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 217 records · Page 12Linked to original sources
PubMed2004

Quantitative functional analysis of protein complexes on surfaces.

A major challenge in cell and molecular physiology research is to understand the mechanisms of biological processes in terms of the interactions, activities and regulation of the underlying proteins. Functional and mechanistic analyses of the large number of proteins that participate in the regulation of cellular processes will require new approaches and techniques for high throughput and multiplexed functional analyses of protein interactions, protein conformational dynamics and protein activity. In this review we focus on the development and application of proteomics and associated technologies for quantitative functional analysis of proteins and their complexes that include: (1) the application of surface plasmon resonance (SPR) imaging for multiplexed, label-free analyses of protein interactions, binding constants for biomolecular interactions and protein activities; and (2) high content analysis of protein motions within functional multiprotein complexes.

Animals↗
PubMed2003

Sequence-function analysis of the K+-selective family of ion channels using a comprehensive alignment and the KcsA channel structure.

Sequence-function analysis of K(+)-selective channels was carried out in the context of the 3.2 A crystal structure of a K(+) channel (KcsA) from Streptomyces lividans (Doyle et al., 1998). The first step was the construction of an alignment of a comprehensive set of K(+)-selective channel sequences forming the putative permeation path. This pathway consists of two transmembrane segments plus an extracellular linker. Included in the alignment are channels from the eight major classes of K(+)-selective channels from a wide variety of species, displaying varied rectification, gating, and activation properties. Segments of the alignment were assigned to structural motifs based on the KcsA structure. The alignment's accuracy was verified by two observations on these motifs: 1), the most variability is shown in the turret region, which functionally is strongly implicated in susceptibility to toxin binding; and 2), the selectivity filter and pore helix are the most highly conserved regions. This alignment combined with the KcsA structure was used to assess whether clusters of contiguous residues linked by hydrophobic or electrostatic interactions in KcsA are conserved in the K(+)-selective channel family. Analysis of sequence conservation patterns in the alignment suggests that a cluster of conserved residues is critical for determining the degree of K(+) selectivity. The alignment also supports the near-universality of the "glycine hinge" mechanism at the center of the inner helix for opening K channels. This mechanism has been suggested by the recent crystallization of a K channel in the open state. Further, the alignment reveals a second highly conserved glycine near the extracellular end of the inner helix, which may be important in minimizing deformation of the extracellular vestibule as the channel opens. These and other sequence-function relationships found in this analysis suggest that much of the permeation path architecture in KcsA is present in most K(+)-selective channels. Because of this finding, the alignment provides a robust starting point for homology modeling of the permeation paths of other K(+)-selective channel classes and elucidation of sequence-function relationships therein. To assay these applications, a homology model of the Shaker A channel permeation path was constructed using the alignment and KcsA as the template, and its structure evaluated in light of established structural criteria.

Bacterial Proteins↗
PubMed1998

Handedness identification from intertubercular sulcus of the humerus by discriminant function analysis.

The accurate determination of skeletal handedness is a critical requirement in physical anthropology and forensic science. To differentiate handedness, discriminant function analysis is applied using the parameters of right and left intertubercular sulci. A total of 200 matched unpaired adult humeri (100 right and 100 left), collected from the Department of Anatomy, were used to measure four parameters of the intertubercular sulcus namely, width (X1), depth (X2), angle of medial wall (X3) and angle of lateral wall (X4) and to note the presence of supratubercular ridge of Meyer (X5). The discriminant function obtained with the significant variables, angle of medial wall (X3), angle of lateral wall (X4) and presence of the supratubercular Meyer (X5) is: Y = 0.093X3 + 0.056X4 + 0.775X5 - 13.46. The accuracy of correct classification using the discriminant function is 89% which is the best starting point for handedness determination approach. The methodology of using discriminant function can be crucial for medicolegal jurisprudence.

Adult↗
PubMed1999

Disruption and basic functional analysis of six novel ORFs of chromosome XV from Saccharomyces cerevisiae.

We report the disruption and functional analysis of six open reading frames (ORFs) from chromosome XV, namely YOL155c, YOL154w, YOL119c, YOL118c, YOR301w and YOR306c, in FY1679 and CEN.PK2 backgrounds. We constructed replacement cassettes and cloned each ORF into the pRS416 centromeric plasmid. No obvious phenotype was observed for the corresponding deleted strains with respect to growth, mating or sporulation. YOL155c encodes a protein with a secretion signal and putative GPI-anchor recognition site and is possibly a cell wall protein, although its deletion did not present morphogenetic defects under any of the conditions tested. Although YOL119c and YOR306c are members of the monocarboxylate permease family, the growth of the double disruptant in acetate, lactate and pyruvate was similar to that of the parental strains.

Amino Acid Sequence↗
PubMed2006

Functional analysis of voice using simultaneous high-speed imaging and acoustic recordings.

We present a comprehensive, functional analysis of clinical voice data derived from both high-speed digital imaging (HSDI) of the larynx and simultaneously acquired acoustic recordings. The goals of this study are to: (1) correlate dynamic characteristics of the vocal folds derived from direct laryngeal imaging with indirectly acquired acoustic measurements; (2) define the advantages of using a combined imaging/acoustic approach for the analysis of voice condition; and (3) identify new quantitative measures to evaluate the regularity of the vocal fold vibration and the complexity of the vocal output -- these measures will be key to successful diagnosis of vocal abnormalities. Image- and acoustic-based analyses are performed using an analytic phase plot approach previously introduced by our group (referred to as 'Nyquist' plot). Fast Fourier Transform (FFT) spectral analyses are performed on the same data for a comparison. Clinical HSDI and acoustic recordings from subjects having normal and specific voice pathologies, including muscular tension dysphonia (MTD) and recurrent respiratory papillomatosis (RRP) were analyzed using the Nyquist plot approach. The results of these analyses show that a combined imaging/acoustic analysis approach provides better characterization of the vibratory behavior of the vocal folds as it correlates with vocal output and pathology.

Humans↗
PubMed1993

Functional analysis of the human neurofilament light chain gene promoter.

We have carried out a structural and functional analysis on the human NF-L (H-NF-L) gene. It contains a methylation-free island, spanning the 5' flanking sequences and the first exon and a number of neuronal-specific DNase I hypersensitive sites have been identified in the upstream region as well as within the body of the gene. Analysis in cell lines and transgenic mice using a combination of these sites has revealed the presence of a conserved element(s) between -300bp and -190bp which is required for neuronal-specific expression.

Animals↗
PubMed2005

Functional analysis of CaIPT1, a sphingolipid biosynthetic gene involved in multidrug resistance and morphogenesis of Candida albicans.

In the present study we describe the isolation and functional analysis of a sphingolipid biosynthetic gene, IPT1, of Candida albicans. The functional consequence of the disruption of both alleles of IPT1 was confirmed by mass analysis of its sphingolipid composition. The disruption of both alleles or a single allele of IPT1 did not lead to any change in growth phenotype or total sphingolipid, ergosterol, or phospholipid content of the mutant cells. The loss of mannosyl diinositol diphosphoceramide [M(IP)(2)C] in the ipt1 disruptant, however, resulted in increased sensitivity to drugs like 4-nitroquinoline oxide, terbinafine, o-phenanthroline, fluconazole, itraconazole, and ketoconazole. The increase in drug susceptibilities of ipt1 cells was linked to an altered sphingolipid composition, which appeared to be due to the impaired functionality of Cdr1p, a major drug efflux pump of C. albicans that belongs to the ATP binding cassette superfamily. Our confocal and Western blotting results demonstrated that surface localization of green fluorescent protein-tagged Cdr1p was affected in ipt1 disruptant cells. Poor surface localization of Cdr1p resulted in an impaired ability to efflux fluconazole and rhodamine 6G. The effect of mannosyl inositol phosphoceramide accumulation in the ipt1 mutant and the absence of M(IP)(2)C from the ipt1 mutant on the efflux of drug substrates was very selective. The efflux of methotrexate, a specific substrate of CaMdr1p, another major efflux pump of major facilitator superfamily, remained unaffected in ipt1 mutant cells. Interestingly, changes in sphingolipid composition affected the ability of mutant cells to form proper hyphae in various media. Taken together, our results demonstrate that an altered composition of sphingolipid, which is among the major constituents of membrane rafts, affects the drug susceptibilities and morphogenesis of C. albicans.

Antifungal Agents↗
PubMed2000

A functional analysis of massive knee replacement after extra-articular resections of primary bone tumors.

We performed a functional analysis of massive knee replacements after extra-articular resection of primary bone tumors. Patients did not score as highly on the Musculoskeletal Tumour Society Score and Knee Society Score (P < or = .01) as patients who had undergone intra-articular resection. Lower scores were achieved for emotional acceptance (P < or = .01), functional restriction (P < or = .05), walking distance (P < or = .05), and managing stairs (P < or = .05). These patients had a significantly greater extension lag (P < or = .01) and greater fixed flexion (P < or = .05). This functional deficit is primarily due to a compromised extensor mechanism inherent in the type of surgical resection necessary to achieve adequate removal of the tumor.

Adolescent↗
PubMed1989

The use of functional analysis of the ribosome as a tool to determine archaebacterial phylogeny.

Forty different antibiotics with diverse kingdom and functional specificities were used to measure the functional characteristics of the archaebacterial translation apparatus. The resulting inhibitory curves, which are characteristic of the cell-free system analyzed, were transformed into quantitative values that were used to cluster the different archaebacteria analyzed. This cluster resembles the phylogenetic tree generated by 16S rRNA sequence comparisons. These results strongly suggest that functional analysis of an appropriate evolutionary clock, such as the ribosome, is of intrinsic phylogenetic value. More importantly, they indicate that the study of the nexus between genotypic and phenotypic (functional) information may shed considerable light on the evolution of the protein synthetic machinery.

Archaea↗
PubMed2004

Functional analysis of Cobra Venom Factor/human C3 chimeras transiently expressed in mammalian cells.

The complement activating venom component Cobra Venom Factor (CVF), a functional and structural homologue of the human complement component C3, forms a stable CVF-dependent C3 convertase complex, which, in contrast to C3-dependent convertase effects continuous activation of the complement and, thereby, decomplementation. In order to elucidate the mechanism underlying the enhanced activity of CVF compared to human C3, we generated two CVF/C3 chimeras and established different affinity-based assay systems for functional analysis of these constructs. To allow for convenient expression and subsequent functional characterisation, the CVF/C3 chimeras as well as CVF and C3 were transiently expressed in mammalian cells. Problems due to the low concentration of the recombinant proteins in the supernatants of transient expressions were circumvented by fusion to peptide tags enabling their efficient immobilisation onto suitable surfaces and subsequent characterisation. In an alternative approach monoclonal antibody fragments generated from a semisynthetic phage display scFv library were employed for concentrating the recombinant proteins by immunoprecipitation. Utilising both approaches all transiently expressed proteins could be characterised for their complement consumption activity. The data obtained with the CVF/C3 chimeras demonstrate that the increased stability of the CVFBb complex is independent of the domains in CVF corresponding to binding sites of factor B and H and the cleavage sites of factor I in the human C3 molecule.

Amino Acid Sequence↗
PubMed1999

Functional analysis of the human D5 dopamine receptor missense and nonsense variants: differences in dopamine binding affinities.

The functional analysis of expressed human gene variants is important in the study of genetic susceptibility to diseases, pharmacogenetic traits and for the investigation of the human genetic diversity at the molecular level. We have performed the analysis of sequence polymorphisms in the human D5 dopamine receptor gene (DRD5) predicting missense and nonsense amino acid changes in the receptor protein. The amino acid substitutions in the human D5 dopamine receptor are: Leu88 to Phe in the putative second transmembrane domain, Ala269 to Val in the third intracellular and Pro330 to Gln in the third extracellular loops, Asn351 to Asp in the seventh transmembrane and Ser453 to Cys in the C-terminal domains and Cys335 to Stop in the third extracellular loop. The two amino acid substitutions in the transmembrane domains had an effect on agonist binding to the human D5 dopamine receptor. Asn351 to Asp resulted in an approximately 10-fold decrease in dopamine and threefold decrease in R(+)-SKF-38393 binding affinities. Leu88 to Phe resulted in a small increase in dopamine binding affinity. Antagonist binding affinities were mostly unaffected by the amino acid substitutions with the exception of Leu88 to Phe, which showed small reductions in binding affinities of SCH-23390 and risperidone. The existence of functionally different variants of the human dopamine receptors might have phenotypic consequences given their importance in central nervous system physiology and pharmacology.

2,3,4,5-Tetrahydro-7,8-dihydroxy-1-phenyl-1H-3-ben↗
PubMed1990

[Functional analysis of mutations on murine chromosome 17 using tertiary trisomy].

Analysis of the functional nature of mutations can be based on their manifestation in organisms with a deletion or a duplication of a particular chromosome segment. With the use of reciprocal translocation T(16;17)43H it is feasible to produce mice with tertiary trisomy for proximal region of chromosome 17. The mutations on chromosome 17 we tested included brachyury (T), hairpin tail (Thp), kinky (Fuki), quaking (qk), tufted (tf), as well as tct (t-complex tail interaction) and tcl (t complex lethal), that are specific for t haplotypes. The set of dominant and recessive mutations was assigned to two groups, one obligatory manifesting itself in the phenotype independently of the number of normal alleles in di- and trisomics, and the other facultative, phenotypically manifesting itself, depending upon the dosage of mutant alleles. A model was derived from analysis of the interaction of the T and Thp mutations with t haplotypes which is to explain the morphogenetic effects of the mutations observed in mice of different genotypes. The tir gene is postulated to reside on chromosome 17 within its framework. It is suggested that the gene dosage ratio at the tir and tct loci determines tail length.

Alleles↗
PubMed1991

Functional analysis of mutations of murine chromosome 17 with the use of tertiary trisomy.

Analysis of the functional nature of mutations can be based on comparisons of their manifestation in organisms with a deletion or duplication of a particular chromosome segment. With the use of reciprocal translocation T(16;17)43H, it is feasible to produce mice with tertiary trisomy of the proximal region of chromosome 17. The mutations on chromosome 17 we tested included brachyury (T), hairpin tail (Thp), kinky (Fuki), quaking (qk), tufted (tf), as well as tct (t complex tail interaction), and tcl (t complex lethal) that are specific to t haplotypes. The set of dominant and recessive mutations was assigned to two groups: one obligatory, manifesting itself in the phenotype independently of the number of normal alleles in di- and trisomics, and the other facultative, phenotypically manifesting itself depending upon the dosage of mutant alleles. A model was derived from analysis of the interaction of the T and Thp mutations with t haplotypes. It seeks to explain the morphogenetic effects of the mutations observed in mice of different genotypes. The tir gene is postulated to reside on chromosome 17 within its framework. It is suggested that the gene dosage ratio at the tir and tct loci determines tail length.

Alleles↗
PubMed1996

Functional analysis of grafts from living donors. Implications for the treatment of older recipients.

OBJECTIVE: Living-related liver transplantation (LRLT) has established efficacy in children. In a larger recipient, LRLT requires the use of a small graft because of limits on the donor hepatectomy. SUMMARY BACKGROUND DATA: The minimum graft weight required for successful transplantation has not been well established, although a characteristic pattern of graft dysfunction has been observed in our patients who receive small grafts. The authors present a clinicopathologic study of small liver grafts obtained from living donors. METHODS: Clinical and histologic data were reviewed for 25 patients receiving LRLT. In five older recipients (small group), the graft represented 50% or less of expected liver weight, whereas in 20 others (large group), the graft represented at least 60% of expected liver weight. A retrospective analysis of graft function was conducted by analyzing clinical parameters and histology. RESULTS: In the small group, 2 of 5 grafts (40%) were lost due to poor function, leading to one patient death (20% mortality), whereas in the large group, 2 of 20 grafts (10%) were lost due to arterial thrombosis without patient mortality. Early ischemic damage related to transplant was comparable with aspartate aminotransferase 203 +/- 23 (small group) and 290 +/- 120 (large group) at 24 hours (p = not significant). Early function was significantly decreased in the small group, with prothrombin time 18.2 +/- 2.2 seconds versus 14.8 +/- 1.6 seconds (large group) on day 3 (p = 0.034). All small group patients developed cholestasis with significantly increased total bilirubin levels at day 7 (16 +/- 5.2 mg% vs. 3.7 +/- 2.7 mg%; p = 0.021) and day 14 (12.0 +/- 7.4 vs. 1.8 +/- 0.7; p = 0.021) compared with the large group. Protocol biopsies in the small group revealed a diffuse ischemic pattern with cellular ballooning on day 7, which progressed to cholestasis in subsequent biopsies. Large group biopsies showed minimal ischemic changes. Three small group patients recovered with normal liver function by 12 weeks. CONCLUSIONS: Clinical recovery after a small-for-size transplant is characterized by significant functional impairment associated with paradoxical histologic changes typical of ischemia. These changes apparently are due to graft injury, which can only be the result of small graft size. These findings have significant implications for the extension of LRLT to adults.

Adolescent↗
PubMed2006

Characterization and functional analysis of a pollen-specific gene st901 in Solanum tuberosum.

A pollen-specific gene, sb401, which was isolated from a cDNA library of in vitro geminated pollen of the diploid potato species Solanum berthaultii, belongs to the class of genes expressed late during pollen development. Using sb401 as a probe, a pollen-specific gene st901 was isolated from the genomic library of a potato species Solanum tuberosum cv. Desiree. Sequencing and RT-PCR analysis showed that the st901 genomic gene is 2,889 bp long, contains three exons and two introns, and encodes a putative polypeptide of 217 residues. The predicted protein sequence contains four imperfect repeated motifs of V-V-E-K-K-N/E-E; the core sequence of the repeats (K-K-N/E-E) resembles a microtubule-binding domain of the microtubule-associated protein MAP1B from mouse. The examination of a promoter-reporter construct in transgenic potato plants revealed that the st901 is expressed exclusively in mature pollen grains, which is consistent with the results of Northern blot and RT-PCR. For analysis of the function of st901, transgenic plants harboring antisense copies of st901 cDNA driven by a native st901 promoter were generated. Suppression of st901 gene in potato resulted in aberrant pollen at maturation and pollen viability of transgenic plants ranged from 4.4 to 14.8%, while that of control plants were more than 90%. These results strongly suggest that st901 has an essential role in pollen development.

Amino Acid Sequence↗
PubMed2005

The effects of reinforcement magnitude on functional analysis outcomes.

The duration or magnitude of reinforcement has varied and often appears to have been selected arbitrarily in functional analysis research. Few studies have evaluated the effects of reinforcement magnitude on problem behavior, even though basic findings indicate that this parameter may affect response rates during functional analyses. In the current study, 6 children with autism or developmental disabilities who engaged in severe problem behavior were exposed to three separate functional analyses, each of which varied in reinforcement magnitude. Results of these functional analyses were compared to determine if a particular reinforcement magnitude was associated with the most conclusive outcomes. In most cases, the same conclusion about the functions of problem behavior was drawn regardless of the reinforcement magnitude.

Autistic Disorder↗
PubMed1995

Functional analysis of linker insertions and point mutations in the alpha-Amy2/54 GA-regulated promoter.

Functional analysis of a gibberellin-regulated wheat alpha-amylase promoter, alpha-Amy2/54, has indicated that three regions were essential for expression. By studying the ability of mutant promoters, containing a randomly inserted 22 bp excision linker, to direct expression in oat aleurone protoplasts we have refined the positions and extents of these three cis elements and also demonstrated the presence of two additional elements. By converting the linker insertions to either single base point mutations or deletions using the class IIS restriction endonuclease BsmI we have shown that nucleotides -119 and -109 within the GARE -121GTAACAGAGTCTGG-108 and nucleotide -152 within the proposed element -156GATTGACTTGACC-144 are essential for high level expression from this promoter.

Base Sequence↗
PubMed1992

Phenotypic and functional analysis of lamina propria mononuclear cells from colonoscopic biopsy specimens in patients with ulcerative colitis.

Phenotypic and functional analysis was performed with lamina propria mononuclear cells (LPMCs) isolated from colonoscopic biopsies in 27 patients with ulcerative colitis (UC). The proportion of T lymphocytes displaying HLA-DR antigens, interleukin 2 (IL-2) receptor, and transferrin receptor was greater in active UC than in control diseases. When LPMCs were cultured with IL-2 or phytohemagglutinin for 72 h, there were no significant differences in the proportion of cells bearing these activation markers between active UC and controls. The proportion of CD56+ cells and lymphokine-activated killer (LAK) cell activity was lower in LPMCs from active UC than in control cells, and depletion of CD56+ cells from control lamina propria cells essentially eliminated LAK cell activity. Mucosal T lymphocytes may be activated in vivo during active inflammation in UC, and lower levels of intestinal LAK cell activity may be related to the decrease of CD56+ cells under these conditions.

Adolescent↗