SEARCH · PubMed Health

Results for “Sequence Count Data”

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 1,027 records · Page 57Linked to original sources

PubMed2000

Reduced expression of PSCA, a member of the LY-6 family of cell surface antigens, in bladder, esophagus, and stomach tumors.

Prostate stem cell antigen (PSCA) is a member of the LY-6 family of surface proteins that is overexpressed in prostate cancer. Using serial analysis of gene expression (SAGE), we identified PSCA as one of the most abundant transcripts in a differentiated urothelial tumor. As assessed by Northern blotting, PSCA is highly expressed in normal urothelium and noninvasive urothelial tumors. In contrast to the previously reported overexpression of PSCA in progressive and invasive forms of prostate cancer, we found a markedly reduced expression in undifferentiated bladder carcinoma. In addition, several aberrant splicing products derived from the PSCA gene were found in urothelial tumors. Furthermore, PSCA mRNA was highly abundant in normal esophagus and stomach, but was undetectable in esophageal or gastric tumors. The PSCA expression appeared to depend on cell contact, since mRNA levels were increased when RT112 bladder carcinoma cells were grown to confluence. Our data suggest that PSCA could serve as a potential marker for the early carcinogenesis in urothelial and gastric tissues and that its expression is specific for epithelial cells.

Alternative Splicing↗

PubMed2004

Consistent cytotoxic-T-lymphocyte targeting of immunodominant regions in human immunodeficiency virus across multiple ethnicities.

Although there is increasing evidence that virus-specific cytotoxic-T-lymphocyte (CTL) responses play an important role in the control of human immunodeficiency virus (HIV) replication in vivo, only scarce CTL data are available for the ethnic populations currently most affected by the epidemic. In this study, we examined the CD8(+)-T-cell responses in African-American, Caucasian, Hispanic, and Caribbean populations in which clade B virus dominates and analyzed the potential factors influencing immune recognition. Total HIV-specific CD8(+)-T-cell responses were determined by enzyme-linked immunospot assays in 150 HIV-infected individuals by using a clade B consensus sequence peptide set spanning all HIV proteins. A total of 88% of the 410 tested peptides were recognized, and Nef- and Gag-specific responses dominated the total response for each ethnicity in terms of both breadth and magnitude. Three dominantly targeted regions within these proteins that were recognized by >90% of individuals in each ethnicity were identified. Overall, the total breadth and magnitude of CD8(+)-T-cell responses correlated with individuals' CD4 counts but not with viral loads. The frequency of recognition for each peptide was highly correlated with the relative conservation of the peptide sequence, the presence of predicted immunoproteasomal cleavage sites within the C-terminal half of the peptide, and a reduced frequency of amino acids that impair binding of optimal epitopes to the restricting class I molecules. The present study thus identifies factors that contribute to the immunogenicity of these highly targeted and relatively conserved sequences in HIV that may represent promising vaccine candidates for ethnically heterogeneous populations.

AIDS Vaccines↗

PubMed1992

Abnormal regulation of the myc gene in myeloid leukemia.

To study the regulation of expression of the myc protooncogene, cells from normal individuals and patients with acute myelogenous leukemia (AML), and chronic phase and blastic crisis of chronic myeloid leukemia (CML) cells were put in overnight culture in the presence or absence of fetal calf serum. Myc expression in normal marrow cells and chronic phase CML cells fell after culture in vitro. In contrast, myc expression was maintained or increased in a majority of the AML and blastic crisis CML specimens. These data demonstrate that the regulation of myc expression is disordered in many AML and blastic crisis specimens but not in chronic phase CML cells.

Base Sequence↗

PubMed2002

Molecular analysis of the Y chromosome AZFc region in Japanese infertile males with spermatogenic defects.

Cytogenetic and molecular studies of azoospermic and oligozoospermic males have suggested the presence of azoospermia factors (AZF) in the human Y chromosome. Deletion in three Y chromosomal regions--AZFa, AZFb and AZFc--has been reported to disrupt spermatogenesis and cause infertility. Several candidate genes responsible for spermatogenesis have been identified in these regions and some of them are thought to be functional in human spermatogenesis. Here we report on clinical and molecular studies of Y chromosome micro-deletions in Japanese. In these studies the data from 157 infertile Japanese men with azoospermia and oligozoospermia was analyzed and divided into 5 categories based on spermatozoa count. Sixteen sets of primers were used for polymerase chain reaction (PCR) to amplify sequence tagged site markers. One common deletion in the AZFc region was identified in infertile men. On the other hand, no deletions around the AZFc region were identified in fertile men. Japanese infertile men in our study had a common deletion in the AZFc region of the Y chromosome. A genomic clone was obtained by PCR screening of the P1 phage artificial chromosome (PAC) library. This clone was analyzed by Southern blotting using a PCR amplified probe of sY240. Our analysis of the genomic sequence of the clone suggests that this locus may contain specific genes for spermatogenesis.

Base Sequence↗

PubMed2025

Rare damaging CCR2 variants are associated with lower lifetime cardiovascular risk.

BACKGROUND: Previous work has shown a role of CCL2, a key chemokine governing monocyte trafficking, in atherosclerosis. However, it remains unknown whether targeting CCR2, the cognate receptor of CCL2, provides protection against human atherosclerotic cardiovascular disease. METHODS: Computationally predicted damaging or loss-of-function (REVEL > 0.5) variants within CCR2 were detected in whole-exome-sequencing data from 454,775 UK Biobank participants and tested for association with cardiovascular endpoints in gene-burden tests. Given the key role of CCR2 in monocyte mobilization, variants associated with lower monocyte count were prioritized for experimental validation. The response to CCL2 of human cells transfected with these variants was tested in migration and cAMP assays. Validated damaging variants were tested for association with cardiovascular endpoints, atherosclerosis burden, and vascular risk factors. Significant associations were replicated in six independent datasets (n = 1,062,595). RESULTS: Carriers of 45 predicted damaging or loss-of-function CCR2 variants (n = 787 individuals) were at lower risk of myocardial infarction and coronary artery disease. One of these variants (M249K, n = 585, 0.15% of European ancestry individuals) was associated with lower monocyte count and with both decreased downstream signaling and chemoattraction in response to CCL2. While M249K showed no association with conventional vascular risk factors, it was consistently associated with a lower risk of myocardial infarction (odds ratio [OR]: 0.66, 95% confidence interval [CI]: 0.54-0.81, p = 6.1 × 10-5) and coronary artery disease (OR: 0.74, 95%CI: 0.63-0.87, p = 2.9 × 10-4) in the UK Biobank and in six replication cohorts. In a phenome-wide association study, there was no evidence of a higher risk of infections among M249K carriers. CONCLUSIONS: Carriers of an experimentally confirmed damaging CCR2 variant are at a lower lifetime risk of myocardial infarction and coronary artery disease without carrying a higher risk of infections. Our findings provide genetic support for the translational potential of CCR2-targeting as an atheroprotective approach.

Humans↗

PubMed1999

Evidence for complex mutations at microsatellite loci in Drosophila.

Fifteen lines each of Drosophila melanogaster, D. simulans, and D. sechellia were scored for 19 microsatellite loci. One to four alleles of each locus in each species were sequenced, and microsatellite variability was compared with sequence structure. Only 7 loci had their size variation among species consistent with the occurrence of strictly stepwise mutations in the repeat array, the others showing extensive variability in the flanking region compared to that within the microsatellite itself. Polymorphisms apparently resulting from complex nonstepwise mutations involving the microsatellite were also observed, both within and between species. Maximum number of perfect repeats and variance of repeat count were found to be strongly correlated in microsatellites showing an apparently stepwise mutation pattern. These data indicate that many microsatellite mutation events are more complex than represented even by generalized stepwise mutation models. Care should therefore be taken in inferring population or phylogenetic relationships from microsatellite size data alone. The analysis also indicates, however, that evaluation of sequence structure may allow selection of microsatellites that more closely match the assumptions of stepwise models.

Animals↗

PubMed1991

A protein secondary structure database (PSS).

A protein secondary structure database (PSS) has been designed to correlate the Protein Sequence Database of the PIR-International with the atomic coordinates and bond connectivities database of the Protein Data Bank in the Brookhaven National Laboratory. The present database includes secondary structures determined by X-ray diffraction analysis, but not predicted structures. The database currently contains data from both the Protein Sequence Database and the Protein Data Bank Database, and will encompass the NMR database in the future. The main characteristics of the database are as follows: (1) the secondary structures, sites, regions and domains of structural interest are displayed together with protein primary structures; and (2) the secondary structure of a desired length of peptide fragment is displayed upon request, as are the peptide fragment(s) that correspond to a defined secondary structure. This database also has software to indicate amino acid pairs having hydrogen bonds and to count the occurrence frequency of each pair as well as the conformational parameters widely used in semi-empirical methods of secondary structure prediction.

Amino Acid Sequence↗

PubMed2002

Molecular typing techniques to characterize the development of a lactic acid bacteria community on vacuum-packaged beef.

The development of a community of lactic acid bacteria from vacuum-packaged beef was investigated during a 6-week storage trial at 2 degrees C. The lactic acid bacteria population was monitored by using molecular techniques to identify a random sample of isolates at biweekly intervals during the storage trial. The polymerase chain reaction and a randomly amplified polymorphic DNA technique were used to identify and distinguish populations of lactic acid bacteria that developed during the storage trial. At week 0, the population of lactic acid bacteria was 3.5 log cfu/120 cm2 and by week 6, the population reached a maximum of 7.6 log cfu/120 cm2. A sampling from the week 0 population indicated a mixed community of Lactobacillus curvatus, Lactobacillus sakei and Leuconostoc spp. However, the sampling from week 6 indicated the population composition had changed to one where a single Leuconostoc strain predominated. This strain demonstrated antagonism towards the growth of other lactic acid bacteria isolated during the study. Additionally, the strain inhibited the growth of foodborne pathogens Escherichia coli O157:H7 and Listeria monocytogenes. DNA sequence data from the 16S rRNA gene suggested that the isolate may be a Leuconostoc gelidum strain.

Animals↗

PubMed2004

Saci-1, -2, and -3 and Perere, four novel retrotransposons with high transcriptional activities from the human parasite Schistosoma mansoni.

Using the data set of 180,000 expressed sequence tags (ESTs) of the blood fluke Schistosoma mansoni generated recently by our group, we identified three novel long-terminal-repeat (LTR)- and one novel non-LTR-expressed retrotransposon, named Saci-1, -2, and -3 and Perere, respectively. Full-length sequences were reconstructed from ESTs and have deduced open reading frames (ORFs) with several uncorrupted features, characterizing them as possible active retrotransposons of different known transposon families. Alignment of reconstructed sequences to available preliminary genome sequence data confirmed the overall structure of the transposons. The frequency of sequenced transposon transcripts in cercariae was 14% of all transcripts from that stage, twofold higher than that in schistosomula and three- to fourfold higher than that in adults, eggs, miracidia, and germ balls. We show by Southern blot analysis, by EST annotation and tallying, and by counting transposon tags from a Serial Analysis of Gene Expression library, that the four novel retrotransposons exhibit a 10- to 30-fold lower copy number in the genome and a 4- to 200-fold-higher transcriptional rate per copy than the four previously described S. mansoni retrotransposons [corrected]. Such differences lead us to hypothesize that there are two different populations of retrotransposons in S. mansoni genome, occupying different niches in its ecology. Examples of retrotransposon fragment inserts were found into the 5' and 3' untranslated regions of four different S. mansoni target gene transcripts. The data presented here suggest a role for these elements in the dynamics of this complex human parasite genome.

Amino Acid Sequence↗

PubMed1995

Expression and mutation analysis of the p53 gene in uterine papillary serous carcinoma.

BACKGROUND: The status of p53 protein expression was determined by immunohistochemistry and correlated with genetic analysis and clinical outcome in patients with uterine papillary serous carcinoma (UPSC). METHODS: Twenty-two patients with UPSC were identified and immunohistochemical staining of p53 protein was performed. Staining was analyzed by quantitating nuclear reactivity in 500 randomly counted cells per specimen. DNA analysis was performed on the tumors using single-strand conformation polymorphism (SSCP) analysis of exons 4-10 of the p53 gene, followed by DNA sequencing of all variants. Clinical data and patient status were ascertained from chart reviews. RESULTS: Sixteen of the 22 (73%) tumors were scored as p53-overexpressing as determined by immunohistochemical analysis. Patients whose tumors overexpressed p53 had a statistically significant shorter survival than those whose tumors did not (P < 0.022). DNA analysis of the 22 tumors revealed five with mutations of the p53 gene. Only three of these mutations were observed in tumors that overexpressed p53. CONCLUSIONS: A relatively large percentage of UPSC tumors exhibited high p53 immunoreactivity. Overexpression is correlated with poor prognosis. Positive immunohistochemistry for p53 protein in UPSC is not necessarily indicative of a genetic mutation.

Aged↗

PubMed1994

A non-isotopic nested polymerase chain reaction method to quantitate minimal residual disease in patients with non-Hodgkin's lymphoma.

The polymerase chain reaction (PCR) is a highly sensitive technique for the detection of lymphoma cells presenting specific rearrangements or translocations, like the t(14;18). However, few methods are available for the quantitative evaluation of clinical samples, especially using nested PCR. In this study, we describe a method for the semiquantitative estimation of low numbers of lymphoma cells using the nested PCR methodology. Samples evaluated consisted of RL cells, a non-Hodgkin's lymphoma cell line harbouring a bcl-2 translocation, mixed with normal mononuclear cells (MC) obtained from bone marrow or peripheral blood. DNA was extracted from samples with RL:MC ratios ranging from 5 x 10(-2) to 5 x 10(-7), and amplified for detection of this translocation. The product of this first amplification reaction was serially diluted 10-fold from 10(0) to 10(-7). Then each fraction was PCR-amplified with nested oligonucleotide primers. Aliquots of the second amplification were electrophoresed on a 2% agarose gel and stained with ethidium bromide. Within the range tested, there was a log-linear relationship between the number of PCR positive bands and the number of translocated cells in each sample. This procedure was highly reproducible in experiments evaluating the interrun and intrarun variability. In addition, there was no interaction with normal cells obtained from peripheral blood or bone marrow, or from different individuals. Furthermore, results were identical with two different cell lines and consistent with patient lymphoma cells obtained from a lymph node biopsy.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗

PubMed1993

Neuronal control of herpes simplex virus latency.

Herpes simplex virus (HSV) is a common neurotropic virus, and latent infection of sensory ganglion neurons readily occurs in humans and in experimentally infected animals. During HSV latency, infectious virus and viral antigen are not detected, and HSV transcription is limited to specific RNA termed latency-associated transcript (LAT). In the present study, the effect of altered nervous system function on HSV latent infection was investigated in dorsal root ganglia (drg) of experimentally infected mice. Latent infection of lumbar drg was established by footpad inoculation of HSV. During latency, sciatic neurectomy was performed in order to modify the in vivo function of latently infected neurons, and HSV LAT and HSV DNA in drg were investigated. Neurectomy has been used in many neurobiological studies to alter neuronal RNA and protein expression. After neurectomy there was a marked decrease in the number of LAT-positive neurons and in the amount of ganglion LAT. This was determined by in situ and RNA (Northern) blot hybridization. The neurectomy-related decrease of HSV LAT was apparent 9-10 days after neurectomy and was more marked after 21 days. The decrease was noted both in drg latently infected with standard thymidine kinase-positive (TK+) HSV and in ganglia infected with mutant TK- HSV. Since TK- HSV is largely reactivation defective, it is concluded that the neurectomy-induced decrease of LAT was probably not the result of in vivo HSV reactivation. It is acknowledged, however, that abortive reactivation by TK- HSV may occur, and decrease of latency may have resulted from neuronal or other host mechanisms subsequent to this. In order to investigate residual HSV latency, in addition to viral transcription, HSV DNA in drg was evaluated by polymerase chain reaction techniques. Decrease of HSV DNA was noted after neurectomy in drg latently infected with either TK+ or TK- HSV. It is suggested that the decrease in LAT expression detected was due to the change in neuronal transcription which is part of the neurectomy-induced axon reaction. Decreased HSV LAT may have led to decreased HSV DNA and latency. The decrease in the molecular markers of HSV latency following neurectomy emphasized the importance of neuronal control mechanisms in the pathogenesis of HSV latent infection.

Animals↗

PubMed1995

Triflavin, an Arg-Gly-Asp-containing peptide, prevents platelet plug formation in in vivo experiments.

Triflavin, an Arg-Gly-Asp-containing peptide from Trimeresurus flavoviridis snake venom (M(r) of 7500 Da) inhibits platelet aggregation through the blockade of fibrinogen binding to activated platelets. The present study demonstrated that the intravenous injection of triflavin (0.1 and 0.25 mg/kg) significantly prolonged the bleeding time about 1.8- to 2.4-fold as compared with control (normal saline) of severed mesenteric arteries in rats, whereas the injection of Gly-Arg-Gly-Asp-Ser (GRGDS) (2-8 mg/kg) failed to increase the bleeding time in this model. Continuous infusion of triflavin (0.08 mg/kg/min) significantly increased the bleeding time about 2.6-fold, and the bleeding time returned to normal within 20 min after the cessation of triflavin infusion. Triflavin (10-20 mg/kg) significantly prolonged the occlusion time of platelet plug formation induced by irradiation of mesenteric venules of fluorescein sodium-pretreated mice. In contrast, trigramin (10-20 mg/kg) and GRGDS (500 and 1000 mg/kg) showed no significant effect. These results suggest that triflavin has an effective antiplatelet effect in vivo and this peptide may be a useful therapeutic agent for arterial thrombosis.

Amino Acid Sequence↗

PubMed2006

Structural correlates of antimicrobial efficacy in IL-8 and related human kinocidins.

Chemokines are small (8-12 kDa) effector proteins that potentiate leukocyte chemonavigation. Beyond this role, certain chemokines have direct antimicrobial activity against human pathogenic organisms; such molecules are termed kinocidins. The current investigation was designed to explore the structure-activity basis for direct microbicidal activity of kinocidins. Amino acid sequence and 3-dimensional analyses demonstrated these molecules to contain iterations of the conserved gamma-core motif found in broad classes of classical antimicrobial peptides. Representative CXC, CC and C cysteine-motif-group kinocidins were tested for antimicrobial activity versus human pathogenic bacteria and fungi. Results demonstrate that these molecules exert direct antimicrobial activity in vitro, including antibacterial activity of native IL-8 and MCP-1, and microbicidal activity of native IL-8. To define molecular determinants governing its antimicrobial activities, the IL-8 gamma-core (IL-8gamma) and alpha-helical (IL-8alpha) motifs were compared to native IL-8 for antimicrobial efficacy in vitro. Microbicidal activity recapitulating that of native IL-8 localized to the autonomous IL-8alpha motif in vitro, and demonstrated durable microbicidal activity in human blood and blood matrices ex vivo. These results offer new insights into the modular architecture, context-related deployment and function, and evolution of host defense molecules containing gamma-core motifs and microbicidal helices associated with antimicrobial activity.

Amino Acid Motifs↗

PubMed2005

Development of a real-time PCR assay targeting the sporulation gene, spo0A, for the enumeration of thermophilic bacilli in milk powder.

Thermophilic bacilli, such as Anoxybacillus, Geobacillus and Bacillus, are common contaminants growing within the processing lines of milk powder producing factories. These contaminants are used as indicator organisms for plant hygiene and specification limits based on their numbers have been implemented to ensure milk powder quality. In this study, we present a SYBR Green-based real-time PCR assay for the rapid detection and enumeration of these thermophilic bacilli in milk powder using the spo0A sporulation gene as quantification target. With this method the detection of thermophilic bacilli in milk powder can be accomplished within 1 h. The detection limit for reconstituted and inoculated milk was 80 vegetative cfu ml(-1) and 640 spores ml(-1), respectively.

Amino Acid Sequence↗

PubMed2004

Identification of a novel alternative splicing form of human netrin-4 and analyzing the expression patterns in adult rat brain.

Netrins are a family of secreted proteins that function as tropic cues directing axon growth and cell migration during neural development. Beta-netrin or netrin-4 (NTN4), the fourth member of this family, was previously reported by Koch (M. Koch, J.R. Murrell, D.D. Hunter, P.F. Olson, W. Jin, D.R. Keene, W.J. Brunken, R.E. Burgeson. A novel member of the netrin family, beta-netrin, shares homology with the beta chain of laminin: identification, expression, and functional characterization. J. Cell Biol. 151 (2000) 221-234) and Yin (Y. Yin, J.R. Sanes, J.H. Miner, Identification and expression of mouse netrin-4. Mech. Dev. 96 (2000) 115-119), respectively. However, whether there is another isoform of netrin-4 and the expression patterns have not been fully determined. Here we report the cloning of a novel isoform of human netrin-4 using rapid amplification of complementary DNA (cDNA) ends (RACE) technique and analysis on the netrin-4 mRNA expression in adult rat brain using in situ hybridization. The new isoform lacks the signal peptide region and might represent a truncated form at the Laminin-N terminal domain of human netrin-4. Examination of the expression pattern of netrin-4 mRNA in adult rat brain revealed that the netrin-4 mRNA was widely expressed in many regions of the brain. High levels of netrin-4 mRNA was found in the pyramidal cell layer of the cerebral cortex, prepiriform cortex, amygdaloid nuclei, pyramidal layer of hippocampus, Purkinje's cells, medial cerebellar nucleus and interposed cerebellar nucleus, medial nucleus of the trapezoid body and mitral cell layer of the olfactory bulb. Moderate signals were present in frontal cortex, several thalamic and hypothalamic nuclei. The widespread expression of netrin-4 in adult rat brain indicates that netrin-4 is not only important for axon guidance during embryonic development, but also critical to neuronal plasticity in adult stage.

Alternative Splicing↗

PubMed2006

Correlation between SIV Tat evolution and AIDS progression in cerebrospinal fluid of morphine-dependent and control macaques infected with SIV and SHIV.

Morphine abuse has been associated with higher virus replication and accelerated disease progression in a non-human primate model of AIDS. In our previous report, we have shown that 50% of morphine-addicted macaques progress rapidly and that 2/3 of the rapid progressors exhibit severe neuropathogenesis. In this report, we examined the sequence evolution of the SIV Tat protein, known to participate in AIDS neuropathology, in the cerebrospinal fluid (CSF) of morphine-dependent and control macaques over the first 20 weeks of infection. The CSF SIV Tat evolution was found to be inversely related with disease progression, and the highly neuropathogenic inoculum clone sequence was the prevalent CSF form in rapid progressors. Divergence from the inoculum clone was significantly greater in both morphine-dependent normal progressors and control macaques than in the morphine-dependent rapid progressors. Furthermore, we also found evidence of a trend that morphine alters the type of mutation, resulting in an enhanced ratio of transitions to transversions (Ts:Tv). Rapid disease exacerbates this trend and appears to influence the distribution of nonsynonymous changes in the first exon of SIV tat, with a clear majority of mutations occurring in the C-terminal half of the protein where the known functionally important domains reside. Thus, morphine abuse may change the nature and extent of mutations that drive viral evolution.

Acquired Immunodeficiency Syndrome↗

PubMed1997

An exported peptide functions intracellularly to contribute to cell density signaling in B. subtilis.

Competence development and sporulation in B. subtilis are partly controlled by peptides that accumulate in culture medium as cells grow to high density. We constructed two genes that encode mature forms of two different signaling molecules, the PhrA peptide that stimulates sporulation, and CSF, the competence- and sporulation-stimulating factor. Both pentapeptides are normally produced by secretion and processing of precursor molecules. The mature pentapeptides were functional when expressed inside the cell, indicating that they normally need to be imported to function. Furthermore, at physiological concentrations (10 nM), CSF was transported into the cell by the oligopeptide permease encoded by spo0K (opp). CSF was shown to have at least three different targets corresponding to its three activities: stimulating competence gene expression at low concentrations, and inhibiting competence gene expression and stimulating sporulation at high concentrations.

ATP-Binding Cassette Transporters↗