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PubMedDate not supplied

Studies of DNA-protein interactions by gel electrophoresis.

The use of gel electrophoresis in studies of nucleic acid-protein (especially DNA-protein) interactions has yielded much qualitative and quantitative information about a variety of such systems. The reduction in mobility of complexes relative to free DNA allows isolation and characterization of the complexes as well as determination of thermodynamic and kinetic properties of the interactions. This article begins with a review of recent applications of the "gel retardation" assay, by way of introduction to experiments in two areas. In the first, a hypothesis is tested regarding whether a DNA molecule with sizable proteins bound very near to each end migrates through a polyacrylamide gel differently than does the corresponding complex having the proteins in the middle of the DNA fragment. The data show little mobility differences for these types of complexes, implying that both may move in a linear, "snakelike", manner through the gel. The experiments also provide results pertaining to questions of DNA bending caused by the binding of the E. coli catabolite activator protein (CAP) and RNA polymerase to the lactose promoter region. It appears that DNA bending by CAP at its wild type lac binding site is retained in complexes where RNA polymerase is bound simultaneously at the lac UV5 promoter.

Cloning, Molecular↗

PubMedDate not supplied

Identification of mouse liver proteins on two-dimensional electrophoresis gels by matrix-assisted laser desorption/ionization mass spectrometry of in situ enzymatic digests.

A number of proteins from a silver-stained two-dimensional (2-D) electrophoresis gel of mouse liver whole-cell lysate were identified by peptide mass mapping and sequence database searching. The excised protein spots were processed by in situ reduction and alkylation, followed by Lys-C digestion. The masses of the resulting peptide mixtures were measured with a matrix-assisted laser desorption/ionization (MALDI) reflection-time-of-flight mass spectrometer. These masses were used successfully to search a protein sequence database. Optimized silver staining and digestion protocols allowed proteins to be identified routinely at the low picomole level. The high mass accuracy and resolution provided by delayed extraction were important for high specificity in the database search. Fragment ion data obtained by MALDI post-source decay (PSD) measurements not only provided confirmation of peptide identification, but could be used to identify the protein from a single peptide without spectral interpretation.

Acrylic Resins↗

PubMed1995

Somatic reversion of some copia-like induced mutations, at the white locus of Drosophila melanogaster, after treatment with alkylating agents.

It has been suggested that transposable elements can be associated with different types of genotoxic effects. For this reason it seems appropriate to outline suitable systems to detect changes in the phenotypic expression of the loci containing transposable elements, as well as those agents that induce such changes. The sex-linked white locus offers a suitable experimental system for studying such events because most of the spontaneous mutations at the white locus are the result of insertions of repeated mobile sequences, and it is easy to follow mutational changes of the locus due to the possibility of detecting even slight changes in eye color. Here we report the results obtained in different strains of Drosophila melanogaster with copia-like induced mutations at the white locus, after treatment with three alkylating agents: ethyl methanesulfonate (EMS), methyl methanesulfonate (MMS), and N-nitroso-N-ethylurea (ENU). The three insertional white mutants used in this work were wa4, wbf, and wsp55, with the wa2 mutation used as control because its mutant phenotype is the result of a point mutation instead of the insertion of a DNA fragment. Our data constitute evidence that EMS, MMS, and ENU induce a clear increase in the frequencies of somatic-revertant sectors in the three strains carrying a white allele with an inserted copia-like element. For the wa2 strain, whose mutant phenotype is the result of a point mutation, only ENU at the highest concentration tested is able to induce a significant increase in the somatic reversion frequency. In addition, our results indicate that the use of D. melanogaster strains with transposable elements in the white locus is suitable for detecting genotoxic damage induced by chemicals.

Alkylating Agents↗

PubMed2001

Constitutive expression of the cyclooxygenase-2 gene in T-cell lines infected with human T cell leukemia virus type I.

Cyclooxygenase-2 (COX-2), an inducible enzyme that catalyzes the formation of prostaglandins and other eicosanoids from arachidonic acid, is constitutively expressed in several human carcinomas. COX-2 expression, however, has not been extensively studied in leukemia. Human T cell leukemia virus type I (HTLV-I) is the etiologic agent of adult T cell leukemia, an aggressive form of human T cell malignancy. We studied COX-2 mRNA expression in various human T-cell lines. Northern blot analysis revealed that COX-2 mRNA steady-state levels were high in 4 of 7 T-cell lines infected with HTLV-I. COX-2 mRNA, however, was not expressed in any of 3 HTLV-I-negative T-cell lines. We also confirmed COX-2 expression in 6 of 7 HTLV-I-positive T-cell lines by reverse transcription-PCR. HTLV-I Tax is known to increase the expression of cellular genes and thus we assayed Tax for its ability to increase transcription from the COX-2 promoter. Although Tax increased transcription of the COX-2 promoter in a T-cell line, Tax expression did not induce COX-2 mRNA expression, indicating that Tax alone is not sufficient for significant accumulation of COX-2 mRNA, which probably requires an additional viral protein. To evaluate the potential role of COX-2 in T cells, the HTLV-I-infected T-cell lines were treated with NS398, a selective COX-2 inhibitor. NS398 treatment inhibited proliferation and induced apoptosis of HTLV-I-infected T-cell lines and downregulated Bcl-2 and Bcl-x(L) mRNA expression, followed by chromosomal DNA fragmentation. Our data suggest that COX-2 is expressed selectively in T-cell lines infected with HTLV-I and that this gene may play a role in cell survival.

Apoptosis↗

PubMed1995

Selective sensitivity of macrophages to cytotoxicity by inhibitors of macromolecular synthesis: induction of apoptosis.

Initial studies designed to measure the effect of inhibiting RNA synthesis by dactinomycin on macrophage functions revealed that the cells were uniformly killed at concentrations that have been routinely used to inhibit RNA synthesis in other cell types. We, thus, determined the dose curve for the cytotoxicity of dactinomycin for macrophages and two other cell types, L929 cells and splenic lymphocytes. Macrophages were extremely sensitive to the cytotoxicity of dactinomycin compared to the other cell types. Submicromolar concentrations that induced 100% cytotoxicity in macrophages caused little death in L929 cells or lymphocytes. Concentrations of dactinomycin that inhibited RNA synthesis by 40% in macrophages induced almost complete cell death but inhibition of over 80% of RNA synthesis in L929 cells or lymphocytes induced no measurable cytotoxicity. Macrophages did take up more dactinomycin than other cells but the amount was not sufficient to account for the large differences in cytotoxicity. We next tested the effects of doxorubicin and cycloheximide and found that macrophages were also extremely sensitive to killing by these compounds, and there was a very close association between the amount of inhibition of protein synthesis and the amount of toxicity. The morphology of macrophages exposed to these agents was consistent with death by apoptosis. This was further supported by assays measuring membrane integrity and DNA fragmentation. These data demonstrate that inhibition of macromolecular synthesis in macrophages, by different mechanisms, causes macrophages to undergo apoptosis. They further suggest that, in contrast to other cell types that require protein synthesis for apoptosis, macrophages require the synthesis of certain proteins to avoid apoptosis.

Animals↗

PubMed2005

Hybrid triple quadrupole-linear ion trap mass spectrometry in fragmentation mechanism studies: application to structure elucidation of buspirone and one of its metabolites.

The use of a hybrid triple quadrupole-linear ion trap (QqQ(LIT)) mass spectrometer system for a comprehensive study of fragmentation mechanisms is described. The anxiolytic drug, buspirone, was chosen as a model compound for this study. With the advent of a QqQ(LIT) instrument, both the traditional quadrupole and the new linear ion trap scans (LIT) could be performed in a single LC run. In the past, a sample had to be run on two different instruments, namely, a triple quadrupole instrument (QqQ) and a 3D ion trap (3D IT) to obtain similar information. With the new QqQ(LIT) technology, collision-induced dissociation (CID) occur in a quadrupole collision cell, q2, and fragment ions are trapped and analyzed in Q3 operated in LIT mode. In this work, high-sensitivity product ion spectra of buspirone were obtained from the one-stage 'Enhanced Product Ion' scan (EPI) with rich product ions and no low mass cut-off. Furthermore, detailed fragmentation pathways were elucidated by further dissociation of each of the fragment ions in the EPI spectrum using MS(3) mode in the same run. The MS(3) scan was performed by incorporating CID in q2, and trapping, cooling, isolation, and resonance-excitation in Q3 when operating in LIT mode. This approach allowed unambiguous assignment of all fragment ions quickly with fewer experiments and easier interpretation than the previous approach. The overall sensitivity for obtaining complete fragment ion data was significantly improved for QqQ(LIT) as compared with that of QqQ and 3D IT mass spectrometers. This is beneficial for structure determination of unknown trace components. The method allowed structure determination of metabolites of buspirone in rat microsomes at 1 microM concentration, which was a 10-fold lower concentration than was needed for QqQ or 3D IT instruments. The QqQ(LIT) instrument provided a simple, rapid, sensitive and powerful approach for structure elucidation of trace components.

Animals↗

PubMed1992

Comparison of holmium and flashlamp pumped dye lasers for use in lithotripsy of biliary calculi.

The characteristics of laser lithotripsy of biliary calculi are compared for a flashlamp pumped dye laser (lambda = 640 nm) and a Cr:Tm:Ho-YAG laser (lambda = 2.1 microns). Data on fragmentation efficiency with respect to laser power and pulse repetition rate are presented for different types of stones. It is shown that both lasers can produce effective stone fragmentation. The laser power required for efficient fragmentation characteristics is significantly less for the visible wavelength laser. However, the problems associated with damage to the fiber tips of the delivery system during operation were found to be less with the near infrared wavelength. The laser power for efficient fragmentation with the dye laser varies significantly for different types of stones while the power for efficient fragmentation with the holmium laser is the same for all stones.

Cholelithiasis↗

PubMed2006

UPLC/MS(E); a new approach for generating molecular fragment information for biomarker structure elucidation.

A new approach to obtain fragmentation information in liquid chromatography/mass spectrometry (LC/MS) studies of small molecules in complex mixtures is presented using simultaneous acquisition of exact mass at high and low collision energy, MS(E). LC/MS-TOF and LC/MS/MS-TOF are powerful tools for the analysis of complex mixtures, especially those for biological fluids allowing the elucidation of elemental composition and fragmentation information. In this example the composition of rat urine was studied using this new approach, allowing the structures of several endogenous components to be confirmed in one analytical run by the simultaneous acquisition of exact mass precursor and fragment ion data. The spectral data obtained using this new approach are comparable to those obtained by conventional LC/MS/MS as exemplified by the identification of endogenous metabolites present in rat urine.

Animals↗

PubMed2006

Detection of new fumonisin mycotoxins and fumonisin-like compounds by reversed-phase high-performance liquid chromatography/electrospray ionization ion trap mass spectrometry.

Fumonisins were produced in a rice culture infected with Fusarium verticillioides. To decrease the possibility of the formation of artifacts, the fumonisins were analyzed by reversed-phase high-performance liquid chromatography with electrospray ionization ion trap tandem mass spectrometry (RP-HPLC/ESI-IT-MS2) immediately after the extraction of the culture material without any sample clean-up. In addition to already known fumonisins, numerous new fumonisin mycotoxins and fumonisin-like compounds were detected. On the basis of the IT-MS2 data, detailed fragmentation pathways including new mechanisms were proposed for the different series of fumonisins. The retention times, the masses of the protonated molecules and of the product ions including the backbones and the characteristic neutral mass losses from the protonated molecules of the new compounds suggested their structures (applying the well-known designation): iso-FA1a,b, iso-FB1a-d, iso-FB2,3a-e, PHFB2a-c, PHFB4a-d, FB5/iso-FB5a-d, FBK1 2TCA, FBK4 2TCA, FC2, iso-FC2,3, PHFC4, FD and FBX series. The relative quantities of fumonisins and fumonisin-like compounds found in the sample extract were expressed as percentages of FB1 (0.02-100%). The backbone of the compound denoted FD contained fewer carbon atoms than the well-known fumonisins with the C19 or C20 backbone and may well be a precursor of the longer compounds. For the compounds denoted FBX (12 compounds), one or two OH groups attached to the fumonisin backbone were esterified by carboxylic acids other than tricarballylic acid, such as cis-aconitic acid, oxalylsuccinic acid and oxalylfumaric acid.

Chromatography, High Pressure Liquid↗

PubMed1998

Cell-specific regulation of transcription of the malic enzyme gene: characterization of cis-acting elements that modulate nuclear T3 receptor activity.

Stimulation of malic enzyme transcription by triiodothyronine (T3) is robust (> 60-fold) in chick embryo hepatocytes, weak (5-fold) in chick embryo fibroblasts that stably overexpress the nuclear T3 receptor-alpha, and still weaker (1-fold) in chick embryo fibroblasts which contain nuclear T3 receptor levels that are similar to those of chick embryo hepatocytes. Using DNase I hypersensitivity, functional transfection, and in vitro DNA-binding analyses, four cis-acting elements were identified in the malic enzyme 5'-flanking DNA that conferred differences in nuclear T3 receptor activity between chick embryo hepatocytes and chick embryo fibroblasts. These cell-specific regulatory elements are located at -3895/-3890, -3761/-3744, -3703/-3686, and -3474/-2715 bp and overlap with DNase I hypersensitive sites that are observed in chromatin of chick embryo hepatocytes. Each element enhances T3 responsiveness of the malic enzyme promoter in chick embryo hepatocytes but has no effect on T3 responsiveness in chick embryo fibroblasts. Three of the cell-specific regulatory elements flank a previously identified DNA fragment (-3889 to -3769 bp; Hodnett et al., Arch. Biochem. Biophys. 334, 309-324, 1996) that contains one major and four minor T3 response elements. The cell-specific regulatory element at -3703/-3686 bp binds to the liver-enriched factor, CCAAT/enhancer-binding protein-alpha, whereas cell-specific regulatory elements at -3895/-3890 and -3761/-3744 bp bind proteins of unknown identity. While the cell-specific regulatory element at -3761/-3744 bp contains sequences that resemble binding sites for CCAAT/enhancer-binding protein, activator protein-1, cyclic AMP response element binding protein, and NF-1, none of these proteins appear to bind to this DNA fragment. These data suggest that cell-specific differences in T3 responsiveness of the malic enzyme gene are mediated in large part by nonreceptor proteins that augment the transcriptional activity of the nuclear T3 receptor in hepatocytes.

Animals↗

PubMed1997

Expression of telomerase RNA, telomerase activity, and telomere length in human gliomas.

To understand the mechanisms of telomere maintenance in human gliomas, telomerase activity, telomerase RNA expression and telomere length of surgically excised glioma samples were analyzed. Sixty-five percent of gliomas exhibited telomerase activity, the occurrence of which was not related to their histological malignancy scale. Not only the telomerase-positive gliomas, but also the telomerase-negative gliomas and normal brain expressed telomerase RNA, suggesting that the presence of telomerase RNA component does not indicate the presence of telomerase activity. Compared with telomerase-positive gliomas, telomerase-negative gliomas had long heterogeneous telomeric terminal restriction fragments. These data suggest that in addition to the telomerase-dependent mechanism, a telomerase-independent mechanism for telomere maintenance may be present in human gliomas.

Astrocytoma↗

PubMed2001

Use of an in silico approach to define the gene structure of eukaryotic adenylyl cyclases.

The limited information available regarding the gene structure of adenylyl cyclases (AC), which catalyze the synthesis of cAMP, suggests a complex arrangement with many exons and large introns such that molecular techniques to define these gene structures are time- and labor-intensive. We report here the use of a computer-based approach involving the assembly of fragmented sequence data generated by the Human Genome Project and nucleic acid analysis software to decipher the gene structure of human and murine AC 6 and other human AC isoforms (ACs 3, 7, and 8). The results, which document 21 exons in human and murine AC 6, human AC 3, 18 exons in AC 8, and 24 exons in AC 7, show substantial conservation of exon organization in the AC family and in particular regions of the AC protein. Application of such in silico methods should prove useful to characterize genes for other ACs and protein families and data provided here should facilitate studies of polymorphisms in AC genes.

Adenylyl Cyclases↗

PubMed2002

Transcriptional regulation of the human TATA binding protein gene.

The human TATA binding protein (TBP) locus consists of a functional domain of three closely linkedhousekeeping genes (TBP, PSMB1 (proteasomal C5 subunit), and PDCD2 (programmed cell death-2)) within a 50-kb interval at chromosome position 6q27. Here we demonstrate that a genomic clone spanning the 20-kb TBP gene, with 12 kb 5' and 3' flanking sequences, was fully functional in stable, transfected L-cells harboring a single copy of this transgene, including after long-term (60 day) culture in the absence of drug selective pressure. Furthermore, we were only able to detect DNaseI hypersensitive sites at the TBP and PSMB1 promoters present within this 44-kb fragment. Our data suggest that this 44-kb genomic region possesses genetic regulatory elements that not only drive ubiquitous expression of TBP but also negate chromatin and DNA methylation induced silencing, which is normally associated with transgenes stably integrated into tissue culture cells.

Chromosomes, Human, Pair 6↗

PubMed1997

Analysis of the in vivo decay of the Escherichia coli dicistronic pyrF-orfF transcript: evidence for multiple degradation pathways.

Messenger RNA decay in Escherichia coli is slowed in pnp-7 (PNPase) rnb-500 (RNase II) rne-1(RNase E) multiple mutants. We have used Northern blots, S1 nuclease protection and primer extension analysis to map 18 endonucleolytic cleavage sites within the pyrF-orfF dicistronic transcript. Although examination of a total of 27 cleavage sites including those determined for the monocistronic trxA transcript revealed a complex pattern, the central four nucleotides within a cluster of 12 residues encompassing the cleavage sites showed a definite A/U preference. Also of interest was the processing of the dicistronic transcript to remove the downstream orfF sequence as a stable but untranslated RNA fragment. The data provide further support for the hypothesis that multiple decay pathways are involved in the decay of a single transcript. In particular, the pyrF-orfF transcript apparently can be degraded either in the 5' to 3' or the 3' to 5' direction. Our results are discussed in light of current models of mRNA decay involving polyadenylation and multiprotein decay complexes.

Endoribonucleases↗

PubMed1993

Reaching for the ring: the study of mitochondrial genome structure.

The linear molecules that comprise most of the mitochondrial DNA (mtDNA) isolated from most organisms result from the artifactual degradation of circular genomes that exist within mitochondria. This view has been adopted by most investigators and is based on DNA fragment mapping data as well as analogy to the genome-sized circular mtDNA molecules obtained in high yield from animals. The alternative view that linear molecules actually represent the major form of DNA within mitochondria is supported by two observations; (1) over a 1000-fold range of genome size among fungi and plants we find the same size distribution of linear mtDNA molecules, and (2) linear mtDNA molecules much larger than genome size can be found for some fungi and plants. The circles that represent only a small fraction of the mtDNA obtained from most eukaryotes could be optional sequence forms unimportant for mitochondrial function; they may also participate in mtDNA replication. The circles might result from incidental recombination events between directly repeated sequences within or between tandemly arrayed genome units on linear mtDNA molecules.

DNA, Mitochondrial↗

PubMed1976

Stabilization of double-stranded DNA molecule by non-histone peptidic effector from calf thymus.

A peptidic effector from calf thymus causes a strong stabilization of DNA double-stranded molecule in vitro. The active factor was isolated from aqueous ultrafiltered thymus extracts and purified by means of chromatography on DEAE-cellulose and then on Dowex 50 WX2. The purified thymic factor was characterized as a peptide of low molecular weight (less than 5000). The biological activity of the thymic factor cannot be attributed to a histone fragment. Melting data of the control DNA and of the DNA-active factor complex in various conditions of ionic strength and dielectric constant of the solution medium are recorded.

Animals↗

PubMed1979

The genome of Bacillus subtilis phage SPP1: the arrangement of restriction endonuclease generated fragments.

SPP1 DNA was cleaved by the restriction endonucleases, BglI, BglII, EcoRI, KpnI, SmaI, and SalI. The molecular weights of the DNA fragments obtained by single enzyme digestion or by consecutive digestion with two enzymes were determined by electron microscopic measurements of contour length and by gel electrophoresis. The major fragments from the six digests could be ordered to give a consistent restriction map of SPP1. The electropherograms of several digests indicated that certain fragments occurred in less than stoichiometric amounts or were heterogeneous in size. Such bands carried a major part of radioactivity, when SPP1 DNA was terminally labelled with P32 prior to degradation by restriction enzymes. These results, and studies of the effect of exonuclease III treatment on restriction enzyme patterns define the terminal restriction fragments. All data obtained support the conclusion drawn in the preceding paper (Morelli et al., 1978 b) that the SPP1 genome is terminally redundant and partially circularly permuted.

Bacillus subtilis↗

PubMed1980

Murine antigen H-2.7: localization of its antigenic determinant to the Ss (C4) molecule.

Murine blood group antigen H-2.7 is encoded by a locus mapping in the vicinity of the S locus which codes for the Ss antigen carried by the fourth component of the complement pathway (C4). Normal mouse serum of H-2.7-positive strains contains a substance which inhibits anti-H-2.7 hemagglutination. This substance cannot be removed by passage of the serum through an anti-Ss immunoabsorbent column indicating that the Ss and H-2.7 antigens are present on separate molecules or molecular fragments in the serum. In contrast, fresh plasma either does not contain the H-2.7-bearing substance at all or it contains it at a far lower concentration than normal serum, although it has a normal level of the Ss-antigen-bearing substance. However, the H-2.7-positive substance appears when the plasma is allowed to stand for several hours, or when it is dialyzed and treated subsequently in a manner favoring spontaneous degradation of complement components. Removal of the Ss substance from the fresh plasma prevents the appearance of the H-2.7 antigen at any time thereafter. These findings indicate that the Ss and H-2.7 antigens are carried by the same molecule or molecular complex. The intact molecule expresses only the Ss antigen; the H-2.7 antigen is either hidden or masked so that it is inaccessible or poorly accessible to H-2.7 antibodies. Degradation of these molecules results in the generation of two fragments, a large fragment carrying the Ss antigen and a smaller H-2.7-positive fragment. The data are consistent with the interpretation that the H-2.7 antigen is encoded by the S locus, and that it is carried by that portion of the C4 molecule split off during complement activation.

Animals↗