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Query: UNIPROT:P06889 (Mol)
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Alveolar macrophages play a critical role in silica-induced lung fibrosis. Silica exposure induces tumor necrosis factor (TNF)-alpha release and nuclear factor (NF)-kappaB activation, and apoptotic mechanisms have been implicated in silica-induced pathogenesis. To characterize potential relationships between these signaling events, we studied their induction in two murine macrophage cell lines. The RAW 264.7 macrophage cell line was more sensitive, and the IC-21 macrophage cell line more tolerant to silica exposure (0.2 or 1 mg/ml for 6 h) as evidenced by significantly higher apoptotic responses in RAW 264.7 (P < 0.05). RAW 264.7 macrophages exhibited enhanced TNF-alpha production and NF-kappaB activation in response to silica, whereas IC-21 macrophages did not produce TNF-alpha in response to silica and did not induce NF-kappaB nuclear binding. Inhibition of NF-kappaB in RAW 264.7 cells with BAY11-7082 significantly increased apoptosis while inhibiting TNF-alpha release. In addition, TNF-alpha and NF-kappaB activation, but not apoptosis, were induced by lipopolysaccharide (LPS) in both cell lines, and NF-kappaB inhibition reduced LPS-induced TNF-alpha release. These data suggest that TNF-alpha induction is dependent on NF-kappaB activation in both cell lines. However, silica can induce apoptosis in murine macrophages, independently of TNF-alpha stimulation, as in IC-21 macrophages. Furthermore, NF-kappaB activation in macrophages may play dual roles, both pro- and antiapoptotic during silica injury.
Am J Respir Cell Mol Biol 2002 Jul
PMID:Silica-induced apoptosis in murine macrophage: involvement of tumor necrosis factor-alpha and nuclear factor-kappaB activation. 1209 Dec 51

The determination of the dose delivered to the body during Total Body Irradiation (TBI) is not easy, as direct measurements are impossible. This article presents the intention to develop a systematic and simple method for absorbed dose determination in(60)Co TBI using mid plane dose factors (MDF) and external measurements, i.e. entrance and exit dose readings by semiconductor detectors. In order to perform the radiation field analysis prior to TBI treatment, a special silicon n-type detector with increased sensitivity (1200 nC/Gy) was used. The dependence of the calibration factor of this detector exposed to different dose rates in standard and TBI conditions was investigated. A theoretical model of anthropomorphic phantoms of cylindrical ellipsoid shape was established. The software made it possible to generalize the applicability of TBI dosimetry to any individual case of real patient data. A quality assurance analysis of dosimetric results of 350 patients, who underwent TBI during a 17-year period, was performed.
Cell Mol Biol Lett 2002
PMID:A dosimetric method of total body irradiation. 1209 80

The Raman spectra (3200-30 cm(-1)) of liquid and solid, and infrared spectra of gaseous and solid chloromethyl silyl dichloride, ClCH2SiHCl2, have been recorded. Variable temperature (-105 to -150 degrees C) studies of the infrared spectra of the sample dissolved in liquid krypton have been carried out. From these data, the enthalpy difference was determined to be 363 +/- 40 cm(-1) (4.34 +/- 0.48 kJ mol(-1)), with the more stable form being the gauche conformer, which is consistent with the prediction from ab initio calculations at both the Hartree-Fock level and with full electron correlation by the perturbation method to second order. It is estimated that 92% of the sample is in the gauche form at ambient temperature. A complete vibrational assignment is proposed for the gauche conformer and several of fundamentals of the trans conformer based on infrared band contours, relative intensities, depolarization values, and group frequencies, which is supported by normal coordinate calculations utilizing the force constants from the ab initio MP2/6-31G(d) calculations. The r0 SiH bond distances of 1.476 and 1.472 A have been obtained for the trans and gauche conformers, respectively, from the silicon-hydrogen stretching frequencies. The optimized geometries have also been obtained from ab initio calculations utilizing several different basis sets with full electron correlation by the perturbation method up to MP2/6-311 + G(2d,2p). The results are discussed and compared to some corresponding results for several related molecules.
Spectrochim Acta A Mol Biomol Spectrosc 2002 Jul
PMID:Spectra and structure of silicon-containing compounds. XXX. Raman and infrared spectra, conformational stability, vibrational assignment of chloromethyl silyl dichloride. 1216 84

Microstructured silicon wafers were employed as miniaturized solid-phase reaction vessels as well as miniaturized micro titer plates. Employing piezoelectric drop-on-demand liquid jets, a combinatorial library of 256 Peptides was synthesized on single beads. The synthesis protocol was associated to the location in the silicon nano-well arrangement. Products were photolytically cleaved in the same well that was used for synthesis and subsequently interrogated for thrombin inhibition in a homogeneous competition assay. The assay procedure was based on drop-on-demand liquid delivery and laser induced fluorescence imaging. The novel format proved useful for the integration of both synthesis and screening into one platform, a prerequisite for an iterative, evolutionary approach towards drug discovery.
Mol Divers 2000
PMID:Single bead parallel synthesis and screening. 1219 67

We analyzed the role of diffusion and cell size on the flux control properties of the glucose-PTS of Escherichia coli, in silicon cells under various metabolic conditions. To our surprise, the influence of the concentration of phosphoryl-donor PEP on the distribution of control was small. We found for cells of bacterial size that PTS-flux control was mainly located in processes taking place in the membrane and that diffusion hardly controlled the flux (< 2.8 %). Enlargement of the cells shifted the control from membrane to cytoplasm and from process rates to diffusion rates, the latter now having a total control of about 38 %. In the presence of glucose, nearly all diffusion flux control resided in the component that links the cytoplasmic processes to those in the membrane.
Mol Biol Rep 2002
PMID:Flux control of the bacterial phosphoenolpyruvate:glucose phosphotransferase system and the effect of diffusion. 1224 Oct 59

Several methods of transformation are currently available for delivering exogenous DNA to plant cells. Agrobacterium-mediated transformation, microprojectile bombardment and direct protoplast transformation are routinely used today. However, each of them has certain disadvantages, which led to research into the development of novel alternative systems such as infiltration, electroporation of cells and tissues, electrophoresis of embryos, microinjection, pollen-tube pathway, silicon carbide- and liposome-mediated transformation. The low efficiency of transformation is considered to be the main reason for the limited popularity of the alternative transformation methods, other than infiltration and silicon carbide-mediated transformation, which seem to be the most promising ones for practice.
Cell Mol Biol Lett 2002
PMID:Alternative methods of plant transformation--a short review. 1237 68

Signaling networks are complex both in terms of the chemical and biophysical events that underlie them, and in the sheer number of interactions. Computer models are powerful tools to deal with both aspects of complexity, but their utility goes beyond simply replicating signaling events in silicon. Their great advantage is as a tool to understanding. The completeness of the description demanded by computer models highlights gaps in knowledge. The quantitative description in models facilitates a mapping between different kinds of analysis methods for complex systems. Systems analysis methods can highlight stable states of signaling networks and describe the transitions between them. Modeling also reveals functional similarities between signaling network properties and other well-understood systems such as electronic devices and neural networks. These suggest various metaphors as a tool to understanding. Based on such descriptions, it is possible to regard signaling networks as systems that decode complex inputs in time, space and chemistry into combinatorial output patterns of signaling activity. This would provide a natural interface to the combinatorial input patterns required by genetic circuits. Thus, a combination of computer modeling methods to capture the complexity and details, and useful abstractions revealed by these models, is necessary to achieve both rigorous description as well as human understanding.
Prog Biophys Mol Biol 2003 Jan
PMID:Understanding complex signaling networks through models and metaphors. 1247 69

The interaction of cyclohexapeptides c(X(1)(1)K(2)X(2)(3)K(4)X(3)(5)K(6)) in water with hydrolysed silicon surfaces were studied by attenuated total reflection Fourier transform infrared (ATR FTIR) spectroscopy and by force field calculations. The band sequences (1800-1500 cm(-1)) for dissolved and adsorbed cyclohexapeptides were recorded and compared with those obtained after flushing with distilled water in order to eliminate the background signal of the peptides in solution. Band analyses and principal component analyses were carried out for the characteristic peptide vibrations in order to evaluate the spectra. In addition, force field calculations were performed to study the binding energies to the surface and to illustrate the possible structures of the cyclohexapeptides. The positively charged lysine side chains of the cyclohexapeptides interact with the OH groups of the surface, as indicated by band shifts. This also was verified by the force field calculations. The bonding stability increases with the number of interacting sites (lysine side chains and other peptide residues) to the surface. These sites are determined by structure and polarity of the cyclohexapeptides.
Spectrochim Acta A Mol Biomol Spectrosc 2003 Mar 01
PMID:Small interacting peptides. Part I. Interaction of cyclohexapeptides with an unspecific SiOH surface: comparison of infrared investigations and force field calculations. 1260 33

Infrared spectra (3500-50 cm(-1)) of gaseous and solid, and Raman spectrum (3500-30 cm(-1)) of liquid vinyldifluorosilane, CH(2)z.dbnd6;CHSiF(2)H, are reported. Both the cis and gauche rotamers have been identified in the fluid phases. From temperature-dependent FT-infrared spectra of krypton solutions, it is shown that the cis conformer is more stable than the gauche form by 119+/-12 cm(-1) (1.42+/-0.14 kJ mol(-1)). At ambient temperature there is 53+/-2% of the gauche conformer present. Complete vibrational assignments are provided for the cis conformer and several modes are identified for the gauche form. Harmonic force constants, fundamental frequencies, infrared intensities, and Raman activities have been obtained from MP2/6-31G(d) calculations with full electron correlation. The optimized geometries and conformational stabilities have also been obtained from ab initio MP2/6-31G(d), MP2/6-311+G(d,p), and MP2/6-311+G(2d,2p) calculations with full electron correlation as well as from density functional theory calculations (DFT) by the B3LYP method. The SiH bond distances (r(0)) of 1.472 and 1.471 A have been obtained for the cis and gauche conformers, respectively, from the silicon-hydrogen stretching frequencies. These results are compared to the corresponding quantities of the corresponding carbon analogue as well as with some similar molecules.
Spectrochim Acta A Mol Biomol Spectrosc 2003 Jul
PMID:Spectra and structure of silicon-containing compounds. Part XXXVIII: Infrared and Raman spectra, vibrational assignment, conformational stability, and ab initio calculations of vinyldifluorosilane. 1278 63

Fluorescent semiconductor nanocrystals (quantum dots [QDs]) are hypothesized to be excellent contrast agents for biomedical assays and imaging. A unique property of QDs is that their absorbance increases with increasing separation between excitation and emission wavelengths. Much of the enthusiasm for using QDs in vivo stems from this property, since photon yield should be proportional to the integral of the broadband absorption. In this study, we demonstrate that tissue scatter and absorbance can sometimes offset increasing QD absorption at bluer wavelengths, and counteract this potential advantage. By using a previously validated mathematical model, we explored the effects of tissue absorbance, tissue scatter, wavelength dependence of the scatter, water-to-hemoglobin ratio, and tissue thickness on QD performance. We conclude that when embedded in biological fluids and tissues, QD excitation wavelengths will often be quite constrained, and that excitation and emission wavelengths should be selected carefully based on the particular application. Based on our results, we produced near-infrared QDs optimized for imaging surface vasculature with white light excitation and a silicon CCD camera, and used them to image the coronary vasculature in vivo. Taken together, our data should prove useful in designing fluorescent QD contrast agents optimized for specific biomedical applications.
Mol Imaging 2003 Jan
PMID:Selection of quantum dot wavelengths for biomedical assays and imaging. 1292 37


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