PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Nested Genes”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 991 records · Page 55Linked to original sources

VH gene usage in immunoglobulin E responses of seasonal rhinitis patients allergic to grass pollen is oligoclonal and antigen driven.

BACKGROUND: IgE is the pivotal-specific effector molecule of allergic reactions yet it remains unclear whether the elevated production of IgE in atopic individuals is due to superantigen activation of B cell populations, increased antibody class switching to IgE or oligoclonal allergen-driven IgE responses. OBJECTIVES: To increase our understanding of the mechanisms driving IgE responses in allergic disease we examined immunoglobulin variable regions of IgE heavy chain transcripts from three patients with seasonal rhinitis due to grass pollen allergy. METHODS: Variable domain of heavy chain-epsilon constant domain 1 cDNAs were amplified from peripheral blood using a two-step semi-nested PCR, cloned and sequenced. RESULTS: The VH gene family usage in subject A was broadly based, but there were two clusters of sequences using genes VH 3-9 and 3-11 with unusually low levels of somatic mutations, 0-3%. Subject B repeatedly used VH 1-69 and subject C repeatedly used VH 1-02, 1-46 and 5a genes. Most clones were highly mutated being only 86-95% homologous to their germline VH gene counterparts and somatic mutations were more abundant at the complementarity determining rather than framework regions. Multiple sequence alignment revealed both repeated use of particular VH genes as well as clonal relatedness among clusters of IgE transcripts. CONCLUSION: In contrast to previous studies we observed no preferred VH gene common to IgE transcripts of the three subjects allergic to grass pollen. Moreover, most of the VH gene characteristics of the IgE transcripts were consistent with oligoclonal antigen-driven IgE responses.

Adult↗

Novel genes expressed in subsets of chemosensory sensilla on the front legs of male Drosophila melanogaster.

Detection of courtship-activating female pheromones by contact chemoreceptors on the front legs of male Drosophila melanogaster is thought to play an important role in triggering courtship behavior. However, the chemosensory organs, cells, and molecules responsible are not known. We have isolated two genes, CheA29a and CheB42a, expressed in nonneuronal auxiliary cells within two nested subsets of chemosensory sensilla on the front legs of sexually mature, adult males. The proteins encoded by the CheA29a and CheB42a genes have no sequence similarity to each other or any other known protein, but they belong to two novel families of proteins encoded by the D. melanogaster genome. Members of the two families are predicted to have a single transmembrane domain at their amino terminus, probably to serve as a signal peptide, suggesting that they are soluble and secreted. Finally, in addition to CheA29a and CheB42a, other genes within each family are expressed preferentially in appendages where chemosensory organs are concentrated, in several cases in a male-specific manner. Our data suggest that CheA29a and CheB42a and other members of these two protein families are involved in male-specific chemical senses, perhaps pheromone response.

Amino Acid Sequence↗

Human immunodeficiency virus type 1 envelope gene structure and diversity in vivo and after cocultivation in vitro.

Nested-primer polymerase chain reaction (PCR) has been applied to the molecular cloning of 4.6-kb half-genome fragments of human immunodeficiency virus type 1 (HIV-1) taken directly from the peripheral blood mononuclear cells (PBMC) of an individual with neurological symptoms of HIV-1 infection. In a similar manner, gp120-coding portions of the envelope gene were cloned after PBMC from the same blood sample were cocultivated with uninfected PBMC for 28 days. The complete 1.6-kb nucleotide sequence of the gp120 gene was determined from each of 35 clones examined. Two of 13 (15%) PBMC-derived gp120 genes and 3 of 22 (14%) coculture-derived gp120 genes were defective as a result of frameshifts and an in-frame stop codon(s). Mean diversity between individual gp120-coding sequences in PBMC was fivefold greater (3.24%) than after coculture (0.65%). A predominant sequence of "strain" was found after coculture that was distinct from the diverse viral genotypes detected in vivo and therefore was selectively amplified during in vitro propagation. Multiple distinct third variable (V3) regions encoding the principal neutralizing domain of the envelope protein were detected in PBMC-derived genes, suggesting the presence of immunologic diversity of HIV env genes in vivo not reflected in the cocultured virus sample. The large size of the HIV fragments generated in this study will permit analysis of the diversity of immunologic reactivity, gene function, and pathogenicity of HIV genomes present within infected individuals, including the functional significance of the loss of diversity that occurs upon coculture.

Acquired Immunodeficiency Syndrome↗

Nested PCR for detection and genotyping of Ehrlichia ruminantium: use in genetic diversity analysis.

Ehrlichia ruminantium, the agent of cowdriosis transmitted by Amblyomma ticks, presents an extensive genetic and antigenic diversity of key importance for vaccine formulation. Two means of nested polymerase chain reaction (PCR) targeting were developed to conduct molecular epidemiology studies in the Caribbean and Africa. The first used a conserved DNA fragment for detection of the pathogen in animals and vectors, and the second relied on the polymorphic map1 gene for genotyping. As compared to a PCR, the nested PCR showed a 2-Log10 improvement of sensitivity and allowed amplification from ticks, blood, brain, and lungs from infected animals, providing a more accurate picture of the tick infection rate. In Guadeloupe, this rate reached 36% (N = 212) instead of 1.7% (N = 224), as previously estimated. Genetic typing was done by restriction fragment length polymorphism or sequencing of map1 amplification products. Molecular epidemiology studies conducted in field sites selected for vaccination trials with inactivated vaccine, revealed the circulation of genetically divergent strains in limited geographical areas. It is known, then, that genetic clustering based on map1 has no predictive value regarding the protective value of a given strain against a new strain. However, tracing the strains by this technique revealed the extent of E. ruminantium diversity that one can expect in a given region, and the method allows differentiation between an inadequate immune response and the challenge by a breakthrough strain on animals dying despite vaccination. Up to now, genetic typing does not avoid cross-protection studies, which were conducted in parallel, although on a more limited scale. The importance of pathogen diversity studies for optimization of vaccine design is discussed as well as the research for new polymorphic genes. These genes may allow better predictions on cross-protection, given the recent completion of the sequence of the full genome of two E. ruminantium strains.

Animals↗

Sequence analysis of a gene product synthesized by Xanthomonas sp. during growth on natural rubber latex.

Xanthomonas sp. secretes an extracellular protein (Mr approximately 70+/-5 kDa) during growth on purified natural rubber [poly(1,4-cis-isoprene)] but not during growth on water-soluble carbon sources such as glucose or gluconate. A 1.3 kbp DNA fragment coding for an internal part of the structural gene of the 70 kDa protein was amplified by nested polymerase chain reaction (PCR) using amino acid sequence information obtained after Edman degradation of selected trypsin-generated peptides of the purified 70 kDa protein. The PCR product was used as a DNA probe to clone the complete structural gene from genomic DNA of Xanthomonas sp. The sequenced DNA contained a 2037 bp open reading frame which coded for a polypeptide of 678 amino acids (Mr 74.6 kDa) and which included the features of the N-terminal signal peptidase cleavage site (Mr approximately 72.9 kDa for the mature protein). Analysis of the amino acid sequence revealed the presence of two heme binding motifs (CXXCH) and a approximately 20 amino acids long sequence that is conserved in the Paracoccus denitrificans and Pseudomonas aeruginosa diheme cytochrome c peroxidases (CCPs). This region includes a histidine residue (H519 in Xanthomonas sp. and H265 and H271 in the Pseudomonas strains, respectively) that is essential for activity in CCPs and that is also conserved in other bacterial oxidases. Blast analysis confirmed the relatedness of the 70 kDa protein to heme-containing oxidases and suggested that it is a member of a new family of relatively large (approximately 500 to approximately 1000 amino acids) extracellular proteins with so far unknown function being only far related in amino acid sequence to P. denitrificans and P. aeruginosa CCPs.

Amino Acid Sequence↗

Mapping the neutralizing epitopes on the glycoprotein of infectious haematopoietic necrosis virus, a fish rhabdovirus.

Twelve neutralizing monoclonal antibodies (MAbs) against the fish rhabdovirus, infectious haematopoietic necrosis virus (IHNV), were used to select 20 MAb escape mutants. The nucleotide sequence of the entire glycoprotein (G) gene was determined for six mutants representing differing cross-neutralization patterns and each had a single nucleotide change leading to a single amino acid substitution within one of three regions of the protein. These data were used to design nested PCR primers to amplify portions of the G gene of the 14 remaining mutants. When the PCR products from these mutants were sequenced, they also had single nucleotide substitutions coding for amino acid substitutions at the same, or nearby, locations. Of the 20 mutants for which all or part of the glycoprotein gene was sequenced, two MAbs selected mutants with substitutions at amino acids 230-231 (antigenic site I) and the remaining MAbs selected mutants with substitutions at amino acids 272-276 (antigenic site II). Two MAbs that selected mutants mapping to amino acids 272-276, selected other mutants that mapped to amino acids 78-81, raising the possibility that this portion of the N terminus of the protein was part of a discontinuous epitope defining antigenic site II. CLUSTAL alignment of the glycoproteins of rabies virus, vesicular stomatitis virus and IHNV revealed similarities in the location of the neutralizing epitopes and a high degree of conservation among cysteine residues, indicating that the glycoproteins of three different genera of animal rhabdoviruses may share a similar three-dimensional structure in spite of extensive sequence divergence.

Amino Acid Sequence↗

Polymorphism of HIV-1 gag (p17) gene from female sex workers in Calcutta, India.

HIV-1 subtype C is the major subtype in India as evidenced from the analysis of specific regions within envelope and gag gene. The matrix protein (p17) of HIV-1 which is involved in several functions like the viral RNA transport, nuclear localization, assembly of pre-integration complex into host nucleus has been used to study the strain diversity among female sexworkers in Calcutta. The gene encoding for the HIV-1 matrix protein, p17 was amplified by nested polymerase chain reaction (PCR) from blood samples of HIV-1 seropositive female sex workers (FSW) in Calcutta, India. Genes of twenty-two samples were sequenced and the phylogenetic analysis with different global strains showed that the majority (seventeen) was clustered with Indian type C. A few samples were found to be close to other C subtypes isolated from South Africa, China and Myanmar. The comparison of Calcutta samples with the samples from other regions of India along with other non-asian subtype C sequences clearly revealed a different cluster of Indian sequences. The two samples, cal 242 and cal 709 was found to be the most divergent type and showed close relatedness with African C subtypes.

Base Sequence↗

[Molecular cloning of TSARG3 gene related to apoptosis in human spermatogenic cells].

OBJECTIVE: To clone a novel gene which is related to human testis spermatogenesis apoptosis. METHODS: To rapidly attain human novel gene full-length cDNA sequence from a human testis cDNA library,the gene-specific primers and the vector-specific primers were designed for nested polymerase chain reaction. Sequencing was performed and the result was analysed. RESULTS: The present authors discovered the TSARG3 gene(GenBank accession number AF419291) from a human testis cDNA library, using a cDNA fragment (GenBank accession number BE644537) as an electronic probe, which was significantly changed in cryptorchidism and represented a novel gene. Furthermore, a mouse homologue of this gene was identified (GenBank accession number AF419292) by using the same method. CONCLUSION: A novel gene named TSARG3 was cloned. It is considered that the function of the new gene is related to human testis spermatogenesis apoptosis.

Amino Acid Sequence↗

Coamplification of hprt cDNA and gamma T-cell receptor sequences from 6-thioguanine resistant human T-lymphocytes.

The nature of mutation at the HPRT locus in human T-lymphocytes in vivo is currently a subject of considerable interest. Determination of clonality in individual mutant T-lymphocytes is essential for the proper interpretation. This requires the molecular analysis of their respective T-cell receptors (TCR). We have developed a polymerase chain reaction (PCR)-based method for coamplification of hprt cDNA and the rearranged gamma T-cell receptor genes from crude cell lysates of individual 6-thioguanine resistant human T-lymphocytes. Following reverse transcription to produce hprt cDNA, the crude cell lysate is treated with proteinase K and subjected to a primary PCR with two sets of amplification primers, one specific for the hprt cDNA and the other for the rearranged gamma TCR gene. A secondary round of PCR, employing appropriate sets of nested amplification primers, are then used to produce sufficient quantities of DNA for both the sequencing and restriction fragment length analysis, of the hprt cDNA and gamma TCR gene respectively.

Adult↗

Detection of Borrelia burgdorferi-specific DNA in urine specimens from patients with erythema migrans before and after antibiotic therapy.

A nested PCR was developed for the detection of Borrelia burgdorferi-specific DNA in the urine of patients with erythema migrans. The target for the nested PCR was a specific region of the flagellin gene; the detection limit was less than five organisms of B. burgdorferi including all three species B. burgdorferi sensu stricto, B. afzelii, and B. garinii. A prospective, controlled, blinded study was performed with 26 patients with erythema migrans to evaluate the nested PCR method with clinical samples. B. burgdorferi-specific DNA could be detected in urine specimens from 22 of 24 patients with erythema migrans (sensitivity, 91.61%). Immediately after therapy, 11 of 19 patients still yielded positive results (58%). Eight weeks after therapy, 2 of 16 patients (13%) were positive by PCR of urine, and 20 weeks after treatment none of seven investigated urine samples was reactive. Essential for the sensitivity that was obtained was the development of a simple DNA extraction procedure. The results of the study indicate that the described method is highly sensitive and allows for the effective control of the efficacy of antibiotic therapy in patients with early Lyme borreliosis.

Adult↗

[Construction of Streptococcus mutans luxS gene allelic exchange plasmid].

OBJECTIVE: It is reported that Streptococcus mutans luxS gene may have an important role in the interspecies quorum sensing system. To construct the S. mutans luxS gene knockout mutant, this research aim to construct the luxS gene allelic exchange plasmid. METHODS: The upstream and downstream flank DNA fragments of S. mutans luxS gene (Xup, Xdn)and the E. coli kanamycin resistance gene (Kana) were enriched by pfu DNA polymerase with "nest PCR" methods. These fragments were ligated into pBluescript SK (+) Phagemids vector with double endonuclease reaction sequentially. RESULTS: With endonuclease reaction and DNA sequencing, it was proved that the objective plasmid, Xukd-pbsk, was constructed correctively and the kanamycin resistance gene could be expressed in vitro. CONCLUSION: The S. mutans luxS gene allelic exchange plasmid is constructed correctively in this research and can be used in the future research of S. mutans luxS gene knockout mutant.

Bacterial Proteins↗

Novel surveillance and cure of a donor-transmitted lymphoma in a renal allograft recipient.

BACKGROUND: In this report we describe a malignant lymphoma of donor origin inadvertently transplanted into two renal allograft recipients, despite standard comprehensive donor screening. The successful clearance of the tumor from both patients and a novel method of surveillance are detailed. METHODS: Initial management consisted of withdrawal of immunosuppression to promote rejection of the allograft and the transplanted tumor in both patients, followed by graft removal. Peripheral blood microchimerism was assessed in both recipients using nested polymerase chain reaction to detect the DYZ3 gene on the Y chromosome (donor male, recipients female). RESULTS: Although microchimerism was detected on day 6 after transplantation and day 1 after explantation, repeat peripheral blood examination at 1, 3, and 6 months after explantation demonstrated no microchimerism. Both patients remain well at 12 months and have been relisted for transplantation. CONCLUSION: Despite inadvertent transplantation of a previously undiagnosed malignancy of donor origin, the recipients' immune response was able to eliminate donor tumor cells after the withdrawal of immunosuppression. Repeated surveillance of peripheral blood from both recipients, using a novel application of the technique of nested polymerase chain reaction to amplify donor DNA, demonstrated no persistence of donor cells, supporting effective eradication of the donor malignancy.

Aged↗

Phylogeny of bipolar Cladonia arbuscula and Cladonia mitis (Lecanorales, Euascomycetes).

Phylogenetic relationships and levels of geographic differentiation of two closely related bipolar taxa, Cladonia arbuscula and Cladonia mitis, were cladistically examined with ITS regions, SSU rDNA introns, partial beta-tubulin, and partial glyceraldehyde 3-phosphate dehydrogenase (GAPDH) genes. In the combined analysis of the four genes, C. arbuscula was paraphyletic, while C. mitis, nested within C. arbuscula, formed a strongly supported monophyletic group. C. arbuscula samples were divided into three separate clades: "arbuscula I," appearing as basal to the other ingroup taxa, "arbuscula II," and "arbuscula III" (the latter represented by only one specimen), which were not correlated with any morphological trait. Only C. mitis specimens formed a morphologically and chemically distinct group. None of the main clades was correlated with geographic origin. The separate analyses were poorly resolved, and in most cases samples from "arbuscula I," "arbuscula II," and "arbuscula III" clades were intermixed. An incongruence test revealed conflict among the four gene regions in almost all cases. Only ITS regions and introns were not significantly incongruent, suggesting lack of recombination within the ribosomal DNA locus. Incomplete lineage sorting and recombination were considered to be the main reasons accounting for the incongruencies. The high proportion of shared polymorphisms between the "arbuscula I" and "arbuscula II" clades, especially found from the beta-tubulin gene and from the ITS regions, and the lack of corroborating morphological characters both indicate a short history of reproductive isolation among the groups. The lack of genetic differentiation among the northern and southern samples within the main clades indicates a relatively recent gene flow, which may have resulted from migrations during the Pleistocene glaciations or from more recent long-distance dispersal.

Ascomycota↗

Amplification of P1 gene by polymerase chain reaction for detection of Mycoplasma pneumoniae.

Mycoplasma pneumoniae is a causative agent of human respiratory tract infection of which the clinical features are not significantly different from those of infections caused by other respiratory pathogens. The diagnosis is based principally on laboratory tests. Since conventional methods such as culture and serological tests are time-consuming, insensitive, and non-specific, polymerase chain reaction (PCR) was employed for laboratory diagnostics. This study was aimed to develop PCR method to detect M. pneumoniae by designing primers to amplify fragment of the P1 adhesin gene. Two protocols, PCR-probe hybridization and nested PCR, were carried out. False-positive result due to amplicon carry over was prevented by using dUTP instead of dTTP and the addition of enzyme uracil DNA glycosylase (UDG). For nested PCR, UDG was added only in the first round reaction mixture. The sensitivity of PCR was 10 fg of M, pneumoniae DNA as detected by agarose gel electrophoresis and increased to be 1 fg as detected by either probe hybridization or nested PCR. The specificity of PCR was tested with DNAs from Mycoplasma spp, a variety of different bacterial genera and human leukocyte. All gave negative results. Considering of the speed, sensitivity, specificity and the prevention of amplicon carryover, the developed PCR-based protocols were suitable and reliable for the detection of M. pneumoniae in routine laboratory.

Base Sequence↗

Improved PCR sensitivity for direct genotyping of Chlamydia trachomatis serovars by using a nested PCR.

Successful amplification of omp1 DNA by PCR is crucial in the genotyping of Chlamydia trachomatis when directly performed with clinical samples (J. Lan, J. M. M. Walboomers, R. Roosendaal, G. J. van Doornum, D. M. McLaren, C. J. L. M. Meijer, and A. J. C. van den Brule, J. Clin. Microbiol. 31:1060-1065, 1993). Several primers flanking the four variable domains of the omp1 gene were selected and tested for sensitivity in several nested PCRs with serial dilutions of serovar G. The optimal sensitivity obtained was 0.1 to 0.01 inclusion-forming units, similar to that obtained in the C. trachomatis plasmid PCR. With this approach, any C. trachomatis PCR-positive sample can be typed.

Bacterial Outer Membrane Proteins↗

[A study on correlation of changing proportion of L:M:S due to the variation of HBV PreS genes and liver injury].

OBJECTIVE: In order to study the correlation between the changing proportion of L:M:S due to the variation of HBV PreS genes and the liver injury. METHODS: We selected three groups of HBV-infected individuals, including acute infection with complete recovery, chronic HBV carriers and chronic severe hepatitis B, each consisting of three cases. The preS genes were amplified from serum samples with half nested PCR. The PCR products were cloned into M13 vectors, and 10 clones were randomly selected for each person and sequenced with routine methods. A total of 90 clones were sequenced and analyzed by DNA homology comparison. RESULTS: We found that there were significant characteristics in HBV-infected individuals with different clinical consequences. (1)Acute hepatitis B: normal proportion of L:M:S, Slightly higher M protein was found in one patient. (2)Chronic HBV carriers: Higher proportion of L:M:S was found by which M protein synthesis decreased. (3)Chronic severe hepatitis B: HBV and deletion of large fragment of preS1 gene may induce abnormally high immunity response, and then cause severe liver injury in these patients. CONCLUSION: These results provide some experimental facts that the possible association between changing proportion of L:M:S and liver injury could be wholly explored.

Hepatitis B↗

[Evaluation of new method for diagnosis of opportunistic fungal infection].

New methods for the possible presence DNA specific for Aspergillus or Trichosporon species were developed. In aspergillus PCR, Aspergillus l8S rRNA encoding gene was amplified from five strains of Aspergillus species by the nested PCR but not from other microorganisms. Results of preliminary investigation of this method demonstrated efficient detections of Aspergillus species in serum samples of rats model of aspergillosis and 29 patients with invasive aspergillosis. In trichosporon PCR, Trichosporon 26S rRNA encoding gene was amplified from two strains of Trichosporon species, and detected by the nested PCR in 64 % of serum samples of patients with trichosporonosis, while glucuronoxylomannan antigen was detected in 55 % of samples. The high sensitivity and specificity of the nested PCR indicate that the assay can provide early diagnosis with sufficient accuracy to be clinically useful for patients with opportunistic fungal infection.

Adult↗

Expression of beta-human chorionic gonadotropin genes in renal cell cancer and benign renal disease tissues.

To study the expression of beta-human chorionic gonadotropin (beta hCG) genes in renal cell carcinomas (RCC) and benign renal disease tissues, nested reverse transcription-polymerase chain reaction (RT-PCR) and restriction endonuclease analysis were employed to detect the expression of beta hCG genes in 44 cases of RCC tissues and 24 cases of benign renal disease tissues. It was found that 52% RCC samples revealed positive for beta hCG mRNA expression. Positive rate in advanced stage and poorly differentiated RCC was higher, but there was no significant difference. The positive rate of beta hCG mRNA expression was 54% in 24 cases of benign renal tissues, including 3 cases out of 6 polycystic kidneys, 7 cases out of 13 renal atrophies, 2 cases out of 2 oncocytomas and 1 case out of 2 pyonephrotic kidneys. beta 7 was most frequently transcribed subtype gene independent on the histology. These findings suggested beta hCG gene transcription is not only involved in RCC but also in benign renal diseases.

Adult↗