Synchrotron radiation hardness studies of PILATUS II.

A synchrotron beam has been used to investigate the radiation tolerance of a PILATUS II module. It has been demonstrated that radiation-induced threshold shifts become significant above 30 Mrad. Individual adjustment of pixel thresholds after irradiation enabled retention of standard behaviour in excess of 40 Mrad. This implies that a module can be continuously irradiated for in excess of 40 days at an individual pixel count rate of 10(6) counts s(-1).

Performance of single-photon-counting PILATUS detector modules.

PILATUS is a silicon hybrid pixel detector system, operating in single-photon-counting mode, that has been developed at the Paul Scherrer Institut for the needs of macromolecular crystallography at the Swiss Light Source (SLS). A calibrated PILATUS module has been characterized with monochromatic synchrotron radiation. The influence of charge sharing on the count rate and the overall energy resolution of the detector were investigated. The dead-time of the system was determined using the attenuated direct synchrotron beam. A single module detector was also tested in surface diffraction experiments at the SLS, whereby its performance regarding fluorescence suppression and saturation tolerance were evaluated, and have shown to greatly improve the sensitivity, reliability and speed of surface diffraction data acquisition.

A spatially resolving x-ray crystal spectrometer for measurement of ion-temperature and rotation-velocity profiles on the Alcator C-Mod tokamak.

A new spatially resolving x-ray crystal spectrometer capable of measuring continuous spatial profiles of high resolution spectra (lambda/d lambda>6000) of He-like and H-like Ar K alpha lines with good spatial (approximately 1 cm) and temporal (approximately 10 ms) resolutions has been installed on the Alcator C-Mod tokamak. Two spherically bent crystals image the spectra onto four two-dimensional Pilatus II pixel detectors. Tomographic inversion enables inference of local line emissivity, ion temperature (T(i)), and toroidal plasma rotation velocity (upsilon(phi)) from the line Doppler widths and shifts. The data analysis techniques, T(i) and upsilon(phi) profiles, analysis of fusion-neutron background, and predictions of performance on other tokamaks, including ITER, will be presented.

Hard-X-ray dark-field imaging using a grating interferometer.

Imaging with visible light today uses numerous contrast mechanisms, including bright- and dark-field contrast, phase-contrast schemes and confocal and fluorescence-based methods. X-ray imaging, on the other hand, has only recently seen the development of an analogous variety of contrast modalities. Although X-ray phase-contrast imaging could successfully be implemented at a relatively early stage with several techniques, dark-field imaging, or more generally scattering-based imaging, with hard X-rays and good signal-to-noise ratio, in practice still remains a challenging task even at highly brilliant synchrotron sources. In this letter, we report a new approach on the basis of a grating interferometer that can efficiently yield dark-field scatter images of high quality, even with conventional X-ray tube sources. Because the image contrast is formed through the mechanism of small-angle scattering, it provides complementary and otherwise inaccessible structural information about the specimen at the micrometre and submicrometre length scale. Our approach is fully compatible with conventional transmission radiography and a recently developed hard-X-ray phase-contrast imaging scheme. Applications to X-ray medical imaging, industrial non-destructive testing and security screening are discussed.

X-ray imaging with the PILATUS 100k detector.

We report on the application of the PILATUS 100K pixel detector for medical imaging. Experimental results are presented in the form of X-ray radiographs using standard X-ray absorption contrast and a recently developed phase contrast imaging method. The results obtained with the PILATUS detector are compared to results obtained with a conventional X-ray imaging system consisting of an X-ray scintillation screen, lens optics, and a charge coupled device. Finally, the results for both systems are discussed more quantitatively based on an image power spectrum analysis.

The PILATUS 1M detector.

The PILATUS 1M detector is a hybrid pixel array detector with over one million pixels that operate in single photon counting mode. The detector, designed for macromolecular crystallography, is the largest pixel array detector currently in use at a synchrotron. It is a modular system consisting of 18 multichip modules covering an area of 21 cm x 24 cm. The design of the components as well as the manufacturing of the detector including the bump-bonding was performed at the Paul Scherrer Institute (PSI). The use of a single photon counting detector for protein crystallography requires detailed studies of the charge collection properties of the silicon sensor. The 18 modules are read out in parallel, leading to a full frame readout-time of 6.7 ms. This allows crystallographic data to be acquired in fine-varphi-slicing mode with continuous rotation of the sample. The detector was tested in several experiments at the protein crystallography beamline X06SA at the Swiss Light Source at PSI. Data were collected both in conventional oscillation mode using the shutter, as well as in a fine-varphi-slicing mode. After applying all the necessary corrections to data from a thaumatin crystal, the processing of the conventional data led to satisfactory merging R-factors of the order of 8.5%. This allows, for the first time, determination of a refined electron density map of a macromolecular biological crystal using a silicon pixel detector.

Improved data acquisition in grazing-incidence X-ray scattering experiments using a pixel detector.

The use of an area detector in grazing-incidence X-ray experiments lends many advantages in terms of both speed and reliability. Here a discussion is given of the procedures established using the PILATUS pixel detector developed at the Swiss Light Source for optimizing data acquisition and analysis of surface diffraction data at the Materials Science beamline, especially with regard to reflectivity measurements, crystal truncation and fractional order rods, and grazing-incidence diffraction experiments.

Collagen XI nucleates self-assembly and limits lateral growth of cartilage fibrils.

Fibrils of embryonic cartilage are heterotypic alloys formed by collagens II, IX, and XI and have a uniform diameter of approximately 20 nm. The molecular basis of this lateral growth control is poorly understood. Collagen II subjected to fibril formation in vitro produced short and tapered tactoids with strong D-periodic banding. The maximal width of these tactoids varied over a broad range. By contrast, authentic mixtures of collagens II, IX, and XI yielded long and weakly banded fibrils, which, strikingly, had a uniform width of about 20 nm. The same was true for mixtures of collagens II and XI lacking collagen IX as long as the molar excess of collagen II was less than 8-fold. At higher ratios, the proteins assembled into tactoids coexisting with cartilage-like fibrils. Therefore, diameter control is an inherent property of appropriate mixtures of collagens II and XI. Collagen IX is not essential for this feature but strongly increases the efficiency of fibril formation. Therefore, this protein may be an important stabilizing factor of cartilage fibrils.

A Pixel-Array Detector for Time-Resolved X-ray Diffraction.

An integrating pixel-array detector for recording time-resolved X-ray diffraction measurements on microsecond timescales has been designed and tested as a 4 x 4 pixel prototype. Operational characteristics and radiation tolerance are discussed. A 100 x 92 array with 151.2 micro m square pixels is currently under construction.

Correlation between lipid plane curvature and lipid chain order.

The 1-palmitoyl-2-oleoyl-phosphatidylethanolamine: 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPE:POPC) system has been investigated by measuring, in the inverted hexagonal (HII) phase, the intercylinder spacings (using x-ray diffraction) and orientational order of the acyl chains (using 2H nuclear magnetic resonance). The presence of 20 wt% dodecane leads to the formation of a HII phase for the composition range from 0 to 39 mol% of POPC in POPE, as ascertained by x-ray diffraction and 2H nuclear magnetic resonance. The addition of the alkane induces a small decrease in chain order, consistent with less stretched chains. An increase in temperature or in POPE proportion leads to a reduction in the intercylinder spacing, primarily due to a decrease in the water core radius. A temperature increase also leads to a reduction in the orientational order of the lipid acyl chains, whereas the POPE proportion has little effect on chain order. A correlation is proposed to relate the radius of curvature of the cylinders in the inverted hexagonal phase to the chain order of the lipids adopting the HII phase. A simple geometrical model is proposed, taking into account the area occupied by the polar headgroup at the interface and the orientational order of the acyl chains reflecting the contribution of the apolar core. From these parameters, intercylinder spacings are calculated that agree well with the values determined experimentally by x-ray diffraction, for the variations of both temperature and POPE:POPC proportion. This model suggests that temperature increases the curvature of lipid layers, mainly by increasing the area subtended by the hydrophobic core through chain conformation disorder, whereas POPC content affects primarily the headgroup interface contribution. The frustration of lipid layer curvature is also shown to be reflected in the acyl chain order measured in the L alpha phase, in the absence of dodecane; for a given temperature, increased order is observed when the curling tendencies of the lipid plane are more pronounced.

High-resolution macromolecular structure determination using CCD detectors and synchrotron radiation.

BACKGROUND: Synchrotron radiation sources have made impressive contributions to macromolecular crystallography. The delay in development of appropriate X-ray detectors has, however, been a significant limitation to their efficient use. New technologies, based on charge-coupled devices (CCDs), provide capabilities for faster, more accurate, automated data collection. RESULTS: A CCD-based X-ray detector has been developed for use in macromolecular crystallography and has been in operation for about one and a half years at the Cornell High Energy Synchrotron Source. It has been used for a variety of crystallographic projects, including a number of high-resolution structural studies. The statistical quality of the data, the detector's ease and efficiency of use, and the growing number of structural results illustrate the practical utility of this new detector system. CONCLUSIONS: The new detector has enhanced capabilities for measuring diffraction patterns from crystals of macromolecules, especially at high resolution, when the X-ray intensities are weak. The survey of results described here ranges from virus crystallography to weakly diffracting small-molecule structure determination and demonstrates the potential of CCD detectors when combined with synchrotron radiation sources.

Collagen fibril structure in lamprey.

X-ray diffraction and electron microscopy are used to compare the molecular and higher order structure of collagen fibrils in three tissues of the lamprey: the dermis, perinotochord and notochord sheath. These lamprey tissues are known to contain five distinct genetic types of fibrillar collagen. The modes of axial and lateral packing of collagen molecules in fibrils of the lamprey tissues demonstrate the three major motifs seen in higher vertebrate D-periodic collagen fibrils. In particular, lamprey dermis was found to have a decreased D period resulting from a molecular tilt that is seen in skins of higher vertebrates. Our results suggest the molecular-packing motifs for collagen fibrils were in place at the dawn of vertebrate evolution and have been conserved since. In contrast, the diameters of fibrils and their spatial orientation in lamprey tissues do not in general, correspond to features found in mammalian tissues. Only for lamprey notochord is there a strong similarity, with fibril diameters and organization closely resembling those seen in type II tissues of higher vertebrates. This suggests that for all tissues except those with type II collagen, higher level organization of fibrils evolved along with the diversification of vertebrates.

Assessment of cell proliferation on porous microcarriers by means of image analysis.

Spherical porous microcarriers (PMCs) made from collagen-glycosaminoglycan crosslinked copolymers have exhibited considerable promise as growth surfaces for the proliferation of anchorage-dependent mammalian cell lines and have demonstrated the ability to entrap anchorage-independent cells. However, quantification of cell growth on PMCs has proved difficult. A method of measuring the proliferation of PMCs, based on image analysis, is presented. Using CV1 and CHO cell lines, samples of PMCs were removed from culture at various times, fixed, embedded and sectioned. The 2 microns sections were stained, photographed and digitized in three colors. A computer program was developed to evaluate digitized PMC cross-sections and to classify pixels as conforming to either background, cytoplasmic, matrix or nuclear parameters, based on a set of classification rules determined by statistical analysis. Growth curves were generated by relating the number of pixels occupied by cellular material to the total number of pixels in the PMC cross-section. The PMCs were found to foster cell proliferation, with cell densities approaching 100% occupancy.

Nonbilayer phases of membrane lipids.

Numerous liquid crystalline biomembrane lipids are known to exhibit non-lamellar phases characterized by curvature of their component lipid monolayers. An understanding of the phase stability of these systems begins with analysis of the energy of bending the monolayers, the interactions which lead to the bending energy, and the geometrical constraints which lead to competing energy terms which arise when the monolayers are bent and packed onto lattices with different structures. Diffraction and other techniques suitable for probing lipid phase structure are described. A phenomenological model is reviewed which successfully explains many of the qualitative features of lipid mesomorphic phase behavior. A key result of this model is that lipid bilayer compositions which are close to the non-lamellar phase boundaries of their phase diagrams are characterized by a frustrated elastic stress which may modulate the activity of imbedded membrane proteins and which may provide a rationale for the prevalence of non-lamellar-tending lipid species in biomembrane bilayers. Areas in need of future research are discussed.

Isolation and partial characterization of collagen chains dimerized by sugar-derived cross-links.

Incubation of tail tendon from a young rat in solutions containing D-ribose resulted in attachment of the monosaccharide to collagen and subsequent cross-link formation at a rate much faster than found for glucose. The collagen rapidly became resistant to solubilization and showed increasing fluorescence. Ribose bound to all major CNBr peptides of collagen, with some preference for the alpha 2-CB3,5 peptide and the triple-helical region of alpha 1-CB6, and was incorporated into higher molecular weight material. Extensive pepsin digestion permitted isolation of dimers of alpha chains cross-linked in triple-helical regions as a result of incubation with ribose. The dimers were identified as beta 11, beta 12, and beta 22 components, and the limited degree of heterogeneity of these components indicated that cross-linking occurred at several sites, some of which must be intermolecular. Isolated beta components were strongly fluorescent with a spectrum similar to that of collagen in aged tissues. Fluorescent dimers with similar characteristics were found in pepsin digests of tail tendons from older rats.

Glycation induces expansion of the molecular packing of collagen.

Exposure of rat tail tendon to a reducing sugar results in covalent attachment of the sugar to collagen, a process termed glycation, and leads to the formation of stable intermolecular cross-links. We have used X-ray diffraction to study the changes in the crystalline unit cell of rat tail tendon collagen brought about by glycation. Ribose was selected as a model compound for most of the study because its reaction with proteins is faster than that of glucose, and therefore more convenient for laboratory studies, but glucose and glyceraldehyde were used as well. A kinetic model describing the process of glycation by ribose and subsequent cross-link formation has been developed. Glycation resulted in an expansion by more than 12% of the unit cell that describes the three-dimensional structure of rat tail tendon collagen. The expansion was in a direction perpendicular to the axes of the rod-shaped molecules, indicating that the intermolecular spacing of the collagen increased. Thus, the structure of collagen in rat tail tendon is significantly altered by glycation in vitro. The expansion was not isotropic, but was directed parallel to the (120) planes, one of the three major planes of the quasi-hexagonal structure that is densely populated by collagen molecules. It is hypothesized that this expansion is brought about by the formation of one, or at most a few, specific intermolecular cross-links in the overlap zone that act to push the molecules apart. It is likely that similar structural changes in collagenous tissues are caused by glycation in vivo during the natural course of aging, and that these changes are accelerated in chronic hyperglycemia such as that associated with diabetes. Analysis of the structure of glycated rat tail tendon potentially can give us new insight into the detailed molecular structure of collagen.

Fibril-forming collagens in lamprey.

Five types of collagen with triple-helical regions approximately 300 nm in length were found in lamprey tissues which show characteristic D-periodic collagen fibrils. These collagens are members of the fibril forming family of this primitive vertebrate. Lamprey collagens were characterized with respect to solubility, mobility on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, carboxylmethyl-cellulose chromatography, peptide digestion patterns, composition, susceptibility to vertebrate collagenase, thermal stability, and segment long spacing-banding pattern. Comparison with fibril-forming collagens in higher vertebrates (types I, II, III, V, and XI) identified three lamprey collagens as types II, V, and XI. Both lamprey dermis and major body wall collagens had properties similar to type I but not the typical heterotrimer composition. Dermis molecules had only alpha 1(I)-like chains, while body wall molecules had alpha 2(I)-like chains combined with chains resembling lamprey type II. Neither collagen exhibited the interchain disulfide linkages or solubility properties of type III. The conservation of fibril organization in type II/type XI tissues in contrast to the major developments in type I and type III tissues after the divergence of lamprey and higher vertebrates is consistent with these results. The presence of type II and type I-like molecules as major collagens and types V and XI as minor collagens in the lamprey, and the differential susceptibility of these molecules to vertebrate collagenase is analogous to the findings in higher vertebrates.

Ultrastructural organization of skin: classification on the basis of mechanical role.

In our previous developmental study on skin we reported that correlations existed between the collagen fibril diameter distribution, glycosaminoglycan content and composition, and mechanical role. In this work we present new but related electron microscope data on the ultrastructure of skins from flounder, marlin, cod, frog, toad, caiman, viper, pigeon, whale and opossum. It is shown that mammalian and avian body skins generally contain relatively sharp unimodal distributions of fibril diameter consistent with a "passive" mechanical role. In contrast most reptilian and fish skins have broad, right-skewed (or bimodal) distributions of fibril diameters compatible with the exotendinous attributes required of an "active" skin. A study of the changing form of the collagen fibril diameter distribution with depth in the dermis is also reported.

Type II collagen of lamprey.

The major collagen in lamprey notochord is type II, as determined by its amino acid composition and solubility properties. This collagen has a distribution of charged residues indistinguishable from higher vertebrate Type II collagens as judged by its SLS banding pattern. Lamprey type II collagen has a higher thermal stability than lamprey skin collagen, in contrast to the identical melting temperatures for these types in mammals. A minor collagen in lamprey notochord has solubility properties, amino acid composition, and electrophoretic mobility similar to that of 1 alpha, 2 alpha, 3 alpha collagen in human cartilage.