Changes in G1-phase populations in human glioblastoma and neuroblastoma cell lines influence p66/Be neutron-induced micronucleus yield

Some photon resistant tumours are sensitive to neutrons but no predictive methods exist which could identify such tumours. In a recent study addressing this clinically important issue, we demonstrated that relative biologic effectiveness (RBE) values for p(66)/Be neutrons estimated from micronucleus (MN) data correlate positively with RBE values obtained from conventional clonogenic survival data. However, not all photon-resistant cell lines showed high RBE values when the MN endpoint was used. Now, we examine how the functional status of the p53 tumour suppressor gene and radiation-induced changes in cell cycle phase populations may contribute to this discrepancy. No significant association was established between p53 status and MN yield for both photon and neutron irradiation. The data demonstrated that neutron-, but not photon-, induced MN yield is dependent on the intrinsic ability of cells to activate a G1-phase arrest. In cell lines of comparable photon sensitivity, those showing more extensive depletion of the G1 population express significantly more micronuclei per unit dose of neutrons. These results suggest that differences in cell cycle kinetics, and not the p53 status, may constitute an important factor in damage induction by high linear energy transfer (LET) irradiation and need to be considered when radiation toxicity in clinical radiobiology or radiation protection is assessed using damage endpoints.     

Design for a binary synapse

The mammalian rod transfers a binary signal, the capture of 0 or 1 photon. In this issue of Neuron, Sampath and Rieke show in mouse that the rod's tonic exocytosis in darkness completely saturates a G protein cascade to close nearly all postsynaptic channels. A full-sized photon event supresses exocytosis sufficiently to allow approximately 30 postsynaptic channels to open simultaneously. Thus, the synapse behaves like a digital gate, whose hallmark is reliability and resistance to noise.     

The photon counting histogram in fluorescence fluctuation spectroscopy.

Fluorescence correlation spectroscopy (FCS) is generally used to obtain information about the number of fluorescent particles in a small volume and the diffusion coefficient from the autocorrelation function of the fluorescence signal. Here we demonstrate that photon counting histogram (PCH) analysis constitutes a novel tool for extracting quantities from fluorescence fluctuation data, i.e., the measured photon counts per molecule and the average number of molecules within the observation volume. The photon counting histogram of fluorescence fluctuation experiments, in which few molecules are present in the excitation volume, exhibits a super-Poissonian behavior. The additional broadening of the PCH compared to a Poisson distribution is due to fluorescence intensity fluctuations. For diffusing particles these intensity fluctuations are caused by an inhomogeneous excitation profile and the fluctuations in the number of particles in the observation volume. The quantitative relationship between the detected photon counts and the fluorescence intensity reaching the detector is given by Mandel's formula. Based on this equation and considering the fluorescence intensity distribution in the two-photon excitation volume, a theoretical expression for the PCH as a function of the number of molecules in the excitation volume is derived. For a single molecular species two parameters are sufficient to characterize the histogram completely, namely the average number of molecules within the observation volume and the detected photon counts per molecule per sampling time epsilon. The PCH for multiple molecular species, on the other hand, is generated by successively convoluting the photon counting distribution of each species with the others. The influence of the excitation profile upon the photon counting statistics for two relevant point spread functions (PSFs), the three-dimensional Gaussian PSF conventionally employed in confocal detection and the square of the Gaussian-Lorentzian PSF for two photon excitation, is explicitly treated. Measured photon counting distributions obtained with a two-photon excitation source agree, within experimental error with the theoretical PCHs calculated for the square of a Gaussian-Lorentzian beam profile. We demonstrate and discuss the influence of the average number of particles within the observation volume and the detected photon counts per molecule per sampling interval upon the super-Poissonian character of the photon counting distribution.     

Validation of Monte carlo Geant4 multithreading code for a 6 MV photon beam of varian linac on the grid computing

AimTo evaluate the computation time efficiency of the multithreaded code (G4Linac-MT) in the dosimetry application, using the high performance of the HPC-Marwan grid to determine with high accuracy the initial parameters of the 6 MV photon beam of Varian CLINAC 2100C.BackgroundThe difficulty of Monte Carlo methods is the long computation time, this is one of the disadvantages of the Monte Carlo methods.Materials and methodsCalculations are performed by the multithreaded code G4Linac-MT and Geant4.10.04.p02 using the HPC-Marwan computing grid to evaluate the computing speed for each code. The multithreaded version is tested in several CPUs to evaluate the computing speed according to the number of CPUs used. The results were compared to the measurements using different types of comparisons, TPR_20.10, penumbra, mean dose error and gamma index.ResultsThe results obtained for this work indicate a much higher computing time saving for the G4Linac-MT version compared to the Geant4.10.04 version, the computing time decreases with the number of CPUs used, can reach about 12 times if 64CPUs are used. After optimization of the initial electron beam parameters, the results of the dose simulations obtained for this work are in very good agreement with the experimental measurements with a mean dose error of up to 0.41% on the PDDs and 1.79% on the lateral dose.ConclusionsThe gain in computation time leads us to perform Monte Carlo simulations with a large number of events which gives a high accuracy of the dosimetry results obtained in this work.     

Explicit Spatiotemporal Simulation of Receptor-G Protein Coupling in Rod Cell Disk Membranes

Dim-light vision is mediated by retinal rod cells. Rhodopsin (R), a G-protein-coupled receptor, switches to its active form (R^?) in response to absorbing a single photon and activates multiple copies of the G-protein transducin (G) that trigger further downstream reactions of the phototransduction cascade. The classical assumption is that R and G are uniformly distributed and freely diffusing on disk membranes. Recent experimental findings have challenged this view by showing specific R architectures, including RG precomplexes, nonuniform R density, specific R arrangements, and immobile fractions of R. Here, we derive a physical model that describes the first steps of the photoactivation cascade in spatiotemporal detail and single-molecule resolution. The model was implemented in the ReaDDy software for particle-based reaction-diffusion simulations. Detailed kinetic in vitro experiments are used to parametrize the reaction rates and diffusion constants of R and G. Particle diffusion and G activation are then studied under different conditions of R-R interaction. It is found that the classical free-diffusion model is consistent with the available kinetic data. The existence of precomplexes between inactive R and G is only consistent with the data if these precomplexes are weak, with much larger dissociation rates than suggested elsewhere. Microarchitectures of R, such as dimer racks, would effectively immobilize R but have little impact on the diffusivity of G and on the overall amplification of the cascade at the level of the G protein.     

Bayesian estimation for species identification in single-molecule fluorescence microscopy

In this article we describe a recursive Bayesian estimator for the identification of diffusing fluorophores using photon arrival-time data from a single spectral channel. We present derivations for all relevant diffusion and fluorescence models, and we use simulated diffusion trajectories and photon streams to evaluate the estimator's performance. We consider simplified estimation schemes that bin the photon counts within time intervals of fixed duration, and show that they can perform well in realistic parameter regimes. The latter results indicate the feasibility of performing identification experiments in real time. It will be straightforward to generalize our approach for use in more complicated scenarios, e.g., with multiple spectral channels or fast photophysical dynamics.     

Photoperiodic time signals during twilight

Abstract. Although daylength has a major effect on flowering and several other aspects of plant development, the actual environmental time signals for the beginning and the end of day are obscure. An intensive spectroradiometric study was carried out in three contrasting environments: namely, unshaded sites, a mature oak woodland and a sugar beet crop. Spectral photon distributions were obtained describing numerous twilight phases and intervening photoperiods throughout the year. From each, absolute photon fluence rates, photon fluence rate ratios and phytochrome photoequilibria were calculated. Although substantial changes in spectral composition occurred during twilight, they were less capable of providing reliable and accurate time signals than the absolute fluence rate; this was especially apparent beneath the canopies. Thus, spectral changes are unlikely to be valuable in photoperiodic perception. The results are discussed in relation to the possible involvement of the known plant photoreceptors in photoperiodism.     

Photo-bleaching and photon saturation in flow cytometry.

In flow cytometry, small particles travel at a high speed through a bright light spot. The high light intensity at the point of measurement causes measurable photon saturation. This observation indicates that the rate at which individual dye molecules emit photons is close to the maximum emission rate. Despite the short exposure time, individual molecules may go through a few hundred excitation cycles while they are in the light beam. The absorbed light dose causes significant dye destruction. This article presents experimental procedures to determine the extent of photon saturation and photo-bleaching of dyes bound to cell nuclei in a flow cytometer. Measurements of Hoechst and propidium iodide bound to chromatin show that the amount of dye bleached per emitted photon is the same at low and high illumination intensities. This finding indicates that photon emission and dye destruction are both the result of the absorption of single excitation photons. The experimental observations allow rough estimates of the lifetime of the excited state and the lifetime of the molecule. The lifetime of the Hoechst 33258 bound to DNA is estimated to be 100 excitation-relaxation cycles. The average propidium iodide molecule lasts approximately 200 excitation-relaxation cycles. The theoretical considerations show that the optimal illumination conditions are different for bleaching and nonbleaching dyes. An optical arrangement for high precision measurements of bleaching dyes is presented.     

Activation of RGS9-1GTPase acceleration by its membrane anchor,R9AP

The GTPase-accelerating protein (GAP) complex RGS9-1.G beta(5) plays an important role in the kinetics of light responses by accelerating the GTP hydrolysis of G alpha(t) in vertebrate photoreceptors. Much, but not all, of this complex is tethered to disk membranes by the transmembrane protein R9AP. To determine the effect of the R9AP membrane complex on GAP activity, we purified recombinant R9AP and reconstituted it into lipid vesicles along with the photon receptor rhodopsin. Full-length RGS9-1.G beta(5) bound to R9AP-containing vesicles with high affinity (K(d) < 10 nm), but constructs lacking the DEP (dishevelled/EGL-10/pleckstrin) domain bound with much lower affinity, and binding of those lacking the entire N-terminal domain (i.e. the dishevelled/EGL-10/pleckstrin domain plus intervening domain) was not detectable. Formation of the membrane-bound complex with R9AP increased RGS9-1 GAP activity by a factor of 4. Vesicle titrations revealed that on the time scale of phototransduction, the entire reaction sequence from GTP uptake to GAP-catalyzed hydrolysis is a membrane-delimited process, and exchange of G alpha(t) between membrane surfaces is much slower than hydrolysis. Because in rod cells different pools exist of RGS9-1.G beta(5) that are either associated with R9AP or not, regulation of the association between R9AP and RGS9-1.G beta(5) represents a potential mechanism for the regulation of recovery kinetics.     

Fluorescence correlation spectroscopy with high count rate and low background: analysis of translational diffusion

An epi-illuminated microscope configuration for use in fluorescence correlation spectroscopy in bulk solutions has been analyzed. For determining the effective sample dimensions the spatial distribution of the molecule detection efficiency has been computed and conditions for achieving quasi-cylindrical sample shape have been derived. Model experiments on translational diffusion of rhodamine 6G have been carried out using strong focusing of the laser beam, small pinhole size and an avalanche photodiode in single photon counting mode as the detector. A considerable decrease in background light intensity and measurement time has been observed. The background light is 40 times weaker than the fluorescence signal from one molecule of Rh6G, and the correlation function with signal-to-noise ratio of 150 can be collected in 1 second. The effect of the shape of the sample volume on the autocorrelation function has been discussed. Correspondence to: R. Rigler     

Explicit Spatiotemporal Simulation of Receptor-G Protein Coupling in Rod Cell Disk Membranes

Dim-light vision is mediated by retinal rod cells. Rhodopsin (R), a G-protein-coupled receptor, switches to its active form (R^∗${\text{R}}^{\ast }$) in response to absorbing a single photon and activates multiple copies of the G-protein transducin (G) that trigger further downstream reactions of the phototransduction cascade. The classical assumption is that R and G are uniformly distributed and freely diffusing on disk membranes. Recent experimental findings have challenged this view by showing specific R architectures, including RG precomplexes, nonuniform R density, specific R arrangements, and immobile fractions of R. Here, we derive a physical model that describes the first steps of the photoactivation cascade in spatiotemporal detail and single-molecule resolution. The model was implemented in the ReaDDy software for particle-based reaction-diffusion simulations. Detailed kinetic in vitro experiments are used to parametrize the reaction rates and diffusion constants of R and G. Particle diffusion and G activation are then studied under different conditions of R-R interaction. It is found that the classical free-diffusion model is consistent with the available kinetic data. The existence of precomplexes between inactive R and G is only consistent with the data if these precomplexes are weak, with much larger dissociation rates than suggested elsewhere. Microarchitectures of R, such as dimer racks, would effectively immobilize R but have little impact on the diffusivity of G and on the overall amplification of the cascade at the level of the G protein.     

Quantum nature of photon signal emitted by Xanthoria parietina and its implications to biology

The properties of living systems are usually described in the semi-classical framework that makes phenomenological division of properties into four classes--matter, psyche, soft consciousness and hard consciousness. Quantum framework provides a scientific basis of this classification of properties. The scientific basis requires the existence of macroscopic quantum entity entangled with quantum photon field of a living system. Every living system emits a photon signal with features indicating its quantum nature. Quantum nature of the signal emitted by a sample of X. parietina is confirmed by analysing photo count distributions obtained in 20000 measurements of photon number in contiguous bins of sizes of 50, 100, 200, 300 and 500 ms. The measurements use a broadband detector sensitive in 300-800 nm range (Photo count distributions of background noise and observed signal are measured similarly. These measurements background noise corrected squeezed state parameters of the signal. The parameters are signal strength expressed in counts per bin, r = 0.06, theta = 2.76 and phi = 0.64. The parameters correctly reproduce photo count distribution of any bin size in 50 ms-6 s range. The reproduction of photo count distributions is a credible evidence of spontaneous emission of photon signal in a quantum squeezed state for macroscopic time by the sample. The evidence is extrapolated to other living systems emitting similar photon signals. It is suggested that every living system is associated with a photon field in squeezed state. The suggestion has far reaching implications to biology and provides two ways of observing and manipulating a living system--either through matter or field or a combination of the two. Some implications and possible scenarios are elaborated.     

Photon Statistics of a Hybrid Quantum Dot-Metal Nanoparticle Cluster

A theoretical study of photon statistics of an optically driven quantum dot located near a metal nanoparticle cluster (composed of one or two nanoparticles) is presented. Considering the system in the weak Rabi frequency regime, an analytical formula for anti-bunching time is derived. Using a photon Green’s function method based on the exact quantization of electromagnetic field in a dissipative medium, the dependence of the anti-bunching time on the geometrical parameters (quantum dot radius and quantum dot distance from the metal nanoparticle) is studied. The results show that these geometrical parameters have pronounced impacts on the photon statistics. Furthermore, our findings reveal that the quantum dot dipole orientation possesses an important role in the quantum dot photon emission.     

Measuring the folding transition time of single RNA molecules

We describe a new, time-apertured photon correlation method for resolving the transition time between two states of RNA in folding--i.e., the time of the transition between states rather than the time spent in each state. Single molecule fluorescence resonance energy transfer and fluorescence correlation spectroscopy are used to obtain these measurements. Individual RNA molecules are labeled with fluorophores such as Cy3 and Cy5. Those molecules are then immobilized on a surface and observed for many seconds during which time the molecules spontaneously switch between two conformational states with different levels of flourescence resonance energy transfer efficiency. Single photons are counted from each fluorophore and cross correlated in a small window around a transition. The average of over 1000 cross correlations can be fit to a polynomial, which can determine transition times as short as the average photon emission interval. We applied the method to the P4-P6 domain of the Tetrahymena group I self-splicing intron to yield the folding transition time of 240 micros. The unfolding time is found to be too short to measure with this method.     

Endogenous enzyme reactions closely related to photon emission in the plant defense response

Lipoxygenase (LOX) and peroxidase (POD) reactions, which are involved in the production of reactive oxygen and radical species, are shown to be associated with ultraweak photon emission in plant defense mechanisms. These enzyme reactions induced high-level ultraweak photon emission in an in vitro reaction system. The application of LOX to sweet potato slices caused photon emission directly in plants. LOX substrate promoted photon emission in chitosan-treated sweet potato, and LOX inhibitor markedly suppressed this emission. Therefore, a LOX-related pathway, including LOX and other downstream reactions, is principally associated with photon emission in plant defense mechanisms.     

Differences in the photoacclimation and photoprotection exhibited by two species of the ciguatera causing dinoflagellate genus,Gambierdiscus

In culture, Gambierdiscus spp. have been shown to prefer irradiances that are relatively low (≤250 μmol photons m⁻² s⁻¹) versus those to which they are frequently exposed to in their natural environment (>500 μmol photons m⁻² s⁻¹). Although several behavioral strategies for coping with such irradiances have been suggested, it is unclear as to how these dinoflagellates do so on a physiological level. More specifically, how do long term exposures (30 days) affect cell size and cellular chlorophyll content, and what is the photosynthetic response to short term, high irradiance exposures (up to 1464 μmol photons m⁻² s⁻¹)? The results of this study reveal that cell size and chlorophyll content exhibited by G. carolinianus increased with acclimation to increasing photon flux density. Additionally, both G. carolinianus and G. silvae exhibited reduced photosynthetic efficiency when acclimated to increased photon flux density. Photosynthetic yield exhibited by G. silvae was greater than that for G. carolinianus across all acclimation irradiances. Although such differences were evident, both G. carolinianus and G. silvae appear to have adequate biochemical mechanisms to withstand exposure to irradiances exceeding 250 μmol photons m⁻² s⁻¹ for at least short periods of time following acclimation to irradiances of up to 150 μmol photons m⁻² s⁻¹.     

Growth,photosynthesis and agar in wild-type strains of Gracilaria verrucosa and G. conferta (Gracilariales,Rhodophyta), as a strain selection experiment

The local species Gracilaria conferta and the foreign G. verrucosa were grown together under a wide range of photon flux density and temperature conditions. Gracilaria verrucosa showed a higher growth rate, especially under low temperatures, and higher photosynthetic performances as well as higher ribulose-1,5-bisphosphate carboxylase activity as compared with G. conferta. Gracilaria verrucosa also showed a better quality and yield of agar, suggesting that this species could be more suitable than G. conferta for outdoor cultivation in Israel and may improve winter growth in ponds. Growth rate and agar quality (gel strength) were rated as the most suitable characteristics influencing the preference of strains for outdoor cultivation.     

Assessment of ionization chamber correction factors in photon beams using a time saving strategy with PENELOPE code

The purpose of this study was to investigate Monte Carlo-based perturbation and beam quality correction factors for ionization chambers in photon beams using a saving time strategy with PENELOPE code. Simulations for calculating absorbed doses to water using full spectra of photon beams impinging the whole water phantom and those using a phase-space file previously stored around the point of interest were performed and compared. The widely used NE2571 ionization chamber was modeled with PENELOPE using data from the literature in order to calculate absorbed doses to the air cavity of the chamber. Absorbed doses to water at reference depth were also calculated for providing the perturbation and beam quality correction factors for that chamber in high energy photon beams. Results obtained in this study show that simulations with phase-space files appropriately stored can be up to ten times shorter than using a full spectrum of photon beams in the input-file. Values of k_Q and its components for the NE2571 ionization chamber showed good agreement with published values in the literature and are provided with typical statistical uncertainties of 0.2%. Comparisons to k_Q values published in current dosimetry protocols such as the AAPM TG-51 and IAEA TRS-398 showed maximum percentage differences of 0.1% and 0.6% respectively. The proposed strategy presented a significant efficiency gain and can be applied for a variety of ionization chambers and clinical photon beams.     

Use of dynamic light scattering to determine second virial coefficient in a semidilute concentration regime

The present work discusses an alternative procedure to obtain static light scattering (SLS) parameters in a dilute and semidilute concentration regime from a dynamic light scattering (DLS) instrument that uses an avalanche photodiode (APD) for recording the scattered intensity signal. An APD enables one to perform both SLS and DLS measurements by photon counting and photon correlation, respectively. However, due to the associated recovery time, the APDs are susceptible to saturation (above 1000 kcps), which may limit the measurements in systems that scatter too much light. We propose an alternative way of obtaining the SLS parameters with instruments that use APD for recording signal intensities.