Discovery of signaling effect of UV-B/C light in the extended UV-A/blue-type action spectra for step-down and step-up photophobic responses in the unicellular flagellate algaEuglena gracilis

Summary Cultures of unicellular algal flagellateEuglena gracilis grown in different conditions were subjected to action spectroscopy for step-down and step-up photophobic responses, respectively. The spectral region was extended into the UV-B/C as well as in the UV-A and visible regions with the Okazaki Large Spectrograph as the monochromatic light source. The photophobic responses of the cells were measured with an individual-cell assay method with the aid of a computerized video motion analyzer. In the UV-A and visible regions, the shapes of the action spectra were the so-called UV-A/blue type. In the newly studied UV-B/C region, new action peaks were found at 270 nm for the step-down response and at 280 nm for the step-up one. The absorption spectrum of flavin adenine dinucleotide (FAD) appeared to fit the action spectrum for the step-up response, whereas the shape of the step-down action spectrum, which has a UV-A peak (at 370 nm) higher than the blue peak (at 450 nm), appeared to be mimicked by the absorption spectrum of a mixed solution of 6-biopterin and FAD. These observations might also account for the fact that the UV-B/C peak wavelength at 270 nm of the action spectrum for the step-down response is shorter by 10 nm than the action spectrum for the step-up response at 280 nm.Abbreviations FAD flavin adenine dinucleotide - FWHM spectral full width at half maximum - NIBB National Institute for Basic Biology - OLS Okazaki Large Spectrograph - PFB paraflagellar body - UV-A ultraviolet light of spectral region between 320 and 400 nm - UV-B/C ultraviolet light of spectral region between 190 and 320 nm     

The nature of very low frequency component of the heart rate variability and the role of sympathetic-parasympathetic interactions

A method of separate monitoring "instant" changes of the VLF, LF and HF power spectral components of heart rate variability, has been developed. The power of the LF and HF spectral components were proved to be continuously changing. The period of these power fluctuations could stay within 15 to 150 sec. Comparison of the heart rate variability spectrum with LF and HF spectral components power fluctuations' spectrums has shown that the frequencies of the LF and HF spectral components power fluctuations stay within the VLF range. The co-operative spectrum form of these fluctuations repeats the form of the VLF peak. In cases when the LF and HF spectral components power fluctuations' periods do not coincide, VLF has two peaks. The frequency of one VLF peak coincides with frequency of the HF power fluctuations, and the frequency of another--with the frequency of LF power fluctuations.     

Spectroscopic study of human lung epithelial cells (A549) in culture: living cells versus dead cells

The noninvasive analysis of living cells grown on 3-dimensional scaffold materials is a key point in tissue engineering. In this work we show the capability of Raman spectroscopy for use as a noninvasive method to distinguish cells at different stages of the cell cycle and living cells from dead cells. The spectral differences between cells in different stages of the cell cycle are characterized mainly by variations in DNA vibrations at 782, 788, and 1095 cm(-1). The Raman spectrum of dead human lung derived (A549 line) cells indicates the breakdown of both phosphodiester bonds and DNA bases. The most sensitive peak for identifying dead cells is the 788 cm(-1) peak corresponding to DNA Obond;Pbond;O backbone stretching. The magnitude of this peak is reduced by 80% in the spectrum of dead cells. Changes in protein peaks suggest significant conformational changes; for example, the magnitude of the 1231 cm(-1) peak assigned to random coils is reduced by 63% for dead cells. The sharp peak of phenylalanine at 1005 cm(-1) drops to half, indicating a decrease of stable proteins associated with cell death. The differences in the 1190-1385 cm(-1) spectral region also suggest a decrease in the amount of nucleic acids and proteins. Using curve fitting, we quantify these spectral differences that can be used as markers of cell death.     

Fluorescence emission spectral shift measurements of membrane potential in single cells.

Previous measurements of transmembrane potential using the electrochromic probe di-8-ANEPPS have used the excitation spectral shift response by alternating excitation between two wavelengths centered at voltage-sensitive portions of the excitation spectrum and recording at a single wavelength near the peak of the emission spectrum. Recently, the emission spectral shift associated with the change in transmembrane potential has been used for continuous membrane potential monitoring. To characterize this form of the electrochromic response from di-8-ANEPPS, we have obtained fluorescence signals from single cells in response to step changes in transmembrane potentials set with a patch electrode, using single wavelength excitation near the peak of the dye absorption spectrum. Fluorescence changes at two wavelengths near voltage-sensitive portions of the emission spectrum and shifts in the complete emission spectrum were determined for emission from plasma membrane and internal membrane. We found that the fluorescence ratio from either dual-wavelength recordings, or from opposite sides of the emission spectrum, varied linearly with the amplitude of the transmembrane potential step between -80 and +60 mV. Voltage dependence of difference spectra exhibit a crossover point near the peak of the emission spectra with approximately equal gain and loss of fluorescence intensity on each side of the spectrum and equal response amplitude for depolarization and hyperpolarization. These results are consistent with an electrochromic mechanism of action and demonstrate how the emission spectral shift response can be used to measure the transmembrane potential in single cells.     

A model-free algorithm for the removal of baseline artifacts

Summary A novel algorithm for removing baseline distortions in NMR spectra is presented. The algorithm approximates the baseline as the median of the noise extrema. Consequently, the method does not require that NMR peaks be discriminated from noise peaks. In addition, no assumptions regarding the source or functional form of the distortion are made. The algorithm is shown to remove the baseline artifacts present in a particularly distorted NOESY spectrum and to reveal peaks which had been obscured by the artifacts. The parameters and spectral characteristics (signal-to-noise ratio, NMR peak density, peak linewidths) governing the resolution of the calculated baselines are also explored.     

Quantitative covariance NMR by regularization

The square root of a covariance spectrum, which offers high spectral resolution along both dimensions requiring only few t ₁ increments, yields in good approximation the idealized 2D FT spectrum provided that the amount of magnetization exchanged between spins is relatively small. When this condition is violated, 2D FT and covariance peak volumes may differ. A regularization method is presented that produces a modified covariance spectrum with cross-peak volumes that closely match their 2D FT analogues. The method is demonstrated for TOCSY spectra with variable mixing times.     

Nitella fluctuation and instability in the membrane potential near threshold.

Excitation of Nitella internodal cell was investigated as an example of the phase transition in an open system far more thermal equilibrium. The power density spectrum of the membrane potential fluctuation had a bulge in a frequency range lower than 1 Hz at the resting state and a peak at approximately 0.03 Hz at a depolarized state near the threshold. A critical oscillation in the membrane potential was observed when threshold was gradually approached from the resting state. Repetitive firing was observed under a step-current of the superthreshold value. The frequency of spectral peaking, critical oscillation, and repetitive firing agree well with each other. The result suggests that the hard-mode instability occurs in the Nitella internodal cell. The membrane impedance had no peak in the same frequency region as the peak of the voltage spectrum. The spectral peak may be ascribed to be electrogenic pump modulated by the metabolic feedback system in photosynthesis.     

Reconstruction of non-uniformly sampled five-dimensional NMR spectra by signal separation algorithm

A method for five-dimensional spectral reconstruction of non-uniformly sampled NMR data sets is proposed. It is derived from the previously published signal separation algorithm, with major alterations to avoid unfeasible processing of an entire five-dimensional spectrum. The proposed method allows credible reconstruction of spectra from as little as a few hundred data points and enables sensitive resonance detection in experiments with a high dynamic range of peak intensities. The efficiency of the method is demonstrated on two high-resolution spectra for rapid sequential assignment of intrinsically disordered proteins, namely 5D HN(CA)CONH and 5D (HACA)CON(CO)CONH.     

Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK

The automated identification of signals in multidimensional NMR spectra is a challenging task, complicated by signal overlap, noise, and spectral artifacts, for which no universally accepted method is available. Here, we present a new peak picking algorithm, CYPICK, that follows, as far as possible, the manual approach taken by a spectroscopist who analyzes peak patterns in contour plots of the spectrum, but is fully automated. Human visual inspection is replaced by the evaluation of geometric criteria applied to contour lines, such as local extremality, approximate circularity (after appropriate scaling of the spectrum axes), and convexity. The performance of CYPICK was evaluated for a variety of spectra from different proteins by systematic comparison with peak lists obtained by other, manual or automated, peak picking methods, as well as by analyzing the results of automated chemical shift assignment and structure calculation based on input peak lists from CYPICK. The results show that CYPICK yielded peak lists that compare in most cases favorably to those obtained by other automated peak pickers with respect to the criteria of finding a maximal number of real signals, a minimal number of artifact peaks, and maximal correctness of the chemical shift assignments and the three-dimensional structure obtained by fully automated assignment and structure calculation.     

Spectra of low-frequency modulation of gyrotron radiation during electron-cyclotron resonance heating of plasma in the L-2M stellarator

Results from experimental studies of the modulation of the gyrotron power during electron cyclotron resonance heating of plasma L-2M stellarator are presented. It is shown that the modulation spectrum consists of separate spectral bands, among which a 20-kHz peak with a spectral density exceeding by one order of magnitude the spectral density of the other peaks is observed. This can be explained by the gyrotron operation being affected by the wave reflected from long-wavelength plasma fluctuations.     

Annotated regions of significance of SELDI-TOF-MS spectra for detecting protein biomarkers

Peak detection is a key step in the analysis of SELDI-TOF-MS spectra, but the current default method has low specificity and poor peak annotation. To improve data quality, scientists still have to validate the identified peaks visually, a tedious and time-consuming process, especially for large data sets. Hence, there is a genuine need for methods that minimize manual validation. We have previously reported a multi-spectral signal detection method, called RS for 'region of significance', with improved specificity. Here we extend it to include a peak quantification algorithm based on annotated regions of significance (ARS). For each spectral region flagged as significant by RS, we first identify a dominant spectrum for determining the number of peaks and the m/z region of these peaks. From each m/z region of peaks, a peak template is extracted from all spectra via the principal component analysis. Finally, with the template, we estimate the amplitude and location of the peak in each spectrum with the least-squares method and refine the estimation of the amplitude via the mixture model.We have evaluated the ARS algorithm on patient samples from a clinical study. Comparison with the standard method shows that ARS (i) inherits the superior specificity of RS, and (ii) gives more accurate peak annotations than the standard method. In conclusion, we find that ARS alleviates the main problems in the preprocessing of SELDI-TOF spectra. The R-package ProSpect that implements ARS is freely available for academic use at http://www.meb.ki.se/ yudpaw.     

Spectral sensitivity of vision and bioluminescence in the midwater shrimp Sergestes similis

In the oceanic midwater environment, many fish, squid, and shrimp use luminescent countershading to remain cryptic to silhouette-scanning predators. The mid-water penaeid shrimp, Sergestes similis Hansen, responds to downward-directed light with a dim bioluminescence that dynamically matches the spectral radiance of oceanic down-welling light at depth. Although the sensory basis of luminescent countershading behavior is visual, the relationship between visual and behavioral sensitivity is poorly understood. In this study, visual spectral sensitivity, based on microspectrophotometry and electrophysiological measurements of photoreceptor response, is directly compared to the behavioral spectral efficiency of luminescent countershading. Microspectrophotometric measurements on single photoreceptors revealed only a single visual pigment with peak absorbance at 495 nm in the blue-green region of the spectrum. The peak electrophysiological spectral sensitivity of dark-adapted eyes was centered at about 500 nm. The spectral efficiency of luminescent countershading showed a broad peak from 480 to 520 nm. Both electrophysiological and behavioral data closely matched the normalized spectral absorptance curve of a rhodopsin with lambda(max) = 495 nm, when rhabdom length and photopigment specific absorbance were considered. The close coupling between visual spectral sensitivity and the spectral efficiency of luminescent countershading attests to the importance of bioluminescence as a camouflage strategy in this species.     

Spectral analysis of fetal heart rhythm in relation to fetal regular mouthing

Fetal heart rate variation during fetal regular mouthing in behavioural state 1F was investigated applying spectral analysis. Periods with and without fetal regular mouthing movements were compared. The power spectrum of the periods with regular mouthing movements showed a peak at the frequency of the clusters of mouthing movements which was absent in the power spectrum of the corresponding periods without movements. The oscillations in the fetal heart rate associated with this peak in the power spectrum were detectable both in the heart rate tracings obtained from the abdominal electrocardiogram and those recorded by means of wide range Doppler ultrasound.     

Refining similarity scoring to enable decoy‐free validation in spectral library searching

Spectral library searching is a maturing approach for peptide identification from MS/MS, offering an alternative to traditional sequence database searching. Spectral library searching relies on direct spectrum‐to‐spectrum matching between the query data and the spectral library, which affords better discrimination of true and false matches, leading to improved sensitivity. However, due to the inherent diversity of the peak location and intensity profiles of real spectra, the resulting similarity score distributions often take on unpredictable shapes. This makes it difficult to model the scores of the false matches accurately, necessitating the use of decoy searching to sample the score distribution of the false matches. Here, we refined the similarity scoring in spectral library searching to enable the validation of spectral search results without the use of decoys. We rank‐transformed the peak intensities to standardize all spectra, making it possible to fit a parametric distribution to the scores of the nontop‐scoring spectral matches. The statistical significance of the top‐scoring match can then be estimated in a rigorous manner according to Extreme Value Theory. The overall result is a more robust and interpretable measure of the quality of the spectral match, which can be obtained without decoys. We tested this refined similarity scoring function on real datasets and demonstrated its effectiveness. This approach reduces search time, increases sensitivity, and extends spectral library searching to situations where decoy spectra cannot be readily generated, such as in searching unidentified and nonpeptide spectral libraries.     

Stability of the heart rate power spectrum over time in the conscious dog

The purpose of this experiment was to test the stability of the heart rate (HR) power spectrum over time in conscious dogs. HR was recorded for 1 h for each of six animals on 2 days. A Fast Fourier transform was used to derive the HR power spectrum for the 12 contiguous 5-min epochs comprising the 1-h recordings. Changes in frequency and amplitude of the various spectral peaks were quantitatively examined. We confirm the presence of two major concentrations of power centered around 0.02 (low frequency peak) and 0.32 Hz (high frequency peak). However, we observed variations in these spectral peaks, especially their amplitudes, both within each hour and from day 1 to day 2. The amplitudes of these two spectral peaks tended to vary reciprocally. HR power spectra based on 5 min of recorded data were also derived from an additional eight animals in both the lying and standing positions; the power spectra from these short recordings were sufficiently sensitive to detect redistributions in power due to changes in posture in all eight dogs. We conclude that: 1) data should be recorded for relatively long periods (e.g., 1 h) to characterize the HR power spectrum; 2) some variability in frequency and amplitude will persist across spectra even when based on longer data bases; 3) care should be taken to ensure that the subject's behavioral state is stable within the recording period; 4) shorter (e.g., 5 min) data bases are not suitable except for detecting relatively robust changes in the HR power spectrum.     

Covariance NMR in higher dimensions: application to 4D NOESY spectroscopy of proteins

Elucidation of high-resolution protein structures by NMR spectroscopy requires a large number of distance constraints that are derived from nuclear Overhauser effects between protons (NOEs). Due to the high level of spectral overlap encountered in 2D NMR spectra of proteins, the measurement of high quality distance constraints requires higher dimensional NMR experiments. Although four-dimensional Fourier transform (FT) NMR experiments can provide the necessary kind of spectral information, the associated measurement times are often prohibitively long. Covariance NMR spectroscopy yields 2D spectra that exhibit along the indirect frequency dimension the same high resolution as along the direct dimension using minimal measurement time. The generalization of covariance NMR to 4D NMR spectroscopy presented here exploits the inherent symmetry of certain 4D NMR experiments and utilizes the trace metric between donor planes for the construction of a high-resolution spectral covariance matrix. The approach is demonstrated for a 4D (13)C-edited NOESY experiment of ubiquitin. The 4D covariance spectrum narrows the line-widths of peaks strongly broadened in the FT spectrum due to the necessarily short number of increments collected, and it resolves otherwise overlapped cross peaks allowing for an increase in the number of NOE assignments to be made from a given dataset. At the same time there is no significant decrease in the positive predictive value of observing a peak as compared to the corresponding 4D Fourier transform spectrum. These properties make the 4D covariance method a potentially valuable tool for the structure determination of larger proteins and for high-throughput applications in structural biology.     

Phototactic responses of anuran amphibians to monochromatic stimuli of equal quantum intensity

The phototactic responses of anuran amphibians to narrow-band monochromatic stimuli of equal quantum intensity were measured for the first time in eight new experiments. The unimodal spectral response, obtained from dark-adapted American toads (Bufo americanus), peaks near 626 THz of frequency (480 nm wavelength). The bimodal, U-shaped spectral response, obtained from dark-adapted tailed frogs (Ascaphus truei), has the anti-mode at about 589 THz (510 nm) and is not merely the spectral mirror-image of the unimodal response. Absolute level of the spectral stimuli of equal quantum intensity did not affect the spectral response of dark-adapted toads, but light-adaptation enhanced a component that has the same spectral peak as the visual pigment absorption spectrum of principal and single cones of the frog's retina.     

Spectral sensitivity and Color Vision in the Bottlenose Dolphin (Tursiops Truncatus)

Spectral sensitivity was measured in air in a bottlenose dolphin using a behavioral training technique. The spectral sensitivity curve shows two maxima in sensitivity, one in the near ultraviolet part of the spectrum and the other one in the bluegreen part at about 490 nm. Two wavelength discrimination tasks showed that the dolphin could discriminate two wavelengths from the peak regions of the two maxima of the spectral sensitivity function, but not between two wavelengths lying within the broad maximum of the curve in the bluegreen part of the spectrum. Possible underlying mechanisms for the shape of the function are discussed.     

Spectral sensitivity and Color Vision in the Bottlenose Dolphin ( Tursiops Truncatus )

Spectral sensitivity was measured in air in a bottlenose dolphin using a behavioral training technique. The spectral sensitivity curve shows two maxima in sensitivity, one in the near ultraviolet part of the spectrum and the other one in the bluegreen part at about 490 nm. Two wavelength discrimination tasks showed that the dolphin could discriminate two wavelengths from the peak regions of the two maxima of the spectral sensitivity function, but not between two wavelengths lying within the broad maximum of the curve in the bluegreen part of the spectrum. Possible underlying mechanisms for the shape of the function are discussed.     

Prediction of peak overlap in NMR spectra

Peak overlap is one of the major factors complicating the analysis of biomolecular NMR spectra. We present a general method for predicting the extent of peak overlap in multidimensional NMR spectra and its validation using both, experimental data sets and Monte Carlo simulation. The method is based on knowledge of the magnetization transfer pathways of the NMR experiments and chemical shift statistics from the Biological Magnetic Resonance Data Bank. Assuming a normal distribution with characteristic mean value and standard deviation for the chemical shift of each observable atom, an analytic expression was derived for the expected overlap probability of the cross peaks. The analytical approach was verified to agree with the average peak overlap in a large number of individual peak lists simulated using the same chemical shift statistics. The method was applied to eight proteins, including an intrinsically disordered one, for which the prediction results could be compared with the actual overlap based on the experimentally measured chemical shifts. The extent of overlap predicted using only statistical chemical shift information was in good agreement with the overlap that was observed when the measured shifts were used in the virtual spectrum, except for the intrinsically disordered protein. Since the spectral complexity of a protein NMR spectrum is a crucial factor for protein structure determination, analytical overlap prediction can be used to identify potentially difficult proteins before conducting NMR experiments. Overlap predictions can be tailored to particular classes of proteins by preparing statistics from corresponding protein databases. The method is also suitable for optimizing recording parameters and labeling schemes for NMR experiments and improving the reliability of automated spectra analysis and protein structure determination.