Simulation of NOESY spectra of DNA segments: A new scaling procedure for iterative comparison of calculated and experimental NOE intensities

Summary A new algorithm for simulation of two-dimensional NOESY spectra of DNA segments has been developed. For any given structure, NOE intensities are calculated using the relaxation matrix approach and a new realistic procedure is suggested for 1:1 comparison of calculated and experimental intensities. The procedure involves a novel method for scaling of calculated NOE intensities to represent volumes of digitised cross peaks in NOESY spectra. A data base of fine structures of all the relevant cross peaks with Lorentzian line shapes and in-phase components, is generated in a digitised manner by two-dimensional Fourier transformation of simulated time domain data, assuming a total intensity of 1.0 for each of the cross peaks. With this procedure, it is shown that the integrated volumes of these digitised cross peaks above any given threshold scale exactly as the total intensity of the respective peaks. This procedure eliminates the repetitive generation of digitised cross peaks by two-dimensional Fourier transformation during the iterative process of structure alteration and NOE intensity calculation and thus enhances the speed of DNA structure optimization. Illustrative fits of experimental and calculated spectra obtained using the new procedure are shown.[/p]     

Automatic procedure for using models of proteins in molecular replacement

In a crystallography experiment, a crystal is irradiated with X-rays whose diffracted waves are collected and measured. The reconstruction of the structure of the molecule in the crystal requires knowledge of the phase of the diffracted waves, information that is lost in the passage from the three-dimensional structure of the molecule to its diffraction pattern. It can be recovered using experimental methods such as heavy-atom isomorphous replacement and anomalous scattering or by molecular replacement, which relies on the availability of an atomic model of the target structure. This can be the structure of the target protein itself, if a previous structure determination is available, or a computational model or, in some cases, the structure of a homologous protein. It is not straightforward to predict beforehand whether or not a computational model will work in a molecular replacement experiment, although some rules of thumb exist. The consensus is that even minor differences in the quality of the model, which are rather difficult to estimate a priori, can have a significant effect on the outcome of the procedure. We describe here a method for quickly assessing whether a protein structure can be solved by molecular replacement. The procedure consists in submitting the sequence of the target protein to a selected list of freely available structure prediction servers, cluster the resulting models, select the representative structures of each cluster and use them as search models in an automatic phasing procedure. We tested the procedure using the structure factors of newly released proteins of known structure downloaded from the Protein Data Bank as soon as they were made available. Using our automatic procedure we were able to obtain an interpretable electron density map in more than half the cases.     

Theory of light diffraction by single skeletal muscle fibers.

A theoretical discussion is presented describing the diffraction of laser light by a single fiber of striated muscle. The complete three-dimensional geometry of the fiber has been taken into consideration. The basic repeated unit is taken as the sarcomere of a single myofibril, including its cylindrical geometry. The single fiber is considered as the sum of myofibrils up to the fiber dimensions. When proper phasing is taken into account, three cases of interest are analyzed. (a) When the adjacent myofibrils are totally aligned with respect to their index of refraction regions (e.g., A and I bands), then the diffraction pattern reflects that of a larger striated cylinder with the dimensions of the fiber. (b) When a particular skew plane develops for the myofibril elements, additional Bragg reflection occurs at certain specific sarcomere lengths, and intensity asymmetry amongst the diffracted orders occurs. (c) When the myofibril phasing changes in a random fashion, while all sarcomeres remain at the same length, then intensity decrease is directly related to the phase deviation from a reference phase point. This condition may well describe a fiber undergoing active isometric contraction.     

Effects of disorder on fibre diffraction patterns

Diffraction patterns from oriented polycrystalline specimens of fibrous polymers sometimes contain features indicating that the constituent microcrystallites are disordered. Such disorder affects the relationship between the crystal structure and the diffracted intensities. Therefore, the effects of disorder must be considered when determining structures from fibre diffraction data. Theory is developed here that describes the intensities diffracted by disordered polycrystalline fibres, and is used to calculate diffraction patterns from stimulated specimens with various kinds of disorder. The results show how Bragg and continuous diffraction are distributed on such diffraction patterns, and implications for structure determination are discussed.     

INTERMITTENT STIMULATION BY LIGHT : III. THE RELATION BETWEEN INTENSITY AND CRITICAL FUSION FREQUENCY FOR DIFFERENT RETINAL LOCATIONS

When measurements of the critical fusion frequency for white light over a large range of intensities are made with the rod-free area of the fovea, the relation between critical frequency and log I is given by a single sigmoid curve, the middle portion of which approximates a straight line whose slope is 11.0. This single relation must be a function of the foveal cones. When the measurements are made with a retinal area placed 5° from the fovea, and therefore containing both rods and cones, the relation between critical frequency and log I shows two clearly separated sections. At the lower intensities the relation is sigmoid and reaches an upper level at about 10 cycles per second, which is maintained for 1.25 log units, and is followed by another sigmoid relationship at the higher intensities similar to the one given by the rod-free area alone. These two parts of the data are obviously separate functions of the rods at low intensities and of the cones at high intensities. This is further borne out by similar measurements made with retinal areas 15° and 20° from the fovea where the ratio of rods to cones is anatomically greater than at 5°. The two sections of the data come out farther apart on the intensity scale, the rod portion being at lower intensities and the cone portion at higher intensities than at 5°. The general form of the relation between critical frequency and intensity is therefore determined by the relative predominance of the cones and the rods in the retinal area used for the measurements.     

Post-refinement method for snapshot serial crystallography

A post-refinement procedure has been devised for ‘snapshot’ diffraction data consisting entirely of partially recorded reflections, each diffraction pattern from a crystal in an orientation unrelated to the others. Initial estimates of the diffraction geometry are used to calculate initial partialities, which are then used to scale the entire dataset together to produce initial estimates of the fully integrated intensities. The geometrical parameters for each pattern are then refined to maximize the agreement between these estimates and the calculated intensities in each pattern, and the procedure repeated iteratively. The performance of the procedure was investigated using simulated data and found to yield a significant improvement in the data quality.     

Intercentral Relations of the Human EEG during Listening to Music

Different musical styles and intensities produce characteristic patterns of changes in the correlation of neocortical biopotentials. Classical music of three intensities and rock music of medium and high intensities were shown to produce asymmetry in the pattern of coherence (Coh) of the cortical activity of listeners: intrahemispheric Coh in the right hemisphere increased, while a decrease in the EEG synchronization prevailed in the left hemisphere. A focus of Coh integration, most pronounced for the γ frequencies, was formed during listening to both classical and rock music (except rock music of a low intensity). Listening to rock music of a low intensity substantially increased the probability of a decrease in intra- and interhemispheric Coh in both hemispheres, which was pronounced in all frequency bands. Listening to rock music changed interhemispheric Coh in a greater percent of cases than listening to classical music.__________Translated from Fiziologiya Cheloveka, Vol. 31, No. 4, 2005, pp. 27–32.Original Russian Text Copyright © 2005 by Sakharov, Davydov, Pavlygina.     

The effect of selective deuteration on magnetization transfer in larger proteins

Summary The effects of selective deuteration on calculated NOESY intensities have been analyzed for the structure of theE. coli trp aporepressor, a 25 kDa protein. It is shown that selectively deuteratedtrp aporepressor proteins display larger calculated NOESY intensities than those for the same interproton distances in the natural abundance protein. The relatively larger magnetization transfer is demonstrated by a comparison of the NOE build-up curves for specific proton pairs, and for the calculated NOE intensities of short-range NOEs to backbone amide protons. This increase in intensity is especially pronounced for the NH¹–NH¹⁺¹ cross peaks in the -helical regions, and particularly for amide protons of two sequential deuterated residues. The effect is shown to be further intensified for longer mixing times. It is also shown that in all cases, each amide proton exhibits stronger NOEs to its own side chain, with an enhanced effect for deuterated derivatives. This theoretical analysis demonstrates that an evaluation of the relative NOE intensities for different selectively deuterated analogs may be an important tool in assigning NMR spectra of large proteins. These results also serve as a guide for the interpretation of NOEs in terms of distances for structure calculations based on data using selectively deuterated proteins.     

A redox-dependent interaction between two electron-transfer partners involved in photosynthesis

Ferredoxin:NADP⁺:reductase (FNR) catalyzes one terminal step of the conversion of light energy into chemical energy during photosynthesis. FNR uses two high energy electrons photoproduced by photosystem I (PSI) and conveyed, one by one, by a ferredoxin (Fd), to reduce NADP⁺ to NADPH. The reducing power of NADPH is finally involved in carbon assimilation. The interaction between oxidized FNR and Fd was studied by crystallography at 2.4 Å resolution leading to a three-dimensional picture of an Fd–FNR biologically relevant complex. This complex suggests that FNR and Fd specifically interact prior to each electron transfer and disassemble upon a redox-linked conformational change of the Fd.     

Calcium Determines the Supramolecular Organization of Fibrillin-rich Microfibrils

Microfibrils are ubiquitous fibrillin-rich polymers that are thought to provide long-range elasticity to extracellular matrices, including the zonular filaments of mammalian eyes. X-ray diffraction of hydrated bovine zonular filaments demonstrated meridional diffraction peaks indexing on a fundamental axial periodicity (D) of ~56 nm. A Ca²⁺-induced reversible change in the intensities of the meridional Bragg peaks indicated that supramolecular rearrangements occurred in response to altered concentrations of free Ca²⁺. In the presence of Ca²⁺, the dominant diffracting subspecies were microfibrils aligned in an axial 0.33-D stagger. The removal of Ca²⁺ caused an enhanced regularity in molecular spacing of individual microfibrils, and the contribution from microfibrils not involved in staggered arrays became more dominant. Scanning transmission electron microscopy of isolated microfibrils revealed that Ca²⁺ removal or addition caused significant, reversible changes in microfibril mass distribution and periodicity. These results were consistent with evidence from x-ray diffraction. Simulated meridional x-ray diffraction profiles and analyses of isolated Ca²⁺-containing, staggered microfibrillar arrays were used to interpret the effects of Ca²⁺. These observations highlight the importance of Ca²⁺ to microfibrils and microfibrillar arrays in vivo.     

Excitation and Optimization Modeling of Surface Plasmon Polaritons in a Concentric Circular Metallic Grating Film

Interaction behavior between surface plasmon polaritons (SPPs) and Hankel-distributed diffracted waves (DWs) on a silver concentric circular grating film is studied using a rigorous coupled-wave technique for circular structure. It is shown that the numerical technique reveals the excitation characteristics of SPPs in the circular metal grating as well as provides an accurate calculation of SPP intensities for further optimization designs. Results show that the SPPs can be excited by various DWs through the control of wavelength and angle of the incident light. The most efficient excitation of SPPs from this circular metal grating structure can be obtained from the +1^st-order DW under a normal incidence with wavelength close to the grating period, and the optimal thickness and duty cycle of the grating are found to be 370 and 0.5 nm, respectively. It is shown that the optimized intensity of SPPs excited from circular metal grating can be higher than that from strip metal grating by over one order of magnitude.     

Active Contours Driven by Multi-Feature Gaussian Distribution Fitting Energy with Application to Vessel Segmentation

Active contour models are of great importance for image segmentation and can extract smooth and closed boundary contours of the desired objects with promising results. However, they cannot work well in the presence of intensity inhomogeneity. Hence, a novel region-based active contour model is proposed by taking image intensities and ‘vesselness values’ from local phase-based vesselness enhancement into account simultaneously to define a novel multi-feature Gaussian distribution fitting energy in this paper. This energy is then incorporated into a level set formulation with a regularization term for accurate segmentations. Experimental results based on publicly available STructured Analysis of the Retina (STARE) demonstrate our model is more accurate than some existing typical methods and can successfully segment most small vessels with varying width.     

Differential Growth and Phototropic Bending in Phycomyces

Using present knowledge of the cell's optical and growth mechanisms, a theoretical bending speed of about 5° min.^-1 is calculated for unilateral irradiation by a single beam of normally incident visible light; this figure is of the magnitude found experimentally. Between beams of light opposed at 180°, the resultant bending speed is given by the difference-to-sum ratio of the light intensities of the two beams. Valid comparisons between cells differing in size, growth speed, or optical properties are made by expressing bending speed as a fraction of each cell's bending response to unilateral irradiation. With multiple beams differing in intensity and azimuth, the resultant bending speed follows from vector addition of phototropic components proportional to the flux fraction of each beam. The bending speed in Oehlkers' experiment where a luminous area is the light source also appears compatible with this rule. In such experiments, the bending speed quantitatively matches the scaled asymmetry of the pattern of flux incident upon the cell. Resolution experiments support the assumption that light intensity enters into steady state phototropic formulations as the first power of I.     

INTENSITY DISCRIMINATION IN THE HUMAN EYE : I. THE RELATION OFΔI/ITO INTENSITY

New measurements of the brightness difference sensibility of the eye corroborate the data of previous workers which show that ΔI/I decreases as I increases. Contrary to previous report, ΔI/I does not normally increase again at high intensities, but instead decreases steadily, approaching a finite limiting value, which depends on the area of the test-field and on the brightness of the surrounding field. On a logarithmic plot, the data of ΔI/I against I for test-fields below 2° are continuous, whereas those for test-fields above 2° show a sharp discontinuity in the region of intensity in which ΔI/I decreases rapidly. This discontinuity is shown to divide the data into predominantly rod function at low intensities, and predominantly cone function at high intensities. Fields below 2° give higher values of ΔI/I at all intensities, when compared with larger fields. Fields greater than one or two degrees differ from one another principally on the low intensity side of the break. Changes in area above this limit are therefore mainly effective by changing the number of rods concerned. This is confirmed by experiments controlling the relative numbers of rods and cones with lights of different wavelength and with different retinal locations. At high intensities ΔI/I is extremely sensitive to changes in brightness of surrounding visual fields, except for large test-fields which effectually furnish their own surrounds. This sensitivity is especially marked for fields of less than half a degree in diameter. Although the effect is most conspicuous for high intensities, the surround brightness seems to affect the relation between variables as a whole, except in very small fields where absence of a surround of adequate brightness results in the distortion of the theoretical relation otherwise found. The theoretical relationship for intensity discrimination derived by Hecht is shown to fit practically all of the data. Changes in experimental variables such as retinal image area, wavelength, fixation, and criterion may be described as affecting the numerical quantities of this relationship.     

X-ray diffraction study of myelin structure in immature and mutant mice

X-ray diffraction patterns were obtained from freshly dissected central and peripheral nerves of quaking, myelin synthesis deficiency ($\text{msd}$), and trembler mutants, as well as immature and adult normal mice. The patterns were compared with respect to strength of myelin diffraction, background scatter level, repeat period, and intensity and linewidth of Bragg reflections. The deficiency of myelin in optic nerves was found to be (in decreasing severity): quaking > immature > trembler ? normal adult; and in sciatic nerves: $\text{trembler > immature > quaking}\text{msd ?}\text{normal}$ adult. Repeat periods about 3 Å less than that for normal adult sciatic myelin were detected in corresponding nerves from immature, quaking, and trembler mice. In some trembler sciatic nerves a second phase having a 190–200 Å period and accounting for about 60% of the total ordered myelin was also evident. Comparison of electron density profiles of membrane units calculated from the repeat periods and diffracted intensities for sciatic myelins indicate structural differences at the molecular level. The main findings are: (1) quaking myelin shows a significant elevation of density in the external protein-water layer between membrane bilayers; (2) the membrane bilayer of immature myelin is ≈ 2 Å thinner than that for normal adult; (3) the membrane bilayer of the more compact phase in trembler myelin is ≈ 5 Å thinner than for normal; and (4) the difference in repeat periods for the two phases present in some of the trembler nerves can be accounted for predominantly by distinct membrane bilayer separations at the external boundary.     

A new label technology for the detection of specific polymerase chain reaction products in a closed tube

A novel signal generation principle suitable for real time and end-point detection of specific PCR products in a closed tube is described. Linear DNA probes were labeled at their 5′-ends with a stable, fluorescent terbium chelate. The fluorescence intensity of this chelate is lower when it is coupled to single-stranded DNA than when the chelate is free in solution. The synthesized probes were used in the real time monitoring of PCR using a prototype instrument that consisted of a fluorometer coupled to a thermal cycler. When the probe anneals to a complementary target amplicon, the 5′→3′ exonucleolytic activity of DNA polymerase detaches the label from the probe. This results in an enhanced terbium fluorescence signal. Since terbium has a long excited state lifetime, its fluorescence can be measured in a time-resolved manner, which results in a low background fluorescence and a 1000-fold signal amplification. The detection method is quantitative over an extremely wide linear range (at least 10–10⁷ initial template molecules). The label strategy can easily be combined with existing label technologies, such as TaqMan 5′-exonuclease assays, in order to carry out multiplex assays that do not suffer from overlapping emission peaks of the fluorophores.     

Salivary alpha amylase and salivary cortisol response to fluid consumption in exercising athletes

The objective of the study was to examine salivary biomarker response to fluid consumption in exercising athletes. Exercise induces stress on the body and salivary alpha amylase (sAA) and salivary cortisol are useful biomarkers for activity in the sympathoadrenal medullary system and the hypothalamic pituitary adrenal axis which are involved in the stress response. Fifteen college students were given 150 ml and 500 ml of water on different days and blinded to fluid condition. The exercise protocol was identical for both fluid conditions using absolute exercise intensities ranging from moderate to high. Saliva was collected prior to exercise, post moderate and post high intensities and analyzed by Salimetrics assays. Exercise was significant for sAA with values different between pre-exercise (85 ± 10 U · ml⁻¹) and high intensity (284 ± 30 U · ml⁻¹) as well as between moderate intensity (204 ± 32 U · ml⁻¹) and high intensity. There was no difference in sAA values between fluid conditions at either intensity. Exercise intensity and fluid condition were each significant for cortisol. Cortisol values were different between pre-exercise (0.30 ± 0.03 ug · dL⁻¹) and high intensity (0.45 ± 0.05 ug · dL⁻¹) as well as between moderate intensity (0.33 ± 0.04 ug · dL⁻¹) and high intensity. Moderate exercise intensity cortisol was lower in the 500 ml condition (0.33 ± 0.03 ug · dL⁻¹) compared with the 150 ml condition (0.38 ± 0.03 ug · dL⁻¹). This altered physiological response due to fluid consumption could influence sport performance and should be considered. In addition, future sport and exercise studies should control for fluid consumption.     

Intriguing effects of selection intensity on the evolution of prosocial behaviors

In many models of evolving populations, genetic drift has an outsized role relative to natural selection, or vice versa. While there are many scenarios in which one of these two assumptions is reasonable, intermediate balances between these forces are also biologically relevant. In this study, we consider some natural axioms for modeling intermediate selection intensities, and we explore how to quantify the long-term evolutionary dynamics of such a process. To illustrate the sensitivity of evolutionary dynamics to drift and selection, we show that there can be a “sweet spot” for the balance of these two forces, with sufficient noise for rare mutants to become established and sufficient selection to spread. This balance allows prosocial traits to evolve in evolutionary models that were previously thought to be unconducive to the emergence and spread of altruistic behaviors. Furthermore, the effects of selection intensity on long-run evolutionary outcomes in these settings, such as when there is global competition for reproduction, can be highly non-monotonic. Although intermediate selection intensities (neither weak nor strong) are notoriously difficult to study analytically, they are often biologically relevant; and the results we report suggest that they can elicit novel and rich dynamics in the evolution of prosocial behaviors.     

Avian magnetic compass can be tuned to anomalously low magnetic intensities

The avian magnetic compass works in a fairly narrow functional window around the intensity of the local geomagnetic field, but adjusts to intensities outside this range when birds experience these new intensities for a certain time. In the past, the geomagnetic field has often been much weaker than at present. To find out whether birds can obtain directional information from a weak magnetic field, we studied spontaneous orientation preferences of migratory robins in a 4 µT field (i.e. a field of less than 10 per cent of the local intensity of 47 µT). Birds can adjust to this low intensity: they turned out to be disoriented under 4 µT after a pre-exposure time of 8 h to 4 µT, but were able to orient in this field after a total exposure time of 17 h. This demonstrates a considerable plasticity of the avian magnetic compass. Orientation in the 4 µT field was not affected by local anaesthesia of the upper beak, but was disrupted by a radiofrequency magnetic field of 1.315 MHz, 480 nT, suggesting that a radical-pair mechanism still provides the directional information in the low magnetic field. This is in agreement with the idea that the avian magnetic compass may have developed already in the Mesozoic in the common ancestor of modern birds.     

声光可调谐滤波器的细胞生物学研究应用

波长选择在荧光光谱仪和显微镜等光学应用中发挥了至关重要的作用。声光可调谐滤波器(AOTF)作为一种电光器件可实现多光源入射波长、功率的同时调制。在声光可调谐滤波器中,压电换能器结合于二氧化碲或石英晶体产生高频声波,改变晶体折射率形成周期性分布。该现象在晶体中生成衍射光栅,使以布拉格角正交入射的光束被高效衍射至一阶光束。当改变施加到晶体的信号频率时将改变折射率变化周期,因此,衍射光的波长随之改变。同时,衍射光强度由施加到晶体的信号振幅决定。本文从声光可调谐滤波器原理和特点出发,总结了声光可调谐滤波器在细胞生物学研究系统中的应用模型。得益于作用时间短、波长分辨率高、无振动部件等特性,声光可调谐滤波器提升了多波长光源功率调制能力,使细胞计数系统具备了细胞高光谱成像能力。所以不仅限于传统细胞生物学研究,包含声光可调谐滤波器件的系统还将在多参数高内涵成像分析、扫描荧光显微术、药物毒理研究等领域成为有力的研究工具。