Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Functional analysis”

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 253 records · Page 14Linked to original sources
PubMed1983

Functional analysis of a herpes simplex virus type 1 promoter: identification of far-upstream regulatory sequences.

We have performed a functional analysis of DNA sequences upstream from the gene for IE mRNA3 of herpes simplex virus type 1. Nucleotide sequences involved in initiation and positive regulation of transcription have been defined by construction of specific deletions in vitro. Transcription was assayed in vivo by microinjection into Xenopus oocytes, or by introduction of plasmid DNA into tissue culture cells and measurement of transient expression. Three functional promoter elements have been defined: i) Sequences between -16 and -37 which are not essential for transcription but are required for accurate initiation. ii) Proximal promoter sequences which are sufficient for transcription initiation in the absence of upstream sequences. iii) Far-upstream promoter sequences (more than 108bp upstream) which increase transcription in oocytes, and contain positive regulatory sequences (-174 to -331) which respond strongly to a factor in the virus inoculum.

Animals↗
PubMed1989

Structure-function analysis of tissue-type plasminogen activator by linker-insertion, point and deletion mutagenesis.

We undertook a structure--function analysis of human tissue plasminogen activator (tPA) using linker-scanning and deletion mutagenesis. Synthetic oligonucleotide linkers were introduced into the tPA cDNA at pre-existing restriction enzyme sites. This generated a series of tPA variants which contained small primary sequence alterations consisting of point mutations, deletions or insertions. The majority of the linker-insertion variants demonstrate a significant reduction in amidolytic and fibrinolytic activity in comparison to wild-type tPA. The exceptions are the variants with linker-inserts placed at the BglII(115) and StyI(277) sites of the tPA cDNA (4SLEG5 and 57LEA58 respectively), which encode insertions at the boundaries of the finger domain. The variants with linker-inserts in the light chain (protease domain) of tPA are the lowest in enzymatic activity. Particularly sensitive to mutation are highly conserved amino acids. Heavy chain deletion variants were constructed from point mutants at the domain boundaries of tPA. Deletion of the kringle domains lowers the fibrinolytic activity to a greater extent than deletion of the finger or growth factor domains. We conclude that alterations in any domain of the tPA molecule, and particularly in the highly conserved residues within these domains, can affect fibrinolytic activity.

Amino Acid Sequence↗
PubMed1994

The significance and future of functional analysis methodologies.

Iwata, Dorsey, Slifer, Bauman, and Richman (1982) presented the first comprehensive and standardized methodology for identifying operant functions of aberrant behavior. This essay discusses the significance functional analysis has had for applied behavior analysis. The methodology has lessened the field's reliance on default technologies and promoted analysis of environment-behavior interactions maintaining target responses as the basis for selecting treatments. It has also contributed to the integration of basic and applied research. Future directions for this research are suggested.

Journal Article↗
PubMed1990

Functional analysis of ARGRI and ARGRIII regulatory proteins involved in the regulation of arginine metabolism in Saccharomyces cerevisiae.

We present here a functional analysis of ARGRI and ARGRIII regulatory proteins which are involved together with ARGRII in specific regulation of arginine anabolic and catabolic pathways. Unlike ARGRII, ARGRI and ARGRIII have no transcriptional activation capacity. The first 60 amino acids of ARGRI (out of 177) are dispensable for its activity. The functional domain of the protein is located in the region of homology with MCM1 and SRF proteins. ARGRIII contains in its C-terminal portion a stretch of 17 aspartate residues which are indispensable for arginine regulation. Gene disruption of the ARGRIII gene impairs the growth of the mutant on rich medium, showing that ARGRIII has a pleiotropic role in the cell.

Arginase↗
PubMedDate not supplied

The reliability of muscle function analysis using different methods of stimulation.

BACKGROUND: The purpose of our study was to determine the reliability of nonvolitional muscle function analysis (MFA) by determining the day-to-day and within-day reliability of conventional electrical stimulation and a newer, magneto-electrical stimulation method, using standard laboratory methodology. METHODS: Ten healthy, human immunodeficiency virus-negative adult men volunteered as subjects. MFA consisted of measuring the maximal relaxation rate, for magneto-electrical stimulation at 1 Hz and conventional electrical stimulation at 20 Hz, and force-frequency ratios using conventional electrical stimulation at 10 Hz:20 Hz and 10 Hz:50 Hz. Within-day and day-to-day reliability were determined by calculating the coefficient of variation (CV) for all subjects. RESULTS: Maximal relaxation rate using magneto-electrical stimulation had a significantly lower CV compared with the other nonvolitional MFA methods (p = .002). CONCLUSIONS: Maximal relaxation rate using magneto-electrical stimulation was more reliable and technically easier than the other muscle function parameters examined. However, the day-to-day CV of muscle function parameters is larger than traditional nutrition assessment techniques. Development within the field should strive to improve testing techniques so that the reliability of MFA will allow definition of a range of normal values against which an individual's value can be compared. Until this is available, the precision and reliability of MFA restrict its use to research and population studies.

Adult↗
PubMed1997

Functional analysis and treatment of elopement.

Elopement is a dangerous behavior because children who run away may encounter life-threatening situations (e.g., traffic). We conducted functional analyses of the elopement of 3 children who had been diagnosed with developmental disabilities. The results identified a maintaining reinforcer for the elopement of 1 child, but the data were difficult to interpret for 2 of the children. Subsequent reinforcer assessments were used to help to clarify the reinforcers for elopement for these 2 children. Results of the functional analyses and reinforcer assessments then were used to develop successful treatments to reduce elopement. The findings are discussed in terms of (a) the application of functional analysis methodology to elopement, (b) the use of reinforcer assessments to identify potential reinforcers when standard functional analyses are undifferentiated, and (c) the utility of assessment-based treatments for elopement.

Behavior Therapy↗
PubMed2003

Molecular characterization and functional analysis of the manganese-containing superoxide dismutase gene (sodA) from Streptococcus thermophilus AO54.

This report describes the isolation, sequencing, and functional analysis of the sodA gene, encoding Mn-superoxide dismutase, from Streptococcus thermophilus AO54. The gene was found to encode a 201 amino acid polypeptide with 88 and 83% identity to SodA from Streptococcus mutans and Streptococcus agalacticae, respectively. Primer extension analysis revealed a transcriptional start site 27 nucleotides upstream of initiation codon. The gene was expressed in Escherichia coli and was able to rescue the growth of a sodAsodB mutant in a minimal-medium containing 10(-6)M paraquat. A sodA mutant of S. thermophilus was constructed and found to be more sensitive to aerobic growth than its parent strain. Supplementing the medium with MnCl(2) improved the growth of the mutant, only under microaerophilic conditions. The results suggest that sodA is essential for the aerobic growth of S. thermophilus. In the absence of functional SodA, manganese ions may provide partial protection against oxygen toxicity.

Amino Acid Sequence↗
PubMed1989

Late regrowth of pituitary adenomas after irradiation and/or surgery. Hazard function analysis.

A retrospective analysis was performed on all patients with pituitary adenomas treated at the Radiation Oncology Center, Mallinckrodt Institute of Radiology, St. Louis, Missouri. Of 210 patients treated from April 1954 through December 1982, 70 were treated with radiotherapy alone (RT), 121 received immediate postoperative RT (2 to 6 weeks), and 19 received RT following surgical failure. The mean follow-up time from the date of diagnosis for those patients alive at the time of last follow-up was 13.0 years (range, 3.0 to 30.0 years). Actuarial progression-free survival was analyzed up to 30 years. The 10-, 20-, and 30-year progression-free survival was 80.5%, 73.5%, and 73.5% for those patients treated with irradiation alone and 92.8%, 71.2%, and 44.0% for those treated with immediate postoperative irradiation. The median time to first failure from initial diagnosis by original treatment was 3.8 years for surgery alone, 4.2 years for RT only, and 10.2 years for surgery plus postoperative RT. Analysis for risk of recurrence per 5-year interval was performed using a hazard function analysis. The risk of recurrence after radiotherapy alone was greatest during the first 5-year interval after treatment and decreased to zero by 20 years. However, the risk of recurrence after primary surgery and postoperative radiotherapy revealed an increasing risk for recurrence up to 30 years after treatment. The concept of "cure" for pituitary adenomas requires extended follow-up.

Actuarial Analysis↗
PubMed1995

Functional analysis and treatment of eye poking.

In four studies we analyzed the eye poking of a youth with profound disabilities. In Study 1, a functional analysis showed that eye poking occurred during the no-attention condition, but not during demand, attention or recreation conditions. The analysis did not identify socially mediated variables involved in the maintenance of eye poking; rather, eye poking may have been maintained by consequences produced directly by the response. In Study 2 we had the student wear goggles to prevent potential reinforcement from finger-eye contact. The results of Study 2 indicated that eye-poking attempts were reduced when the student wore goggles. We then tested in Study 3 the effects of two alternative topographies of stimulation. Study 3 demonstrated that eye poking was reduced when a video game was provided as a competing source of visual stimulation, and that music was less effective in reducing eye poking. In Study 4, a contingency analysis using the video game was conducted in an attempt to (a) reduce the frequency of eye poking and (b) study whether the video game functioned as a reinforcer. The results of Study 4 demonstrated substantive reductions in the frequency of eye poking, and suggested that the video game served as a reinforcer.

Acoustic Stimulation↗
PubMed2002

Large-scale structure-function analysis of the Arabidopsis RPM1 disease resistance protein.

The Arabidopsis RPM1 gene confers resistance against Pseudomonas syringae expressing either the AvrRpm1 or the AvrB type III effector protein. We present an exhaustive genetic screen for mutants that no longer recognize avrRpm1. Using an inducible avrRpm1 expression system, we identified 110 independent mutations. These mutations represent six complementation groups. None discriminates between avrRpm1 and avrB recognition. We identified 95 rpm1 alleles and present a detailed structure--function analysis of the RPM1 protein. Several rpm1 mutants retain partial function, and we deduce that their residual activity is dependent on the level of avrRpm1 signal. In these mutants, the hypersensitive response remains activated if the signal goes above a certain threshold. Missense mutations in rpm1 are highly enriched in the nucleotide binding domain, suggesting that this region plays a key role either in the hypersensitive response associated with RPM1 activation or in RPM1 stability. Cluster analysis of rpm1 alleles defines functionally important residues that are highly conserved between nucleotide binding site leucine-rich repeat R proteins and those that are unique to RPM1. Regions of RPM1 to which no loss-of-function alleles map may represent domains in which variation is tolerated and may contribute to the evolution of new R gene specificities.

Alleles↗
PubMed1995

Sex determination from the pubis by discriminant function analysis.

A total of 122 adult human pubes (66 males and 56 females) are used in this study of a discriminant function analysis for determining sex from four pubic measurements: the angle formed by the middle line of the superior ramus and inferior ramus of pubis (in degrees, X1), subpubic angle (in degrees, X2), the minimum distance from the symphyseal surface to the obturator (in millimeters, X3), and the minimum thickness of the ischiopubic ramus (in millimeters, X4). The method introduced by Fisher is used. Using the formula Y = 0.270 mean1-0.985mean2-0.761mean3 + 1.806mean4,F = 200 F = 200 (F > F0.01(4,117), P < 0.01), section point -32.47, an accuracy of 100% could be achieved for 230 pubes (130 males, 100 females).

Discriminant Analysis↗
PubMed1991

Functional analysis of cis-elements, auxin response and early developmental profiles of the mannopine synthase bidirectional promoter.

The dual MAS1'-2' promoter regulating two divergently transcribed mannopine synthase genes has been widely employed in plant expression vectors. As part of an effort towards its rational design as a genetic engineering tool, we have undertaken a functional analysis of the promoter by deletion mutagenesis and by the use of hybrid promoter constructs. Our results indicate that the central region of the intergenic promoter is composed of at least four domains. Three of these contain complementary sequences, which can potentially hybridize to form alternative palindromic structures. These three domains can function cooperatively, and in an orientation-independent manner, in imparting a sevenfold higher expression level at the 2' end relative to the corresponding 1'. The remaining domain is characterized by tracts of repeated A/T-rich elements, and appears to confer the weak activity at the MAS1' promoter end. However, even though this A/T-rich DNA segment is functional, our deletion analysis provided strong evidence that it is completely dispensable for wild-type promoter activity. In addition, the relative distances between these enhancer domains and the 1'-2' TATA-proximal regions can have a pronounced influence on the level of expression in both directions. In young tobacco seedlings, the two promoter ends are expressed in similar, if not identical, tissues in the aerial parts of the plants, but major differences can be observed in roots. Transient expression assays using hybrid promoter constructs showed that cis-elements that can respond to auxin induction signals are redundant in nature, in that they are dispersed throughout the promoter and showed no obvious consensus sequence.

2,4-Dichlorophenoxyacetic Acid↗
PubMed2004

Total potential source contribution function analysis of trace elements determined in aerosol samples collected near Lake Huron.

Aerosol samples were collected at the rural Burnt Island Ontario Integrated Air Deposition Network air sampling station on the northern shore of Lake Huron from 1992 through 1994. The samples were analyzed for trace elements by neutron activation analysis, and the air concentrations of over 30 elements were determined. Total potential source contribution function analysis (TPSCF) was used to determine the most probable geographical location of these aerosols' origin. The TPSCF results for As, In, Sb, Se, Sn, and Zn are highlighted in this paper. Source regions for these elements ranged from Alma, Quebec, Canada to Carrollton, GA. Because of large seasonal variations in the concentrations of the atmospheric concentrations of these elements, TPSCFvalues were calculated for the summer and winter halves of the year as well as the entire year.

Aerosols↗
PubMed1999

Genetic and functional analysis of genes required for the post-modification of the polyketide antibiotic TA of Myxococcus xanthus.

The antibiotic TA of Myxococcus xanthus is a complex macrocyclic polyketide, produced through successive condensations of acetate by a type I PKS (polyketide synthase) mechanism. The genes encoding TA biosynthesis are clustered on a 36 kb DNA fragment, which has been cloned and analysed. The chemical structure of TA and the mechanism by which it is synthesized indicate the need for several post-modification steps, which are introduced into the carbon chain of the polyketide to form the final bioactive molecule. These include the addition of several carbon atoms originating from acetate carbonyl, three C-methylations, O-methylation and a specific hydroxylation. This paper reports the analysis of five genes which are involved in the post-modification of TA. Their functional analysis, by specific gene disruption, suggests that they may be essential for the production of the active antibiotic. The characteristics and organization of the genes suggest that they may be involved in the addition of the carbon atoms which arise from acetate.

Amino Acid Sequence↗
PubMed2003

Comparative functional analysis of rat TGF-beta1 and Xenopus laevis TGF-beta5 promoters suggest differential regulations.

We have carried out a comparative functional analysis of the rat TGF-beta1 and Xenopus laevis TGF-beta5 promoters across several mammalian and amphibian cell lines. Progressive deletion constructs of both the promoters have been made using a PCR based approach and the basal promoter activities studied in Xenopus tadpole cell line (XTC), Xenopus adult kidney fibroblast cell line (A6), human hepatoma cell line (HepG2), normal rat kidney cell line (NRK), and Chinese hamster ovary cell line (CHO). Data suggests that the basal promoter activity of TGF-beta1 is low as compared to TGF-beta5 promoter in XTC cells but comparable in A6 cells, while TGF-beta5 promoter shows nearly negligible activity as compared to TGF-beta5 promoter in all the tested mammalian cell lines. Moreover, TGF-beta5 promoter is found to be repressed in XTC cells on treatment with TGF-beta5 protein. Thus, the regulation of TGF-beta1 and TGF-beta5 promoters is distinct in amphibian and mammalian species. We therefore suggest that contrary to the suggested functional equivalence of TGF-beta1 and TGF-beta5 proteins, TGF-beta1 and TGF-beta5 genes have distinct functions in their respective species.

Animals↗
PubMed1979

[Comparative clinical study of 3 technics of functional analysis of occlusion].

The object of our research is to compare clinically and objectively three articulators: -- the Dentatus, semiadjustable articulator which employs dynamico-static records -- the T.M.J., fully adjustable articulator which employs dynamico-cinematic stereographic endobuccal records -- the Denar, fully adjustable articulator which employs dynamico-cinematic pantographic extrabuccal records. We expressly avoided repeating the mechanical and mathematical analysis of the possibilities and limitations of the articulator and copying the previous researches which always imply quasi-perfection in the behaviour of the patient, in the manipulations of the dental surgeon and in the physical qualities of the articulator and materials used. Our comparative research claims to respect all the variables which occur in the carrying out of an actual case and which are inherent in the patient, the dental surgeon, the articulator and the materials used. In carrying out our research we followed two essential conditions: -- We decided to follow, first of all, a strictly clinical plan using successively the three articulators in the analysis of the occlusal function (carried out twice) for each of the six patients and comparing the results obtained for each articulator and for each patient. -- We decided, next, that this comparative research should be strictly objective. To this end, we did not set out to form an opinion, on the basis of clinical impressions, favourable or unfavourable to the different characteristics of the three articulators. We limited ourselves, on the contrary, to measuring, superposing and making a comparative analysis of the results obtained with the three articulators for the same analysis of the occlusal function.

Dental Arch↗
PubMed1987

Structure-function analysis of fos protein: a single amino acid change activates the immortalizing potential of v-fos.

We have undertaken a detailed structure-function analysis of v-fos protein, taking the ability to induce transformation and immortalization as criteria of biological activity. Our results demonstrate that the evolutionarily conserved center region of fos, comprising ca. 28% of the protein, is indispensable for its function. A single amino acid change (Glu 138----Val 138) in this region activates the immortalizing potential of v-fos without affecting its transforming capacity. The presence of additional either N- or C-terminal amino acids, however, is required for efficient expression of a stable protein, and significantly increases its biological activity. In contrast, sequences in the C-terminal half (between positions 228 and 267) strongly downmodulate the transforming activity of v-fos protein without decreasing its immortalizing potential.

Amino Acids↗
PubMed2002

Functional analysis and molecular model of the human urate transporter/channel, hUAT.

Recombinant protein, designated hUAT, the human homologue of the rat urate transporter/channel (UAT), functions as a highly selective urate channel in lipid bilayers. Functional analysis indicates that hUAT activity, like UAT, is selectively blocked by oxonate from its cytosolic side, whereas pyrazinoate and adenosine selectively block from the channel's extracellular face. Importantly, hUAT is a galectin, a protein with two beta-galactoside binding domains that bind lactose. Lactose significantly increased hUAT open probability but only when added to the channel's extracellular side. This effect on open probability was mimicked by glucose, but not ribose, suggesting a role for extracellular glucose in regulating hUAT channel activity. These functional observations support a four-transmembrane-domain structural model of hUAT, as previously predicted from the primary structure of UAT. hUAT and UAT, however, are not functionally identical: hUAT has a significantly lower single-channel conductance and open probability is voltage independent. These differences suggest that evolutionary changes in specific amino acids in these highly homologous proteins are functionally relevant in defining these biophysical properties.

Adenosine↗