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At least 433 records · Page 24Linked to original sources
PubMed2000

Structure-function analysis of the dolichyl phosphate-mannose: protein O-mannosyltransferase ScPmt1p.

Protein O-mannosylation is an essential protein modification. It is initiated at the endoplasmic reticulum by a family of dolichyl phosphate-mannose:protein O-mannosyltransferases (Pmts), which is evolutionarily conserved from yeast to humans. Saccharomyces cerevisiae Pmt1p is an integral membrane protein of the endoplasmic reticulum. ScPmt1p forms a complex with ScPmt2p that is required for maximum transferase activity. Recently, we proposed a seven-transmembrane structural model for ScPmt1p. A large, hydrophilic, endoplasmic reticulum-oriented segment is flanked by five amino-terminal and two carboxyl-terminal membrane-spanning domains. Based on this model, a structure-function analysis of ScPmt1p was performed. Deletion mutagenesis identified the N-terminal third of the transferase as being essential for the formation of a functional ScPmt1p-ScPmt2p complex. Deletion of the central hydrophilic loop eliminates mannosyltransferase activity, but not ScPmt1p-ScPmt2p interactions. Alignment of all fully characterized PMT family members revealed that this central loop region contains three highly conserved peptide motifs, which can be considered as signatures of the PMT family. In addition, a number of invariant amino acid residues were identified throughout the entire protein sequence. In order to evaluate the functional significance of these conserved residues site-directed mutagenesis was performed. We show that several amino acid substitutions in the conserved motifs significantly reduce ScPmt1p activity. Further, the invariant residues Arg-64, Glu-78, Arg-138, and Leu-408 are essential for ScPmt1p function. In particular, Arg-138 is crucial for ScPmt1p-ScPmt2p complex formation.

Amino Acid Sequence↗
PubMed2026

Molecular profiling of coronary stent testenosis: A systematic review and functional analysis of implicated genes.

BACKGROUND: Coronary stent restenosis occurs in approximately 5% of patients treated with drug-eluting stents (DES) and is associated with adverse clinical outcomes. Elucidating the genetic mechanisms underlying restenosis may support precision medicine approaches to improve patient management.This systematic review aimed to synthesize evidence on genes and biological pathways associated with DES-related restenosis and to perform functional analysis of the implicated genes using bioinformatics tools. METHODS: The review was conducted according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews guidelines. A systematic search of PubMed, Scopus, and Web of Science was performed for human studies investigating genetic or genomic factors in coronary restenosis, with the last search conducted in March 2024. Eligibility criteria included original studies reporting genetic associations with DES restenosis. Screening and data extraction were performed by a single reviewer. Identified genes underwent gene set enrichment analysis using Enrichr (Ma'ayan Laboratory, Computational Systems Biology) and ClueGo extension on Cytoscape (National Resource for Network Biology). RESULTS: Seventeen studies met the inclusion criteria. The studies highlighted multiple genes involved in extracellular matrix remodeling, inflammatory signaling, and the renin-angiotensin system. Gene enrichment analysis confirmed the overrepresentation of these biological pathways in DES-associated restenosis. CONCLUSIONS: This systematic review synthesizes the genetic and molecular contributors to DES-associated restenosis and identifies potential targets for future research and personalized therapies. No external funding was received, and the protocol was not registered.

Humans↗
PubMed1996

Functional analysis of human/chicken transferrin receptor chimeras indicates that the carboxy-terminal region is important for ligand binding.

Chimeric human/chicken transferrin receptors have been constructed using the polymerase chain reaction. Different regions of the 671-residue external domain of the human transferrin receptor were replaced by the corresponding sequences from the chicken transferrin receptor. As chicken transferrin receptors do not bind human transferrin, functional analysis of such chimeric receptors provides an approach to define the ligand-binding site of the human transferrin receptor. Four of 16 chimeric human/chicken transferrin receptors expressed in chick embryo fibroblasts were efficiently transported to the plasma membrane and displayed on the cell surface. Studies of the four chimeric receptors indicated that binding of human transferrin was abolished if the carboxy terminal 192 amino acids of the human transferrin receptor (residues 569-760) were replaced with the corresponding region from the chicken transferrin receptor. Further, a chimeric receptor in which the carboxy-terminal 72 residues were derived from the chicken transferrin receptor exhibited a 16-fold decrease in binding affinity for human transferrin. In contrast, analysis of the other two chimeric receptors showed that 340 amino acids of the human transferrin receptor external domain more proximal to the transmembrane region (residues 151-490) could be replaced with the corresponding region from the chicken transferrin receptor without loss of high-affinity ligand binding. In contrast, two mAbs against the human transferrin receptor external domain, B3/25 and D65.3, that do not compete with transferrin binding, do not bind the chimeric transferrin receptors in which the membrane proximal part is replaced by chicken sequences, while they do bind the two other chimeric transferrin receptors with high affinity. These data indicate that sequence differences in the carboxy-terminal region of human and chicken transferrin receptor external domains are important for the species specificity of transferrin binding and imply that this portion of the human transferrin receptor is critical for ligand binding.

Animals↗
PubMed2000

Functional analysis of the CD4(+) T-cell response to Epstein-Barr virus: T-cell-mediated activation of resting B cells and induction of viral BZLF1 expression.

In contrast to the major role played by Epstein-Barr virus (EBV)-specific CD8(+) cytotoxic T-cell responses in immunosurveillance, recent studies have offered the apparently paradoxical suggestion that development of EBV-driven human B-cell lymphoproliferative disorders and tumors in SCID/hu mice is dependent on the presence of T cells, in particular CD4(+) T cells. This study presents a functional analysis of the CD4(+) T-cell response to EBV and shows that while CD4(+) T cells may be cytotoxic, they also express Th2 cytokines and CD40 ligand (gp39) and possess B-cell helper function. We show that EBV-specific CD4(+) T cells can provide non-HLA-restricted help for activation of resting B cells via a gp39-CD40-dependent pathway and are able to induce expression of BZLF1, a viral lytic cycle transactivator in latently infected resting B cells, ultimately resulting in rapid outgrowth of transformed B-cell colonies. These results support the proposal that CD4(+) T cells may play a key role in reactivation of latent EBV infection and may thus contribute to the pathogenesis of EBV-driven lymphoproliferative disorders.

Antiviral Agents↗
PubMed2005

Functional analysis of two divalent metal-dependent regulatory genes dmdR1 and dmdR2 in Streptomyces coelicolor and proteome changes in deletion mutants.

In Gram-positive bacteria, the expression of iron-regulated genes is mediated by a class of divalent metal-dependent regulatory (DmdR) proteins. We cloned and characterized two dmdR genes of Streptomyces coelicolor that were located in two different nonoverlapping cosmids. Functional analysis of dmdR1 and dmdR2 was performed by deletion of each copy. Deletion of dmdR1 resulted in the derepression of at least eight proteins and in the repression of three others, as shown by 2D proteome analysis. These 11 proteins were characterized by MALDI-TOF peptide mass fingerprinting. The proteins that show an increased level in the mutant correspond to a DNA-binding hemoprotein, iron-metabolism proteins and several divalent metal-regulated enzymes. The levels of two other proteins--a superoxide dismutase and a specific glutamatic dehydrogenase--were found to decrease in this mutant. Complementation of the dmdR1-deletion mutant with the wild-type dmdR1 allele restored the normal proteome profile. By contrast, deletion of dmdR2 did not affect significantly the protein profile of S. coelicolor. One of the proteins (P1, a phosphatidylethanolamine-binding protein), overexpressed in the dmdR1-deleted mutant, is encoded by ORF3 located immediately upstream of dmdR2; expression of both ORF3 and dmdR2 is negatively controlled by DmdR1. Western blot analysis confirmed that dmdR2 is only expressed when dmdR1 is disrupted. Species of Streptomyces have evolved an elaborated regulatory mechanism mediated by the DmdR proteins to control the expression of divalent metal-regulated genes.

Amino Acid Sequence↗
PubMed1995

Preparation and a structure-function analysis of human ciliary neurotrophic factor.

Ciliary neurotrophic factor (CNTF) is a trophic protein that promotes survival and/or differentiation of a variety of neuronal cell types including sensory, sympathetic, and motor neurons. CNTF, leukemia inhibitory factor (LIF), interleukin-6 (IL-6) and oncostatin M (OSM) share a predicted common helical framework and partially identical receptor components. In this study, we present the preparation and structure--functional analysis of recombinant human CNTF. The human CNTF gene was expressed under the control of the PL promoter in Escherichia coli, and the mutants were constructed by insertion, deletion and site-directed mutagenesis. The recombinant proteins were purified from bacteria via DEAE A-50 and Sephacryl S-200 chromatography, and their survival promoting activities were determined using cultures of embryonic chick dorsal root ganglion (DRG) neurons. Insertion at position 23 with APGL, or at position 79 with PRGA, or substitution of 162L163Q for PIDG resulted in proteins with no neurotrophic activity. However, insertion at position 186 with PRGI did not alter human CNTF activity. Deletion of the carboxy-terminal amino acid 186-200 did not reduce the biological activity, but elimination of the amino acid 162-186 abolished the activity. The mutant substituting of 17 Cys for Ser was found to display a biological activity equivalent to that of the wild type. Our data provided experimental confirmation for the structural prediction of CNTF.

Amino Acid Sequence↗
PubMed2001

Functional analysis of neurofibromatosis 2 (NF2) missense mutations.

Neurofibromatosis 2 (NF2) is a tumor predisposition syndrome in which affected individuals develop nervous system tumors at an increased frequency. The most common tumor in individuals with NF2 is the schwannoma, which is composed of neoplastic Schwann cells lacking NF2 gene expression. Moreover, inactivation of the NF2 gene is observed in nearly all sporadic schwannomas, suggesting that the NF2 gene is a critical growth regulator for Schwann cells. In an effort to gain insights into the function of the NF2 gene product, merlin or schwannomin, we performed a detailed functional analysis of eight naturally occurring non-conservative missense mutations in the NF2 gene. Using a regulatable expression system in rat schwannoma cells, we analyzed proliferation, actin cytoskeleton-mediated events and merlin folding. In this report, we demonstrate that mutations clustered in the predicted alpha-helical region did not impair the function of merlin whereas those in either the N- or C-terminus of the protein rendered merlin inactive as a negative growth regulator. These results suggest that the key functional domains of merlin lie within the highly conserved FERM domain and the unique C-terminus of the protein.

Amino Acid Substitution↗
PubMed2003

Molecular cloning, mapping, and functional analysis of the bovine sulfate transporter SLC26a2 gene.

Sulfate is one of the most important macronutrients in cells and the major sulfur source in many organisms as well as one of the most abundant anions in the serum. As sulfate is a hydrophilic anion, movement across the lipid bilayer is mediated by transporters that regulate efflux and influx. Here, we report the molecular cloning, mapping, and functional analysis of the bovine solute carrier/sulfate transporter SLC26a2 gene, the first member of this family to be cloned in cattle. A recombinant phage library was screened, and single phages harbouring the SLC26a2 gene was isolated and sequenced. A fragment of 6295 base pairs (bp) of the bovine SLC26a2 gene harbouring exon 2 and exon 3 was used for further analysis. Similar to the human, ovine, mouse, and rat SLC26a2 gene, the bovine ortholog consists of two coding exons. The open reading frame harbours 2202 nucleotides (nt), coding for a protein of 734 amino acids with a calculated molecular weight of 81.5 kilodaltons (kDa) and a statistical isoelectric point (pI) of 8.77. The bovine SLC26a2 gene was mapped to chromosome 7q23-q24 (BTA 7q23-q24) by fluorescence in situ hybridisation (FISH) analysis. Two point mutations were identified comparing the DNAs of 300 Holstein Frisian cattle, one of them resulting in an isoleucine to serine amino acid exchange at position 520. The Ile520Ser exchange influences the sulfate uptake as measured in primary fibroblasts isolated from testis and in immortalized fibroblastoid bovine cell lines.

Amino Acid Sequence↗
PubMed2004

Functional analysis of a rice putative voltage-dependent Ca2+ channel, OsTPC1, expressed in yeast cells lacking its homologous gene CCH1.

We isolated a cDNA (OsTPC1) from rice that was homologous to AtTPC1, a putative voltage-dependent Ca(2+) channel (VDCC) gene of Arabidopsis thaliana. The hydropathy profile of its deduced amino acid sequence showed significant structural features of the alpha 1-subunit of animal VDCCs. Functional analysis using a heterologous yeast expression system showed that OsTPC1 facilitates Ca(2+) permeation. The K(m) value for Ca(2+) of OsTPC1, 47.5 micro M, was comparable to that of intrinsic CCH1, a candidate VDCC in yeast. Ca(2+) permeation by OsTPC1 was inhibited by verapamil, a VDCC blocker. These findings indicate for the first time that OsTPC1 is a putative VDCC in rice.

Amino Acid Sequence↗
PubMed1998

Transgenic animal models for the functional analysis of vasoactive peptides.

The interplay of vasoactive peptide systems is an essential determinant of blood pressure regulation in mammals. While the endothelin and the renin-angiotensin systems raise blood pressure by inducing vasoconstriction and sodium retention, the kallikrein-kinin and the natriuretic-peptide systems reduce arterial pressure by eliciting vasodilatation and natriuresis. Transgenic technology has proven to be very useful for the functional analysis of vasoactive peptide systems. As an outstanding example, transgenic rats overexpressing the mouse Ren-2 renin gene in several tissues become extremely hypertensive. Several other transgenic rat and mouse strains with genetic modifications of components of the renin-angiotensin system have been developed in the past decade. Moreover, in recent years gene-targeting technology was employed to produce mouse strains lacking these proteins. The established animal models as well as the main insights gained by their analysis are summarized in this review.

Angiotensinogen↗
PubMed1998

Structure-function analysis of integrase interactor 1/hSNF5L1 reveals differential properties of two repeat motifs present in the highly conserved region.

Retroviral integrase (IN) catalyzes the integration of retroviral cDNA into host chromosome. Ini1 (integrase interactor 1) is a host protein that specifically binds and stimulates in vitro joining activity of HIV-1 IN. Ini1 has homology to yeast transcription factor SNF5 and is a component of the analogous mammalian SWI/SNF complex that can remodel chromatin. Little is known about the function of Ini1 in mammalian cells. To gain insight into the functional domains of Ini1, and to understand the details of protein-protein interactions of IN and Ini1, a structure-function analysis of Ini1 was initiated. By means of the yeast two-hybrid system, the minimal IN binding domain of Ini1 was characterized. One of the two repeat motifs present in the highly conserved regions of Ini1 was found necessary and sufficient to bind to IN in yeast as well as in vitro. Because IN binds to only one of the two repeat motifs in this conserved region of Ini1, it appears that the IN-Ini1 interaction is very specific and functionally significant. Characterization of DNA-binding properties of Ini1 revealed that Ini1 can bind to plasmid DNA, binding more readily to supercoiled DNA than to the relaxed circular DNA. The minimal domain for DNA binding was localized to a region upstream of repeat 1. The DNA binding activity of Ini1 is not required for its ability to interact with IN. The finding that the two repeat motifs of Ini1 display differential binding to HIV-1 IN and that this discrete component of mammalian SWI/SNF complex binds to DNA will help understand the role of Ini1 in HIV-1 integration and in cellular process.

Amino Acid Sequence↗
PubMed1985

The research diagnostic criteria for endogenous depression and the dexamethasone suppression test: a discriminant function analysis.

Most studies examining the validity of the Research Diagnostic Criteria (RDC) for endogenous depression have been negative. RDC endogenous subtyping is not associated with short- or long-term treatment outcome, family history of affective disorder, or premorbid personality disorder. Studies examining its relationship to the dexamethasone suppression test (DST) are mixed; half report a significant association, and half do not. The RDC endogenous diagnosis may lack validity either because the criteria do not represent, or are not specific to, the endogenous subtype, or the diagnostic algorithm is inappropriate. In the present study, we conduct a discriminant function analysis on the 10 criteria for the endogenous subtype using DST results as the independent variable. We constructed a new diagnostic algorithm and cross-validated it on a second patient sample. In both samples the discriminant function classification was significantly associated with DST results, whereas the RDC algorithm was not.

Adult↗
PubMed1991

Functional analysis and treatment of aberrant behavior.

This article reviewed and discussed various methodologies used for the analysis of variables maintaining aberrant behavior. Previous research had succeeded in identifying a wide variety of environmental events which may contribute to an individual's maladaptive responding. These general classes of variables are summarized and presented with relevant examples. We conclude with suggestions for conducting a comprehensive functional analysis using descriptive and experimental methods leading to the development and evaluation of analysis-derived interventions.

Behavior Therapy↗
PubMed2003

The predictive value of modified computerized thromboelastography and platelet function analysis for postoperative blood loss in routine cardiac surgery.

UNLABELLED: Hemorrhage after cardiopulmonary bypass (CPB) remains a clinical problem. Point-of-care tests to identify hemostatic disturbances at the bedside are desirable. In the present study, we evaluated the predictive value of two point-of-care tests on postoperative bleeding after routine cardiac surgery. Prospectively, 255 consecutive patients were studied to compare the ability of modified thromboelastography (ROTEG) as well as a platelet function analyzer (PFA-100) to predict postoperative blood loss. Measurements were performed at three time points: preoperatively, during CPB, and after protamine administration with three modified thromboelastography and PFA tests. The best predictors of increased bleeding tendency were the tests performed after CPB. The angle alpha is the best predictor (area under the receiver operating characteristic curve 0.69) and, in combination with the adenosine diphosphate-PFA test, the predictive accuracy is enhanced (area under the receiver operating characteristic curve 0.73). The negative predictive value for the angle alpha is 82%, although the positive predictive value is small (41%). Thromboelastography is a better predictor than PFA. In routine cardiac surgery, impaired hemostasis as identified by point-of-care tests does not inevitably lead to hemorrhage postoperatively. However, patients with normal test results are unlikely to bleed for hemostatic reasons. Bleeding in these patients is probably caused surgically. The high negative predictive value supports early identification and targeted treatment of surgical bleeding by distinguishing it from a significant coagulopathy. IMPLICATIONS: Thrombelastography and platelet function analysis in routine cardiac surgery demonstrate high negative predictive values for postoperative bleeding, which supports early identification and targeted treatment of surgical bleeding by distinguishing it from a significant coagulopathy. The positive predictive values are small. The best predictors are thrombelastography values obtained after cardiopulmonary bypass.

Aged↗
PubMed1996

Functional analysis of the human guanylin gene promoter.

Guanylin (GCAP-I, guanylate cyclase activating peptide I) and uroguanylin (GCAP-II, guanylate cyclase activating peptide II) are regulatory peptides involved in the regulation of the intestinal chloride / water balance. They share significant structural homology to the E. coli enterotoxin STa, which binds to the particulate guanylyl cyclase C causing diarrhea in mammals. In this study we report the functional analysis of the guanylin / GCAP-I gene promoter region. By means of the luciferase reporter gene assay, we demonstrate a strong promoter activity in T84 cells. Especially the first 160 bp of the 5'-flanking region of the gene seem to be essential for gene induction. Our findings are the basis for further identification of important regulatory elements of the corresponding gene.

Base Sequence↗
PubMed2006

Advances in cloning, functional analysis and heterologous expression of fungal polyketide synthase genes.

Fungal polyketides comprise a diverse group of secondary metabolites that play an important role for drug discovery, as pigments, and as mycotoxins. Their biosynthesis is governed by multidomain enzymes, so-called fungal type I polyketide synthases (PKS). Investigating the molecular basis of polyketide biosynthesis in fungi is of great importance for ecological and pharmacological reasons. In addition, cloning, functional analysis and expression of fungal PKS genes also set the basis for engineering the yet largely untapped biosynthetic potential.

Fungal Proteins↗
PubMed2001

Three-dimensional modeling for functional analysis of cardiac images: a review.

Three-dimensional (3-D) imaging of the heart is a rapidly developing area of research in medical imaging. Advances in hardware and methods for fast spatio-temporal cardiac imaging are extending the frontiers of clinical diagnosis and research on cardiovascular diseases. In the last few years, many approaches have been proposed to analyze images and extract parameters of cardiac shape and function from a variety of cardiac imaging modalities. In particular, techniques based on spatio-temporal geometric models have received considerable attention. This paper surveys the literature of two decades of research on cardiac modeling. The contribution of the paper is three-fold: 1) to serve as a tutorial of the field for both clinicians and technologists, 2) to provide an extensive account of modeling techniques in a comprehensive and systematic manner, and 3) to critically review these approaches in terms of their performance and degree of clinical evaluation with respect to the final goal of cardiac functional analysis. From this review it is concluded that whereas 3-D model-based approaches have the capability to improve the diagnostic value of cardiac images, issues as robustness, 3-D interaction, computational complexity and clinical validation still require significant attention.

Diagnostic Imaging↗
PubMed1995

In vivo functional analysis of the mouse estrogen receptor gene promoter: a transgenic mouse model to study tissue-specific and developmental regulation of estrogen receptor gene transcription.

Understanding the molecular and morphological basis of estrogen responsiveness in the various tissues and organs that make up an adult organism and its onset during ontogenesis requires identification of the genetic controls that determine timed expression of the estrogen receptor (ER) gene in multiple cell types. With this goal in mind, we describe here the results of the functional analysis of the mouse (m) ER gene promoter, carried out in vivo in transgenic mice. The mER gene promoter was cloned and spliced to the coding sequence of the bacterial lacZ gene (fused to the nuclear localization signal of SV40 large T: nls-beta-GAL) and then stably reintegrated into the genome of mice. Analysis of beta-GAL mRNA and protein expression in multiple organs of both female and male transgenic animals was then performed. Results show that the transgenic mER promoter, much like the endogenous one, is active in several organs and tissues of adult female and male mice. The first 0.4 kilobases of 5'-flanking DNA (up to -364) are sufficient to direct widespread expression of the transgene in mouse organs. This indicates that genetic elements functional in various cell types are included in this segment. Furthermore, the first exon and intron of the mER gene are necessary to achieve sexually dimorphic expression of the transgene in neurons located at specific sites within the central nervous system. These mER promoter transgenic mice will be useful in mapping estrogen- responsive cell types under different physiological and pathological conditions in vivo, in defining ontogenesis of estrogen action in the mouse, and in studying the mechanisms that regulate ER gene transcription.

Animals↗