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Results for “Enhancer mapping”

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At least 919 records · Page 51Linked to original sources

PubMed1999

Utility of chicken-specific microsatellite primers for mapping the turkey genome.

As part of the University of Minnesota's initiative to map the turkey genome, we are currently evaluating chicken microsatellite loci for use in mapping the turkey genome. To date, 141 primer pairs have been tested for amplification at six different combinations of temperature and MgCl2 concentration. Microsatellite primer pairs from the Chicken Comprehensive Mapping Kit #2, and additional unpublished chromosome 1 and 2 primers were screened. Analyzable PCR products were produced from 78 of the 141 (55%) primer combinations. In the majority of cases (68%), PCR fragments obtained from the turkey were similar in size to respective chicken loci. The presence of dinucleotide repeats (CA/TG repeats) was determined by Southern hybridization with a (TG)15, oligonucleotide probe. Five of 12 (41.63%) turkey fragments hybridized under low stringency conditions. The length of the dinucleotide repeats in the turkey, relative to the chicken sequences, were found to correspond directly with hybridization intensity. Amplification of homologous loci was confirmed by direct sequencing and subsequent alignment of the turkey and chicken sequences. The results of this study indicate that the use of chicken-specific microsatellite primers will rapidly and significantly enhance construction of a genetic map for the turkey.

Animals↗

PubMedDate not supplied

Drug abuse treatment process components that improve retention.

BACKGROUND: Longer retention has been the most consistent predictor of favorable drug abuse treatment outcomes, but key therapeutic and patient engagement indicators of treatment process need to be more clearly established. METHODS: An integrative model representing treatment dynamics was tested for explaining long-term program retention. It was based on a multisite sample of 527 daily opioid users who remained in methadone maintenance a minimum of 3 months. All had been assigned randomly to a counseling condition at admission (i.e., cognitively enhanced or standard), and information obtained from patient files, as well as periodic assessments completed by patients and their counselors in the first 90 days after admission were the sources of predictors. RESULTS: Counseling enhancements (using node-link mapping, a visual representation tool for improving communication and problem solving) contributed to stronger therapeutic relationships between counselor and patient, which in turn had a positive reciprocal relationship with patient engagement (session attendance). Pretreatment motivation measured at intake was also related to higher engagement. More positive therapeutic relationships (in months 1 and 2) led to lower levels of during-treatment drug use (defined from urinalysis results in months 2 and 3), and better session attendance and therapeutic relationships both predicted longer retention. In addition, lower drug use during treatment was related to longer retention. CONCLUSIONS: Major conceptual domains of drug abuse treatment process were identified in community-based programs and their interrelationships with retention specified. As intermediate (during treatment) criteria, they can help guide functional improvements in program effectiveness as illustrated with our counseling enhancements.

Humans↗

PubMed1989

[Quantified EEG and psychometric effects of 3 doses of dexfenfluramine in the young adult].

In an acute, double-blind placebo-controlled study, three groups of nine healthy subjects were included. Each group received, in randomized and weekly intervals, a single oral dose of dexfenfluramine (15 mg, 30 mg or 60 mg) or placebo. Psychometric and EEG studies were carried out before as well as 1, 2, 3, 4, 5 and 6 h after drug administration. Changes from predrug to postdrug conditions for each time were determined by the ratio of absolute spectral power and compared to the evolution of power spectra under placebo conditions. Statistical evaluation was done with ANOVA. Dexfenfluramine induced a dose-dependent decrease of power spectra for theta and alpha 1 bands and an increase for the beta band. Topographic brain mapping of these significant changes displayed a central and posterior decrease for theta and alpha 1 bands, and a temporal localization for the beta-power. Maps of relative power-enhanced changes were seen in absolute power and provided false displays. Psychometric evaluation of dexfenfluramine effects only showed trends to extraversion and increased mood scores but no statistical significance was found. Arousal and performance tests were unchanged. These results suggest that qEEG variations are more sensitive to serotonergic drug effects than psychometric investigations. It appears that spontaneous EEG power spectra variations with time must be accounted for by drug evaluation. Absolute power variations are more reliable than relative power. Methodological implications are discussed.

Adult↗

PubMed2006

An RNA map predicting Nova-dependent splicing regulation.

Nova proteins are a neuron-specific alternative splicing factors. We have combined bioinformatics, biochemistry and genetics to derive an RNA map describing the rules by which Nova proteins regulate alternative splicing. This map revealed that the position of Nova binding sites (YCAY clusters) in a pre-messenger RNA determines the outcome of splicing. The map correctly predicted Nova's effect to inhibit or enhance exon inclusion, which led us to examine the relationship between the map and Nova's mechanism of action. Nova binding to an exonic YCAY cluster changed the protein complexes assembled on pre-mRNA, blocking U1 snRNP (small nuclear ribonucleoprotein) binding and exon inclusion, whereas Nova binding to an intronic YCAY cluster enhanced spliceosome assembly and exon inclusion. Assays of splicing intermediates of Nova-regulated transcripts in mouse brain revealed that Nova preferentially regulates removal of introns harbouring (or closest to) YCAY clusters. These results define a genome-wide map relating the position of a cis-acting element to its regulation by an RNA binding protein, namely that Nova binding to YCAY clusters results in a local and asymmetric action to regulate spliceosome assembly and alternative splicing in neurons.

Alternative Splicing↗

PubMed1995

Sequence identity locates CEBPD and FGFR1 to mapped human loci within proximal 8p.

The gene loci for human CEBPD (CCAAT enhancer binding protein, delta chain) and FGFR1 (fibroblast growth factor receptor) have been identified within two genetically mapped cosmids by sequence homology between rare cutter site regions and data base sequences for these loci. Cell hybrid and fluorescence in situ hybridization mapping places both of these loci within the chromosome region 8p11.2-->p11.1.

Animals↗

PubMed1986

Analysis of the spatial organization of microtubule-associated proteins.

We have developed microdensitometer-computer correlation techniques to analyze the arrangement of microtubule arms and bridges (i.e., microtubule-associated proteins [MAPs]). A microdensitometer was used to scan immediately adjacent to the wall of longitudinally sectioned microtubules in positive transparency electron micrographs. Signal enhancement procedures were applied to the digitized densitometer output to produce a binary sequence representing the apparent axial spacing of MAP projections. These enhanced records were analyzed in two ways. (a) Autocorrelograms were formed for each record and correlogram peaks from a group of scans were pooled to construct a peak frequency histogram. (b) Cross-correlation was used to optimize the match between each enhanced record and templates predicted by different models of MAP organization. Seven symmetrical superlattices were considered as well as single axial repeats. The analyses were repeated with randomly generated records to establish confidence levels. Using the above methods, we analyzed the intrarow bridges of the Saccinobaculus axostyle and the MAP2 projections associated with brain microtubules synthesized in vitro. We confirmed a strict 16-nm axial repeat for axostyle bridges. For 26 MAP2 records, the only significant match was to a 12-dimer superlattice model (P less than 0.002). However, we also found some axial distances between MAP2 projections which were compatible with the additional spacings predicted by a 6-dimer superlattice. Therefore, we propose that MAP2 projections are arranged in a "saturated 12-dimer, unsaturated 6-dimer" superlattice, which may be characteristic of a wide variety of MAPs.

Animals↗

PubMed2002

[Mutation of LoopAB in HuIFN 1c/86D and enhancement of antiviral activity].

BACKGROUND: Based on the earlier mapping of the epitope recognized by neutralizing antibody, the authors directly replaced binding domain of IFN in AB-loop for enhancement of biological activity. METHODS: Two unique restriction sites (EcoR? and BsE?) were created into region flanking LoopAB. Casette mutagesis, restriction enzyme digestion, DNA sequencing, antiviral activity assay and antiproliferative activity assay have been used in the project. RESULTS: The mutated residues M31?D,D32?P of LoopAB in parent IFN were produced. The recombinant phagemid pCANTAB5E/3132IFN 1c/86D and expression plasmid PBV322-132IFN 1c/86D were constructed respectively by replacing the corresponding LoopAB with DNA fragment mutated in the residues M31?D,D32?P, which have been confirmed. The recombinant protein has been expressed in E.coli JM103. The crude 3132IFN 1c/86D has been assayed on human WISH cells challenged with VSV and on HeLa cells by colorimetric MTT. 3132IFN 1c/86D showed 8-old antiviral activity compared to that of parent IFN 1c/86D, while IFN?induced growth inhibition of both types had no difference. CONCLUSIONS: The authors concluded that a mutant IFN with enhanced antiviral activity can be obtained via a targeted replacement of receptor binding domain in AB-loop.

Amino Acid Substitution↗

PubMed1991

CBF measured by Xe-CT: approach to analysis and normal values.

Normal reference values and a practical approach to CBF analysis are needed for routine clinical analysis and interpretation of xenon-enhanced computed tomography (CT) CBF studies. We measured CBF in 67 normal individuals with the GE 9800 CT scanner adapted for CBF imaging with stable Xe. CBF values for vascular territories were systematically analyzed using the clustering of contiguous 2-cm circular regions of interest (ROIs) placed within the cortical mantle and basal ganglia. Mixed cortical flows averaged 51 +/- 10ml.100g-1.min-1. High and low flow compartments, sampled by placing 5-mm circular ROIs in regions containing the highest and lowest flow values in each hemisphere, averaged 84 +/- 14 and 20 +/- 5 ml.100 g-1.min-1, respectively. Mixed cortical flow values as well as values within the high flow compartment demonstrated significant decline with age; however, there were no significant age-related changes in the low flow compartment. The clustering of systematically placed cortical and subcortical ROIs has provided a normative data base for Xe-CT CBF and a flexible and uncomplicated method for the analysis of CBF maps generated by Xe-enhanced CT.

Adult↗

PubMed1985

Upstream promoter element of the human metallothionein-IIA gene can act like an enhancer element.

Initiation of transcription by RNA polymerase II in eukaryotes is strongly increased by cis-acting genetic elements, known as activators or enhancers. Enhancers, first detected in simian virus 40 (SV40), were subsequently also found to control the expression of several cellular genes. The human metallothionein-IIA (hMT-IIA) gene, although inducible by heavy metals and glucocorticoids, is widely expressed in most cell types in the absence of inducers. Here we show that the high basal level of transcription of the hMT-IIA gene is due to the presence of an enhancer element within the hMT-IIA promoter region. The structural and functional organization of this cellular enhancer element in two direct repeats is strikingly similar to that of the enhancer element of SV40. This suggests a possible functional and evolutionary relationship between enhancers and upstream promoter elements.

Acetyltransferases↗

PubMed1993

Immunoglobulin heavy chain enhancer is located near or in an initiation zone of chromosomal DNA replication.

In several animal viruses, enhancers have been implicated in both DNA replication and transcriptional activation. The linkage of the two mechanisms appears intimate, in that common DNA binding factors can be shared. The immunoglobulin heavy chain (Igh) intronic [heavy chain joining region (JH)-mu chain constant region (C mu)] enhancer (E mu) is required for tissue-specific transcription of Igh genes and is essential for somatic recombination of diversity (D) and J segments. We show here that E mu is located at or near an origin of chromosomal DNA replication, which is more active in B lymphocytes than fibroblasts. E mu does not fulfill two criteria demonstrated for some cellular origins. E mu can initiate but not maintain autonomous replicating activity in B cells. E mu is unable to impart early replication timing to a transfected VDJ-C mu Igh locus in B cells. Instead we propose that E mu-associated ori activity contributes to tissue-specific Igh expression through local effects on chromatin structure leading to subsequent accessibility of transcription and/or recombination factors for the enhancer.

3T3 Cells↗

PubMed2000

The antenatal ward care delivery map: a team model approach.

We begin by defining the concept of a 'CareMap', before briefly examining the context in which CareMaps emerged, as well as both their potential applications and the benefits arising from their implementation in health care services. We identify and discuss the history of, and critical aspects involved in, the development of the Antenatal Ward Care Delivery Map for the Mater Mothers' Hospital, Brisbane. We will address the multiple applications of, and specific benefits arising from, the formulation and implementation of the Antenatal Ward Care Delivery Map. Additionally, the relationship between the Care Delivery Map and other projects aimed at enhancing and maintaining high quality service delivery for patients across the continuum of care, will be explored. We examine the benefits of utilising the Care Delivery Map in professional education for clinical staff, as well as for health care consumers and their families. In conclusion, future projects enabled through the development of the Care Delivery Map are identified, as well as areas requiring further research.

Continuity of Patient Care↗

PubMed1998

E1A represses apolipoprotein AI enhancer activity in liver cells through a pRb- and CBP-independent pathway.

The apolipoprotein AI (apoAI) promoter/enhancer contains multiple cis -acting elements on which a variety of hepatocyte-enriched and ubiquitous transcription factors function synergistically to regulate liver-specific transcription. Adenovirus E1A proteins repress tissue-specific gene expression and disrupt the differentiated state in a variety of cell types. In this study expression of E1A 12Sor 13S in hepatoblastoma HepG2 cells repressed apoAI enhancer activity 8-fold. Deletion mapping analysis showed that inhibition by E1A was mediated by the apoAI promoter site B. E1A selectively inhibited the ability of HNF3beta and HNF3alpha to transactivate reporter genes controlled by the apoAI site B and the HNF3 binding site from the transthyretin promoter. The E1A-mediated repression of HNF3 activity was not reversed by overexpression of HNF3beta nor did E1A alter nuclear HNF3beta protein levels or inhibit HNF3 binding to DNA in mobility shift assays. Overexpression of two cofactors known to interact with E1A, pRb and CBP failed to overcome inhibition of HNF3 activity. Similarly, mutations in E1A that disrupt its interaction with pRb or CBP did not compromise its ability to repress HNF3beta transcriptional activity. These data suggest that E1A inhibits HNF3 activity by inactivating a limiting cofactor(s) distinct from pRb or CBP.

Adenovirus E1A Proteins↗

PubMed1995

Hydrogen peroxide preferentially enhances the tyrosine phosphorylation of epidermal growth factor receptor.

We found that hydrogen peroxide (H2O2) enhances EGF receptor tyrosine phosphorylation in intact cells as well as solubilized membrane of an EGF receptor hyperproducing cell line NA. An antioxidant MnCl2 effectively inhibited this enhancement. Interestingly, overall phosphorylation of the EGF receptor enhanced by H2O2 was half that of the EGF-enhanced phosphorylation when the receptor immunoprecipitated from [32P]orthophosphate-labeled cells was examined. Tryptic phospho-peptide mapping of these receptors revealed that EGF enhanced the phosphorylation on five specific residues including serine 671, 1,046 and 1,047, threonine 669 and tyrosine 1,173, whereas H2O2 enhanced the phosphorylation remarkably on tyrosine 1,173 and three other residues and only moderately on serine 1,046 and 1,047 and threonine 669. Thus, H2O2 preferentially enhances the tyrosine phosphorylation of EGF receptor through oxidant stress.

Amino Acid Sequence↗

PubMed1997

Mapping the chicken genome.

Most economically important traits are genetically complex and controlled by numerous genes. A quality genetic map is a prerequisite for identifying quantitative trait loci (QTL) that contain the genes involved in these traits. Currently, there are two internationally recognized reference families that are used to build genetic maps. In this paper, the East Lansing (EL) genetic map is described in detail. Presently, the EL genetic map contains 617 genetic markers, of which 589 are resolved into 41 linkage groups. The map coverage within linkage groups is over 2,700 cM, which is about the estimated size of the chicken genome. There are 322 microsatellite markers, which greatly enhances the utility of this genetic map for genome-wide QTL searches. Also, 101 genes have been mapped, which will aid in the development of a comparative map. Further efforts to improve the genetic map and the potential for the map to identify QTL are discussed.

Animals↗

PubMed1978

The limitations of epicardial mapping as a guide to the surgical therapy of ventricular tachycardia.

The adequacy of intraoperative epicardial mapping as a guide to surgical procedures performed to terminate ventricular arrhythmias was investigated. Ligation of the anterior septal or left anterior descending coronary artery in 28 dogs produced ventricular arrhythmias that were studied 24-36 hours following occlusion. The sites of origin of 26 tachycardias were determined to be in the subendocardium by using extensive epicardial, endocardial and intramural mapping techniques and were verified by demonstrating unaltered activation sequences during pacing from these earliest sites. Epicardial breakthrough followed earliest directly recordable ventricular activity by as little as 7 msec. Without endocardial mapping many of these tachycardias would have been incorrectly identified as originating in the fascicles or epicardium. The sites of epicardial breakthrough were anatomically distant from the sites of origin by a markedly varying extent (5mm to 6cm). Two rhythms might be close in their sites of earliest epicardial appearance yet distant on the endocardium or vice versa. We conclude that epicardial mapping may not be sufficient to identify or predict the origins of many ventricular tachycardias and that the success of surgery to abolish these arrhythmias may be enhanced by preoperative and intraoperative endocardial mapping.

Animals↗

PubMed1988

Mapping of the rib5 gene in Saccharomyces cerevisiae using UV light as an enhancer of rad52-mediated chromosome loss.

Rib5 mutants of S. cerevisiae are blocked at the end of the riboflavin biosynthetic pathway. Using UV light to increase rad52-mediated chromosome loss, we have assigned the rib5 mutation to chromosome II. Tetrad analysis of crosses between rib5 and other markers on chromosome II shows that the RIB5 gene is located on the right arm of this chromosome, closely linked to HIS7.

Chromosome Mapping↗

PubMed2003

The Cerefy Neuroradiology Atlas: a Talairach-Tournoux atlas-based tool for analysis of neuroimages available over the internet.

The article introduces an atlas-assisted method and a tool called the Cerefy Neuroradiology Atlas (CNA), available over the Internet for neuroradiology and human brain mapping. The CNA contains an enhanced, extended, and fully segmented and labeled electronic version of the Talairach-Tournoux brain atlas, including parcelated gyri and Brodmann's areas. To our best knowledge, this is the first online, publicly available application with the Talairach-Tournoux atlas. The process of atlas-assisted neuroimage analysis is done in five steps: image data loading, Talairach landmark setting, atlas normalization, image data exploration and analysis, and result saving. Neuroimage analysis is supported by a near-real-time, atlas-to-data warping based on the Talairach transformation. The CNA runs on multiple platforms; is able to process simultaneously multiple anatomical and functional data sets; and provides functions for a rapid atlas-to-data registration, interactive structure labeling and annotating, and mensuration. It is also empowered with several unique features, including interactive atlas warping facilitating fine tuning of atlas-to-data fit, navigation on the triplanar formed by the image data and the atlas, multiple-images-in-one display with interactive atlas-anatomy-function blending, multiple label display, and saving of labeled and annotated image data. The CNA is useful for fast atlas-assisted analysis of neuroimage data sets. It increases accuracy and reduces time in localization analysis of activation regions; facilitates to communicate the information on the interpreted scans from the neuroradiologist to other clinicians and medical students; increases the neuroradiologist's confidence in terms of anatomy and spatial relationships; and serves as a user-friendly, public domain tool for neuroeducation. At present, more than 700 users from five continents have subscribed to the CNA.

Atlases as Topic↗

PubMed1998

Serotonergic repression of mitogen-activated protein kinase control of the calcitonin gene-related peptide enhancer.

We have investigated the mechanisms underlying regulation of the calcitonin gene-related peptide (CGRP) cell-specific enhancer. Recently, we reported that this enhancer is inhibited by serotonin type-1 (5-HT1) agonists, similar to currently used antimigraine drugs. We have now tested whether this repression involves a mitogen-activated protein (MAP) kinase pathway. We first demonstrate that the CGRP enhancer is strongly (10-fold) activated by a constitutively active MAP kinase kinase (MEK1), yielding reporter activities 100-fold above the enhancerless control. The involvement of a MAP kinase pathway was confirmed by down-regulation of reporter activity upon cotransfection of a dominant negative Ras. Activation of the enhancer by MEK1 was blocked in a dose-dependent manner by the 5-HT1 receptor agonist CGS 12066A (CGS). Since it is not known whether the CGRP enhancer factors are immediate targets of MAP kinases, we then used EIk-1- and c-Jun-dependent reporter genes that are directly activated by the ERK (extracellular signal-regulated kinases) and JNK (c-Jun N-terminal kinase) MAP kinases. CGS treatment repressed the activation of both of these reporters, suggesting that at least two MAP kinases are the immediate targets of CGS-mediated repression. We further demonstrate that 5-HT1 agonists inactivate ERK by dephosphorylation, even in the presence of constitutively activated MEK1. This inactivation appears to be due to a marked increase in the level of MAP kinase phosphatase-1. These results have defined a novel and general mechanism by which 5-HT1 receptor agonists can repress MAP kinase activation of target genes, such as CGRP.

Animals↗