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At least 631 records · Page 35Linked to original sources
PubMed1996

Functional analysis of the DNA-stimulated ATPase domain of yeast SWI2/SNF2.

The yeast SWI2/SNF2 polypeptide is a subunit of the SWI/SNF protein complex that is required for many transcriptional activators to function in a chromatin context. SWI2 is believed to be the founding member of a new subfamily of DNA-stimulated ATPases/DNA helicases that includes proteins that function in DNA repair (RAD5, RAD16, ERCC6), recombination (RAD54), transcription (MOT1, ISWI, brm, BRG1, hBRM) and cell cycle control (STH1). We have created a set of 16 mutations within the SWI2 ATPase domain and have analyzed the functional consequences of these mutations in vivo. We have identified residues within each of the seven ATPase motifs that are required for SWI2 function. We have also identified crucial residues that are interspersed between the known ATPase motifs. In contrast, we identify other highly conserved residues that appear to be dispensable for SWI2 function. We also find that single amino acid changes in ATPase motifs IV and VI lead to a dominant negative phenotype. None of the 12 SWI2 mutations that disrupt SWI2 activity in vivo alter the assembly of the SWI/SNF complex. These studies provide an invaluable framework for biochemical analysis of the SWI2 ATPase and for functional analysis of other SWI2 family members.

Adenosine Triphosphatases↗
PubMed2003

Biochemical and functional analysis of CTR1, a protein kinase that negatively regulates ethylene signaling in Arabidopsis.

CTR1 encodes a negative regulator of the ethylene response pathway in Arabidopsis thaliana. The C-terminal domain of CTR1 is similar to the Raf family of protein kinases, but its first two-thirds encodes a novel protein domain. We used a variety of approaches to investigate the function of these two CTR1 domains. Recombinant CTR1 protein was purified from a baculoviral expression system, and shown to possess intrinsic Ser/Thr protein kinase activity with enzymatic properties similar to Raf-1. Deletion of the N-terminal domain did not elevate the kinase activity of CTR1, indicating that, at least in vitro, this domain does not autoinhibit kinase function. Molecular analysis of loss-of-function ctr1 alleles indicated that several mutations disrupt the kinase catalytic domain, and in vitro studies confirmed that at least one of these eliminates kinase activity, which indicates that kinase activity is required for CTR1 function. One missense mutation, ctr1-8, was found to result from an amino acid substitution within a new conserved motif within the N-terminal domain. Ctr1-8 has no detectable effect on the kinase activity of CTR1 in vitro, but rather disrupts the interaction with the ethylene receptor ETR1. This mutation also disrupts the dominant negative effect that results from overexpression of the CTR1 amino-terminal domain in transgenic Arabidopsis. These results suggest that CTR1 interacts with ETR1 in vivo, and that this association is required to turn off the ethylene-signaling pathway.

Alleles↗
PubMed2006

Mutational and functional analysis of an essential subdomain of the adenovirus E1A N-terminal transcription repression domain.

Adenovirus early gene 1A (E1A) possesses a potent transcriptional repression function within the first 80 amino acids (E1A 1-80). Our previous analysis of subdomain 1 (residues 1 to 30) revealed strong correlations between residues required for repression and for disruption of TBP-TATA complexes. Here, we report a functional analysis of subdomain 2 (48 to 60) by alanine-scanning mutagenesis. 53Ala, 54Pro, 55Glu, and 56Asp are required for repression in vitro and in vivo and for efficient interaction with p300 but not for disruption of TBP-TATA. These combined results suggest a model for E1A transcription repression. E1A through subdomains 1 and 2 uses coactivators like p300 as scaffolds to access E1A repressible promoters. At the promoter, subdomain 1 interacts with TBP to disrupt TBP-TATA and abort transcription initiation. In further support of this model, we show that E1A 1-80 bound to the p300-binding site retains the ability to interact with TBP.

Adenovirus E1A Proteins↗
PubMed2005

Functional analysis of recombinant Bbeta15C and Bbeta15A fibrinogens demonstrates that Bbeta15G residue plays important roles in FPB release and in lateral aggregation of protofibrils.

BACKGROUND AND OBJECTIVES: Analysis of dysfibrinogens has improved our understanding of molecular defects and their effects on the function of intact fibrinogen. To eliminate the influence of plasma heterozygous molecules, we synthesized and analyzed recombinant-variant fibrinogens. METHODS: We synthesized two recombinant-variant fibrinogens with a single amino acid substitution at the 15Gly residue in the Bbeta-chain: namely, Bbeta15Cys and Bbeta15Ala. RESULTS: Western blotting analysis of purified fibrinogen revealed the existence of a small amount of a dimeric form only for Bbeta15Cys fibrinogen. For Bbeta15Cys fibrinogen, functional analysis indicated (a) no thrombin-catalyzed fibrinopeptide B (FPB) release and (b) markedly impaired lateral aggregation in thrombin- and reptilase-catalyzed fibrin polymerizations. For Bbeta15Ala fibrinogen, such analysis indicated slight impairments of both thrombin-catalyzed FPB release and lateral aggregation in thrombin-catalyzed fibrin polymerization, but nearly normal lateral aggregation in reptilase-catalyzed fibrin polymerization. These impaired lateral aggregations were accompanied by thinner fibrin fiber diameters (determined by scanning electron microscopy of the corresponding fibrin clots). CONCLUSION: We conclude that a region adjacent to Bbeta15Gly plays important roles in lateral aggregation not only in desA fibrin polymerization, but also in desAB fibrin polymerization, and we speculate that the marked functional differences between Bbeta15A and Bbeta15C fibrinogens in FPB release and fibrin polymerization might not only be due to the presence of a substituted cysteine residue in Bbeta15C fibrinogen, but also to the existence of disulfide-bonded forms. Finally, our data indicate that the Bbeta15Gly residue plays important roles in FPB release and lateral aggregation of protofibrils.

Alanine↗
PubMed2006

A methodology for the structural and functional analysis of signaling and regulatory networks.

BACKGROUND: Structural analysis of cellular interaction networks contributes to a deeper understanding of network-wide interdependencies, causal relationships, and basic functional capabilities. While the structural analysis of metabolic networks is a well-established field, similar methodologies have been scarcely developed and applied to signaling and regulatory networks. RESULTS: We propose formalisms and methods, relying on adapted and partially newly introduced approaches, which facilitate a structural analysis of signaling and regulatory networks with focus on functional aspects. We use two different formalisms to represent and analyze interaction networks: interaction graphs and (logical) interaction hypergraphs. We show that, in interaction graphs, the determination of feedback cycles and of all the signaling paths between any pair of species is equivalent to the computation of elementary modes known from metabolic networks. Knowledge on the set of signaling paths and feedback loops facilitates the computation of intervention strategies and the classification of compounds into activators, inhibitors, ambivalent factors, and non-affecting factors with respect to a certain species. In some cases, qualitative effects induced by perturbations can be unambiguously predicted from the network scheme. Interaction graphs however, are not able to capture AND relationships which do frequently occur in interaction networks. The consequent logical concatenation of all the arcs pointing into a species leads to Boolean networks. For a Boolean representation of cellular interaction networks we propose a formalism based on logical (or signed) interaction hypergraphs, which facilitates in particular a logical steady state analysis (LSSA). LSSA enables studies on the logical processing of signals and the identification of optimal intervention points (targets) in cellular networks. LSSA also reveals network regions whose parametrization and initial states are crucial for the dynamic behavior. We have implemented these methods in our software tool CellNetAnalyzer (successor of FluxAnalyzer) and illustrate their applicability using a logical model of T-Cell receptor signaling providing non-intuitive results regarding feedback loops, essential elements, and (logical) signal processing upon different stimuli. CONCLUSION: The methods and formalisms we propose herein are another step towards the comprehensive functional analysis of cellular interaction networks. Their potential, shown on a realistic T-cell signaling model, makes them a promising tool.

Animals↗
PubMed1995

Cloning and functional analysis of TipE, a novel membrane protein that enhances Drosophila para sodium channel function.

Voltage-dependent sodium channels are involved in the initiation and propagation of action potentials in many excitable cells. Here we report that tipE, a gene defined by a temperature-sensitive paralytic mutation in Drosophila, encodes a novel integral membrane protein that dramatically stimulates functional expression in Xenopus oocytes of the Drosophila sodium channel alpha subunit encoded by the paralytic (para) locus. Using a heat shock promoter to control tipE+ gene expression in transgenic flies, we demonstrate that tipE+ gene expression is required during pupal development to rescue adult paralysis. In addition, we demonstrate a role for the tipE gene product in adults.

Amino Acid Sequence↗
PubMed2000

Functional analysis of cardiovascular renin-angiotensin system using a gain or loss of function approach.

The study of the effect of autocrine-paracrine vasoactive modulators on cardiovascular biology is very difficult in vivo, because in vivo studies are limited. In particular, characterization of the role of components of the renin-angiotensin system (RAS) in vivo is limited by the difficulty in manipulating individual components of the RAS as well as by methodological limitations in studying the function of a local RAS in the absence of any contribution by the circulatory system. Recent progress in in vivo gene transfer technologies has provided us with the opportunity to study cellular responses to the manipulation of the individual components (i.e., by overexpression or inhibition). Many researchers have recently developed various in vivo gene transfer techniques for cardiovascular applications. Using in vivo gene transfer approaches, the roles of various tissues in the RAS, such as cardiac angiotensin, have been identified. Such an approach may increase our understanding of the biology and pathobiology of the autocrine-paracrine system. This review discusses the potential utility of in vivo gene transfer methods.

Angiotensins↗
PubMed1990

Structure-function analysis of the human interferon gamma. The COOH terminus is not essential for functional activity.

The structure-function relationships for the human interferon gamma (HuIFN-gamma) were studied using recombinant variants that had various deletions at the carboxyl terminus. Four COOH-terminal deletion variants were constructed that contained the amino-terminal 122, 117, 111, and 106 amino acid residues. These variants were constructed by specific DNA modifications and were expressed in Escherichia coli. The deletion of 21 amino acid residues resulted in only 2- and 3-fold reduction in the antiviral and antiproliferative specific activities, respectively. Thus, the carboxyl-terminal 21 residues are not directly involved in the function of the HuIFN-gamma. The level of intracellular accumulation was also decreased by 3-5-fold. Further deletions of 26, 32, and 37 residues from the COOH terminus resulted in the lack of detectable activity as well as in 50-100-fold reduction in the level of accumulation in the bacterial cell. However, each of the modified plasmids was found to have comparable efficiency in directing the production of the respective variant molecules relative to the full-length HuIFN-gamma molecule in an in vitro transcription-translation assay. Thus, the failure of some of the deletion variant molecules to accumulate in the E. coli cell is likely due to their instability in vitro. The loss of the COOH-terminal 21 amino acid residues of HuIFN-gamma also resulted in a substantial reduction in the ability of the molecule to be renatured in vitro from the treatment with chaotrophic agents, a method frequently used to extract and purify recombinant polypeptides from E. coli host. The latter result may account for some earlier reports which inferred the involvement of the COOH terminus in the functions of the HuIFN-gamma molecule due to their failure to detect activity upon deletions of only 11-18 residues.

Amino Acid Sequence↗
PubMed2005

Direct observation of a transverse vibrational mechanism for negative thermal expansion in Zn(CN)2: an atomic pair distribution function analysis.

The instantaneous structure of the cyanide-bridged negative thermal expansion (NTE) material Zn(CN)(2) has been probed using atomic pair distribution function (PDF) analysis of high energy X-ray scattering data (100-400 K). The temperature dependence of the atomic separations extracted from the PDFs indicates an increase of the average transverse displacement of the cyanide bridge from the line connecting the Zn(II) centers with increasing temperature. This allows the contraction of non-nearest-neighbor Zn...Zn' and Zn...C/N distances despite the observed expansion of the individual direct Zn-C/N and C-N bonds. Thus, this analysis provides definitive structural confirmation that an increase in the average displacement of bridging atoms is the origin of the NTE behavior. The lattice parameters reveal a slight reduction in the NTE behavior at high temperature from a minimum coefficient of thermal expansion (alpha = dl/ldT) of -19.8 x 10(-6) K(-1) below 180 K, which is attributed to interaction between the doubly interpenetrated frameworks that comprise the structure.

Journal Article↗
PubMed2000

Obstructive sleep apnea (OSA): a cephalometric analysis of severe and non-severe OSA patients. Part II: A predictive discriminant function analysis.

One hundred male obstructive sleep apnea (OSA) patients were classified into 2 groups on the basis of apnea-hypopnea index (AHI) as severe (AHI > or = 50) and non-severe (AHI < 50). A comprehensive cephalometric analysis of cervicocraniofacial skeletal and upper airway soft tissue morphology was performed in 51 non-severe and 49 severe OSA patients. In addition, a multivariate statistical method (principal component, analysis and predictive discriminant analysis) was performed to identify the components that could correctly differentiate the severe from the non-severe OSA patients. Eight principal components (PCs) of cervicocraniofacial skeletal morphology, 4 PCs of hyoid bone position and head posture, and 7 PCs of upper airway soft tissue morphology, together with the selected demographic variables, were deduced to formulate a linear canonical discriminant function. The equation of a 9-variable model was generated as follows: PDF score = 4.127 - 0.144 (Body Mass Index) - 0.376 (PC1.1) + 0.311 (PC1.4) + 0.214 (PC1.5) + 0.075 (PC 2.1) - 1.309 (PC2.3) + 0.708 (PC3.2) - 0.059 (PC3.3) + 0.609 (PC3.6). The cutoff score was -0.03899. The overall rate of correct classification was 83%. The results showed that Body Mass Index and 8 other PCs contributed significantly to the OSA severity. These analyses are proven to be a useful adjunctive diagnostic tool to select optimal treatment regimens for OSA patients with varying degrees of severity.

Aged↗
PubMed1997

Suitability of replacement markers for functional analysis studies in Saccharomyces cerevisiae.

The complete yeast sequence contains a large proportion of genes whose biological function is completely unknown. One approach to elucidating the function of these novel genes is by quantitative methods that exploit the concepts of metabolic control analysis. An important first step in such an analysis is to determine the effects of deleting individual genes on the growth rate (or fitness) of Saccharomyces cerevisiae. Since the specific growth-rate effects of most genes are likely to be small, they are most readily determined by competition against a standard strain in chemostat cultures where the true steady state demanded by metabolic control analysis may be achieved. We have constructed two different standard strains in which the HO gene is replaced by either HIS3 or kanMX. We demonstrate that HO is a selectively neutral site for gene replacement. However, there is a significant marker effect associated with HIS3 which, moreover, is dependent on the physiological conditions used for the competition experiments. In contrast, the kanMX marker exhibited only a small effect on specific growth rate (< or = +/- 4%). These data suggest that nutritional markers should not be used to generate deletion mutants for the quantitative analysis of gene function in yeast but that kanMX replacements may be used, with confidence, for such studies.

Anti-Bacterial Agents↗
PubMed2000

Functional analysis of ligand-binding and signal transduction domains of CD69 and CD23 C-type lectin leukocyte receptors.

CD69 and CD23 are leukocyte receptors with distinctive pattern of cell expression and functional features that belong to different C-type lectin receptor subfamilies. To assess the functional equivalence of different domains of these structurally related proteins, a series of CD69/CD23 chimeras exchanging the carbohydrate recognition domain, the neck region, and the transmembrane and cytoplasmic domains were generated. Biochemical analysis revealed the importance of the neck region (Cys68) in the dimerization of CD69. Functional analysis of these chimeras in RBL-2H3 mast cells and Jurkat T cell lines showed the interchangeability of structural domains of both proteins regarding Ca2+ fluxes, serotonin release, and TNF-alpha synthesis. The type of the signal transduced mainly relied on the cytoplasmic domain and was independent of receptor oligomerization. The cytoplasmic domain of CD69 transduced a Ca2+-mediated signaling that was dependent on the extracellular uptake of Ca2+. Furthermore, a significant production of TNF-alpha was induced through the cytoplasmic domain of CD69 in RBL-2H3 cells, which was additive to that promoted via FcepsilonRI, thus suggesting a role for CD69 in the late phase of reactions mediated by mast cells. Our results provide new important data on the functional equivalence of homologous domains of these two leukocyte receptors.

Animals↗
PubMed1984

Home health care cost-function analysis.

An exploratory home health care (HHC) cost-function model is estimated using State rate-setting data for the 74 traditional (nonprofit) Connecticut agencies. The analysis demonstrates U-shaped average costs curves for agencies' provision of skilled nursing visits, with substantial diseconomies of scale in the observable range. It is determined from the estimated cost function that the sample representative agency is providing fewer visits than optimal, and its marginal cost is significantly below average cost. The finding that an agency's costs are predominantly related to output levels, with little systematic variation due to other agency or patient characteristics, suggests that the economic inefficiency in a cost-based HHC reimbursement policy may be substantial.

Analysis of Variance↗
PubMed1995

Protein backbone dynamics revealed by quasi spectral density function analysis of amide N-15 nuclei.

Spectral density functions J(0), J(omega N), and J(omega H + omega N) of individual amide N-15 nuclei in proteins were approximated by a quasi spectral density function (QSDF). Using this function, the backbone dynamics were analyzed for seven protein systems on which data have been published. We defined J(0; omega N) as the difference between the J(0) and the J(omega N) values, which describes motions slower than 50 (or 60) MHz, and J(omega N; omega H+N) as the difference between the J(omega N) and the J(omega H + omega N) values, which describes motions slower than 450 (or 540) MHz. The QSDF analysis can easily extract the J(0; omega N) of protein backbones, which have often some relation to biologically relevant reactions. Flexible N-terminal regions in eglin c and glucose permease IIA and a loop region in eglin c showed smaller values of both the J(0; omega N) and the J(omega N; omega H+N) as compared with the other regions, indicating increases in motions faster than nanosecond. The values of the J(0; omega N) for the backbone of the FK506 binding protein showed a large variation in the apoprotein but fell in a very narrow range after the binding of FK506. Characteristic increase or decrease in the values of J(0) and J(omega N) was observed in two or three residues located between secondary structures.

Calmodulin↗
PubMed2003

Use of differential item functioning analysis to assess the equivalence of translations of a questionnaire.

In cross-national comparisons based on questionnaires, accurate translations are necessary to obtain valid results. Differential item functioning (DIF) analysis can be used to test whether translations of items in multi-item scales are equivalent to the original. In data from 10,815 respondents representing 10 European languages we tested for DIF in the nine translations of the EORTC QLQ-C30 emotional function scale when compared to the original English version. We tested for DIF using two different methods in parallel, a contingency table method and logistic regression. The DIF results obtained with the two methods were similar. We found indications of DIF in seven of the nine translations. At least two of the DIF findings seem to reflect linguistic problems in the translation. 'Imperfect' translations can affect conclusions drawn from cross-national comparisons. Given that translations can never be identical to the original we discuss how findings of DIF can be interpreted and discuss the difference between linguistic DIF and DIF caused by confounding, cross-cultural differences, or DIF in other items in the scale. We conclude that testing for DIF is a useful way to validate questionnaire translations.

Adult↗
PubMed2006

ROC and loss function analysis in sequential testing.

Sequential testing is applied to reduce costs in SP-based tests (OSCEs). Initially, all candidates take a screening test consisting of a part of the OSCE. Candidates who fail the screen sit the complete test, whereas those who pass the screen are qualified as a pass of the complete test. The procedure may result in a reduction of testing resources, but at the cost of false positives (candidates who pass the screen but would fail the complete test). In a diagnostic test an optimum cutpoint is obtained by minimizing the weighted sum of false negatives and false positives using Receiver Operator Characteristic (ROC) analysis. However, in the sequential procedure there are no false negatives, because the result of the complete test is considered the final outcome. Several authors ignored this difference and applied classic ROC analysis to a sequential test. Earlier, we doubted the validity of the procedure and proposed to set the cutpoint by minimizing the loss, defined as the weighted sum of the screen negatives and the false positives. Recently, Regehr and Colliver (2003) argued that under certain theoretically derived conditions the use of the loss formula in sequential testing is functionally identical to using classic ROC analysis. The current study shows (a) the conclusion of Regehr and Colliver is based on assumptions that can be challenged, and (b) ROC analysis indeed can be used in sequential testing, but only if the procedure is modified according to the results of a corresponding loss function analysis.

Diagnostic Tests, Routine↗
PubMed2004

Genomic organization and functional analysis of murine PKD2L1.

Mutations in genes that encode polycystins 1 or 2 cause polycystic kidney disease (PKD). Here, we report the genomic organization and functional expression of murine orthologue of human polycystin-2L1 (PKD2L1). The murine PKD2L1 gene comprises 15 exons in chromosome 19C3. Coexpression of PKD2L1 together with polycystin-1 (PKD1) resulted in the expression of PKD2L1 channels on the cell surface, whereas PKD2L1 expressed alone was retained within the endoplasmic reticulum (ER). This suggested that interaction between PKD1 and PKD2L1 is essential for PKD2L1 trafficking and channel formation. Deletion analysis at the cytoplasmic tail of PKD2L1 revealed that the coiled-coil domain was important for trafficking by PKD1. Mutagenesis within two newly identified ER retention signal-like amino acid sequences caused PKD2L1 to be expressed at the cell surface. This indicated that the coiled-coil domain was responsible for retaining PKD2L1 within the ER. Functional analysis of murine PKD2L1 expressed in HEK 293 cells was undertaken using calcium imaging. Coexpression of PKD1 and PKD2L1 resulted in the formation of functional cation channels that were opened by hypo-osmotic stimulation, whereas neither molecule formed functional channels when expressed alone. We conclude that PKD2L1 forms functional cation channels on the plasma membrane by interacting with PKD1. These findings raise the possibility that PKD2L1 represents the third genetic locus that is responsible for PKD.

Amino Acid Sequence↗
PubMed2000

Atlantic salmon HNF-3/forkhead: cDNA sequence, evolution, expression, and functional analysis.

We report the isolation and characterization of a cDNA encoding an HNF-3 family member (as HNF-3) from Atlantic salmon (Salmo salar L). The important functional domains of HNF-3 proteins that have been characterized previously are revealed by segments of high identity along the alignment of the asHNF-3 with winged helix/forkhead amino acid sequences isolated from other species. A comparison of asHNF-3 cDNA and genomic DNA indicated that there were no introns present in the asHNF-3 gene. Expression of asHNF-3 protein in adult salmon tissues was not exclusive to liver but was also present in the pancreas and intestine. An RT-PCR analysis performed on salmon development showed that asHNF3 expression is detectable before gastrulation at the mid blastula transition stage. Functional analysis of the asHNF-3 protein using a characterized HNF-3 consensus binding site demonstrated that the protein can recognize and bind to specific HNF-3 consensus sequences. We also report the identification of a novel HNF3 binding site in the promoter of the Atlantic salmon transferrin gene.

Amino Acid Sequence↗