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Results for “Enhancer mapping”

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PubMed1994

A comprehensive human linkage map with centimorgan density. Cooperative Human Linkage Center (CHLC).

In the last few years there have been rapid advances in developing genetic maps for humans, greatly enhancing our ability to localize and identify genes for inherited disorders. Through the collaborative efforts of three large groups generating microsatellite markers and the efforts of the 110 CEPH collaborators, a comprehensive human linkage map is presented here. It consists of 5840 loci, of which 970 are uniquely ordered, covering 4000 centimorgans on the sex-averaged map. Of these loci, 3617 are polymerase chain reaction-formatted short tandem repeat polymorphisms, and another 427 are genes. The map has markers at an average density of 0.7 centimorgan, providing a resource for ready transference to physical maps and achieving one of the first goals of the Human Genome Project--a comprehensive, high-density genetic map.

Chromosome Mapping↗

PubMed2004

Gene targeting at the chromosomal immunoglobulin locus: a model system for the study of mammalian homologous recombination mechanisms.

Plasmid DNA transfected into mammalian cells can integrate into mammalian chromosomes by homologous recombination. This phenomenon, known as gene targeting, can be used as a tool to investigate mammalian homologous recombination mechanisms. The chromosomal immunoglobulin (Ig) genes as they are presented in mouse hybridoma cells have several advantages that render them particularly amenable to gene targeting. Here, we present the basic methods currently in use in our laboratory that exploit this system to investigate mammalian gene targeting mechanisms.

Animals↗

PubMed1991

[Effects of verticillatine on cerebral blood flow, cerebral vascular resistance and blood pressure in anesthetized dogs and cats].

The effects of verticillatine (Ver), hexamethonium (Hex) and nimodipine (Nim) on mean arterial pressure (MAP), cerebral blood flow (CBF) and cerebrovascular resistance (CVR) were determined in pentobarbital anesthetized animals using the method of electromagnetic flow meter in dogs and hydrogen clearance in cats. Ver or Nim iv induced significant reduction of MAP and CVR. CBF was increased in dogs and unaltered in cats. The Hex treated dogs and cats exhibited a fall of MAP and CBF with enhancement of CVR. In cats after middle cerebral artery occlusion (MCAO), regional cerebral blood flow (rCBF) was reduced from 190 +/- 70 to 90 +/- 20 ml.kg-1.min-1. Ver and Nim iv caused similar changes of MAP and CVR to those before MCAO. The results suggest that Ver and Nim may have vasodilation effect and improve the cerebral circulation. Thus, they would be beneficial to patients suffering from hypertension.

Animals↗

PubMed2002

Assessing myocardial viability and infarct transmurality with left ventricular electromechanical mapping in patients with stable coronary artery disease: validation by delayed-enhancement magnetic resonance imaging.

BACKGROUND: This study was designed to define myocardial viability and establish practical cut-off values for differentiating normal myocardial tissue from subendocardial and transmural scar tissue by using electromechanical mapping (EMM). We validated our results by delayed-enhancement cardiac MRI (DE-MRI). METHODS AND RESULTS: We prospectively studied 15 ambulatory patients with stable coronary disease who were candidates for cardiac catheterization. Within 48 hours of EMM, DE-MRI was performed. Using EMM software, we created a bull's eye precisely matched to that generated by DE-MRI. Segment by segment, we compared the MRI results to the corresponding unipolar voltage value for that same segment in the EMM bull's eye. Of 300 total segments, 275 were compared. The segments were divided into normal (n=211), subendocardial scar (n=49), and transmural scar (n=15). We found that subendocardial (6.8+/-2.9 mV) and transmural (4.6+/-1.9 mV) scar segments had significantly less unipolar voltage than normal (11.6+/-4.5 mV) segments (P<0.05 for each comparison). When normal myocardium was compared with myocardium with subendocardial scar, the threshold for differentiating between the two areas was 7.9 mV (sensitivity, 80%; specificity, 80%). Comparison of normal tissue to transmural scar yielded a threshold of 6.9 mV (sensitivity, 93%; specificity, 88%). CONCLUSIONS: Our results demonstrate that normal myocardium can be accurately distinguished from myocardium with subendocardial or transmural infarcts on the basis of unipolar voltage values obtained through EMM. This is the first study to validate these results by using cardiac DE-MRI in humans.

Adult↗

PubMed1997

Induction of nerve growth factor synthesis by sphingomyelinase and ceramide in primary astrocyte cultures.

Astrocytes synthesize nerve growth factor (NGF) in response to pro-inflammatory cytokines. To further study the signaling mechanism involved in this induction of NGF production, the sphingomyelin (SM) pathway was studied. Addition of exogenous neutral SMase (Staphylococcus aureus) or C2-ceramide to primary cultures of newborn rat cortical astrocytes elicited a dose-response increase of NGF synthesis, with maximal effect at 1 U/ml and 25 microM, respectively. Induction of NGF synthesis by SMase and ceramide was shown to be independent of classical PKC activity. Intracellular cAMP-raising agents, such as forskolin and 3-isobutyl-1-methylxanthine, partially prevented the SMase- and C2-ceramide-induced secretion of NGF to the cell supernatant. PD098059 and apigenin, inhibitors of the mitogen-activated protein (MAP) kinase pathway, produced a dose-response inhibition of the SMase- and C2-cer-induced release of NGF. This observation points to the possibility that regulation of NGF synthesis and secretion by the SMase pathway may be mediated downstream by the MAP kinase cascade. As a matter of fact, pre-treatment of astrocytes with SMase or C8-ceramide led to an increased phosphorylation of raf-1. Moreover, MAP kinase activity was enhanced in astrocytes treated with SMase or both ceramides. In conclusion, results suggest that the SMase pathway may control NGF synthesis in the central nervous system, and raise the possibility of an involvement of the MAP kinase cascade in this process.

Animals↗

PubMed1998

Regulators of pseudohyphal differentiation in Saccharomyces cerevisiae identified through multicopy suppressor analysis in ammonium permease mutant strains.

Nitrogen-starved diploid cells of the yeast Saccharomyces cerevisiae differentiate into a filamentous, pseudohyphal growth form. Recognition of nitrogen starvation is mediated, at least in part, by the ammonium permease Mep2p and the Galpha subunit Gpa2p. Genetic activation of the pheromone-responsive MAP kinase cascade, which is also required for filamentous growth, only weakly suppresses the filamentation defect of Deltamep2/Deltamep2 and Deltagpa2/Deltagpa2 strain. Surprisingly, deletion of Mep1p, an ammonium permease not previously thought to regulate differentiation, significantly enhances the potency of MAP kinase activation, such that the STE11-4 allele induces filamentation to near wild-type levels in Deltamep1/Deltamep1 Deltamep2/Deltamep2 and Deltamep1/Deltamep1 Deltagpa2/Deltagpa2 strains. To identify additional regulatory components, we isolated high-copy suppressors of the filamentation defect of the Deltamep1/Deltamep1 Deltamep2/Deltamep2 mutant. Multicopy expression of TEC1, PHD1, PHD2 (MSS10/MSN1/FUP4), MSN5, CDC6, MSS11, MGA1, SKN7, DOT6, HMS1, HMS2, or MEP2 each restored filamentation in a Deltamep1/Deltamep1 Deltamep2/Deltamep2 strain. Overexpression of SRK1 (SSD1), URE2, DAL80, MEP1, or MEP3 suppressed only the growth defect of the Deltamep1/Deltamep1 Deltamep2/Deltamep2 mutant strain. Characterization of these genes through deletion analysis and epistasis underscores the complexity of this developmental pathway and suggests that stress conditions other than nitrogen deprivation may also promote filamentous growth.

Carrier Proteins↗

PubMed1993

Redox regulation of a src family protein tyrosine kinase p56lck in T cells.

Protein tyrosine phosphorylation was examined after T cells were exposed to oxidative stress in vitro to investigate the possible involvement of redox regulation in T-cell signaling. Oxidative reagents such as hydrogen peroxide (H2O2) and diamide, which oxidize the free sulfhydryl groups in the cells, markedly induced tyrosine phosphorylation of multiple cellular proteins, especially a 55-kDa protein, of cultured peripheral blood T lymphocytes (PBL blasts). The 55-kDa molecule phosphorylated by diamide turned out to be a src family protein tyrosine kinase, p56lck. The immune complex kinase assay showed that the kinase activity of p56lck of diamide-treated PBL blasts was enhanced. The tryptic peptide mapping of p56lck demonstrated that diamide induced the phosphorylation both at Tyr-394 (autophosphorylation site) and at Tyr-505 (negative regulatory site). Taken together, the tyrosine phosphorylation and presumably kinase activity of p56lck were swiftly enhanced by oxidative stress, indicating that T cells have a redox-sensitive signaling mechanism, which is partly mediated by the lymphocyte-specific protein tyrosine kinase p56lck.

Cells, Cultured↗

PubMedDate not supplied

Automated enhancement of description logic-defined terminologies to facilitate mapping to ICD9-CM.

Compositional (post-coordinated) terminologies are one potential solution to the problem of content completeness. However, they have the potential to render data incomparable. For computers to determine that compositional expressions are comparable, the relations between the composed components that are understood implicitly by human readers must be represented explicitly for computer manipulation. We discuss a technique for discovering and formalizing the implicit semantic relationships in two vocabularies: the International Classification of Disease Version 9 Clinical Modification (ICD9-CM), and SNOMED-Reference Terminology (SNOMED-RT). The results of this technique are used to augment the existing SNOMED-RT relation ontology, which is a necessary step in automated concept mapping between systems. The reference terminology must contain all the semantics implicit in the classification in order to map concepts between the two representations. We also provide an explicit representation of the implied semantics of ICD9-CM. This tabulation will be useful for other knowledge engineering efforts involving ICD9-CM.

Automation↗

PubMed1988

Fine-structure mapping of the three mouse alpha-fetoprotein gene enhancers.

Multiple cellular enhancers have been identified previously in the 5'-flanking region of the mouse alpha-fetoprotein gene by transient expression assay. In this report the enhancers have been localized to three regions 200 to 300 base pairs in length at 2.5, 5.0, and 6.5 kilobases of DNA upstream of the transcriptional start site. Nucleotide sequence analysis of the three enhancers revealed areas of homology among them, the most significant of which were two regions of 10 and 18 nucleotides in length. Two of the enhancers were analyzed in detail and shown to be composed of multiple nonidentical domains, none of which was sufficient for full enhancer activity; rather, they acted in an additive fashion in generating the full activity of the enhancer. The tissue-specific activity of the enhancer at -2.5 kilobases was assessed by comparing the activities of subdomains in liver- and non-liver-derived cell lines and was found to be the result of both positive elements within the enhancer and at least one negative element to its 5' end. In contrast, the tissue specificity of the enhancer at -5.0 kilobases was maintained when the minimal essential region was tested alone. The nucleotide sequence similarities, as well as the differences among the enhancers, may explain their differing biological activities both in tissue culture and in vivo.

Animals↗

PubMed2000

Enhanced video image guidance for biopsy using the safety map.

We present the system design and the methods of video-based guidance to assist with brain tumor biopsy procedures. The system comprises of a three-dimensional (3-D) position sensor, a CCD camera, a liquid crystal display (LCD) and a graphics computer equipped with a video capture board. The markers for positional measurement are attached to the CCD camera, a surgical tool, and the patient head. In order to be integrated into the camera-viewing capacity, 3-D images of the head and guidance indicators are visualized to form a life like video image. For reliable guidance, we also use the surgical plan, called the "safety map", which is a sphere surface highlighting the covering area of anatomically significant tissues and obstacles around the target for the indication of the biopsy needle's insertion starting-point. The safety map can be visualized in exactly the same way as it would be in a real life situation. The preliminary experiments were performed at the National Cancer Center. A high degree of flexibility in terms of views was created by using general apparatuses which are a CCD camera and a LCD. The display of the safety map enabled a successful completion of both craniotomy and biopsy needle insertion procedures.

Biopsy, Needle↗

PubMed2001

Multimodal contribution to speech perception revealed by independent component analysis: a single-sweep EEG case study.

In this single-sweep electroencephalographic case study, independent component analysis (ICA) was used to investigate multimodal processes underlying the enhancement of speech intelligibility in noise (for monosyllabic English words) by visualizing facial motion concordant with the audio speech signal. Wavelet analysis of the single-sweep IC activation waveforms revealed increased high-frequency energy for two ICs underlying the visual enhancement effect. For one IC, current source density analysis localized activity mainly to the superior temporal gyrus, consistent with principles of multimodal integration. For the other IC, activity was distributed across multiple cortical areas perhaps reflecting global mappings underlying the visual enhancement effect.

Adult↗

PubMed2000

SAPKs regulation of ischemic preconditioning.

The role of stress-activated protein kinases (SAPKs), c-Jun NH(2)-terminal kinase (JNK) and p38 mitogen-activated protein (MAP) kinase, in preconditioning (PC) was examined with the use of isolated rat hearts subjected to four cyclic episodes of 5-min ischemia and 10-min reperfusion followed by 30-min ischemia and 2-h reperfusion (I/R). A group of hearts was preperfused with 100 microM curcumin, a c-Jun and JNK1 inhibitor, or 5 microM SB 203580, a p38 MAP kinase inhibitor. Another group of hearts was preperfused with 20 microM anisomycin, a stimulator for both JNK and p38 MAP kinases. I/R increased the protein levels of JNK1, c-Jun, and p38 MAP kinase. PC also enhanced the induction of these kinases, but subsequent I/R-mediated increase was blocked by PC. Curcumin blocked I/R- and PC-mediated increase in JNK1 and c-Jun protein levels, whereas it had no effects on p38 MAP kinase. SB 203580, on the other hand, was equally effective in reducing the p38 MAP kinase activation but exerted no effects on JNK1 and c-Jun induction. I/R-mediated increased myocardial infarction was reduced by any of the following compounds: anisomycin, curcumin, and SB 203580. The cardioprotective effects of PC were abolished by either curcumin or SB 203580. The results demonstrate that PC is mediated by a signal-transduction pathway involving both JNK1 and p38 MAP kinase. Activation of SAPKs, although transient, is obligatory for PC.

Animals↗

PubMed1991

[Effects of intracarotid injection of adenosine on respiration blood pressure and renal sympathetic nerve activity].

Changes of mean arterial pressure (MAP), heart rate (HR), respiration and renal sympathetic nerve activity (RSNA) induced by close-arterial administration of adenosine to carotid body (CB) were observed in 33 anesthetized rabbits. The results were as follows: (1) In response to intracarotid injections of adenosine, MAP decreased in a dose-dependent manner, while the frequency of respiration increases with little change in depth. Following carotid sinus denervation, intracarotid injection of adenosine still resulted in a decrease of MAP but with no changes in respiration. (2) By adding adenosine to perfusate of the isolated carotid sinus, both MAP and HR decreased, but these effects could be abolished by inactivation of carotid body. (3) MAP decreased and RSNA enhanced during perfusing adenosine into carotid sinus. These effects could be abolished by the section of sinus nerve or inactivation of CB. From the results obtained, it is considered that adenosine is capable of activating CB, decreasing MAP and heart rate but with a concomitant increases in respiration and RSNA.

Adenosine↗

PubMed2000

The mouse mammary tumor virus transcription enhancers for hematopoietic progenitor and mammary gland cells share functional elements.

Expression of mouse mammary tumor virus (MMTV)-encoded superantigens in B lymphocytes is required for viral transmission and pathogenesis. We have previously established a critical role of an enhancer element within the long terminal repeat (LTR) for MMTV sag gene expression in B-lymphoid progenitor cells. We now demonstrate enhancer activity of this element in a promyelocytic progenitor cell line. We also map the position of the enhancer within the U3 region of the MMTV LTR and show that the progenitor cell enhancer shares functional elements with a previously described mammary gland-specific enhancer.

Animals↗

PubMed1996

A metric map of humans: 23,500 loci in 850 bands.

High-resolution maps integrated with the enhanced location data base software (LDB+) give improved estimates of genetic parameters and reveal characteristics of cytogenetic bands. Chiasma interference is intermediate between Kosambi and Carter-Falconer levels, as in Drosophila and the mouse. The autosomal genetic map is 2832 and 4348 centimorgans in males and females, respectively. Telomeric T-bands are strikingly associated with male recombination and gene density. Position and centromeric heterochromatin have large effects, but nontelomeric R-bands are not significantly different from G-bands. Several possible reasons are discussed. These regularities validate the maps, despite their high resolution and inevitable local errors. No other approach has been demonstrated to integrate such a large number of loci, which are increasing at about 45% per year. The maps and the data and software from which they are constructed are available through the Internet (http:@cedar.genetics.soton.ac.uk/public_html). Successive versions of this location data base may also be accessed on CD-ROM.

Chromosome Banding↗

PubMed1998

Modulation of MAP kinase signaling and growth characteristics by the overexpression of protein kinase C in NIH3T3 cells.

This study was performed to examine effects of the overexpression of protein kinase C (PKC) isoforms (i.e., beta I, beta II, gamma, delta, eta, and zeta) on mitogen-activated protein (MAP) kinase (Erk-1 and -2) signaling and growth characteristics of NIH3T3 cells. Phorbol ester (PMA) activated endogenous and ectopically expressed PKC alpha, beta I, beta II, gamma, delta, epsilon, and eta. Overexpression of the examined PKC isoforms enhanced PMA-induced MAP kinase activation. Potentiation of MAP kinase activation was also observed upon stimulation of cells with platelet-derived growth factor (PDGF) although there was no indication for the activation PKC isoforms by PDGF. Inhibition of PKC blocked PMA- but not PDGF-induced MAP kinase activation. Thus, potentiation of PDGF-induced MAP kinase activation appears to be independent to PKC activity, while PMA-induced MAP kinase activation requires PKC activity. The ability of PKC isoforms to potentiate MAP kinase activation is not related to the growth characteristics of cells because individual PKC isoforms differentially regulated maximum density and proliferation of cells.

3T3 Cells↗

PubMed1988

The echo-transponder electrode catheter: a new method for mapping the left ventricle.

The ability to locate catheter position in the left ventricle with respect to endocardial landmarks might enhance the accuracy of ventricular tachycardia mapping. An echo-transponder system (Telectronics, Inc.) was compared with biplane fluoroscopy for left ventricular endocardial mapping. A 6F electrode catheter was modified with the addition of a piezoelectric crystal 5 mm from the tip. This crystal was connected to a transponder that received and transmitted ultrasound, resulting in a discrete artifact on the two-dimensional echocardiographic image corresponding to the position of the catheter tip. Catheters were introduced percutaneously into the left ventricle of nine anesthetized dogs. Two-dimensional echo-transponder and biplane fluoroscopic images were recorded on videotape with the catheter at multiple endocardial sites. Catheter location was marked by delivering radiofrequency current to the distal electrode, creating a small endocardial lesion. Catheter location by echo-transponder and by fluoroscopy were compared with lesion location without knowledge of other data. Location by echo-transponder was 8.7 +/- 5.1 mm from the center of the radiofrequency lesion versus 14 + 7.8 mm by fluoroscopy (n = 15, p = 0.023). Echo-transponder localization is more precise than is biplane fluoroscopy and may enhance the accuracy of left ventricular electrophysiologic mapping.

Animals↗

PubMed2006

[Oxygen-enhanced MRI of the lung: optimized calculation of difference images].

BACKGROUND: In oxygen-enhanced lung MRI, difference maps of acquisitions during inhalation of room air and pure oxygen are calculated to assess lung function. The purpose of this study was to analyze how the calculation of these difference maps depends on the delayed signal change after switching the gas supply. METHODS: Ten healthy volunteers were examined with an ECG and respiratory-triggered T1-weighting inversion recovery HASTE sequence with parallel imaging. Four blocks with 20 repetitions of up to 6 coronal slices were continuously acquired; in blocks 1 and 3 room air was supplied, in blocks 2 and 4 oxygen. Data were postprocessed, discarding between 0 and 19 repetitions after each change of gas supply before calculating the relative signal difference. RESULTS: The averaged relative signal difference increases from 9.4 to 17.4% when the number of discarded acquisitions increases; the ratio of signal difference and spatial standard deviation reaches a maximum at 5-8 discarded acquisitions. CONCLUSIONS: An optimized ratio of signal difference and statistical error is found if about 5-8 of 20 respiratory-triggered repetitions are discarded after each change of gas supply for the calculation of difference maps.

Adult↗