Crystal structure of the DNA-binding domain of Mbp1, a transcription factor important in cell-cycle control of DNA synthesis

BACKGROUND

During the cell cycle, cells progress through four distinct phases, G1, S, G2 and M; transcriptional controls play an important role at the transition between these phases. MCB-binding factor (MBF), a transcription factor from budding yeast, binds to the so-called MCB (MluI cell-cycle box) elements found in the promoters of many DNA synthesis genes, and activates the transcription of those at the G1-->S phase transition. MBF is comprised of two proteins, Mbp1 and Swi6.

RESULTS

The three-dimensional structure of the N-terminal DNA-binding domain of Mbp1 has been determined by multiwavelength anomalous diffraction from crystals of the selenomethionyl variant of the protein. The structure is composed of a six-stranded beta sheet interspersed with two pairs of alpha helices. The most conserved core region among Mbp1-related transcription factors folds into a central helix-turn-helix motif with a short N-terminal beta strand and a C-terminal beta hairpin.

CONCLUSIONS

Despite little sequence similarity, the structure within the core region of the Mbp1 N-terminal domain exhibits a similar fold to that of the DNA-binding domains of other proteins, such as hepatocyte nuclear factor-3gamma and histone H5 from eukaryotes, and the prokaryotic catabolite gene activator. However, the structure outside the core region defines Mbp1 as a larger entity with substructures that stabilize and display the helix-turn-helix motif.

[Three-dimensional finite element stress analysis of magnetical retaining and bar retaining in overdenture implants]

The purpose of this study was to determine which type of denture retaining implants can produce better biomechanical effect on the bone tissue. Two mechanical models of magnetically retained complete overdenture supported by osseo-integrated implant and bar-retained complete over denture supported by osseo-integrated implant were made. The peak stress in mandibular peri-implant bone tissue of the models were studied under the same loading conditions vertically and horizontally by three-dimensional FEM stress analysis. The results were as follows: (1) Both types of dentures retention can produce significant stress effect on the peri-implant and other regions of the jaw bone and (2) Magnetical retention is more beneficial to maintenance both of peri-implant bone tissue and long-term success of denture supported by osseo-integrated implant than bar retention does.

Interactions between single-stranded DNA binding protein and oligonucleotide analogs with different backbone chemistries

Chemical modification of backbone structures has been an important strategy in designing oligonucleotides capable of improved antisense effects. However, altered backbone chemistry may also affect the binding of oligonucleotides to key cellular proteins, and thus may impact on the overall biological action of antisense agents. In this study we have examined the binding of oligonucleotides having four different backbone chemistries to single-strand binding protein (SSB), a protein having a key role in DNA repair and replication. The oligomers tested had the same sequence, while the internucleoside linkages were phosphodiester (PO), phosphorothioate (PS), phosphorodithioate (PS2), or methylphosphonate (MP). We found that both PS and PS2 oligomers bound to SSB with higher affinity than PO oligonucleotides, while MP oligonucleotides did not bind appreciably at the concentrations tested. Oligonucleotide length was also an important factor in binding to SSB, but sequence was less critical. These observations indicate that backbone chemistry is an important factor in interactions between oligonucleotides and critical cellular proteins, and thus may be a key determinant of the biological effects of antisense oligonucleotides.

The transcriptional integrator CREB-binding protein mediates positive cross talk between nuclear hormone receptors and the hematopoietic bZip protein p45/NF-E2

Thyroid hormone (T3) and retinoic acid (RA) play important roles in erythropoiesis. We found that the hematopoietic cell-specific bZip protein p45/NF-E2 interacts with T3 receptor (TR) and RA receptor (RAR) but not retinoid X receptor. The interaction is between the DNA-binding domain of the nuclear receptor and the leucine zipper region of p45/NF-E2 but is markedly enhanced by cognate ligand. Remarkably, ligand-dependent transactivation by TR and RAR is markedly potentiated by p45/NF-E2. This effect of p45/NF-E2 is prevented by maf-like protein p18, which functions positively as a heterodimer with p45/NF-E2 on DNA. Potentiation of hormone action by p45/NF-E2 requires its activation domain, which interacts strongly with the multifaceted coactivator cyclic AMP response element protein-binding protein (CBP). The region of CBP which interacts with p45/NF-E2 is the same interaction domain that mediates inhibition of hormone-stimulated transcription by AP1 transcription factors. Overexpression of the bZip interaction domain of CBP specifically abolishes the positive cross talk between TR and p45/NF-E2. Thus, positive cross talk between p45/NF-E2 and nuclear hormone receptors requires direct protein-protein interactions between these factors and with CBP, whose integration of positive signals from two transactivation domains provides a novel mechanism for potentiation of hormone action in hematopoietic cells.

Visual instrument image-quality assessment with rotationally symmetric difference of Gaussians

We performed contrast-sensitivity measurements using rotationally symmetric, variable contrast difference-of-Gaussians targets, viewed through specially designed telescopes that presented various amounts of monochromatic aberrations. The contrast-sensitivity ratios between aberrated and unaberrated cases were correlated with instrument-based measures of image quality. The radius that encircles 84% of the energy of the point-spread function was found to give the best correlation with the subjective data.

Antitumor effects of internal iliac arterial infusion of platinum compounds in a rabbit cervical cancer model

OBJECTIVE

To compare three platinum compounds for their antitumor effects on cervical cancer after systemic and intra-arterial infusion.

METHODS

Adult female rabbits with squamous cell carcinoma of the uterine cervix received infusions of 1.7 mg/kg cisplatin, 10 mg/kg carboplatin, or 6 mg/kg cis-diammine (glycolato)platinum (254-S) via the internal iliac artery or ear vein. Platinum concentrations in the tumor and tumor size were measured after internal iliac arterial or intravenous (i.v.) infusion with these platinum compounds.

RESULTS

The platinum concentration in the tumor after intra-arterial infusion was significantly higher than that after i.v. infusion for cisplatin. However, the tumor concentrations of platinum for carboplatin and 254-S did not differ between the infusion methods. The platinum concentration 20 minutes after i.v. infusion was significantly higher for 254-S than for cisplatin or carboplatin. The platinum concentration 7 days after intra-arterial infusion was significantly higher with cisplatin than with carboplatin or 254-S. Tumor size 7 days after intra-arterial infusion was significantly smaller than that after i.v. infusion for cisplatin (1.85 +/- 0.54 versus 5.60 +/- 2.60 cm2; P < .05). Tumor size was significantly smaller with 254-S than with cisplatin or carboplatin using the i.v. infusion method (2.40 +/- 0.21 cm2 for 254-S, 5.60 +/- 2.60 cm2 for cisplatin, and 5.13 +/- 1.59 cm2 for carboplatin, P < .05.

CONCLUSIONS

Intra-arterial infusion seems to be a suitable route of administration for cisplatin, whereas i.v. infusion appears to have an advantage for 254-S in the treatment of cervical cancer.

Glutathione S-transferase-pi expression and glutathione concentration in ovarian carcinoma before and after chemotherapy

BACKGROUND

To clarify the role of glutathione (GSH) in the chemotherapy resistance of ovarian carcinoma, the authors examined the expression of glutathione S-transferase-pi (GST-pi) and the concentration of glutathione in tumors before and after chemotherapy in the same patients.

METHODS

The cohort for this study comprised 20 patients with ovarian carcinoma who had residual disease after primary surgery. These patients received two to three courses of postoperative chemotherapy, then underwent surgery for a second time. Chemotherapy consisted of 50 mg/m2 cisplatin, 40 mg/m2 doxorubicin, and 400 mg/m2 cyclophosphamide. The expression of GST-pi in tumors was determined by immunohistochemical staining and Western blot analysis. GSH concentration was measured by an enzymatic assay.

RESULTS

Of the 20 patients, 10 responded to chemotherapy and 10 did not. Immunohistochemical staining for GST-pi was positive in 3 tumors among the 10 responders and in 7 tumors among the 10 nonresponders, but Western blot analysis detected GST-pi expression in all tumors. Among the responders, GST-pi after chemotherapy increased in one patient, was unchanged in two patients, and decreased in seven patients. Among nonresponders, GST-pi increased in six patients, was unchanged in one patient, and decreased in three patients. The ratio of GST-pi density in tumors after chemotherapy to GST-pi density before chemotherapy was significantly higher in nonresponders than in responders (2.0 +/- 1.1 vs. 0.6 +/- 0.4). The concentration of GSH in tumors was widely distributed, but it was found that the ratio of GSH concentration in each tumor after chemotherapy to GSH concentration before chemotherapy was significantly higher for nonresponders than for responders (3.0 +/- 1.3 vs. 0.6 +/- 0.3).

CONCLUSIONS

Increased levels of GST-pi expression after chemotherapy are linked to drug resistance in patients with ovarian carcinoma.

Down-regulation of IL-12, not a shift from a T helper-1 to a T helper-2 phenotype, is responsible for impaired IFN-gamma production in mammary tumor-bearing mice

Altered cytokine production has been implicated in the down-regulation of cell-mediated immunity in mice bearing large mammary tumors. In several diseases, an imbalance between helper T lymphocytes Th1 and Th2 and their cytokines has been suggested as a contributing factor. In this study, although IFN-gamma from splenic T cells of D1-DMBA-3 mammary tumor-bearing mice was greatly diminished, other cytokine levels remained unchanged, indicating no clear shift between the Th1, Th2, or Th3 phenotypes. The IFN-gamma levels can be restored in vitro by addition of rIL-12 to cultured splenocytes from tumor bearers. Furthermore, IL-12 production is greatly down-regulated in macrophages from tumor-bearing mice as detected by ELISA, and this correlates with diminished expression of IL-12 p40 chain RNA. The mammary tumor used in our studies produces several factors, including granulocyte macrophage-CSF, PGE2, and phosphatidyl serine, that can affect the immune system. Addition of these tumor-derived factors in vitro to macrophages from normal mice resulted in decreased levels of IL-12 protein in cultures treated with PGE2 or phosphatidyl serine. These results indicate that the down-regulation of T cell-produced IFN-gamma in this tumor model is the result of decreased IL-12 production caused by tumor-derived factors and not a shift from the Th1 to the Th2 phenotype.

Combination effect of granisetron and methylprednisolone for preventing emesis induced by cytotoxic agents

To evaluate the combined effect of granisetron and methylprednisolone against acute emesis induced by cytotoxic agents, we investigated the clinical response and the urinary excretion of 5-HIAA in 85 patients with ovarian cancer who received the same anticancer chemotherapeutic regimen in a prospective randomized trial. Each patient received one of three different regimens (granisetron alone, methylprednisolone plus granisetron, and metoclopramide alone). The combination therapy of granisetron and methylprednisolone is effective for preventing acute emesis induced by cytotoxic chemotherapy.

Clinical responses and platinum concentrations in tumors after intra-arterial and intravenous administration of cisplatin in the same patients with cervical cancer

We evaluated 3 patients with advanced cervical cancer treated with cisplatin intra-arterially and intravenously. The dose of cisplatin was 50 mg/m2 in each infusion. Chemotherapy was repeated at 4-week intervals for three to four courses. The clinical response and the tumor concentration of platinum were evaluated in each course. All patients who received the intra-arterial infusion of cisplatin were judged to be responders, whereas none of them responded to the intravenous infusion. The platinum concentration in tumor tissue was significantly higher after intra-arterial infusion of cisplatin (1.97 +/- 0.04 vs. 2.86 +/- 0.10 microg/g). Although there were no apparent differences in side effects between intra-arterial and intravenous routes, 2 of 3 patients rejected an intra-arterial route. The present study suggests that intra-arterial administration of cisplatin may be useful in treating locally advanced cervical cancer.

Down-regulation of IL-12, not a shift from a T helper-1 to a T helper-2 phenotype, is responsible for impaired IFN-gamma production in mammary tumor-bearing mice

Altered cytokine production has been implicated in the down-regulation of cell-mediated immunity in mice bearing large mammary tumors. In several diseases, an imbalance between helper T lymphocytes Th1 and Th2 and their cytokines has been suggested as a contributing factor. In this study, although IFN-gamma from splenic T cells of D1-DMBA-3 mammary tumor-bearing mice was greatly diminished, other cytokine levels remained unchanged, indicating no clear shift between the Th1, Th2, or Th3 phenotypes. The IFN-gamma levels can be restored in vitro by addition of rIL-12 to cultured splenocytes from tumor bearers. Furthermore, IL-12 production is greatly down-regulated in macrophages from tumor-bearing mice as detected by ELISA, and this correlates with diminished expression of IL-12 p40 chain RNA. The mammary tumor used in our studies produces several factors, including granulocyte macrophage-CSF, PGE2, and phosphatidyl serine, that can affect the immune system. Addition of these tumor-derived factors in vitro to macrophages from normal mice resulted in decreased levels of IL-12 protein in cultures treated with PGE2 or phosphatidyl serine. These results indicate that the down-regulation of T cell-produced IFN-gamma in this tumor model is the result of decreased IL-12 production caused by tumor-derived factors and not a shift from the Th1 to the Th2 phenotype.

Characterization of the gene for an immunodominant 72 kDa lipoprotein of Mycoplasma mycoides subsp. mycoides small colony type

With the aim of characterizing specific immunogenic proteins of Mycoplasma mycoides subsp. mycoides small colony (SC) type, the aetiological agent of contagious bovine pleuropneumonia, a gene encoding a major immunogenic protein of 72 kDa named P72 was cloned and expressed in Escherichia coli. The expressed protein was of the same apparent molecular mass as that produced by the parent strain. The predicted molecular mass of P72, based on the DNA-deduced amino acid sequence, was 61.118 kDa, significantly lower than the apparent molecular mass of endogenous or recombinant P72 on SDS-PAGE. Analysis of the amino acid sequence revealed a typical prokaryotic signal peptidase II-membrane lipoprotein lipid attachment site and a transmembrane structure domain in the leader sequence at the amino-terminal end of the protein. P72 was shown to be a lipoprotein and its surface location was confirmed by trypsin treatment of whole cells. An unassigned gene encoding a peptide with some similarity to P72 was found on the genome sequence of M. capricolum subsp. capricolum but not on that of Mycoplasma genitalium. The P72 gene was detected in 11/11 M. mycoides subsp. mycoides SC strains. Antiserum against recombinant P72 reacted strongly with 12/12 strains of M. mycoides subsp. mycoides SC, weakly with Mycoplasma bovine group 7 strain PG50, but not with other members of the 'mycoides cluster' or closely related mycoplasmas. Cows experimentally contact-infected with M. mycoides subsp. mycoides SC developed a humoral response against P72 within 35 d. P72 is a specific antigenic membrane lipoprotein of M. mycoides subsp. mycoides SC with potential for use in development of diagnostic reagents. It seems to belong to a family of lipoproteins of the "mycoides cluster'.

A structural basis for the preferential binding of hemimethylated DNA by HhaI DNA methyltransferase

The crystal structure of HhaI methyltransferase complexed with non-palindromic duplex DNA, containing a hemimethylated recognition sequence, and with the cofactor analog S-adenosyl-L-homocysteine (AdoHcy), has been determined. The structure provides an explanation for the stronger affinities of DNA methyltransferases for hemimethylated DNA than for unmethylated or fully methylated DNA in the presence of AdoHcy. The unmethylated target 2'-deoxycytidine flips out of the DNA helix and the CH group at position 5 makes van der Waals' contacts with the sulfur atom of AdoHcy. Selectivity/preference for hemimethylated over fully methylated DNA may thus reflect interactions among the chemical substituent (H or CH3) at the C5 position of the flipped cytosine, protein and the bound AdoHcy. The 5-methyl-2'-deoxycytidine on the complementary strand remains in the DNA helix, with the methyl group almost perpendicular to the carboxylate group of Glu239, which is part of the sequence recognition loop. Thus, selectivity/preference for hemimethylated over unmethylated DNA appears to result largely from van der Waals' contacts between the planar Glu239 carboxylate and the methyl group of the 5-methyl-2'-deoxycytidine. Furthermore, the positive electrostatic potential originating from the bound AdoHcy extends to the DNA phosphate groups flanking the flipped cytosine. The increased binding to DNA by long-range electrostatic interactions should also occur with the methyl donor S-adenosyl-L-methionine.

Cytokine production by lymphoreticular cells from mammary tumor bearing mice: the role of tumor-derived factors

Mammary tumor development has multiple effects on the T cell, B cell and macrophage compartments of the hosts as evidenced by the alterations in their phenotype and functions. Cytokines are known to modulate the immune system, thus a study of the production of these factors has great relevance to tumor immunity. Here we present evidence that tumor progression causes a profound dysregulation of the cytokine production by various lymphoreticular cells. Furthermore, the tumors themselves are capable of secreting factors that can directly or indirectly affect the cells of the immune system, thereby resulting in the immunosuppressive and other deleterious effects that favor the progress of the neoplastic disease.

Enzymatic C5-cytosine methylation of DNA: mechanistic implications of new crystal structures for HhaL methyltransferase-DNA-AdoHcy complexes

The refined crystal structures of HhaI methyltransferase complexed with cognate unmethylated or methylated DNA together with S-adenosyl-L-homocysteine, along with the previously-solved binary and covalent ternary structures, offer a detailed picture of the active site at individual stages throughout the reaction cycle. This picture supports and extends a proposed mechanism for C5-cytosine methylation that may be general for the whole family of C5-cytosine methyltransferases. The structures of the two new complexes have been refined to crystallographic R-factors of 0.189 and 0.178, respectively, at 2.7 A resolution. We observe that both unmethylated 2'-deoxycytidine and 5-methyl-2'-deoxycytidine flip out of the DNA helix and fit into the active site of the enzyme. The catalytic sulfur atom of Cys81 interacts strongly with C6. The C5 methyl group of the flipped 5-methyl-2'-deoxycytidine is bent approximately 50 degrees out of the plane of the cytosine ring and towards the sulfur atom of S-adenosyl-L-homocysteine. This unusual position is probably due to partial sp3 character at C5 and C6 and to steric effects of the conserved amino acid residues Pro80 and Cys81. Two water molecules are held near the hydrophobic edge (C5 and C6) of the flipped cytosine by two conserved amino acid residues (Gln82 and Asn304) and the phosphoryl oxygen atom of the phosphate group 3' to the flipped nucleotide, and one of them may serve as the general base for eliminating the proton from C5. Protonation of the cytosine N3 during the methylation reaction may involve Glu119, which itself might be protonated via a water-mediated interaction between the terminal carboxyl group of Glu119 and the amino group of the methionine moiety of S-adenosyl-L-methionine. The cofactor thus plays two key roles in the reaction.

Charge-state reduction with improved signal intensity of oligonucleotides in electrospray ionization mass spectrometry

The shift of charge states of oligonucleotide negative ions formed in electrospray ionization mass spectrometry to higher mass-to-charge ratio has been accomplished by addition of organic acids and bases to the solution to be electrosprayed. The use of acetic acid or formic acid combined with piperidine and imidazole effectively reduced charge states. Signal intensity and stability were enhanced greatly when the infused solution contained a high percentage of acetonitrile. In addition, the cocktail that contained imidazole, piperidine, and acetic acid in 80% acetonitrile not only reduced charge states, but also substantially suppressed Na adduction. Several oligonucleotides that varied in base composition and length were investigated, and studies of mixtures showed a significant reduction in spectral complexity.

Characterization of the murine antibody response to peptides representing the variable domains of the major outer membrane protein of Chlamydia pneumoniae

In an attempt to gain more knowledge about the immunogenicity of the variable domains (VDs) of the major outer membrane protein (MOMP) of Chlamydia pneumoniae, peptides representing these areas were used to immunize BALB/c and C57BL/6 mice. Antisera to the peptides and to peptides conjugated to keyhole limpet hemocyanin (KLH) were characterized by their ability to recognize the immunizing peptide and elementary bodies (EBs) of C. pneumoniae by enzyme-linked immunosorbent assay (ELISA) and Western blot (immunoblot). In addition, antiserum was analyzed for its molecular specificity by a pepscan as well as its in vitro neutralizing ability. In general, results obtained with antisera to the peptides paralleled the results obtained with the antisera to the KLH-conjugated peptides except that the titers or strength of reaction in the assays was less. Antisera to the VDs in both strains of mice gave ELISA titers to the homologous VD peptide ranging from 1,000 to >64,000. The strength of reactivity with the reduced MOMP as judged by Western blot, in most cases, paralleled the ELISA titer to the peptide. However, only antisera raised in both strains of mice to the VD1 and VD4 peptides reacted strongly with the EBs, suggesting surface exposure of these VDs. In addition, antisera to VD3 from C57BL/6 mice gave strong reactivity to EBs. By pepscan analysis antisera from both strains of mice reacted with several VD1 and VD3 octameric peptides, with weaker reactivity being seen with the octameric peptides in the other two VDs. This was in contrast to antisera raised to EBs of C. pneumoniae TW-183, which identified two immunogenic regions, one in VD1 and the other mapped to VD4. While antisera raised to EBs strongly neutralized the infectivity of C. pneumoniae, none of the peptide antisera was able to neutralize. In addition, peptides to the VDs were not able to block the neutralizing ability of the antisera to EBs of C. pneumoniae. Therefore, these results suggest that the VDs of the MOMP of C. pneumoniae are surface exposed but do not elicit neutralizing antibodies when linear peptides representing them are used as the immunogen.

Mass spectrometric characterization of sequence-specific complexes of DNA and transcription factor PU.1 DNA binding domain

Electrospray ionization mass spectrometry (ESI-MS) has been used to study the noncovalent interaction of the 13.5-kDa DNA binding domain of PU.1 (PU.1-DBD) with specific double-stranded DNA (dsDNA) target molecules. Mixtures of PU.1-DBD protein and wild-type target DNA sequence yielded ESI-MS spectra showing only protein-dsDNA complex ions of 1:1 stoichiometry and free dsDNA. When PU.1-DBD protein, wild type target DNA, and a mutant target DNA lacking the consensus sequence were mixed, only the 1:1 complex with the wild-type DNA was observed, consistent with gel electrophoresis mobility shift assay results, demonstrating the observation of sequence-specific protein-dsDNA complexes using ESI-MS.

Direct measurement of oligonucleotide binding stoichiometry of gene V protein by mass spectrometry

The binding stoichiometry of gene V protein from bacteriophage f1 to several oligonucleotides was studied using electrospray ionization-mass spectrometry (ESI-MS). Using mild mass spectrometer interface conditions that preserve noncovalent associations in solution, gene V protein was observed as dimer ions from a 10 mM NH4OAc solution. Addition of oligonucleotides resulted in formation of protein-oligonucleotide complexes with stoichiometry of approximately four nucleotides (nt) per protein monomer. A 16-mer oligonucleotide gave predominantly a 4:1 (protein monomer: oligonucleotide) complex while oligonucleotides shorter than 15 nt showed stoichiometries of 2:1. Stoichiometries and relative binding constants for a mixture of oligonucleotides were readily measured using mass spectrometry. The binding stoichiometry of the protein with the 16-mer oligonucleotide was measured independently using size-exclusion chromatography and the results were consistent with the mass spectrometric data. These results demonstrate, for the first time, the observation and stoichiometric measurement of protein-oligonucleotide complexes using ESI-MS. The sensitivity and high resolution of ESI-MS should make it a useful too] in the study of protein-DNA interactions.

[Simultaneous rhinoplasty and blepharoplasty]

Simultaneous rhinoplasty and blepharoplasty are the commonest facial cosmetic operation. The paper presents 73 cases who underwent this procedure with satisfactory results from Jan. 1989 to Nov. 1993. The authors described operation steps, e.g., making lacuna in the dorsum, lengthening nasal columella, nasal tip plasty. It was emphasized that the pretarsal flap should contain complete network of the superficial fascia, and the soft tissue underneath be trimmed. All the dissection should be kept in the same cleavage, which would reduce intraoperative bleeding and postoperative edema.