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Results for “Functional analysis”

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At least 181 records · Page 10Linked to original sources

PubMed2001

Direct functional analysis of epitope-specific CD8+ T cells in peripheral blood.

The functional status of virus-specific CD8+ T cells is important for the outcome and the immunopathogenesis of viral infections. We have developed an assay for the direct functional analysis of antigen-specific CD8+ T cells, which does not require prolonged in vitro cultivation and amplification of T cells. Whole blood samples were incubated with peptide antigens for <5 h, followed by staining with peptide-MHC tetramers to identify epitope-specific T cells. The cells were also stained for the activation marker CD69 or for the production of cytokines such as interferon-gamma (IFNgamma) or tumor necrosis factor-alpha (TNFalpha). With the combined staining with tetramer and antibodies to CD69 or cytokines the number of antigen-specific CD8+ T cells as well as the functional response of each individual cell to the cognate antigen can be determined in a single experiment. Virus-specific CD8+ T cells that are nonfunctional, as well as those that are functional under the same stimulating conditions can be simultaneously detected with this assay, which is not possible by using other T-cell functional assays including cytotoxicity assay, intracellular cytokine staining, and enzyme-linked immunospot (ELISPOT) assay.

Antigens, Viral↗

PubMed1996

Functional analysis of the cellobiohydrolase I promoter of the filamentous fungus Trichoderma reesei.

Functional analysis of the cellulase promoter cbh1 of the filamentous fungus Trichoderma reesei was carried out using the Escherichia coli lacZ gene as a reporter. An assay based on cultivation on solid medium in microtiter plates was developed that allows rapid and reliable semiquantitative analysis of beta-galactosidase expression of a large number of transformants. A series of deletions and specifically designed alterations were made covering 2.2 kb of the cbh1 promoter. Removal of sequences upstream of nucleotide -500 in relation to the initiator ATG abolished glucose repression. Mutation of a single hexanucleotide sequence 5'GTGGGG at nucleotide -720 was sufficient for derepression. This site is similar to the binding sites of the glucose repressors MIG1 of Saccharomyces cerevisiae and CREA/CREI of filamentous fungi. Removal of the glucose repressor site did not affect sophorose induction. Sophorose induction of the promoter was retained even in deletion derivatives lacking sequences upstream of position -161, which retained about 70 bp upstream of the transcription start point and only 30 bp upstream of the TATA box.

Base Sequence↗

PubMed2002

Recombinational DNA Repair in Cancer and Normal Cells: The Challenge of Functional Analysis.

A major goal of current cancer research is to understand the functional consequences of mutations in recombinational DNA repair genes. The introduction of artificial recombination substrates into living cells has evolved into a powerful tool to perform functional analysis of DNA double strand break (DSB) repair. Here, we review the principles and practice of current plasmid assays with regard to the two major DSB repair pathways, homologous recombination and nonhomologous end-joining. A spectrum of assay types is available to assess repair in a wide variety of cell lines. However, several technical challenges still need to be overcome. Understanding the alterations of DSB repair in cancers will ultimately provide a rational basis for drug design that may selectively sensitize tumor cells to ionizing radiation and chemotherapy, thereby achieving therapeutic gain.

Journal Article↗

PubMed1995

Functional analysis and treatment of escape-maintained aggression correlated with sleep deprivation.

Functional analysis identified the consequences that maintained aggressive behavior and the relationship between these consequences and sleep deprivation for an individual with severe mental retardation. Results showed that aggression was maintained by negative reinforcement contingencies (escape from demand) and that aggression was more severe when sleep deprivation was present. A multicomponent intervention resulted in reductions of aggression for up to 7 months.

Adult↗

PubMed1997

Functional analysis of episodic self-injury correlated with recurrent otitis media.

A functional analysis examined the consequences that maintained episodic self-injury and the relationship between those consequences and otitis media for a child with moderate developmental disabilities. Results indicated that self-injury occurred only during periods of otitis media. Otitis media may have served as an establishing operation related to escape from ambient noise.

Adult↗

PubMed1999

Functional analysis and treatment of problem behavior exhibited by elementary school children.

A functional analysis involving antecedent events was conducted with 4 students who had been identified as having behavior problems. Off-task behavior was measured while task difficulty and level of adult attention were manipulated during analogue sessions. Results revealed two patterns: Three students displayed higher rates of off-task behavior during difficult tasks, and 1 displayed higher rates of off-task behavior during sessions with low attention. Improved behavior was observed when students were taught an alternative behavior that matched the assessment results.

Attention↗

PubMed2002

Teacher acquisition of functional analysis methodology.

The current study examined methods for training teachers to use functional analysis methods. Teachers first received written and verbal instructions detailing attention and demand conditions. They then received training that included modeling, rehearsal, and performance feedback. Finally, probes were taken during ongoing class instruction. Results indicate that teachers acquired the skills and used them in classroom settings.

Behavior Therapy↗

PubMed1977

[Functional analysis in stomatology].

A survey of diagnostic details is made on which functional analysis is based. Symptoms connected with the temporo-mandibular joint, muscle palpation, radiological demonstration of the temporo-mandibular joint, and registration of the positional jaw relation are especially dealt with. The methods of examination which are prerequisite to a safe diagnosis are critically evaluated.

Dental Articulators↗

PubMed1983

Multiple discriminant function analysis of sex and race in the postcranial skeleton.

Terry Collection femora and innominates of 260 American Whites and Blacks (65 males and 65 females of each race) were analyzed by multiple discriminant function analysis. A stepwise procedure produced three optimal discriminant functions using 15 of our 32 measurements. These functions correctly identified 95% of the sample. The first two-one for sex and one for race-are statistically and biologically significant and form the basis of our analysis. The sexing function manifested both size and shape elements. Prominent among the former was joint size--acetabular diameter and epicondylar diameter of the femur. The shape elements included form of the greater sciatic notch and of the inferomedial aspect of the pubic body. The racing function highlighted a pattern of greater innominate dimensions, exclusive of the acetabular joint, in Whites. This was in contrast to the greater length of the Black femur. Overall, the function seems to express the established differences between the races in the ratio of lower limb length to torso length. While these functions have been applied successfully to forensic cases with confirmed identifications, questions regarding the breadth of applicability of discriminant functions make it desirable to validate our results on new material from the Terry and other collections.

Analysis of Variance↗

PubMed2001

Application of nano-diffraction to local atomic distribution function analysis of amorphous materials.

A method is proposed for the local atomic distribution function analysis of amorphous materials. This method is based on local halo-electron diffraction intensity analysis with nano-sized electron probes as small as 25 to approximately 3 nm, taking advantage of the intensity recording with imaging plate. Nanodiffraction and selected area electron diffraction (SAED) patterns from an amorphous SiNx (x approximately 4/3) thin film were taken using a conventional transmission electron microscope operated at 200 kV and recorded on imaging plates. An intensity correction to omit inelastic intensity was made using electron energy-loss spectroscopy. When a beam-convergence angle is larger than 1 x 10(-3) rad, the Wiener-filter deconvolution method becomes helpful in producing atomic pair distribution functions (PDFs) from the nano-diffraction intensity profiles that are more similar to the PDF from the SAED intensity. This technique was applied to the analysis of local amorphous structures of SiO2 layers formed by an oxygen-ion implantation into single crystal SiC.

Journal Article↗

PubMed2005

Functional analysis of tardive dyskinesia: implications for assessment and treatment.

We conducted an analogue functional analysis contrasting motor tasks with varying types of social consequences for movements associated with tardive dyskinesia (TD) in 2 men who had been diagnosed with developmental disabilities and TD. Our findings suggest that TD-related movements were not a function of social reinforcement contingencies. However, motor-activation tasks decreased TD-related movements, suggesting a possible novel intervention.

Antipsychotic Agents↗

PubMed1995

In vivo functional analysis of the Ras exchange factor son of sevenless.

The Son of sevenless (Sos) protein functions as a guanine nucleotide transfer factor for Ras and interacts with the receptor tyrosine kinase Sevenless through the protein Drk, a homolog of mammalian Grb2. In vivo structure-function analysis revealed that the amino terminus of Sos was essential for its function in flies. A molecule lacking the amino terminus was a potent dominant negative. In contrast, a Sos fragment lacking the Drk binding sites was functional and its activity was dependent on the presence of the Sevenless receptor. Furthermore, membrane localization of Sos was independent of Drk. A possible role for Drk as an activator of Sos is discussed and a Drk-independent interaction between Sos and Sevenless is proposed that is likely mediated by the pleckstrin homology domain within the amino terminus.

Animals↗

PubMed2006

GOFFA: gene ontology for functional analysis--a FDA gene ontology tool for analysis of genomic and proteomic data.

BACKGROUND: Gene Ontology (GO) characterizes and categorizes the functions of genes and their products according to biological processes, molecular functions and cellular components, facilitating interpretation of data from high-throughput genomics and proteomics technologies. The most effective use of GO information is achieved when its rich and hierarchical complexity is retained and the information is distilled to the biological functions that are most germane to the phenomenon being investigated. RESULTS: Here we present a FDA GO tool named Gene Ontology for Functional Analysis (GOFFA). GOFFA first ranks GO terms in the order of prevalence for a list of selected genes or proteins, and then it allows the user to interactively select GO terms according to their significance and specific biological complexity within the hierarchical structure. GOFFA provides five interactive functions (Tree view, Terms View, Genes View, GO Path and GO TreePrune) to analyze the GO data. Among the five functions, GO Path and GO TreePrune are unique. The GO Path simultaneously displays the ranks that order GOFFA Tree Paths based on statistical analysis. The GO TreePrune provides a visual display of a reduced GO term set based on a user's statistical cut-offs. Therefore, the GOFFA visual display can provide an intuitive depiction of the most likely relevant biological functions. CONCLUSION: With GOFFA, the user can dynamically interact with the GO data to interpret gene expression results in the context of biological plausibility, which can lead to new discoveries or identify new hypotheses. AVAILABILITY: GOFFA is available through ArrayTrack softwarehttp://edkb.fda.gov/webstart/arraytrack/.

Genomics↗

PubMed1997

Functional analysis of immunoreceptor tyrosine-based activation motif (ITAM)-mediated signal transduction: the two YxxL segments within a single CD3zeta-ITAM are functionally distinct.

Functional analysis of the immunoreceptor tyrosine-based activation motif (ITAM) derived from the membrane-proximal ITAM of CD3zeta demonstrates that mutations at either the tyrosine or leucine residues in the N-terminal YxxL segment of the ITAM abolish all signal transduction functions of this ITAM. In contrast, mutations at the tyrosine or leucine residues in the C-terminal YxxL segment abrogate signals for interleukin (IL)-2 production but do not prevent tyrosine phosphorylation of the N-terminal tyrosine of the ITAM, lck association with the ITAM, activation of phospholipase C-gamma1 or calcium mobilization. Cross-linking of chimeric receptors containing a C-terminal YxxL leucine mutation induces tyrosine phosphorylation of ZAP70 but without stable binding to the phosphorylated ITAM. These results indicate that the two YxxL segments in an ITAM are functionally distinct and that both are essential for ZAP70 binding and IL-2 production. Furthermore, tyrosine phosphorylation of ZAP70 per se is not sufficient to trigger the downstream events leading to IL-2 production. Substitution of an alanine for the bulky side chain at the Y+1 position of the N-terminal YxxL segment reduces the receptor cross-linking requirement necessary to achieve cellular activation and the absolute dependence on lck in this process. Our results reveal that both the number of ITAM as well as the specific amino acid residues within a single ITAM determine the extent of chimeric receptor cross-linking required to trigger tyrosine phosphorylation-dependent signaling events.

Amino Acid Sequence↗

PubMed1992

Functional analysis of human papillomavirus type 16 E7 by complementation with adenovirus E1A mutants.

Functional analysis of human papillomavirus type 16 E7 protein by complementation with adenovirus E1A mutants in baby rat kidney cells has shown that the retinoblastoma gene product (RB)-binding region of E7 can substitute in trans for that of E1A. An N-terminal E7 mutant was unable to complement an E1A mutant unable to bind p300, indicating that the two mutants were defective for functionally equivalent activities. E7 proteins with mutations within the RB-binding region were also unable to complement either the non-p300-binding E1A mutant or the N-terminal E7 mutant, suggesting that these mutations affect more than just RB binding.

Adenovirus Early Proteins↗

PubMed1998

Drug-induced phenotypes provide a tool for the functional analysis of yeast genes.

The post-genome sequencing era of Saccharomyces cerevisiae is defined by the analysis of newly discovered open reading frames of unknown function. In this report, we describe a genetic method for the rapid identification and characterisation of genes involved in a given phenotype. This approach is based on the ability of overexpressed genomic DNA fragments to cure an induced phenotype in yeast. To validate this concept, yeast cells carrying a yeast DNA library present on multicopy plasmid vectors were screened for resistance to the antifungal drug ketoconazole. Among 1.2 million colonies 13 clones tested positive, including those expressing the lanosterol C-14 demethylase, known to be a cellular target for azole drugs, and the cytochrome-c oxidase of mitochondria, regulating the respiratory chain electron transport. Several other resistant clones were identified, which code for yeast proteins of so far unknown function. These genes may represent potential candidates for antifungal drug effects. Together with the availability of the entire yeast genome sequence, the described genetic screening method is a powerful tool for the effective functional analysis of yeast genes.

Antifungal Agents↗

PubMed1994

Functional analysis of transcription of the Mycobacterium tuberculosis 16S rDNA-encoding gene.

A functional analysis of Mycobacterium tuberculosis 16S ribosomal RNA (rRNA) transcription and processing was undertaken in this study. RNA:DNA hybridizations indicated that the maximum transcriptional activity of rRNA-encoding genes (rDNA) corresponded to the earliest period of exponential growth. Transcription start points (tsp) were mapped by primer extension analysis of RNA from M. tuberculosis H37Rv and M. tuberculosis H37Ra. An identical pattern of rRNA transcription and processing was exhibited in laboratory-grown cultures of M. tuberculosis H37Rv and H37Ra. One promoter represents the structural equivalent of the Escherichia coli rrn P2 promoter. The precursor transcripts are processed into mature 16S rRNA through a pathway that includes recognition of RNA secondary structure by ribonuclease III (RNase III) in the stem structure surrounding the 16S rRNA indicating that at least this RNA processing step is conserved in mycobacteria and E. coli. The 16S rDNA promoter region from H37Rv was cloned upstream from the promoterless chloramphenicol (Cm) acetyltransferase (CAT)-encoding gene (cat) in a shuttle plasmid vector, pSD7. The promoter-fusion construct, pSD7.16S, was characterized by CAT assays, measurement of percent survival in Cm-containing medium and in vivo transcription analysis in M. smegmatis. The M. smegmatis transformant exhibited a CAT activity of 16,669 nmol/min per mg protein, suggesting that the 16S promoter was of exceptionally high strength. Two tsp utilized in M. tuberculosis were also employed in M. smegmatis. The cat mRNA synthesized under the direction of the ribosomal promoter was less stable, as compared to genome-derived rRNA.

Base Sequence↗

PubMed1989

A comparison of dummy variable versus traditional multiple discriminant function analysis.

The authors compare the use of dummy variable and traditional multiple discriminant function analysis when dealing with research questions where ratio or nominal scale independent variables can be used. A healthcare-related example of using dv MDF is given and the authors conclude that it is superior to traditional MDF for determining variable importance and developing market segment profiles.

Analysis of Variance↗