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 379 records · Page 21Linked to original sources
PubMed1995

Sequence and functional analysis of a 7.2 kb DNA fragment containing four open reading frames located between RPB5 and CDC28 on the right arm of chromosome II.

In a coordinated approach, several laboratories sequenced Saccharomyces cerevisiae chromosome II during the European BRIDGE project. Here we report on the sequence and functional analysis of a 7217 bp fragment located on the right arm of chromosome II between RPB5 and CDC28. The fragment contains four open reading frames probably encoding proteins of 79.2 kDa (corresponding gene YBR156c), 12.1 kDa (YBR157c), 62.7 kDa (YBR158w) and 38.7 kDa (YBR159w). All four open reading frames encode new proteins, as concluded from data base searches. The respective genes were destroyed by gene replacement in one allele of diploid cells. After sporulation and tetrad analysis, the resulting mutant haploid strains were investigated. No phenotype with respect to spore germination, viability, carbohydrate utilization, and growth was found for YBR157c, encoding the smallest open reading frame investigated. Gene replacement within the YBR156c gene encoding a highly basic and possibly nuclear located protein was lethal. Ybr158 revealed similarities to the Grrl (Cat80) protein with respect to the leucine-rich region. Cells harboring a mutation in the YBR158w gene showed strongly reduced growth as compared to the wild-type cells. The protein predicted from YBR159w shared 33% identical amino acid residues with the human estradiol 17-beta-hydroxysterol dehydrogenase 3. Haploid ybr159c mutants were only able to grow at reduced temperatures, but even under these conditions the mutants grew slower than wild-type strains.

Amino Acid Sequence↗
PubMed2006

Comparative structure-function analysis of cytolethal distending toxins.

Cytolethal distending toxins (CDTs) constitute a family of bacterial proteins that enter eukaryotic cells with genotoxic activity leading to cell cycle arrest and apoptosis. CDTs are widespread, having been found in a variety of Gram-negative pathogens with a broad tissue tropism. The recently determined crystal structure of the Haemophilus ducreyi CDT provides a powerful starting point for analysis of the structure and function in this toxin family. In this study, we apply comparative modeling and structural analysis to extend the experimental structural information to multiple CDT toxins from a diverse species. Analysis of structurally and functionally important residues in the active subunit, CdtB, and putative cell delivery elements, CdtA and CdtC, begins to establish the fundamental, mechanistic elements of this unique holotoxin. The results reveal that key structural features with important functional consequences are highly conserved across different CDTs, providing a blueprint for directed examination of functional hypotheses in a variety of pathogenic contexts.

Amino Acid Sequence↗
PubMed1998

Structure and function analysis of Pseudomonas plant cell wall hydrolases.

Hydrolysis of the major structural polysaccharides of plant cell walls by the aerobic soil bacterium Pseudomonas fluorescens subsp. cellulosa is attributable to the production of multiple extracellular cellulase and hemicellulase enzymes, which are the products of distinct genes belonging to multigene families. Cloning and sequencing of individual genes, coupled with gene sectioning and functional analysis of the encoded proteins have provided a detailed picture of structure/function relationships and have established the cellulase-hemicellulase system of P. fluorescens subsp. cellulosa as a model for the plant cell wall degrading enzyme systems of aerobic cellulolytic bacteria. Cellulose- and xylan-degrading enzymes produced by the pseudomonad are typically modular in structure and contain catalytic and noncatalytic domains joined together by serine-rich linker sequences. The cellulases include a cellodextrinase; a beta-glucan glucohydrolase and multiple endoglucanases, containing catalytic domains belonging to glycosyl hydrolase families 5, 9, and 45; and cellulose-binding domains of families II and X, both of which are present in each enzyme. Endo-acting xylanases, with catalytic domains belonging to families 10 and 11, and accessory xylan-degrading enzymes produced by P. fluorescens subsp. cellulosa contain cellulose-binding domains of families II, X, and XI, which act by promoting close contact between the catalytic domain of the enzyme and its target substrate. A domain homologous with NodB from rhizobia, present in one xylanase, functions as a deacetylase. Mananase, arabinanase, and galactanase produced by the pseudomonad are single domain enzymes. Crystallographic studies, coupled with detailed kinetic analysis of mutant forms of the enzyme in which key residues have been altered by site-directed mutagenesis, have shown that xylanase A (family 10) has 8-fold alpha/beta barrel architecture, an extended substrate-binding cleft containing at least six xylose-binding pockets and a calcium-binding site that protects the enzyme from thermal inactivation, thermal unfolding, and attack by proteinases. Kinetic studies of mutant and wild-type forms of a mannanase and a galactanase from P. fluorescens subsp. cellulosa have enabled the catalytic mechanisms and key catalytic residues of these enzymes to be identified.

Amino Acid Sequence↗
PubMed2002

Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamily.

2',3' Cyclic nucleotide phosphodiesterases are enzymes that catalyze at least two distinct steps in the splicing of tRNA introns in eukaryotes. Recently, the biochemistry and structure of these enzymes, from yeast and the plant Arabidopsis thaliana, have been extensively studied. They were found to share a common active site, characterized by two conserved histidines, with the bacterial tRNA-ligating enzyme LigT and the vertebrate myelin-associated 2',3' phosphodiesterases. Using sensitive sequence profile analysis methods, we show that these enzymes define a large superfamily of predicted phosphoesterases with two conserved histidines (hence 2H phosphoesterase superfamily). We identify several new families of 2H phosphoesterases and present a complete evolutionary classification of this superfamily. We also carry out a structure- function analysis of these proteins and present evidence for diverse interactions for different families, within this superfamily, with RNA substrates and protein partners. In particular, we show that eukaryotes contain two ancient families of these proteins that might be involved in RNA processing, transcriptional co-activation and post-transcriptional gene silencing. Another eukaryotic family restricted to vertebrates and insects is combined with UBA and SH3 domains suggesting a role in signal transduction. We detect these phosphoesterase modules in polyproteins of certain retroviruses, rotaviruses and coronaviruses, where they could function in capping and processing of viral RNAs. Furthermore, we present evidence for multiple families of 2H phosphoesterases in bacteria, which might be involved in the processing of small molecules with the 2',3' cyclic phosphoester linkages. The evolutionary analysis suggests that the 2H domain emerged through a duplication of a simple structural unit containing a single catalytic histidine prior to the last common ancestor of all life forms. Initially, this domain appears to have been involved in RNA processing and it appears to have been recruited to perform various other functions in later stages of evolution.

2',3'-Cyclic-Nucleotide Phosphodiesterases↗
PubMed1988

Structure-function analysis of murine interferon-alpha: antiviral properties of novel hybrid interferons.

As described earlier the protein products of the murine interferon (IFN) genes MuIFN-alpha 1, -alpha 2, and -alpha 4 differ in their antiviral activity on hamster (CHO) and mouse (L929) cells. For structure-function analysis, hybrids were prepared between the three genes using common restriction enzyme sites. Natural and hybrid genes were transiently expressed in monkey COS cells. Under the conditions used IFN constituted 20-30% of the total amount of secreted proteins. Using a panel of hybrids either between alpha 1 and alpha 2 or between alpha 1, alpha 2, and alpha 4, the amino-terminal region of the protein, from amino acids 10 to 58, was found to determine its antiviral activity on hamster cells. On mouse cells, the antiviral activities of hybrids between alpha 4 and either alpha 1 or alpha 2 were compared. The high activity of alpha 4 (five to ten times that of alpha 1 or alpha 2) was not transmitted to hybrids having the amino-terminal part of alpha 4, but coincided with the presence of the alpha 4 carboxy-terminal region in all but one hybrid construct. The deletion of five amino acids (positions 103-107) located in this region of alpha 4 did not affect antiviral activity when introduced into MuIFN-alpha 2 and a MuIFN-alpha 42 hybrid by site-directed mutagenesis.

Animals↗
PubMed1985

Functional analysis of tight junction organization.

The functional basis of tight junction design has been examined from the point of view that this rate-limiting barrier to paracellular transport is a multicompartment system. Review of the osmotic sensitivity of these structures points to the need for this sort of analysis for meaningful correlation of structure and function under a range of conditions. A similar conclusion is drawn with respect to results from voltage-clamping protocols where reversal of spontaneous transmural potential difference elicits parallel changes in both structure and function in much the same way as does reversal of naturally occurring osmotic gradients. In each case, it becomes necessary to regard the junction as a functionally polarized structure to account for observations of its rectifying properties. Lastly, the details of experimentally-induced junction deformation are examined in light of current theories of its organization; arguments are presented in favor of the view that the primary components of intramembranous organization (as viewed with freeze-fracture techniques) are lipidic rather than proteinaceous.

Animals↗
PubMed1997

A system for functional analysis of Ebola virus glycoprotein.

Ebola virus causes hemorrhagic fever in humans and nonhuman primates, resulting in mortality rates of up to 90%. Studies of this virus have been hampered by its extraordinary pathogenicity, which requires biosafety level 4 containment. To circumvent this problem, we developed a novel complementation system for functional analysis of Ebola virus glycoproteins. It relies on a recombinant vesicular stomatitis virus (VSV) that contains the green fluorescent protein gene instead of the receptor-binding G protein gene (VSVDeltaG*). Herein we show that Ebola Reston virus glycoprotein (ResGP) is efficiently incorporated into VSV particles. This recombinant VSV with integrated ResGP (VSVDeltaG*-ResGP) infected primate cells more efficiently than any of the other mammalian or avian cells examined, in a manner consistent with the host range tropism of Ebola virus, whereas VSVDeltaG* complemented with VSV G protein (VSVDeltaG*-G) efficiently infected the majority of the cells tested. We also tested the utility of this system for investigating the cellular receptors for Ebola virus. Chemical modification of cells to alter their surface proteins markedly reduced their susceptibility to VSVDeltaG*-ResGP but not to VSVDeltaG*-G. These findings suggest that cell surface glycoproteins with N-linked oligosaccharide chains contribute to the entry of Ebola viruses, presumably acting as a specific receptor and/or cofactor for virus entry. Thus, our VSV system should be useful for investigating the functions of glycoproteins from highly pathogenic viruses or those incapable of being cultured in vitro.

Animals↗
PubMed1983

Psychotic and neurotic depression: discriminant function analysis and five-year outcome.

A consecutive series of 94 patients recently admitted to hospital from a defined catchment area and diagnosed as having a depressive illness were examined using standardized techniques for eliciting mental state, etc. The overlap between psychotic and neurotic diagnoses was 8.5% on discriminant function analysis of mental state items. A sub-sample of 71 patients was given a comprehensive postal and case record follow-up 5 years later. When patients developing organic and other complicating illnesses were excluded, those suffering from psychotic depression showed a significantly poorer outcome, as defined by relapse and required lengths of hospital care, than those diagnosed as suffering from neurotic depression.

Adult↗
PubMed1997

Functional analysis of paired box missense mutations in the PAX6 gene.

Mutations in the human PAX6 gene produce various phenotypes, including aniridia, Peters' anomaly, autosomal dominant keratitis and familial foveal dysplasia. The various phenotypes may arise from different mutations in the same gene. To test this theory, we performed a functional analysis of two missense mutations in the paired domain: the R26G mutation, previously reported in a case of Peters' anomaly, and an unreported I87R mutation, which we identified in a patient with aniridia. While both the R26 and the I87 positions are conserved in the paired boxes of all known PAX genes, X-ray crystallography has shown that only R26 makes contact with DNA. We showed that the R26G mutant failed to bind a subset of paired domain binding sites but, surprisingly, bound other sites and successfully transactivated promoters containing those sites. In contrast, the I87R mutant had lost the ability to bind DNA at all tested sites and failed to transactivate promoters. Our data support the haploid-insufficiency hypothesis of aniridia, and the hypothesis that R26G is a hypomorphic allele.

3T3 Cells↗
PubMed1980

[Functional analysis of depressive states: integration of cognitive and behavioral contributions (author's transl)].

The article provides a review of the main contributions both of behaviorally--and cognitively--oriented litterature on depressive states and depressive behaviors. These various data are organised so as to form into a tool for the functional analysis of depression: symptoms--structures--releasing factors--mechanisms--maintaining and aggravating factors. Synthetic tables at the end of the article constitute a first attempt at a clinical report allowing the pratician to evaluate the contributions--as well as the limits--of a behavioral approach of the depression phenomenom.

Behavior↗
PubMed1989

Transient expression of the angiotensin II receptor: a rapid and functional analysis of a calcium-mobilizing seven-transmembrane domain receptor in COS-7 cells.

The mas oncogene/angiotensin II receptor was subcloned into a mammalian expression vector pCDM8 and used to transiently transfect monkey kidney derived COS-7 cells. As a result, the mas transfected COS-7 cells expressed a functional angiotensin II receptor capable of transducing an increase in intracellular Ca2+ following stimulation with angiotensin II. The angiotensin II stimulated changes in Ca2+ could be measured 24 hours after transfection in both a fluorimeter and a fluorescence activated cell sorter. These results describe a rapid method for the functional analysis of the 7-transmembrane domain receptor genes.

Angiotensin II↗
PubMed1999

Characterization and functional analysis of Arabidopsis TFIIA reveal that the evolutionarily unconserved region of the large subunit has a transcription activation domain.

TFIIA has initially been identified as a component of transcription initiation complex of RNA polymerase II. Its role in transcription has been controversial. In this paper, we report the characterization and functional analysis of both the Arabidopsis TFIIA large and small subunits. Sequence analysis revealed that Arabidopsis TFIIA is structurally more related to animal than to yeast counterparts. Arabidopsis has at least two genes for the large subunit and one for the small subunit. Both types of genes are constitutively transcribed in various plant organs. The proteins encoded by the cDNA interact each other in yeast 2-hybrid system. Only the N-terminal part of the large subunit is necessary for the interaction with the small subunit. Recombinant Arabidopsis TFIIA polypeptides bind to TBP-DNA complex in gel shift assays. The large subunit of TFIIA can stimulate transcription in yeast and in plant cells when fused to a DNA-binding domain binding to cis sequences upstream of a minimal promoter. This trans-activating activity is localized to a 35 amino acid segment within the evolutionarily unconserved central region.

Amino Acid Sequence↗
PubMed1991

Controlling extremely dangerous aggressive outbursts when functional analysis fails.

This article describes and illustrates a treatment program aimed at addressing intermittent extremely dangerous aggressive behavior in an 11-year-old girl who was blind, multiply handicapped, and profoundly mentally retarded. In the month preceding treatment she had injured a peer, a paid careprovider, and her mother. Functional analysis produced no clear antecedents to aggression. Punishment was used to introduce a superordinate contingency. Differential reinforcement of alternative behavior combined with contingent restraint reduced, then eliminated aggression. Follow-up at an age equivalent of 4 years, 6 months indicated a continued absence of aggression. Results are discussed in regards to the balance between research methodology, agency policy, right to effective treatment, and social validity.

Aggression↗
PubMed2005

[Cloning and functional analysis of the stable plasmid pBMB175 in Bacillus thuringiensis subsp. tenebrionis strains YBT-1765].

A 15.2 kb plasmid pBMB175 from Bacillus thuringiensis subsp. tenebrionis strains YBT-1765 was cloned and the restriction map was constructed. The mini-replicating region of pBMB175 was located in a 1151 bp fragment by functional analysis. The sequence of a 4152 bp fragment which contained the mini-replicating region was analyzed and results showed that the fragment had three potential open reading frames (ORF1, ORF2 and ORF3). Sequence comparison and homology search revealed that ORF1 (767AA) has 20% approximately 30% similarity to UvrD-helicase, RecD and RecB family proteins; no homology was found between ORF2 (149AA) and other known proteins; ORF3 shared 34% identification to a potential protein (ORF7) in pGI3. Deletion and sequence analysis presumed that the protein encoded by ORF2 maybe a new replication protein. Above all, pBMB175 likely belongs to a new plasmid family with a new replicon. The recombinant plasmid harboring the mini-replicating region is very stable, even after growth for more than 40 generations without selection, so it might be used as a cloning and expression vector.

Bacillus thuringiensis↗
PubMed2005

Functional analysis of the baculovirus host range gene, hrf-1.

The hrf-1 gene from Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV) prevents translation arrest and promotes Autographa californica multiple nucleopolyhedrovirus (AcMNPV) replication in IPLB-Ld652Y cells (Ld652Y), a non-permissive L. dispar cell line. There are no motifs in the predicted protein sequence to suggest how it might function and the only homolog identified is encoded by another baculovirus, Orgyia pseudotsugata multiple nucleopolyhedrovirus (OpMNPV). In this study, we report a functional analysis of the hrf-1 protein. AcMNPV bearing carboxy- or amino-terminally truncation hrf-1, and hrf-1 mutated by two-amino acid insertions did not replicate Ld652Y cells. Neither OpMNPV hrf-1 nor an OpMNPV/LdMNPV chimeric hrf-1 supported AcMNPV replication. Mutations in a highly acidic domain of hrf-1, in which aspartic acid residues were replaced with alanine, had varied effects on hrf-1 function. They had no effect, abolished hrf-1 function completely, or partially supported protein synthesis in infected Ld652Y cells. A slight increase in protein synthesis was achieved by increasing the expression of hrf-1 acidic domain mutant proteins. Together, these results indicate a critical role for hrf-1 structure and suggest a functional role for the acidic domain.

Animals↗
PubMed1999

Structural and functional analysis of the rat metallothionein III genomic locus.

Metallothionein III (MT III) has been reported to suppress neuronal growth in a rat in vitro model system. The protein and its specific mRNA are detected predominantly in the brain, differentiating MT III from the well-characterised archetypal metallothioneins. Isolation, sequencing and functional analysis of the rat MT III genomic locus indicated that, although the organisation of the gene was conserved between MT III and the more conventional metallothioneins, the 5' flanking region of the MT III gene was distinct. Within this region, a number of putative regulatory elements were identified, including the metal regulatory elements (MREs) characteristic of metallothionein promoters. However, despite their conservation in sequence with active elements, the MREs of MT III were unresponsive to zinc. A 'silencing element' was revealed within a 250 bp section of the MT III promoter which suppressed gene expression in two brain cell lines. The operation of this silencing region in conjunction with the inactive MREs may explain the distinct expression profile observed for MT III within the central nervous system and during neuronal development.

Animals↗
PubMed1985

Functional analysis of fractionated Drosophila Kc cell tRNA gene transcription components.

We have previously described the partial purification of RNA polymerase III transcription components from Drosophila Kc cell extracts (Burke, D. J., Schaack, J., Sharp, S., and Söll, D. (1983) J. Biol. Chem. 258, 15224-15231). Here we report further physical and functional analysis of the two transcription-required fractions designated as factors B and C. Using stable complex formation-competition experiments with ordered addition of these transcription components, we have shown that factor C associates rapidly with the tRNA gene, but will not form a stable complex with the DNA in the absence of factor B. Reconstitution experiments of the individual Drosophila Kc cell factors with those from human HeLa cells demonstrated that the HeLa factor B, combined with Kc factor C, can form active transcription complexes. These now exhibit a property of the Drosophila system, a strong dependence on sequences in the 5'-flanking regions of tRNA genes. However, the Kc factor B (which has an apparent molecular weight of 260,000 as judged by gel filtration analysis) is not compatible with the HeLa factor C. These results, together with the isolation of a large complex containing all necessary transcription components, emphasize the importance of the interaction of these components for both stable complex formation and transcription initiation.

Animals↗