains is CGA instead of AGA. This result is in accordance with our previous hypothesis that there is a drift in vivo from GPGR to GPGQ motif on the tipof V3-loop of HIV-1 subtype B strain in this arm with the elapse of time.

Amino Acid Sequence↗

PubMed2004

The calculative nature of microbe-mineral interactions.

Microorganisms continually redefine themselves at many levels, including the molecule, cell, and community. Although it was initially assumed that this resulted from the genesis of information within DNA alone, it has since been shown that innovation originates at multiple levels. This occurs through calculative units, each unit consisting of two proliferating structures, one nested within the other and each undergoing changes in structural geometry that affect the proliferation rate of the other. For example, the recombination of genetic structures affects the proliferation of community structures, and the recombination of community structures affects the proliferation of genetic structures. The proliferation of a nested series of structures (e.g., genes proliferating within cells, cells proliferating within communities, communities proliferating within ecosystems) results in a logic circuit that calculates the form and function of each structural element in the series. In this situation each element functions as both a habitat and an inhabitant (environment and organism), and it is this dichotomy that determines the balance of nature. Nested geological structures, such as minerals and continents, also proliferate and redefine themselves in much the same way. Microbe-mineral interactions thus link nested biological calculations to an analogous set of nested geological calculations. Examples include the microorganisms involved in the nucleation (proliferation) of ferric hydroxides, carbonates, silicates, and ice crystals.

Bacteria↗

PubMed1997

[Immunohistochemical and immunogenetic analysis of ocular adnexal lymphoid proliferations].

We examined 20 cases (21 specimens) of ocular adnexal lymphoid proliferations, using the histological, immunohistochemical and molecular genetic methods. The latter two protocols were performed to detect the light chains restriction of immunoglobulin with peroxidase-antiperoxidase (PAP) methods, and the clonality of immunoglobulin heavy chain gene with the hemi-nested polymerase chain reaction (PCR) method, respectively. Although in 8 cases it could not be morphologically determined whether they were neoplastic or not, clonality was revealed in 1 case with immunohistochemistry and in 4 cases with PCR. Two cases showed discordant results between immunohistochemistry and PCR probably due to somatic mutation of the framework region of the immunoglobulin heavy chain gene. Therefore, we, concluded that examination with these methods contribute to a better understanding of the nature of the ocular adnexal lymphoid proliferations. Furthermore, the immunoglobulin gene PCR method is very useful in practical examination, as it can be used with formalin-fixed paraffin-embedded specimens.

Adult↗

PubMed2005

[Receptor selection and B cell immune tolerance].

The immune system of mammalian has developed sophisticated mechanism to deal with diverse unknown antigens by random rearrangement of V, D and J antigen gene fragments. The immune self-tolerance is the mechanism to avoid self-destruction by the gene rearrangement generated autoreactive lymphocytes. Until recently it was believed that autoreactive lymphocytes are either deleted or rendered unable to respond by the supposed cell or clone selection mechanism. However, recent findings from a number of laboratories suggest instead of cell selection but receptor selection plays an essential role in immune self-tolerance. Receptor selection is carried out by secondary or nested rearrangement of antigen receptor gene fragments, and can occur at different stages of lymphocyte differentiation. Furthermore, secondary rearrangement of receptor gene also plays an important role in shaping immune response after the interaction of receptor with antigen by altering its specificity.

Autoimmune Diseases↗

PubMed2005

Detection and identification of Flavobacterium psychrophilum from gill washings and benthic diatoms by PCR-based sequencing analysis.

A nested polymerase chain reaction (PCR) amplification technique was used to detect Flavobacterium psychrophilum from washings of fish gill surfaces and benthic diatoms as environmental samples. Gill washing samples were prepared from kawamutsu, Zacco temminckii (Temminck & Schlegel) and oikawa, Z. platypus (Temminck & Schlegel). Benthic diatom samples were collected from stone surfaces. All samples were collected from rivers in Wakayama Prefecture, Japan from November 2003 to January 2004. Following simple DNA extraction using a chelating resin, nested PCR techniques targeting 16S-rDNA and gyrB regions were performed, and PCR products were cloned and sequenced. With nested PCR amplification for the 16S-rDNA gene, ambiguous PCR products were detected from two of six samples, and by cloning and sequencing analysis were found not to be DNA fragments amplified from F. psychrophilum. Using nested PCR for the gyrB gene, however, five of six samples were clearly positive for F. psychrophilum in agarose gel electrophoresis, and were found to be identical with nucleotide sequences of F. psychrophilumgyrB deposited in DNA databases by sequencing analysis. Results indicate that nested PCR for the gyrB region is a useful technique to detect low levels of F. psychrophilum from environmental samples contaminated with many other organisms.

Animals↗

PubMed2002

Analysis of p53 mutations and Helicobacter pylori infection in human and animal models.

BACKGROUND: p53 gene mutations are believed to play a critical role in the development of gastric carcinoma. We examined the relation between Helicobacter pylori infection and p53 gene mutations of the gastric mucosa in human and animal models. METHODS: To detect the original p53 DNA sequences of the Japanese monkey and Mongolian gerbil, the p53 genes of these animals were amplified using the nested polymerase chain reaction method with primers for the human p53 gene. Direct DNA sequencing of exons 5, 6, 7, and 8 of the p53 genes was performed by the dideoxy terminator method for gastric mucosa of humans, the Japanese monkey, and the Mongolian gerbil. The expression of p53 was examined immunohistochemically in a Japanese monkey model. RESULTS: Mutations of the p53 gene were identified in 52.4% of human H. pylori-positive mucosa and in 100% of monkey H. pylori-positive mucosa. However, no mutations of the p53 gene were found in the H. pylori-positive gastric mucosa of Mongolian gerbils. There were no mutations in H. pylori-negative gastritis mucosa of humans, monkeys, or Mongolian gerbils. Nuclear staining of p53 was seen in the glandular cells of the H. pylori-infected mucosa of Japanese monkeys, especially in the neck region of the glands. CONCLUSIONS: These findings demonstrate that the H. pylori infection can induce p53 point mutations in humans and the Japanese monkey and appear to be involved in the pathway leading to dysplasia or carcinoma. However, our direct DNA sequencing method showed no p53 mutations in the Mongolian gerbil model at present. Further studies with this model are needed.

Animals↗

PubMed1993

Delineation of positive and negative control elements within the promoter region of the murine leukemia inhibitory factor (LIF) gene.

Leukaemia inhibitory factor (LIF) is a multifunctional growth and differentiation factor with activities in both the adult and the embryo. The expression of LIF appears to be tightly regulated, as the levels of constitutive expression in most tissues and cell lines is extremely low. In this report we have identified three sequence elements within the 5'-flanking region of the murine LIF gene which control the constitutive action of the LIF promoter. A nested set of DNA fragments from the LIF gene 5'-flanking region was placed upstream of the chloramphenicol acetyltransferase (CAT) gene and assayed for their ability to direct chloramphenicol acetyltransferase (CAT) expression in STO-fibroblasts. The essential promoter of the LIF-gene, giving rise to low levels of CAT expression, was found to require the major start-site of transcription (+1), a TATA-box (-31) and up to 72 additional 5' nucleotides (-32 to -103). A negative regulatory element which abolished CAT-activity was identified between positions -360 and -249. The SV40 enhancer element was able to override this apparent negative element. In addition, an apparent positive control element in the LIF 5'-flanking region, between positions -860 and -661 was identified which was also able to override this negative effect.

Animals↗

PubMed2003

Doxycycline-regulated lentiviral vector system with a novel reverse transactivator rtTA2S-M2 shows a tight control of gene expression in vitro and in vivo.

Regulated expression of therapeutic genes is required for long-term gene therapy applications for many disorders. Here we describe a doxycycline (dox)-regulated lentiviral vector system consisting of two HIV-1-based self-inactivating viruses. One of the vectors is constitutively expressing a novel improved version of the tetracycline reverse transactivator rtTA2(S)-M2 and the other has a rtTA responsive promoter driving the expression of beta-galactosidase gene (lacZ). The rtTA2(S)-M2 has highly improved properties with respect to specificity, stability and inducibility. Functionality of the system by dox was confirmed after in vitro cotransduction of Chinese hamster ovary and human endothelial hybridoma (EAhy926) cells. Regulation of the system showed tight control of the gene expression. Dose dependence for dox was seen with concentrations that can be obtained in vivo with doses normally used in clinical practice. LacZ expression could be switched on/off during long-term (3 months) culturing of cotransduced cells. The system was next tested in vivo after cotransduction into rat brain and studying expression of the lacZ gene in dox-treated and control rats. Nested RT-PCR confirmed that the tight control of the gene expression was achieved in vivo. Also, X-gal staining showed positive cells in the dox-treated rats, but not in the controls 10 days after cotransduction with 4 days preceding treatment with dox. It is concluded that our doxycycline-regulated vector system shows significant potential for long-term gene therapy treatments.

Animals↗

PubMed2001

Helicobacter pylori in water systems for human use in Mexico City.

Helicobacter pylori infection is associated with peptic ulcers and gastric cancer in humans. Transmission of H. pylori is still not certain with some epidemiological data suggesting water as a possible transmission route. The objective of this study was to detect H. pylori 16S rRNA gene in five water systems in the Mexico City area. Samples were taken between 1997 and 2000 from extraction wells (system 1), from dams used as water sources, both pre- and post-treatment (systems 2 and 3), treated wastewater (system 4) and non-treated wastewater (system 5). Detection of the H. pylori 16S rRNA gene in water samples was carried out using nested PCR in 139 water samples and confirmed by using cagA gene detection by PCR-hybridisation. The results showed the presence of H. pylori in 58 (42%) of the water samples in total with a prevalence of 68% in system 1, 100% in system 2, 0% in system 3, 17% in system 4 and 20% in system 5. This first stage showed the presence of H. pylori in the tested water systems; nevertheless, viability of the microorganism in water and vegetables needs to be confirmed as well as demonstration of a relationship between human and environmental strains.

Agriculture↗

PubMed2001

[Extraction of RNA from Stored Bone Marrow Smears for Detecting Expression of the WT1 Gene in MDS Patients]

RNA was extracted from stored bone marrow smears, expression of WT1 gene in the patients with MDS was examined by means of nest RT-PCR. The results showed WT1 gene was highly expressed in some cases of MDS. Expression rates were higher in the patients with RAEB and RAEB-t than those patients with RA and RAS. WT1 expression is related to the advance of MDS. The detection of WT1 gene expression by RT-PCR might be useful for assessing disease progress in the patients with MDS.

Journal Article↗

PubMed2005

[Single nucleotide polymorphisms of HIV coreceptor CCR5 gene in Chinese Yi ethnic group and its association with HIV infection].

OBJECTIVE: To investigate the single nucleotide polymorphism (SNP) of HIV-1 coreceptor CCR5 gene in Chinese Yi ethnic group and the association between these SNPs and HIV/AIDS. METHODS: Peripheral blood samples of 102 HIV negative persons of Chinese Yi nationality, 87 males amd 15 females, aged 23 (12-37), and 68 HIV carriers, 61 males and 7 females, aged 27 (17-51). The regulatory and structural regions of the HIV coreceptor CCR5 gene were amplified from the genomic DNA by nested PCR, each of the two regions was divided into three gene fragments which were overlapped. High throughput DHPLC was used for screening of unknown mutations in each gene fragment. The PCR products showing different peak traces from wild types in DHPLC were sequenced by forward and reverse primers respectively. The sequences were analyzed with the help of Sequence Navigator software to search for SNP loci. Statistical analysis by SPSS and PPAP softwares were made to study the association between these SNPs and HIV infection. RESULTS: Five SNPs (A77G, G316A, T532C, C921T, and G668A) and a AGA deletion of the 686-688 nucleotides were discovered in the coding region of this gene in Chinese Yi ethnic group. C921T mutation was a nonsense mutation, and the other SNPs (A77G, G316A, T532C, and G668A) are sense mutation, with the amino acid changes of K26R, G106R, C178R, and R223Q. Only the frequency of R223Q allelic gene was high (0.08) but those of the others were low (less than 0.01). There was no significant difference in the allele frequency between the HIV negative and HIV positive groups (all P > 0.05). Five SNP loci (T58934G, G59029A, T59353C, G59402A, and C59653T) were found in the regulatory region of CCR5 gene with high allelic frequencies of 0.1912-0.2941. Between the HIV negative and HIV positive groups, there were no differences in the SNP loc (all P > 0.05). Statistical analysis of the association between the linkage of mutation loci with HIV infection suggested a significant difference in the haplotype frequency of T59353C-G59402A between the HIV negative and HIV positive groups of the Yi population. CONCLUSION: A high throughput screening method of detecting unknown genetic mutation DHPLC can effectively analyze the SNP of CCR5 regulatory and structural regions in Chinese Yi ethnic group.

Acquired Immunodeficiency Syndrome↗

PubMed2026

Gravity-driven millifluidic platform for magnetic solid-phase extraction of Enterocytozoon hepatopenaei DNA from complex shrimp hepatopancreas.

Effective detection of Enterocytozoon hepatopenaei (EHP) in aquaculture is currently hindered by the lack of field-deployable extraction methods capable of processing complex, inhibitor-rich hepatopancreatic tissue. This study presents a gravity-driven millifluidic platform for the rapid extraction of EHP genomic DNA using an optimized, surfactant-compatible magnetic solid-phase extraction (MSPE) chemistry. Utilizing 5% PEG 8000 and 2.0 M NaCl, the platform facilitates the selectively capture of DNA from inhibitor-rich crustacean lysates. The 3D-printed device employs a tilting rocking plate to generate passive, gravity-driven flow, maintaining homogeneous magnetic bead suspension and maximizing solid-phase capture efficiency without external pumps. The integrated platform achieved a DNA yield of 2804.33 ± 15.31 ng/μL, a 5.9-fold increase over manual magnetic bead extraction. TaqMan quantitative PCR (qPCR) validation targeting the EHP SSU rRNA gene was developed. Using a standard curve spanning 101 to 107 plasmid copies (Ct = -3.611 log10 [copy] + 42.309, R2 = 0.998, amplification efficiency 89.2%), the on-chip MSPE achieved a validated analytical limit of detection (LOD) of 1 spore per reaction (100% detection rate, n = 21), whereas a commercial CTAB-based DNA extraction kit failed to achieve a validated LOD even at 10 spores (85.7%, 18/21). Nested PCR targeting the SWP gene was employed for field evaluation. A pilot study across two cohorts (N = 40) demonstrated consistent detection of confirmed EPH-positive cases; however, the small sample size precludes definitive diagnostic accuracy claims. With a total processing time under 30 min, this platform provides a high-efficiency extraction module. Future work will couple the device with isothermal amplification (e.g., LAMP or RPA) to realize a sample-to-answer system for resource-limited aquaculture.

Aquaculture diagnostics↗

PubMed2003

Incongruent nuclear and mitochondrial phylogeographic patterns in the Timarcha goettingensis species complex (Coleoptera, Chrysomelidae).

Phylogeographic analyses have mostly been based on single-gene genealogies but it is unclear how conclusions from such studies depend on the choice of gene markers. We conducted a nested geographical clade analysis [A.R. Templeton, E. Routman and C.A. Phillips (1995) Genetics 140: 767-782] based on nuclear rDNA internal transcribed spacer region 2 (ITS2) sequences in the Timarcha goettingensis species complex (Coleoptera, Chrysomelidae), and compared the inferences with an updated version of previously published results using mitochondrial cytochrome oxidase II (COIl) sequences. Inferences from ITS2 suggest that patterns of marker distribution are mostly explained by restricted gene flow with isolation by distance. In contrast, COII revealed a history of geographical structure resulting from episodic population contiguous-range expansions. Both markers also show different genealogical patterns, which are associated to the effects of genetic introgression in a putative hybrid zone between two major lineages in the complex. Altogether, these differences are attributed to distinct population and/or evolutionary dynamics of the markers, and offer a more accurate phylogeographic description for the T. goettingensis complex.

Animals↗

PubMed2004

Fetal origin of single nucleated erythroblasts and free DNA in the peripheral blood of pregnant women.

OBJECTIVES: To investigate the feasibility of using single fetal nucleated erythroblasts (FNRBCs) and free DNA in maternal blood for non-invasive prenatal diagnosis. METHODS: Single FNRBCs were isolated from 51 of 116 samples of maternal blood analyzed by micromanipulation after density gradient centrifugation. Furthermore, the nested polymerase chain reaction (PCR) method was used to amplify the SRY gene of single FNRBCs. Primer extension pre-amplification and nested PCR were used to amplify the SRY gene of the plasma DNA extracted from 65 samples of maternal blood. RESULTS: The detection rate of single FNRBCs was 90.20% (46/51). The concordance rates between real fetal sex and sex determined by amplification of the SRY gene from single cells and from free DNA analysis were 82.61% (38/46) and 90.77% (59/65), respectively. CONCLUSIONS: Single nucleated erythroblasts and free DNA in maternal blood are of fetal origin and can be valuable fetal material sources for non-invasive prenatal diagnosis.

Adult↗

PubMed1998

[Construction and screening of type 1 human immunodeficiency virus specific phage antibodies combinatorial library].

UNLABELLED: Human monoclonal antibodies to type 1 immunodeficiency virus (HIV-1) gp120 were generated from phage antibody combinatorial library. METHODS: The human immunoglobulin heavy chain Fd and light chain k genes were amplified by half-nested PCR from PBMC of patient infected with HIV. Phage antibody combinatorial library was constructed with the Fd and k chain genes using Pcomb3 as vector. The affinity selection and ELISA were adopted for generating specific phage antibodies. Partial DNA of a positive clone was sequenced and its soluble Fab was expressed in E coli. HIV-1 specific phage antibodies combinatorial library were constructed using the Fd and k genes and Pcomb3 vector. The library capacity was about 1.95 x 10(7). The specific phage antibodies were highly enriched after three rounds of biopanning selection against HIV-1 gp120 and 32% positive clones were detected by ELISA screening. DNA fragment coding for CH1 and CL derived from a positive clone was sequenced and its product was successfully expressed as soluble Fab which was specific for HIV-1 gp120. The HIV-1 specific phage antibody combinatorial library, and human monoclonal antibodies to HIV-1 gp120 have been used as tools for screening of neutralizing antibody to HIV-1, and the methods seem to be very crucial and applicable.

Amino Acid Sequence↗

PubMed2006

[Sequence analysis of the CTL epitopes in transmembrane region of latent membrane protein 2 of Epstein-Barr virus derived from nasopharyngeal carcinoma cells].

BACKGROUND & OBJECTIVE: Epstein-Barr virus (EBV) in nasopharyngeal carcinoma (NPC) cells expresses Epstein-Barr nuclear antigen 1 (EBNA1), latent membrane protein 1 (LMP1), and LMP2. LMP2 is an ideal target for immunotherapy because LMP2 mRNA is detected in 100% nasopharyngeal carcinoma cells and LMP2 protein shows stronger immunogenity than the rest 2 viral proteins. This study was to analyze the sequence of CTL epitopes in the transmembrane region of LMP2 to optimize LMP2-targeted immunotherapy. METHODS: Genomic DNA was extracted from 20 biopsies of NPC and 3 biopsies of normal nasopharynx from Cantonese. The transmembrane region of LMP2 gene was amplified with hemi-nest polymerase chain reaction (PCR), and then sequenced directly. RESULTS: As compared with prototype B95.8 cells, the transmembrane region of LMP2 gene, derived from Cantonese NPC and normal nasopharynx tissues, had 14 base pair substitutions, resulting in 6 amino acid substitutions. Among these substitutions, 3 changed amino acids were located in 4 HLA-restricted CTL epitopes (SSC, TYG, CLG, and VMS). Among these polymorphisms, the VMS variation was first identified. The sequence changes of the LMP2 derived from NPC was the same as those of the LMP2 from normal nasopharynx, indicating that those variations were due to geographic-associated polymorphisms rather than NPC-associated mutations. CONCLUSION: Polymorphisms of LMP2 exist in EBV derived from Cantonese, resulting in 4 CTL epitope variations, which implicates that the effect of LMP2 polymorphisms should be considered when LMP2-targeted vaccine is designed for immunotherapy.

Amino Acid Substitution↗