Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “functional experiments”

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 811 records · Page 45Linked to original sources
PubMed2004

What can we learn from highly purified neutrophils?

Neutrophil purification has traditionally been performed by centrifugation of leucocytes through density gradients. These reliable methods produce populations that are typically >95% pure neutrophils, and have allowed the widespread study of the function of these cells. Our recent work has suggested that residual monocytes may play a more important role than has been previously realized, and suggest that for some functional experiments, further purification of cells is required to understand fully the neutrophil phenotype.

Animals↗
PubMed2003

Response to culture aeration mediated by the nitrate and nitrite sensor NarQ of Escherichia coli K-12.

Respiratory enzyme synthesis in enterobacteria is controlled in response to electron acceptor availability. The iron-sulphur protein Fnr and the sensor-regulator proteins ArcB-ArcA control respiratory gene transcription in response to oxygen and quinone pool redox status respectively. The sensor-regulator proteins NarX-NarL and NarQ-NarP control anaerobic respiratory gene expression in response to nitrate and nitrite. Our laboratory recently engineered the lac operon to replace the primary operator O1-lac with the NarL and NarP protein binding site from the nirB operon. Expression of the lacZ gene from this construct is repressed by nitrate in Nar+ strains. Here, we found that lacZ gene expression was repressed in aerated cultures of narQ+narX null strains. This repression was not observed in narX+narQ+ or narX+narQ null strains. Thus, the NarQ sensor responds to aeration as well as to nitrate and nitrite. The NarX and NarQ sensors are composed of three distinct modules: an amino-terminal sensory module, a carboxyl-terminal transmitter module and a central module of unknown function. Experiments with NarX-NarQ hybrid proteins suggest that the NarQ protein central module is necessary for response to aeration. The physiological significance of this additional sensory role for the NarQ sensor remains obscure.

Binding Sites↗
PubMed1994

Abscisic acid promotes novel DNA-binding activity to a desiccation-related promoter of Craterostigma plantagineum.

Abscisic acid-treated callus of the resurrection plant Craterostigma plantagineum tolerates extreme desiccation. Nuclear proteins from tolerant callus bind specific sequence elements in the promoter region of the ABA and desiccation-inducible CDeT27-45 gene. One specific region of the promoter, which is protected from DNAase I treatment by DNA-binding activities, is different from previously reported ABA response elements. Four complexes of nuclear proteins and this DNA region are detected by electrophoretic mobility shift assay: two of these complexes (I and II) are readily detectable in untreated samples and are increased by ABA treatment while two other complexes (III and IV) accumulate only following ABA treatment and are prevented from accumulating by protein synthesis inhibitors. When a fragment containing the novel binding site is deleted from the wild-type promoter the ABA responsiveness of the promoter is removed; however, gain of function experiments using synthetic promoters in a protoplast transient assay suggest that besides the binding site other promoter elements are required. A second region of the promoter, containing the sequence element ACGT which is found in abscisic acid response elements, is also bound by nuclear proteins. The level of this second binding activity is similar in both untreated and ABA- treated cells and promoter/reporter gene constructs which contain only the four ACGT elements of the CDeT27-45 promoter are not ABA responsive in a C. plantagineum transient assay system.

Abscisic Acid↗
PubMed1997

Light-induced transcriptional repression of the pea AS1 gene: identification of cis-elements and transfactors.

Here, we examine the cis-elements and trans-factors affecting the expression of asparagine synthetase (AS) genes whose transcription is negatively regulated by light. The promoters for the AS1 and AS2 genes of pea were isolated, sequenced, and functionally dissected for their ability to confer regulated expression to the GUS reporter gene in transgenic tobacco. Histochemical analysis of transgenic plants demonstrated that the AS1 and AS2 promoters show identical patterns of cell-specific expression. The more highly active AS1 promoter was further demonstrated to confer negative light-regulation to the GUS gene in transgenic tobacco. Deletion analysis and gain-of-function experiments showed that 124 bp of the AS1 promoter was sufficient to confer light-activated repression to a heterologous promoter. Potential conserved transcription regulatory elements, Box B, Box C, and Box C' within this region were shown to bind to nuclear proteins by gel shift analysis. A light-specific DNA:protein interaction was detected with Box B. The nuclear factors that bind to Box C and C' elements of AS1 are competed by a putative repressor element 'RE1' defined previously in the oat phytochrome gene whose transcription is also repressed by light. The Box B and C/C'-Box/RE1-binding factors were found in nuclear extracts of tobacco, pea, and Arabidopsis and may therefore be universal factors involved in light-activated transcriptional repression.

Aspartate-Ammonia Ligase↗
PubMed1999

Identification of three kinds of mutually related composite elements conferring S phase-specific transcriptional activation.

Conservation of the Oct motif (CGCGGATC) is a remarkable feature of plant histone gene promoters. Many of the Oct motifs are paired with a distinct motif, Hex, TCA or CCAAT-box, constituting the type I element (CCACGTCANCGATCCGCG), type II element (TCACGCGGATC) and type III element (GATCCGCG-N14-ACCAATCA). To clarify the roles of these Oct-containing composite elements (OCEs) in cell cycle-dependent and tissue-specific expression, we performed gain-of-function experiments with transgenic tobacco cell lines and plants harboring a derivative of the 35S core promoter/beta-glucuronidase fusion gene in which three or four copies of an OCE had been placed upstream. Although their activities were slightly different, results showed that each of the three types of OCEs could confer the ability to direct S phase-specific expression on a heterologous promoter. In transgenic plants, the type I and III elements exhibited a similar activity, directing expression in meristematic tissues, whereas the activity of the type II element appeared to be restricted to young cotyledons and maturating guard cells. Mutational analyses demonstrated that the co-operation of Oct with another module (Hex, TCA or CCAAT-box) was absolutely required for both temporal and spatial regulation. Thus, OCEs play a pivotal role in regulation of the expression of plant histone genes.

Base Sequence↗
PubMed2000

Characterization of cis-elements required for vascular expression of the cinnamoyl CoA reductase gene and for protein-DNA complex formation.

Cinnamoyl-CoA reductase (CCR) catalyses the first specific step in the biosynthesis of monolignols, the monomeric units of lignins. We examined the developmental regulation of the Eucalyptus gunnii EgCCR promoter by analysing the expression of EgCCR-GUS fusions in tobacco. EgCCR promoter activity was strongest in lignified organs (stems and roots) consistent with the EgCCR mRNA level in these organs. Histochemical analysis showed expression in vascular tissues (cambium, young differentiating xylem, ray cells, internal and external phloem) of stems and roots in agreement with in situ hybridization data. Promoter deletion analysis and gain-of-function experiments identified the sequences between positions -119 and -77 as necessary and sufficient for expression in vascular tissues of stems. Electrophoretic mobility-shift assays showed that this region is specifically recognized by nuclear proteins present in tobacco stems, giving rise to two retarded complexes, LMC1 and LMC2. Using overlapping EgCCR fragments and mutated oligonucleotides as competitors in gel-shift assays, two DNA-protein interaction sites were mapped. Finally, the role of protein-protein interactions in the formation of the LMC1 and LMC2 complexes was investigated using the detergent sodium deoxycholate, and protein fractionation onto a heparin Sepharose column.

Aldehyde Oxidoreductases↗
PubMed2002

Identification and regulation of high light-induced genes in Chlamydomonas reinhardtii.

We have used restriction fragment differential display for isolating genes of the unicellular green alga Chlamydomonas reinhardtii that exhibit elevated expression on exposure of cells to high light. Some of the high light-activated genes were also controlled by CO2 concentration. Genes requiring both elevated light and low CO2 levels for activation encoded both novel polypeptides and those that function in concentrating inorganic carbon (extracellular carbonic anhydrase, low CO2-induced protein, ABC transporter of the MRP subfamily). All the genes in this category were shown to be under the control of Cia5, a protein that regulates the responses of C. reinhardtii to low-CO2 conditions. Genes specifically activated by high light, even under high-CO2 conditions, encoded a 30 kDa chloroplast membrane protein, a serine hydroxymethyltransferase, a nuclease, and two proteins of unknown function. Experiments using DCMU, an inhibitor of photosynthetic electron transport, and mutants devoid of either photosystem I or photosystem II activity, showed aberrant expression of all the genes regulated by both CO2 and high light, suggesting that redox plays a role in controlling their expression. In contrast, there was little effect of DCMU or lesions that block photosynthetic electron transport on the activity of genes that were specifically controlled by high light.

Amino Acid Sequence↗
PubMed2003

Two cis-acting elements necessary and sufficient for gibberellin-upregulated proteinase expression in rice seeds.

In germinating rice seeds, a cysteine proteinase (REP-1), synthesized in aleurone-layer cells, is a key enzyme in the degradation of the major storage protein, glutelin. The expression of the gene for REP-1 (Rep1) is induced by gibberellins (GAs) and repressed by abscisic acid (ABA). To identify GA-responsive elements in the Rep1 promoter, we developed a transient expression system in rice aleurone cells. Deletion and point-mutation analyses indicated that the GA-response complex was composed of TAACAGA, TAACGTA, and two copies of CAACTC. The two former sequences were identical to GAREs conserved in the promoter of genes for alpha-amylase and proteinases in cereals. The latter, termed as CAACTC regulatory elements (CAREs), were novel GAREs. Gain-of-function experiments revealed that two pairs of GARE and CARE were necessary and sufficient to confer GA inducibility. The sequences were also required for effective transactivation by the transcription factor OsGAMyb. Four copies of either GARE or CARE showed transactivation neither by OsGAMyb nor by GA induction. CARE and GARE were also found in the promoters of a rice alpha-amylase gene, RAmy1A, and a barley proteinase gene, EPB1, which are expressed in germinating seeds. Mutations of CARE in their promoters caused a loss of GA inducibility and GAMyb transactivation, suggesting that CARE is the regulatory element for GA-inducible expression of hydrolase genes in the germinating seeds.

Base Sequence↗
PubMed2003

Target genes for OBP3, a Dof transcription factor, include novel basic helix-loop-helix domain proteins inducible by salicylic acid.

Overexpression of a salicylic-acid (SA)-inducible Arabidopsis DNA binding with one finger (Dof) transcription factor, called OBF-binding protein 3 (OBP3; AtDof3.6), has previously been shown to result in growth defects. In this study, suppressive subtraction hybridization (SSH) was used to isolate genes induced in an OBP3-overexpression line and several putative clones, called OBP3-responsive genes (ORGs), were isolated. The link with the induced expression levels of these genes and OBP3 overexpression was confirmed by analysing additional OBP3-overexpression lines. ORG1 through ORG4 are novel genes, while ORG5 is an extensin gene, AtExt1. While ORG4 has no similarity with other proteins in the database, ORG1 has weak similarity in different regions of the predicted protein with CDC2 and fibrillin. ORG2 and ORG3 share 80% overall identity in their deduced amino acid sequences and contain a basic helix-loop-helix DNA-binding domain, suggesting that ORG2 and ORG3 may be transcription factors. The expression of the ORG1, ORG2 and ORG3 genes was co-regulated under all conditions examined including upregulation by SA and downregulation by jasmonic acid (JA). Fifteen OBP3-silenced lines were generated to further explore the function of OBP3. Although there were no visible phenotypic changes in any of these lines, the expression of ORG1, ORG2 and ORG3 was reduced. Among the ORG genes, ORG1, ORG2 and ORG3 contained the highest number of potential Dof-binding sites in the promoter region, and their expression was significantly increased within 3 h after induction of OBP3 expression using an inducible promoter system, and closely reflected the expression levels of the exogenous OBP3 protein. The results from the gain-of-function and loss-of-function experiments suggest that the ORG1, ORG2 and ORG3 genes are direct target genes of OBP3.

Amino Acid Sequence↗
PubMed1999

The role of Xmsx-2 in the anterior-posterior patterning of the mesoderm in Xenopus laevis.

Many molecules are involved in defining mesodermal patterning of the Xenopus embryo. In this paper, evidence is provided that a member of the msx family of genes, the Xmsx-2 gene, is involved in anterior-posterior patterning of the mesoderm. A comparison of its sequence to another previously cloned msx-2 Xenopus homolog, Xhox-7.1' [45] showed that they are closely related. The Xmsx-2 gene is first expressed at midgastrulation predominantly in the dorsal part of the embryo. It showed a complex pattern of spatial expression, consistent with a role in patterning of the anterior-posterior axis. This inference is confirmed by gain-of-function experiments in which overexpressed msx-2 mRNA in developing Xenopus embryos resulted in embryos lacking anterior structures. Analysis of markers in mutant embryos showed that genes involved in ventral-posterior patterning such as Xhox-3, Xwnt-8, and Xvent-1 were upregulated, confirming the posteriorized nature of the embryos. We believe that the Xmsx-2 gene is involved in refining the patterning of the anterior-posterior part of the dorsal mesoderm after the initial signals determining the dorsal or ventral nature of the mesoderm have been specified.

Amino Acid Sequence↗
PubMed2000

Species differences in the actions of sensory neuropeptides on contractility of the smooth muscle of the rat and guinea-pig prostate.

1. The present review describes the actions of sensory neuropeptides on the contractility of the rat and guinea-pig prostate gland and discusses the differences in sensitivity of the smooth muscle of the prostates taken from these species to these neuropeptides. 2. Nerve fibres immunoreactive for the tachykinins substance P and neurokinin A, as well as for the sensory neuropeptide calcitonin gene-related peptide (CGRP), are sparsely distributed throughout the fibromuscular stroma of the prostate gland in both the rat and guinea-pig. 3. In functional experiments, tachykinin agonists potentiate electrical field stimulation-induced contractile responses of prostates taken from guinea-pigs, but have no effect on those taken from rats. This potentiation is through stimulation of tachykinin NK1-receptors. 4. Conversely, CGRP inhibits electrical field stimulation-induced contractile responses of prostates taken from rats, but has no effect on those taken from guinea-pigs. 5. It is concluded that although the sensory innervation to the prostate glands of the rat and guinea-pig appears similar, the nature and sensitivity of the contractile response of the prostatic smooth muscle to applied sensory neuropeptides is vastly different in the two species.

Animals↗
PubMed1999

Role of Pax-5 in the regulation of a mid-hindbrain organizer's activity.

The mes-metencephalic boundary (isthmus) has been suggested to act as an organizer in the development of the optic tectum. Pax-5 was cloned as a candidate for regulator of the organizing center. Isthmus-specific expression of Pax-5 and analogy with the genetic cascade in Drosophila suggest that Pax-5 may be at a higher hierarchical position in the gene regulation cascade of tectum development. To examine this possibility, a gain-of-function experiment on Pax-5 was carried out. In ovo electroporation on E2 chick brain with the eucaryotic expression vector that encodes chick Pax-5 cDNA was used. Not only was a considerable amount of Pax-5 expressed ectopically in the transfected brain, but irregular bulging of the neuroepithelium was induced in the diencephalon and mesencephalon. At Pax-5 misexpressing sites, uptake of BrdU was increased. Histological examination of E7 transfected brain revealed that Pax-5 caused transdifferentiation of diencephalon into the tectum-like structure. In the bulges of the E7 mesencephalon, differentiation of laminar structure was repressed when compared to the normal side. In transfected embryos, En-2, Wnt-1 and Fgf8 were up-regulated ectopically, and Otx2 was down-regulated in the diencephalon to mesencephalon. Moreover, Ephrin-A2, which is expressed specifically in the tectum with a gradient highest at the caudal end, is suggested to be involved in pathfinding of the retinal fibers, and was induced in the bulges. When the mouse Fgf8 expression vector was electroporated, Pax-5 and chick Fgf8 were also induced ectopically. These results suggest that Pax-5, together with Fgf8, hold a higher position in the genetic hierarchy of the isthmus organizing center and regulate its activity.

Amino Acid Sequence↗
PubMed1999

Genetic and epigenetic regulation of NMDA receptor expression in the rat visual cortex.

The susceptibility of cortical networks to use-dependent modifications declines with age (critical period) and this decline of neuronal plasticity during development is paralleled by the shortening of NMDA receptor EPSCs. We showed previously in the somatosensory cortex that the shortening of NMDA receptor kinetics correlates with a developmentally-regulated increase in the NR2A subunit expression. Here we examine whether this developmental regulation of NR2A expression is related to the duration of critical periods and whether it is influenced by experience. Functional NMDA receptors and their molecular characteristics are studied in identified layer IV neurons of rat visual cortex. In this structure the time course of the critical period differs from that in the somatosensory cortex and can be changed by sensory deprivation, thus permitting examination of correlations between the time course of receptor expression and the duration of the critical period. We find that the developmental expression of the NR2A subunit is delayed compared with the somatosensory cortex, in agreement with the prolonged critical period in the visual cortex. Moreover, sensory deprivation further delays the developmental change in the NMDA receptor subunit composition, demonstrating the activity dependence of this process and strengthening the correlation between changes in subunit composition and the time course of the critical period.

Aging↗
PubMed2001

Paracellin-1 is critical for magnesium and calcium reabsorption in the human thick ascending limb of Henle.

BACKGROUND: A new protein, named paracellin 1 (PCLN-1), expressed in human thick ascending limb (TAL) tight junctions, possibly plays a critical role in the control of magnesium and calcium reabsorption, since mutations of PCLN-1 are present in the hypomagnesemia hypercalciuria syndrome (HHS). However, no functional experiments have demonstrated that TAL magnesium and calcium reabsorption were actually impaired in patients with HHS. METHODS: Genetic studies were performed in the kindred of two unrelated patients with HHS. Renal magnesium and calcium reabsorption in TAL were analyzed in one homozygous affected patient of each family, one patient with extrarenal hypomagnesemia (ERH), and two control subjects (CSs). RESULTS: We found two yet undescribed mutations of PCLN-1 (Gly 162 Val, Ala 139 Val). In patients with HHS, renal magnesium and calcium reabsorptions were impaired as expected; NaCl renal conservation during NaCl deprivation and NaCl tubular reabsorption in diluting segment were intact. Furosemide infusion in CS markedly increased NaCl, Mg, and Ca urinary excretion rates. In HHS patients, furosemide similarly increased NaCl excretion, but failed to increase Mg and Ca excretion. Acute MgCl(2) infusion in CS and ERH patient provoked a dramatic increase in urinary calcium excretion without change in NaCl excretion. When combined with MgCl(2) infusion, furosemide infusion remained able to induce normal natriuretic response, but was unable to increase urinary magnesium and calcium excretion further. In HHS patients, calciuric response to MgCl(2) infusion was blunted. CONCLUSION: This study is the first to our knowledge to demonstrate that homozygous mutations of PCLN-1 result in a selective defect in paracellular Mg and Ca reabsorption in the TAL, with intact NaCl reabsorption ability at this site. In addition, the study supports a selective physiological effect of basolateral Mg(2+) and Ca(2+) concentration on TAL divalent cation paracellular permeability, that is, PCLN-1 activity.

Adolescent↗
PubMed2002

Behaviors and outcomes of acute confusion in hospitalized patients.

The purpose of this study was to describe behaviors associated with acute confusion (AC) in hospitalized patients and to determine whether acutely confused patients experience more adverse outcomes compared with their nonconfused counterparts. Using a prospective design, 117 subjects were followed throughout hospital stay. Subjects who developed AC were more likely to fall, be incontinent, have a urinary catheter, and experience functional decline. Mortality was higher in subjects with AC. Contrary to popular belief, acutely confused patients exhibited decreased psychomotor activity. Nurses can be trained to recognize AC using a standardized protocol to improve outcomes for this vulnerable population.

Acute Disease↗
PubMed2006

Parathyroid imaging: how good is it and how should it be done?

Hypersecretion of parathormone in primary hyperparathyroidism is common, occurring in approximately 1 in 500 women and 1 in 2,000 men per year in their fifth to seventh decades of life. This has been suggested from the literature to be primarily the result of a parathyroid adenoma (80-85% of cases), hyperplasia involving more than 1 gland, usually with all 4 glands being involved (10-15% of cases), or the result, albeit rarely, of parathyroid carcinoma (0.5-1% of cases). Surgical removal of the hypersecreting gland is the primary treatment; this procedure is best performed by a skilled surgeon who would normally find the abnormality in 95% of cases. Imaging, however, should be used to identify the site of abnormality, potentially reducing inpatient stay and improving the patient experience. Functional imaging of parathyroid tissue using thallium was introduced in the 1980s but has largely been superceded by the use of (99m)Tc-labeled isonitriles. The optimum techniques have used (99m)Tc-sestamibi with subtraction imaging or washout imaging. A recent systematic review reported the percentage sensitivity (95% confidence intervals) for sestamibi in the identification of solitary adenomas as 88.44 (87.48-89.40), multigland hyperplasia 44.46 (41.13-47.8), double adenomas 29.95 (-2.19 to 62.09), and carcinoma 33 (33). This review does not separate the washout and subtraction techniques. The subtraction technique using (99m)Tc-sestamibi and (123)I is the optimal technique enabling the site to be related to the thyroid tissue when the parathyroid gland is in the neck in a normal position. If there is an equivocal scan then confirmation with high resolution ultrasound should be used. With ectopic glands, the combined use of single-photon emission computed tomography may then provide anatomical information to enable localization of the functional abnormality. In patients who have had surgical exploration by an experienced parathyroid surgeon in a unit with an experienced nuclear medicine team and negative sestamibi imaging, it is reasonable to image the patient with (11)C methionine. It is debatable whether patients with a high likelihood of secondary hyperparathyroidism should be imaged. The only possible justification for this is to exclude an ectopic site. There is no substitute for an experienced surgeon and an experienced imaging unit to provide a parathyroid service.

Adenoma↗
PubMed2005

Calcineurin regulates bone formation by the osteoblast.

Two of the most commonly used immunosuppressants, cyclosporine A and tacrolimus (FK506), inhibit the activity of a ubiquitously expressed Ca(2+)/calmodulin-sensitive phosphatase, calcineurin. Because both drugs also cause profound bone loss in humans and in animal models, we explored whether calcineurin played a role in regulating skeletal remodeling. We found that osteoblasts contained mRNA and protein for all isoforms of calcineurin A and B. TAT-assisted transduction of fusion protein TAT-calcineurin Aalpha into osteoblasts resulted in the enhanced expression of the osteoblast differentiation markers Runx-2, alkaline phosphatase, bone sialoprotein, and osteocalcin. This expression was associated with a dramatic enhancement of bone formation in intact calvarial cultures. Calcineurin Aalpha(-/-) mice displayed severe osteoporosis, markedly reduced mineral apposition rates, and attenuated colony formation in 10-day ex vivo stromal cell cultures. The latter was associated with significant reductions in Runx2, bone sialoprotein, and osteocalcin expression, paralleled by similar decreases in response to FK506. Together, the gain- and loss-of-function experiments indicate that calcineurin regulates bone formation through an effect on osteoblast differentiation.

Animals↗
PubMed2006

Prion protein (PrPc) positively regulates neural precursor proliferation during developmental and adult mammalian neurogenesis.

The misfolding of the prion protein (PrP(c)) is a central event in prion diseases, yet the normal function of PrP(c) remains unknown. PrP(c) has putative roles in many cellular processes including signaling, survival, adhesion, and differentiation. Given the abundance of PrP(c) in the developing and mature mammalian CNS, we investigated the role of PrP(c) in neural development and in adult neurogenesis, which occurs constitutively in the dentate gyrus (DG) of the hippocampus and in the olfactory bulb from precursors in the subventricular zone (SVZ)/rostral migratory stream. In vivo, we find that PrP(c) is expressed immediately adjacent to the proliferative region of the SVZ but not in mitotic cells. In vivo and in vitro studies further find that PrP(c) is expressed in multipotent neural precursors and mature neurons but is not detectable in glia. Loss- and gain-of-function experiments demonstrate that PrP(c) levels correlate with differentiation of multipotent neural precursors into mature neurons in vitro and that PrP(c) levels positively influence neuronal differentiation in a dose-dependent manner. PrP(c) also increases cellular proliferation in vivo; in the SVZ, PrP(c) overexpresser (OE) mice have more proliferating cells compared with wild-type (WT) or knockout (KO) mice; in the DG, PrP(c) OE and WT mice have more proliferating cells compared with KO mice. Our results demonstrate that PrP(c) plays an important role in neurogenesis and differentiation. Because the final number of neurons produced in the DG is unchanged by PrP(c) expression, other factors must control the ultimate fate of new neurons.

Aging↗