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PubMed1993

Rapid high-sensitivity peptide mapping by liquid chromatography-mass spectrometry.

Toward a complete LC-MS mapping system for peptides and proteins, we have coupled a precision-flow microbore HPLC system to an electrospray single quadrupole mass spectrometer. The HPLC system allows fast separation of protein digests with UV detection at the low pmol level. A 2 microliters/min portion (1:25) of the effluent is passed into a high-sensitivity electrospray MS system. The electrospray source allows for molecular mass associated ions (MH+, MH2(2+), MH3(3+), etc.) to be generated as well as collision induced dissociation of these ions before MS analysis. After LC-MS runs, with or without partial fragmentation, the data generated are largely interpreted by identification of predicted peptides, incompletely digested peptides, unusual peptide cleavages, and so on, using appropriate integrated software (PEPMAP, PEPMATCH). Examples of peptide mapping at the low pmol level using this integrated system will be shown (e.g., of the protein human growth hormone and of the glycoprotein, tissue plasminogen activator).

Amino Acid Sequence↗

PubMed1995

Apoptosis in chicken embryos induced by the infectious bursal disease virus.

Fifteen-day-old fertile eggs (specific pathogen-free) were inoculated with the infectious bursal disease virus (IBDV) by the allantoic route and were opened and examined 2, 4 or 6 days later. The bursas of Fabricius (BFs) were collected and processed for DNA extraction, flow cytometry, and light and electron microscopy. Cellular DNA was subjected to electrophoresis on 1.5% agarose gel and stained with ethidium bromide. Intense internucleosomal DNA fragmentation was detected in IBDV-infected bursas. Cytograms from cell suspensions derived from infected BFs displayed an increased population of cells with either high density and small size (apoptotic cells) or small size and high uptake of ethidium bromide (necrotic cells). Light and electron microscopical examination of the IBDV-infected BFs revealed death of lymphoid cells without surrounding inflammatory reaction, but with condensation of nuclear chromatin, crescent formation, and nuclear and cellular fragmentation. These data indicated that infection of chicken embryos with IBDV induced apoptosis in bursal lymphoid cells.

Animals↗

PubMed1984

Distribution and metabolism of dermorphin in rats.

Dermorphin distribution and metabolism were studied in rats injected with high doses of the peptide and with 125I-dermorphin, using RIA methods, HPLC extraction and -counting. Dermorphin rapidly disappeared from plasma (half-life: 1.3 min). In vivo and in vitro experiments demonstrated that the peptide was destroyed in liver and kidney. The highest percent (11%) of injected dermorphin has been found in the bile collected over 1 hour. HPLC analysis showed that bile contained also breakdown products (di, tri, and tetra N-terminal peptide fragments). Reported data suggested that intact dermorphin can be eliminated more slowly than breakdown products.

Animals↗

PubMed1996

The FHIT gene 3p14.2 is abnormal in lung cancer.

To determine the role of the FHIT gene, which encompasses the fragile site at 3p14.2, we analyzed 59 tumors of the small cell and non-small cell type by reverse transcription of FHIT mRNA, followed by PCR amplification and sequencing of products. Allelic losses affecting the gene were evaluated by microsatellite polymorphism analysis and genomic alterations by hybridization using cDNA and genomic probes. Small cell lung tumors (80%) and non-small cell lung cancers (40%) showed abnormalities in RNA transcripts of FHIT, and 76% of the tumors exhibited loss of FHIT alleles. Abnormal lung tumor transcripts lack two or more exons of the FHIT gene. Small cell lung cancer tumors and cell lines were analyzed by Southern blotting and showed rearranged BamHI fragments. These data suggest a critical role of the FHIT gene in lung carcinogenesis.

Amino Acid Sequence↗

PubMed1998

Philadelphia-negative chronic myelogenous leukemia in a patient with a unique complex translocation: 46,XY,t(9;12;15)(q34;12;q21).

Chronic myelogenous leukemia (CML) is associated with an acquired karyotypic abnormality, the Philadelphia (Ph) chromosome, in 95% of cases. The Ph chromosome is the product of a balanced translocation that results in a hybrid gene that is considered essential for the pathogenesis of this disease. We have found a complex translocation involving chromosomes 9, 12, and 15 in a 42-year-old Haitian male with the clinical findings of CML. Complex translocations have been shown to result in the masking of the Ph chromosome. We used a mixture of two BCR-specific DNA probes for Southern blot analysis in order to test this hypothesis in our patient. High-molecular weight DNA was digested with the restriction enzymes BglII, BamHI and HindIII. The BglII digestion revealed the presence of two abnormal fragments of 3.9 and 3.0 kb and the BamHI digestion an abnormal 15-kb fragment. These data suggest there is a breakpoint in region 2 of M-bcr. The identification of this breakpoint confirms our hypothesis that a rearrangement involving 22q11 has occurred in the leukemic cells of our patient. A secondary translocation involving chromosomes 12 and 15 has hidden the effects of this translocation. Combined cytogenetic and molecular analysis establishes the karyotype of our patient as 46,XY,t(9;12;15;22)(q34;q12;q21;q11).

Adult↗

PubMed1999

PCR for specific detection of haemorrhagic enteritis virus of turkeys, an avian adenovirus.

A hexon gene based PCR was developed for specific amplification of DNA sequences from the haemorrhagic enteritis virus (HEV) of turkeys. The hexon genes of different avian adenoviruses were compared for primer construction. Two regions with low sequence homology between HEV and fowl adenovirus (FAV) hexon genes were selected for primer localisation. In correlation with the known sequence data a fragment of 1647 bp was amplified from a live vaccine and spleens of turkeys suffering from haemorrhagic enteritis (HE). All other avian adenoviruses which are able to infect turkeys, i.e. FAV and turkey adenoviruses (TAV), were negative. This is the first PCR for specific detection of HEV DNA which should be useful for rapid diagnosis and epidemiological investigations of HEV infections in turkeys.

Animals↗

PubMed2002

Dynamics of therapeutic ultrasound contrast agents.

Novel therapeutic contrast agents offer great potential for localized drug delivery. Localized delivery should significantly improve the efficacy of drug delivery and reduce any toxic exposure to the healthy tissue. This work describes a preliminary theoretical description of agents, such as those developed by the ImaRx Corporation, enclosed by a relatively thick fluid shell. A theoretical extension is made to a generalized Rayleigh-Plesset formulation that allows it to be solved for an encapsulating liquid shell of arbitrary thickness and density. The equation is used to investigate the role of shell thickness, density and viscosity on the radial dynamics and velocity of the inner and outer radii. Comparisons are made with experimental measurements of the maximum radial expansions for agents with triacetin shells. For a seven-cycle driving acoustic pulse with a center frequency of 1.5 MHz and peak amplitude of 1.6 MPa, the equation predicts maximum expansions from 5.5 to 1.3 times the initial radius for agents 1 to 10 microm, respectively, in initial radius with a 500-nm (28.0 cP) encapsulating shell. These predictions have reasonable agreement with the maximum radial expansions obtained from optical experimental data of fragmenting and intact agents. Approximate agreement between theory and experiment for a similar range of agent sizes is also demonstrated for a pulse with the same pressure amplitude at 2.5 MHz. At 2.5 MHz, smaller radial expansion amplitudes from 1.1 to 4.1 times the initial radius were found for agents 1 to 10 microm in initial radius, respectively. Discrepancies are attributed to shape instabilities and their associated fragmentation effects not incorporated in the equation. A significant difference in the inner and outer wall velocities is predicted for agents with a 500-nm triacetin shell. A 2.5 microm initial radius agent driven with a seven-cycle pulse at 2.5 MHz and 1.6 MPa achieves a maximum negative inner wall velocity of 364 m/s and outer wall velocity of 63 m/s. For parameters that correspond to large differences between the inner and outer wall velocities, fragmentation is typically observed experimentally.

Contrast Media↗

PubMed1997

Apoptotic vs. nonapoptotic cytotoxicity induced by hydrogen peroxide.

The regulation of cellular cytotoxicity induced by hydrogen peroxide (H2O2) over a wide concentration range was assessed. Three distinct patterns were detected: the highest concentrations (> 10 mM) rapidly induced a necrotic form of death characterized by smeared patterns of DNA digestion and morphological evidence of primary cytoplasm and plasma membrane damage; In contrast, 10 and 5 mM H2O2 induced endonucleosomal DNA digestion concurrently with cytotoxicity and target cell death was associated with morphologic evidence of apoptosis. Apoptosis was inhibited by cycloheximide, emetine, aminobenzamide (ABA), aurintricarboxylic acid, and calcium depletion. The lowest concentrations of H2O2 (0.5 and 0.1 mM)-induced delayed cytotoxicity (at 24 or 48 hr), which was not associated with DNA ladder formation or morphologic evidence of apoptosis, but was inhibited by ABA. Enforced expression of BCL-2 induced resistance to 0.5 and 0.1 mM H2O2 but had no effect on cytotoxicity induced by 5 and 10 mM. Exposure of isolated nuclei to H2O2 in the absence of calcium or magnesium failed to induce endonucleosomal fragmentation. These data indicate that distinct pathways of H2O2-induced cytotoxicity can be distinguished by their different concentration dependences, and that BCL-2 can protect against some forms of H2O2-induced cytotoxicity.

Animals↗

PubMed2003

Efficacy of Vitamin D compounds to modulate estrogen receptor negative breast cancer growth and invasion.

In estrogen receptor (ER) positive breast cancer cells such as MCF-7 cells, the anti-tumor effects of 1,25(OH)(2)D(3) (1,25D(3)) may be secondary to disruption of estrogen mediated survival signals. If so, then sensitivity to 1,25D(3) mediated growth arrest could be reduced in estrogen independent breast cancer cells. The aim of these studies was to determine the effects of 1,25D(3) and EB1089 on the ER negative, invasive human breast cancer cell line SUM-159PT. 1,25D(3) and EB1089 reduced SUM-159PT cell growth subsequent to elevation of p27 and p21 levels. 1,25D(3) mediated apoptosis of SUM-159PT cells was associated with an enrichment of membrane bound bax, a redistribution of cytochome c from the mitochondria to the cytosol and PARP cleavage. 1,25D(3) and EB1089 also inhibited SUM-159PT cell invasion through an 8 microM Matrigel membrane. In pre-clinical studies, EB1089 dramatically reduced the growth of SUM-159PT xenografts in nude mice. The decreased size of tumors from EB1089 treated mice was associated with decreased proliferation and increased DNA fragmentation. Our data support the concept that Vitamin D(3) compounds trigger apoptosis by mechanisms independent of estrogen signaling. These studies indicate that Vitamin D(3) based therapeutics may be beneficial, alone or in conjunction with other agents, for the treatment of estrogen independent breast cancer.

Animals↗

PubMed2004

Control of actin turnover by a salmonella invasion protein.

Salmonella force their way into nonphagocytic host intestinal cells to initiate infection. Uptake is triggered by delivery into the target cell of bacterial effector proteins that stimulate cytoskeletal rearrangements and membrane ruffling. The Salmonella invasion protein A (SipA) effector is an actin binding protein that enhances uptake efficiency by promoting actin polymerization. SipA-bound actin filaments (F-actin) are also resistant to artificial disassembly in vitro. Using biochemical assays of actin dynamics and actin-based motility models, we demonstrate that SipA directly arrests cellular mechanisms of actin turnover. SipA inhibits ADF/cofilin-directed depolymerization both by preventing binding of ADF and cofilin and by displacing them from F-actin. SipA also protects F-actin from gelsolin-directed severing and reanneals gelsolin-severed F-actin fragments. These data suggest that SipA focuses host cytoskeletal reorganization by locally inhibiting both ADF/cofilin- and gelsolin-directed actin disassembly, while simultaneously stimulating pathogen-induced actin polymerization.

Actin Depolymerizing Factors↗

PubMed1991

Three DNA sequencing methods using capillary gel electrophoresis and laser-induced fluorescence.

Capillary gel electrophoresis is demonstrated for the four-spectral-channel sequencing technique of Smith, the two-spectral-channel sequencing technique of Prober, and the one-spectral-channel sequencing technique of Richardson and Tabor. Sequencing rates up to 1000 bases/h are obtained at electric field strengths of 465 V/cm. At lower electric field strengths, capillary electrophoresis produces useful data for fragments greater than 550 nucleotides in length with 2 times better resolution than slab gel electrophoresis. An on-column detector produces detection limits of 200 zmol (1 zmol = 10(-21) mol = 600 molecules) for the four-spectral-channel technique. A postcolumn detector, based on the sheath flow cuvette, produces detection limits of 20 and 2 zmol for the two- and one-spectral-channel techniques, respectively.

Base Sequence↗

PubMed2003

Oligonucleotide-functionalized gold nanoparticles as probes in a dry-reagent strip biosensor for DNA analysis by hybridization.

The highly specific molecular recognition properties of oligonucleotides are combined with the unique optical properties of gold nanoparticles for the development of a dry-reagent strip-type biosensor that enables visual detection of double stranded DNA within minutes. The assay does not require instrumentation and avoids the multiple incubation and washing steps performed in most current assays. Gold nanoparticle reporters with oligo(dT) attached to their surface form an integral part of the strip. Biotinylated PCR products (233 bp or 495 bp) are hybridized (5 min) with a poly(dA)-tailed oligo and applied on the strip, which is then immersed in the appropriate buffer. As the buffer migrates upward, it rehydrates the nanoparticles that are linked to the target DNA through poly(dA)/(dT) hybridization. Capture of the hybrids by immobilized streptavidin in the test zone of the strip generates a characteristic red band. A second red band is formed, by hybridization, in the control zone of the strip to indicate proper test performance. The sensor offers at least 8 times higher detectability than ethidium bromide staining of agarose gels and provides confirmation of the amplified fragments. Quantitative data are obtained by densitometric analysis of the bands. As low as 2 fmol of amplified DNA were detectable by the strip sensor. Also, 500 copies of prostate-specific antigen cDNA were detected by combining PCR and the strip sensor. The sensor was used successfully for detection of hepatitis C virus in plasma samples from 20 patients. The strip detected 16 out of 16 positive samples and gave no signal for 4 samples that were negative for the virus. To our knowledge, this is the first dry-reagent system that makes use of oligonucleotide-conjugated gold nanoparticles as probes.

Biosensing Techniques↗

PubMed1985

DNA methylation in mammalian nuclei.

A novel system to study the methylation of newly synthesized DNA in isolated nuclei was developed. Approximately 2.5% of cytosine residues incorporated into nascent DNA became methylated by endogenous methylase(s), and the level of DNA modification was reduced by methylation inhibitors. DNA synthesis and methylation were dependent on separate cytosol factors. The cytosol factor or factors required for DNA methylation were sensitive to trypsin digestion and were precipitable by (NH4)2SO4, suggesting that they were proteinaceous. Time-course experiments revealed a short lag of approximately 20 s between synthesis and methylation in nuclei. The DNAs produced in these nuclei were a mixed population of low molecular weight fragments and higher molecular weight fragments shown to be short extension of existing replicons. The methylation level found in low molecular weight DNA was lower than that found in bulk L1210 DNA, indicating that further methylation events might take place after ligation of small fragments. These data suggest that newly synthesized DNA is a good substrate for methylase enzymes and that nuclear cytoplasmic interactions may be important in controlling inheritance of methylation patterns.

Animals↗

PubMed1979

Nucleosome organization during germ cell development in the sea cucumber Holothuria tubulosa.

Conformational changes that occur in chromatin from developing germ cells of the echinoderm Holothuria tubulosa have been probed with micrococcal nuclease. The results indicate that the extent of DNA degradation to acid-soluble nucleotides is highest in chromatin at the early stages of gonad growth, being drastically subdued in the mature sperm cell. Production of nucleosomal particles also varies with development, involving at least 70% of the chromatin at the final stage of maturation, whereas in immature germ cells it remains much lower. In contrast, electrophoretic analysis for DNA size has shown that the average nucleosome repeat length, about 227 base pairs, does not change throughout the maturation process. However, kinetics of the enzyme reaction have revealed that, although brief digestion of chromatin from both immature gonads and sperm yields comparable series of higher oligomers, extensive digest patterns differ widely. Sperm chromatin, highly protected, releases a 275 base pair intermediate fragment, wholly absent in immature gonads. The 145 base pair core released in both chromatins is not further digested in sperm. In comparison to sperm chromatin, that of immature germ cells is much more susceptible to fragmentation, yielding the usual set of smaller subnucleosomal fragments. These data suggest the induction of differential accessibilities of chromatin DNA with maturation, which is not accompanied by displacement of the histone complement. The histone variants present in this species may well be instrumental in the process.

Animals↗

PubMed2001

Synthesis and characterization of phosphorescent cyclometalated iridium complexes.

The preparation, photophysics, and solid state structures of octahedral organometallic Ir complexes with several different cyclometalated ligands are reported. IrCl3.nH2O cleanly cyclometalates a number of different compounds (i.e., 2-phenylpyridine, 2-(p-tolyl)pyridine, benzoquinoline, 2-phenylbenzothiazole, 2-(1-naphthyl)benzothiazole, and 2-phenylquinoline), forming the corresponding chloride-bridged dimers, CwedgeN2Ir(mu-Cl)2IrCwedgeN2 (CwedgeNis a cyclometalated ligand) in good yield. These chloride-bridged dimers react with acetyl acetone (acacH) and other bidentate, monoanionic ligands such as picolinic acid (picH) and N-methylsalicylimine (salH), to give monomeric CwedgeN2Ir(LX) complexes (LX = acac, pic, sal). The emission spectra of these complexes are largely governed by the nature of the cyclometalating ligand, leading to lambda(max) values from 510 to 606 nm for the complexes reported here. The strong spin-orbit coupling of iridium mixes the formally forbidden 3MLCT and 3pi-pi* transitions with the allowed 1MLCT, leading to a strong phosphorescence with good quantum efficiencies (0.1-0.4) and room temperature lifetimes in the microsecond regime. The emission spectra of the CwedgeN2Ir(LX) complexes are surprisingly similar to the fac-IrCwedgeN3 complex of the same ligand, even though the structures of the two complexes are markedly different. The crystal structures of two of the CwedgeN2Ir(acac) complexes (i.e., CwedgeN = ppy and tpy) have been determined. Both complexes show cis-C,C', trans-N,N' disposition of the two cyclometalated ligands, similar to the structures reported for other complexes with a "CwedgeN2Ir" fragment. NMR data (1H and 13C) support a similar structure for all of the CwedgeN2Ir(LX) complexes. Close intermolecular contacts in both (ppy)2Ir(acac) and (tpy)2Ir(acac) lead to significantly red shifted emission spectra for crystalline samples of the ppy and tpy complexes relative to their solution spectra.

Journal Article↗

PubMed2006

Mass spectrometric and quantum chemical studies of the thermodynamics and bonding of neutral and ionized LnCl, LnCl2, and LnCl3 species (Ln = Ce, Lu).

The mass spectral patterns of CeCl3(g) and LuCl3(g) and appearance energies for the identified ions were measured using a Nier-type mass spectrometer coupled with a Knudsen cell. The molecular ion CeCl3+ was found to be considerably less stable in comparison to LuCl3+. Partial pressures and sublimation enthalpies of LnCl3(s) to monomeric LnCl3(g) and dimeric Ln2Cl6(g) species were obtained in the ranges of 882-1028 (Ln = Ce) and 850-1004 K (Ln = Lu). The contribution of dimeric Ce2Cl6(g) species to equilibrium vapors of CeCl3(s) is considerably smaller than the Lu2Cl6(g) contribution in LuCl3(s) vapors. The measurements were supplemented by quantum chemical ab initio studies of structures, energetics, and vibrational frequencies of neutral and singly ionized LnCl, LnCl2, and LnCl3 species (Ln = Ce, Lu). The theoretical appearance energies of different ions, calculated from the energies of the gaseous species, are in good agreement with experimental data. The fragmentation energies of LnCl, LnCl2, and LnCl3 were also computed and compared with the mass spectral patterns of respective vapor species. The Mulliken and natural bond orbital electron population methods were applied for the systematic analysis of the bonding scheme in molecules and cations.

Journal Article↗

PubMed1981

Synthesis and DNA binding of [3-[2'-(2-acetamidoethyl)-2,4'-bithiazole-4-carboxamido]propyl[dimethylsulfonium chloride, a fragment of bleomycin A2.

[3-[2'-(2-Acetamidoethyl)-2,4'-bithiazole-4-carboxamido]propyl]dimethylsulfonium chloride (1), the acetyl derivative of the cationic terminal dipeptide of bleomycin A2, has been synthesized and its binding to DNA and poly(dA-dT) has been studied by proton NMR and fluorescence spectroscopy. The spectral perturbations which occur upon binding of the compound to either nucleic acid indicate that that portion of bleomycin which binds to the nucleic acid can, for the most part, be mimicked by the fragment. The data are discussed in terms of the structure of the drug and the drug-nucleic acid complex.

Binding Sites↗

PubMed1997

Cisplatin-DNA adduct determination in the hepatic albumin gene as compared to whole genomic DNA.

A quantitative time-resolved fluorometriC PCR-stop assay has been used to determine cisplatin-DNA adducts in a 1.612 kb region and a polymorphic 1.85 kb region of the rat liver albumin gene containing parts of exons B and C and all of the BC intron. The values were compared to adducts in the whole rat liver genome determined by atomic absorbance spectrometry (AAS). Initial validation of the PCR-stop assay involved modification of purified rat liver DNA in vitro to desired levels by incubation with different concentrations of cisplatin. In these DNA samples, cisplatin-DNA adduct levels determined in the 1612 base pair fragment by PCR-stop assay were shown to be similar to those determined in the whole genomic DNA by AAS. In freshly isolated primary rat hepatocytes cultured for 2 h with 50, 75, 100, and 150 microM cisplatin, adduct levels determined by the PCR-stop assay were similar to those measured by AAS. Cultured MH1C1 rat hepatoma cells, which express albumin, had a polymorphism in the rat albumin gene such that the fragment amplified with the same primers was about 1.85 kb (13% larger). When MH1C1 cells were exposed to 5, 15, 25, 50, and 75 microM cisplatin for 24 h, 50% cell kill was at 21.0 +/- 5.5 microM cisplatin. For doses of 15-75 microM cisplatin, the cisplatin-DNA adduct levels in this fragment, measured by PCR-stop assay, were about one-half of those in the whole genomic DNA measured by AAS. In addition, MH1C1 cells exposed to 150 microM cisplatin for 4 h and subsequently incubated with fresh medium for 24 h showed no change in adduct level in whole genomic DNA during this time but showed a 29% adduct removal in the 1.85 kb fragment. The data demonstrate that this 1.85 kb region containing expressed regions of the albumin gene has undergone both less adduction and more rapid adduct removal, as compared to the MH1C1 genome as a whole.

Albumins↗