Negative Control Regions Research Articles

Lack of association between cortical amyloid deposition and glucose metabolism in early stage Alzheimer´s disease patients.

BackgroundBeta amyloid (Aβ) causes synaptic dysfunction leading to neuronal death. It is still controversial if the magnitude of Aβ deposition correlates with the degree of cognitive impairment. Diagnostic imaging may lead to a better understanding the role of Aβ in development of cognitive deficits. The aim of the present study was to investigate if Aβ deposition in the corresponding brain region of early stage Alzheimer´s disease (AD) patients, directly correlates to neuronal dysfunction and cognitive impairment indicated by reduced glucose metabolism.Patients and methodsIn 30 patients with a clinical phenotype of AD and amyloid positive brain imaging, 2-[18F] fluoro-2-deoxy-d-glucose (FDG) PET/CT was performed. We extracted the average [18F] flutemetamol (Vizamyl) uptake for each of the 16 regions of interest in both hemispheres and computed the standardized uptake value ratio (SUVR) by dividing the Vimazyl intensities by the mean signal of positive and negative control regions. Data were analysed using the R environment for statistical computing and graphics.ResultsAny negative correlation between Aβ deposition and glucose metabolism in 32 dementia related and corresponding brain regions in AD patients was not found. None of the correlation coefficient values were statistically significant different from zero based on two-sided p- value.ConclusionsRegional Aβ deposition did not correlate negatively with local glucose metabolism in early stage AD patients. Our findings support the role of Aβ as a valid biomarker, but does not permit to conclude that Aβ is a direct cause for an aberrant brain glucose metabolism and neuronal dysfunction.

Post op shoulders with shearwave assessment

Introduction Little is known about the morphology of healing rotator cuff after surgical repair. Shear wave elastography ultrasound (SWEUS) is a relatively new technique that evaluates tissue elasticity by applying an acoustic radiation force impulse (ARFI). The aim of this study was to evaluate in a temporal fashion the stiffness of the repaired supraspinatus tendon post arthroscopic repair using shear wave elastography ultrasound imaging (SWEUS). Methods An intra-inter reliability trial showed that SWEUS (Siemens Acuson S2000 HELIX; Siemens Medical Solutions, Mountain View, California) was very reliable at assessing the supraspinatus tendon (r > 0.9). The mean (± SEM) stiffness of normal human supraspinatus tendon was 9.96 ± 0.02 m/s. To evaluate the healing tendon fifty participants (30 males and 20 females) were enrolled one week post arthroscopic rotator cuff repair. The mean age was 57 (range 24-85) years old. A grey-scale ultrasound image of the supraspinatus tendon was recorded. Shearwave elastography ultrasound was applied and a sample box positioned within the supraspinatus tendon to assess the post operative supraspinatus tendon, in three specific areas, using a standardized protocol by a single sonographer. In addition, the humeral head (positive control) and the deltoid muscle (negative control) were evaluated on each occasion. Each sample recorded the velocity(m/s), depth of the sampling box (cm) and elasticity (kPa). These assessments were repeated at 8 days, 6 weeks, 12 weeks and 6 months post operative rotator cuff repair. Results Of 50 patients, 3 re-tore their tendons at 6 weeks and 1 re-tore at 12 weeks. Shearwave values of the positive (9.9 m/s ± 0.03) and negative (3.7 m/s ± 0.15) control regions were unchanged throughout the study. The lateral tendon in the anatomical footprint (lateral region) and the tendon medial to the footprint increased in stiffness in an exponential fashion over 6 months (p Conclusion The tendon stiffness as assessed by shearwave elastography increased as the supraspinatus tendon healed in a consistent uniform fashion post rotator cuff repair at the lateral insertion and the tendon medial to the insertion. At six months the average stiffness was 80% of normal supraspinatus tendon.

Identification of promoter regions in the Arabidopsis thaliana atExt1 extensin gene controlling late responses to wounding and pathogen attack

The Arabidopsis thaliana (L.) Heynh. atExt1 extensin gene is expressed in a cell and tissue-specific manner, in response to developmental cues, and is inducible by a wide range of biotic and abiotic stresses. Over-expression of this gene has been shown to alter stem morphology and to limit the invasiveness of virulent bacterial pathogens, indicating that this cell wall protein gene plays an important role in plant development and defense. A detailed sequence analysis of 3.2 kb of the atExt1 gene promoter region has identified a large number of putative 5′cis-acting elements. Based on the location of clusters of putative promoter control elements, seven atExt1 5′ promoter truncations were constructed, fused upstream of the β-glucuronidase (GUS) reporter gene, and transformed into A. thaliana. Transgenic plants carrying the various promoter constructs were challenged by wounding and pathogen attack and analysed for GUS expression - this analysis revealed a complex pattern of regulation, involving positive and negative control regions. Northern analysis using wounded tissues from transgenic Arabidopsis plants carrying the 3.2 kb-promoter::GUS construct confirmed the transcriptional activation of the transgene.

Direct regulation ofknotgene expression by Ultrabithorax and the evolution of cis-regulatory elements inDrosophila

The regulation of development by Hox proteins is important in the evolution of animal morphology, but how the regulatory sequences of Hox-regulated target genes function and evolve is unclear. To understand the regulatory organization and evolution of a Hox target gene, we have identified a wing-specific cis-regulatory element controlling the knot gene, which is expressed in the developing Drosophila wing but not the haltere. This regulatory element contains a single binding site that is crucial for activation by the transcription factor Cubitus interruptus (Ci), and a cluster of binding sites for repression by the Hox protein Ultrabithorax (UBX). The negative and positive control regions are physically separable, demonstrating that UBX does not repress by competing for occupancy of Ci-binding sites. Although knot expression is conserved among Drosophila species, this cluster of UBX binding sites is not. We isolated the knot wing cis-regulatory element from D. pseudoobscura, which contains a cluster of UBX-binding sites that is not homologous to the functionally defined D. melanogaster cluster. It is, however, homologous to a second D. melanogaster region containing a cluster of UBX sites that can also function as a repressor element. Thus, the knot regulatory region in D. melanogaster has two apparently functionally redundant blocks of sequences for repression by UBX, both of which are widely separated from activator sequences. This redundancy suggests that the complete evolutionary unit of regulatory control is larger than the minimal experimentally defined control element. The span of regulatory sequences upon which selection acts may, in general, be more expansive and less modular than functional studies of these elements have previously indicated.

CArG elements control smooth muscle subtype-specific expression of smooth muscle myosin in vivo.

Expression of smooth muscle myosin heavy chain (SM-MHC) is tightly controlled depending on the differentiated state of smooth muscle cells (SMCs). To better understand the mechanisms that regulate transcription of the SM-MHC gene in vivo, we tested the function of several conserved CArG elements contained within the -4200 to +11,600 region of this gene that we had previously shown to drive SMC-specific expression in transgenic mice. CArG1 in the 5'-flanking sequence was required for all SMCs, while CArG2 and a novel intronic CArG element were differentially required in SMC subtypes. Of particular note, mutation of the intronic CArG selectively abolished expression in large arteries. A promoter construct containing three repeats of a conserved 227-bp intronic CArG-containing region was sufficient to direct transcription in vascular SMCs in transgenic mice, although this construct was also expressed in skeletal and cardiac muscle. These results support a model in which transcriptional regulation of SM-MHC is controlled by multiple positive and negative modular control regions that differ between SMCs and non-SMCs and among SMC subtypes. We also demonstrated that the CArG elements of the endogenous SM-MHC gene were bound by SRF in chromatin.

Identification of a Nuclear Factor-I Family Protein-binding Site in the Silencer Region of the Cartilage Matrix Protein Gene

Cartilage matrix protein (CMP) is synthesized by chondrocytes in a developmentally regulated manner. Here we have dissected promoter upstream elements involved in its transcriptional regulation. We show that although the 79-base pair CMP minimal promoter is promiscuous, 1137 base pairs of 5'-flanking region are capable of directing tissue- and developmental stage-specific transcription when fused to a reporter gene. This results from two positive control regions which, in proliferating chondrocytes, relieve the repression mediated by two non-tissue-specific negative control regions. Characterization of the promoter proximal silencer by DNase I footprinting and gel shifts revealed the presence of two elements, SI and SII, which bound mesenchymal cell proteins. Methylation interference analysis indicated a gapped palindromic binding site similar to nuclear factor I (NF-I) family proteins within SI, but only a half-site within SII. Gel shift assays with specific NF-I and mutated SI competitors, binding of recombinant NF-I, as well as supershift analysis with NF-I-specific antiserum verified the binding of NF-I family proteins to the SI element. Double-stranded SI and SII oligonucleotides inserted in single copy in either orientation were found to repress both homologous and heterologous promoters upon transfection into mesenchymal cells. Transcriptional repression also occurred when a consensus NF-I site itself was fused to the CMP minimal promoter. We conclude that NF-I-related protein(s) can mediate transcriptional repression in cells of mesenchymal origin.

The Bel1 protein of human foamy virus contains one positive and two negative control regions which regulate a distinct activation domain of 30 amino acids.

The Bel1 transactivator is essential for the replication of human foamy virus (HFV). To define the functional domains of HFV Bel1, we generated random missense mutations throughout the entire coding sequence of Bel1. Functional analyses of 24 missense mutations have revealed the presence of at least two functional domains in Bel1. One domain corresponds to a basic amino acid-rich motif which acts as a bipartite nuclear targeting sequence. A second, central domain corresponds to a presumed effector region which, when mutated, leads to dominant-negative mutants and/or lacks transactivating ability. In addition, deletion analyses and domain-swapping experiments further showed that Bel1 protein contains a strong carboxy-terminal activation domain. The activating region is also capable of functioning as a transcription-activating domain in yeast cells, although it does not bear any significant sequence homology to the well-characterized acidic activation domain which is known to function only in yeast and mammalian cells. We also demonstrated that the regions of Bel1 from residues 1 to 76 and from residues 153 to 225 repressed transcriptional activation exerted by the Bel1 activation domain. In contrast, the region from residues 82 to 150 appears to overcome an inhibitory effect. These results indicate that Bel1 contains one positive and two negative regulatory domains that modulate a distinct activation domain of Bel1. These regulatory domains of Bel1 cannot affect the function of the VP16 activation domain, suggesting that these domains specifically regulate the activation domain of Bel1. Furthermore, in vivo competition experiments showed that the positive regulatory domain acts in trans. Thus, our results demonstrate that Bel1-mediated transactivation appears to undergo a complex regulatory pathway which provides a novel mode of regulation for a transcriptional activation domain.

Proteins binding to the 5′-flanking regulatory elements of the human β-globin gene

The binding of nuclear proteins prepared from mouse erythroid tissue in different developmental stages to the 5′-flanking regulatory elements of human β-globin gene, two negative control regions(NCR1, -610 to -490 bp; NCR2, -338 to -233bp), was identified. Two stage specific protein factors corresponding to embryonic and fetal stages were found to be capable of binding to NCR2. These data provided evidence that the cis acting elements of the 5′-flanking region might be involved in the developmental control of β globin gene and NCR2 might be responsible in part for the silence of β-globin gene in the embryonic and fetal stages.

Identification of two silencers flanking an AP-1 enhancer in the vimentin promoter

We have studied the 5′ upstream sequences required for the transcriptional regulation of the hamster gene encoding the intermediate filament protein, vimentin. Although vimentin is regarded as the intermediate filament protein of mesothelial tissue, it is also produced in most cultured cells. The human mammary carcinoma cell line, MCF-7, belongs to the exceptions. It contains no vimentin, and the complete upstream promoter region is inactive in this particular cell line. By using transient transfection of chimeric constructs into MCF-7 and HeLa cells, and subsequent chloramphenicol acetyltransferase assays, we were able to show the presence of two negative control regions flanking a double AP1 enhancer element. Our data indicate that these elements exert their effect irrespective of orientation and position, suggesting that they are silencers. In vitro footprinting assays, gel mobility assays and Southwestern (protein-DNA) blotting revealed the presence of trans-acting factors interacting with both silencer elements. The silencing effect was particularly pronounced in MCF-7 cells, although DNA-binding proteins are present in HeLa cells as well.

Human AH locus polymorphism and cancer: inducibility of CYP1A1 and other genes by combustion products and dioxin

The polymorphism of mammalian aromatic hydrocarbon (Ah) responsiveness appears to be correlated with genetic differences in risk of bronchogenic carcinoma caused by cigarette smoking. The human polymorphism has been uncovered, largely as the result of corresponding genetic differences characterized first in the mouse. The murine Ah locus has been defined as the gene encoding the aromatic hydrocarbon-responsive (Ah) receptor, responsible for the inducibility of a battery of at least six genes, two of which encode P450 enzymes. The high-affinity receptor and, hence, more highly induced levels of P450, can result in greater concentrations of polycyclic aromatic reactive intermediates that form DNA adducts and, ultimately, mutation fixation (tumour initiation). The Ah receptor is also likely to participate in growth and differentiation signal transduction pathways (tumour promotion). Positive and negative control regions flanking the murine Cyp 1a-1 and human CYP1A1 (cytochrome P(1)450) genes have been identified. A DNA motif approximately 1 kb upstream of the transcription start site appears to affect the translatability of the CYP1A1 mRNA and activity of the enzyme. Expression of the CYP1A1 or CYP1A2 enzyme in mouse hepatoma Hepa-1 cells lacking endogenous CYP1A1 activity represses constitutive transcription of not only the endogenous Cyp1a-1 gene but other genes in the dioxin-inducible [Ah] battery. Human polymorphisms involving a Msp I site 450 bp downstream from the last CYP1A1 exon have been described in Japan, the Eastern Mediterranean, Norway and the USA. The '1.9 allele' is associated with an increased incidence of Kreyberg Type I bronchogenic carcinomas in Japan and has recently been correlated with a valine-to-isoleucine substitution at position 462 in the haeme-binding region. This allele is about 3 times more frequent in Japan than in Caucasians of Norway and the USA, in which no correlation has been found between this allele and lung cancer. More work is needed to clarify these findings. Isolation and sequencing of the human Ah receptor cDNA, and the subsequent screening of populations for polymorphisms, hold great promise for predicting interindividual risk of cancer caused by smoking and other environmental pollutants.

Identification of Positive and Negative Regulatory Regions Controlling Expression of the Cartilage Matrix Protein Gene

A complex pattern of regulation of the cartilage matrix protein gene was revealed by transient expression experiments. A minimal promoter from positions -15 to +64 functioned in chondrocytes and fibroblasts. An enhancer located in the first intron exerted chondrocyte-specific stimulation on the minimal promoter activity. The same fragment, however, had a negative effect in fibroblasts. Between -334 and -15, a silencer was found which inhibited the gene expression driven from its homologous as well as heterologous promoters both in chondrocytes and fibroblasts. Additional positive and negative control regions were mapped further upstream of the promoter.

Identification of positive and negative regulatory regions controlling expression of the cartilage matrix protein gene.

A complex pattern of regulation of the cartilage matrix protein gene was revealed by transient expression experiments. A minimal promoter from positions -15 to +64 functioned in chondrocytes and fibroblasts. An enhancer located in the first intron exerted chondrocyte-specific stimulation on the minimal promoter activity. The same fragment, however, had a negative effect in fibroblasts. Between -334 and -15, a silencer was found which inhibited the gene expression driven from its homologous as well as heterologous promoters both in chondrocytes and fibroblasts. Additional positive and negative control regions were mapped further upstream of the promoter.

Autoregulation plus upstream positive and negative control regions associated with transcriptional activation of the mouse P1(450) gene.

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is known to interact with a cytosolic receptor and, in turn, activate transcription of the mouse P1(450) gene. Various lengths of DNA upstream of the P1(450) gene were inserted into the pSV0-cat expression vector, with and without addition of the Harvey murine sarcoma virus (Ha-MSV) 72-bp repeat enhancer element. The constructs were cotransfected with pSV2-neo into mouse hepatoma wild-type cells and two variant cell lines. One variant is believed to result from a mutation in the P1(450) structural gene and expresses high levels of P1(450) mRNA constitutively; the other variant has a defect in nuclear translocation of the inducer-receptor complex. After selection in G418, the cells were treated with control medium, TCDD, cycloheximide, or TCDD plus cycloheximide and then assayed for chloramphenicol acetyltransferase (CAT) activity. The data are consistent with the presence of several functional regions within the upstream sequence: a promoter region, a region that is negatively autoregulated, possible repressor-binding and inducer-receptor complex-binding sites, and an upstream activation element that is required for transcriptional activation by TCDD. The Ha-MSV enhancer can substitute for this upstream activation element.