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PubMed1997

Dantrolene sodium reverses the increase in cAMP response element and TPA responsive element DNA-binding activity in the rabbit brain following haloperidol administration and heat stress.

Using electrophoretic mobility-shift assay (EMSA), we examined DNA-binding activity of cAMP response element (CRE), onto its responsive element CRE, as well as TPA responsive element (TRE) in the medial hypothalamus and striatum of the experimental rabbits administered with haloperidol under heat stress exposure and studied the effects of dantrolene sodium to the transcriptional factor. In EMSA with nuclear extracts from the rabbit brain, the DNA-binding activities of CRE and TRE in medial hypothalamus and striatum increased following haloperidol and heat stress. These increases were maintained by coadministration with atropine. The treatment with dantrolene sodium markedly reversed such increases. The alterations of activities of these transcriptional factors may reflect the therapeutic effect of dantrolene sodium.

Animals↗
PubMed2003

Quantitative computed tomography-based finite element models of the human lumbar vertebral body: effect of element size on stiffness, damage, and fracture strength predictions.

This study investigated the numerical convergence characteristics of specimen-specific "voxel-based" finite element models of 14 excised human cadaveric lumbar vertebral bodies (age: 37-87; M = 6, F = 8) that were generated automatically from clinical-type CT scans. With eventual clinical applications in mind, the ability of the model stiffness to predict the experimentally measured compressive fracture strength of the vertebral bodies was also assessed. The stiffness of "low"-resolution models (3 x 3 x 3 mm element size) was on average only 4% greater (p = 0.03) than for "high"-resolution models (1 x 1 x 1.5 mm) despite interspecimen variations that varied over four-fold. Damage predictions using low- vs high-resolution models were significantly different (p = 0.01) at loads corresponding to an overall strain of 0.5%. Both the high (r2 = 0.94) and low (r2 = 0.92) resolution model stiffness values were highly correlated with the experimentally measured ultimate strength values. Because vertebral stiffness variations in the population are much greater than those that arise from differences in voxel size, these results indicate that imaging resolution is not critical in cross-sectional studies of this parameter. However, longitudinal studies that seek to track more subtle changes in stiffness over time should account for the small but highly significant effects of voxel size. These results also demonstrate that an automated voxel-based finite element modeling technique may provide an excellent noninvasive assessment of vertebral strength.

Adult↗
PubMed2006

A penetration-based finite element method for hyperelastic 3D biphasic tissues in contact. Part II: finite element simulations.

The penetration method allows for the efficient finite element simulation of contact between soft hydrated biphasic tissues in diarthrodial joints. Efficiency of the method is achieved by separating the intrinsically nonlinear contact problem into a pair of linked biphasic finite element analyses, in which an approximate, spatially and temporally varying contact traction is applied to each of the contacting tissues. In Part I of this study, we extended the penetration method to contact involving nonlinear biphasic tissue layers, and demonstrated how to derive the approximate contact traction boundary conditions. The traction derivation involves time and space dependent natural boundary conditions, and requires special numerical treatment. This paper (Part II) describes how we obtain an efficient nonlinear finite element procedure to solve for the biphasic response of the individual contacting layers. In particular, alternate linearization of the nonlinear weak form, as well as both velocity-pressure, v-p, and displacement-pressure, u-p, mixed formulations are considered. We conclude that the u-p approach, with linearization of both the material law and the deformation gradients, performs best for the problem at hand. The nonlinear biphasic contact solution will be demonstrated for the motion of the glenohumeral joint of the human shoulder joint.

Anisotropy↗
PubMed2004

Technical note: A novel boundary condition using contact elements for finite element based deformable image registration.

Deformable image registration is an important tool for image-guided radiotherapy. Physics-model-based deformable image registration using finite element analysis is one of the methods currently being investigated. The calculation accuracy of finite element analysis is dependent on given boundary conditions, which are usually based on the surface matching of the organ in two images. Such a surface matching, however, is hard to obtain from medical images. In this study, we developed a new boundary condition to circumvent the traditional difficulties. Finite element contact-impact analysis was employed to simulate the interaction between the organ of interest and the surrounding body. The displacement loading is not necessarily specified. The algorithm automatically deforms the organ model into the minimum internal energy state. The analysis was performed on CT images of the lung at two different breathing phases (exhalation and full inhalation). The result gave the displacement vector map inside the lung. Validation of the result showed satisfactory agreement in most parts of the lung. This approach is simple, operator independent and may provide improved accuracy of the prediction of organ deformation.

Algorithms↗
PubMed1981

Genetic elements novel for Corynebacterium diphtheriae: specialized transducing elements and transposons.

It was shown in an accompanying paper (Buck and Groman, J. Bacteriol. 148: 131-142, 1981) that gamma-tsr-1 phage stocks produced by heat induction of lysogens are a mixture of two phages which differ in the content of their deoxyribonucleic acid (DNA). This difference is evidenced by the appearance of "heterogeneous" (HET) fragments in restriction enzyme digests of gamma-tsr-1 phage DNA. It was estimated that 20 to 80% of the phage in these lysates produced HET fragments. The appearance of HET fragments correlated with the appearance of a DNA insertion (DI-1) in the gamma phage genome as revealed in heteroduplexes of DNA from gamma-tsr-1 and beta corynebacteriophages. The HET fragments were seen in DNA from heat-induced lysates, but not in DNA from phage stocks produced by lytic infection. By DNA-DNA hybridization analysis it was shown that a fraction of gamma-tsr-1 phages from heat-induced lysates carried an insertion of bacterial DNA in the vegetative phage attachment site (attP), and that this insertion was responsible for the formation of HET fragments. Since the phage produced by this event carried a complete phage genome plus a small segment of bacterial DNA, they were called transducing elements. On the basis of these facts it was concluded that heat-induced gamma-tsr-1 prophage was excised at an abnormal site at a very high frequency. Abnormal excision was highly specific, and the change in excision specificity occurred simultaneously with the spontaneous mutation of the phage to heat inducibility. From this and other data it was postulated that a mutation in the immune repressor was reponsible for an alteration in the specificity of the normal excision process. This distinguishes the mechanism of formation of gamma-tsr-1 transducing elements from that employed by other phages. A second DNA insertion (DI-2) in the tox (diphtheria toxin) gene of gamma-tsr-1 and gamma-tsr-2 was also identified as an insertion of bacterial DNA. The DI-2 insertion had a stem-and-loop structure similar to that seen in heteroduplexes visualizing transposons or insertion elements. It seems likely that gamma wild-type phage, which is mutant for tox, was originally tox(+), but that transposition of bacterial DNA into the gene inactivated it.

Attachment Sites, Microbiological↗
PubMed2004

The bcr1 DNA repeat element is specific to the Bacillus cereus group and exhibits mobile element characteristics.

Bacillus cereus strains ATCC 10987 and ATCC 14579 harbor an approximately 155-bp repeated element, bcr1, which is conserved in B. cereus, B. anthracis, B. thuringiensis, and B. mycoides but not in B. subtilis and B. licheniformis. In this study, we show by Southern blot hybridizations that bcr1 is present in all 54 B. cereus group strains tested but absent in 11 Bacillus strains outside the group, suggesting that bcr1 may be specific and ubiquitous to the B. cereus group. By comparative analysis of the complete genome sequences of B. cereus ATCC 10987, B. cereus ATCC 14579, and B. anthracis Ames, we show that bcr1 is exclusively present in the chromosome but absent from large plasmids carried by these strains and that the numbers of full-length bcr1 repeats for these strains are 79, 54, and 12, respectively. Numerous copies of partial bcr1 elements are also present in the three genomes (91, 128, and 53, respectively). Furthermore, the genomic localization of bcr1 is not conserved between strains with respect to chromosomal position or organization of gene neighbors, as only six full-length bcr1 loci are common to at least two of the three strains. However, the intergenic sequence surrounding a specific bcr1 repeat in one of the three strains is generally strongly conserved in the other two, even in loci where bcr1 is found exclusively in one strain. This finding indicates that bcr1 either has evolved by differential deletion from a very high number of repeats in a common ancestor to the B. cereus group or is moving around the chromosome. The identification of bcr1 repeats interrupting genes in B. cereus ATCC 10987 and ATCC 14579 and the presence of a flanking TTTAT motif in each end show that bcr1 exhibits features characteristic of a mobile element.

Bacillus anthracis↗
PubMed1989

A unique enhancer element for the trans activator (p40tax) of human T-cell leukemia virus type I that is distinct from cyclic AMP- and 12-O-tetradecanoylphorbol-13-acetate-responsive elements.

The trans activator (p40tax) of human T-cell leukemia virus type I (HTLV-I) is a transcriptional factor that activates the long terminal repeat (LTR) of HTLV-I and interleukin-2 receptor alpha. We examined the HTLV-I enhancer responsible for tax-mediated trans activation and identified (A/T)(G/C)(G/C)CNNTGACG(T/A) as a plausible tax-responsive element (TRE). The putative TRE in the LTR was found to be different from the elements required for activation by cycle AMP and 12-O-tetradecanoylphorbol-13-acetate, although these elements overlapped each other. The TRE was also different from a binding site of an NF-kappa B-like factor that was identified in the interleukin-2 receptor alpha promoter and human immunodeficiency virus LTR as a TRE. The latter result was further demonstrated by the failure of the NF-kappa B sequence to compete with the TRE of the LTR in a protein-binding assay. These findings indicate that tax function and its cascade can modulate activities of various enhancer sequences, which are probably regulated by distinct DNA-binding factors.

Base Sequence↗
PubMed1993

The intracisternal A-particle upstream element interacts with transcription factor YY1 to activate transcription: pleiotropic effects of YY1 on distinct DNA promoter elements.

Murine intracisternal A-particle long terminal repeats contain an intracisternal A-particle upstream enhancer (IUE) element that binds to a 65-kDa IUE binding protein (IUEB) present in both undifferentiated F9 embryonal carcinoma cells and differentiated parietal endoderm-like PYS-2 cells. This IUE element confers a CpG methylation-sensitive IUEB binding and enhancer activity. Using gel retardation, methylation interference, CpG methylation sensitivity binding, and cotransfection assays, we have now identified the 65-kDa IUEB as YY1 (also called NF-E1, delta, or UCRBP), a zinc finger protein related to the Krüppel family. YY1 binds to a number of similar but distinct DNA motifs, and cotransfection assays indicate that these motifs have different enhancer potentials in PYS-2 cells. The relative strengths of these elements are as follows: IUE > kappa E3' from the human immunoglobulin kappa light-chain 3' enhancer > upstream conserved region from the Moloney murine leukemia virus promoter. Results of DNA binding assays suggest that the differences in enhancer potentials are due to the different binding affinities of YY1 to the various motifs and the binding of two other transcription factors to the IUE sequence.

Animals↗
PubMed1990

Invertrons, a class of structurally and functionally related genetic elements that includes linear DNA plasmids, transposable elements, and genomes of adeno-type viruses.

Invertrons are genetic elements composed of DNA with inverted terminal repeats at both ends, covalently bonded to terminal proteins involved in the initiation of DNA replication at both their 5' termini when they exist in the cytoplasm of their host in free form. They function as viruses, linear DNA plasmids, transposable elements, and sometimes combinations of two of these properties. They differ from retroviruses and related retro-type transposons which have direct repeats on both their genomic ends and exploit RNA intermediates for replication of their DNA. A model for replication and integration of invertrons is presented, as well as a model for transposition of transposable elements.

Adenoviridae↗
PubMed2002

Estrogen activates the high-density lipoprotein receptor gene via binding to estrogen response elements and interaction with sterol regulatory element binding protein-1A.

The effects of E2 on the high-density lipoprotein receptor (HDL-R) scavenger receptor class B type I (SR-BI) gene were examined. Four putative estrogen response element half-site motifs (ERE(1/2)) (-2176, -1726, -1622, and -1211, designated ERE(1/2)-1, 2, 3, and 4, respectively) were identified in the HDL-R SR-BI promoter. Transfection studies and mutation analysis demonstrated that E2 significantly increased HDL-R SR-BI promoter activity and that mutating ERE(1/2)-1, 2, and 4 resulted in a loss of E2 responsiveness. Both ER alpha and ER beta formed specific complexes with ERE(1/2)-1, 2, and 4 but did not bind ERE(1/2)-3 in vitro. Interestingly, ERE(1/2)-3 was the motif shown not to be important for E2-activation of the HDL-R SR-BI promoter in the mutational analysis studies. The influence of SREBP-1a (sterol regulatory element binding protein-1a) on E2 regulation of the HDL-R SR-BI gene was also examined. SREBP-1a was able to bind directly to the ERE(1/2) motifs and enhanced ER binding when both ER subtypes were present. ER alpha and beta also bound to a sterol response element motif, but they did not enhance SREBP-1a binding. Cotransfection studies demonstrated that the presence of the three factors, ER alpha, ER beta, and SREBP-1a, enhanced the overall luciferase activity produced from the HDL-R SR-BI promoter construct in the presence of only one of the factors. Interaction of SREBP-1a with both ERs was demonstrated using a mammalian two-hybrid assay. The data confirmed that E2 through the ERs can positively regulate the HDL-R SR-BI through binding and activation of three ERE(1/2) motifs and identified SREBP-1a as a potential coactivator of the E2-ER-dependent effects on the HDL-R SR-BI gene.

Blotting, Western↗
PubMed2007

Transcriptional regulation of the cholesterol side chain cleavage cytochrome P450 gene (CYP11A1) revisited: binding of GATA, cyclic adenosine 3',5'-monophosphate response element-binding protein and activating protein (AP)-1 proteins to a distal novel cluster of cis-regulatory elements potentiates AP-2 and steroidogenic factor-1-dependent gene expression in the rodent placenta and ovary.

The first and key enzyme controlling the synthesis of steroid hormones is cholesterol side chain cleavage cytochrome P450 (P450scc, CYP11A1). This study sought to elucidate overlooked modes of regulation of P450scc transcription in the rodent placenta and ovary. Transcription of P450scc requires two clusters of cis-regulatory elements: a proximal element (-40) known to bind either activating protein 2 (AP-2) in the placenta, or steroidogenic factor 1 in the ovary, and a distal region of the promoter (-475/-447) necessary for potentiation of the AP-2/steroidogenic factor 1-dependent activity up to 7-fold. In primary cultures of mouse trophoblast giant cells and rat ovarian granulosa cells, binding of trans-factors to the distal regulatory sequences generated transcriptional activity in a tissue-specific pattern: in the placenta, cAMP response element (CRE)-binding protein 1 (CREB-1) and GATA-2 binding generates promoter activity in a cAMP-independent manner, whereas in ovarian cells, CREB-1 and GATA-4 are required for FSH responsiveness. However, as ovarian follicles advance toward ovulation, elevated Fra-2 expression replaces CREB-1 function by binding the same CRE(1/2) motif. Our findings suggest that upon onset of follicular recruitment, CREB-1 mediates FSH/cAMP signaling, which switches to cAMP-independent expression of P450scc in luteinizing granulosa cells expressing Fra-2. In the placenta, the indispensable role of CREB-1 was demonstrated by use of dominant-negative CREB-1 mutant, but neither cAMP nor Ser133 phosphorylation of CREB-1 is required for P450scc transcription. These observations suggest that placental regulation of P450scc expression is subjected to alternative signaling pathway(s) yet to be found.

Activating Transcription Factor 1↗
PubMed1991

A binding site for the cyclic adenosine 3',5'-monophosphate-response element-binding protein as a regulatory element in the grp78 promoter.

The 78-kDa glucose-regulated protein (GRP78) is ubiquitously expressed in many cell types. Its promoter contains multiple protein-binding sites and functional elements. In this study we examined a high affinity protein-binding site spanning bp -198 to -180 of the rat grp78 promoter, using nuclear extracts from both B-lymphoid and HeLa cells. This region contains a sequence TGACGTGA which, with the exception of one base, is identical to the cAMP-response element (CRE). Site-directed mutagenesis reveals that this sequence functions as a major basal level regulatory element in hamster fibroblast cells and is also necessary to maintain high promoter activity under stress-induced conditions. By gel mobility shift analysis, we detect two specific protein complexes. The major specific complex I, while immunologically distinct from the 42-kDa CRE-binding protein (CREB), binds most strongly to the grp site, but also exhibits affinity for the CRE consensus sequence. As such, complex I may consist of other members of the CREB/activating transcription factor protein family. The minor specific complex II consists of CREB or a protein antigenically related to it. A nonspecific complex III consists of the Ku autoantigen, an abundant 70- to 80-kDa protein complex in HeLa nuclear extracts. By cotransfection experiments, we demonstrate that in F9 teratocarcinoma cells, the grp78 promoter can be transactivated by the phosphorylated CREB or when the CREB-transfected cells are treated with the calcium ionophore A23187. The differential regulation of the grp78 gene by cAMP in specific cell types and tissues is discussed.

B-Lymphocytes↗
PubMed2006

Mode superposition transient dynamic analysis for dental implants with stress-absorbing elements: a finite element analysis.

The purpose of this study was to analyze the dynamic behavior of a dental implant with a stress-absorbing element, using dynamic analysis. Two model types, stress-absorbing model with a resilient stress absorber made of polyoxymethylene and non-stress-absorbing model with rigid titanium, were employed. In both model types, the implant was 4.0 mm in diameter and 13.0 mm in length and placed in the mandibular first molar region. Shapes of the finite element implant and implant-bone were modeled using computer-aided design. All calculations for the dynamic analysis were performed using the finite element method. It was found that the stress-absorbing model had a lower natural frequency than the non-stress-absorbing model. In addition, the stress-absorbing model had a higher damping effect than the non-stress-absorbing model. It was concluded that mode superposition transient dynamic analysis is a useful technique for determining dynamic behavior around dental implants.

Dental Implants↗
PubMed2005

Identification of androgen-responsive element ARE and Sp1 element in the maspin promoter.

Maspin is a serine protease inhibitor (serpin) with tumor-suppressing function in mammary gland. It is down-regulated in primary prostate cancer cells and lost in metastatic cells. To better understand the transcriptional regulation of maspin gene, the 860bp (-765 approximately +95) of its promoter sequence was amplified by PCR from the human genomic DNA. Then this 860bp sequence and a series of deletions from 5' and 3' ends were inserted into the upstream of luciferase reporter gene respectively. Results from dual luciferase reporter assay and electrophoretic mobility shift assay indicated that there were a negative androgen-responsive element (ARE) in the region of -277 to -262 and a positive Sp1 element in the region of +14 to +35, respectively. In addition, androgen receptor (AR) can recognize and bind to the ARE element, and then inhibit the activity of maspin promoter.

Androgens↗
PubMed2005

Selective mineral elements concentration of the intestinal mucosa role of the lysosomes of duodenal enterocytes in the handling of mineral elements after intragastric administration.

Intragastric administration to rats of four soluble lanthanides cerium, lanthanum, europium, thulium and of three soluble elements of group IIIA aluminium, indium and gallium has been shown in previous studies. In this work two new rare earths gadolinium and terbium were studied using the same protocols and the same methods (transmission electron microscopy and ion microanalysis). among the previously studied elements, some of them were administered simultaneously on the one hand aluminium and indium, and on the other hand, lanthanum and cerium. These metals were looked for in intestinal mucosa, liver and kidney. The results showed: a) gadolinium and terbium were selectively concentrated in lysosomes of duodenal enterocytes, precipitated as non-soluble phosphate salts and eliminated with the cell's turn-over in less than 48 hr; b) Administered simultaneously, they precipitated in the same lysosome. c/ none of them was observed in the liver or kidney even with high dose. This study brings up to nine the number of elements forming a non-soluble phosphate salts, explaining their precipitation in lysosomes. None of them have a physiological role, two are toxic (aluminium and indium). This rapid intralysosomal concentration is an efficient mechanism which limits the diffusion of the foreign substances through the digestive barrier, then permits their elimination along with the cytoptose phenomenon in the intestinal lumen.

Animals↗
PubMed2006

[A modifier of the Bg element of the Bg-rbg transposable element system of maize].

A modifier of the Bg autonomous element of the Bg-rbg system of transposable elements has been found in the genotype of the inbred maize strain 346. In the presence of this modifier (termed Mbg), the frequency of reversion of mutable allele o2-lf in combination with the Bg-lf element increases by 7-24 times. An increase in the Mbg dosage by three times increases the o2-lf reversion frequency by a factor of about two. The presence of Mbg and Bg-lf in the same genotype before meiosis is necessary for the expression of the Mbg modifying effect. The possible nature and mechanism of action of the novel modifier are discussed.

Alleles↗
PubMed1991

Involvement of lysine residues 289 and 291 of the cAMP-responsive element-binding protein in the recognition of the cAMP-responsive element.

The molecular interactions resulting in specific binding of trans-acting factors to distinct cis-acting elements is not well understood. Here we report our attempt to understand the involvement of distinct amino acid residues of the basic domain of cAMP-responsive element-binding protein (delta CREB) in the determination of binding toward the cAMP-responsive element (CRE). Using in vitro mutagenesis, we constructed site-directed mutants of distinct amino acid residues within the DNA contact region of delta CREB. The activities of the mutant proteins were analyzed by gel retardation, methylation interference, and CRE competition analyses. We demonstrate that a single lysine to glutamine substitution at positions 289 and 291 of delta CREB alters the methylation interference pattern of the mutant protein for the CRE site. Additional mutants constructed at these positions demonstrate that only identical basic residues at both positions 289 and 291 of delta CREB can restore the wild type methylation interference pattern of the mutant delta CREB protein for the CRE site. These observations point to the importance of the lysine residues at positions 289 and 291 in the process of CRE binding. In addition, this observation suggests that the symmetrical nature of the CRE site is reflected in the DNA contact region of the protein.

Amino Acid Sequence↗
PubMedDate not supplied

[Levels of oligo-elements and trace elements in patients at the time of admission in intensive care units].

Routinely, the macronutrient contribution is thoroughly studied when a patient is included in a total parenteral nutrition (TPN) program. However, it must be kept in mind that along with macronutrients, micronutrients, oligoelements and vitamins are also administered, and these must be taken into account. At present, for instance, the importance of oligoelements has become evident, and clinical conditions of oligoelement deficiency have been described in many cases even when the minimum daily requirements had been met. This study centers on the importance of evaluating oligoelement and trace element levels when patients are admitted into the ICU and were included into a total parenteral nutrition (TPN) program. An assessment of the serum calcium (Ca), phosphorus (P), magnesium (Mg), zinc (Zn), copper (Cu), iron (Fe) and transferrin (Tfe) levels was done on 55 septic patients who underwent abdominal surgery was done on admission to the ICU. Transferrin was measured of serve as an indicator of metabolic damage. A description of the methods used in analytical assessment, a presentation of normal values, the statistical management of each of the elements under study and the interpretation of the results obtained has been done. The discussion is based on the changes detected in the patients' serum levels on admission to the unit, showing low iron, transferrin, zinc and calcium values and normal magnesium, phosphorus and copper figures. The conclusion arrived at suggests that the daily parenteral supplements of these elements should be higher than those recommended by the American Medical Association (AMA) and by other authors.

Female↗