Five-color-based high-information-content fingerprinting of bacterial artificial chromosome clones using type IIS restriction endonucleases.

We have developed a high-information-content fingerprinting (HICF) system for bacterial artificial chromosome (BAC) clones using a Type IIS restriction endonuclease, HgaI, paired with a Type II restriction endonuclease, RsaI. In the method described, unknown five-base overhangs generated with HgaI are partially or fully sequenced by modified fluorescent dideoxy terminators. Using an in-lane size standard labeled with a fifth dye, fragments are characterized by both the size and the sequence of its terminal one to five bases. The enhanced information content associated with this approach significantly increases the accuracy and efficiency of detecting shared fragments among BAC clones. We have compared data obtained from this method to predicted HICF patterns of 10 fully sequenced BACs. We have further applied HICF to 555 BAC clones to assemble contigs spanning 16p11.2 to 16p13.1 of human chromosome 16.

Troglitazone improves psoriasis and normalizes models of proliferative skin disease: ligands for peroxisome proliferator-activated receptor-gamma inhibit keratinocyte proliferation.

BACKGROUND: Psoriasis is often treated with agents that activate nuclear hormone receptors for glucocorticoids, retinoids, and vitamin D. The peroxisome proliferator-activated receptor-gamma (PPARgamma) is a related nuclear hormone receptor that can be activated by its ligands, including the thiazolidinediones. OBJECTIVE: To assess whether treatment with troglitazone, a currently available thiazolidinedione used to treat diabetes mellitus, has an effect on psoriasis in normoglycemic patients and whether ligands for PPARgamma have an effect on models of psoriasis. DESIGN: Open-label administration of troglitazone in patients with psoriasis and evaluation of drug actions in cellular, organ, and transplant models of psoriasis. SETTING: University and community hospital outpatient departments and university laboratories. PATIENTS: Patients with chronic, stable plaque psoriasis and control subjects. Five patients with psoriasis received troglitazone (none withdrew); 10 different untreated patients and 10 controls provided tissue samples. INTERVENTIONS: Oral troglitazone therapy at various dosages in patients with psoriasis; also, use of troglitazone, ciglitazone, and 15-deoxy-delta-12,14-prostaglandinJ2 in psoriasis models. MAIN OUTCOME MEASURES: Investigator-determined clinical results in patients and cell counts and histological evidence in models. RESULTS: All patients' psoriasis improved substantially during troglitazone therapy. Peroxisome proliferator-activated receptor-gamma was expressed in human keratinocytes; ligands for PPARgamma inhibited the proliferation of normal and psoriatic human keratinocytes in culture. Troglitazone treatment normalized the histological features of psoriatic skin in organ culture and reduced the epidermal hyperplasia of psoriasis in the severe combined immunodeficient mouse and human skin transplant model of psoriasis (P<.05 compared with untreated controls). CONCLUSIONS: Peroxisome proliferator-activated receptor-gamma might be a useful intracellular target for the treatment of psoriasis; further study is needed to assess the clinical value of ligands for PPARgamma, including troglitazone.

New energy transfer dyes for DNA sequencing.

We have synthesized a set of four energy transfer dyes and demonstrated their use in automated DNA sequencing. The donor dyes are the 5- or 6-carboxy isomers of 4'-aminomethylfluorescein and the acceptor dyes are a novel set of four 4,7-dichloro-substituted rhodamine dyes which have narrower emission spectra than the standard, unsubstituted rhodamines. A rigid amino acid linker, 4-aminomethylbenzoic acid, was used to separate the dyes. The brightness of each dye in an automated sequencing instrument equipped with a dual line argon ion laser (488 and 514 nm excitation) was 2-2.5 times greater than the standard dye-primers with a 2 times reduction in multicomponent noise. The overall improvement in signal-to-noise was 4- to 5-fold. The utility of the new dye set was demonstrated by sequencing of a BAC DNA with an 80 kb insert. Measurement of the extinction coefficients and the relative quantum yields of the dichlororhodamine components of the energy transfer dyes showed their values were reduced by 20-25% compared with the dichlororhodamine dyes alone.

Effects of thiazolidinediones on growth and differentiation of human aorta and coronary myocytes.

Thiazolidinediones, insulin-sensitizing agents that lower insulin and lipid levels in insulin-resistant states, block agonist-induced Ca2+ entry into vascular smooth muscle (VSM) cells in vitro and lower blood pressure in animals and humans in vivo. In this study, we investigated the effects of ciglitazone and troglitazone on cell growth and DNA synthesis (as thymidine incorporation), and differentiation in cultured human aorta (haVSM) and human coronary artery (hcaVSM) VSM cells. Mitotically quiescent haVSM cells were stimulated with serum or platelet-derived growth factor (PDGF). Ciglitazone (40 micromol/L) inhibited haVSM cell proliferation by 84 +/- 16% (mean +/- SEM) (P < .05, n = 3), and serum and PDGF stimulated [3H]-thymidine incorporation by 91 +/- 18% (P < .03, n = 3) and 73 +/- 14% (P < .03, n = 4), respectively. Troglitazone (5 micromol/L) inhibited proliferation of haVSM cells by 78 +/- 14% (P < .05, n = 3) and hcaVSM cells by 91 +/- 18% (P < .05, n = 3). Proliferating VSM cells (synthetic phenotype) expressed small amounts of alpha-actin, whereas nonproliferating VSM cells (contractile phenotype) exhibited abundant alpha-actin. Exposure of proliferating haVSM cells to 40 micromol/L ciglitazone induced a marked increase in alpha-actin staining, consistent with transition to the well differentiated, contractile phenotype. To the extent that thiazolidinediones similarly affect growth factor-induced proliferation and differentiation of arterial myocytes in vivo, these agents may be useful in treating atherosclerosis and in preventing restenosis after angioplasty.

Fluorescence energy-transfer cyanine heterodimers with high affinity for double-stranded DNA. II. Applications to multiplex restriction fragment sizing.

Energy-transfer cyanine dyes, a thiazsole orange-thiazole-indolenine (butylTOTIN) and a thiazole orange-thiazole blue heterodimer (pentylTOTAB), form high-affinity complexes with double-stranded (ds)DNA with donor fluorescence (lambdaF(max)527 nm) quenched >90% and with acceptor fluorescence emission above 650 nm (S. C. Benson, Z. Zeng, and A. N. Glaser (1995) Anal. Biochem. 231, 247-255). After separation by agarose gel electrophoresis, bands of precomplexed dsDNA-dye restriction fragments containing 10 pg of dsDNA are readily detected with a laser-excited confocal-fluorescence gel scanner (R. A. Mathies et al. (1994) Rev. Sci. Instrum. 65, 807-812) following donor excitation at 488 nm (argon ion laser) or direct acceptor excitation at 647 nm (krypton ion laser). Accurate two-color multiplex sizing of restriction fragments is obtained with 488-nm excitation with dsDNA fragments precomplexed with thiazole orange dimer (TOTO) as unknowns (detected at 500-565 nm, green channel) and dsDNA fragments stained with the energy-transfer cyanine dyes (detected at 645-750 nm, red channel) as internal standards. There is negligible cross talk of fluorescence between the red and green channels and no significant dye migration in mixtures of prelabeled standard and unknown fragments.

Fluorescence energy-transfer cyanine heterodimers with high affinity for double-stranded DNA. I. Synthesis and spectroscopic properties.

We have designed, synthesized, and characterized fluorescent cyanine heterodimers that exploit resonance energy transfer to achieve strong emission above 650 nm with 488-nm excitation. Thiazole orange serves as the common fluorescence donor in these dyes and thiazole-indolenine, thiazole blue, or symmetric thiazole blue as acceptors. The donor and acceptor chromophores are linked by a polymethylene linker containing quaternary amino groups. These heterodimers have a high affinity for double-stranded DNA (dsDNA). The donor emission in the dsDNA-bound dyes is quenched by over 85%. The affinity for dsDNA and the quenching of donor fluorescence were optimized by varying the length of the linker between the donor and acceptor. Complexes of dsDNA fragments with such optimized dyes dissociated very slowly (t(0.5) > 300 min) during agarose gel electrophoresis.

High-sensitivity capillary electrophoresis of double-stranded DNA fragments using monomeric and dimeric fluorescent intercalating dyes.

Fluorescence-detected capillary electrophoresis separations of phi X174/HaeIII DNA restriction fragments have been performed using monomeric and dimeric intercalating dyes. Replaceable hydroxyethyl cellulose solutions were used as the separation medium. Confocal fluorescence detection was performed following 488-nm laser excitation. The limits of DNA detection for on-column staining with monomeric dyes (ethidium bromide, two propidium dye derivatives, oxazole yellow, thiazole orange, and a polycationic thiazole orange derivative) were determined. The thiazole orange dyes provide the most sensitive detection with limiting sensitivities of 2-4 amol of DNA base pairs per band, and detection of the 603-bp fragment was successful, injecting from phi X174/HaeIII samples containing only 1-2 fg of this fragment per microliter. Separations of preformed DNA-dimeric dye complexes were also performed. The breadth of the bands observed in separations of preformed DNA-dimeric dye complexes is due to the presence of DNA fragments with different numbers of bound dye molecules that can be resolved as closely spaced subbands in many of our separations. The quality of these DNA-dye complex separations can be dramatically improved by performing the electrophoresis with 9-aminoacridine (9AA) in the column and running buffers. The optimum concentrations of 9AA for the separation of complexes preformed with the dimeric dyes TOTO, EthD, TOTAB, and YOYO were determined to be 100, 1, 1, and 0.5 microM, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)

Heterodimeric DNA-binding dyes designed for energy transfer: stability and applications of the DNA complexes.

Spectroscopic studies of the complexes of double-stranded (ds) DNA with the polymethylene-amine linked heterodimers thiazole orange-thiazole blue, thiazole orange-ethidium, and fluorescein-ethidium, in each case show efficient energy transfer from donor to acceptor chromophores (Benson, S.C., Singh, P. and Glazer, A.N. (1993) accompanying manuscript). A quantitative assay of the stability of such complexes during gel electrophoresis is presented. The off-rate of dye from complexes formed at an initial dsDNA bp:dye ratio > or = 10:1 follows strict first-order kinetics. The t0.5 values for the dissociation of a series of related dyes provide a quantitative criterion for the design of DNA-binding fluorophores. Complexes of dsDNA with the monomeric propidium and cyanine dyes, [1-(9-amino-4,7-diazanonyl)-3,8-diamino-6-phenyl-phenanthridinium bromide trihydrobromide] and (N,N'-tetramethyl-1,3-propanediamino)propyl thiazole orange [4-[3-methyl-2,3-dihydro-(benzo-1,3-thiazole)-2-methylidenyl]-1-(4 ,4,8-trimethyl-4,8-diazanonyl)-quinolinium diiodide], are much more stable than those with their widely used counterparts, ethidium and thiazole orange. Applications of the new dyes in post-staining of gels and in the multiplex detection of DNA restriction fragments are presented.

Heterodimeric DNA-binding dyes designed for energy transfer: synthesis and spectroscopic properties.

Heterodimeric dyes are described which bind tightly to double-stranded (dsDNA) with large fluorescence enhancements. These dyes are designed to exploit energy transfer between donor and acceptor chromophores to tune the separation between excitation and emission wavelengths. The dyes described here absorb strongly at the 488 nm argon ion line, but emit at different wavelengths, and can be applied to multiplex detection of various targets. The chromophores in these dyes, a thiazole orange-thiazole blue heterodimer (TOTAB), two different thiazole orange-ethidium heterodimers (TOED1 and TOED2), and a fluorescein-ethidium heterodimer (FED), are in each case linked through polymethyleneamine linkers. The emission maxima of the DNA-bound dyes lie at 662 (TOTAB), 614 (TOED 2), and 610 nm (FED). The dyes showed a > 100 fold enhancement of the acceptor chromophore fluorescence on binding to dsDNA and no sequence selectivity. In comparison with direct 488 nm excitation of the constituent monomeric dyes, in the heterodimers the fluorescence of the acceptor chromophores was greatly enhanced and the emission of the donor chromophores quenched by over 90%. The acceptor emission per DNA-bound dye molecule was constant from 100 DNA bp:dye to 20 bp:dye and decreased sharply at higher dye:DNA ratios.

Immunogold detection of glycoprotein antigens in sea urchin embryos.

Four developmental stages of sea urchin embryos were labeled with colloidal gold in an attempt to elucidate the intracellular trafficking patterns within the cells that produce the glycoprotein matrix of the embryonic spicule. The primary mesenchyme cells (PMCs) form a syncytium and secrete an organic matrix on which calcium carbonate is laid down to form an endoskeletal spicule. The organic matrix has been isolated and characterized as glycoprotein consisting of four major bands. Polyclonal antibodies to these glycoproteins were used to label embryos from the mesenchyme blastula, early gastrula, late gastrula, and plutei stages of development. The label is concentrated in the Golgi complex and associated vesicles, in secretory vesicles, and in the organic matrix. The density of the labeling increases as development proceeds.

The effect of cyclic AMP on the accumulation of newly synthesized protein in the extracellular matrix of PFHR-9 teratocarcinoma cells.

The effect of elevated cyclic AMP levels on the accumulation of newly synthesized extracellular matrix protein was examined in PFHR-9 cells producing Type IV collagen. The effect of dbcAMP, 8-BrcAMP, IBMX and forskolin on the synthesis of total protein, non-collagen protein and collagen were compared. DbcAMP increased the accumulation of total protein but did not affect the distribution of collagen and non-collagen protein. 8-BrcAMP, IBMX and forskolin also increased collagen and non-collagen accumulation. However, the effect on collagen was significantly greater with 8-BrcAMP and IBMX. Consequently, 8-BrcAMP and IBMX resulted in an increased percent collagen synthesis in the extracellular matrix. Elevated cAMP levels had no effect on cell proliferation or DNA synthesis but did produce a significant effect on cell morphology.

Regulation of lung fibroblast proliferation and protein synthesis by bronchiolar lavage in experimental silicosis.

Male Sprague-Dawley rats were subjected to a single, intratracheal instillation of 30 mg Min-U-Sil silica in sterile saline and were sacrificed 3, 7, or 14 days following instillation. Control animals were instilled with sterile saline only. Silica instillation produced an inflammatory reaction followed by histological changes characteristic of lung fibrosis. Thickened alveolar septa associated with inflammatory cells transforming into large multifocal fibrotic nodules were detected in silica-exposed animals. Increased numbers of bronchoalveolar cells (principally macrophages), elevated levels of protein (principally serum albumin), and lysozyme, proteolytic (trypsin-like), and myeloperoxidase activities were detected in lavage fluids obtained from animals instilled with silica. These factors (except for lysozyme activity) were elevated above control levels from 3 to 7 days postinstillation and declined to near control levels by Day 14. The rate of DNA, collagen, and noncollagen protein synthesis was significantly elevated in lung tissue minces from silica-treated rats 3 and 7 days after instillation. Elevated levels of total protein, and lung collagen in particular, were observed 9 weeks after insult. Lavage fluid from silica-instilled rats stimulates DNA synthesis in cultures of proliferating and quiescent rat lung fibroblasts. Lavage fluid from silica-instilled rats also stimulates lung fibroblasts to increase collagen and noncollagen protein synthesis.

Regulation of lung fibroblast proliferation and collagen synthesis by alveolar macrophages in experimental silicosis. I: Effect of macrophage conditioned medium from silica instilled rats.

Alveolar macrophages were lavaged from silica or saline instilled rats 0, 3, 7 and 14 days after exposure. Macrophages were cultured for twenty-four hours and the conditioned media assayed for the ability to stimulate rat lung fibroblast proliferation and collagen synthesis. Macrophages remained viable throughout the culture period. DNA synthesis was significantly elevated by macrophage conditioned media (MCM) from silica instilled rats (S-MCM) compared to untreated fibroblasts or fibroblasts exposed to MCM from saline instilled control animals (C-MCM). Stimulation of DNA synthesis was not observed when S-MCM was exposed to non-proliferating fibroblasts. Collagen synthesis quantitated as 3H-hydroxyproline accumulation or percent collagen synthesis was also increased by day 3 and day 7 S-MCM. Specific activity measurements of intracellular 3H-proline minimized the possibility that the increase in 3H-proline incorporation into collagen was a reflection of increased proline transport. Non-collagen protein synthesis was also increased in fibroblasts exposed to day 14 S-MCM. These results suggest that alveolar macrophages elaborate factors following silica exposure capable of altering the DNA and protein synthetic activity of lung fibroblasts. These changes in fibroblast DNA and protein metabolism are similar to those observed for lung tissue in vivo and lend further support to the hypothesis of macrophage mediation of the pulmonary response following silica exposure.

The organic matrix of the skeletal spicule of sea urchin embryos.

The micromeres that arise at the fourth cell division in developing sea urchin embryos give rise to primary mesenchyme, which in turn differentiates and produces calcareous endoskeletal spicules. These spicules have been isolated and purified from pluteus larvae by washing in combinations of ionic and nonionic detergents followed by brief exposure to sodium hypochlorite. The spicules may be demineralized and the integral matrix dissolves. The matrix is composed of a limited number of glycoproteins rich in aspx, glux, gly, ser, and ala, a composition not unlike that found in matrix proteins of biomineralized tissues of molluscs, sponges, and arthropods. There is no evidence for collagen as a component of the matrix. The matrix contains N-linked glycoproteins of the complex type. The matrix arises primarily from proteins synthesized from late gastrulation onward, during the time that spicule deposition occurs. The mixture of proteins binds calcium and is an effective immunogen. Electrophoresis of the glycoproteins on SDS-containing acrylamide gels, followed by blotting and immunocytochemical detection, reveals major components of approximately 47, 50, 57, and 64 kD, and several minor components. These same components may be detected with silver staining or fluorography of amino acid-labeled proteins. In addition to providing convenient molecular marker for the study of the development of the micromere lineage, the spicule matrix glycoproteins provide an interesting system for investigations in biomineralization.

Glucocorticoids stimulate collagen and noncollagen protein synthesis in cultured vascular smooth muscle cells.

The effect of glucocorticoids on collagen synthesis was examined in cultured bovine aortic smooth muscle (BASM) cells. BASM cells treated with 0.1 microM dexamethasone during their proliferative phase (11 d) were labeled with [3H]proline for 24 h, and the acid-precipitable material was incubated with bacterial collagenase. Dexamethasone produced an approximate twofold increase in the incorporation of proline into collagenase-digestible protein (CDP) and noncollagen protein (NCP) in the cell layer and medium. The stimulation was present in both primary mass cultures and cloned BASM. An increase in CDP and NCP was detected at 0.1 nM, while maximal stimulation occurred at 0.1 microM. Only cells exposed to dexamethasone during their log phase of growth (1-6 d after plating) showed the increase in CDP and NCP when labeled 11 d after plating. The stimulatory effect was observed in BASM cells treated with the natural bovine glucocorticoid, cortisol, dexamethasone, and testosterone, but was absent in cells treated with aldosterone, corticosterone, cholesterol, 17 beta-estradiol, and progesterone. The increase in CDP and NCP was absent in cells treated with the inactive glucocorticoid, epicortisol, and totally abolished by the antagonist, 17 alpha-hydroxyprogesterone, suggesting that the response was mediated by specific cytoplasmic glucocorticoid receptors. Dexamethasone-treated BASM cells showed a 4.5-fold increase in the specific activity of intracellular proline, which was the result of a twofold increase in the uptake of proline and depletion of the total proline pool. After normalizing for specific activity, dexamethasone produced a 2.4- and 2.8-fold increase in the rate of collagen and NCP synthesis, respectively. Cells treated with dexamethasone secreted 1.7-fold more collagen protein in 24 h compared to control cultures. The BASM cells secreted 70% Type I and 30% Type III collagen into the media as assessed by two-dimensional gel electrophoresis. The ratio of these two types was not altered by dexamethasone. The results of the present study demonstrate that glucocorticoids can act directly on vascular smooth muscle cells to increase the synthesis and secretion of collagen and NCP.