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Results for “Enhancer mapping”

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PubMed1993

Mutation of the C/EBP binding sites in the Rous sarcoma virus long terminal repeat and gag enhancers.

Several C/EBP binding sites within the Rous sarcoma virus (RSV) long terminal repeat (LTR) and gag enhancers were mutated, and the effect of these mutations on viral gene expression was assessed. Minimal site-specific mutations in each of three adjacent C/EBP binding sites in the LTR reduced steady-state viral RNA levels. Double mutation of the two 5' proximal LTR binding sites resulted in production of 30% of wild-type levels of virus. DNase I footprinting analysis of mutant DNAs indicated that the mutations blocked C/EBP binding at the affected sites. Additional C/EBP binding sites were identified upstream of the 3' LTR and within the 5' end of the LTRs. Point mutations in the RSV gag intragenic enhancer region, which blocked binding of C/EBP at two of three adjacent C/EBP sites, also reduced virus production significantly. Nuclear extracts prepared from both chicken embryo fibroblasts (CEFs) and chicken muscle contained proteins binding to the same RSV DNA sites as did C/EBP, and mutations that prevented C/EBP binding also blocked binding of these chicken proteins. It appears that CEFs and chicken muscle contain distinct proteins binding to these RSV DNA sites; the CEF binding protein was heat stable, as is C/EBP, while the chicken muscle protein was heat sensitive.

Animals↗

PubMed1998

Human immunodeficiency virus tat modulates the Flk-1/KDR receptor, mitogen-activated protein kinases, and components of focal adhesion in Kaposi's sarcoma cells.

Kaposi's sarcoma (KS) spindle cell growth and spread have been reported to be modulated by various cytokines as well as the human immunodeficiency virus (HIV) gene product Tat. Recently, HIV-1 Tat has been shown to act like a cytokine and bind to the Flk-1/KDR receptor for the vascular endothelial growth factor A (VEGF-A), which is expressed by KS cells. We have characterized signal transduction pathways stimulated by HIV-1 Tat upon its binding to surface receptors on KS cells. We observed that stimulation in KS 38 spindle cells resulted in tyrosine phosphorylation and activation of the Flk-1/KDR receptor. We also report that HIV-1 Tat treatment enhanced the phosphorylation and association of proteins found in focal adhesions, such as the related adhesion focal tyrosine kinase RAFTK, paxillin, and p130(cas). Further characterization revealed the activation of mitogen-activated protein kinase, c-Jun amino-terminal kinase (JNK), and Src kinase. HIV-1 Tat contains a basic domain which can interact with growth factor tyrosine kinase receptors and a classical RGD sequence which may bind to and activate the surface integrin receptors for fibronectin and vitronectin. We observed that stimulation of KS cells with basic as well as RGD sequence-containing Tat peptides resulted in enhanced phosphorylation of RAFTK and activation of MAP kinase. These studies reveal that Tat stimulation activates a number of signal transduction pathways that are associated with cell growth and migration.

Calcium-Calmodulin-Dependent Protein Kinases↗

PubMed2001

Cyclical regulation of GnRH gene expression in GT1-7 GnRH-secreting neurons by melatonin.

The pineal hormone melatonin plays an important role in the neuroendocrine control of reproductive physiology, but its effects on hypothalamic GnRH neurons are not yet known. We have found that GT1-7 GnRH-secreting neurons express membrane-bound G protein-coupled melatonin receptors, mt1 (Mel-1a) and MT2 (Mel-1b) as well as the orphan nuclear receptors ROR alpha and RZR beta. Melatonin (1 nM) significantly downregulates GnRH mRNA levels in a 24-h cyclical manner, an effect that is specifically inhibited by the melatonin receptor antagonist luzindole (10 microM). Repression of GnRH gene expression by melatonin appears to occur at the transcriptional level and can be mapped to the GnRH neuron-specific enhancer located within the 5' regulatory region of the GnRH gene. Using transient transfection of GT1-7 cells, downregulation of GnRH gene expression by melatonin was further localized to five specific regions within the GnRH enhancer including -1827/-1819, -1780/-1772, -1746/-1738, -1736/-1728, and -1697/-1689. Interestingly, the region located at -1736/-1728 includes sequences that correspond to two direct repeats of hexameric consensus binding sites for members of the ROR/RZR orphan nuclear receptor family. To begin to dissect the mechanisms involved in the 24-h cyclical regulation of GnRH transcription, we have found that melatonin (10 nM) induces rapid internalization of membrane-bound mt1 receptors through a beta-arrestin 1-mediated mechanism. These results provide the first evidence that melatonin may mediate its neuroendocrine control on reproductive physiology through direct actions on the GnRH neurons of the hypothalamus, both at the level of GnRH gene expression and through the regulation of G protein-coupled melatonin receptors.

Animals↗

PubMed1998

POU transcription factors control expression of CNS stem cell-specific genes.

Multipotential stem cells throughout the developing central nervous system have common properties. Among these is expression of the intermediate filament protein nestin and the brain fatty acid binding protein (B-FABP). To determine if common mechanisms control transcription in CNS stem cells, the regulatory elements of these two genes were mapped in transgenic mice. A 257 basepair enhancer of the rat nestin gene is sufficient for expression throughout the embryonic neuroepithelium. This enhancer contains two sites bound by the class III POU proteins Brn-1, Brn-2, Brn-4, and Tst-1. Only one of the two POU sites is required for CNS expression. An adjacent hormone response element is necessary for expression in the dorsal midbrain and forebrain. The regulatory sites of the B-FABP gene are strikingly similar to those of the nestin gene. A hybrid POU/Pbx binding site is recognized in vitro by Pbx-1, Brn-1 and Brn-2. This site is essential for expression in most of the CNS. In addition, a hormone response element is necessary for forebrain expression. Both the nestin and B-FABP genes therefore depend on POU binding sites for general CNS expression, with hormone response elements additionally required for activity in the anterior CNS. These data indicate that regulation by POU proteins and hormone receptors is a general mechanism for CNS stem cell-specific transcription.

Animals↗

PubMed2001

Revealing the unseen: the organizer region of the nucleolus.

We carried out a high-resolution ultrastructural analysis of the nucleolus in mouse P815 cells by combining specific DNA and RNA staining, anti-fibrillarin immunolabeling, contrast enhancement by energy filtering TEM and phosphorus mapping by ESI to visualize nucleic acids. We demonstrated that specifically contrasted DNA, fibrillarin and phosphorus overlap within the nucleolar dense fibrillar component. Moreover, we describe a 'DNA cloud' consisting of an inner core of DNA fibers (fibrillar center) and a periphery made of extremely thin fibrils overlapping the anti-fibrillarin immunolabeling (dense fibrillar component). This highly sensitive approach has allowed us to demonstrate, for the first time, the exact distribution of DNA within the decondensed interphase counterpart of the NOR, which includes both the fibrillar center and the dense fibrillar component.

Animals↗

PubMed2003

The role of octadecanoids and functional mimics in soybean defense responses.

Oxylipins of the jasmonate pathway and synthetic functional analogs have been analyzed for their elicitor-like activities in an assay based on the induced accumulation of glyceollins, the phytoalexins of soybean (Glycine max L.), in cell suspension cultures of this plant. Jasmonic acid (JA) and its methyl ester showed weak phytoalexin-inducing activity when compared to an early jasmonate biosynthetic precursor, 12-oxo-phytodienoic acid (OPDA), as well as to the bacterial phytotoxin coronatine and certain 6-substituted indanoyl-L-isoleucine methyl esters, which all were highly active. Interestingly, different octadecanoids and indanoyl conjugates induced the accumulation of transcripts of various defense-related genes to different degrees, indicating distinct induction competencies. Therefore, these signaling compounds and mimics were further analyzed for their effects on signal transduction elements, such as the transient enhancement of the cytosolic Ca2+ concentration and MAP kinase activation, which are known to be initiated by a soybean pathogen-derived beta-glucan elicitor. In contrast to the beta-glucan elicitor, none of the other compounds tested triggered these early signaling elements. Moreover, endogenous levels of OPDA and JA in soybean cells were shown to be unaffected after treatment with beta-glucans. Thus, OPDA and JA, which are functionally mimicked by coronatine and a variety of 6-substituted derivatives of indanoyl-L-isoleucine methyl ester, represent highly efficient signaling compounds of a lipid-based pathway not deployed in the beta-glucan elicitor-initiated signal transduction.

Acetates↗

PubMed2006

A societal outcomes map for health research and policy.

The linkages between decisions about health research and policy and actual health outcomes may be extraordinarily difficult to specify. We performed a pilot application of a "road mapping" and technology assessment technique to perinatal health to illustrate how this technique can clarify the relations between available options and improved health outcomes. We used a combination of data-mining techniques and qualitative analyses to set up the underlying structure of a societal health outcomes road map. Societal health outcomes road mapping may be a useful tool for enhancing the ability of the public health community, policymakers, and other stakeholders, such as research administrators, to understand health research and policy options.

Health Policy↗

PubMed1983

Exaggerated hypotensive responses to calcium antagonists in spontaneously hypertensive rats.

The hypotensive effects of intravenous injection and infusion of diltiazem, l- and d-verapamil were investigated in conscious and anaesthetized rats with spontaneous hypertension (SHR) and normal blood pressure (NT-WKY). The inhibitory actions of these calcium-influx blockers on the pressor responses to angiotensin II (AII) and noradrenaline (NA) were also examined in anaesthetized SHR and NT-WKY. The intravenous injections of these three drugs (0.03, 0.1, 0.3, 1.0 mg/kg) lowered mean arterial pressure (MAP) in a dose related manner in conscious NT-WKY and SHR. The small dose of the blockers administered by intravenous infusion (0.02 mg/kg per min) also decreased MAP in both groups. The potency of the antihypertensive action was in the order l-verapamil greater than d-verapamil = diltiazem. The fall in blood pressure expressed as percentage of the initial MAP produced by the compounds was significantly enhanced in SHR compared to NT-WKY. The pressor responses to AII (0.03, 0.1, 0.3, 1.0 micrograms/kg i.v.) were suppressed by the intravenous infusion of 20 micrograms/kg per min with l-verapamil but not with d-verapamil, diltiazem and vehicle in NT-WKY, while no calcium blocker significantly diminished the vasopressor action of AII in SHR. The pressor effects of NA (0.3, 1.0, 3.0, 10.0 micrograms/kg i.v.) were inhibited by the same doses of l-verapamil and diltiazem but not with d-verapamil and vehicle in NT-WKY. Diltiazem reduced the response to NA in SHR but the other compounds (l- and d-verapamil) did not alter the pressor response to NA in SHR. The pressor responses to arginine vasopressin (3, 10, 30 and 100 mU/kg i.v.) were not altered by diltiazem infusion in either SHR or NT-WKY. It is concluded that these compounds are different in the potency of their hypotensive action and also the inhibition of the pressor responses to AII and NA. Calcium entry blockers are more effective antihypertensive agents in SHR than in NT-WKY. It appears that their inhibitory effects on the responses to AII and NA do not explain the exaggerated hypotensive responses in SHR.

Action Potentials↗

PubMed2001

Semantic features of an enterprise interface terminology for SNOMED RT.

OBJECTIVE: To evaluate the utility of SNOMED RT in support of a natural language interface for encoding of clinical assessments. METHOD: Using a random sample of clinical terms from the UNMC Lexicon, I mapped the terminology into canonical data entries using SNOMED RT. Working from the source term language, I evaluated lexical mapping to the SNOMED term set, and the function of the SNOMED RT semantic network in support of a language-based clinical coding interface. RESULTS: Ambiguity in the source terms was low at 0.3%. Lexical (language-based) mapping could account for only 48.8% of meaning from the source terms. The RT semantic network accounted for 39.5% of meaning, and supplementing the lexical map this led to 80.2% capture of source content. Error rates in the segment of RT which I reviewed were low at 0.6%. 97.6% of source content could be accurately captured in SNOMED RT. CONCLUSION: SNOMED RT supported an accurate and reliable representation of clinical assessment data in this sample. The semantic network of RT substantially enhanced the encoding of concepts relative to lexical mapping. However these data suggest that natural language encoding with SNOMED RT in an enterprise environment is unlikely at this time.

Natural Language Processing↗

PubMed2002

[Molecular biology of drug dependence and behavioral sensitization].

Molecular mechanisms in the development of drug abuse and dependence were reviewed by taking behavioral sensitization induced by psychostimulants like amphetamines and cocaine as a typical example. Behavioral sensitization is characterized by three main features, progressive quantitative and qualitative changes in responsiveness to the drug, very long-lastingness, and development of vulnerability to other drugs and nonspecific physical and psychological stressors, in other words, cross-sensitization. These serial changes in response to the drug during abuse must result from plastic changes in the brains of abusers. As to subcellular neurochemical mechanisms of sensitization, the activation of three main cascades is indispensable, 1) D1 dopamine (DA) receptors/PKA/phospho-34Thr-DARPP-32/PP-1 cascade activated by psychostimulant-induced enhancement of DA release in the accumbens, 2) NMDA receptors and CaM-KII activated by enhanced release of glutamate, 3) activation of MAP kinase cascade by BDNF and beta 1 subunit of G protein. These, in turn, activate several transcription factors, including delta-Fos B, and affect transcription and translation of 4th or later messengers. Finally, these result in the rearrangement of neural networks, where the tone of the A10 dopamine pathway from the ventral tegmentum area to the accumbens is strengthened, and regulation by glutamatergic afferents from the frontal cortex, amygdala and hippocampus shifts into abnormal positive regulation. As amphetamines increase expression of some plasticity-related genes (e.g. synaptophysin, stathmin and arc), synaptogenesis, neuritic sprouting and elongation must develop during behavioral sensitization. These plastic changes with structural modification of neural networks in the CNS during drug abuse could induce and reinforce psychological dependence and susceptibility to drug-induced psychoses, which become increasingly intractable.

Brain↗

PubMed1994

Transcellular activation of the HTLV promoter by human hematopoietic cells.

We examined the ability of hematopoietic cells to transactivate the HTLV promoter by a transcellular mechanism. HeLa cells containing a CAT reporter gene driven by the HTLV-2 promoter were cocultivated with hematopoietic cells of the B-(Raji), T-(HuT78, Jurkat) and monocyte/promyelocytic (THP-1, U937 and HL60) lineages. Cocultivation with U937 and HuT78 cells constitutively and significantly transactivated the HTLV-2 promoter, while no effect was observed with the other lines. However, activation of other T-cell lines (CEM, Jurkat, Molt-3 and MT-4) with a combination of phorbolester and phytohemagglutinin also resulted in potent transactivation. Supernatant from HuT78 cells exhibited detectable transactivating activity, suggesting that the activation is mediated by a secreted factor(s). This factor also transactivates the HTLV-1 promoter. We used a panel of HTLV-1 LTR deletion mutants to map the responsive elements to this factor(s). Unlike the response element to the HTLV transactivator protein, Tax, which can be mapped to a small region in the enhancer, maximal transactivation by the cellular factor(s) required the complete U3 sequence. Transcellular activation of the HTLV promoter by activated T-cells may play a role in the development of leukemia in HTLV infected individuals.

Deltaretrovirus↗

PubMed1998

Synaptic competition during the reformation of a neuromuscular map.

We have been studying the mechanisms whereby pools of motor neurons establish a rostrocaudal bias in the position of their synapses in some skeletal muscles. The serratus anterior (SA) muscle of the rat displays a rostrocaudal topographic map before birth, and the topography is re-established after denervation. In this report, we explore the potential role of synaptic competition between innervating axons as a means of generating topographic specificity. We followed the progress of the reformation of this map in neonatal animals under conditions that enhanced the likelihood of observing synaptic competition. This was accomplished by forcing caudal axons to regenerate ahead of rostral axons onto a surgically reduced SA muscle. In this way, caudal (C7) motor neurons had unopposed access to vacated synaptic sites on the remaining rostral half of the SA before the return of the rostral (C6) axons. Intracellular recording revealed that 2 d after the second denervation, most of the reinnervated end plates contained only axons from the C7 branch; the remaining reinnervated end plates received input from C6 only or were multiply innervated by C6 and C7 axons. After 6 d, the pattern was reversed, with most end plates innervated exclusively by C6. After 17 d, axons from C6 were the sole input to reinnervated end plates. During the transition from C7- to C6-dominated input, at end plates coinnervated by C6 and C7 axons, the average quantal content from C6 was the same as that from C7; after 7 d, the quantal content of C6 was greater than that of C7. We have thus developed an experimental situation in which the outcome of synaptic competition is predictable and can be influenced by the positional labels associated with axons from different levels in the spinal cord.

Animals↗

PubMed2003

Mitogen-activated protein kinase pathway is involved in androgen-independent PSA gene expression in LNCaP cells.

BACKGROUND: Prostate specific antigen (PSA) is regulated by growth factors and hormones through functional androgen responsive elements in the promoter region of the PSA gene. However, the molecular basis for androgen independent PSA elevation in hormone refractory prostate cancer is unknown. The purpose of this study was to investigate the role of MAP kinase activation in androgen independent regulation of PSA expression. METHODS: LNCaP cells transfected with MEK1 expression vector with or without the MAP kinase inhibitor U0126 under low androgen conditions were analyzed by luciferase assay and electrophoretic mobility shift assay (EMSA). RESULTS: Transfection experiments of the proximal PSA promoter linked to Luc-reporter identified one region designated as "B" motif centered at -60 bp to be essential for basal activation. Co-transfection with the MEK1 activated vector enhanced PSA expression, while mutation of the "B" motif totally abrogated this induction. EMSA showed a specific DNA-protein complex, but Sp1 family members and AR do not interact with the "B" region by supershift analysis. CONCLUSIONS: Our data suggest that enhanced androgen-independent PSA gene expression in MAP kinase-induced LNCaP cells is mediated, at least in part, by the "B" motif of the PSA promoter.

Androgens↗

PubMed1992

Chromosomal localization in man and rat of the genes encoding the liver-enriched transcription factors C/EBP, DBP, and HNF1/LFB-1 (CEBP, DBP, and transcription factor 1, TCF1, respectively) and of the hepatocyte growth factor/scatter factor gene (HGF).

By means of somatic cell hybrids segregating either human or rat chromosomes, we determined the chromosome localization of three genes encoding transcription factors expressed in hepatocytes, namely, C/EBP (CCAAT/enhancer binding protein), DBP (D site of albumin promoter binding protein), and HNF1/LFB-1 (designated transcription factor 1, gene symbol: TCF1), and of the hepatocyte growth factor gene, which is identical to the mitogenic and chemotactic factor designated scatter factor (gene symbol:HGF). The CEBP and DBP genes, encoding two related transcription factors, were found to be syntenic both on human chromosome 19 and on rat chromosome 1. These results provide further evidence for conservation of synteny on these two chromosomes (and on mouse chromosome 7). The TCF1 gene was found to be located on chromosome 12 in both man and rat, thereby defining a new segment of homology between these two species (and a segment of mouse chromosome 5). The HGF gene was mapped to rat chromosome 4, confirming homology between this chromosome and human chromosome 7, which carries the human HGF gene.

Animals↗

PubMed2005

Improved BOLD detection in the medial temporal region using parallel imaging and voxel volume reduction.

Using gradient-echo EPI, signal dropout due to macroscopic off resonance effects can prevent blood-oxygenation-level-dependent (BOLD) signal change detection. The anterior medial temporal lobe (MTL) is located near these susceptibility gradients and therefore shows considerable signal dropout with GE-EPI. Reducing the volume of the image voxel reduces susceptibility-related signal dropout. However, this is accompanied by a prohibitive reduction in signal-to-noise ratio (SNR). To compensate for SNR loss with smaller voxels, we used a multi-channel MRI receiver with an array of receive-only 16-element surface coils at 3 T. We demonstrate that the reduction of susceptibility artifacts, through use of high resolution images, coupled with the gains in image SNR from the array coil improves the temporal signal-to-noise ratio (TSNR) and enhances the contrast-to-noise ratio (CNR). Furthermore, a comparison of 2 mm with 4-mm-thick axial images both with the same in-plane resolution showed that thinner slices enhanced TSNR and CNR throughout the ventral-medial regions of the temporal lobes, with the greatest improvement in the most anterior regions of the MTL. Further improvements were seen when adjacent 2 mm slices were combined to match overall voxel volume. These results demonstrate that BOLD investigation of anterior MTL function can be enhanced by decreasing voxel size but only in combination with the SNR gained by using the 16-channel head coil system.

Adult↗

PubMed2003

The effect of acute hypoxemia and hypotension on adenosine-mediated depression of evoked hippocampal synaptic transmission.

The present study was designed to investigate the relative contributions of arterial P(O(2)), local cerebral blood flow, and oxygen delivery to the adenosine A(1) receptor-mediated depression of evoked synaptic transmission recorded in the rat hippocampus. Urethane-anesthetized rats were given a unilateral common carotid artery occlusion and then placed in a stereotaxic apparatus for stimulation and recording of bilateral hippocampal field excitatory postsynaptic potentials (fEPSPs). Arterial blood gases, mean arterial blood pressure (MAP), and bilateral hippocampal blood flow (HBF) were also measured. Arterial P(O(2)), HBF, and oxygen delivery were manipulated using normoxic hypotension, hypoxic hypotension, and hypoxic normotension. Both hypoxic hypotension and normoxic hypotension resulted in decreased HBF, decreased oxygen delivery, and a depression of the evoked fEPSP limited to the hippocampus ipsilateral to the occlusion. The enhanced HBF and oxygen delivery associated with increased MAP resulted in a restoration and maintenance of hippocampal fEPSPs despite sustained hypoxemia. The adenosine A(1) receptor-mediated depression of the fEPSP was more strongly correlated with changes in HBF and oxygen delivery than with arterial P(O(2)). We propose that adenosine plays an important role mediating the depression of neuronal activity associated with reduced oxygen delivery characteristically observed in ischemic brain tissue.

Acute Disease↗

PubMed2006

Pedagogical efficiency of melodic contour mapping technology as it relates to vocal timbre in singers of classical music repertoire.

The purpose of this investigation was to ascertain the pedagogical viability of computer-generated melodic contour mapping systems in the classical singing studio, as perceived by their resulting effect (if any) on vocal timbre when a singer's head and neck remained in a normal singing posture. The evaluation of data gathered during the course of the study indicates that the development of consistent vocal timbre produced by the classical singing student may be enhanced through visual/kinesthetic response to melodic contour inversion mapping, as it balances the singer's perception of melodic intervals in standard musical notation. Unexpectedly, it was discovered that the system, in its natural melodic contour mode, may also be useful for teaching a student to sing a consistent legato line. The results of the study also suggest that the continued development of this new technology for the general teaching studio, designed to address standard musical notation and a singer's visual/kinesthetic response to it, may indeed be useful.

Adolescent↗

PubMed1997

The potent enhancer activity of the polycythemic strain of spleen focus-forming virus in hematopoietic cells is governed by a binding site for Sp1 in the upstream control region and by a unique enhancer core motif, creating an exclusive target for PEBP/CBF.

The polycythemic strain of the spleen focus-forming virus (SFFVp) contains the most potent murine retroviral enhancer configuration known so far for gene expression in myeloerythroid hematopoietic cells. In the present study, we mapped two crucial elements responsible for the high activity of the SFFVp enhancer to an altered upstream control region (UCR) containing a GC-rich motif (5'-GGGCGGG-3') and to a unique enhancer core (5'-TGCGGTC-3'). Acquisition of these motifs accounts for half of the activity of the complete retroviral enhancer in hematopoietic cells, irrespective of the developmental stage or lineage. Furthermore, the UCR motif contains the major determinant for the enhancer activity of SFFVp in embryonic stem (ES) cells. Using electrophoretic mobility shift assays, we show that the UCR of SFFVp, but not of Friend murine leukemia virus, is targeted by the ubiquitous transcriptional activator, Sp1. The core motif of SFFVp creates a specific and high-affinity target for polyomavirus enhancer binding protein/core binding factor (PEBP/CBF) and excludes access of CAAT/enhancer binding protein. Cotransfection experiments with ES cells imply that PEBP/CBF cooperates with the neighboring element, LVb (the only conserved Ets consensus in the SFFVp enhancer), and that the Sp1 motif in the UCR stimulates transactivation through the Ets-PEBP interaction. Putative secondary structures of the retroviral enhancers are proposed based on these data.

Animals↗