Computerized method for nonrigid MR-to-PET breast-image registration.

We have developed and tested a new simple computerized finite element method (FEM) approach to MR-to-PET nonrigid breast-image registration. The method requires five-nine fiducial skin markers (FSMs) visible in MRI and PET that need to be located in the same spots on the breast and two on the flanks during both scans. Patients need to be similarly positioned prone during MRI and PET scans. This is accomplished by means of a low gamma-ray attenuation breast coil replica used as the breast support during the PET scan. We demonstrate that, under such conditions, the observed FSM displacement vectors between MR and PET images, distributed piecewise linearly over the breast volume, produce a deformed FEM mesh that reasonably approximates nonrigid deformation of the breast tissue between the MRI and PET scans. This method, which does not require a biomechanical breast tissue model, is robust and fast. Contrary to other approaches utilizing voxel intensity-based similarity measures or surface matching, our method works for matching MR with pure molecular images (i.e. PET or SPECT only). Our method does not require a good initialization and would not be trapped by local minima during registration process. All processing including FSMs detection and matching, and mesh generation can be fully automated. We tested our method on MR and PET breast images acquired for 15 subjects. The procedure yielded good quality images with an average target registration error below 4mm (i.e. well below PET spatial resolution of 6-7 mm). Based on the results obtained for 15 subjects studied to date, we conclude that this is a very fast and a well-performing method for MR-to-PET breast-image nonrigid registration. Therefore, it is a promising approach in clinical practice. This method can be easily applied to nonrigid registration of MRI or CT of any type of soft-tissue images to their molecular counterparts such as obtained using PET and SPECT.

Action spectrum for subliminal light control of adaptation in Phycomyces phototropism.

Adaptation processes enable phototropism and other blue light responses of Phycomyces to operate over a 10-decade range of fluence rate. Phototropic latency, used routinely to monitor the kinetics of sensitivity recovery after a step down in fluence rate, can be shortened by application of dim light for 35 min during the early part of the latency period. This light is termed subliminal, because it does not elicit phototropism under these experimental conditions; rather, it exerts its influence on the underlying adaptation kinetics. Fluence rate-response data for this latency reduction, obtained at 17 wavelengths of subliminal light from 347 to 742 nm, showed a variety of shapes that could be fit by zero, one, or two sigmoidal components, plus a constant term. At most wavelengths, the fluence-rate threshold for latency reduction by subliminal light tended to be well below the absolute threshold for phototropism, indicating that this effect is highly sensitive. An action spectrum for the sensitivity of the subliminal light effect, derived from the fluence rate-response curves, shows major peaks around 400 and 500 nm and a broad band from 570 to 670 nm, followed by a steep absorption edge. The sensitivity in the near ultraviolet region is relatively very low. The magnitude of the latency reduction also depends strongly on wavelength with a maximum at about 450 nm. The fluence-rate response data and the action spectrum--which is markedly different from that for phototropism and other blue-light responses of Phycomyces--indicate the participation of multiple pigments, or pigment states, in the photocontrol of adaptation.

Effect of calcium on dark adaptation in Phycomyces phototropism.

Adaptation processes enable phototropism of Phycomyces to operate over a 10-decade range of blue-light intensity (1 nW m-2-10 W m-2). To investigate the influence of calcium on dark adaptation, the phototropic latency method was employed with the modification that sporangiophores were temporarily immersed in solutions containing CaCl2 or LaCl3. Following such treatment, the time course of bending was found to have two components with distinct latencies and bending rates. After immersion in darkness for 30 min in LaCl3 solution or 1 h in a solution of CaCl2, MgCl2, or the calcium chelator EGTA, each sporangiophore was adapted to a blue light beam (1 W m-2) for 45 min by rotation around its vertical axis. Cessation of rotation defined the onset of the phototropic stimulus, at which time the intensity was reduced by as much as 10(3)-fold. For a 10(2)-fold reduction (to 10(-2) W m-2), immersion in CaCl2 (10-100 microM) reduces the latency 13 min for the early bending component and 18 min for the late component, whereas treatment with the calcium-channel blocker lanthanum (0.1-11 microM LaCl3) increases the latency 12 min for the early component and 13 min for the late component. EGTA (10 microM) also had an inhibitory effect, increasing the latency of the first and the second components by 7 and 10 min, respectively. In experiments performed similarly, but without the light adaptation treatment after immersion, no differences between calcium-treated and control sporangiophores were found. The bending rates of both components show only a weak dependence on calcium.(ABSTRACT TRUNCATED AT 250 WORDS)

Growth rate fluctuations in phycomyces sporangiophores.

The growth rate of the Phycomyces sporangiophore fluctuates under constant environmental conditions. These fluctuations underlie the well-characterized sensory responses to environmental changes. We compared growth fluctuations in sporangiophores of unstimulated wild type and behavioral mutants by use of maximum entropy spectral analysis, a mathematical technique that estimates the frequency and amplitude of oscillations in a time series. The mutants studied are believed to be altered near the input ("night-blind") or output ("stiff" and "hypertropic") of the photosensory transduction chain. The maximum entropy spectrum of wild type shows a sharp drop-off in spectral density above 0.3 millihertz, several minor peaks between 0.3 and 10 millihertz, and a broad maximum near 10 millihertz. Similar spectra were obtained for a night-blind mutant and a hypertropic mutant. In contrast, the spectra of three stiff mutants, defective in genes madD, madE, or madG, had distinctive peaks near 1.6 mHz and harmonics of this frequency. A madF stiff mutant, which is less stiff than madD, madE, and madG mutants, had a spectrum intermediate between wild type and the three other stiff mutants. Our results indicate that alterations in one or more steps associated with growth regulation output cause the Phycomyces sporangiophore to express a rhythmic growth rate.

Action spectra of the light-growth response in three behavioral mutants of Phycomyces.

Null-point action spectra of the light-growth response were measured for three mutants of Phycomyces blakesleeanus (Burgeff) and compared with the action spectrum of the wild type (WT). The action spectrum for L150, a recently isolated "night-blind" mutant, differs from the WT spectrum. The L150 action spectrum has a depression near 450 nm and small alterations in its long-wavelength cutoff, the same spectral regions where its photogravitropism action spectrum is altered. This indicates that the affected gene product influences both phototropism and the light-growth response. For L85, a "hypertropic" (madH) mutant, the light-growth-response action spectrum is very similar to that of WT even though the photogravitropism action spectrum of L85 has been shown previously to be altered in the near-UV region. The affected gene product in this mutant appears to affect phototropic transduction but not light-growth-response transduction. The action spectrum of C110, a "stiff" (madE) mutant, differs significantly from the WT spectrum near 500 nm, the same spectral region where sporangiophores of madE mutants have been shown to have small alterations in second-derivative absorption spectra. This indicates that the madE gene product may be physically associated with a photoreceptor complex, as predicted by system-analysis studies.

Photoinduced accumulation of carotene in Phycomyces.

Blue light stimulates the accumulation of beta-carotene (photocarotenogenesis) in the fungus Phycomyces blakesleeanus. To be effective, light must be given during a defined period of development, which immediately precedes the cessation of mycelial growth and the depletion of the glucose supply. The competence periods for photocarotenogenesis and photomorphogenesis in Phycomyces are the same when they are tested in the same mycelium. Photocarotenogenesis exhibits a two-step dependence on exposure, as if it resulted from the additon of two separate components with different thresholds and amplitudes. The low-exposure component produces a small beta-carotene accumulation, in comparison with that of dark-grown mycelia. The high-exposure component has a threshold of about 100 J· m(-2) blue light and produces a large beta-carotene accumulation, which is not saturated at 2·10(6) J·m(-2). Exposure-response curves were obtained at 12 wavelengths from 347 to 567 nm. The action spectra of the two components share general similarities with one another and with those of other Phycomyces photoresponses. The small, but significant differences in the action spectra of the two components imply that the respective photosystems are not identical. Light stimulates the carotene pathway in the carB mutants, which contain the colourless precursor phytoene, but not beta-carotene. Carotenogenesis is not photoinducible in carA mutants, independently of their carotene content. This and other observations on various car mutants indicate that light prevents the normal inhibition of the pathway by the carA and carS gene products. The chromophore(s) for photocarotenogenesis are presumably flavins, and not carotenes.

Action spectra of the light-growth response of Phycomyces.

The light-growth response of Phycomyces blakesleeanus (Burgeff) is a transient change in elongation rate of the sporangiophore caused by a change in light intensity. Previous investigators have found that the light-growth response has many features in common with phototropism; the major difference is that only the light-growth response is adaptive. In order to better understand the light-growth response and its relationship to phototropism, we have developed a novel experimental protocol for determining light-growth-response action spectra and have examined the effect of the reference wavelength and intensity on the shape of the action spectrum. The null-point action spectrum obtained with broadband-blue reference light has a small peak near 400 nm, a flat region from 430 nm to 470 nm, and an approximately linear decline in the logarithm of relative effectiveness above 490 nm. The shape of the action spectrum is different when 450-nm reference light is used, as has been shown previously for the phototropic-balance action spectrum. However, the action spectrum of the light-growth response differs from that for phototropic balance, even when the same reference light (450 nm) is used. Moreover, for the light-growth response, the relative effectiveness of 383-nm light decreases as the intensity of the 450-nm reference light increases; this trend is the opposite of that previously found for phototropic balance. The dependence of the lightgrowth-response action spectrum on the reference wavelength, its difference from the phototropic-balance action spectrum, and the reference-intensity dependence of the relative effectiveness at 383 nm may be attributable to dichroic effects of the oriented photoreceptor(s), and to transduction processes that are unique to the light-growth response.

Action spectra for photogravitropism of Phycomyces wild type and three behavioral mutants (L150, L152, and L154).

We have measured fluence rate-response curves and action spectra for photogravitropism in Phycomyces wild type and in three recently isolated mutants with elevated phototropic thresholds. The action spectra were determined from least-squares fits of a sigmoidal function to the fluence rate-response data for each wavelength. The action spectrum for wild type has maxima near 383, 413, 452, and 490 nm and minima near 397, 425, and 469 nm. This photogravitropism action spectrum is very similar to the Phycomyces phototropic balance action spectrum between 413 but has significantly higher effectiveness below 400 nm and above 490 nm. These differences may be caused by dichroic effects of the oriented receptor pigment and/or by multiple receptor pigments. The action spectra of the three mutants differ significantly from one another and from that of wild type. Relative to the wild type spectrum, all three mutants exhibit a suppression in effectiveness near 425 nm, which is near the transmission peak of the broadband blue filter used to isolate the mutants.

Electrophoretic analysis of proteins from Phycomyces mutants with abnormal tropisms.

Certain phototropism mutants of Phycomyces blakesleeanus show defective bending responses (tropisms) to stimuli besides light, such as gravity, wind, and barriers. These so-called "stiff" mutants are affected in four genes (madD to madG). Using two-dimensional gel electrophoresis, we have analyzed polypeptides from microsomal and soluble fractions obtained from the wild type, four single mutants, and six double mutants affected in all pairwise combinations of the four genes. Consistent differences in spot patterns for madE and madF mutants were found in microsomal fractions but not in soluble fractions. In madE mutants, two spots designated E1 (52 kDa, pI 6.65) and E2 (50 kDa, pI 6.65) were altered. E1 appeared denser in the wild type than in the madE mutants, while the reverse was true for E2. The spots E1 and E2 are probably under regulatory control by madE, perhaps involving posttranslational modification. A protein spot, F1 (53 kDa, pI 6.1), was present on the wild-type gels but absent from all gels for madF mutants. The F1 polypeptide probably represents the madF gene product.

Light-controlled adaptation kinetics in Phycomyces: evidence for a novel yellow-light absorbing pigment.

When sporangiophores of the fungus Phycomyces blakesleeanus adapt from high to low fluence rate, dark adaptation (sensitivity recovery) can be accelerated by dim subliminal light [Galland et al. (1989) Photochem. Photobiol. 49, 485-491]. We measured fluence rate-response curves for this acceleration under the following conditions. After sporangiophores were initially adapted symmetrically to a fluence rate of 1 W m-2 (447 nm), they were exposed to unilateral subliminal light (subthreshold for phototropism) of variable wavelength and fluence rate, and then to unilateral test light (447 nm) of fluence rate either 10(-3) or 10(-5) W m-2. The duration of the subliminal light was chosen so that phototropism would not occur during this period. Phototropic latencies could be shortened by subliminal light that was less intense than the test light by several orders of magnitude. In experiments with the final unilateral light of fluence rate 10(-3) W m-2, the 447 nm subliminal light had a threshold (for the acceleration effect) of about 10(-11) W m-2. Yellow light of wavelength 575 nm, which itself is extremely ineffective for phototropism was extremely effective in shortening phototropic latencies in response in response to the test light. At 575 nm, the threshold was about 2 x 10(-12) W m-2. Conversely, near-UV light of wavelength 347 nm, which is highly effective for phototropism, was relatively ineffective (threshold approximately 7 x 10(-8) W m-2) in shortening the phototropic latency. Our results suggest the presence of a novel yellow-light absorbing pigment in Phycomyces that specifically regulates dark adaptation.(ABSTRACT TRUNCATED AT 250 WORDS)

Subliminal light control of dark adaptation kinetics in Phycomyces phototropism.

The dark adaptation kinetics of Phycomyces phototropism depend critically on the experimental protocol. When sporangiophores that had been light-adapted to a fluence rate of 1 W m-2 at 447 nm were exposed to dim unilateral light, the adaptation kinetics showed exponential decay (6 min time constant). However, when light-adapted sporangiophores were kept for variable intervals in darkness (i.e. in presence of traditional red safelight) and then exposed to dim unilateral test light, the decay kinetics of adaptation were biexponential with a rapid decay during the first minute (1 min time constant), followed by a slow recovery (11 min time constant). Thus, the dim subliminal light given after the sporangiophores had been adapted to 1 W m-2, was actually perceived, and exerted control over the dark-adaptation process. The observed acceleration of dark-adaptation kinetics constitutes a novel light effect of the sporangiophore. At wavelength 383 nm this effect was not observed. Because a beta-carotene lacking mutant, L91 (genotype carB), was unmodified in dark-adaptation kinetics measured in the presence or absence of subliminal light, it appears that beta-carotene is not involved in the photocontrol of adaptation.

System analysis of Phycomyces light-growth response: madC, madG, and madH mutants.

The light-growth response of Phycomyces has been studied further with the sum-of-sinusoids method in the framework of the Wiener theory of nonlinear system identification. The response was treated as a black box with the logarithm of light intensity as the input and elongation rate as the output. The nonlinear input-output relation of the light-growth response can be represented mathematically by a set of weighting functions called kernels, which appear in the Wiener intergral series. The linear (first-order) kernels of wild type, and of single and double mutants affected in genes madA to madG were determined previously with Gaussian white noise test stimuli, and were used to investigate the interactions among the products of these genes (R.C. Poe, P. Pratap, and E.D. Lipson. 1986. Biol. Cybern. 55:105.). We have used the more precise sum-of-sinusoids method to extend the interaction studies, including both the first- and second-order kernels. Specifically, we have investigated interactions of the madH ("hypertropic") gene product with the madC ("night blind") and madG ("stiff") gene products. Experiments were performed on the Phycomyces tracking machine. The log-mean intensity of the stimulus was 6 x 10(-2) W m-2 and the wavelength was 477 nm. The first- and second-order kernels were analyzed in terms of nonlinear kinetic models. The madH gene product was found to interact with those of madC and madG. This result extends previous findings that themadH gene product is associated with the input and the ouput of the sensory transduction complex for the lightgrowth response.

System analysis of Phycomyces light-growth response in single and double night-blind mutants.

The sum-of-sinusoids method of nonlinear system identification has been applied to the light-growth response of the Phycomyces sporangiophore. Experiments were performed on the Phycomyces tracking machine with the wild-type strain with single and double mutants affected in genes madA, madB, and madC. The sum-of-sinusoids test stimuli were applied to the logarithm of the light intensity. The log-mean intensity level was 10(-1) W m-2 and the wavelength was 477 nm. The system identification results are in the form of first- and second-order frequency kernels, which are related to temporal kernels that appear in the Wiener functional series. The first-order kernels agree well with those obtained previously by the white noise method. In particular, the madA madB and madB madC double mutants show very weak responses. With the superior precision of the sum-of-sinusoids methods, we have achieved sufficient resolution to measure and analyze their second-order kernels. The first- and second-order frequency kernels were interpreted by system analysis methods involving a nonlinear parametric model. In addition a nonparametric hypothesis concerning interactions of gene products was tested. Results from the interaction tests confirm the earlier conclusion that the madB and madC gene products interact. In addition, with the enhanced precision and with the extension to nonlinear analysis, we have found evidence of interaction of the madA gene product with the madB and madC gene products. Thus all three genes appear to have mutual interactions, presumably because of their close physical association in a photoreceptor complex.

High-and low-intensity photosystems in Phycomyces phototropism: Effects of mutations in genes madA, madB, and madC.

Sporangiophores of Phycomyces blakesleeanus Burgeff that have been grown in darkness and are then suddenly exposed to unilateral light show a two-step bending response rather than a smooth, monotonic response found in light-adapted specimens (Galland and Lipson, 1987, Proc. Natl. Acad. Sci. USA 84, 104-108). The stepwise bending is controlled by two photosystems optimized for the low-and high-intensity ranges. These two photosystems have now been studied in phototropism mutants with defects in genes madA, madB, and madC. All three mutations raise the threshold of the low-intensity (low-fluence) photosystem by about 10(6)-fold and that of the high-intensity (high-fluence) system by about 10(3)-fold. Estimates for the light-adaptation time constants of the low-and high-intensity photosystems show that the mutants are affected in adaptation. In the mutants, the light-adaptation kinetics are only slightly affected in the low-intensity photosystem but, for the high-intensity photosystem, the kinetics are considerably slower than in the wild type.

Photomorphogenesis inPhycomyces: Fluence-response curves and action spectra.

Blue light regulates vegetative reproduction inPhycomyces blakesleeanus Bgff. by inhibiting the development of microphores and stimulating that of macrophores. Fluence-response curves were obtained at twelve different wavelengths. Each response exhibits a two-step ("biphasic") dependence on fluence, as if it resulted from the addition of two separate components with different thresholds, midpoints, and amplitudes. The absolute threshold is close to 10 photons·µm(2). The threshold fluence of the low-intensity component is about 10(4) times smaller than that of the high-intensity component. The action spectra for each of the two components of the two responses share general similarities, but exhibit significant differences that might be taken to favour four separate photosystems. Additional complexity is indicated by the wavelength dependence of the saturation levels.

Blue-light reception in Phycomyces phototropism: evidence for two photosystems operating in low- and high-intensity ranges.

Phototropism in the fungus Phycomyces is mediated by two photosystems that are optimized for the low-intensity region (below 10(-6) W X m-2) and the high-intensity region (above 10(-6) W X m-2). These photosystems can be distinguished under special experimental conditions, in which sporangiophores grown in the dark are suddenly exposed to continuous unilateral light. With this treatment, the bending occurs in two steps. Below 10(-6) W X m-2, an early-response component (15-min latency) and a late-response component (50- to 70-min latency) are observed that are mediated by photosystem I. Above 10(-6) W X m-2, the early component is augmented by an intermediate component with a 40-min delay that is mediated by photosystem II. The two photosystems are distinguished further by their wavelength sensitivities and adaptation kinetics. Photosystem I is more effective at 334, 347, and 550 nm than photosystem II, but it is less effective at 383 nm. At wavelength 450 nm, the dark-adaptation kinetics associated with photosystem I are approximately half as fast as those associated with photosystem II. However, the light-adaptation kinetics of photosystem I are approximately equal to 3 times faster than the kinetics associated with photosystem II. The existence of two photosystems clarifies several behavioral features of Phycomyces and helps explain how the sporangiophore can manage the full range of 10 decades.

System analysis of Phycomyces light-growth response with sum-of-sinusoids test stimuli.

The light-growth response of Phycomyces has been studied with the sum-of-sinusoids method of nonlinear system identification (Victor, J.D., and R.M. Shapley, 1980, Biophys. J., 29:459). This transient response of the sporangiophore has been treated as a black-box system with one input (logarithm of the light intensity, I) and one output (elongation rate). The light intensity was modulated so that log I, as a function of time, was a sum of sinusoids. The log-mean intensity was 10(-4) W m-2 and the wavelength was 477 nm. The first- and second-order frequency kernels, which represent the linear and nonlinear behavior of the system, were obtained from the Fourier transform of the response at the appropriate component and combination frequencies. Although the first-order kernel accounts for most of the response, there remains a significant nonlinearity beyond the logarithmic transducer presumed to occur at the input of the sensory transduction chain. From the analysis of the frequency kernels, we have derived a dynamic nonlinear model of the light-growth response system. The model consists of a nonlinear subsystem followed by a linear subsystem. The model parameters were estimated from a combined nonlinear least-squares fit to the first- and second-order frequency kernels.

System analysis of Phycomyces light-growth response. Wavelength and temperature dependence.

The light-growth response of the Phycomyces sporangiophore was studied further with the sum-of-sinusoids method of nonlinear system identification. The first- and second-order frequency kernels, which represent the input-output relation of the system, were determined at 12 wavelengths (383-529 nm) and 4 temperatures (17 degrees, 20 degrees, 23 degrees, and 26 degrees C). The parametric model of the light-growth response system, introduced in the preceding paper, consists of nonlinear and linear dynamic subsystems in cascade. The model parameters were analyzed as functions of wavelength and temperature. At longer wavelengths, the system becomes more nonlinear. The latency and the bandwidth (cutoff frequency) of the system also vary significantly with wavelength. In addition, the latency decreases progressively with temperature (Q10 = 1.6). At low temperature (17 degrees C), the bandwidth is reduced. The results indicate that about half of the latency is due to physical processes such as diffusion, and the other half to enzymatic reactions. The dynamics of the nonlinear subsystem also vary with wavelength. The dependence of various model components on wavelength supports the hypothesis that the light-growth response, as well as phototropism, are mediated by multiple interacting photoreceptors.

System analysis of Phycomyces light-growth response. Photoreceptor and hypertropic mutants.

The light-growth responses of Phycomyces behavioral mutants, defective in genes madB, madC, and madH, were studied with the sum-of-sinusoids method of system identification. Modified phototropic action spectra of these mutants have indicated that they have altered photoreceptors (P. Galland and E.D. Lipson, 1985, Photochem. Photobiol. 41:331). In the two preceding papers, a kinetic model of the light-growth response system was developed and applied to wild-type frequency kernels at several wavelengths and temperatures. The present mutant studies were conducted at wavelength 477 nm. The log-mean intensity was 6 X 10(-2)W m-2 for the madB and madC night-blind mutants, and 10(-4)W m-2 for the madH hypertropic mutant. The prolonged light-growth responses of the madB and madC mutants are reflected in the reduced dynamic order of their frequency kernels. The linear response of the hypertropic mutant is essentially normal, but its nonlinear behavior shows modified dynamics. The behavior of these mutants can be accounted for by suitable modifications of the parametric model of the system. These modifications together support the hypothesis that an integrated complex mediates sensory transduction in the light responses and other responses of the sporangiophore.

Modified Light-Induced Absorbance Changes in dim Y Photoresponse Mutants of Trichoderma.

A brief pulse of blue light induces the common soil fungus Trichoderma harzianum to sporulate. Photoresponse mutants with higher light requirements than the wild type are available, including one class, dim Y, with modified absorption spectra. We found blue-light-induced absorbance changes in the blue region of the spectrum, in wild-type and dim Y mutant strains. The light-minus-dark difference spectra of the wild type and of several other strains indicate photoreduction of flavins and cytochromes, as reported for other fungi and plants. The difference spectra in strains with normal photoinduced sporulation have a prominent peak at 440 nm. After actinic irradiation, this 440 nanometer difference peak decays rapidly in the dark. In two dim Y photoresponse mutants, the difference spectra were modified; in one of these, LS44, the 440 nanometer peak was undetectable in difference spectra. Detailed study of the dark-decay kinetics in LS44 and the corresponding control indicated that the 440 nanometer difference peak escaped detection in LS44 because it decays faster than in the control. The action spectrum of the 440 nm difference peak is quite different from that of photoinduced sporulation. The light-induced absorbance changes are thus unlikely to be identical to the primary photochemical reaction triggering sporulation. Nevertheless, these results constitute genetic evidence that physiologically relevant pigments participate in these light-induced absorbance changes in Trichoderma.