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  • 1
    Electronic Resource
    Electronic Resource
    Analysis of density functionals and their density tails in H2 (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 69 (1998), S. 541-550 
    Details
    ISSN: 0020-7608
    Keywords: density functional theory ; long-range behavior ; electron density ; Kohn-Sham ; orbital energy ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The total energy, internuclear distance, vertical ionization potential, and electron density function were determined for the hydrogen molecule (H2) with a configuration interaction calculation, a Hartree-Fock calculation, all 22 density functional theory (DFT) methods built into Gaussian 92/DFT, and the Davidson and Jones natural orbital expansion of the Kolos and Roothaan wave function. These data were used to explore the performance of DFT methods in modeling the chemical bond. We noted that although the vertical ionization potentials suggested by the highest occupied molecular orbital energies of DFT methods are generally quite poor, the medium-range bahavior of the electron density from DFT methods is close to that of more accurately determined electron densities. Accordingly, we propose a method of finding an approximate vertical ionization potential for a density functional calculation from the medium-range behavior of the electron density. We explain why the density functionals' electron densities decay in a manner different from that which their orbital energies lead us to expect and explore the relationship between the errors in the exchange-correlation potentials, electron densities, and the orbital energies.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 69: 541-550, 1998
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  • 2
    Electronic Resource
    Electronic Resource
    PTH-responsive osteoblast nuclear matrix architectural transcription factor binds to the rat type I collagen promoterThe first two authors contributed equally to this work. (1998)
    New York, N.Y. : Wiley-Blackwell
    Journal of Cellular Biochemistry 69 (1998), S. 336-352 
    Details
    ISSN: 0730-2312
    Keywords: architectural transcription factor ; nuclear matrix ; osteoblast ; parathyroid hormone ; type I collagen ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: In connective tissue, cell structure contributes to type I collagen expression. Differences in osteoblast microarchitecture may account for the two distinct cis elements regulating basal expression, in vivo and in vitro, of the rat type I collagen α1(I) polypeptide chain (COL1A1). The COL1A1 promoter conformation may be the penultimate culmination of osteoblast structure. Architectural transcription factors bind to the minor groove of AT-rich DNA and bend it, altering interactions between other trans-acting proteins. Similarly, nuclear matrix (NM) proteins bind to the minor groove of AT-rich matrix-attachment regions, regulating transcription by altering DNA structure. We propose that osteoblast NM architectural transcription factors link cell structure to promoter geometry and COL1A1 transcription. Our objective was to identify potential osteoblast NM architectural transcription factors near the in vitro and in vivo regulatory regions of the rat COL1A1 promoter. Nuclear protein-promoter interactions were analyzed by gel shift analysis and related techniques. NM extracts were derived from rat osteosarcoma cells and from rat bone. The NM protein, NMP4, and a soluble nuclear protein, NP, both bound to two homologous poly(dT) elements within the COL1A1 in vitro regulatory region and proximal to the in vivo regulatory element. These proteins bound within the minor groove and bent the DNA. Parathyroid hormone increased NP/NMP4 binding to both poly(dT) elements and decreased COL1A1 mRNA in the osteosarcoma cells. NP/NMP4-COL1A1 promoter interactions may represent a molecular pathway by which osteoblast structure is coupled to COL1A1 expression. J. Cell. Biochem. 69:336-352. © 1998 Wiley-Liss, Inc.
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  • 3
    Electronic Resource
    Electronic Resource
    Differential stability of proteolytically active and inactive recombinant metalloproteinase in Chinese hamster ovary cells (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 53 (1997), S. 594-600 
    Details
    ISSN: 0006-3592
    Keywords: CHO ; mammalian cells ; metalloproteinase ; recombinant protein production ; expression stability ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Stability of heterologous protein expression during production is critical for regulatory approval of vaccine and therapeutic products. Leishmania GP63, a zinc metalloproteinase that is a potential vaccine candidate, has been expressed on the surface of Chinese hamster ovary (CHO) cells. Flow cytometry was used to follow the stability of GP63 expression. Expression of proteolytically active GP63 (GP63WT) was unstable whether or not methotrexate (MTX) selection was maintained. In contrast, expression of an active site mutant (GP63E265D) was stable under MTX selection. In the absence of selection, the decline in GP63E265D expression was more gradual than the loss of GP63WT expression. Different molecular mechanisms accounted for these losses and resulted in higher growth rate nonproducer populations. A dynamic population model was used to calculate the conversion rates of GP63WT producers to nonproducers. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 53: 594-600, 1997.
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  • 4
    Electronic Resource
    Electronic Resource
    Identification of a vitamin D3 response element in the fibronectin gene that is bound by a vitamin D3 receptor homodimer (1996)
    New York, N.Y. : Wiley-Blackwell
    Journal of Cellular Biochemistry 60 (1996), S. 322-333 
    Details
    ISSN: 0730-2312
    Keywords: fibronectin ; VDR ; homodimer ; vitamin D regulation ; transcription ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: Fibronectin (FN) is an important adhesive noncollagenous glycoprotein involved in maintenance of the extracellular matrix and cell adhesiveness, loss of which has been implicated in the metastatic potential of cells. Regulation of FN occurs at the transcriptional level by the active metabolite of vitamin D3, 1,25-dihydroxyvitamin D3 (1,25-(OH)2D3). Transient transfection of homologous and heterologous promoter reporter constructs into ROS 17/2,8 (rat osteosarcoma), NIH 3T3 (mouse fibroblast), and MCF-7 (human mammary carcinoma) cell lines showed a consistent two- to threefold induction of transcription when stimulated with 1,25-(OH)2D3. These heterologous promoter transfection studies with gel shift analysis locate a third, natural DR6-type vitamin D responsive element (VDRE) at nucleotide positions -171 to -154 in the murine FN promoter. Interestingly, this VDRE is also present in rat and human FN promoters. This study shows that 1,25-(OH)2D3 induces FN transcription from an existing elevated basal transcriptional activity by acting through two putative hexameric core binding motifs which bind VDR homodimers. Furthermore, the FN VDRE is the first homodimer-type VDRE that is not overlaid by a DR3-type structure. © 1996 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
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  • 5
    Electronic Resource
    Electronic Resource
    G/C element contributes to the cell line-specific expression of the proximal osteocalcin promoter (1995)
    New York, N.Y. : Wiley-Blackwell
    Journal of Cellular Biochemistry 58 (1995), S. 499-508 
    Details
    ISSN: 0730-2312
    Keywords: osteocalcin promoter ; G/C element ; collagen type I (α1) promoter ; osteoblast ; ORE-1 ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: Sequential activation of cell type-specific genes occurs during osteoblast development. The promoter of one such gene, osteocalcin, has been widely studied, but the DNA sequences that govern osteoblast-specific expression have not been defined. The proximal osteocalcin promoter linked to pTKCAT directs strong promoter activity in osteoblast-like ROS17/2.8 cells and comparatively weak promoter activity in nonosteoblastic NIH3T3 cells. To identify sequences important in conferring cell-specific expression of the osteocalcin gene, a deletion series of the human proximal promoter was constructed and the activities assessed in ROS17/2.8 and NIH3T3 cells. These studies identified a 30 bp sequence within the proximal promoter (osteocalcin repressor element-1 [ORE-1]) which is responsible for repressing the transcriptional activity in NIH3T3 cells. In electrophoretic mobility shift assays from both NIH3T3 and ROS17/2.8 cells, a protein complex bound to the ORE-1 that was related to a complex which binds the G/C-rich repressor element in the collagen type I (α1) promoter. In addition, there was a second complex from NIH3T3 cells but not ROS17/2.8 cells that bound the ORE-1 fragment. The presence of this additional factor in NIH3T3 cells parallels the observation that constructs carrying the ORE-1 sequence have repressed promoter activity relative to the analogous constructs lacking the ORE-1 when transfected into NIH3T3 and suggests that the NIH3T3-specific factor is a repressor. These data indicate that the G/C element in the ORE-1 contributes to the repression of osteocalcin gene transcription in a nonosteoblast cell line. The high homology between the ORE-1 sequence and a related sequence and a related sequence in the collagen type I (α2) proximal promoter suggests that homologous regions in other osteoblast-expressed genes may function similarly.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcb.240580413
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  • 6
    Electronic Resource
    Electronic Resource
    rHox: A homeobox gene expressed in osteoblastic cells (1995)
    New York, N.Y. : Wiley-Blackwell
    Journal of Cellular Biochemistry 59 (1995), S. 486-497 
    Details
    ISSN: 0730-2312
    Keywords: homeobox gene ; rHox ; rat ; osteocalcin ; collagen I α 1 ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: Homeodomain proteins are characterized by a conserved domain with a helix-turn-helix motif. These proteins act as regulatory factors in tissue differentiation and proliferation. However, their role in the regulation of osteoblast differentiation is unknown. In this study we have identified and characterized a homeobox gene in osteoblast-like cells. This gene, termed rHox, was isolated from a cDNA library derived from rat osteoblast-like cells. The nucleotide sequence of the 1,375 base pair (bp) cDNA contains a noncoding leader sequence of 329 bp, a 735 bp open reading frame, and 312 bp of 3′ noncoding sequence. Sequence comparison demonstrates that rHox is identical to the mouse Pmx gene (also called MHox) at the amino acid level and 90% homologous at the nucleotide level. Both Southwestern blotting and gel shift analyses indicate that rHox has potential to bind both the collagen l α 1 and the osteocalcin promoters. Transfection experiments using an rHox expression vector showed a strong repression of target promoter activity, regardless of whether the target promoters contained homeodomain binding reponse elements. These data suggest that rHox is a potent negative regulator of gene expression, although the specific role of rHox in bone gene regulation remains to be determined. © 1995 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcb.240590409
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  • 7
    Electronic Resource
    Electronic Resource
    1α,25-Dihydroxyvitamin D3 receptor as a mediator of transrepression of retinoid signaling (1997)
    New York, N.Y. : Wiley-Blackwell
    Journal of Cellular Biochemistry 67 (1997), S. 287-296 
    Details
    ISSN: 0730-2312
    Keywords: vitamin D3 receptor ; regulation of transcription ; retinoid signaling transrepression ; tumor necrosis factor-α receptor type I ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: The receptors for retinoic acid (RA) and for 1α,25-dihydroxyvitamin D3 (VD), RAR, RXR, and VDR are ligand-inducible members of the nuclear receptor superfamily. These receptors mediate their regulatory effects by binding as dimeric complexes to response elements located in regulatory regions of hormone target genes. Sequence scanning of the tumor necrosis factor-α type I receptor (TNFαRI) gene identified a 3′ enhancer region composed of two directly repeated hexameric core motifs spaced by 2 nucleotides (DR2). On this novel DR2-type sequence, but not on a DR5-type RA response element, VD was shown to act through its receptor, the vitamin D receptor (VDR), as a repressor of retinoid signalling. The repression appears to be mediated by competitive protein-protein interactions between VDR, RAR, RXR, and possibly their cofactors. This VDR-mediated transrepression of retinoid signaling suggests a novel mechanism for the complex regulatory interaction between retinoids and VD. J. Cell. Biochem. 67:287-296, 1997. © 1997 Wiley-Liss, Inc.
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  • 8
    Electronic Resource
    Electronic Resource
    Identification of an osteocalcin gene promoter sequence that binds AP1 (1996)
    New York, N.Y. : Wiley-Blackwell
    Journal of Cellular Biochemistry 60 (1996), S. 447-457 
    Details
    ISSN: 0730-2312
    Keywords: osteocalcin promoter ; AP1 ; osteoblast ; vitamin D induction ; DNA binding ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: Osteoblasts are differentiated cells that produce bone matrix components including the bone-specific protein osteocalcin. The osteocalcin gene promoter has become a model for understanding how genes are regulated, specifically in osteoblasts. One model for cell-specific regulation suggests that osteoblast-expressed genes are regulated through common promoter sequences which bind osteoblast-specific transcriptional activators. The phenotype suppression model suggests osteoblast-specific promoters are switched off through the action of the common transcriptional activator AP1. We previously demonstrated that a short sequence element (OSCARE-2) in the osteocalcin promoter was homologous to a repressive element in the collagen type 1 (α1) promoters. In this paper we use electrophoretic mobility shift (EMS) assays to examine DNA-protein interactions in the OSCARE-2 sequence. In EMS assays, OSCARE-2 binds a complex of proteins, including AP1. This supports the role of AP1 sites in contributing to the regulation of the osteocalcin promoter. Exogenous c-JUN protein bound to OSCARE-2 and increasing c-JUN incubated with nuclear extract amounts caused a progressive increase in a higher-molecular-weight complex, consistent with c-JUN involvement in protein-protein as well as DNA-protein interactions. Anti-c-FOS antibody was capable of supershifting OSCARE-2 DNA-protein complexes produced using osteoblast-like cell nuclear extracts. In addition, EMS assays of nuclear proteins from osteoblast-like cells indicated that 1,25 (OH)2D3-inducible proteins are bound to OSCARE-2. Osteocalcin promoter constructs showed that OSCARE-2 contributed to the 1,25 (OH)2D3 response, albeit in a minor way. These data support the role of AP1 protein as a regulator of osteoblast-specific gene expression during osteoblast development. © 1996 Wiley-Liss, Inc.
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  • 9
    Electronic Resource
    Electronic Resource
    Negative-ion mass spectrometry in a commercial gas chromatography/ion-trap mass spectrometer system (1995)
    New York, NY : Wiley-Blackwell
    Rapid Communications in Mass Spectrometry 9 (1995), S. 1302-1309 
    Details
    ISSN: 0951-4198
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Physics
    Notes: Commercial gas chromatography quadrupole ion-trap mass spectrometer (GC/ITMS) instruments have been used in a novel way for the study of negative ions formed from perfluorotributyl-amine and polychlorinated biphenyl compounds. Negative ions, formed during a normal electron impact ionization period in which 70 eV electrons were used, were isolated in an ion trap by the application of a negative DC voltage to the ring electrode that caused all positive ions to be ejected from the ion trap; in the subsequent analytical scan, negatives ions were detected with an electron multiplier biased normally so as to detect positive ions. The major negative-ion species detected from FC-43 were m/z 252 to m/z 633; 34 other negative-ion species were detected also, though in low abundance. The observed negative-ion mass range extended from m/z 252 to m/z 633. The signal-to-noise ratio of negative-ion mass spectra was enhanced by operation of the GC/MS instrument in GC mode and averaging the mass spectra acquired. In an examination of 3 hexachlorobiphenyl compounds, the molecular anion cluster around m/z 360 for the non-ortho-substituted congener 169 was observed with a signal-to-noise ratio of ca. 20 for 90 pg injected on column: the response for congener 169 was greater than that for congener 156 (mono-ortho-substituted) which, in turn, was greater than that for congener 153 (di-ortho-substituted).
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/rcm.1290091316
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  • 10
    Electronic Resource
    Electronic Resource
    Mechanisms regulating Raf-1 activity in signal transduction pathways (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Molecular Reproduction and Development 42 (1995), S. 507-514 
    Details
    ISSN: 1040-452X
    Keywords: Signal transduction ; Serine/threonine kinases ; Cancer ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: Raf-1 is a key protein involved in the transmission of developmental and proliferative signals generated by receptor and nonreceptor tyrosine kinases. Biochemical and genetic studies have demonstrated that Raf-1 functions downstream of activated tyrosine kinases and Ras and upstream of mitogen-activated protein kinase (MAPK) and MAPK kinase (MKK or MEK) in many signaling pathways. A major objective of our laboratory has been to determine how Raf-1 becomes activated in response to signaling events. Using mammalian, baculovirus, and Xenopus systems, we have examined the roles that phosphorylation and protein-protein interactions play in regulating the biological and biochemical activity of Raf-1.Our studies have provided evidence that the activity of Raf-1 can be modulated by both Ras-dependent and Ras-independent pathways. Recently, we reported that Arg89 of Raf-1 is a residue required for the association of Raf-1 and Ras. Mutation of this residue disrupted interaction with Ras and prevented Ras-mediated, but not protein kinase C-or tyrosine kinase-mediated, enzymatic activation of Raf-1 in the baculovirus expression system. Further analysis of this mutant demonstrated that kinase-defective Raf-1 proteins interfere with the propagation of proliferative and developmental signals by binding to Ras and blocking Ras function.Our findings have also shown that phosphorylation events play a role in regulating Raf-1. We have identified sites of in vivo phosphorylation that positively and negatively alter the biological and enzymatic activity of Raf-1. In addition, we have found that some of these phosphorylation sites are involved in mediating the interaction of Raf-1 with potential activators (Fyn and Src) and with other cellular proteins (14-3-3). Results from our work suggest that Raf-1 is regulated at multiple levels by several distinct mechanisms. © 1995 wiley-Liss, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/mrd.1080420420
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