Identification of known and novel genes whose expression is regulated by endogenous retinoic acid during early embryonic development of the mouse. (33/182)

Retinoic acid (RA) derived from vitamin A is necessary for, among other things, mammalian embryonic development. Although the impact of RA-dependent gene-regulation on embryonic development has been examined through genetic disruption of the retinoid receptors, the understanding of the underlying molecular mechanism remain unclear, in part, due to the difficulty in identifying RA-regulated genes in an intact embryo. We report here that RA-regulated genes can be identified from total RA-deficient embryos created by retinol-binding protein antisense (RBP-AS) oligodeoxynucleotide treatment in conjunction with differential display. Of the 28 genes isolated, 15 genes matched known genes in the GenBank database and the others either represented EST sequences or encoded novel genes. Semi-quantitative reverse transcriptase-polymerase chain reaction verified that the mRNA levels of mouse DN 38, COL VI 3 alpha, cul-1, alpha-tropomyosin, and PP2A-C alpha were substantially increased, whereas mouse Msh 2, Ndufa2, Ribosomal protein S19, sFRP-1, GDAP-10 and mSmcD were significantly decreased in vitamin A deficient (VAD) embryos compared to the control embryos. The utility of the method is exemplified by our finding that several genes in the Wnt signaling pathway are vitamin A regulated in day 9.0 post coitum (p.c.) embryos.  (+info)

Determination of affinity, stoichiometry and sequence selectivity of minor groove binder complexes with double-stranded oligodeoxynucleotides by electrospray ionization mass spectrometry. (34/182)

Electrospray mass spectrometry was evaluated regarding the reliability of the determination of the stoichiometries and equilibrium association constants from single spectra. Complexes between minor groove binders (Hoechst 33258, Hoechst 33342, DAPI, netropsin and berenil) and 12mer oligonucleotide duplexes with a central sequence (A/T)4 flanked by G/C base pairs were chosen as model systems. To validate the electrospray ionization mass spectrometry (ESI-MS) method, comparisons were made with circular dichroism and fluorescence spectroscopy measurements. ESI-MS allowed the detection of minor (2 drug + DNA) species for Hoechst 33258, Hoechst 33342, DAPI and berenil with duplex d(GGGG(A/T)4GGGG). d(CCCC(A/T)4CCCC), which were undetectable with the other techniques. Assuming that the duplexes and the complexes have the same electrospray response factors, the equilbrium association constants of the 1:1 and 2:1 complexes were determined by ESI-MS, and the values show a good quantitative agreement with fluorescence determined constants for Hoechst 33258 and Hoechst 33342. It is also shown that ESI-MS can quickly give reliable information on the A/T sequence selectivity of a drug: the signal of a complex is directly related to the affinity of the drug for that particular duplex. The potential of ESI-MS as a qualitative and quantitative affinity screening method is emphasized.  (+info)

Transfection efficiency and toxicity of polyethylenimine in differentiated Calu-3 and nondifferentiated COS-1 cell cultures. (35/182)

In the present study, we evaluated polyethylenimine (PEI) of different molecular weights (MWs) as a DNA complexing agent for its efficiency in transfecting nondifferentiated COS-1 (green monkey fibroblasts) and well-differentiated human submucosal airway epithelial cells (Calu-3). Studying the effect of particle size, zeta potential, presence of serum proteins or chloroquine, it appeared that transfection efficiency depends on the experimental conditions and not on the MW of the PEI used. Comparing transfection efficiencies in both cell lines, we found that PEI was 3 orders of magnitude more effective in COS-1 than in Calu-3 cells, because Calu-3 cells are differentiated and secrete mucins, which impose an additional barrier to gene delivery. Transfection efficiency was strongly correlated to PEI cytotoxicity. Also, some evidence for PEI-induced apoptosis in both cell lines was found. In conclusion, our results indicate that PEI is a useful vector for nonviral transfection in undifferentiated cell lines. However, results from studies in differentiated bronchial epithelial cells suggest that PEI has yet to be optimized for successful gene therapy of cystic fibrosis (CF).  (+info)

TGF-beta1 inhibits multiple caspases induced by TNF-alpha in murine osteoblastic MC3T3-E1 cells. (36/182)

Tumor necrosis factor alpha (TNF-alpha) is a proinflammatory cytokine that induces apoptosis in a number of cell systems, including osteoblasts. Transforming growth factor beta1 (TGF-beta1) is an abundant growth factor that is known to stimulate bone formation. This study was designed to examine the role of TGF-beta1 on TNF-alpha-induced apoptosis in murine osteoblastic MC3T3-E1 cells. Total RNA was extracted from MC3T3-E1 cells treated with 20 ng/ml of TNF-alpha, 10 ng/ml of TGF-beta1, or combination, for 6 h. TNF-alpha exerted a variety of effects on the apoptotic gene expression in osteoblasts. Ribonuclease protection assays (RPA) revealed that TNF-alpha upregulated the mRNA levels of caspase-1, -7, -11, -12, and FAS. Western blot analysis showed enhanced processing of caspase-1, -7, -11, and -12, with the appearance of their activated enzymes 24 h after TNF-alpha treatment. In addition, caspase-3-like activity was significantly activated following TNF-alpha treatment. Levels of cleaved poly(ADP-ribose) polymerase and FAS protein were also elevated by TNF-alpha. Finally, Hoechst staining, terminal deoxynucleotidyl-transferase nick-end labeling (TUNEL) assay, and oligonucleosome ELISA all indicated that TNF-alpha induced apoptosis. In contrast, the addition of TGF-beta1 attenuated all of the aforementioned effects of TNF-alpha. Our results demonstrate that TGF-beta1 can decrease TNF-alpha-induced apoptosis in murine osteoblasts at least in part by attenuating TNF-alpha-induced caspase gene expression.  (+info)

Quantifying DNA concentrations using fluorometry: a comparison of fluorophores. (37/182)

Detection of low concentrations of DNA is important in vision research because many animal models only provide scant samples of ocular tissue. Quantitative analysis of low concentrations of double stranded DNA is now feasible using fluorometry with newer fluorophores. This technique offers a rapid way to evaluate the DNA content of samples based on the measurement of fluorescence enhancement emitted by fluorophore-bound DNA and is more sensitive than absorption spectrometry. The purpose of this study was to compare the sensitivity of several different fluorophores for measuring DNA concentrations by fluorometry. Based on our studies, we conclude that SYBR Green I and PicoGreen are substantially more sensitive for quantifying DNA concentrations than ethidium bromide and Hoechst 33258.  (+info)

Global chromosome positions are transmitted through mitosis in mammalian cells. (38/182)

We investigated positioning of chromosomes during the cell cycle in live mammalian cells with a combined experimental and computational approach. By non-invasive labeling of chromosome subsets and tracking by 4D imaging, we could show that no global rearrangements occurred in interphase. Using the same assay, we also observed a striking order of chromosomes throughout mitosis. By contrast, our computer simulation based on stochastic movements of individual chromosomes predicted randomization of chromosome order in mitosis. In vivo, a quantitative assay for single chromosome positioning during mitosis revealed strong similarities between daughter and mother cells. These results demonstrate that global chromosome positions are heritable through the cell cycle in mammalian cells. Based on tracking of labeled chromosomes and centromeres during chromosome segregation and experimental perturbations of chromosomal order, we propose that chromosome specific timing of sister chromatid separation transmits chromosomal positions from one cell generation to the next.  (+info)

Water at DNA surfaces: ultrafast dynamics in minor groove recognition. (39/182)

Water molecules at the surface of DNA are critical to its equilibrium structure, DNA-protein function, and DNA-ligand recognition. Here we report direct probing of the dynamics of hydration, with femtosecond resolution, at the surface of a DNA dodecamer duplex whose native structure remains unperturbed on recognition in minor groove binding with the bisbenzimide drug (Hoechst 33258). By following the temporal evolution of fluorescence, we observed two well separated hydration times, 1.4 and 19 ps, whereas in bulk water the same drug is hydrated with time constants of 0.2 and 1.2 ps. For comparison, we also studied calf thymus DNA for which the hydration exhibits similar time scales to that of dodecamer DNA. However, the time-resolved polarization anisotropy is very different for the two types of DNA and clearly elucidates the rigidity in drug binding and difference in DNA rotational motions. These results demonstrate that hydration at the surface of the groove is a dynamical process with two general types of trajectories; the slowest of them (approximately 20 ps) are those describing dynamically ordered water. Because of their ultrafast time scale, the "ordered" water molecules are the most weakly bound and are accordingly involved in the entropic (hydration/dehydration) process of recognition.  (+info)

A novel method for DNA molecular counting. (40/182)

We have developed a new method for counting DNA molecules using 'capillary-plates' consisting of a large number of small glass-capillary 'channels' fused together in parallel. PCR mixtures containing serially diluted DNA templates with the DNA indicator dye Hoechst 33258 were poured into the plates and sealed with silicone rubber-plates. Following 40 PCR cycles, fluorescence microscopy revealed that the fluorescence in some channels had increased about three-times more than in others at template concentrations of 1 fM or lower. No bright fluorescence was observed in the absence of template. The relationship between the proportion of fluorescent channels in the capillary-plates and the template concentrations was linear according to Poisson probabilities in the range of 0.1-1,000 aM. These results demonstrate the amplification of single templates in the channels, and that a small number of templates could be quantified by counting the proportion of positive channels on the capillary-plates.  (+info)