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 397 records · Page 22Linked to original sources
PubMed1995

Nucleotide sequence and functional analysis of regulatory region of the lumP and the lux operon from Photobacterium leiognathi.

The lumP gene is linked to the lux operon, but runs in the opposite direction in Photobacterium leiognathi PL741. The gene order of the lumP and the lux operon is < -lumP-R & R-luxC-luxD-luxA-luxB-luxN-luxE- > (R & R: regulatory region). The nucleotide sequence of the regulatory region (827-bp) between the lumP and the lux operon was determined. Sequence analysis illustrates that the regulatory region includes two divergent promoter systems, PR-promoter system for the lux operon (R-operon) and PL-promoter system for the lumP or lum operon (L-operon). Functional analysis of the regulatory region shows that the PR- and PL-promoter systems both are able to lead the gene expression. The deletion experiment result elicits that the PR- and PL-promoter are coordinatively and negatively regulated; the PR- and PL-promoter might be competing for recognition by RNA polymerase to initiate transcription. The fact of the LumP responsible for the spectral blue shift in P. leiognathi implied that the lumP gene closedly linked to the lux operon is for coordinative regulation with the lux operon. In addition, the glucose repression on the PR-promoter system shows that the expression of the lux operon is regulated by cAMP-CRP induction in E. coli.

Base Sequence↗
PubMed1994

Molecular and functional analysis of a lymphocyte chemoattractant factor: association of biologic function with CD4 expression.

Lymphocyte chemoattractant factor (LCF) is a lymphocyte cell product that stimulates a migratory response in CD4+ lymphocytes, monocytes, and eosinophils. In concert with its chemoattractant activity, LCF induces human T-lymphocyte expression of interleukin 2 receptor. Here we describe the molecular cloning of cDNA encoding human LCF. It is a novel interleukin with no significant homology to any previously described cytokine families. There is an absolute requirement for both autoaggregation of LCF monomers and for membrane-expressed CD4 molecules for LCF-induced migration in lymphocytes.

Amino Acid Sequence↗
PubMed2003

Sex determination from the talus of South african whites by discriminant function analysis.

The field of forensic anthropology involves the building of an antemortem profile of an individual from skeletal remains. This includes sex and race determination and age and stature estimation. Since most bones that are conventionally used for sex determination are often recovered either in a fragmented or incomplete state, it has become necessary to use denser bones that are often recovered intact, eg, the patella, calcaneus, and talus. Thus the aim of this study is to assess the sex-determining ability of each of the measurements of the talus and derive discriminant function equations for sex determination in the South African white population. Sixty male and 60 female tali of South African whites obtained from the Raymond A. Dart Collection of Human Skeletons were used. Nine measurements were taken on each talus. Descriptive statistics and discriminant function analysis were performed on the acquired data. The basic statistics showed that all measurements were sexually dimorphic. Univariate, stepwise, and direct discriminant function equations were generated for use in sex determination. The level of average accuracy of sex classification was 80% to 82% for the univariate method, 85% to 88% for the stepwise method, and 81% to 86% for the direct method. It is concluded that the talus of South African whites is useful for sex determination.

Adolescent↗
PubMed2004

Identification and functional analysis of Hyphantria cunea nucleopolyhedrovirus iap genes.

Hyphantria cunea nucleopolyhedrovirus (HycuNPV) infection protected SpIm cells from actinomycin D (ActD)-induced apoptosis as early as 4 h postinfection. Analysis by Southern hybridization revealed that the HycuNPV genome possessed three members of inhibitor of apoptosis genes (iaps) that were designated as hycu-iap1, hycu-iap2, and hycu-iap3 because of their amino acid sequence homology with iaps identified in other baculoviruses. Functional analysis of Hycu-IAPs by transient expression assay in Sf9 cells revealed that Hycu-IAP3 blocked apoptosis induced by actinomycin D and rescued replication of p35 deficient-mutant AcMNPV, while Hycu-IAP1 and Hycu-IAP2 did not show any anti-apoptotic functions. Knockdown of hycu-iap3 expression by RNAi during HycuNPV infection in SpIm cells induced apoptosis. These results indicate that Hycu-IAP3 is essential for blockage of apoptosis during HycuNPV infection of permissive SpIm cells.

Amino Acid Sequence↗
PubMed2000

Sex determination by discriminant function analysis of the right tibia in the prehispanic population of the Canary Islands.

This study has been performed in order to define standards usable to determine the sex of prehispanic individuals from the Canary Islands from their skeletal remains. Osteometric information at the right tibia was obtained from 59 complete skeletons from Gran Canaria, housed in the Museo Canario (Las Palmas), 45 males and 14 females (this constitutes the totality of complete prehispanic skeletons known from Gran Canaria). The parameters measured were: tibial length, proximal and distal epiphyseal breadth, transverse and anteroposterior diameter, perimeter at the nutrition foramen levels and minimum shaft perimeter. These parameters were subjected to different SPSS discriminant function analysis, combining all of them, or only the proximal or distal ones, without tibial length, etc., in order to obtain functions usable even if only bone fragments are available. Transverse diameter, proximal epiphyseal breadth and minimum shaft perimeter showed the highest discriminant power. The functions obtained showed high average accuracies, ranging from 94.9 to 98.3%, with female accuracies of 100%. The functions obtained were further applied to a test prehispanic population (ten males and ten females) from El Hierro. Overall accuracies of the functions when applied to this population ranged from 65 to 94.7%, with female accuracies ranging 80% to 100%.

Atlantic Islands↗
PubMed2006

Molecular cloning, characterization and functional analysis of a 2C-methyl- D-erythritol 2, 4-cyclodiphosphate synthase gene from ginkgo biloba.

2C-methyl-D-erythritol 2, 4-cyclodiphosphate synthase (MECPS, EC: 4.6.1.12) is the fifth enzyme of the non-mevalonate terpenoid pathway for isopentenyl diphosphate biosynthesis and is involved in the methylerythritol phosphate (MEP) pathway for ginkgolide biosynthesis. The full-length mecps cDNA sequence (designated as Gbmecps) was cloned and characterized for the first time from gymnosperm plant species, Ginkgo biloba, using RACE (rapid amplification of cDNA ends) technique. The full-length cDNA of Gbmecps was 874 bp containing a 720 bp open reading frame (ORF) encoding a peptide of 239 amino acids with a calculated molecular mass of 26.03 kDa and an isoelectric point of 8.83. Comparative and bioinformatic analyses revealed that GbMECPS showed extensive homology with MECPSs from other species and contained conserved residues owned by the MECPS protein family. Phylogenetic analysis indicated that GbMECPS was more ancient than other plant MECPSs. Tissue expression pattern analysis indicated that GbMECPS expressed the highest in roots, followed by in leaves, and the lowest in seeds. The color complementation assay indicated that GbMECPS could accelerate the accumulation of beta-carotene. The cloning, characterization and functional analysis of GbMECPS will be helpful to understand more about the role of MECPS involved in the ginkgolides biosynthesis at the molecular level.

Amino Acid Sequence↗
PubMed1999

RESEARCH: Evaluating Sustainability of Watershed Resources Management Through Wetland Functional Analysis.

/ Unsustainable agricultural policies and water and soil resource schemes have drained two thirds of Mediterranean wetlands since 1920. An outstanding example is Karla in Greece, a former internationally important wetland that was drained in 1962 causing environmental, social, and water and soil problems. The objective of this study was to assess the functions and values of Karla, at three periods of its history, and to relate them to major events in the management of the water and soil resources of its watershed. Information on wetland and watershed features was collectedfrom historical records and field visits. The results showed that the wetland in its pristine state had performed five functions to a high degree, one (groundwater recharge) to a moderate degree, and one (flood storage) to a low degree. Flood-control works, uncontrolled pumping, etc., in 1936-1961 degraded all functions except microclimate modification while, the bird support function was moderately altered. Drainage works in 1962 left a very small artificially flooded wetland with only four functions performed to an insignificant degree. Value degradation followed function degradation. It was concluded that past resource management has been nonintegrated. No consideration was given to the multiple functions and values of Karla. Previous restoration proposals involved the reinstatement of one or two functions only. The appropriate restoration scheme for Karla must be multiobjective and based on the integrated resource management of its own and the neighboring watersheds.KEY WORDS: Soil and water resources; Sustainability; Watershed management; Wetland functional analysis; Karla wetlandhttp://link.springer-ny.com/link/service/journals/00267/bibs/24n2p193.html

Journal Article↗
PubMed1983

Clonal expansion and functional analysis of virus-specific T lymphocytes from cerebrospinal fluid in measles encephalitis.

T cells were directly cloned from the cerebrospinal fluid (CSF) of a patient with acute measles encephalitis by limiting dilution in the presence of irradiated feeder cells and T cell growth factor (TCGF). A total of 42 colonies was established. Functional analysis revealed 27 of them to be derived from a cytotoxic T lymphocyte as demonstrated by the ability to exert phytohaemagglutinin (PHA)-dependent cytotoxicity against uninfected allogeneic PHA blasts. Twenty-three of the cytotoxic colonies were specific for measles virus and restricted to self HLA-A or -B antigens. Three clones were also found to give measles virus-specific proliferative responses. The results show that the CSF in measles encephalitis contains a highly enriched population of in vivo sensitized antigen-specific T cells. We propose that the clinical symptoms in measles encephalitis are caused by a T cell-mediated reaction against virus-infected brain cells.

Child↗
PubMed2005

Functional analysis of transactivation by mutants of hepatitis B virus X gene in human hepatocellular carcinoma.

The X protein of the hepatitis B virus transactivates various cellular and viral promoters and enhancers. In this study, wild-type and mutants of the X gene, including the point mutations at codons 130 (AAG-->ATG, lysin-->methionine) and 131 (GTC-->ATC, valine-->isoleucine), commonly found in patients with human hepatocellular carcinoma (HCC), or deletions encompassing the same region, were cloned and inserted into expression vectors. Functional analysis of the mutants of the X gene was performed on the long terminal repeat of the Rous sarcoma virus in a transient transfection assay. A transactivating function was observed in the vector containing point mutations at codons 130 and 131 at the same level as that of wild-type X gene. Two constructs, each containing a different type of 8-nucleotide deletion mutant (codons 128-130 or 130-132,) dramatically lost their transactivating function. These findings suggest that the transactivating function is not necessarily associated with the development of HCC, and that not only transactivation by the X gene but also the mutation-enhanced oncogenic potential of the gene products could contribute to hepatocarcinogenesis.

Animals↗
PubMed2004

Functional analysis of the matricellular protein SPARC with novel monoclonal antibodies.

SPARC (osteonectin, BM-40) is a matricellular glycoprotein that is expressed in many embryogenic and adult tissues undergoing remodeling or repair. SPARC modulates cellular interaction with the extracellular matrix (ECM), inhibits cell adhesion and proliferation, and regulates growth factor activity. To explore further the function and activity of this protein in tissue homeostasis, we have developed several monoclonal antibodies (MAbs) that recognize distinct epitopes on SPARC. The MAbs bind to SPARC with high affinity and identify SPARC by ELISA, Western blotting, immunoprecipitation, immunocytochemistry, and/or immunohistochemistry. The MAbs were also characterized in functional assays for potential alteration of SPARC activity. SPARC binds to collagen I and laminin-1 through an epitope defined by MAb 293; this epitope is not involved in the binding of SPARC to collagen III. The other MAbs did not interfere with the binding of SPARC to collagen I or III or laminin-1. Inhibition of the anti-adhesive effect of SPARC on endothelial cells by MAb 236 was also observed. Functional analysis of SPARC in the presence of these novel MAbs now confirms that the activities ascribed to this matricellular protein can be assigned to discrete subdomains.

Animals↗
PubMed2003

Functional analysis of the Mycobacterium tuberculosis MprAB two-component signal transduction system.

The mechanisms utilized by Mycobacterium tuberculosis to establish, maintain, or reactivate from latent infection in the host are largely unknown but likely include genes that mediate adaptation to conditions encountered during persistence. Previously, a two-component signal transduction system, mprAB, was found to be required in M. tuberculosis for establishment and maintenance of persistent infection in a tissue- and stage-specific fashion. To begin to characterize the role of this system in M. tuberculosis physiology and virulence, a functional analysis of the mprA and mprB gene products was initiated. Here, evidence is presented demonstrating that sensor kinase MprB and response regulator MprA function as an intact signal-transducing pair in vitro and in vivo. Sensor kinase MprB can be autophosphorylated, can donate phosphate to MprA, and can act as a phospho-MprA phosphatase in vitro. Correspondingly, response regulator MprA can accept phosphate from MprB or from small phosphodonors including acetyl phosphate. Mutagenesis of residues His249 in MprB and Asp48 in MprA abolished the ability of these proteins to be phosphorylated in vitro. Introduction of these alleles into Mycobacterium bovis BCG attenuated virulence in macrophages in vivo. Together, these results support a role for the mprAB two-component system in M. tuberculosis physiology and pathogenesis. Characterization of two-component signal transduction systems will enhance our understanding of processes regulated by M. tuberculosis during acute and/or persistent infection in the host.

Animals↗
PubMed2006

Isolation and characterization of Xenopus laevis homologs of the mouse inv gene and functional analysis of the conserved calmodulin binding sites.

The homozygous inv (inversion of embryonic turning) mouse mutant shows situs inversus and polycystic kidney disease, both of which result from the lack of the inv gene. Previously, we suggested that inv may be important for the left-right axis formation, not only in mice but also in Xenopus, and that calmodulin regulates this inv protein function. Here, we isolated and characterized two Xenopus laevis homologs (Xinv-1 and Xinv-2) of the mouse inv gene, and performed functional analysis of the conserved IQ motifs that interact with calmodulin. Xinv-1 expresses early in development in the same manner as mouse inv does. Unexpectedly, a full-length Xenopus inv mRNA did not randomize cardiac orientation when injected into Xenopus embryos, which is different from mouse inv mRNA. Contrary to mouse inv mRNA, Xenopus inv mRNA with mutated IQ randomized cardiac orientation. The present study indicates that calmodulin binding sites (IQ motifs) are crucial in controlling the biological activity of both mouse and Xenopus inv proteins. Although mouse and Xenopus inv genes have a quite similar structure, the interaction with calmodulin and IQ motifs of Xenopus inv and mouse inv proteins may regulate their function in different ways.

Amino Acid Sequence↗
PubMed2005

Functional analysis of p53 tumor suppressor in yeast.

The p53 tumor suppressor protein is a transcription factor that mediates the cell's response to various kinds of stress by preventing cell division and/or inducing apoptosis. p53 gene mutations have been detected in nearly 50% of human cancers. These gene aberrations are mostly missense point mutations located predominantly in the central DNA-binding domain. In addition to the classical inactivating mutations, there are also dominant-negative, gain-of-function, temperature-sensitive, and cold-sensitive, discriminating, superactive p53 mutations, and some mutations that do not inactivate p53 activity. Several approaches have been developed for detection and analyses of p53 mutations: first, immunochemical methods have been developed to detect p53 protein levels; second, molecular analyses targeting changes in DNA structure are utilized; and third, functional assays are used to explore the biological properties of the p53 protein. Functional analysis of separated alleles in yeast targets the transactivation capability of the p53 protein expressed in yeast cells. This method uses p53 mRNA isolated from cells and tissues to produce a p53 product by RT-PCR. This method has undergone continuous improvement and now serves as a powerful tool for distinguishing various functional types of p53 mutations. Understanding the exact impact of p53 mutation on its function is an important prerequisite for establishment of efficient anti-cancer therapies.

DNA Mutational Analysis↗
PubMed2001

Pectin: cell biology and prospects for functional analysis.

Pectin is a major component of primary cell walls of all land plants and encompasses a range of galacturonic acid-rich polysaccharides. Three major pectic polysaccharides (homogalacturonan, rhamnogalacturonan-I and rhamnogalacturonan-II) are thought to occur in all primary cell walls. This review surveys what is known about the structure and function of these pectin domains. The high degree of structural complexity and heterogeneity of the pectic matrix is produced both during biosynthesis in the endomembrane system and as a result of the action of an array of wall-based pectin-modifying enzymes. Recent developments in analytical techniques and in the generation of anti-pectin probes have begun to place the structural complexity of pectin in cell biological and developmental contexts. The in muro de-methyl-esterification of homogalacturonan by pectin methyl esterases is emerging as a key process for the local modulation of matrix properties. Rhamnogalacturonan-I comprises a highly diverse population of spatially and developmentally regulated polymers, whereas rhamnogalacturonan-II appears to be a highly conserved and stable pectic domain. Current knowledge of biosynthetic enzymes, plant and microbial pectinases and the interactions of pectin with other cell wall components and the impact of molecular genetic approaches are reviewed in terms of the functional analysis of pectic polysaccharides in plant growth and development.

Cell Wall↗
PubMed2000

Identification and functional analysis of three isoforms for the Na+-dependent phosphate co-transporter (NaPi-2) in rat kidney.

We have isolated three unique NaPi-2-related protein cDNAs (NaPi-2alpha, NaPi-2beta and NaPi-2gamma) from a rat kidney library. NaPi-2alpha cDNA encodes 337 amino acids which have high homology to the N-terminal half of NaPi-2 containing three transmembrane domains. NaPi-2beta encodes 327 amino acids which are identical to the N-terminal region of NaPi-2 containing four transmembrane domains, whereas the 146 amino acids in the C-terminal region are completely different. In contrast, NaPi-2gamma encodes 268 amino acids which are identical to the C-terminal half of NaPi-2. An analysis of phage and cosmid clones indicated that the three related proteins were produced by alternative splicing in the NaPi-2 gene. In a rabbit reticulocyte lysate system, NaPi-2alpha, beta and gamma were found to be 36, 36 and 29 kDa polypeptides, respectively. NaPi-2alpha and NaPi-2gamma were glycosylated and revealed to be 45 and 35 kDa proteins, respectively. A functional analysis demonstrated that NaPi-2gamma and alpha markedly inhibited NaPi-2 activity in Xenopus oocytes. The results suggest that these short isoforms may function as a dominant-negative inhibitor of the full-length transporter.

Animals↗
PubMed2005

Physical map of the Azoarcus sp. strain BH72 genome based on a bacterial artificial chromosome library as a platform for genome sequencing and functional analysis.

Azoarcus sp. strain BH72 is a Gram-negative proteobacterium of the beta subclass; it is a diazotrophic endophyte of graminaceous plants and can provide significant amounts of fixed nitrogen to its host plant Kallar grass. We aimed to obtain a physical map of the Azoarcus sp. strain BH72 chromosome to be directly used in functional analysis and as a part of an Azoarcus sp. BH72 genome project. A bacterial artificial chromosome (BAC) library was constructed and analysed. A representative physical map with a high density of marker genes was developed in which 64 aligned BAC clones covered almost the entire genome.

Azoarcus↗
PubMed2000

Structure-function analysis of SUV39H1 reveals a dominant role in heterochromatin organization, chromosome segregation, and mitotic progression.

SUV39H1, a human homologue of the Drosophila position effect variegation modifier Su(var)3-9 and of the Schizosaccharomyces pombe silencing factor clr4, encodes a novel heterochromatic protein that transiently accumulates at centromeric positions during mitosis. Using a detailed structure-function analysis of SUV39H1 mutant proteins in transfected cells, we now show that deregulated SUV39H1 interferes at multiple levels with mammalian higher-order chromatin organization. First, forced expression of full-length SUV39H1 (412 amino acids) redistributes endogenous M31 (HP1beta) and induces abundant associations with inter- and metaphase chromatin. These properties depend on the C-terminal SET domain, although the major portion of the SUV39H1 protein (amino acids 89 to 412) does not display affinity for nuclear chromatin. By contrast, the M31 interaction surface, which was mapped to the first 44 N-terminal amino acids, together with the immediately adjacent chromo domain, directs specific accumulation at heterochromatin. Second, cells overexpressing full-length SUV39H1 display severe defects in mitotic progression and chromosome segregation. Surprisingly, whereas localization of centromere proteins is unaltered, the focal, G(2)-specific distribution of phosphorylated histone H3 at serine 10 (phosH3) is dispersed in these cells. This phosH3 shift is not observed with C-terminally truncated mutant SUV39H1 proteins or with deregulated M31. Together, our data reveal a dominant role(s) for the SET domain of SUV39H1 in the distribution of prominent heterochromatic proteins and suggest a possible link between a chromosomal SU(VAR) protein and histone H3.

Cell Cycle Proteins↗