Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Sequence Count Data”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 127 records · Page 7Linked to original sources
PubMed1994

The natural history of HIV-1 infection: virus load and virus phenotype independent determinants of clinical course?

Virus load and virus phenotype have both been indicated as major determinants of disease progression in HIV-1 infection. In this study HIV-1 RNA copy numbers in serum, virus phenotype, and CD4+ cell counts were analyzed longitudinally in a group of 20 seroconverters progressing to AIDS within 5.5 years. In this group 12 individuals developed AIDS without syncytium-inducing (SI) viruses ever being isolated, while 8 individuals showed a non-SI (NSI) to SI phenotypic switch prior to AIDS development. HIV-1 RNA copy numbers in sera of all progressors were stable and high from seroconversion until development of AIDS. Twenty-one seroconverters remaining asymptomatic for more than 5.5 years were selected as nonprogressing controls, and both progressors and nonprogressors were evaluated at seroconversion and early in infection (3 years post seroconversion). Comparative analysis revealed that at the point of seroconversion HIV-1 RNA copy numbers in sera from NSI progressors, SI progressors, and nonprogressors were not significantly different, nor were their CD4+ cell counts. At seroconversion all individuals harbored viruses with an NSI phenotype. In contrast to the progressors, HIV-1 RNA copy numbers in sera of nonprogressors had declined significantly during the early period of infection. At the second time point RNA copy numbers in the sera of NSI progressors and nonprogressors differed significantly (P = 0.0005), while RNA copy numbers in the sera of SI progressors and nonprogressors did not. However, at this time point the CD4+ cell counts of SI progressors were significantly lower than those from nonprogressors (P = 0.002), while the CD4+ cell counts of NSI progressors and nonprogressors did not differ significantly. These results show that early in HIV-1 infection progressors and nonprogressors are distinguishable. NSI progressors can be distinguished from nonprogressors on the basis of serum HIV-1 RNA load and S1 progressors on the basis of CD4+ cell decline. In addition, a significant decrease in the number of HIV-1 RNA copies in the early phase of infection seems to postpone the development of AIDS.

Acquired Immunodeficiency Syndrome↗
PubMed1994

Elevated numbers of gamma-delta (gamma delta+) T lymphocytes in children with immune thrombocytopenic purpura.

Immune thrombocytopenic purpura (ITP) in childhood is a heterogeneous clinical disorder characterized by immune-mediated platelet destruction. Although generally considered to involve autoreactive B lymphocytes which produce antiplatelet antibodies, there is increasing evidence that T lymphocytes also play an important role in this autoimmune process. We studied 11 children with acute ITP and 19 children with chronic ITP and observed elevated numbers of TCR gamma delta+ T lymphocytes in several patients. In the three children with the highest elevations (TCR gamma delta+/CD3+ percentage ranging from 37.8 to 48.1% at initial evaluation), the expanded cell population exclusively expressed the surface V delta 2/V gamma 9 heterodimer and had enhanced in vitro proliferation to mycobacterial extracts and IL-2. Analysis of the nucleotide sequences used by these TCR gamma delta+ cells demonstrated a diverse set of VDDJC gene rearrangements, indicating polyclonal expansion of cells reminiscent of a superantigen response. There was a close correlation between the number of TCR gamma delta+ T lymphocytes and the degree of thrombocytopenia in each patient. TCR gamma delta+ T lymphocytes may be important in the pathogenesis of immune-mediated platelet destruction in some children with ITP.

Adolescent↗
PubMed1992

Regulatory aspects of clonally expanded B-1 (CD5+ B) cells.

B-1 (CD5+ B) cells appear early in ontogeny, produce mainly unmutated polyreactive antibodies, and are capable of self-renewal. B-1 cells clonally expand with age and are the malignant cell in chronic lymphocytic leukemia. In this report immunological analysis of B-1 malignancies in NZB mice, a murine model of chronic lymphocytic leukemia, is related to current information on B-1 cells. B-1 clones from NZB mice produce high levels of interleukin-10, detected at the RNA level by semi-quantitative polymerase chain reaction. In addition, the B-1 malignant clones in NZB mice and their hybrids, are negative for B220/6B2 expression, the B-specific antigenic form of CD45 which is a membrane-associated phosphatase involved in lymphocyte activation. Both the autocrine production by B-1 cells of interleukin-10 and altered CD45 expression may be responsible for the clonal expansion of these cells, as well as the accompanying T cell expansion. We report the establishment of an in vitro cytotoxic CD8+ T cell line derived from an NZB with a B-1 malignancy. The effect of B-1 cell-derived interleukin-10 on subsets of T lymphocytes may account for the immunoregulatory properties of B-1 cells. In addition, the NZB malignancies were also characterized for immunoglobulin variable region sequence and antigen specificity. The B-1 malignancies produced immunoglobulin derived from unmutated germline sequences with no N base substitutions. It appears that both the immunoglobulin and interleukin-10 produced by the B-1 malignant cell in NZB mice may have immunoregulatory properties. A study of B-1 malignancies may shed light on the immunoregulatory properties of non-clonally expanded normal B-1 cells.

Animals↗
PubMed1992

Homologous tachyphylaxis to bradykinin and its interference with allergic pleurisy in actively sensitized rats.

After recovery from a first intraplantar or intrathoracic stimulation with bradykinin, repeated daily provocation with this peptide resulted in a progressive loss of its ability to cause paw or pleural oedema, reaching 0-20% of the control within seven and four consecutive provocations, respectively. The phenomenon was shown to be time reversible, since the unresponsiveness ceased when stimulations were discontinued, and localized, since paw oedema evoked by the peptide was not modified after desensitization of either the contralateral paw or the pleural cavity. Furthermore desensitization to bradykinin did not influence the pleurisy elicited by either histamine (200 micrograms/cavity), 5-hydroxytryptamine (5-HT) (100 microgram/cavity) or platelet-activating factor (PAF) (1 microgram/cavity), suggesting that the desensitization was selective. In contrast, when actively sensitized animals were submitted to bradykinin-induced tachyphylaxis, pleural exudation and leukocyte influx induced by antigen were drastically reduced, strongly implying bradykinin in this process. We demonstrated that repeated daily stimulation with bradykinin cause selective, local and reversible auto-refractoriness, which may be useful as a tool in attempting to evaluate the role of this peptide in inflammation.

Amino Acid Sequence↗
PubMed1996

Detection and quantification of blood-derived CD8+ T lymphocytes secreting tumor necrosis factor alpha in response to HLA-A2.1-binding melanoma and viral peptide antigens.

We applied an enzyme-linked immunospot (ELISPOT) assay for the detection and quantification of blood-derived CD8+ T cells recognizing peptide antigens presented by HLA-A2.1. CD8+ T lymphocytes were isolated from peripheral blood and were stimulated for 40 h with peptide-loaded A2.1-positive 0.174 x CEM.T2 cells. Tumor necrosis factor alpha (TNF-alpha) secreted by single T cells in response to antigen contact was trapped on nitrocellulose membranes precoated with anti-TNF-alpha antibodies and was then immunochemically visualized as spots. With this assay, up to 25% of cloned cytolytic T lymphocytes (CTL) were detected during the test period that recognized defined melanoma antigens in association with HLA-A2.1. CD8+ lymphocytes responsive to a known immunogenic HLA-A2.1-binding peptide from reverse transcriptase of the human immunodeficiency virus (HIV) were only detectable in HIV-infected patients, but not in anti-HIV-negative donors. T cells reacting with a peptide derived from a mutated cyclin-dependent kinase 4 (CDK4-R24C) were exclusively detected among CD8+ lymphocytes isolated from blood of the patient, whose melanoma had previously been found to carry the CDK4-R24C allele. T cells responding to HLA-A2.1-associated peptides of normal melanocyte differentiation antigens tyrosinase and Melan-A/MART-1 were found at low frequencies in almost all donors tested, which might reflect a natural autoimmunity to these antigens. However, in a melanoma patient we found a few days after surgery of melanoma metastases high frequencies of T cells against Melan-A/MART-1 and tyrosinase peptides (up to 38 per 10(5) CD8+ T cells), which gradually decreased during the following months. In an HIV-infected patient with progressive disease we observed a loss of T cells reactive with the HIV reverse transcriptase peptide. These observations provide evidence that peptide-dependent TNF-alpha spot formation in vitro resulted from previous antigen exposure in vivo. Therefore, the TNF-alpha ELISPOT assay might be useful in monitoring antigen-specific T lymphocyte responses during the natural course of diseases as well as during therapeutic interventions aiming at the induction of protective T cell immunity. In addition, it might help to identify immunodominant T cell epitopes.

Amino Acid Sequence↗
PubMed1991

A computer-aided procedure for measuring Lashley III maze performance.

As an animal swims through the Lashley III maze, an observer types into a Macintosh computer the path taken. The computer program, Observe Software, then breaks the string of choices into two-step sequences and counts the number of such sequences. These data are then sent to a spreadsheet, where the sequences are sorted into forward and backward responses. Forward choices are Correct Path, T Choice Errors and Cul Entry Errors. All backward choices are errors, by definition. They are classified as T Choices, Cul Entries, Cul Exits, and Return to Start. The animal's behavior is then described by the various error classes plus a measure called Learning Index. Examples of learning by rats and mice are presented.

Animals↗
PubMed1992

Disseminated "Mycobacterium genavense" infection in patients with AIDS.

We describe 18 patients with advanced HIV infection, most of whom had a chronic illness characterised by fever, diarrhoea, and massive loss of weight. Biopsy and necropsy samples revealed abundant acid-fast microorganisms in intestines, liver, spleen, lymph nodes, and many other tissues, which did not grow on solid media, although limited growth was observed in liquid blood cultures. Using primers complementary to bacterial 16S rRNA we amplified DNA sequences from tissue and leucocyte extracts and from blood-culture bottles. The sequences obtained were unique and suggest that the microorganism is a new member of the genus Mycobacterium, for which we propose the name "Mycobacterium genavense". Disseminated infection with "M genavense" should be considered in the differential diagnosis of HIV-infected patients with extreme immunosuppression, wasting, and fever.

Acquired Immunodeficiency Syndrome↗
PubMed1994

Evaluation of the effect of Sm28GST-derived peptides in murine hepatosplenic schistosomiasis: interest of the lipopeptidic form of the C-terminal peptide.

Among the synthetic peptides derived from the 28-kDa Schistosoma mansoni glutathione S-transferase (Sm28GST), immunization with the C-terminal peptide comprising amino acid residues 190-211 induced a reduction in splenomegaly, in the number of hepatic eggs and in hepatic fibrosis in mice infected by Schistosoma mansoni. The absence of antibodies specific for the Sm28GST or for the 190-211 peptide observed in our conditions of immunization with this peptide argued in favour of the involvement of cellular-dependent mechanisms in the reduction in hepatic pathology. This was confirmed by the passive transfer of 190-211 peptide-specific T-cell enriched spleen cells which reproduced the protective effect conferred by immunization with the 190-211 peptide. These 190-211 peptide-specific cells produced little IL4 and high levels of IFN-gamma, a potent inhibitor of collagen synthesis. Furthermore, the use of a lipopeptidic form of the 190-211 peptide significantly improved the reduction in hepatic pathology obtained with the uncoupled peptide and induced a durable protective response. These results provide encouraging information for the possible use of synthetic peptides in the immunoprophylaxis of Schistosomiasis.

Amino Acid Sequence↗
PubMed1996

Detection of Cryptosporidium parvum oocysts in faeces: comparison of conventional coproscopical methods and the polymerase chain reaction.

Conventional and coproscopical methods were compared with the polymerase chain reaction (PCR) for the detection of Cryptosporidium oocysts in bovine faeces. Oocysts were not detected in samples seeded with 10,000 oocysts following formol ether sedimentation and examination using auramine phenol (AP) or by immunofluorescent (IF) staining. When oocysts were concentrated using sucrose flotation the threshold of detection was 4000 oocysts per gram for both staining methods. Following salt flotation 4000 oocysts per gram could be reliably detected by AP staining but the detection limit was increased to 6000 oocysts per gram using IF staining. The recovery of oocysts was significantly less than expected for all techniques. A specific PCR coupled with immunomagnetic particle separation (IMS) of samples detected five oocysts per ml of diluted faeces, which corresponds to 80-90 oocysts per gram. Even allowing for the dilution of formed faecal samples, required for IMS, this represents an increase in sensitivity of several orders of magnitude over the conventional corpodiagnostic methods.

Animals↗
PubMed2006

Characterization of novel Bruton's tyrosine kinase gene mutations in Central European patients with agammaglobulinemia.

X-linked agammaglobulinemia (XLA) is an immunodeficiency disorder caused by mutations in the gene coding for Bruton's tyrosine kinase (BTK). In this study we investigated 10 male patients with XLA-compatible phenotype (agammaglobulinemia and undetectable B cells in peripheral blood) from 9 unrelated Central European families. We identified seven different mutations, six of which were novel. One previously described point mutation caused a premature stop codon (p.C464X), two point mutations resulted in amino acid exchanges (p.W588R; p.G419E), and two point mutations affected splice sites (c.305-1G>A; c.391+1G>A). We further detected one deletion (c.1921_1927del CGTCCCA) and one large duplication. The duplication resulted from Alu element-induced unequal homologous recombination, which was only detectable by extended analysis of cDNA, while direct sequencing of genomic DNA gave a false negative result. Western blot analysis revealed that the patients with the p.W588R and the p.G419E amino acid substitutions, respectively, produced full length BTK, but in clearly diminished amounts. The patient with the 7bp deletion expressed low amounts of protein which might represent truncated BTK. All other genomic alterations resulted in complete loss of BTK protein. In two patients from unrelated families BTK protein expression was normal and no Btk gene mutation was detected. The results of this study further substantiate the importance of using elaborate molecular analysis with different detection techniques to obtain an explicit molecular diagnosis in patients with suspected XLA.

Adult↗
PubMed2006

Allobilharzia visceralis gen. nov., sp. nov. (Schistosomatidae-Trematoda) from Cygnus cygnus (L.) (Anatidae).

In Iceland, the examination of whooper swans (Cygnus cygnus L.) viscera resulted in the detection of adult digenean flukes of the family Schistosomatidae. The mature worms occurring in the blood vessels of the large intestine and mesenterium caused vascular lesions, around the eggs deposited in the intestinal mucosa and liver granulomatous reactions developed. The morphology of the isolated schistosomes shows certain similarity with the flukes of the genus Trichobilharzia; in males reduced gynecophoral canal, and on both sexes both suckers and spatulate ends are present. However, the Icelandic flukes possess other morphological features which are distinct from the genus: the point of caecal reunion in males takes place posterior to gynecophoral canal and the genital pore is behind acetabulum and anterior to caecal reunion. In order to evaluate the identity of Icelandic schistosomes, sequencing of ITS region of DNA was performed, and the obtained sequence was deposited in GenBank under the accession no. DQ067561. Following phylogenetic analysis of relationship between the sequence of Icelandic flukes and database sequences of other bird schistosome genera (Trichobilharzia, Gigantobilharzia and Dendritobilharzia) showed different position of Icelandic worms in the phylogenetic tree. In conclusion, our study revealed new genus and species of schistosome flukes--Allobilharzia visceralis gen. et sp. n.

Animals↗
PubMed2006

Characterisation of a SAT-1 outbreak of foot-and-mouth disease in captive African buffalo (Syncerus caffer): clinical symptoms, genetic characterisation and phylogenetic comparison of outbreak isolates.

African buffalo (Syncerus caffer) play an important role in the maintenance of the SAT types of foot-and-mouth disease (FMD) in southern Africa. These long-term carriers mostly become sub-clinically infected, maintaining the disease and posing a threat to other susceptible wildlife and domestic species. During an unrelated bovine tuberculosis experiment using captive buffalo in the Kruger National Park (KNP), an outbreak of SAT-1 occurred and was further investigated. The clinical signs were recorded and all animals demonstrated significant weight loss and lymphopenia that lasted 100 days. In addition, the mean cell volume and mean cell haemoglobin values were significantly higher than before the outbreak started. Virus was isolated from several buffalo over a period of 167 days post infection and the molecular clock estimated to be 3 x 10(-5) nucleotide substitutions per site per day. Seven amino acid changes occurred of which four occurred in hypervariable regions previously described for SAT-1. The genetic relationship of the outbreak virus was compared to buffalo viruses previously obtained from the KNP but the phylogeny was largely unresolved, therefore the relationship of this outbreak strain to others isolated from the KNP remains unclear.

Amino Acid Sequence↗
PubMed1999

PCR-based quantitation of Cryptosporidium parvum in municipal water samples.

A PCR method for the quantitation of Cryptosporidium parvum oocysts in municipal drinking water samples was investigated. Quantitative PCR uses an internal standard (IS) template with unknown target numbers to compare to standards of known concentrations in a standard curve. The IS template was amplified using the same primers used to amplify a portion of a 358 bp gene fragment that encodes a repetitive oocyst wall protein in C. parvum. Municipal water samples spiked with known numbers of C. parvum oocysts were tested by quantitative PCR using the IS and the Digene SHARP Signal System Assay for PCR product detection. The absorbance readings for target DNA and IS templates versus the number of molecules of the target DNA were plotted to generate standard curves for estimating oocyst numbers. The method allowed the quantitation of oocysts from log 3 to log 5 spiked into municipal water samples.

Animals↗
PubMed2000

Mutations in the tyrosine phosphatase CD45 gene in a child with severe combined immunodeficiency disease.

The hematopoietic-specific transmembrane protein tyrosine phosphatase CD45 functions to regulate Src kinases required for T- and B-cell antigen receptor signal transduction. So far, there have been no reports to our knowledge of a human deficiency in a tyrosine-specific phosphatase. Here, we identified a male patient with a deficiency in CD45 due to a large deletion at one allele and a point mutation at the other. The point mutation resulted in the alteration of intervening sequence 13 donor splice site. The patient presented at 2 months of age with severe combined immunodeficiency disease. The population of peripheral blood T lymphocytes was greatly diminished and unresponsive to mitogen stimulation. Despite normal B-lymphocyte numbers, serum immunoglobulin levels decreased with age. Thus, CD45 deficiency in humans results in T- and B-lymphocyte dysfunction.

Antigens, CD↗
PubMed1994

Cloning, sequencing, expression and inflammatory activity in skin of ovine interleukin-8.

Ovine IL-8 (oIL-8) cDNA was obtained by probing a spleen cell cDNA library with human IL-8 (hIL-8) cDNA. The oIL-8 cDNA was 1434 base pairs long with a single open reading frame encoding a 101 amino acid precursor protein of relative molecular mass 11,268. The inferred amino acid sequence has 78, 82, 84 and 67% similarity with human, rabbit, porcine and guinea-pig IL-8, respectively. By analogy with the most prevalent form of hIL-8, a 72 amino acid form of oIL-8 was expressed as a fusion protein containing glutathione-S-transferase and purified by affinity chromatography on a glutathione-Sepharose column yielding 8 mg IL-8/L broth culture. The fusion protein lacked chemotactic activity for ovine neutrophils, whereas the 72 amino acid form of oIL-8 was equipotent with rhIL-8. At 6 and 24 h after intradermal injection of 10(-9) mol oIL-8, there was intense accumulation of neutrophils, and very mild accumulation of eosinophils, CD5, CD4 and T19 (a gamma delta TCR subset) cells but not CD8 cells. The availability of roIL-8 and its cDNA probes will permit the role of this important member of the IL-8 family of chemotactic cytokines to be determined in inflammatory diseases of sheep.

Amino Acid Sequence↗
PubMed1998

Vaccination of cattle against the Boophilus microplus using a mucin-like membrane glycoprotein.

An antigen, BMA7, which induced partial immunity against tick infestation has been isolated from Boophilus microplus using two different protein fractionation protocols, accompanied by vaccination and parasite challenge trails. The antigen is a 63 kDa glycoprotein isolated from semi-engorged adult female ticks. Though significant, the induced immunity is less striking than that previously reported for antigen Bm86 from the same parasite. However, co-vaccination with Bm86 and BMA7 can enhance immunity over that seen with a commercial vaccine based on Bm86 alone. Limited peptide sequence information shows significant variation in the BMA7 protein occurs. The antigen has approximately 36 kDa of glycosylation, in both N-linked and O-linked oligosaccharides. There is evidence that both polypeptide and oligosaccharide are antigenic, but the chemical nature of the protective antigenic sites is not clear. There is little or no immunological response to the antigen during natural infestation with parasites, suggesting the antigen is 'concealed' and protective immunity dependent on artificial vaccination. The antigen has some similarities with the vertebrate mucins. It is widely distributed in tick tissues and membrane bound but its function is currently unknown.

Amino Acid Sequence↗