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 109 records · Page 6Linked to original sources

PubMed2001

[Analysis of several genes using primer extension preamplification based on individual cell].

OBJECTIVE: To analyze several genes at the same time in one individual cell using primer extension preamplification (PEP). METHODS: The whole genome of individual cell was preamplified by PEP using 10 base random oligonucleotides. The aliquots(5 mu liter) from PEP were used to amplify SRY, ZP(3), RhCE, RhD and F VIII genes by nested PCR. RESULTS: The five genes could be amplified following PEP-PCR. Lymphocyte of four genotypes were diagnosed by PEP-PCR; correct diagnoses were obtained in 95.6%. CONCLUSION: At least five genes can be analyzed by PEP-PCR based on one individual cell in this laboratory. This method could be used in preimplantation genetic diagnosis and noninvasive prenatal diagnosis.

Female↗

PubMed2005

[Experimental study on the pathological effect of Helicobacter pylori on liver tissues].

OBJECTIVE: To observe whether H. pylori inoculated by oral route could arrive in livers and cause liver inflammation as an independent etiological factor. METHODS: C57BL/6 mice were orally inoculated with H. pylori SS1 strains and fed for 8 months. H. pylori colonization and pathologic consequences were studied in the liver and gallbladder tissues of the mice; the blood, liver tissue and gastric mucosa were obtained and cultured for H. pylori growth; The bacterial DNA extracted from the liver, bile and blood was examined by nested PCR for H. pylori genes. 16S rRNA PCR amplicons were sequenced and compared with the sequencing results of 16S rRNA PCR amplicons of the bacteria cultured from gastric mucosa and the inoculated H. pylori SS1. RESULTS: The bacterial DNA extracted from the liver, bile and blood of the infected mice was detected for H. pylori genes by nested PCR. Six of the 15 samples were positive (40%) in the liver, 6 of 10 samples in the bile (60%), and 2 of 10 samples in the blood (20%). Sequencing results of 16S rRNA PCR products of the livers showed 100% homogeneity when compared with the cultured H. pylori from gastric mucosa and inoculated H. pylori SS1. H. pylori was found in 4 liver tissues of the 15 infected mice (26.7%) and 6 in the gallbladders (40%). Infiltrations of lymphocyte cells along hepatic sinusoids and a lower degree infiltration around interlobular arteries and veins were observed; ballooning degeneration was also observed in some hepatocytes. CONCLUSION: H. pylori inoculated by oral route could arrive in the liver and cause inflammation as an independent etiological factor. The routes which the microorganisms took to reach the livers may involve hematogenous and/or biliary system dissemination.

Animals↗

PubMed2005

Microarray analysis of host gene-expression during intracellular nests formation of Trypanosoma cruzi amastigotes.

The intracellular pathogens utilize numerous cellular components of host cells to advance the infection as well as to enter the host cell. Analyzing the host cellular response enables us to get a better understanding of the pathogenesis, and subsequently indicate possible therapeutic targets. We therefore analyzed gene-expression profile of NIH3T3 fibroblast cells infected by Trypanosoma, a representative intracellular pathogen similar to Leishmania, using custom-designed cDNA microarray consisting of 1,701 mKIAA cDNAs. Focusing on intracellular nest formation of Trypanosoma cruzi amastigotes, we profiled the host gene-expression at 8 days post-infection and found several degrees of change in 16 mKIAA genes. Among these genes, 10 were up-regulated and 6 were down-regulated. Assuming that these genes had important roles in the infection's progression, we performed semi-quantitative RT-PCR analysis and con-firmed the gene expression change of 4 genes. Furthermore, 5 genes were mapped on cadherin signaling pathway using pathway analysis software. These results indicate significance of the host cellular pathway in the proliferative stage of Trypanosoma cruzi amastigotes.

Animals↗

PubMed2000

Detection of lymph node metastasis of oesophageal cancer by RT-nested PCR for SCC antigen gene mRNA.

With recent development in molecular biology, reverse transcriptase polymerase chain reaction (RT-PCR) has been applied to detect occult lymph node metastasis, but there have been few reports concerning oesophageal cancer. The objective of this study is to investigate the usefulness of the squamous cell carcinoma (SCC) antigen gene as a marker with RT-nested PCR to detect occult lymph node metastases of oesophageal cancer. The SCC antigen has been widely used as a serum tumour marker and was reported as a target gene to detect tumour cells in peripheral blood in cervical cancer. In this study, 620 lymph nodes from 14 oesophageal cancer patients were analysed. The results of RT-nested PCR were compared with that of pathological and immunohistochemical examinations. In the test of sensitivity, the RT-nested PCR detected 10(1) of SCC antigen producing cells in 10(7) peripheral blood mononucleocytes and was not found in 43 control lymph nodes. The pathological examination, immunohistochemical examination and the RT-nested PCR detected 36, 45 and 65 nodes respectively. The RT-nested PCR detected statistically more lymph nodes than the pathological or immunohistochemical examination. The sensitivity and specificity seem higher in squamous cell carcinoma cases. The SCC antigen gene is one of the more useful markers for RT-nested PCR to detect occult lymph node metastases of oesophageal cancer.

Antigens, Neoplasm↗

PubMed1994

Functional analysis of the connexin43 gene promoter in vivo and in vitro.

Connexin43 is the principal gap junction protein found in the mammalian heart. The regulation of connexin43 gene expression may be an important determinant of normal and altered cardiac development and electrophysiology. We constructed a series of chimeric luciferase reporter genes containing nested deletions from the human connexin43 gene (-2400 to -50 basepairs, relative to transcription initiation). The transcriptional activity of the chimeric genes was assayed in several cell types and systems, including rat cardiocytes in vitro and adult rat heart in vivo. In both systems, high levels of luciferase activity required at least 175 base-pairs of 5'-flanking sequence. Constructs including 2400 base-pairs of upstream sequence increased activity two-fold in vivo, but not in vitro. Chimeric genes were also assayed in cultured cardiac non-myocytes. This population of cells accumulates significant levels of connexin43 mRNA when propagated in vitro and promoter constructs were correspondingly active. Elements within the proximal promoter may also confer tissue-specificity. Transfectional analysis of the SKHep1 cell line, which does not express connexin43, demonstrated reduced reporter gene activity, especially for the longest constructs. These studies begin to define the cis-acting elements of the connexin43 gene which regulate its strength and specificity of transcription.

Animals↗

PubMed2002

Gene flow, dispersal, and nested clade analysis among populations of the stonefly Peltoperla tarteri in the southern Appalachians.

We examined the genetic structure and phylogeography of populations of the stonefly Peltoperla tarteri in the Southern Appalachians to determine the extent and likely mechanism for dispersal of this stream insect. A 454-base-pair (bp) portion of the mitochondrial control region was sequenced from a minimum of 20 individuals from eight populations. Pairwise FST and exact tests showed high levels of differentiation among almost all populations except those on the same stream. amova analysis detected significant genetic differentiation between streams within drainages (phi(SD) = 0.14, P < 0.001), and there was a slight positive correlation between aquatic distance and genetic distance (r = 0.295, P = 0.03). According to nested clade analysis, the present day pattern of genetic variation in P. tarteri is the result of a historical range expansion coupled with restricted gene flow with isolation by distance. Together, these analyses suggest that adult dispersal is limited and that movement by larvae is the primary dispersal mechanism for P. tarteri.

Animals↗

PubMed2026

Nested co-expression network analysis identifies compact gene clusters in a black box.

MOTIVATION: Digital analysis of biological systems requires methods capable of identifying both broad and nested gene modules reflecting complex biological processes. Existing transcriptomic methods often miss compact gene sets corresponding to subprocesses in specialized cell types, limiting insights into functional heterogeneity. RESULTS: We present Nested-WGCNA, a two-stage unsupervised network analysis algorithm designed to identify coarse-grained and fine-grained gene modules. Applied to bulk RNA-Seq data, Nested-WGCNA reveals stable modules reproducible across datasets. When validated against scRNA-Seq data, these modules correspond to both major and minor immune cell subtypes. Application to immunotherapy response datasets uncovers predictive and prognostic biomarkers, highlighting its utility in treatment stratification and biomarker discovery. AVAILABILITY: The NestedWGCNA source code and analysis pipeline are available on GitHub (https://github.com/ilyada/NestedWGCNA) and archived on Zenodo (https://doi.org/10.5281/zenodo.18959244).

Algorithms↗

PubMed2000

Analytical sensitivity, reproducibility of results, and clinical performance of five PCR assays for detecting Chlamydia pneumoniae DNA in peripheral blood mononuclear cells.

Chlamydia pneumoniae has been associated with atherosclerosis and coronary artery disease (CAD), and its DNA has been detected in atheromatous lesions of the aorta, carotid, and coronary arteries by a variety of PCR assays. The objective of this study was to compare the performances of five published PCR assays in the detection of C. pneumoniae in peripheral blood mononuclear cells (PBMCs) from patients with coronary artery disease. The assays included two conventional PCRs, one targeting a cloned PstI fragment and one targeting the 16S rRNA gene; two nested PCRs, one targeting the 16S rRNA gene and one targeting ompA; and a touchdown enzyme time release (TETR) PCR, targeting the 16S rRNA gene. All PCRs had similar analytical sensitivities and detected a minimum of 0.005 inclusion-forming units (IFU) of C. pneumoniae; the ompA nested PCR and the TETR PCR were slightly more sensitive and detected 0.001 IFU. Assay reproducibility was examined by testing 10 replicates of C. pneumoniae DNA by each assay. All five assays showed excellent reproducibility at high levels of DNA, with scores of 10 out of 10 for 0.01 IFU, but exhibited decreased reproducibility for smaller numbers of C. pneumoniae IFU for all tests. Pairwise comparison of test results indicated that there was a significant difference between tests (Cochran Q = 32.0, P<0.001), with the PstI fragment (P<0.001) and 16S rRNA (P = 0.002) assays having lower reproducibility than the nested ompA and TETR assays. To further analyze assay sensitivity, C. pneumoniae-infected U-937 mononuclear cells were added to whole blood, and extracted mononuclear-cell DNA was tested by each assay. All five assays showed similar sensitivities, detecting 15 infected cells; three assays detected 3 infected cells, while all assays were negative at the next dilution (1.5 infected cells). A striking difference in performance of the five assays was seen, however, when PBMCs from CAD patients were tested for C. pneumoniae DNA. The ompA nested PCR detected C. pneumoniae DNA in 11 of 148 (7.4%) specimens, the 16S rRNA nested PCR detected 2 positives among the 148 specimens (1.4%) (P<0.001), and the other 3 assays detected no positive specimens (P<0.001, compared with the ompA assay). These results indicate that analytical sensitivity alone does not predict the ability of an assay to detect C. pneumoniae in whole-blood-derived PBMCs. Before standardized assays can be used in wide-scale epidemiological studies, further characterization of these assays will be required to improve our understanding of their performance in the detection of C. pneumoniae in clinical material.

Bacterial Outer Membrane Proteins↗

PubMed2006

[Study on fetal SRY gene in maternal plasma using nested polymerase chain reaction].

OBJECTIVE: To develop a nested polymerase chain reaction (PCR) technique for fetal SRY gene identification using cell-free fetal DNA in maternal plasma. METHODS: Peripheral blood samples were obtained from 30 pregnant women and cell-free DNA was extracted by the phenol/chloroform method from plasma. The nested PCR was carried out to amplify the fragment of SRY gene by two sets of PCR primer pairs. Direct sequencing analysis was then performed on the PCR product. RESULTS: Among the 17 women bearing male fetuses, SRY sequences were detected in 15 plasma samples after nested PCR amplification, while none of the 13 women bearing female fetuses had the positive results. The accuracy and sensitivity were 93.3% (28/30) and 88.2% (15/17), respectively. CONCLUSION: The phenol/chloroform extraction for fetal DNA in maternal plasma was effective and simple. And the nested PCR amplification of SRY sequence is a convenient and low-cost approach for the non-invasive early prenatal diagnosis of sex-linked inheritant diseases.

Adult↗

PubMed2005

Identification of anaplastic lymphoma kinase variant translocations using 5'RACE.

Anaplastic lymphoma kinase (ALK) is abnormally expressed in anaplastic large cell lymphoma (ALCL) and its expression associated with chromosomal translocations involving the ALK gene at 2p23. These translocations lead to the synthesis of novel chimeric proteins that retain the C-terminal portion of ALK, where the tyrosine kinase domain is located. In most of these tumors, the t(2;5)(p23;q35) translocation causes fusion of the ALK gene to the 5' region of the nucleophosmin (NPM) gene, but other different ALK partners have been identified, including nonmuscle tropomyosin (TPM3), TRK-fused gene (TFG), 5' aminoimidazole-4-carboxamide ribonucleotide formyltranferase/IMP cyclohydrolase (ATIC), clathrin heavy chain gene (CLTC), and moesin (MSN). The characterization of these ALK partners has been performed using different molecular methods, including the 5' Rapid Amplification of complementary deoxyribonucleic acid (cDNA) Ends (5'RACE) polymerase chain reaction (PCR)-based technique. This approach allows the potential amplification and identification of either 5' or 3' mRNA ends from an internal known sequence. In ALK translocations, identification of the 5' gene involved has been performed using primers designed within the known 3' catalytic domain of the ALK. Initial reaction consists in a first-strand cDNA synthesis primed using a gene-specific antisense primer (ALK1), performing the cDNA conversion of specific messenger ribonucleic acids, and maximizing the potential for complete extension to the 5'-end of the message. After cDNA synthesis, the first-strand product is purified from unincorporated dNTPs and ALK1. Terminal deoxynucleotidyl transferase is used to add homopolymeric tails to the 3' ends of the cDNA. Tailed cDNA is then amplified by PCR using a nested gene-specific primer (ALK2), which anneals 3' to ALK1, and a complementary homopolymer containing an anchor primer (i.e., AAP), which permits amplification from the homopolymeric tail. This allows amplification of unknown sequences between the ALK2 and the 5' end of the mRNA. Further, nested PCRs usually are required to confer an adequate level of specificity to the process to permit the characterization of RACE products. The reamplification is achieved by using a nested gene-specific primer (ALK3), which anneals 3' to ALK2, and a universal amplification primer, which anneals to the 5' sequence previously introduced by the AAP primer.

Anaplastic Lymphoma Kinase↗

PubMed2005

Morphological irregularities and features of resistance to apoptosis in the dcp-1/pita double mutated egg chambers during Drosophila oogenesis.

In the present study, we demonstrate the most novel characteristic morphological features of Drosophila egg chambers lacking both dcp-1 and pita functions in the germline cells. Dcp-1 is an effector caspase and it has been previously shown to play an important role during Drosophila oogenesis [McCall and Steller, 1998 : Science 279 : 230-234; Laundrie et al., 2003 : Genetics 165 : 1881-1888; Peterson et al., 2003 : Dev Biol 260 : 113-123]. The completion of sequencing and annotation of the Drosophila genome has revealed that the dcp-1 gene is nested within an intron of another distinct gene, called pita, a member of the C2H2 zinc finger protein family that regulates transcriptional initiation. The dcp-1(-/-)/pita(-/-) nurse cells exhibit euchromatic nuclei (delay of apoptosis) during the late stages of oogenesis, as revealed by conventional light and electron microscopy. The phalloidin-FITC staining discloses significant defects in actin cytoskeleton arrangement. The actin bundles fail to organize properly and the distribution of actin filaments in the ring canals is changed compared to the wild type. The oocyte and the chorion structures have been also modified. The oocyte nucleus is out of position and the chorion appears to contain irregular foldings, while the respiratory filaments obtain an altered morphology. The dcp-1(-/-)/pita(-/-) egg chambers do not exhibit the rare events of spontaneously induced apoptosis, observed for the wild type flies, during mid-oogenesis. Interestingly, the mutated egg chambers are protected by staurosporine-induced apoptosis in a percentage of 40%, strongly suggesting the essential role of dcp-1 and/or pita during mid-oogenesis.

Actins↗

PubMed2006

Detection of ovine lentivirus in the cumulus cells, but not in the oocytes or follicular fluid, of naturally infected sheep.

The aim of this study was to examine the Maedi-Visna virus (MVV) infection status of oocytes, cumulus cells, and follicular fluid taken from 140 ewes from breeding flocks. MVV proviral-DNA and MVV RNA were detected using nested-PCR and RT-PCR MVV gene amplification, respectively in the gag gene. Nested-PCR analysis for MVV proviral-DNA was positive in peripheral blood mononuclear cells in 37.1% (52/140) of ewes and in 44.6% (125/280) of ovarian cortex samples. The examination of samples taken from ovarian follicles demonstrated that 8/280 batches of cumulus cells contained MVV proviral-DNA, whereas none of the 280 batches of oocytes taken from the same ovaries and whose cumulus cells has been removed, was found to be PCR positive. This was confirmed by RT-PCR analysis showing no MVV-viral RNA detection in all batches of oocytes without cumulus cells (0/280) and follicular fluid samples taken from the last 88 ovaries (0/88). The purity of the oocyte fraction and the efficacy of cumulus cell removal from oocytes was proved by absence of granulosa cell-specific mRNA in all batches of oocytes lacking the cumulus cells, using RT-PCR. This is the first demonstration that ewe cumulus cells harbor MVV genome and despite being in contact with these infected-cumulus cells, the oocytes and follicular fluid remain free from infection. In addition, the enzymatic and mechanical procedures we used to remove infected-cumulus cells surrounding the oocytes, are effective to generate MVV free-oocytes from MVV-infected ewes.

Animals↗

PubMed2002

Choroidal tubercles in disseminated tuberculosis diagnosed by the polymerase chain reaction of aqueous humor. A case report and review of the literature.

PURPOSE: Disseminated tuberculosis occurs due to the hematogenous spread of pulmonary tuberculosis systemically. Polymerase chain reaction (PCR) of various body fluids has been found to be beneficial in the diagnosis of disseminated tuberculosis, including intraocular tuberculosis. We describe the role of PCR of the aqueous aspirate in a case of disseminated tuberculosis involving the choroid. METHODS: Single-step PCR fusing primers coding for the IS6110 gene and nested PCR (nPCR) for the detection of the MPB64 gene were performed on the aqueous aspirate in a case of disseminated tuberculosis with miliary involvement of the choroid. RESULTS: On PCR, the aqueous aspirate showed the Mycobacterium tuberculosis genome, thereby confirming the diagnosis of intraocular tuberculosis. CONCLUSION: PCR is a highly sensitive and specific diagnostic test and PCR of intraocular specimens like the aqueous can be supportive of the diagnosis of miliary tuberculosis of the choroid.

Aqueous Humor↗

PubMed1996

Genomic analysis of human multigene families using chromosome-specific vectorette PCR.

We report a technique for the rapid determination of genomic structure of individual members of human interspersed multigene families which circumvents the requirement for genomic clone isolation. In this approach, vectorette libraries were constructed from human/rodent somatic cell hybrid DNA harbouring single members of the gene family. Using these libraries as PCR templates with nested gene-specific primers in combination with a common vectorette primer resulted in the amplification of gene-specific products suitable for the subsequent determination of intron/exon structure. We have applied this technique to characterise members of two gene families.

Chromosomes↗

PubMed2000

[Detection of bcl-2/JH gene rearrangement by semi-nested polymerase chain reaction from fresh tumor samples in patients with laryngeal squamous cell carcinomas].

OBJECTIVE: To evaluate the clinical implications of bcl-2/JH gene rearrangement in laryngeal squamous cell carcinomas (LSCC). METHODS: Bcl-2/JH gene rearrangement analysis in fresh tumor samples was performed in 60 patients with LSCC by semi-nested polymerase chain reaction(PCR). RESULTS: The results showed that bcl-2/JH gene rearrangement was found in 37 out of 60 patients. The breakpoint was located within the major breakpoint region(mbr) in 33 of the 60 patients and the remaining patients had bcl-2 translocation within the minor cluster region(mcr). The results of the study showed that the rearrangement rate of bcl-2 gene was not related to the grade of differentiation, clinical stage, and neck lymph-node metastasis (P > 0.05), and it was related to heavy smoking (P < 0.05). CONCLUSION: Detection of bcl-2/JH gene rearrangement could reveal that bcl-2/JH fusion gene in LSCC is an important molecular biological marker and has a significant role in occurrence and development of LSCC.

Adult↗

PubMed1997

Detection of alphafetoprotein-expressing cells in the blood of patients with hepatoma and hepatitis.

The presence of tumour cells in the blood circulation may predict disease recurrence and metastasis. We have evaluated the specificity and sensitivity of detecting hepatoma cells in blood using nested polymerase chain reaction with primers specific for the alphafetoprotein (AFP) gene. The nested polymerase chain reaction amplified a 270-base pair AFP DNA fragment from cDNA of Hep 3B hepatoma cells. In a reconstitution experiment, AFP mRNA was detected from peripheral mononuclear cells isolated from 10 ml of blood containing as few as ten Hep 3B cells. Peripheral mononuclear cells from the blood of 20 hepatoma patients were analysed, and 19 patients showed positive AFP mRNA expression. Seven of 13 samples from hepatitis patients also showed positive AFP mRNA expression. All five paired samples of peripheral blood or umbilical cord blood from pregnant mothers and their babies, respectively, showed positive AFP expression. None of 22 control samples was positive. The presence of AFP mRNA in the blood of hepatitis or hepatoma patients suggests the presence of circulating hepatoma cells or hepatocytes in the circulation. The high incidence of AFP mRNA in the blood of hepatoma patients supports the notion of early haematogenous spreading of the disease.

Feasibility Studies↗

PubMed1992

Communal nesting patterns in mice implicate MHC genes in kin recognition.

House mice (Mus musculus domesticus) form communal nests and appear to nurse each other's pups indiscriminately. Communal nesting probably functions to reduce infanticide, but it also makes females vulnerable to exploitation if nursing partners fail to provide their fair share of care. Kinship theory predicts that females will preferentially form communal nests with relatives to minimize exploitation and further increase inclusive fitness. Here we provide evidence from seminatural populations that females prefer communal nesting partners that share allelic forms of major histocompatibility complex genes. Such behaviour would lead to the selection of close relatives as communal nesting partners. Although criteria for the demonstration of kin recognition are currently embroiled in controversy, this is the first vertebrate study to meet Grafen's restrictive requirements: discrimination is based on genetic similarity at highly polymorphic loci, incidental correlations due to relatedness are experimentally controlled, and strong reasons exist for expecting the assayed behaviour to be kin-selected.

Animals↗

PubMed2002

Is the saitohin gene involved in neurodegenerative diseases?

Recently, a single nucleotide polymorphism that results in an amino acid change (Q7R) was identified in a previously undescribed gene, named saitohin, nested within the tau gene. We analyzed the distribution of this polymorphism in 499 patients with Alzheimer's disease, 91 patients with frontotemporal dementia, and 402 controls. This polymorphism was in complete disequilibrium with the well-defined extended tau haplotype. We failed to replicate the association between the RR genotype and late-onset Alzheimer's disease, but we found a trend toward an association between the QQ genotype and frontotemporal dementia. Thus, the saitohin Q allele, which is a novel determinant of the tau H1 haplotypes, might represent a causative factor involved in the determinism of several tauopathies.

Adult↗