Optical diffractometry in bone research

A new method of quantitative evaluation and comparison for bone tissue histological studies is described. Optical diffractometry allows numerical evaluation of dimensions of structures being studied and also permits study by discriminant analysis.     

Aggregation kinetics of bovine serum albumin studied by FTIR spectroscopy and light scattering

To investigate which type of structural and conformational changes is involved in the aggregation processes of bovine serum albumin (BSA), we have performed thermal aggregation kinetics in D(2)O solutions of this protein. The tertiary conformational changes are followed by Amide II band, the secondary structural changes and the formation of beta-aggregates by the Amide I' band and, finally, the hydrodynamic radius of aggregates by dynamic light scattering. The results show, as a function of pD, that: tertiary conformational changes are more rapid as pD increases; the aggregation proceeds through formation of ordered aggregates (oligomers) at pD far from the isoelectric point of the protein; disordered structures add as the pD decreases. Moreover, beta-aggregates seem to contribute only to oligomers formation, as showed by the good correlation between kinetics of scattering intensity and IR absorption intensity. These results indicate for BSA a general mechanism of aggregation composed by partial unfolding of the tertiary structure and by the decrease of alpha-helix and random coil contents in favor of beta-sheet aggregates. This mechanism strictly depends on pD and gives rise to almost two distinct types of macromolecular aggregates.     

Spectroscopic studies of D-α-tocopherol concentration-induced transformation in egg phosphatidylcholne vesicles

The effects of embedding up to 60 mol% of α-tocopherol (α-Toc) on the morphology and structure of the egg phosphatidylcholine (PC) membrane were studied using spectroscopic techniques. The resulting vesicles were subjected to turbidometric and dynamic light scattering measurements to evaluate their size distribution. The α-Toc intrinsic fluorescence and its quenching was used to estimate the tocopherol position in the membrane. Optical microscopy was used to visualize morphological changes in the vesicles during the inclusion of tocopherol into the 2 mg/ml PC membrane. The incorporation of up to 15 mol% of tocopherol molecules into PC vesicles is accompanied by a linear increase in the fluorescence intensity and the simultaneous formation of larger, multilamellar vesicles. Increasing the tocopherol concentration above 20 mol% induced structural and morphological changes leading to the disappearance of micrometer-sized vesicles and the formation of small unilamellar vesicles of size ranging from 30 to 120 nm, mixed micelles and non-lamellar structures.     

Myosin head orientation: a structural determinant for the Frank-Starling relationship

The cellular mechanism underlying the Frank-Starling law of the heart is myofilament length-dependent activation. The mechanism(s) whereby sarcomeres detect changes in length and translate this into increased sensitivity to activating calcium has been elusive. Small-angle X-ray diffraction studies have revealed that the intact myofilament lattice undergoes numerous structural changes upon an increase in sarcomere length (SL): lattice spacing and the I(1,1)/I(1,0) intensity ratio decreases, whereas the M3 meridional reflection intensity (I(M3)) increases, concomitant with increases in diastolic and systolic force. Using a short (～10 ms) X-ray exposure just before electrical stimulation, we were able to obtain detailed structural information regarding the effects of external osmotic compression (with mannitol) and obtain SL on thin intact electrically stimulated isolated rat right ventricular trabeculae. We show that over the same incremental increases in SL, the relative changes in systolic force track more closely to the relative changes in myosin head orientation (as reported by I(M3)) than to the relative changes in lattice spacing. We conclude that myosin head orientation before activation determines myocardial sarcomere activation levels and that this may be the dominant mechanism for length-dependent activation.     

The Structural Dilemma of Bulk Polyethylene: An Intermediary Structure

Background

The Fourier space (reciprocal space) image of bulk polyethylene consists of lines superimposed on the coherent diffuse background. The mixed character of the image indicates the complex nature of these compounds. The inability in detecting full images of reciprocal space of polymeric substances without Compton radiation and the other undesirable diffuse scatterings has misled the structural analysis (structural characterisation) of these materials.

Principal Findings

We propose the use of anomalous diffractometry where, it is possible to obtain a real image of reciprocal space without Compton radiation and other undesirable scatterings. By using classical diffractometry techniques this procedure is not possible. This methodology permitted us to obtain the “Direct Delta function”, in the case of polycrystalline substances that was not previously detected. A new procedure was proposed to interpret the image of reciprocal space of bulk polyethylene. The results show the predominance of the geometry of local order determination compared to the crystal unit cell. The analysis of x-ray diffraction images illustrates that the elementary structural unit is a tetrahedron. This structural unit illustrates the atoms in the network scatter in a coherent diffuse manner. Moreover, the interference function derived from the coherent diffuse scattering dampens out quickly and the degree of randomness is superior to a liquid state. The radial distribution function derived from this interference function shows bond shortening in the tetrahedron configuration. It is this particular effect, which stabilises polyethylene.

Conclusion

Here we show by anomalous diffractometry that the traditional concept of the two-phase or the crystal-defect model is an oversimplification of the complex reality. The exploitation of anomalous diffractometry has illustrated that polyethylene has an intermediate ordered structure.     

Nanosecond retinal structure changes in K-590 during the room-temperature bacteriorhodopsin photocycle: picosecond time-resolved coherent anti-stokes Raman spectroscopy.

Time-resolved vibrational spectra are used to elucidate the structural changes in the retinal chromophore within the K-590 intermediate that precedes the formation of the L-550 intermediate in the room-temperature (RT) bacteriorhodopsin (BR) photocycle. Measured by picosecond time-resolved coherent anti-Stokes Raman scattering (PTR/CARS), these vibrational data are recorded within the 750 cm-1 to 1720 cm-1 spectral region and with time delays of 50-260 ns after the RT/BR photocycle is optically initiated by pulsed (< 3 ps, 1.75 nJ) excitation. Although K-590 remains structurally unchanged throughout the 50-ps to 1-ns time interval, distinct structural changes do appear over the 1-ns to 260-ns period. Specifically, comparisons of the 50-ps PTR/CARS spectra with those recorded with time delays of 1 ns to 260 ns reveal 1) three types of changes in the hydrogen-out-of-plane (HOOP) region: the appearance of a strong, new feature at 984 cm-1; intensity decreases for the bands at 957 cm-1, 952 cm-1, and 939 cm-1; and small changes intensity and/or frequency of bands at 855 cm-1 and 805 cm-1; and 2) two types of changes in the C-C stretching region: the intensity increase in the band at 1196 cm-1 and small intensity changes and/or frequency shifts for bands at 1300 cm-1 and 1362 cm-1. No changes are observed in the C = C stretching region, and no bands assignable to the Schiff base stretching mode (C = NH+) mode are found in any of the PTR/CARS spectra assignable to K-590. These PTR/CARS data are used, together with vibrational mode assignments derived from previous work, to characterize the retinal structural changes in K-590 as it evolves from its 3.5-ps formation (ps/K-590) through the nanosecond time regime (ns/K-590) that precedes the formation of L-550. The PTR/CARS data suggest that changes in the torsional modes near the C14-C15 = N bonds are directly associated with the appearance of ns/K-590, and perhaps with the KL intermediate proposed in earlier studies. These vibrational data can be primarily interpreted in terms of the degree of twisting of the C14-C15 retinal bond. Such twisting may be accompanied by changes in the adjacent protein. Other smaller, but nonetheless clear, spectral changes indicate that alterations along the retinal polyene chain also occur. The changes in the retinal structure are preliminary to the deprotonation of the Schiff base nitrogen during the formation of M-412. The time constant for the ps/ns K-590 transformation is estimated from the amplitude change of four vibrational bands in the HOOP region to be 40-70 ns.     

Change in intensity of respiration in development of some invertebrates

We studied the dynamic of respiration intensity during ontogenesis of flat worms (Dugesia tigrina), molluscs (Anodonta piscinalis and Viviparus viviparus, and insects (Leptinotarsa decemlineata). In planarians that reproduce vegetatively, the intensity of respiration increases just after fission and decreases at the subsequent phases of growth. In A. piscinalis, this index of metabolism increases during embryonic and early larval development and decreases at the later developmental stages. In V. viviparus, which develops in the female genital tract, the intensity of respiration remains unchanged during embryogenesis and decreases during late embryogenesis and subsequent phases of growth. In L. decemlineata, the intensity of respiration increases during embryonic and early larval development and then decreases to undergo cyclic changes times to molts. This index markedly decreases in the pupae, increases in the beginning of imaginal period, and then again decreases.     

The effects of aging on the intimal region of the human saphenous vein: insights from multimodal microscopy and quantitative image analysis

We hypothesized that structural remodeling associated with advancing age occurs in human saphenous veins. To address this hypothesis, we have identified structural remodeling in human saphenous veins by applying histochemistry, fluorescence staining and quantitative image analysis to specifically assess intimal area, intimal cellularity and intimal collagen content and organization. Saphenous veins were collected from patients undergoing coronary artery bypass graft surgery. Area measurements and cellularity were quantified using the image analysis software Stereo Investigator, employing planimetry and counting frames, respectively. Collagen content and organization were quantified in MetaMorph image analysis software based on measurements of color (hue, saturation, and intensity) from polarized light images. Intimal area and cellularity showed no statistically significant increases with age; in contrast, total collagen content showed a significant decrease with advancing age. Furthermore, collagen fiber types also demonstrated a statistically significant alteration with age; increases in age resulted in decreases in larger collagen fibers. No significant changes in small collagen fibers were identified. These results raise the possibility that age-associated structural alterations in total collagen content, specifically collagen fiber size, could be a factor in the etiology of age-associated venous diseases.     

Deviation of the living system from the stationary state during oogenesis

Summary The changes in respiration and glycolysis of whole oocytes and homogenates of oocytes during oogenesis have been studied.The respiration rate of whole oocytes increases during oocyte growth and decreases during oocyte maturation. The respiration rate of homogenates also increases during oocyte growth and does not change during egg maturation. At all oogenesis stages the respiration rate of homogenates is higher than the respiration rate of whole oocytes.Respiration intensity increases during the small growth stage and decreases during the following stages of oogenesis. Respiration intensity of homogenates under optimal conditions changes in a similar way. Respiration intensity under physiological conditions diminishes during oogenesis from 70% at the small growth stage to 42% in unfertilised eggs.The rate of glycolysis in whole oocytes and homogenates of oocytes increases during the growth period of oocytes but does not change during egg maturation.Glycolysis intensity of the whole oocytes increases at the large growth stage—stage of cytoplasmic vacuolisation—and becomes less during the following stages. Glycolysis intensity in homogenates under optimal conditions is much higher than the glycolysis intensity of whole oocytes and it decreases slightly during oogenesis. The efficiency of glycolysis in oocytes under physiological conditions is very low. It increases from the stage of cytoplasmic vacuolisation (3.6%) to the stage at which vitellogenesis starts (20%) and diminishes at the following stages.The data obtained are considered in the light of the Prigogine and Wiame interpretation of a thermodynamic theory of development.     

Structural alteration of the endothelial glycocalyx: contribution of the actin cytoskeleton

The endothelial glycocalyx is a carbohydrate–protein layer that lines the luminal surface of the endothelium. It anchors to the cell membrane via its core proteins that share extended link to the actin cytoskeleton. It is widely accepted that those protein domains and the attached carbohydrates are susceptible to pathological changes. It is unclear, however, to what extent the actin cytoskeleton contributes to the glycocalyx stability. In this study, we investigate the role of the actin cytoskeleton in the maintenance of the glycocalyx under static and laminar flow conditions in vitro. Our results show that in the static culture medium neither rapid actin depolymerisation nor prolonged actin disturbance leads to glycocalyx disruption from the apical surface of human umbilical vein endothelial cells. However, when endothelial cells are exposed to laminar flow for 24 h, the glycocalyx is seen to shift to the downstream peripheral region of the cell surface. The mean fluorescence intensity decreases to \(91.9 \pm 2.5\%\) of the control. When actin depolymerisation is introduced, the intensity decreases significantly to \(54.7 \pm 1.3\%\), indicating a severe disruption of the glycocalyx. Similar changes are observed in human aortic endothelial cells, where the intensity of the glycocalyx is reduced to \(72.8 \pm 1.6\%\) of the control. Collectively, we demonstrate that the actin cytoskeleton contributes to structural stability of the glycocalyx under shear stress. Our results can be used to develop new strategies to prevent shedding of the glycocalyx in cardiovascular diseases.     

Long-range interactions between DNA-bound ligands

We have studied the interaction of the A:T specific minor-groove binding ligand 4′, 6-diamidino-2-phenylindole (DAPI) with synthetic DNA oligomers containing specific binding sites in order to investigate possible long-range interactions between bound ligands. We find that DAPI binds cooperatively to the oligomers. The degree of cooperativity increases with increasing number of binding sites and decreases with the separation between them. This dependence is paralleled by changes in the induced circular dichroism spectrum of DAPI, which decreases in intensity at 335 nm and increases at 365 nm. These results are consistent with an allosteric interaction of DAPI with DNA, where bound ligands cooperatively alter the structure of the DNA molecule. This structural change seems possible to induce under various conditions, including physiological. One consequence of allosteric binding is that ligands bound at a distance from each other sense each other's presence and influence each other's properties. If some regulatory proteins the same conformational change as DAPI, novel mechanisms for controlling gene expression can be anticipated.     

Cofilin increases the torsional flexibility and dynamics of actin filaments

We have measured the effects of cofilin on the conformation and dynamics of actin filaments labeled at Cys374 with erythrosin-iodoacetemide (ErIA), using time-resolved phosphorescence anisotropy (TPA). Cofilin quenches the phosphorescence intensity of actin-bound ErIA, indicating that binding changes the local environment of the probe. The cofilin concentration-dependence of the phosphorescence intensity is sigmoidal, consistent with cooperative actin filament binding. Model-independent analysis of the anisotropies indicates that cofilin increases the rates of the microsecond rotational motions of actin. In contrast to the reduction in phosphorescence intensity, the changes in the rates of rotational motions display non-nearest-neighbor cooperative interactions and saturate at substoichiometric cofilin binding densities. Detailed analysis of the TPA decays indicates that cofilin decreases the torsional rigidity (C) of actin, increasing the thermally driven root-mean-square torsional angle between adjacent filament subunits from approximately 4 degrees (C = 2.30 x 10(-27) Nm2 radian(-1)) to approximately 17 degrees (C = 0.13 x 10(-27) Nm2 radian(-1)) at 25 degrees C. We favor a mechanism in which cofilin binding shifts the equilibrium between thermal ErIA-actin filament conformers, and facilitates two distinct structural changes in actin. One is local in nature, which affects the structure of actin's C terminus and is likely to mediate nearest-neighbor cooperative binding and filament severing. The second is a change in the internal dynamics of actin, which displays non-nearest-neighbor cooperativity and increases the torsional flexibility of filaments. The long-range effects of cofilin on the torsional dynamics of actin may accelerate P(i) release from filaments and modulate interactions with other regulatory actin filament binding proteins.     

Laser light-scattering analysis of protoplasmic streaming in the slime mold Physarum polycephalum

Laser light scattering is shown to be an effective means of obtaining a rapid, objective assessment of dynamic changes in the intact plasmodium of the myxomycete Physarum polycephalum during bidirectional (shuttle) streaming. The motion of material in a 100 mum diameter region of a plasmodial vein was studied by following changes in the autocorrelation function of the fluctuations in the scattered light intensity. The autocorrelation function was recorded at 10 s intervals and analyzed to follow changes in the flow velocity of protoplasm associated with shuttle streaming. Rhythmic velocity changes and a "beating" pattern of velocity maxima were readily observed. In an attempt to locate the site of underlying structural changes in the vein responsible for the changing pattern of flow, the average scattered intensity was separated into components derived from moving and stationary scatterers. Periodic variations in the light intensity due to stationary scatterers are related to the streaming cycle and indicate the occurrence of important structural changes in the vein walls. Two possible interpretations of the data are offered; one involving gross dynamic changes in vein structure, the other involving the formation, contraction, or breakdown of fibrillar material in the vein wall during the streaming cycle.     

Structuro-functional changes in bushy interoceptors during protracted anoxia

The bushy receptors of the frog urinary bladder respond to the effect of 60-minute-long anoxia with a complex combination of morphological. tinctorial and electrophysiological reactions. A biphase change in dynamics of bioelectrical activity takes place (an initial increase of frequency with its successive decrease), prolongation of the vital staining periods with methylene blue, change in the character of staining and decoloration of the receptory plates: increase in homogeneity and in intensity of staining, discontinuance of granuloformation and weakening of processes of the plates mobility. The ultrastructural changes are mainly concerned with mitochondria, where either crists reduce and osmiophility decreases, or increases. A part of mitochondria does not change. Certain heterogeneity in reactive changes of the receptors is noted. This is considered as manifestation of functional heterogeneity of the receptory units and their structural elements.     

Small-angle neutron scattering study of the ultrastructure of chloroplast thylakoid membranes - Periodicity and structural flexibility of the stroma lamellae

The multilamellar organization of freshly isolated spinach and pea chloroplast thylakoid membranes was studied using small-angle neutron scattering. A broad peak at ~0.02?(-1) is ascribed to diffraction from domains of ordered, unappressed stroma lamellae, revealing a repeat distance of 294?±7? in spinach and 345?±11? in pea. The peak position and hence the repeat distance of stroma lamellae is strongly dependent on the osmolarity and the ionic strength of the suspension medium, as demonstrated by varying the sorbitol and the Mg(++)-concentration in the sample. For pea thylakoid membranes, we show that the repeat distance decreases when illuminating the sample with white light, in accordance with our earlier results on spinach, also regarding the observation that addition of an uncoupler prohibits the light-induced structural changes, a strong indication that these changes are driven by the transmembrane proton gradient. We show that the magnitude of the shrinkage is strongly dependent on light intensity and that the repeat distance characteristic of the dark state after illumination is different from the initial dark state. Prolonged strong illumination leads to irreversible changes and swelling as reflected in increased repeat distances. The observed reorganizations are discussed within the frames of the current structural models of the granum-stroma thylakoid membrane assembly and the regulatory mechanisms in response to variations in the environmental conditions in vivo. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.     

Iron-binding ligands in the catalytic site of protocatechuate 3,4-dioxygenase

The tryptophan fluorescence maximum for holoprotocatechuate 3,4-dioxygenase(holo PCD) is blue-shifted slightly (3 nm) from that of the apoenzyme. In the preparation of apoenzyme, increases in tryptophan fluorescence intensity coincided with decreases in enzyme activity and decreases in iron content. The tryptophan emission intensity of reconstituted enzyme having full enzyme activity was about 90% of that of the holoenzyme. Although apo PCD has similar molecular weight, amino acid content and essentially the same gross quaternary conformation as holo PCD, the absence of iron in apo PCD causes the changes in emission intensity of tryptophan. Findings indicate that some tryptophan residues may be (or may be near) the iron-binding ligands in the catalytic site of protocatechuate 3,4-dioxygenase.     

A single-step competitive binding assay for mapping of single DNA molecules

Optical mapping of genomic DNA is of relevance for a plethora of applications such as scaffolding for sequencing and detection of structural variations as well as identification of pathogens like bacteria and viruses. For future clinical applications it is desirable to have a fast and robust mapping method based on as few steps as possible. We here demonstrate a single-step method to obtain a DNA barcode that is directly visualized using nanofluidic devices and fluorescence microscopy. Using a mixture of YOYO-1, a bright DNA dye, and netropsin, a natural antibiotic with very high AT specificity, we obtain a DNA map with a fluorescence intensity profile along the DNA that reflects the underlying sequence. The netropsin binds to AT-tetrads and blocks these binding sites from YOYO-1 binding which results in lower fluorescence intensity from AT-rich regions of the DNA. We thus obtain a DNA barcode that is dark in AT-rich regions and bright in GC-rich regions with kilobasepair resolution. We demonstrate the versatility of the method by obtaining a barcode on DNA from the phage T4 that captures its circular permutation and agrees well with its known sequence.     

Physiological color change in squid iridophores

Evidence is presented that changes in the optical properties of active iridophores in the dermis of the squid Lolliguncula brevis are the result of changes in the ultrastructure of these cells. At least two mechanisms may be involved when active cells change from non-iridescent to iridescent or change iridescent color. One is the reversible change of labile, detergent-resistant proteinaceous material within the iridophore platelets, from a contracted gel state (non-iridescent) to an expanded fluid or sol state when the cells become iridescent. The other is a change in the thickness of the platelets, with platelets becoming significantly thinner as the optical properties of the iridophores change from non-iridescent to iridescent red, and progressively thinner still as the observed iridescent colors become those of shorter wavelengths. Optical change from Rayleigh scattering (non-iridescent) to structural reflection (iridescent) may be due to the viscosity change in the platelet material, with the variations in observed iridescent colors due to changes in the dimensions of the iridophore platelets.     

Rapid vasoregulatory mechanisms in exercising human skeletal muscle: dynamic response to repeated changes in contraction intensity

We tested the hypothesis that vasoregulatory mechanisms exist in humans that can rapidly adjust muscle blood flow to repeated increases and decreases in exercise intensity. Six men and seven women (age, 24.4+/-1.3 yr) performed continuous dynamic forearm handgrip contractions (1- to 2-s contraction-to-relaxation duty cycle) during repeated step increases and decreases in contraction intensity. Three step change oscillation protocols were examined: Slow (7 contractions per contraction intensityx10 steps); Fast (2 contractions per contraction intensityx15 steps); and Very Fast (1 contraction per contraction intensityx15 steps). Forearm blood flow (FBF; Doppler and echo ultrasonography), heart rate (ECG), and mean arterial pressure (arterial tonometry) were examined for the equivalent of a cardiac cycle during each relaxation phase (FBFrelax). Mean arterial pressure and heart rate did not change during repeated step changes (P=0.352 and P=0.190). For both Slow and Fast conditions, relaxation phase FBFrelax adjusted immediately and repeatedly to both increases and decreases in contraction intensity, and the magnitude and time course of FBFrelax changes were virtually identical. For the Very Fast condition, FBFrelax increased with the first contraction and thereafter slowly increased over the course of repeated contraction intensity oscillations. We conclude that vasoregulatory mechanisms exist in human skeletal muscle that are capable of rapidly and repeatedly adjusting muscle blood flow with ongoing step changes in contraction intensity. Importantly, they demonstrate symmetry in response magnitude and time course with increasing versus decreasing contraction intensity but cannot adjust to very fast exercise intensity oscillations.     

Effect of reduced and oxidized glutathione on physico-chemical properties of erythrocyte membranes]

The parameters describing the structural and functional state of membranes depending on the level of reduced glutathione in erythrocytes were studied. It was shown, that the decrease in the concentration of reduced intracellular glutathione in erythrocytes upon metabolic depletion (prolonged incubation of cells at 37 degrees C in the absence of glucose) or a rapid irreversible depletion of glutathione with 1-chloro-2,4-dinitrobenzene enhances lipid peroxidation processes in membranes, inhibits the membrane-bound NAD.H methemoglobin reductase activity and decreases the intensity of 1,6-diphenyl-1,3,5-hexatrien fluorescence. The data obtained suggest that the depletion of reduced intracellular glutathione causes changes in the physicochemical state of the erythrocyte membrane: the accumulation of lipid peroxidation products, changes in the physical state of lipid bilayer and the inhibition of membrane-bound NAD.H-methemoglobin reductase activity.