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Results for “Enhancer mapping”

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PubMed1989

Somatostatin gene expression in pancreatic islet cells is directed by cell-specific DNA control elements and DNA-binding proteins.

Somatostatin is a peptide synthesized in the pancreatic islets, nervous system, gastrointestinal tract, and thyroid gland. Factors that control islet cell-specific expression of the somatostatin gene were analyzed by expression of fusion genes consisting of 5' rat somatostatin gene sequences linked to coding sequences of the receptor genes, bacterial chloramphenicol acetyltransferase, and human growth hormone. Fusion genes containing 900 and 250 base pairs (bp) of 5'-flanking DNA were preferentially expressed at 5-10-fold higher levels in somatostatin-producing islet cell lines, as compared with islet cell lines that produced insulin and glucagon, and in three non-islet cell lines. A deletional mutation consisting of only 65 bp of 5'-flanking sequence of the rat somatostatin gene expressed in all islet cell lines but not in non-islet lines, indicating the existence of a negative-acting islet cell-specific element located between nucleotides -250 and -65. The 65-bp sequence contains the octameric cAMP-responsive enhancer (CRE) TGACGTCA (nucleotides -48 to -41). Fine mapping of sequences responsible for islet-specific expression by substitution of synthetic oligonucleotide cassettes revealed full retention of expression by deletion to nucleotides -48 and complete loss of expression at nucleotides -42 of the CRE. Substitution of the 9 bp adjacent 3' to the CRE of the somatostatin gene (nucleotides -40 to -32) with the corresponding sequence located 3' to the CRE of the glucagon gene abolished expression. By gel mobility shift and DNaseI footprinting analyses, proteins in extracts of islet cells bound to the 24 bp including the CRE and downstream adjacent 9 bp (nucleotides -58 to -35). An additional upstream region of DNA was protected from DNase I digestion (nucleotides -110 to -80). Proteins from non-islet cells bound to the region from nucleotides -58 to -35, but patterns of DNase I protection differed from those using proteins from islet cells. These observations indicate that several DNA-binding proteins interact with cis-acting elements located between 35 and 58 bp upstream of the transcriptional start site of the rat somatostatin gene to determine islet cell-specific gene expression. CRE-binding protein(s) is ubiquitous among phenotypically different cells, and expression of the somatostatin gene in non-somatostatin-producing islet cells appears to be inhibited by a negative-acting element located upstream of the CRE.

8-Bromo Cyclic Adenosine Monophosphate↗

PubMed1987

Heterogeneous distribution of neurotensin-like immunoreactive neurons and fibers in the midbrain periaqueductal gray of the rat.

The midbrain periaqueductal gray (PAG) has been shown to be a site where various manipulations induce pain suppression. Recent physiological evidence (Behbehani and Pert, 1984; Behbehani et al., 1987) suggests that neurotensin has pronounced physiological actions in PAG and effects pain suppression. We have performed immunohistochemical studies in order to determine the magnitude and distribution of neurotensin-like immunoreactive (NT-IR) cell bodies and fibers in PAG. NT-IR cell bodies were common throughout PAG, although there were more in the caudal than the rostral half. NT-IR neurons were much more numerous in the ventral than the dorsal half of PAG, and some appeared to be located within the dorsal raphe nucleus. The pattern of NT-IR fibers was analyzed with the aid of image enhancement/analysis and densitometry. The fibers were found to be heterogeneously distributed, being most heavily concentrated in the region adjacent to the cerebral aqueduct in the caudal two-thirds of PAG. The distribution of NT fibers closely matches sites where exogenously applied NT elicits long-lasting excitation of PAG neurons (Behbehani et al., 1987). Based on the known physiological and behavioral actions of NT in PAG, the present anatomical results suggest that NT acts on elements located predominantly in the medial and ventrolateral parts of PAG. Neurons activated by NT may project directly to the nucleus raphe magnus and adjacent ventral medulla (Behbehani and Pert, 1984) to activate neurons that project to the spinal cord and modulate nociceptive circuits.

Animals↗

PubMed1983

Specific in situ phosphorylation of plectin in detergent-resistant cytoskeletons from cultured Chinese hamster ovary cells.

Plectin (Mr = 300,000) was found to be an abundant polypeptide component of Chinese hamster ovary cells accounting for up to 1% of cellular protein. Seventy-five per cent of the plectin were present in cytoskeletons prepared by extraction of attached cells with 0.15% Triton X-100. As shown by immunofluorescence microscopy, plectin's spatial arrangement within these cytoskeletal preparations appeared well preserved, though slightly more filamentous compared to nonextracted cells. Upon in situ incubation of cytoskeletons with [gamma-32P] ATP followed by solubilization and immunoprecipitation, plectin was identified as one of the major phosphoacceptors. A basic phosphorylation of the protein was accomplished by a type I cAMP-independent protein kinase, while a cAMP-dependent protein kinase enhanced its phosphorylation up to 2-fold. Peptide mapping revealed that the two kinases phosphorylated different molecular sites. Peptide maps generated from cytoskeletal plectin phosphorylated in vitro using [gamma-32P]ATP and plectin phosphorylated in vivo using 32Pi were virtually identical demonstrating that the in situ phosphorylation of plectin in preparations of cytoskeletons was specific. Moreover, the specific radioactivity of cytoskeletal plectin was three times higher than that of detergent-extracted plectin, suggesting that phosphorylation is important for the protein's association with the cytoskeleton.

Animals↗

PubMed1993

[Localization of E(wa) in Drosophila melanogaster using rearrangement].

The white-apricot (wa) allele differs from the wild type white gene by the presence of the retrovirus-like transposable element copia within the transcription unit. The activity of wa is reduced in trans by a semidominant mutation in the gene Enhancer-of white-apricot (E(wa)). The map position of E(wa) is refined by analyzing recombination among three genes: px, E(wa) and sp. The recombinational distance between E(wa) and sp is 0.2 cM, which places E(wa) at 2-106.8. To localize E(wa) cytologically, four Y; 2 translocations, one 1;2 translocation and three 2R deficiency stocks were crossed to the suitable E(wa) stocks and the wa sons were scored for intensity of pigment and the speck at the axis of wings. The E(wa) was placed in the distal portion of 60B. The one E(wa) mutation and two sp mutations derived from our gamma-ray mutagenesis were used for examination of polytene chromosome. The former was a revertant which has a cytologically visible insertion of material from an unknown source at 60B5-13, most likely in the 60B8-9. It is likely that this insertion is within the E(wa) gene. The latter shows breakpoint at 60C1-2, where is likely the location of the sp gene. Combining the data of both cytological localization and recombinational mapping, the E(wa) was localized at 60B5-13, most likely in the 60B8-9, the left of sp but very close to it.

Animals↗

PubMed1997

Test-retest analysis with functional MR of the activated area in the human visual cortex.

PURPOSE: To investigate the intersubject and intrasubject variability of the activated area in the visual cortex with functional MR imaging. METHODS: Double-section gradient-echo MR images were acquired at 1.5 T in 28 healthy volunteers using the fast low-angle shot (FLASH) technique. Visual stimulation was obtained with light-emitting diode (LED) goggles. Eighteen volunteers were studied twice. The size of the activated areas in the visual cortex and the increase in signal were measured. A reproducibility ratio for size (R[size]) and for location (R[overlap]) was calculated on a scale of 0.0 to 1.0. RESULTS: Activation was seen in 89% of the subjects. The size of the activated area was widely variable among subjects: mean, 460 +/- 284 mm2; range, 0 to 1029 mm2 in the first study in all volunteers. Signal increases ranged from 3.2% to 10.9%, with a mean of 6.6 +/- 1.7%. The mean values of intrasubject variability testing were R(size) = 0.83 +/- 0.16 and R(overlap) = 0.31 +/- 0.11. CONCLUSION: Functional MR imaging with the FLASH technique is useful in identifying certain cortical areas that have quite variable locations among subjects. This study provides reference data for the intrasubject and intersubject variability of the activation pattern of the visual cortex.

Adult↗

PubMed1989

Subchronic methamphetamine treatment enhances methamphetamine- or cocaine-induced dopamine efflux in vivo.

Intracerebral dialysis was used to study the mechanism underlying behavioral sensitization. Rats were divided into two groups: a control group that received intraperitoneal injections of saline and an experimental group that was given methamphetamine (MAP) (4 mg/kg) once a day for 14 days. Seven days after the last injection, dopamine (DA) and its metabolites were measured in striatal dialysates obtained from awake freely moving rats. A challenge injection of MAP (4 mg/kg) caused a marked increase in the extracellular concentrations of DA, and the extent of the increase was significantly greater in MAP-pretreated rats than in the saline-pretreated controls. A challenge injection of cocaine (20 mg/kg) also caused a significantly greater increase in extracellular DA levels in MAP-pretreated rats than in saline-pretreated rats. These results suggest that an enhancement in striatal DA efflux may play an important role in MAP-induced behavioral sensitization and cross-sensitization to cocaine.

Animals↗

PubMed2000

Regional fine mapping of HMG17 to chromosomal band 1p35.

HMG17, a member of the high-mobility group of proteins, is ubiquitously expressed in higher eukaryotes. This protein has been shown to enhance transcriptional activity of many other genes. Recently, the HMG17 gene has been mapped to chromosomal band 1p36.1. Because this region is frequently involved in chromosomal aberrations of various human neoplasms, two PAC clones containing an HMG17 sequence were isolated. By fluorescence in situ hybridization (FISH) on prometaphase spreads, HMG17 was mapped to chromosomal band 1p35.

Chromosome Banding↗

PubMed1987

CT appearance of experimental thalamic radiofrequency lesion in dog.

The location and extent of thalamic lesions following thalamotomy can be identified as a large low density area in the acute stage to a small spot in the chronic stage. Stereotactic experimental radiofrequency lesions were placed in the thalamus of 35 mongrel dogs. CT images and whole brain specimens were obtained on days 0, 3, 7, 10, 14, 21 and 60. The appropriate time to map the lesions in the thalamus was thought to be about day 14, because of the thalamic size ratio and the correction of the ventricular deformity. The histological area of the lesion at day 14 corresponded better to the contrast-enhanced area than to that of the plain CT. These results suggest that the lesion demonstrated by contrast-enhanced CT scans at day 14 gives the best anatomical mapping of the actual histological defect.

Animals↗

PubMed1980

Localization of the plasmid (pKM101) gene(s) involved in recA+lexA+-dependent mutagenesis.

Twenty Tn5 insertion mutants of the drug resistance plasmid pKM101 have been isolated that are unable to enhance mutagenesis with ultraviolet (UV) irradiation or methyl methanesulfonate. By restriction mapping, the Tn5 insertion in each of these pKM101 mutants was shown to be within a 1.9 kb region of the plasmid genome. We have termed this segment of the pKM101 map the muc (mutagenesis: UV and chemical) gene(s). Characterization of these mutants indicated that any Tn5 insertion within the muc gene(s) abolished the ability of pKM101 to: (a) enhance spontaneous, UV and chemical mutagenesis, (b) increase host survival following UV-irradiation, (c) increase the survival of UV-irradiated phage plated on irradiated or unirradiated cells, and (d) suppress the repair and mutagenesis deficiencies of a umuC- mutant. Possible models to explain the role of the pKM101 muc gene(s) in mutagenesis and repair are discussed.

Bacteriophage lambda↗

PubMed2001

Computerized radiographic mass detection--part II: Decision support by featured database visualization and modular neural networks.

Based on the enhanced segmentation of suspicious mass areas, further development of computer-assisted mass detection may be decomposed into three distinctive machine learning tasks: 1) construction of the featured knowledge database; 2) mapping of the classified and/or unclassified data points in the database; and 3) development of an intelligent user interface. A decision support system may then be constructed as a complementary machine observer that should enhance the radiologists performance in mass detection. We adopt a mathematical feature extraction procedure to construct the featured knowledge database from all the suspicious mass sites localized by the enhanced segmentation. The optimal mapping of the data points is then obtained by learning the generalized normal mixtures and decision boundaries, where a is developed to carry out both soft and hard clustering. A visual explanation of the decision making is further invented as a decision support, based on an interactive visualization hierarchy through the probabilistic principal component projections of the knowledge database and the localized optimal displays of the retrieved raw data. A prototype system is developed and pilot tested to demonstrate the applicability of this framework to mammographic mass detection.

Artificial Intelligence↗

PubMed1991

Yeast artificial chromosome vectors for efficient clone manipulation and mapping.

The yeast artificial chromosome (YAC) cloning system allows the cloning of exogenous DNA several hundred kilobases in length. To enhance the usefulness of this technology, yeast artificial chromosome vectors have been designed for efficient clone characterization, manipulation, and mapping. The vectors contain a polylinker with unique EcoRI, BglII, NotI, EagI, SacII, SalI, NruI, NheI, and ClaI cloning sites and T7 bacteriophage promoters positioned to allow the generation of riboprobes from the exogenous DNA ends. Centric and acentric vector arms were constructed as separate plasmids to allow the recovery of both ends of the YAC insert DNA directly in Escherichia coli. In addition, YACs generated using this vector system contain a yeast gene (SUP 11) that allows visual monitoring of YAC stability and copy number.

Animals↗

PubMed2005

Hedonic hot spot in nucleus accumbens shell: where do mu-opioids cause increased hedonic impact of sweetness?

Mu-opioid systems in the medial shell of the nucleus accumbens contribute to hedonic impact ("liking") for sweetness, food, and drug rewards. But does the entire medial shell generate reward hedonic impact? Or is there a specific localized site for opioid enhancement of hedonic "liking" in the medial shell? And how does enhanced taste hedonic impact relate to opioid-stimulated increases in food intake? Here, we used a functional mapping procedure based on microinjection Fos plumes to localize opioid substrates in the medial shell of the nucleus accumbens that cause enhanced "liking" reactions to sweet pleasure and that stimulate food intake. We mapped changes in affective orofacial reactions of "liking"/"disliking" elicited by sucrose or quinine tastes after D-Ala2-N-Me-Phe4-Glycol5-enkephalin (DAMGO) microinjections in rats and compared hedonic increases to food intake stimulated at the same sites. Our maps indicate that opioid-induced increases in sucrose hedonic impact are generated by a localized cubic millimeter site in a rostrodorsal region of the medial shell. In contrast, all regions of the medial shell generated DAMGO-induced robust increases in eating behavior and food intake. Thus, our results identify a locus for opioid amplification of hedonic impact and reveal a distinction between opioid mechanisms of food intake and hedonic impact. Opioid circuits for stimulating food intake are widely distributed, whereas hedonic "liking" circuits are more tightly localized in the rostromedial shell of the nucleus accumbens.

Animals↗

PubMed2000

Mitogen-activated protein kinase activates human placental lactogen-B enhancer by an NF-IL6-dependent pathway.

Computer analysis of the human placental lactogen-B (hPL-B) enhancer reveals two putative binding sites for the transcription factor NF-IL6, but the role of NF-IL6 in the regulation of the enhancer is unknown. Using gel mobility shift and supershift assays, we demonstrated that NF-IL6 binds to both enhancer sites. Transient transfection studies indicated that the transcription factor NF-IL6 stimulates hPL-B enhancer activity by 4.4-fold in primary cultures of human trophoblast cells and by 32.0- and 8.4-fold in JAR and BeWo choriocarcinoma cells, respectively. Overexpression of MEK (mitogen-activated protein [MAP] kinase kinase), which is known to stimulate phosphorylation of NF-IL6, induced a 3.6-fold increase in hPL-B enhancer activity. The induction by MEK was completely inhibited by an expression plasmid for a dominant/negative mutant of NF-IL6 or by mutation of the NF-IL6 binding sites on the enhancer. PD98059, an inhibitor of MEK, inhibited hPL release from cultured trophoblast cells by about 50%. Taken together, these results indicate that MAP kinase stimulates the hPL-B enhancer by an NF-IL-6-dependent pathway.

CCAAT-Enhancer-Binding Proteins↗

PubMed1993

Selecting DNA fragments for mutation detection by temperature gradient gel electrophoresis: application to the p53 gene cDNA.

Temperature gradient gel electrophoresis (TGGE) and related methods are widely employed to detect mutations in DNA fragments. DNA melting map calculations and GC clamps have been used to enhance the detection of mutations. While generally successful, these methods have not always revealed base changes within a DNA fragment. Previous work suggested that mutations are detected if they are in a DNA's first melting domain, and the melting domain is well separated from final strand dissociation. Two criteria from the DNA melting theory were established to determine when both of these conditions are met. The criteria involve calculating the derivative melting curve as well as the melting map of a DNA sequence. The approach was applied to the cDNA sequence of the human p53 gene. Mutations in the p53 gene are common in human cancers and are generally located in four 'hot spot' regions. Calculations indicated that three DNA fragments are needed to detect base substitutions in the four hot-spot regions. Predicted melting behavior was experimentally tested with eight single base substitutions distributed among the four hot-spot regions. All mutations tested behaved as predicted and were detected by vertical TGGE. Heteroduplex DNAs formed by melting and reannealing various ratios of wild type and mutant DNA fragments were also examined. Results indicated that point mutations can be detected by ethidium bromide staining from samples containing 10% mutant and 90% wild-type sequences.

Base Sequence↗

PubMed2005

Transforming growth factor-beta promotes pro-fibrotic behavior by serosal fibroblasts via PKC and ERK1/2 mitogen activated protein kinase cell signaling.

OBJECTIVE: To assess the role of fibroblasts, transforming growth factor (TGF)-beta, and cell signal pathways in promoting fibrosis in Crohn's disease (CD). SUMMARY BACKGROUND DATA: Intestinal strictures are a major source of morbidity in CD. Fibroblasts found at sites of stricture promote fibrogenesis. The mechanisms underlying this pro-fibrotic behavior remain elusive. METHODS: Fibroblasts were isolated from strictured and macroscopically normal serosa in patients with CD and from normal serosa in patients with colorectal cancer. Whole cell connective tissue growth factor (CTGF) and fibronectin expression were determined by Western blot analysis. Fibroblast type I collagen expression was evaluated by real-time PCR, while fibroblast contractile activity was measured using fibroblast populated collagen lattices. Cells were stimulated with TGF-beta1 and inhibitors of the protein kinase C (PKC) and ERK 1/2 mitogen activated protein (MAP) kinase cell signaling pathways. RESULTS: Stricture fibroblasts displayed enhanced constitutive expression of fibronectin. TGF-beta promoted fibroblast CTGF, fibronectin, and type I collagen expression and enhanced fibroblast contractile activity. Inhibition of PKC reduced basal collagen expression and contractile activity in Crohn's fibroblasts and attenuated the effect of TGF-beta on fibroblast CTGF, fibronectin, and collagen I expression as well as fibroblast contractility. ERK 1/2 inhibition had a similar effect on TGF-beta-induced CTGF and fibronectin expression. CONCLUSIONS: TGF-beta is a critical pro-fibrotic growth factor in CD, and its effects are mediated via PKC and ERK 1/2 MAP kinase cell signaling. These pathways may represent novel therapeutic targets for patients with CD characterized by recurrent intestinal stricture formation.

Adult↗

PubMed2006

Performance evaluation of partial differential equation models in electronic speckle pattern interferometry and the delta-mollification phase map method.

The ordinary differential equation (ODE) and partial differential equation (PDE) image- processing methods have been applied to reduce noise and enhance the contrast of electronic speckle pattern interferometry fringe patterns. We evaluate the performance of a few representative PDE denoising models quantitatively with two parameters called image fidelity and speckle index, and then we choose a good denoising model. Combining this denoising model with the ODE enhancement method, we make it possible to perform contrast enhancement and denoising simultaneously. Second, we introduce the delta-mollification method to smooth the unwrapped phase map. Finally, based on PDE image processing, delta mollification and some traditional techniques, an approach of phase extraction from a single fringe pattern is tested for computer-simulated and experimentally obtained fringe patterns. The method works well under a high noise level and limited visibility and can extract accurate phase values.

Journal Article↗

PubMed1998

Inhibition of the mitogen-activated protein kinase pathway triggers B16 melanoma cell differentiation.

In B16 melanoma cells, mitogen-activated protein (MAP) kinases are activated during cAMP-induced melanogenesis (Englaro, W., Rezzonico, R., Durand-Clément, M., Lallemand, D., Ortonne, J. P., and Ballotti, R. (1995) J. Biol. Chem. 270, 24315-24320). To establish the role of the MAP kinases in melanogenesis, we studied the effects of a specific MAP kinase kinase (MEK) inhibitor PD 98059 on different melanogenic parameters. We showed that PD 98059 inhibits the activation of MAP kinase extracellular signal-regulated kinase 1 by cAMP, but does not impair the effects of cAMP either on the morphological differentiation, characterized by an increase in dendrite outgrowth, or on the up-regulation of tyrosinase that is the key enzyme in melanogenesis. On the contrary, PD 98059 promotes by itself cell dendricity and increases the tyrosinase amount and activity. Moreover, down-regulation of the MAP kinase pathway by PD 98059, or with dominant negative mutants of p21(ras) and MEK, triggers a stimulation of the tyrosinase promoter activity and enhances the effect of cAMP on this parameter. Conversely, activation of the MAP kinase pathway, using constitutive active mutants of p21(ras) and MEK, leads to an inhibition of basal and cAMP-induced tyrosinase gene transcription. These results demonstrate that the MAP kinase pathway activation is not required for cAMP-induced melanogenesis. Furthermore, the inhibition of this pathway induces B16 melanoma cell differentiation, while a sustained activation impairs the melanogenic effect of cAMP-elevating agents.

Animals↗

PubMed2001

Chemokine stromal cell-derived factor-1alpha modulates VLA-4 integrin-dependent adhesion to fibronectin and VCAM-1 on bone marrow hematopoietic progenitor cells.

Stromal cell-derived factor-1alpha (SDF-1alpha) is a potent chemoattractant for hematopoietic progenitor cells (HPC), suggesting that it could play an important role during their migration within or to the bone marrow (BM). The integrin VLA-4 mediates HPC adhesion to BM stroma by interacting with CS-1/fibronectin and VCAM-1. It is required during hematopoiesis and homing of HPC to the BM. As HPC migration in response to SDF-1alpha might require dynamic regulation of integrin function, we investigated if SDF-1alpha could modulate VLA-4 function on BM CD34(hi) cells.CD34(hi) BM cells and hematopoietic cell lines were tested for the effect of SDF-1alpha on VLA-4-dependent adhesion to CS-1/fibronectin and VCAM-1, as well as to BM stroma. CD34(hi) BM cells that adhered to VLA-4 ligands after SDF-1alpha treatment were characterized in colony-forming and long-term culture-initiating cell (LTC-IC) assays.SDF-1alpha rapidly (1 minute) and transiently upregulated the adhesion of CD34(hi) BM cells and hematopoietic cell lines to both CS-1/fibronectin and VCAM-1, and to BM stromal cells. The upregulation of VLA-4-dependent cell adhesion by SDF-1alpha targeted primitive LTC-IC as well as committed CD34(hi) cells. SDF-1alpha-triggered enhancement in VLA-4 function was inhibited by pertussis toxin (PTx) and cytochalasin D, indicating the involvement of G(i) protein downstream signaling and an intact cytoskeleton. Instead, activation of p44/42 MAP kinases by SDF-1alpha did not functionally correlate with enhancement of VLA-4-dependent cell adhesion. Modulation of VLA-4-mediated CD34(hi) BM cell adhesion by SDF-1alpha could play a key role in their migration within and to the BM and therefore influence their proliferation and differentiation.

Animals↗