Messenger RNA half-life measurements in mammalian cells.

The recognition of the importance of mRNA turnover in regulating eukaryotic gene expression has mandated the development of reliable, rigorous, and "user-friendly" methods to accurately measure changes in mRNA stability in mammalian cells. Frequently, mRNA stability is studied indirectly by analyzing the steady-state level of mRNA in the cytoplasm; in this case, changes in mRNA abundance are assumed to reflect only mRNA degradation, an assumption that is not always correct. Although direct measurements of mRNA decay rate can be performed with kinetic labeling techniques and transcriptional inhibitors, these techniques often introduce significant changes in cell physiology. Furthermore, many critical mechanistic issues as to deadenylation kinetics, decay intermediates, and precursor-product relationships cannot be readily addressed by these methods. In light of these concerns, we have previously reported transcriptional pulsing methods based on the c-fos serum-inducible promoter and the tetracycline-regulated (Tet-off) promoter systems to better explain mechanisms of mRNA turnover in mammalian cells. In this chapter, we describe and discuss in detail different protocols that use these two transcriptional pulsing methods. The information described here also provides guidelines to help develop optimal protocols for studying mammalian mRNA turnover in different cell types under a wide range of physiologic conditions.

Development of light-responsive porous polycarbonate membranes for controlled caffeine delivery

For controlled caffeine release, light-responsive membranes were developed. It was possible to produce membranes that reduced their caffeine permeability resistance by about 97% when irradiated with UV-light compared to measurements at daylight. This was achieved by grafting polymers possessing photochromic units onto track-edged polycarbonate membranes. Covalently linked coatings on porous polycarbonate membranes were obtained by plasma activation of the membrane surface followed by plasma-induced graft polymerization. Copolymerization of spiro-compounds during the coating process as well as postmodification of preformed coatings with spiropyran resulted in photochromic membranes. For the copolymerization process, the synthesis of five photochromic methacrylic and acrylic spiropyrans and spirooxazines was successfully performed. Additionally, a spiropyran with carboxylic acid functionality was synthesized for the postmodification process. This enabled us to postmodify polymeric materials containing alcohol or amine groups to obtain photochromic materials. UV-irradiation of these light-responsive membranes resulted in a strong colouration of the membrane, in a reduction of surface tension, which resulted in a decreased caffeine permeability resistance. The membranes were characterized using XPS for the elemental composition of the coating, contact angle measurements for the surface tension, solid-state UV/VIS measurements for the determination of the kinetic and stability properties, and two-photon microscopy for the localisation of the photochromic substance in the porous membrane.

Comparison of globules prepared from high dilutions of various starting materials by ultraviolet light spectroscopy

Background: High and ultra-high dilutions of various starting materials, e.g. copper sulfate, Hypericum perforatum and sulfur, showed significant differences in ultraviolet light (UV) transmission from controls and amongst different dilution levels [1,2]. Verum and placebo globules of Aconitum napellus 30c or calcium carbonate/quercus e cortice 6x from the same packs as used in previous clinical trials and dissolved in water could be distinguished by UV spectroscopy [3]. However, it was unclear whether the differences in UV absorbance originated from specific characteristics of the starting materials, from differences in the production of verum and placebo globules, and/or other unknown interference factors. Aims: The aim of this study was to investigate whether globules produced with high and ultra-high dilutions (6x, 12x, 30c, 200c, 200CF (centesimal discontinuous fluxion), 10,000CF) of various starting materials (Aconitum napellus, Atropa belladonna, phosphorus, sulfur, Apis mellifica, quartz) could be distinguished by UV spectroscopy. Methodology: The globules were specially produced for this study by Spagyros AG (Gümligen, Switzerland) and differed only in the starting materials of the dilutions (but not in the batch of globules or ethanol used). Globules were dissolved in water at 10 mg/ml, in quadruplicates, approximately 22 h prior to the measurements. Absorbance of the samples in the UV range (from 190 to 340 nm) was measured in a randomized order with a Shimadzu double beam UV-1800 spectrophotometer equipped with an auto sampler. Samples of each starting material were prepared and measured on 5 independent days. The daily variations of the spectrophotometer as well as the drift during the measurements were corrected for. The average absorbance from 200 to 340 nm was compared among various starting materials within equal dilution levels using a Kruskal-Wallis test. Results: Statistically significant differences were found among 30c (Figure 1), 200c and 200CF dilutions of the various starting materials. No differences were found among 6x, 12x and 10,000CF dilutions. Conclusions: Globules prepared from high dilutions of various starting materials may show significantly different UV absorbance when dissolved in water. References [1] Wolf U, Wolf M, Heusser P, Thurneysen A, Baumgartner S. Homeopathic preparations of quartz, sulfur and copper sulfate assessed by UV-spectroscopy. Evid Based Complement Alternat Med. 2011;2011:692798. [2] Klein SD, Sandig A, Baumgartner S, Wolf U. Differences in median ultraviolet light transmissions of serial homeopathic dilutions of copper sulfate, Hypericum perforatum, and sulfur. Evid Based Complement Alternat Med. 2013;2013:370609. [3] Klein SD, Wolf U. Investigating homeopathic verum and placebo globules with ultraviolet spectroscopy. Forsch Komplementmed. 2013, accepted.

Quantitative analysis of fluorescence lifetime measurements of the macula using the fluorescence lifetime imaging ophthalmoscope in healthy subjects.

PURPOSE Fundus autofluorescence (FAF) cannot only be characterized by the intensity or the emission spectrum, but also by its lifetime. As the lifetime of a fluorescent molecule is sensitive to its local microenvironment, this technique may provide more information than fundus autofluorescence imaging. We report here the characteristics and repeatability of FAF lifetime measurements of the human macula using a new fluorescence lifetime imaging ophthalmoscope (FLIO). METHODS A total of 31 healthy phakic subjects were included in this study with an age range from 22 to 61 years. For image acquisition, a fluorescence lifetime ophthalmoscope based on a Heidelberg Engineering Spectralis system was used. Fluorescence lifetime maps of the retina were recorded in a short- (498-560 nm) and a long- (560-720 nm) spectral channel. For quantification of fluorescence lifetimes a standard ETDRS grid was used. RESULTS Mean fluorescence lifetimes were shortest in the fovea, with 208 picoseconds for the short-spectral channel and 239 picoseconds for the long-spectral channel, respectively. Fluorescence lifetimes increased from the central area to the outer ring of the ETDRS grid. The test-retest reliability of FLIO was very high for all ETDRS areas (Spearman's ρ = 0.80 for the short- and 0.97 for the long-spectral channel, P < 0.0001). Fluorescence lifetimes increased with age. CONCLUSIONS The FLIO allows reproducible measurements of fluorescence lifetimes of the macula in healthy subjects. By using a custom-built software, we were able to quantify fluorescence lifetimes within the ETDRS grid. Establishing a clinically accessible standard against which to measure FAF lifetimes within the retina is a prerequisite for future studies in retinal disease.

Pion emission from the T2K replica target: method, results and application

The T2K long-baseline neutrino oscillation experiment in Japan needs precise predictions of the initial neutrino flux. The highest precision can be reached based on detailed measurements of hadron emission from the same target as used by T2K exposed to a proton beam of the same kinetic energy of 30 GeV. The corresponding data were recorded in 2007-2010 by the NA61/SHINE experiment at the CERN SPS using a replica of the T2K graphite target. In this paper details of the experiment, data taking, data analysis method and results from the 2007 pilot run are presented. Furthermore, the application of the NA61/SHINE measurements to the predictions of the T2K initial neutrino flux is described and discussed.

The Deep Blue Color of HD 189733b: Albedo Measurements with Hubble Space Telescope/Space Telescope Imaging Spectrograph at Visible Wavelengths

We present a secondary eclipse observation for the hot Jupiter HD 189733b across the wavelength range 290-570 nm made using the Space Telescope Imaging Spectrograph on the Hubble Space Telescope. We measure geometric albedos of Ag = 0.40 ± 0.12 across 290-450 nm and Ag < 0.12 across 450-570 nm at 1σ confidence. The albedo decrease toward longer wavelengths is also apparent when using six wavelength bins over the same wavelength range. This can be interpreted as evidence for optically thick reflective clouds on the dayside hemisphere with sodium absorption suppressing the scattered light signal beyond ~450 nm. Our best-fit albedo values imply that HD 189733b would appear a deep blue color at visible wavelengths.

Energy and charge transfer dynamics in DNA based light harvesting antennae

DNA can serve as a versatile scaffold for chromophore assemblies. For example, light-harvesting antennae have been realized by incorporating phenanthrene and pyrene building blocks into DNA strands. It was shown that by exciting at 320 nm (absorption of phenanthrene), an emission at 450 nm is observed which corresponds to a phenanthrene-pyrene exciplex. The more phenanthrenes are added into the DNA duplex, the higher is the fluorescence intensity with no significant change in quantum yield. This shows that phenanthrene acts as a donor and efficiently transfers the excitation energy to the pyrene. Up to now, the mechanism of this energy transfer and exciplex formation is not known. Therefore, we first aim at studying the photo-cycle of such DNA assemblies through transient absorption spectroscopy. Based on the results, we will explore ways to manipulate the energy transfer by application of intense THz fields. Ground as well as excited state Stark effect dynamics will be investigated.

Thermal dependence of luminescence lifetimes and radioluminescence in quartz

During time-resolved optical stimulation experiments (TR-OSL), one uses short light pulses to separate the stimulation and emission of luminescence in time. Experimental TR-OSL results show that the luminescence lifetime in quartz of sedimentary origin is independent of annealing temperature below 500 °C, but decreases monotonically thereafter. These results have been interpreted previously empirically on the basis of the existence of two separate luminescence centers LH and LL in quartz, each with its own distinct luminescence lifetime. Additional experimental evidence also supports the presence of a non-luminescent hole reservoir R, which plays a critical role in the predose effect in this material. This paper extends a recently published analytical model for thermal quenching in quartz, to include the two luminescence centers LH and LL, as well as the hole reservoir R. The new extended model involves localized electronic transitions between energy states within the two luminescence centers, and is described by a system of differential equations based on the Mott–Seitz mechanism of thermal quenching. It is shown that by using simplifying physical assumptions, one can obtain analytical solutions for the intensity of the light during a TR-OSL experiment carried out with previously annealed samples. These analytical expressions are found to be in good agreement with the numerical solutions of the equations. The results from the model are shown to be in quantitative agreement with published experimental data for commercially available quartz samples. Specifically the model describes the variation of the luminescence lifetimes with (a) annealing temperatures between room temperature and 900 °C, and (b) with stimulation temperatures between 20 and 200 °C. This paper also reports new radioluminescence (RL) measurements carried out using the same commercially available quartz samples. Gaussian deconvolution of the RL emission spectra was carried out using a total of seven emission bands between 1.5 and 4.5 eV, and the behavior of these bands was examined as a function of the annealing temperature. An emission band at ∼3.44 eV (360 nm) was found to be strongly enhanced when the annealing temperature was increased to 500 °C, and this band underwent a significant reduction in intensity with further increase in temperature. Furthermore, a new emission band at ∼3.73 eV (330 nm) became apparent for annealing temperatures in the range 600–700 °C. These new experimental results are discussed within the context of the model presented in this paper.

Yellow laser light generation by frequency doubling of the output from a master oscillator fiber power amplifier system

We present a power-scalable approach for yellow laser-light generation based on standard Ytterbium (Yb) doped fibers. To force the cavity to lase at 1154 nm, far above the gain-maximum, measures must be taken to fulfill lasing condition and to suppress competing amplified spontaneous emission (ASE) in the high-gain region. To prove the principle we built a fiber-laser cavity and a fiber-amplifier both at 1154 nm. In between cavity and amplifier we suppressed the ASE by 70 dB using a fiber Bragg grating (FBG) based filter. Finally we demonstrated efficient single pass frequency doubling to 577 nm with a periodically poled lithium niobate crystal (PPLN). With our linearly polarized 1154 nm master oscillator power fiber amplifier (MOFA) system we achieved slope efficiencies of more than 15 % inside the cavity and 24 % with the fiber-amplifier. The frequency doubling followed the predicted optimal efficiency achievable with a PPLN crystal. So far we generated 1.5 W at 1154nm and 90 mW at 577 nm. Our MOFA approach for generation of 1154 nm laser radiation is power-scalable by using multi-stage amplifiers and large mode-area fibers and is therefore very promising for building a high power yellow laser-light source of several tens of Watt.

MEMLS3&a: Microwave Emission Model of Layered Snowpacks adapted to include backscattering

The Microwave Emission Model of Layered Snowpacks (MEMLS) was originally developed for microwave emissions of snowpacks in the frequency range 5–100 GHz. It is based on six-flux theory to describe radiative transfer in snow including absorption, multiple volume scattering, radiation trapping due to internal reflection and a combination of coherent and incoherent superposition of reflections between horizontal layer interfaces. Here we introduce MEMLS3&a, an extension of MEMLS, which includes a backscatter model for active microwave remote sensing of snow. The reflectivity is decomposed into diffuse and specular components. Slight undulations of the snow surface are taken into account. The treatment of like- and cross-polarization is accomplished by an empirical splitting parameter q. MEMLS3&a (as well as MEMLS) is set up in a way that snow input parameters can be derived by objective measurement methods which avoid fitting procedures of the scattering efficiency of snow, required by several other models. For the validation of the model we have used a combination of active and passive measurements from the NoSREx (Nordic Snow Radar Experiment) campaign in Sodankylä, Finland. We find a reasonable agreement between the measurements and simulations, subject to uncertainties in hitherto unmeasured input parameters of the backscatter model. The model is written in Matlab and the code is publicly available for download through the following website: http://www.iapmw.unibe.ch/research/projects/snowtools/memls.html.

Diagnostic performance of a new red light LED device for approximal caries detection

The aim of this study was to test a newly developed LED-based fluorescence device for approximal caries detection in vitro. We assembled 120 extracted molars without frank cavitations or fillings pairwise in order to create contact areas. The teeth were independently assessed by two examiners using visual caries detection (International Caries Detection and Assessment System, ICDAS), bitewing radiography (BW), laser fluorescence (LFpen), and LED fluorescence (Midwest Caries I.D., MW). The measurements were repeated at least 1 week later. The diagnostic performance was calculated with Bayesian analyses. Post-test probabilities were calculated in order to judge the diagnostic performance of combined methods. Reliability analyses were performed using kappa statistics for nominal data and intraclass correlation (ICC) for absolute data. Histology served as the gold standard. Sensitivities/specificities at the enamel threshold were 0.33/0.84 for ICDAS, 0.23/0.86 for BW, 0.47/0.78 for LFpen, and 0.32/0.87 for MW. Sensitivities/specificities at the dentine threshold were 0.04/0.89 for ICDAS, 0.27/0.94 for BW, 0.39/0.84 for LFpen, and 0.07/0.96 for MW. Reliability data were fair to moderate for MW and good for BW and LFpen. The combination of ICDAS and radiography yielded the best diagnostic performance (post-test probability of 0.73 at the dentine threshold). The newly developed LED device is not able to be recommended for approximal caries detection. There might be too much signal loss during signal transduction from the occlusal aspect to the proximal lesion site and the reverse.