Sequence-specific solution structure of d-GGTACGCGTACC

Complete resonance assignments of nonexchangeable base protons and sugar protons in d-GGTACGCGTACC at 500 MHz have been obtained by two-dimensional correlated spectroscopy (COSY) and nuclear Overhauser enhancement spectroscopy (NOESY). The characteristic phase-sensitive multiplet patterns of the ntrasugar cross peaks in the omega 1-scaled COSY spectrum have been used to estimate several scalar coupling constants (J). These coupling constants combined with the intranucleotide COSY cross peak intensities have been used to identify the sugar pucker of individual nucleotide units. In most cases, the deoxyribose rings adopt a conformation close to O4'-endo. Spin-diffusion has been monitored from the buildup of the normalized volumes of NOE cross peaks in NOESY spectra as a function of mixing time. A set of 55 intranucleotide and internucleotide interproton distances have been estimated from the low mixing time NOESY spectrum (tau m = 75 ms). The estimated intranucleotide proton-proton distances have been used to determine the individual glycosidic dihedral angles of the nucleotide units which lie in the anti domain. It is observed that the molecule adopts an overall conformation close to that of the B-form although there are differences in the intricate details.     

A fast SEQUEST cross correlation algorithm

The SEQUEST program was the first and remains one of the most widely used tools for assigning a peptide sequence within a database to a tandem mass spectrum. The cross correlation score is the primary score function implemented within SEQUEST and it is this score that makes the tool particularly sensitive. Unfortunately, this score is computationally expensive to calculate, and thus, to make the score manageable, SEQUEST uses a less sensitive but fast preliminary score and restricts the cross correlation to just the top 500 peptides returned by the preliminary score. Classically, the cross correlation score has been calculated using Fast Fourier Transforms (FFT) to generate the full correlation function. We describe an alternate method of calculating the cross correlation score that does not require FFTs and can be computed efficiently in a fraction of the time. The fast calculation allows all candidate peptides to be scored by the cross correlation function, potentially mitigating the need for the preliminary score, and enables an E-value significance calculation based on the cross correlation score distribution calculated on all candidate peptide sequences obtained from a sequence database.     

Use of a light-induced respiratory transient to measure the optical cross section of photosystem I in chlorella

A method has been developed whereby the magnitude of a transient in O₂ uptake attributable to photosystem (PS) I activity, following single-turnover laser flashes of varying energy, can be used to measure the optical cross section of PSI. As measurements are made under the identical physiological conditions for which the cross section of PSII has previously been determined (AC Ley, DC Mauzerall 1982 Biochim Biophys Acta 680: 96-105), it is now possible to simultaneously measure the cross section of both photosystems in intact, photosynthetically competent cells, without the use of inhibitors or artificial mediators of electron transport. Plots of light-saturation behavior of the respiratory oscillation following pulses at 596 nanometers indicate a mean optical cross section similar to that of PSII at this wavelength, but suggest significant heterogeneity in the cross section of PSI. If this method measures only PSI activity, this result implies that there exist units with different numbers of identical chromophores, or units having populations of chromophores with different absorption spectra.     

13C NMR assignments of the protonated carbons of [d(TAGCGCTA)]2 by two-dimensional proton-detected heteronuclear correlation

The resonances of the protonated carbons of [d(TAGCGCTA)]2 have been assigned by the two-dimensional proton-detected double-quantum heteronuclear correlation experiment [( 1H-13C]-DQCOSY). 13C-coupled and 13C-decoupled versions of the experiment were used. The assignment method is discussed in detail. The deoxyribose cross peaks segregate into five well-resolved regions, and the base cross peaks have distinct features that are helpful for assignments. The cross peaks from the 1H-13C pairs at the Cyd5, Ado2 and ThdCH3 base positions fall in separate regions of the spectrum from each other; they also are resolved from the closely spaced Ado8, Guo8, Cyd6 and Thd6. Additional parameters for distinction of the base signals are their differing J-coupling values and long-range coupling patterns.     

Multivariate analysis of simultaneously active motor units in human skeletal muscle

The joint activity of simultaneously active motor units was analyzed, using several methods including interunit interval and expectation density functions. The results show that there is no significant interaction between any motor units and, except for a slight coupling, the units fire independently of one another. The coupling is weak but pervasive and affects motor units overlapping and disjoint territories. Synchronous action potentions were recorded at sites whose distance is greater than the acknowledged diameter of motor unit territories. It is proposed that these expansive motor units and the viscoelastic properties of muscle are responsible for smooth contractions in human muscle.This work was supported in part by the Social Rehabilitation Service through the Krusen Research Center, Temple University, Philadelphia, Pennsylvania, while Dr. Shiavi was with the Biomedical Engineering and Science Program, Drexel University, Philadelphia, Pennsylvania, and the Krusen Research Center.     

A simulation study to examine the use of cross-correlation as an estimate of surface EMG cross talk.

Cross-correlation between surface electromyogram (EMG) signals is commonly used as a means of quantifying EMG cross talk during voluntary activation. To examine the reliability of this method, the relationship between cross talk and the cross-correlation between surface EMG signals was examined by using model simulation. The simulation results illustrate an increase in cross talk with increasing subcutaneous fat thickness. The results also indicate that the cross-correlation function decays more rapidly with increasing distance from the active fibers than cross talk, which was defined as the normalized EMG amplitude during activation of a single muscle. The influence of common drive and short-term motor unit synchronization on the cross-correlation between surface EMG signals was also examined. While common drive did not alter the maximum value of the cross-correlation function, the correlation increased with increasing motor unit synchronization. It is concluded that cross-correlation analysis is not a suitable means of quantifying cross talk or of distinguishing between cross talk and coactivation during voluntary contraction. Furthermore, it is possible that a high correlation between surface EMG signals may reflect an association between motor unit firing times, for example due to motor unit synchronization.     

Detecting Protein Complexes in Living Cells from Laser Scanning Confocal Image Sequences by the Cross Correlation Raster Image Spectroscopy Method

We describe a general method for detecting molecular complexes based on the analysis of single molecule fluorescence fluctuations from laser scanning confocal images. The method detects and quantifies complexes of two different fluorescent proteins noninvasively in living cells. Because in a raster scanned image successive pixels are measured at different times, the spatial correlation of the image contains information about dynamic processes occurring over a large time range, from the microseconds to seconds. The correlation of intensity fluctuations measured simultaneously in two channels detects protein complexes that carry two molecules of different colors. This information is obtained from the entire image. A map of the spatial distribution of protein complexes in the cell and their diffusion and/or binding properties can be constructed. Using this cross correlation raster image spectroscopy method, specific locations in the cell can be visualized where dynamics of binding and unbinding of fluorescent protein complexes occur. This fluctuation imaging method can be applied to commercial laser scanning microscopes thereby making it accessible to a large community of scientists.     

Simultaneous on/off regulation of transgenes located on a mammalian chromosome with Cre-expressing adenovirus and a mutant loxP

The site-specific recombinase Cre has often been used for on/off regulation of expression of transgenes introduced into the mammalian chromosome. However, this method is only applicable to the regulation of a single gene and cannot be used to simultaneously regulate two genes, because site-specific recombination occurs from the target loxP sequence of one regulating unit to the loxP sequence of any other unit and would eventually disrupt the structure of both regulating units. We previously reported a mutant loxP sequence with a two base substitution called loxP V (previously called loxP 2272), with which wild-type loxP cannot recombine but with which the identical mutant loxP recombines efficiently. In the present study we isolated cell lines bearing two regulating units on a chromosome containing a pair of wild-type loxP sequences or mutant loxP V sequences. After infection with Cre-expressing recombinant adenovirus AxCANCre, expression of a gene in each regulating unit was simultaneously turned on and off. Southern analyses showed that both regulating units were processed simultaneously and independently, even after infection with a limited amount of AxCANCre. The results showed that simultaneous regulation of gene expression on a mammalian chromosome mediated by Cre can be achieved by using mutant loxP V and wild-type loxP. This method may be a useful approach for conditional transgenic/knockout animals and investigation of gene function involving two genes simultaneously. Another possible application is for preparation of a new packaging cell line of viral vectors through simultaneous production of toxic viral genes.     

Accurate measurements of coupling constants from two-dimensional nuclear magnetic resonance spectra of proteins and determination of phi-angles

A new and simple method to measure 3JHNH alpha coupling constants of proteins by adding and subtracting traces from corresponding two-dimensional nuclear Overhauser enhanced spectroscopy and two-dimensional correlated spectroscopy cross peaks after scaling is proposed. The optimal scaling for the addition and the subtraction of the two traces is obtained by minimizing an error function. The method was proven to give accurate and precise measurements of coupling constants when tested with a series of simulated spectra. The accuracy of the method was better than 0.1 Hz for all test cases including the limiting case of J = 2.0 Hz and line-width = 11.0 Hz. The accuracy of the method was better than 0.1 Hz for all test cases including The 3JHNH alpha coupling constants were measured in two-dimensional nuclear magnetic resonance spectra of the two proteins barley serine proteinase inhibitor (CI-2) and the bacterial ribonuclease (barnase) of Bacillus amyloliquefaciens. The experimentally measured coupling constants were used to calculate the constants in a Karplus equation to be: 3JHNH alpha = 6.7 cos2(phi-60) -1.3 cos(phi-60) +1.5. These constants are in good accordance with those obtained for basic pancreatic trypsin inhibitor (BPTI). In addition, special emphasis is given to the measurements of positive phi-angles, and to the contribution of molecular dynamics on the apparent coupling constants.     

Two-category model of task allocation with application to ant societies

In many network models of interacting units such as cells or insects, the coupling coefficients between units are independent of the state of the units. Here we analyze the temporal behavior of units that can switch between two 'category' states according to rules that involve category-dependent coupling coefficients. The behaviors of the category populations resulting from the asynchronous random updating of units are first classified according to the signs of the coupling coefficients using numerical simulations. They range from isolated fixed points to lines of fixed points and stochastic attractors. These behaviors are then explained analytically using iterated function systems and birth-death jump processes. The main inspiration for our work comes from studies of non-hierarchical task allocation in, e.g., harvester ant colonies where temporal fluctuations in the numbers of ants engaged in various tasks occur as circumstances require and depend on interactions between ants. We identify interaction types that produce quick recovery from perturbations to an asymptotic behavior whose characteristics are function of the coupling coefficients between ants as well as between ants and their environment. We also compute analytically the probability density of the population numbers, and show that perturbations in our model decay twice as fast as in a model with random switching dynamics. A subset of the interaction types between ants yields intrinsic stochastic asymptotic behaviors which could account for some of the experimentally observed fluctuations. Such noisy trajectories are shown to be random walks with state-dependent biases in the 'category population' phase space. With an external stimulus, the parameters of the category-switching rules become time-dependent. Depending on the growth rate of the stimulus in comparison to its population-dependent decay rate, the dynamics may qualitatively differ from the case without stimulus. Our simple two-category model provides a framework for understanding the rich variety of behaviors in network dynamics with state-dependent coupling coefficients, and especially in task allocation processes with many tasks.     

Closed-loop control of muscle length through motor unit recruitment in load-moving conditions

Neuroprostheses aimed at restoring lost movement in the limbs of spinal cord injured individuals are being developed in this laboratory. As part of this program, we have designed a digital proportional-integral-derivative controller integrated with a stimulation system which effects recruitment of motor units according to the size principle. This system is intended to control muscle length while shortening against fixed loads. Feline sciatic nerves were exposed and stimulated with ramp, triangular, sinusoidal, staircase and random signals as test inputs. Changes in muscle length and effective time delay under different conditions were measured and analyzed. Differences of tracking quality between open- and closed-loop conditions were examined through analysis of variance as well as the differences between small (250g) and large (1kg) loads. The results showed that parameters used to compare muscle length output to the input signals were dramatically improved in the closed-loop trials as compared to the open-loop condition. Mean squared correlation coefficients between input and output signals for ramp signals increased by 0.019, and for triangular signals by 0.12. Mean peak cross correlation between input and output signals for sinusoidal waveforms increased by 0.06, with decreases in time to peak cross correlation (effective time delay) from 195 to 38ms. In slow random signals (power up to 0.5Hz), peak cross correlation went from 0.74 to 0.89, and time-to-peak cross correlation decreased from 205 to 55ms. In fast random signals (power up to 1Hz), peak cross correlation went from 0.82 to 0.89, and time-to-peak cross correlation from 200 to 65ms. For staircase signals, both rise times and mean steady-state errors decreased. It was found that, once the length range was set, the load weight had no effect on tracking performance. Analysis of mean square error demonstrated that for all signals tested, the feedback decreased the tracking error significantly, whereas, again, load had no effect. The results suggest that tracking is vastly improved by using a closed-loop system to control muscle length, and that load does not affect the quality of signal tracking as measured by standard control system analysis methods.     

De novo determination of protein structure by NMR using orientational and long-range order restraints

Orientational and novel long-range order restraints available from paramagnetic systems have been used to determine the backbone solution structure of the cytochrome c' protein to atomic resolution in the complete absence of restraints derived from the nuclear Overhauser effect. By exploiting the complementary geometric dependence of paramagnetic pseudocontact shifts and the recently proposed Curie-dipolar cross correlated relaxation effect, in combination with orientational constraints derived from residual dipolar coupling, autorelaxation rate ratios and secondary structure constraints, it is possible to define uniquely the fold and refine the tertiary structure of the protein (0.73 A backbone rmsd for 82/129 amino acid residues) starting from random atomic Cartesian coordinates. The structure calculation protocol, developed using specific models to describe the novel constraint interactions, is robust, requiring no precise a priori estimation of the various interaction strengths, and provides unambiguous convergence based only on the value of the target function. Tensor eigenvalues and their component orientations are allowed to float freely, and are thus simultaneously determined, and found to converge, during the structure calculation.     

Spatial correlation analysis of atrial activation patterns during sustained atrial fibrillation in conscious goats

In this study we applied both linear and nonlinear spatial correlation measures to characterize epicardial activation patterns of sustained atrial fibrillation in instrumented conscious goats. It was investigated if nonlinearity was involved in the spatial coupling of atrial regions and to what extent fibrillation was organized in the experimental model of sustained atrial fibrillation (AF) in instrumented goats. Data were collected in five goats during experiments to convert AF by continuous infusion of cibenzoline. Spatial organization during AF was quantified with the linear spatial cross correlation function and the nonlinear spatial cross redundancy which was calculated using the Grassberger-Procaccia correlation integral. Two different types of correlation were evaluated to distinguish simultaneous interaction from non-simultaneous interaction, for instance resulting from propagation of fibrillation waves. The nonlinear association length and the linear correlation length were estimated along the principal axes of iso-correlation contours in two-dimensional correlation maps of the nonlinear spatial redundancy and the linear spatial correlation function, respectively. To quantitatively assess the degree of nonlinearity, the association length was also estimated from the linearized spatial redundancy using multivariate surrogate data. The differences between the nonlinear and linearized association lengths indicated that a nonlinear component in the spatial organization of AF predominantly existed in the right atrium. The degree of organization characterized by association length along the short principal axis was higher in the right atrium (15 +/- 7 mm) than in the left atrium (8 +/- 4 mm). The spatial extension of coherent atrial patches was estimated from a surface of association equal to the area spanned by the principal axes of iso-correlation contours from the redundancy, including the effects from non-simultaneous interaction. Interpreting this area as the spatial domain of a fibrillation wavelet, the results suggest that the mapped region was activated on average by two wavelets in the left atrium and by one wavelet in the right atrium. Therefore, the activation pattern of sustained AF in goats was relatively organized, consistent with type II of AF. It is suggested that the surface of association is a measure of the number of independent wavelets present in the atria during sustained AF, and that larger association lengths result from fewer and larger reentrant circuits.     

Simultaneous on/off regulation of transgenes located on a mammalian chromosome with Cre-expressing adenovirus and a mutant loxP

The site-specific recombinase Cre has often been used for on/off regulation of expression of transgenes introduced into the mammalian chromosome. However, this method is only applicable to the regulation of a single gene and cannot be used to simultaneously regulate two genes, because site-specific recombination occurs from the target loxP sequence of one regulating unit to the loxP sequence of any other unit and would eventually disrupt the structure of both regulating units. We previously reported a mutant loxP sequence with a two base substitution called loxP V (previously called loxP 2272), with which wild-type loxP cannot recombine but with which the identical mutant loxP recombines efficiently. In the present study we isolated cell lines bearing two regulating units on a chromosome containing a pair of wild-type loxP sequences or mutant loxP V sequences. After infection with Cre-expressing recombinant adenovirus AxCANCre, expression of a gene in each regulating unit was simultaneously turned on and off. Southern analyses showed that both regulating units were processed simultaneously and independently, even after infection with a limited amount of AxCANCre. The results showed that simultaneous regulation of gene expression on a mammalian chromosome mediated by Cre can be achieved by using mutant loxP V and wild-type loxP. This method may be a useful approach for conditional transgenic/knockout animals and investigation of gene function involving two genes simultaneously. Another possible application is for preparation of a new packaging cell line of viral vectors through simultaneous production of toxic viral genes.     

NMR studies of the conformation of the natural sweetener rebaudioside A

Rebaudioside A is a natural sweetener from Stevia rebaudiana in which four β-d-glucopyranose units are attached to the aglycone steviol. Its ¹H and ¹³C NMR spectra in pyridine-d₅ were assigned using 1D and 2D methods. Constrained molecular dynamics of solvated rebaudioside using NMR constraints derived from ROESY cross peaks yielded the orientation of the β-d-glucopyranose units. Hydrogen bonding was examined using the temperature coefficients of the hydroxyl chemical shifts, ROESY and long-range COSY spectra, and proton-proton coupling constants.     

Correlations of neuronal spike discharges of VL neurons during spontaneous firing and during the activity evoked by peripheral stimulation

The temporal relations between simultaneously recorded neurons of the nucleus ventralis lateralis (VL) of cat thalamus were studied. The interaction and the functional connections between individual VL neurons are described. This was achieved with an application of cross correlation techniques. The response patterns of different individual neurons to somatic sensory and photic stimuli were also analyzed. For the purpose of classifying neurons as thalamocortical relay cells (T-C) and non relay cells (N-C) which do not project to the motor sensory cortex antidromic cortical stimulation was used. This stimulation was also used as conditioning one when proceeded peripheral stimuli. To analyze the nonspecific specific interactions upon single neurons conditioning photic stimuli were applied. The results show that T-C neurons are antidromically excited from a wide cortical areas and that the functional interaction between T-C neurons is mediated by a shared input from common sources. It is further postulated that N-C cells interposed between relay neurons subserve the functions of gating units modifying the neuronal network of lateral ventral nucleus of the thalamus.     

Oxidative capacity and capillary density of diaphragm motor units

Motor units in the cat diaphragm (DIA) were isolated in situ by microdissection and stimulation of C5 ventral root filaments. Motor units were classified based on their isometric contractile force responses and fatigue indexes (FI). The muscle fibers belonging to individual units (i.e., the muscle unit) were identified using the glycogen-depletion method. Fibers were classified as type I or II based on histochemical staining for myofibrillar adenosine triphosphatase (ATPase) after alkaline preincubation. The rate of succinate dehydrogenase (SDH) activity of each fiber was determined using a microphotometric procedure. The location of capillaries was determined from muscle cross sections stained for ATPase after acid (pH = 4.2) preincubation. The capillarity of muscle unit fibers was determined by counting the number of capillaries surrounding fibers and by calculating the number of capillaries per fiber area. A significant correlation was found between the fatigue resistance of DIA units and the mean SDH activity of muscle unit fibers. A significant correlation was also observed between DIA unit fatigue resistance and both indexes of muscle unit fiber capillarity. The mean SDH activity and mean capillary density of muscle unit fibers were also correlated. We conclude that DIA motor unit fatigue resistance depends, at least in part, on the oxidative capacity and capillary density of muscle unit fibers.     

Determination of antithyroid antibodies by an immunoenzymatic method; an adaptation for expressing results in international units]

Solid phase immunoenzymatic methods (ELISA) have been developed for the determination of antithyroglbulin (ATG), antimicrosomal (AMc) and antimembrane (ATMA) antibodies in blood serum. The results have been expressed in international units (IU). The level of nonspecific reaction was determined on the basis of 30 samples of blood serum obtained from healthy donors. The double standard deviation values amounted to 8 IU for antithyroglobulin antibodies, 17 IU for antimicrosomal antibodies and 53 IU for antimembrane antibodies at the serum dilution of 1:100. The values of double standard deviation obtained for the healthy donors correspond to the borderline between the positive serum samples and those containing no autoantibodies. The level of autoantibodies in patients with autoimmune diseases of the thyroid varied considerably ranging from complete absence to several thousand units per milliliter in single cases. Antithyroglobulin antibodies were determined simultaneously by using the described method and the commercial kit (Walker, Cambridge) and the results obtained by the two methods were compared. A linear correlation with the correlation coefficient r = 0.93, p < 0.001 was obtained. A good but nonlinear correlation was demonstrated with the methods expressing the results in titre values.     

收敛交叉映射方法及其在生态学中的应用

收敛交叉映射(CCM)是一种分析非线性系统中时间序列变量间因果关系的方法。其不同于传统的线性系统分析方法,是通过对变量进行状态空间重构来获取变量的历史信息,随着时间序列不断增长,当其估计性能呈现收敛的性质时,可以判断因果关系的存在。本文介绍了CCM的发展史及其较传统的格兰杰因果检验的优点,详细阐明了CCM的原理、算法过程和实现途径。CCM作为一种针对变量间具有弱到中等强度耦合关系的系统分析方法,可以用来有效地解决非线性生态系统多变量间复杂的因果关系问题。将该方法应用于具有空间信息的多点位时间序列变量间因果分析时,应充分考虑点位间的空间自相关性,与可以去除变量及序列间空间相关性的方法相结合,从而确保CCM对变量因果关系的分析更加准确,结果也更具有信服力。     

Wavelet based correlation and coherence analysis reveals frequency dependent motor unit conduction velocity of the abductor pollicis brevis muscle

The purpose of this study was to investigate the motorunit conduction velocity (CV) as a function of frequency. A wavelet based correlation and coherence analysis was introduced to measure CV as a function of frequency. Based on the most simple assumption that the power spectra of the motor unit action potential is shifted to higher frequencies with increasing CV, we hypothesized that there would be a monotonic or linear trend of increasing CV with frequency. This trend was only confirmed at higher frequencies. At lower frequencies the trend was often reversed leading to a decrease in CV with increasing frequency. Thus the CV was high at low frequencies, went through a minimum at about 170 Hz and increased at higher frequencies, as expected. The observed CV at low frequencies could not be fully explained by assuming non-propagating signals or variable groups of motor units. We concluded that spectra and CV contain partly independent information about the muscles and that the wavelet based method provides the tools to measure them both simultaneously.