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At least 163 records · Page 9Linked to original sources

Monitoring of anti-vaccine CD4 T cell frequencies in melanoma patients vaccinated with a MAGE-3 protein.

Quantitative evaluation of T cell responses of patients receiving antitumoral vaccination with a protein is difficult because of the large number of possible HLA-peptide combinations that could be targeted by the response. To evaluate the responses of patients vaccinated with protein MAGE-3, we have developed an approach that involves overnight stimulation of blood T cells with autologous dendritic cells loaded with the protein, sorting by flow cytometry of the T cells that produce IFN-gamma, cloning of these cells, and evaluation of the number of T cell clones that secrete IFN-gamma upon stimulation with the Ag. An important criterion is that T cell clones must recognize not only stimulator cells loaded with the protein, but also stimulator cells transduced with the MAGE-3 gene, so as to exclude the T cells that recognize contaminants generated by the protein production system. Using this approach it is possible to measure T cell frequencies as low as 10(-6). We analyzed the frequencies of anti-vaccine CD4 T cells in five metastatic melanoma patients who had been injected with a MAGE-3 protein without adjuvant and showed evidence of tumor regression. Anti-MAGE-3 CD4 T cells were detected in one of the five patients. The frequency of the anti-MAGE-3 CD4 T cells was estimated at 1/60,000 of the CD4 T cells in postvaccination blood samples, representing at least an 80-fold increase in the frequency found before immunization. The frequencies of one anti-MAGE-3 CD4 T cell clonotype were confirmed by PCR analysis on blood lymphocytes. The 13 anti-MAGE-3 clones, which corresponded to five different TCR clonotypes, recognized the same peptide presented by HLA-DR1.

Amino Acid Sequence↗

Carriage of DRB1*13 is associated with increased posttreatment IgE levels against Schistosoma mansoni antigens and lower long-term reinfection levels.

Praziquantel treatment for Schistosoma mansoni infection enhances Th2 responsiveness against parasite Ags, but also increases the variance in Ab isotype levels. This effect may arise partly from genetic heterogeneity. In this study, associations between HLA polymorphisms at three loci (HLA-DQB1, HLA-DQA1, and HLA-DRB1) and posttreatment Ig responses to S. mansoni Ags were assessed in 199 individuals aged 7-50 years from Uganda. Blood samples were assayed for IgG1, IgG4, and IgE levels against soluble worm Ag (SWA), soluble egg Ag, tegument Ag, and a recombinant tegumental Ag (rSm 22.6) 7 wk after treatment. Multivariate ANOVA analysis initially revealed associations between carriage of DRB1*13 and increased levels of IgG1, IgG4, and IgE against SWA, tegument Ag, and rSM22.6. Subsequent analysis of covariance, which controlled for correlations between isotype levels and also included pretreatment IL-4, IL-5, and IL-13 responsiveness against SWA as covariates, revealed an independent association only between DRB1*13 and a factor score summarizing IgE levels to worm-derived Ags, which was strongest in adults. A post hoc age- and sex-stratified analysis revealed lower reinfection intensities at 1 year, 22 mo, and 6 years after the first round of treatment among carriers of DRB1*13. These results indicate that genetic background has a prominent influence on the posttreatment Th2 immune response to S. mansoni Ags, as well as a downstream association with long-term reinfection levels.

Adolescent↗

Phylogenetic relationships among isolates of Cryptosporidium: evidence for several new species.

Isolates of Cryptosporidium were characterized using nucleotide sequence analysis of the 18S rRNA and dihydrofolate reductase genes and also random-amplified polymorphic DNA analysis. Phylogenetic analysis confirmed the validity of the species of Cryptosporidium examined in this study such as Cryptospordium muris and Cryptosporidium baileyi, and also reinforced evidence from numerous researchers worldwide suggesting that Cryptosporidium parvum is not a single uniform species. The data obtained provided strong support for the validity of Cryptosporidium felis. Evidence suggests that the newly identified marsupial and pig genotypes may also be distinct and valid species, but biological studies are required for confirmation.

Animals↗

Copro-diagnosis of Echinococcus granulosus infection in dogs by amplification of a newly identified repeated DNA sequence.

Diagnosis of Echinococcus granulosus infection in dogs by detecting adult worms recovered post mortem or purged from the intestines after treatment with arecoline is not suitable for mass screening. Large-scale diagnosis by detection of copro-antigens is useful but only with relatively high intensity infections, and only by genus. To provide a more sensitive and specific diagnosis, a polymerase chain reaction (PCR) assay was developed, that amplified a target repeated sequence (EgG1 Hae III) newly identified in the genome of the common sheep strain of E. granulosus. This repeated sequence consists of approximately 6,900 copies, arranged in tandem, in groups of 2-6 repeats. The corresponding primers used in the PCR easily detected a single egg with no cross-amplification of DNA from closely related cestodes, including E. multilocularis and Taenia spp. Fecal samples from naturally infected dogs, with 2-10,000 E. granulosus worms at necropsy, were all PCR positive, while E. multilocularis or Taenia spp. positive controls as well as non-endemic controls were all PCR negative. This copro-PCR assay was demonstrated to be 100% specific and also detected all necropsy-positive E. granulosus-infected dogs. It is suggested that this copro-PCR assay has the potential for pre-mortem diagnosis of E. granulosus infection even in areas where E. granulosus and E. multilocularis are co-endemic.

Animals↗

[Evaluation of usefulness of different methods for detection of Cryptosporidium in human and animal stool samples].

There are many methods for detection of Cryptosporidium oocysts. Most of them (more than 20) enable the microscopic detection of Cryptosporidium oocysts in faecal smears. Such a great variability of diagnostic methods may lead to confusion as far as the choice of an appropriate technique by a given laboratory is concerned. This study evaluated the diagnostic usefulness of Cryptosporidium oocysts and coproantigen detection methods in the diagnosis of cryptosporidiosis in human (266 stool specimen) and animals (205 from cattle, 160 from sheep, 30 from horses, 80 from cats, 227 from dogs and 11 from wild animals). The total number of human and animal stool specimens processed was 266 and 713, respectively. In this study the usefulness of several diagnostic methods was compared. The following techniques were taken into account: wet mounts, hematoxylin staining, four different specific methods (modified Zeihl-Neelsen, Kinyoun's, safranin-methylene blue, as well as carbol-methyl violet and tartrazyne) and commercially available kit based on enzyme-linked immunoassay (ProspecT(r) Cryptosporidium Microplate Assay). The final number of positive specimens was 123. Out of them 77 were positive in all specific methods. The oocysts found in stool specimens were measured. Humans were infected with C. parvum and animals with C. parvum, C. andersoni or C. felis. The statistical analysis has shown that EIA test was a better than microscopy method for identification of Cryptosporidium in faecal samples in human and wild animal. Sensitivity and specificity are important factors for the choice of a proper diagnostic method for Cryptosporidium detection, however other factors such as cost, simplicity and ease of interpretation of results are also important considerations.

Animals↗

[Anti-schistosomiasis effect induced by full length DNA vaccine coding paramyosin of Schistosoma japonicum in C57BL/6 mice].

OBJECTIVE: To observe the anti-schistosomiasis effect in mice immunized with Sjc97 DNA vaccine. METHODS: C57BL/6 mice were vaccinated intramuscularly with the Sjc97 DNA twice at an interval of 3 weeks, and challenged with 30 +/- 2 cercariae of Schistosoma japonicum three weeks after immunization. Mice in blank plasmid vector control and infection control groups were also infected with same number of cercariae. The mice were sacrificed 7 weeks after challenge infection. The size of single egg granulomas in livers was measured with micrometer. The level of hyaluronic acid (HA) and laminin (LN) in sera of the mice was determined by ELISA. PCR-ELISA was used to examine the expression of TGF-beta1 mRNA in liver. RESULTS: The mean hepatic egg granuloma diameters of the three groups, the Sjc97 DNA, blank plasmid vector and infection control, were 183.75 +/- 42.36 microns, 303.12 +/- 37.36 microns and 304.38 +/- 53.23 microns, respectively. The hepatic granuloma was significantly smaller in the Sjc97 DNA group than that in control. The level of HA and LN in sera of Sjc97 DNA vaccinated mice was markedly lower than those in the two control groups (P < 0.01). The amount of TGF-beta1 mRNA isolated from the livers of mice in Sjc97 DNA group decreased significantly. CONCLUSION: The results showed that Sjc97 DNA vaccine may act as an effective inhibitor against formation of egg granuloma and reduce immunopathological damage caused by Schistosoma japonicum in the host.

Animals↗

Mapping of a new immunodominant human linear B-cell epitope on the vpu protein of the human immunodeficiency virus type 1.

A random fragment expression library was used to identify and map a new human epitope on the vpu protein of the human immunodeficiency virus type 1 (HIV-1). The epitope was mapped to the central part of the protein within amino acids (aa) 37-50 comprising the sequence N-KIDRLIDRLI-ERAE-C. A alpha-galactosidase-vpu fusion protein representing aa 37-68 of vpu was used to screen 356 human serum samples from HIV-1-infected persons for antibodies to the novel epitope. A total of 125 (35.1%) of the samples reacted with this region of vpu. Antibodies against this region were significantly more prevalent among samples from individuals with CD4 cell counts < 400 cells/microliters than individuals with CD4 cell counts > or = 400 cells/microliters (37.6 vs. 17.6%; p < 0.0146, Fisher's exact test). Thus, the presence of antibodies against this epitope of vpu appears to be associated with a progressed state of disease.

Amino Acid Sequence↗

Phenotype/genotype correlations in Gaucher disease type I: clinical and therapeutic implications.

Gaucher disease is the most frequent lysosomal storage disease and the most prevalent genetic disease among Ashkenazi Jews. Gaucher disease type 1 is characterized by marked variability of the phenotype and by the absence of neuronopathic involvement. To test the hypothesis that this phenotypic variability was due to genetic compounds of several different mutant alleles, 161 symptomatic patients with Gaucher disease type 1 (> 90% Ashkenazi Jewish) were analyzed for clinical involvement, and their genotypes were determined. Qualitative and quantitative measures of disease involvement included age at onset of the disease manifestations, hepatic and splenic volumes, age at splenectomy, and severity of bony disease. Highly statistically significant differences (P < .005) were found in each clinical parameter in patients with the N370S/N370S genotype compared with those patients with the N370S/84GG, N370S/L444P, and N370S/? genotypes. The symptomatic N370S homozygotes had onset of their disease two to three decades later than patients with the other genotypes. In addition, patients with the latter genotypes have much more severely involved livers, spleens, and bones and had a higher incidence of splenectomy at an earlier age. These predictive genotype analyses provide the basis for genetic care delivery and therapeutic recommendations in patients affected with Gaucher disease type 1.

Adolescent↗

Increased frequency of abnormal gamma delta T cells in blood of patients with inflammatory bowel diseases.

We have previously reported a preferential usage of V delta 1/V gamma 8 on TCR-gamma-delta-bearing intraepithelial lymphocytes of the normal human intestine as well as in the inflamed synovial tissue of patients with rheumatoid arthritis. The aim of the present study was to analyze V gene segment usage by gamma delta T cells of the intestine and peripheral blood (PB) from patients with inflammatory bowel disease. Freshly isolated lymphocytes were analyzed by flow cytometry using a panel of V gene subset-specific mAbs. The relative proportion of PB TCR-gamma delta+ cells was increased in patients with Crohn's disease as compared with controls. Interestingly, an increased proportion of PB gamma delta T cells of patients with ulcerative colitis or CrD expressed V delta and V gamma genes typically used by intraepithelial lymphocytes. Thus, increased proportions of V delta 1+ and V gamma 8+ cells were found in the PB of both patient groups. The majority of TCR-gamma delta+ intraepithelial lymphocytes (IEL) in inflamed and noninflamed intestine expressed V delta 1/V gamma 8, and a substantial proportion of V gamma(2,3,4)+ cells were found. These observations suggest a disease-associated appearance of "gut-like" gamma delta T cells in the periphery. Moreover, two patients had a large proportion of gamma delta T cells in their PB of which the majority expressed two distinct V gamma proteins. Both of these patients had a short duration of disease (1 and 10 mo, respectively) and the relative proportion of gamma delta T cells decreased in concert with stabilization of disease. Interestingly, one of the patients had a clonal expansion of a V gamma dual-expressing gamma delta T cell in the PB.

Base Sequence↗

enoLOGOS: a versatile web tool for energy normalized sequence logos.

enoLOGOS is a web-based tool that generates sequence logos from various input sources. Sequence logos have become a popular way to graphically represent DNA and amino acid sequence patterns from a set of aligned sequences. Each position of the alignment is represented by a column of stacked symbols with its total height reflecting the information content in this position. Currently, the available web servers are able to create logo images from a set of aligned sequences, but none of them generates weighted sequence logos directly from energy measurements or other sources. With the advent of high-throughput technologies for estimating the contact energy of different DNA sequences, tools that can create logos directly from binding affinity data are useful to researchers. enoLOGOS generates sequence logos from a variety of input data, including energy measurements, probability matrices, alignment matrices, count matrices and aligned sequences. Furthermore, enoLOGOS can represent the mutual information of different positions of the consensus sequence, a unique feature of this tool. Another web interface for our software, C2H2-enoLOGOS, generates logos for the DNA-binding preferences of the C2H2 zinc-finger transcription factor family members. enoLOGOS and C2H2-enoLOGOS are accessible over the web at http://biodev.hgen.pitt.edu/enologos/.

Amino Acids↗

Proportionality-based association metrics in count compositional data.

Compositional data comprise vectors that describe the constituent parts of a whole. Data arising from various -omics platforms such as 16S and RNA sequencing are compositional in nature. In this kind of data, correlations between features on raw counts have no meaningful interpretation. Metrics of proportionality were formulated to address this problem. However, an inherent bias arises when these metrics are calculated empirically on count-based measures due to variability in read depths. We quantify the bias introduced by empirically calculating proportionality-based association metrics in count data. Additionally, we propose a means of estimating these metrics within a logit-normal multinomial model in pursuit of more accurate estimates. The model-based estimates are shown to outperform empirical estimates in simulated data and are applied to a mouse embryonic stem cell single-cell sequencing dataset, as well as a pediatric-onset multiple sclerosis metagenomic dataset.

Animals↗

Detection of Paragonimus heterotremus eggs in experimentally infected cats by a polymerase chain reaction-based method.

A polymerase chain reaction (PCR) procedure for the detection of Paragonimus heterotremus eggs in stool samples was developed and compared with Stoll's egg count method. The primers were designed on the basis of a previously constructed pPH-13-specific DNA probe, which produced an approximate 0.5-kb amplified product. This PCR method could detect as few as 5 eggs in 0.6 g of artificially inoculated feces of a healthy control cat or as little as 1 x 10(-4) ng of P. heterotremus genomic DNA. The assay had 100% sensitivity in all infected cats. The method did not yield an approximate 0.5-kb product with DNA from other parasites such as Gnathostoma spinigerum, Trichinella spiralis, Fasciola gigantica, Echinostoma malayanum, Opisthorchis viverrini, Dirofilaria immitis, and Taenia saginata; exceptions were Paragonimus siamensis and Paragonimus westermani. In addition, no genomic DNA from Escherichia coli, Burkholderia pseudomallei, Acinetobacter anitratus, Mycobacterium tuberculosis, Staphylococcus aureus, beta-Streptococcus grA, and Proteus mirabilis or from the vertebrate and invertebrate hosts of P. heterotremus was amplified in the PCR assay. This assay has great potential for application in clinical epidemiological studies.

Animals↗

Discordant outcomes following failure of antiretroviral therapy are associated with substantial differences in human immunodeficiency virus-specific cellular immunity.

Many individuals chronically infected with human immunodeficiency virus type 1 (HIV-1) experience a recrudescence of plasma virus during continuous combination antiretroviral therapy (ART) due either to the emergence of drug-resistant viruses or to poor compliance. In most cases, virologic failure on ART is associated with a coincident decline in CD4(+) T lymphocyte levels. However, a proportion of discordant individuals retain a stable or even increasing CD4(+) T lymphocyte count despite virological failure. In order to address the nature of these different outcomes, we evaluated virologic and immunologic variables in a prospective, single-blinded, nonrandomized cohort of 53 subjects with chronic HIV-1 infection who had been treated with continuous ART and monitored intensively over a period of 19 months. In all individuals with detectable viremia on ART, multiple drug resistance mutations with similar impacts on viral growth kinetics were detected in the pol gene of circulating plasma virus. Further, C2V3 env gene analysis demonstrated sequences indicative of CCR5 coreceptor usage in the majority of those with detectable plasma viremia. In contrast to this homogeneous virologic pattern, comprehensive screening with a range of antigens derived from HIV-1 revealed substantial immunologic differences. Discordant subjects with stable CD4(+) T lymphocyte counts in the presence of recrudescent virus demonstrated potent virus-specific CD4(+) and CD8(+) T lymphocyte responses. In contrast, subjects with virologic failure associated with declining CD4(+) T lymphocyte counts had substantially weaker HIV-specific CD4(+) T lymphocyte responses and exhibited a trend towards weaker HIV-specific CD8(+) T lymphocyte responses. Importantly the CD4(+) response was sustained over periods as long as 11 months, confirming the stability of the phenomenon. These correlative data lead to the testable hypothesis that the consequences of viral recrudescence during continuous ART are modulated by the HIV-specific cellular immune response.

Adult↗

Change-point analysis of neuron spike train data.

In many medical experiments, data are collected across time, over a number of similar trials, or over a number of experimental units. As is the case of neuron spike train studies, these data may be in the form of counts of events per unit of time. These counts may be correlated within each trial. It is often of interest to know if the introduction of an intervention, such as the application of a stimulus, affects the distribution of the counts over the course of the experiment. In such investigations, each trial generates a sequence of data that may or may not contain a change in distribution at some point in time. Each sequence of integer counts can be viewed as arising from a Poisson process and are therefore independently distributed or as an integer-valued time series that allows for correlations between these counts. The main aim of this paper is to show how the ensemble of sample paths may be used to make inference about the distribution of the instantaneous times of change in a given population. This will be accomplished using a Bayesian hierarchical model for these change-points in time. A bonus of these models is they also allow for inference about the probability of a change in each unit and the magnitude of the effects, if any. The use of such change-point models on integer-valued time series is illustrated on neuron spike train data, although the methods can be applied to other situations where integer-valued processes arise.

Action Potentials↗

Radioimager quantification of oligonucleotide hybridization with DNA immobilized on transfer membrane: application to the identification of related sequences.

The radioimager scintillating optical fiber imager was used to quantify the hybridization parameters of a 35-mer oligonucleotide probe with target DNAs immobilized on transfer membranes. The amount of the immobilized target DNA remaining accessible to hybridization (Rt) was shown to be about 4% of the spotted DNA. The time course of the hybridization of a target DNA reacting with an excess of full-match probe exhibited a first-order kinetics, in which rate constant k was the highest for the hybridization temperature close to the calculated Tm. The effect of temperature on the hybridization kinetics of the probe sharing 37 to 100% identity with the immobilized target DNA was assessed: A significant fall of both the rate constant k and Rt values at the plateau was observed when the identity shared by the target DNA and the probe decreased from 100 to 71%. The highest k and Rt values were also obtained for temperatures closest to the calculated Tm. A good estimate of the degree of sequence identity may be calculated from the corresponding hybridization signals. Washing procedure did not improve the discrimination between related sequences, except for closely similar sequences. Practical conclusions for the detection of sequences belonging to gene families are presented.

Base Sequence↗

Degradation of chlorpyrifos contaminated soil by bioslurry reactor operated in sequencing batch mode: bioprocess monitoring.

Bioslurry reactor (SS-SBR) was studied for the degradation of chlorpyrifos contaminated soil using native mixed microflora, by adopting sequencing batch mode (anoxic-aerobic-anoxic) operation. Reactor operation was monitored for a total cycle period of 72 h consisting of 3 h of FILL, 64 h REACT, 2 h of SETTLE, and 3 h of DECANT with chlorpyrifos concentrations of 3000 micrpg/g, 6000 microg/g and 12000 microg/g. At 3000 microg/g of chlorpyrifos concentration, 91% was degraded after 72 h of the cycle period, whereas in the case of 6000 microg/g of chlorpyrifos, 82.5% was degraded. However, for 12000 microg/g of chlorpyrifos, only 14.5% degradation was observed. The degradation rate was rapid at lower substrate concentration and 12000 microg/g of substrate concentration was found to be inhibitory. Chlorpyrifos removal rate was slow during the initial phase of the sequence operation. Half-life of chlorpyrifos degradation (t0.5) was estimated to be 6.3 h for 3000 microg/g of substrate, 17.5 h for 6000 microg/g and 732.2 h for 12000 microg/g. Process performance was assessed by monitoring chlorpyrifos concentration and biochemical process parameters viz., pH, oxidation and reduction potential (ORP), dissolved oxygen (DO), oxygen consumption rate (OCR) and microbial count (CFU) during sequence operation. From the experimental data obtained it can be concluded that the rate-limiting step with the bioslurry phase reactor in the process of chlorpyrifos degradation may be attributed to the concentration of substrate present in either soil or liquid phase. Periodic operations (SBR) by varying individual components of substrate with time in each process step place micro-organisms under nutritional changes from feast to famine and maintains a wide distribution in the population of micro-organisms resulting in high uptake of the substrate in the bioslurry reactor.

Bacteria, Aerobic↗

Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence features of the regions of 1,191,918 bp covered by seventeen physically assigned P1 clones.

A total of 17 P1 and TAC clones each containing a marker(s) specifically mapped on chromosome 5 were isolated from P1 and TAC libraries of the Arabidopsis thaliana Columbia genome, and their nucleotide sequences were determined according to the shot gun-based strategy and precisely located on the physical map of chromosome 5. The total length of the clones sequenced in this study was 1,191,918 bp. As we have previously reported the sequence of 2,662,078 bp by analysis of 33 P1 clones, the total length of the sequences of chromosome 5 determined so far is now 3,853,996 bp. The sequences determined in this study were subjected to similarity search against protein and EST databases and analysis with computer programs for gene modeling, and a total of 310 potential protein-coding genes and/or gene segments with known or predicted functions were identified. The positions of exons which do not show apparent similarity to known genes were also predicted by computer-aided analysis. An average density of the assigned genes and/or gene segments was 1 gene/3,845 bp. Introns were identified in 78% of the potential protein genes, and the average number per gene and the average length of the introns were 3.7 and 185 bp, respectively. The numbers of the Arabidopsis ESTs matched to each of the predicted genes have been counted to monitor the transcription level. The sequence data and gene information are available on the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.

Arabidopsis↗