Neutron off-plane scattering of aligned membranes. I. Method Of measurement.

We describe a method of measuring neutron scattering of aligned membranes with the momentum transfer oriented parallel or partly perpendicular to the plane of the membranes. The method obtains the complete information for the structures within fluid membranes obtainable by scattering. Data from alamethicin- and magainin-induced pores are presented. Although the in-plane scattering curves of these two peptides are similar to each other, their off-plane scattering patterns are strikingly distinct. Magainin pores exhibit intermembrane correlations.     

Core-Shell Modeling of Light Scattering by Vesicles: Effect of Size,Contents, and Lamellarity

Having a fast, reliable method for characterizing vesicles is vital for their use as model cell membranes in biophysics, synthetic biology, and origins of life studies. Instead of the traditionally used Rayleigh-Gans-Debye approximation, we use an exact extended Lorenz-Mie solution for how core-shell particles scatter light to model vesicle turbidity. This approach enables accurate interpretations of simple turbidimetric measurements and is able to accurately model highly scattering vesicles, such as larger vesicles, those with multiple layers, and those with encapsulated material. We uncover several surprising features, including that vesicle lamellarity has a larger effect on sample turbidity than vesicle size and that the technique can be used to measure the membrane thickness of vesicles. We also examine potential misinterpretations of turbidimetry and discuss when measurements are limited by forward and multiple scattering and by the geometry of the instrument.     

A miniaturized wide-angle 2D cytometer.

BACKGROUND: We present an optical waveguide based cytometer that is capable of simultaneously collecting the light scattered by cells over a wide range of solid angles. Such comprehensive scattering data are a prerequisite for the microstructural characterization of cells. METHODS: We use latex beads as cell mimics, and demonstrate the ability of this new cytometer to collect back-scattered light in two dimensions (2D). This cytometer is based on a liquid-core optical waveguide, excited by prism coupling, that also serves as the microfluidic channel. In principle, our use of a hemispherical lens allows the collection of scattered light from 0 to 180 degrees in 2D. RESULTS: The experimentally observed positions of the intensity peaks of the back-scattered light agree well with theoretical prediction of scattering from both 4.0- and 9.6-mum diameter latex beads. The position of the bead, relative to the axes of the hemispherical lens and the microchannel, strongly affects the scattering pattern. We discuss a computational method for determining these offsets. CONCLUSIONS: We show that wide-angle 2D light scattering patterns of cell-sized latex beads can be observed in a microfluidic-based optical cytometer that uses leaky waveguide mode excitation. This chip-based system is compatible with emerging chip-based technologies.     

Plasmon light scattering in biology and medicine: new sensing approaches, visions and perspectives

Surface plasmons are collective oscillations of free electrons at metallic surfaces. These oscillations can give rise to the intense colors of solutions of plasmon resonance nanoparticles and/or very intense scattering. While the use of plasmonic particle absorption based bioaffinity sensing is now widespread throughout biological research, the use of their scattering properties is relatively ill explored. We refer to the use, utility and control of surface plasmons as plasmonics. In this review and forward-looking article, we discuss the current opinions and uses of plasmonics, as well as speculate on areas of future research. These include the use of plasmon scatter for long-range immunosensing and macromolecular conformation studies, as well as the ability to Stokes shift plasmon scatter, a plasmonics phenomenon recently referred to as metal-enhanced fluorescence.     

Characterization of bacteria by multiparameter flow cytometry.

An arc-lamp based flow cytometer was used to obtain high resolution measurements of the light scattering characteristics and DNA contents of eight different bacteria. Light scatter profiles of bacteria are a useful first step when flow cytometry is used to characterize organisms. Scanning and transmission electron microscopy of the bacterial samples demonstrate that the structural basis of the light scattering profiles is not always clear, i.e. some organisms appear to have anomalous light scattering characteristics. The use of a third measurement parameter, DNA content, allowed much better discrimination of the organisms. Flow cytometry shows great promise as a method for the rapid discrimination and identification of bacterial populations.     

Calculations of scattered light from rigid polymers by Shifrin and Rayleigh-Debye approximations.

We show that the commonly used Rayleigh-Debye method for calculating light scattering can lead to significant errors when used for describing scattering from dilute solutions of long rigid polymers, errors that can be overcome by use of the easily applied Shifrin approximation. In order to show the extent of the discrepancies between the two methods, we have performed calculations at normal incidence both for polarized and unpolarized incident light with the scattering intensity determined as a function of polarization angle and of scattering angle, assuming that the incident light is in a spectral region where the absorption of hemoglobin is small. When the Shifrin method is used, the calculated intensities using either polarized or unpolarized scattered light give information about the alignment of polymers, a feature that is lost in the Rayleigh-Debye approximation because the effect of the asymmetric shape of the scatterer on the incoming polarized electric field is ignored. Using sickle hemoglobin polymers as an example, we have calculated the intensity of light scattering using both approaches and found that, for totally aligned polymers within parallel planes, the difference can be as large as 25%, when the incident electric field is perpendicular to the polymers, for near forward or near backward scattering (0 degrees or 180 degrees scattering angle), but becomes zero as the scattering angle approaches 90 degrees. For randomly oriented polymers within a plane, or for incident unpolarized light for either totally oriented or randomly oriented polymers, the difference between the two results for near forward or near backward scattering is approximately 15%.     

Aggregation and denaturation of antibodies: a capillary electrophoresis, dynamic light scattering, and aqueous two-phase partitioning study

Protein denaturation and aggregation are well-known problems in the pharmaceutical industry. As the protein aggregates, it loses its biological activity and creates problems in its administration to patients. In this paper, we explore the use of aqueous two-phase systems, capillary zone electrophoresis, and dynamic light scattering for the monitoring of protein denaturation and aggregation. Our studies focus on human IgG and HSA. Capillary zone electrophoresis was used to monitor changes in the charge to size ratio of the proteins upon denaturation and dynamic light scattering was used to detect the presence of any aggregates and to monitor the size of the proteins. The information obtained from aqueous two-phase partitioning is similar to that obtained from capillary zone electrophoresis. The simplicity of aqueous two-phase system and its low cost (compared to the other analytical techniques) suggest that it can be routinely used for the quality control of some pharmaceutical preparations.     

Resonance Raman Spectroscopy of Extreme Nanowires and Other 1D Systems

This paper briefly describes how nanowires with diameters corresponding to 1 to 5 atoms can be produced by melting a range of inorganic solids in the presence of carbon nanotubes. These nanowires are extreme in the sense that they are the limit of miniaturization of nanowires and their behavior is not always a simple extrapolation of the behavior of larger nanowires as their diameter decreases. The paper then describes the methods required to obtain Raman spectra from extreme nanowires and the fact that due to the van Hove singularities that 1D systems exhibit in their optical density of states, that determining the correct choice of photon excitation energy is critical. It describes the techniques required to determine the photon energy dependence of the resonances observed in Raman spectroscopy of 1D systems and in particular how to obtain measurements of Raman cross-sections with better than 8% noise and measure the variation in the resonance as a function of sample temperature. The paper describes the importance of ensuring that the Raman scattering is linearly proportional to the intensity of the laser excitation intensity. It also describes how to use the polarization dependence of the Raman scattering to separate Raman scattering of the encapsulated 1D systems from those of other extraneous components in any sample.     

Analysis of the hierarchical structure of biological tissues by scanning X-ray scattering using a micro-beam.

The outstanding mechanical properties of biological tissues such as wood or bone are mainly due to their hierarchical structure and to their optimization at all levels of hierarchy. It is therefore essential to characterize the structure at all levels to understand the complex behavior of such tissues. Structures down to the micrometer level are accessible to light or scanning electron microscopic observation. In the case of bone this includes, for example, morphometry of the trabecular architecture or the bone mineral density distribution in cortical and trabecular bone. To characterize the sub-micrometer structure of, e.g., the collagen-mineral composite in the case of bone or the cellulose microfibrils in the case of wood, other methods, such as transmission electron microscopy or X-ray scattering are necessary. The recent availability of extremely brilliant synchrotron X-ray sources has led to the development of the new techniques of scanning small-angle X-ray scattering and scanning X-ray microdiffraction, which are capable of providing structural information on the micrometer and the nanometer level, simultaneously. As a basic principle of the method the specimen is scanned across an X-ray beam which has a diameter of few micrometers. Measuring the X-ray absorption at each position provides an image of the specimen (microradiography) with resolution similar to light microscopy, in the micrometer range. Moreover, the X-ray scattering pattern is analyzed at each specimen position to provide parameters characterizing the structure in the nanometer range. The present paper reviews the principles of the techniques and demonstrates their application to biological materials, such as wood or bone.     

Differential polarization imaging. V. Numerical aperture effects and the contribution of preferential scattering and absorption to the circular dichroism images.

Chiral objects which scatter and absorb preferentially left versus right circularly polarized light give rise to bright-field circular dichroism (CD) images containing contributions from both these two phenomena. These contributions are separated and characterized mathematically, and the effect of the dimensions of the chiral object on their relative magnitude is discussed. CD images of the long-range chiral organization of the thylakoid membranes in chloroplasts are obtained at two different wavelengths to illustrate the diverse wavelength dependence of the preferential absorption and scattering contributions to the images. The bright field CD images not only depend on the magnitude and sign of the preferential scattering and preferential absorption contributions, but also on the numerical aperture of the lens used. This dependence is obtained formally and a method to extract the angle dependent preferential scattering contributions to the images is presented. The validity of this method is confirmed experimentally.     

Analysis of laser scattering pattern as an early measure of apoptosis.

Light scattering pattern analysis (LSPA) was applied in the current study for accurate and sensitive detection of subtle changes in cell size, which occur in mouse thymocytes undergoing apoptosis. The decrease in cell diameter as measured by LSPA was found to be an early signal of apoptosis preceding the externalization of phosphatidylserine on the outer membrane. When apoptosis was induced by dexamethasone, the change in cell size was dose and time dependent, and could be blocked by pretreatment of the thymocytes with N-acetylcysteine (NAC). This implies that the scattering pattern, when combined with fluorescent markers such as annexine-V, may be a powerful tool for early detection of apoptosis. Another advantage gained by the use of this method is the ability to repeatedly trace the same cells and to monitor the kinetics of their size changes.     

The DFPase from Loligo vulgaris in sugar surfactant-based bicontinuous microemulsions: structure, dynamics, and enzyme activity

The enzyme diisopropyl fluorophosphatase (DFPase) from the squid Loligo vulgaris is of great interest because of its ability to catalyze the hydrolysis of highly toxic organophosphates. In this work, the enzyme structure in solution (native state) was studied by use of different scattering methods. The results are compared with those from hydrodynamic model calculations based on the DFPase crystal structure. Bicontinuous microemulsions made of sugar surfactants are discussed as host systems for the DFPase. The microemulsion remains stable in the presence of the enzyme, which is shown by means of scattering experiments. Moreover, activity assays reveal that the DFPase still has high activity in this complex reaction medium. To complement the scattering experiments cryo-SEM was also employed to study the microemulsion structure.     

Pesticides,caution, and experimentation in st. Vincent,Eastern Caribbean

Understanding the problem of pesticide misuse in the Third World requires analysis of both political- economic forces and local- level variations in peasant behavior and attitudes. This study, based on 12 months of fieldwork during 1988–1989, examines growing agrochemical dependence and misuse in St. Vincent and the Grenadines in the East Caribbean. Consistent with findings from other political-economic studies, this research documents the influence of the state, export agriculture, consumer pressure, and foreign aid in leading to increased chemical use in agriculture. This study also considers the extent to which farmer behavior and attitudes limit or exacerbate the problems that can accompany increased pesticide use. Some researchers emphasize that farmers are careless and indiscriminate when using pesticides, thereby contributing to pesticide-related problems. In contrast, data from the village level reveal that although some farmers are careless, others are cautious in their use of pesticides, a pattern reflective of variability among farmers in pesticide- use practices and attitudes in general. By exploring the issue of variability in patterns of pesticide use among villagers, this paper emphasizes the utility of the concepts of individuality and experimentation in agriculture in examining problems of pesticide misuse.     

Improved technique for calculating X-ray scattering intensity of biopolymers in solution: Evaluation of the form,volume, and surface of a particle

An improved cube method has been developed for calculating the intensity of diffuse x-ray scattering of macromolecules in solution using a certain set of their atomic coordinates. The technique is based on the ideas of B. Lee and F. M. Richards [(1971) J. Mol. Biol. 55 , 374–400] and Richards [(1977) Annu. Rev. Biophys. Bioeng. 6 , 151–176] on the possibility of estimating the molecular and accessible surface of a particle by “rolling” a sphere, simulating a water molecule, on its molecular surface. It is shown that this technique is more advantageous than earlier versions of the cube methods. The improved technique for calculating scattering curves was utilized for several globular proteins, and for the first time, reliable scattering curves were obtained for protein-“bound” water complexes. In the case of globular proteins and tRNA, this technique has permitted a strict evaluation of their accessible surfaces, their volumes, and, apparently for the first time, their complete molecular surfaces.     

X-ray scattering from labeled membranes.

We present a new method for the determination of structural parameters in biological membranes. Recording the continuous scattering of heavy-atom labeled membranes and applying elementary Fourier methods we obtain the scattering of the heavy-atom distribution alone. The details of this distribution are explored by developing a simple model and testing for cases relevant to biological membranes. We find that the intensity distribution is highly sensitive to many key parameters. The increased signal from heavy-atom labeling and the use of an improved x-ray system make it possible to record patterns from dilute membrane suspensions. Thus determination of these parameters is possible in the same environment where many membrane biochemical studies are performed. Application of the method is made to a model lipid bilayer membrane, dipalmitoyl phosphatidylcholine by labeling with UO2++ ions. We determine the precise distance between UO2++ layers on either side of the membrane as well as the width of the label on each side. This determination permits estimation of phosphate separation across single labeled bilayers in an aqueous suspension.     

Structural insights into the beta-mannosidase from T. reesei obtained by synchrotron small-angle X-ray solution scattering enhanced by X-ray crystallography

A molecular envelope of the beta-mannosidase from Trichoderma reesei has been obtained by combined use of solution small-angle X-ray scattering (SAXS) and protein crystallography. Crystallographic data at 4 A resolution have been used to enhance informational content of the SAXS data and to obtain an independent, more detailed protein shape. The phased molecular replacement technique using a low resolution SAXS model, building, and refinement of a free atom model has been employed successfully. The SAXS and crystallographic free atom models exhibit a similar globular form and were used to assess available crystallographic models of glycosyl hydrolases. The structure of the beta-galactosidase, a member of a family 2, clan GHA glycosyl hydrolases, shows an excellent fit to the experimental molecular envelope and distance distribution function of the beta-mannosidase, indicating gross similarities in their three-dimensional structures. The secondary structure of beta-mannosidase quantified by circular dichroism measurements is in a good agreement with that of beta-galactosidase. We show that a comparison of distance distribution functions in combination with 1D and 2D sequence alignment techniques was able to restrict the number of possible structurally homologous proteins. The method could be applied as a general method in structural genomics and related fields once protein solution scattering data are available.     

Time-Gated Optical Projection Tomography Allows Visualization of Adult Zebrafish Internal Structures

Optical imaging through biological samples is compromised by tissue scattering and currently various approaches aim to overcome this limitation. In this paper we demonstrate that an all optical technique, based on non-linear upconversion of infrared ultrashort laser pulses and on multiple view acquisition, allows the reduction of scattering effects in tomographic imaging. This technique, namely Time-Gated Optical Projection Tomography (TGOPT), is used to reconstruct three dimensionally the internal structure of adult zebrafish without staining or clearing agents. This method extends the use of Optical Projection Tomography to optically diffusive samples yielding reconstructions with reduced artifacts, increased contrast and improved resolution with respect to those obtained with non-gated techniques. The paper shows that TGOPT is particularly suited for imaging the skeletal system and nervous structures of adult zebrafish.     

Affinity precipitation of proteins by surfactant-solubilized, ligand-modified phospholipids.

The use of ligand-modified phospholipids solubilized in aqueous solution by nonionic surfactant for affinity precipitation of proteins is described. Avidin was precipitated by contact with solutions in which dimyristoylphosphatidylethanolamine (DMPE) functionalized with biotin (DMPE-B) was solubilized in octaethylene glycol mono-n-dodecyl ether (C12E8) solutions. The nonionic surfactant solubilizes the phospholipid in micelles above its critical micelle concentration (CMC) and in small submicellar aggregates below this concentration. At C12E8 concentrations significantly exceeding its CMC, determined to be about 100 microM, precipitation of avidin by solubilized DMPE-B is not observed. In this regime, binding of protein by DMPE-B was monitored by a hyperchroic shift in the protein's UV-visible spectrum at 231.5 nm. The data were analyzed using a model that considers the four binding sites on the protein to be independent and identical in binding strength for DMPE-B. Below the CMC of C12E8, precipitation is observed and is monitored by increasing turbidity of the solution. The kinetics of precipitation and the aggregate size measured by quasielastic light scattering were analyzed using Smoluchowski kinetics and the Mie scattering theory. These results help establish more completely the factors that influence the precipitation of proteins by ligand-modified phospholipids, and they are helpful in specifying conditions for the precipitation of other proteins.     

Optical changes in unilamellar vesicles experiencing osmotic stress.

Membrane properties that vary as a result of isotropic and transmembrane osmolality variations (osmotic stress) are of considerable relevance to mechanisms such as osmoregulation, in which a biological system "senses" and responds to changes in the osmotic environment. In this paper the light-scattering behavior of a model system consisting of large unilamellar vesicles of dioleoyl phosphatidyl glycerol (DOPG) is examined as a function of their osmotic environment. Osmotic downshifts lead to marked reductions in the scattered intensity, whereas osmotic upshifts lead to strong intensity increases. It is shown that these changes in the scattering intensity involve changes in the refractive index of the membrane bilayer that result from an alteration in the extent of hydration and/or the phospholipid packing density. By considering the energetics of osmotically stressed vesicles, and from explicit analysis of the Rayleigh-Gans-Debye scattering factors for spherical and ellipsoidal shells, we quantitatively demonstrate that although changes in vesicle volume and shape can arise in response to the imposition of osmotic stress, these factors alone cannot account for the observed changes in scattered intensity.