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 721 records · Page 40Linked to original sources
PubMed2006

Biochemical and genetic analysis of the gamma-resorcylate (2,6-dihydroxybenzoate) catabolic pathway in Rhizobium sp. strain MTP-10005: identification and functional analysis of its gene cluster.

We identified a gene cluster that is involved in the gamma-resorcylate (2,6-dihydroxybenzoate) catabolism of the aerobic bacterium Rhizobium sp. strain MTP-10005. The cluster consists of the graRDAFCBEK genes, and graA, graB, graC, and graD were heterologously expressed in Escherichia coli. Enzymological studies showed that graD, graA, graC, and graB encode the reductase (GraD) and oxygenase (GraA) components of a resorcinol hydroxylase (EC 1.14.13.x), a maleylacetate reductase (GraC) (EC 1.3.1.32), and a hydroxyquinol 1,2-dioxygenase (GraB) (EC 1.13.11.37). Bioinformatic analyses suggested that graE, graR, and graK encode a protein with an unknown function (GraE), a MarR-type transcriptional regulator (GraR), and a benzoate transporter (GraK). Quantitative reverse transcription-PCR of graF, which encodes gamma-resorcylate decarboxylase, revealed that the maximum relative mRNA expression level ([5.93 +/- 0.82] x 10(-4)) of graF was detected in the total RNA of the cells after one hour of cultivation when gamma-resorcylate was used as the sole carbon source. Reverse transcription-PCR of graDAFCBE showed that these genes are transcribed as a single mRNA and that the transcription of the gene cluster is induced by gamma-resorcylate. These results suggested that the graDAFCBE genes are responsible as an operon for the growth of Rhizobium sp. strain MTP-10005 on gamma-resorcylate and are probably regulated by GraR at the transcriptional level. This is the first report of the gamma-resorcylate catabolic pathway in an aerobic bacterium.

Base Sequence↗
PubMed2006

Functional analysis of Arabidopsis thaliana RHM2/MUM4, a multidomain protein involved in UDP-D-glucose to UDP-L-rhamnose conversion.

UDP-L-rhamnose is required for the biosynthesis of cell wall rhamnogalacturonan-I, rhamnogalacturonan-II, and natural compounds in plants. It has been suggested that the RHM2/MUM4 gene is involved in conversion of UDP-D-glucose to UDP-L-rhamnose on the basis of its effect on rhamnogalacturonan-I-directed development in Arabidopsis thaliana. RHM2/MUM4-related genes, RHM1 and RHM3, can be found in the A. thaliana genome. Here we present direct evidence that all three RHM proteins have UDP-D-glucose 4,6-dehydratase, UDP-4-keto-6-deoxy-D-glucose 3,5-epimerase, and UDP-4-keto-L-rhamnose 4-keto-reductase activities in the cytoplasm when expressed in the yeast Saccharomyces cerevisiae. Functional domain analysis revealed that the N-terminal region of RHM2 (RHM2-N; amino acids 1-370) has the first activity and the C-terminal region of RHM2 (RHM2-C; amino acids 371-667) has the two following activities. This suggests that RHM2 converts UDP-d-glucose to UDP-L-rhamnose via an UDP-4-keto-6-deoxy-D-glucose intermediate. Site-directed mutagenesis of RHM2 revealed that mucilage defects in MUM4-1 and MUM4-2 mutant seeds of A. thaliana are caused by abolishment of RHM2 enzymatic activity in the mutant strains and furthermore, that the GXXGXX(G/A) and YXXXK motifs are important for enzymatic activity. Moreover, a kinetic analysis of purified His(6)-tagged RHM2-N protein revealed 5.9-fold higher affinity of RHM2 for UDP-D-glucose than for dTDP-D-glucose, the preferred substrate for dTDP-D-glucose 4,6-dehydratase from bacteria. RHM2-N activity is strongly inhibited by UDP-L-rhamnose, UDP-D-xylose, and UDP but not by other sugar nucleotides, suggesting that RHM2 maintains cytoplasmic levels of UDP-D-glucose and UDP-L-rhamnose via feedback inhibition by UDP-L-rhamnose and UDP-D-xylose.

Amino Acid Motifs↗
PubMed2003

Isolation and functional analysis of the 5'-flanking region of carrot top1beta gene coding for the beta isoform of DNA topoisomerase I.

We have isolated and functionally characterized the promoter region of the top1beta gene encoding carrot (Daucus carota) DNA topoisomerase Ibeta. The major transcription start site was mapped by primer extension analysis 164 nt upstream the ATG translation start codon. Sequence analysis of the 5'-upstream region of the gene revealed the presence of a canonical TATA-like box at position -35 bp and several cis-acting sequences, including a (CT)n element in the leader region of the gene, a myb-related motif and the Dof element NtBBF-1, which correlate with the inducible expression pattern of this gene. Functional reporter analysis of the top1beta 5'-flanking region was performed in both carrot and Arabidopsis thaliana transfected protoplasts. The region at -719 to +161 was sufficient to confer high expression level in both species. The transient expression assay in protoplasts induced to stop dividing confirmed that the promoter, whose activity is low in quiescent cells, is activated when protoplasts are induced to proliferate by exogenous application of growth factors.

5' Flanking Region↗
PubMed2004

Bessel-function analysis of the optimized star coupler for uniform power splitting.

An optimized N x N planar optic star coupler that utilizes directional coupling of arrayed waveguides for uniform power splitting is analyzed on the basis of special properties of the involved Bessel-function series. The analysis has provided a remarkably simple, novel basic design formula for such a device with much needed physical insights into the unique diffraction properties. For the analysis of diffraction from the end of directionally coupled arrayed waveguides, many useful formulas around the Bessel functions, such as the addition theorem and the Kepler-Bessel series, have been given in new forms.

Journal Article↗
PubMed1998

New modalities of regional and global left ventricular function analysis: state of the art.

Study of left ventricular (LV) regional and global function represents a main point of the cardiologic evaluation. This article presents an overview of the state of the art in quantitative analysis of ventricular wall motion and describes the different techniques available in clinical settings; we also present the personal experience of the authors in comparing conventional 2-dimensional (2D) echocardiography with other recently developed, more sophisticated techniques. Conventional 2D echocardiography mainly depends on the operator's ability. Moreover, the physiologic regional pattern of myocardial wall motion in different segments of left ventricle is still not completely known as well as the heart's rotational and translational movements. Qualitative and quantitative transesophageal echocardiography allows a better and more accurate evaluation of regional wall motion, and improves the on-line border detection feasibility even in patients with poor transthoracic echocardiographic window. The automated system for on-line endocardial border detection, color kinesis, and the power Doppler are, at the moment, promising techniques. Using magnetic resonance imaging as a "gold standard" for the study of global and regional left ventricular function, the investigators describe personal experiences with tissue Doppler imaging and a new computerized system for tissue Doppler images postprocessing analysis.

Adolescent↗
PubMed2001

Functional analysis of glucose-dependent insulinotropic polypeptide fusion proteins.

To generate functional fluorescently tagged glucose-dependent insulinotropic polypeptide (GIP), a series of GIP expression constructs were devised. These included G1 (complete preprohormone), G2 (lacking the C-terminal extension), G3 (lacking both N- and C-terminal extensions), G4 (G2 fused to green fluorescent protein, GFP), and G5 (G3 fused to GFP). Expression of G5 in bacteria generated immunopositive GIP together with GFP fluorescence, while G4 generated only fluorescence without immunoreactivity. Transfection of NIH3T3 cells with cDNAs of G1, G3, G5, but not G2, G4, and EGFP, resulted in immunologically detectable GIP formation, although fluorescence could be detected in the latter two. GIP as well as GIP-GFP secreted by NIH3T3 cells significantly stimulated intracellular cAMP accumulation and Ca(2+) mobilization in SaOS2 cells. The GIP receptor antagonist GIP(7-30) abolished these responses. These results suggest that a GIP-GFP fusion protein seven times larger than the native peptide retains function and may be used as an in vivo probe to detect GIP receptor distribution and to explore GIP's biological roles.

3T3 Cells↗
PubMed1990

Elucidation of the Erwinia uredovora carotenoid biosynthetic pathway by functional analysis of gene products expressed in Escherichia coli.

The most important function of carotenoid pigments, especially beta-carotene in higher plants, is to protect organisms against photooxidative damage (G. Britton, in T. W. Goodwin, ed., Plant Pigments--1988, 1988; N. I. Krinsky, in O. Isler, H. Gutmann, and U. Solms, ed., Carotenoids--1971, 1971). beta-Carotene also functions as a precursor of vitamin A in mammals (G. A. J. Pitt, in I. Osler, H. Gutmann, and U. Solms, ed., Carotenoids--1971, 1971). The enzymes and genes which mediate the biosynthesis of cyclic carotenoids such as beta-carotene are virtually unknown. We have elucidated for the first time the pathway for biosynthesis of these carotenoids at the level of enzyme-catalyzed reactions, using bacterial carotenoid biosynthesis genes. These genes were cloned from a phytopathogenic bacterium, Erwinia uredovora 20D3 (ATCC 19321), in Escherichia coli and located on a 6,918-bp fragment whose nucleotide sequence was determined. Six open reading frames were found and designated the crtE, crtX, crtY, crtI, crtB, and crtZ genes in reference to the carotenoid biosynthesis genes of a photosynthetic bacterium, Rhodobacter capsulatus; only crtZ had the opposite orientation from the others. The carotenoid biosynthetic pathway in Erwinia uredovora was clarified by analyzing carotenoids accumulated in E. coli transformants in which some of these six genes were expressed, as follows: geranylgeranyl PPiCrtB----prephytoene PPiCrtE----phytoeneCrtI---- lycopeneCrtY----beta-caroteneCrtZ----zeaxanthinCrtX--- -zeaxanthin-beta- diglucoside. The carotenoids in this pathway appear to be close to those in higher plants rather than to those in bacteria. Also significant is that only one gene product (CrtI) for the conversion of phytoene to lycopene is required, a conversion in which four sequential desaturations should occur via the intermediates phytofluene, zeta-carotene, and neurosporene.

Amino Acid Sequence↗
PubMed2004

Functional analysis of Drosophila melanogaster gene regulatory sequences by transgene coplacement.

The function of putative regulatory sequences identified by comparative genomics can be elucidated only through experimentation. Here the effectiveness of using heterologous gene constructs and transgene coplacement to characterize regulatory sequence function is demonstrated. This method shows that a sequence in the Adh 3'-untranslated region negatively regulates expression, independent of gene or chromosomal context.

Alcohol Dehydrogenase↗
PubMed2006

Functional analysis of the chemokine receptor CCR3 on airway epithelial cells.

The function of chemokine receptors on structural cells is only partially known. We previously reported the expression of a functional CCR3 receptor on airway epithelial cells (EC). We speculated that CCR3 might drive wound repair and expression of inflammatory genes in epithelium. The human airway EC lines BEAS-2B, 16-HBE, and primary bronchial EC were used to test the effect of in vitro challenge with the CCR3 ligands CCL11/eotaxin, CCL24/eotaxin-2, or CCL26/eotaxin-3 on 1) wound repair, using an established wound model; 2) cell proliferation and chemotaxis, using specific fluorometric assays; and 3) gene expression, using pathway-specific arrays for inflammatory and profibrotic cytokines, chemokines, and chemokine receptor genes. Agonist specificity was tested by cell pretreatment with an AstraZeneca CCR3 antagonist (10(-8) - 10(-6) M). CCL24 challenge significantly accelerated epithelial wound closure, with similar effects exerted by CCL11 and CCL26. This effect was time dependent, submaximal at 1 nM, and comparable in potency to epidermal growth factor. CCL24 induced a concentration-dependent increase in EC proliferation and chemotaxis, with significant effects observed at 10 nM. The AstraZeneca compound selectively inhibited these CCL24-mediated responses. CCL11 induced the up-regulation of several profibrogenic molecules such as fibroblast growth factor 1 and 5 and of several CC and CXC chemokines. Epithelial immunostaining for CCR3 was stronger in bronchial biopsies of asthmatics displaying marked inflammatory changes than in nondiseased samples. Epithelial CCR3 participates in key functions for wound repair, amplifies the expression of profibrogenic and chemokine transcripts, and appears up-regulated in inflamed asthmatic airways.

Cell Line↗
PubMed1983

Reliability of the nasopharyngeal fiberscope (NPF) for assessing velopharyngeal function: analysis by judgment.

The reliability and validity of data about velopharyngeal function obtained with the nasopharyngeal fiberscope was assessed in normal subjects. The experimental design included data reduction procedures that are likely to have clinical utility (clinical ratings). The results indicated that relative velar movement and size of the velopharyngeal port may be reliably and validly estimated using the procedures. However NPF estimates of lateral pharyngeal wall movement were not reliable. Finally, the data indicated that velar movement and size of V-P port were consistent within subjects and tasks across data collection sessions. Data about consistency of lateral wall movement across sessions was inconclusive, however. Additional research involving similar procedures with subjects who have morphologic deficits is indicated.

Cineradiography↗
PubMed1997

Functional analysis of V3A and related areas in human visual cortex.

Using functional magnetic resonance imaging (fMRI) and cortical unfolding techniques, we analyzed the retinotopy, motion sensitivity, and functional organization of human area V3A. These data were compared with data from additional human cortical visual areas, including V1, V2, V3/VP, V4v, and MT (V5). Human V3A has a retinotopy that is similar to that reported previously in macaque: (1) it has a distinctive, continuous map of the contralateral hemifield immediately anterior to area V3, including a unique retinotopic representation of the upper visual field in superior occipital cortex; (2) in some cases the V3A foveal representation is displaced from and superior to the confluent foveal representations of V1, V2, V3, and VP; and (3) inferred receptive fields are significantly larger in human V3A, compared with those in more posterior areas such as V1. However, in other aspects human V3A appears quite different from its macaque counterpart: human V3A is relatively motion-selective, whereas human V3 is less so. In macaque, the situation is qualitatively reversed: V3 is reported to be prominently motion-selective, whereas V3A is less so. As in human and macaque MT, the contrast sensitivity appears quite high in human areas V3 and V3A.

Anatomy, Cross-Sectional↗
PubMed1977

The cruciate ligaments of the canine stifle: an anatomical and functional analysis.

Fifty canine stifles were used to study the anatomy and function of the cruciate ligaments. The morphology of the ligaments and the shape of their bony attachments were determined by dissection. The relative tension of the ligaments in flexion and extension was determined by identifying the points of attachment of ligament fibers with small pins and making multiple radiographs as the stifle was taken through a range of motion. The distance between these points was then measured and the linear changes in the ligaments were defined. Measurements of rotation, craniocaudal displacement, extension, and flexion were made before and after cutting of one or both ligaments. It was found that both cruciate ligaments were composed of 2 component parts and that the geometry of their femoral attachments was responsible for a reciprocal loosening and tightening of these components through a range of motion. It was also found that transection of one or both cruciate ligaments resulted in marked joint instability.

Animals↗
PubMed2002

Functional analysis of the TFIID-specific yeast TAF4 (yTAF(II)48) reveals an unexpected organization of its histone-fold domain.

Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAF(II)s), nine of which contain histone-fold domains (HFDs). The C-terminal region of the TFIID-specific yTAF4 (yTAF(II)48) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 (dTAF(II)110) and human TAF4 (hTAF(II)135). A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. Temperature-sensitive mutations in the yTAF4 HFD alpha2 helix or the CCTD can be suppressed upon overexpression of yTAF12 (yTAF(II)68). Moreover, coexpression in Escherichia coli indicates direct yTAF4-yTAF12 heterodimerization optimally requires both the yTAF4 HFD and CCTD. The x-ray crystal structure of the orthologous hTAF4-hTAF12 histone-like heterodimer indicates that the alpha3 region within the predicted TAF4 HFD is unstructured and does not correspond to the bona fide alpha3 helix. Our functional and biochemical analysis of yTAF4, rather provides strong evidence that the HFD alpha3 helix of the TAF4 family lies within the CCTD. These results reveal an unexpected and novel HFD organization in which the alpha3 helix is separated from the alpha2 helix by an extended loop containing a conserved functional domain.

Amino Acid Sequence↗
PubMed2004

Pharmacogenomics of drug transporters: a new approach to functional analysis of the genetic polymorphisms of ABCB1 (P-glycoprotein/MDR1).

In the 21st century, emerging genomic technologies (i.e., bioinformatics, functional genomics, and pharmacogenomics) are shifting the paradigm of drug discovery research and improving the strategy of medical care for patients. In order to realize the personalized medicine, it is critically important to understand molecular mechanisms underlying inter-individual differences in the drug response, namely, pharmacological effect vs. side effect. Evidence is now accumulating to strongly suggest that drug transporters are one of the determinant factors governing the pharmacokinetic profile of drugs. Effort has been made to identify genetic variation in drug transporter genes. In particular, genetic variations of the human ABCB1 (P-glycoprotein/MDR1) gene have been most extensively studied. Hitherto more than fifty single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms in the ABCB1 gene have been reported. However, at the present time, information is still limited with respect to the actual effect of those genetic polymorphisms on the function of ABCB1. In this context, we have undertaken functional analyses of ABCB1 polymorphisms. To quantify the impact of genetic polymorphisms on the substrate specificity of ABCB1, we have developed a high-speed screening system and a new structure-activity relationship (SAR) analysis method. This review addresses functional aspects of the genetic polymorphism of ABCB1 and provides the standard method to evaluate the effect of polymorphisms on the function.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2026

Genome-Wide Identification of the R2R3-MYB Gene Family in Solanum americanum and Functional Analysis of Its Role in Fruit Coloration.

Anthocyanins are key secondary metabolites responsible for fruit coloration in plants, and their biosynthesis is largely regulated by R2R3-MYB transcription factors. However, the R2R3-MYB regulators controlling fruit anthocyanin accumulation in wild Solanum species remain poorly understood. Here, Solanum americanum was used to identify candidate R2R3-MYB genes associated with fruit coloration through genome-wide identification, phylogenetic analysis, synteny analysis, expression profiling, and virus-induced gene silencing (VIGS). A total of 122 SaMYB genes were identified, and phylogenetic analysis revealed that SaMYB proteins clustered with Arabidopsis thaliana R2R3-MYB members in conserved subgroups, suggesting evolutionary conservation of this family. Synteny analysis identified 37 syntenic gene pairs among SaMYB genes, and the Ka/Ks values of all analyzable gene pairs were below 1, indicating that these duplicated genes are subject to functional constraint. Integrated analysis of phylogenetic relationships, protein structures, promoter cis-elements, and fruit developmental expression patterns identified SaMYB59 and SaMYB106 as candidate regulators of anthocyanin accumulation. VIGS analysis demonstrated that silencing SaMYB106 reduced purple coloration, decreased anthocyanin content, and downregulated the expression of the structural gene DFR. These results indicate that SaMYB106 functions as a positive regulator of fruit anthocyanin accumulation in S. americanum. This study provides insights into the molecular basis of fruit coloration in wild Solanum species.

Solanum americanum↗
PubMed1997

Cloning and functional analysis of rat cyclin D2 promoter: multiple prolactin-responsive elements.

Structure and function of the promoter region of rat cyclin D2 gene were investigated by cloning, sequence analysis and DNA mobility shift assay using nuclear extracts of prolactin-stimulated Nb2 cells. The results show that the expression of rat cyclin D2 gene is not dependent on the TATA-box but is stimulated by multiple transcription factors induced by prolactin at an immediate-early stage of the cell cycle.

Amino Acid Sequence↗
PubMed1995

Murine models of neoplasia: functional analysis of the tumour suppressor genes Rb-1 and p53.

Loss of function of one or both of the two tumour suppressor genes p53 and RB-1 has been recognised as an important step in the development of a variety of human neoplasias for some time. By virtue of the ability to manipulate the genome of murine embryonic stem cells in culture, it has become possible to generate strains of mice which bear inactivations of the murine counterparts of these genes. This article attempts to bring together some of the many results obtained from these murine strains which are shedding light both on the normal role played by both of these genes and the consequences of their dysfunction. Surprisingly neither gene product is revealed to have an indispensable role at the level of the single cell. Hence, even though the Rb-1 gene product clearly has an important role in cell cycle regulation animals constitutively deficient in this gene develop relatively normally for the first 10 days of embryogenesis. It is only at and beyond this stage of development that a requirement for Rb-1 becomes clear, in the regulation of certain cell populations through control of both proliferation and apoptosis. That loss of function of Rb-1 is associated with tumorigenesis is confirmed by the development of tumours of the pituitary gland within heterozygotes. The retinas of these animals, the target organ for tumorigenesis in human RB-1 heterozygotes, remain unaffected. The majority of mice homozygous for an inactivating p53 mutation survive to birth, but then rapidly succumb to tumorigenesis. Heterozygotes also develop tumours, but with a delayed time course and altered spectrum. Analysis of several tissue types from the mutant animals has shown p53 to be crucial for the normal induction of apoptosis following DNA damage, and it is thought that failure of this process is a key predisposing step towards tumorigenesis within the mutant animals. Finally, studies on these and other transgenic strains have revealed interactions between pathways governed by these two genes. For example, the fate of Rb-1 deficient cells has been shown, in some tissues at least, to be dependent upon the functional status of p53.

Animals↗