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At least 199 records · Page 11Linked to original sources

Causal transfer function analysis to describe closed loop interactions between cardiovascular and cardiorespiratory variability signals.

Although the concept of transfer function is intrinsically related to an input-output relationship, the traditional and widely used estimation method merges both feedback and feedforward interactions between the two analyzed signals. This limitation may endanger the reliability of transfer function analysis in biological systems characterized by closed loop interactions. In this study, a method for estimating the transfer function between closed loop interacting signals was proposed and validated in the field of cardiovascular and cardiorespiratory variability. The two analyzed signals x and y were described by a bivariate autoregressive model, and the causal transfer function from x to y was estimated after imposing causality by setting to zero the model coefficients representative of the reverse effects from y to x. The method was tested in simulations reproducing linear open and closed loop interactions, showing a better adherence of the causal transfer function to the theoretical curves with respect to the traditional approach in presence of non-negligible reverse effects. It was then applied in ten healthy young subjects to characterize the transfer functions from respiration to heart period (RR interval) and to systolic arterial pressure (SAP), and from SAP to RR interval. In the first two cases, the causal and non-causal transfer function estimates were comparable, indicating that respiration, acting as exogenous signal, sets an open loop relationship upon SAP and RR interval. On the contrary, causal and traditional transfer functions from SAP to RR were significantly different, suggesting the presence of a considerable influence on the opposite causal direction. Thus, the proposed causal approach seems to be appropriate for the estimation of parameters, like the gain and the phase lag from SAP to RR interval, which have a large clinical and physiological relevance.

Adult↗

Functional analysis of pathogenicity genes in a genomics world.

Genome-wide mutational and expression analyses have been performed in yeast and provide a model for large-scale analysis of gene function in filamentous fungi. The recent completion of the Neurospora crassa genome offers a resource for comparative analysis with plant pathogenic filamentous fungi. These advances have important implications for molecular genetic studies of pathogenicity genes.

Fungal Proteins↗

Functional analysis of the Saccharomyces cerevisiae YFR021w/YGR223c/YPL100w ORF family suggests relations to mitochondrial/peroxisomal functions and amino acid signalling pathways.

Saccharomyces cerevisiae YFR021w, YGR223c and YPL100w are paralogous ORFs of unknown function. Phenotypic analysis of overexpression, single-, double- and triple-ORF deletion strains under various growth conditions indicated mitochondria-related functions for all three ORFs. Two-hybrid screens of a yeast genomic library identified potentially interacting proteins for the three ORFs. Among these, the transcriptional activator Rtg3p interacted with both Yfr021wp and Ypl100wp and both ORF single deletions reduced the constitutive expression of the RTG-regulated CIT2 and DLD3 genes and caused typical retrograde response of CIT2 and DLD3 under growth conditions requiring functional mitochondria, indicating that YFR021w and YPL100w are also involved in unidentified mitochondrial functions. Ptr3p, a component of the amino acid sensor Ssy1p/Ptr3p, was also found as a two-hybrid interactant of Yfr021wp. Of the three single-ORF deletions, ypl100w Delta exhibited ptr3 Delta-similar phenotypes. These findings, combined with the fact that RTG-dependent expression is modulated by specific amino acids, suggested possible relations of Yfr021wp and Ypl100wp to amino acid signalling pathways. Under most conditions examined, the effects of the single- and double-ORF deletions indicated that YFR021w, YPL100w and YGR223c are not parts of the same pathway. We found no unique phenotype attributed to the deletion of YGR223c. However, its function interferes with the function of the other two ORFs, as revealed by the effects of double- and triple-ORF deletions.

Amino Acid Sequence↗

ErmineJ: tool for functional analysis of gene expression data sets.

BACKGROUND: It is common for the results of a microarray study to be analyzed in the context of biologically-motivated groups of genes such as pathways or Gene Ontology categories. The most common method for such analysis uses the hypergeometric distribution (or a related technique) to look for "over-representation" of groups among genes selected as being differentially expressed or otherwise of interest based on a gene-by-gene analysis. However, this method suffers from some limitations, and biologist-friendly tools that implement alternatives have not been reported. RESULTS: We introduce ErmineJ, a multiplatform user-friendly stand-alone software tool for the analysis of functionally-relevant sets of genes in the context of microarray gene expression data. ErmineJ implements multiple algorithms for gene set analysis, including over-representation and resampling-based methods that focus on gene scores or correlation of gene expression profiles. In addition to a graphical user interface, ErmineJ has a command line interface and an application programming interface that can be used to automate analyses. The graphical user interface includes tools for creating and modifying gene sets, visualizing the Gene Ontology as a table or tree, and visualizing gene expression data. ErmineJ comes with a complete user manual, and is open-source software licensed under the Gnu Public License. CONCLUSION: The availability of multiple analysis algorithms, together with a rich feature set and simple graphical interface, should make ErmineJ a useful addition to the biologist's informatics toolbox. ErmineJ is available from http://microarray.cu.genome.org.

Animals↗

Functional analysis of the expression of the 3'-phosphoglycerate kinase pgk gene in Aspergillus nidulans.

A functional analysis of the Aspergillus nidulans 3-phosphoglycerate kinase pgk promoter was undertaken using gene fusions to the lacZ gene of Escherichia coli, and introducing these into a beta-galactosidase-deficient strain of A. nidulans. Expression of a particular gene fusion in transformed strains depends upon the site of integration of the vector into the genome, and when specifically targeted to the catabolic quinate dehydrogenase qutE (selective marker) locus is directly proportional to its copy number. The analysis of transformed strains with single copies of pgk promoter deletion--lacZ fusions at the qutE locus identified three constitutive, positively acting sequence elements in the pgk gene. Sequence located between -161 and -120 nucleotides relative to the transcript start site +1, and including an element with a seven-out-of-eight nucleotide match (AAGCAAAT; -131 to -124) to the consensus eukaryotic octamer sequence ATGCAAAT, is essential for expression, and deletion of the complete 41-nucleotide sequence abolishes transcription. Sequence encompassing codons 14 to 183 and including the two introns of pgk contributes approximately one-third of the total activity, and far upstream sequence 5' to position -638 contributes approximately a further one-third total activity. In addition, sequence located -638 to -488 nucleotides, which includes an apparent consensus feature of A. nidulans glycolytic genes, affects carbon source-dependent regulation of expression. This region is required for an approximately 50% increase in pgk expression when A. nidulans is grown on gluconeogenic compared with glycolytic carbon sources.

Aspergillus nidulans↗

Incremental value of the exercise treadmill test in determining the extent of coronary artery disease: a discriminant function analysis.

This study was undertaken to determine whether it was possible to use a multivariate discriminant function analysis to assess the severity of coronary artery disease in patients with angina pectoris. One hundred and forty-three patients diagnosed as having angina pectoris who formed a 'learning group' were subjected to an exercise test on a treadmill using a Bruce protocol. The items of data from the test least likely to be influenced by beta blockade were considered for the analysis along with two discrete variables (the gender and the use of beta blockers). All the patients subsequently underwent coronary angiography and the severity of the coronary artery disease was graded according to a scoring system. In addition, patients in 'learning group' were classified into two 'Groups', (I) those with normal vessels or with disease in one or two of the major arteries, (II) those with disease in the left main stem or in all three major arteries. The multivariate analysis yielded a score based upon 4 factors: (i) gender, (ii) percentage increase in double product at the highest level of exercise achieved, (iii) duration of ST depression in the recovery period and (iv) the summation of the ST depression in the standard electrocardiogram excluding lead aVR. There was a significant overall correlation between the discriminant function score and the coronary artery score for severity of the disease. In addition, it was found that, of patients having discriminant function score below 0, 96% (69/72) were in Group I. The post-test risk of a positive test was 0.005.(ABSTRACT TRUNCATED AT 250 WORDS)

Adrenergic beta-Antagonists↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

[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↗

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↗