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The morphology and structure of giant starch granules from the pseudo-bulbs of Phajus grandifolius were investigated, using a number of microscopy techniques together with synchrotron radiation microdiffration analysis. Most of the granules, which had sizes between 100 and 200 microm, occurred as ogival particles with the hilum or proximal end located at the apex of the granules. A small percentage of granules held a protuberance extending orthogonally to the underlying parent granule. Growth rings were observed in all granules: strongly curved close to the hilum, but planar toward the distal end of the granules or in the protuberances. Specific mechanical disruption followed by enzymatic digestion revealed the susceptibility of the disorganized parts of the growth rings, which were preferentially carved away during the digestion, leaving behind the better-organized domains. Microdiffraction analysis achieved with synchrotron radiation revealed the crystalline features of the granules and provided orientation maps of the amylopectin molecules in the various parts of the granules. In simple ogival granules the amylopectin molecules were uniformly oriented with their axes running from the hilum toward the distal end of the granule. In granules with a protuberance, the axes of the amylopectin molecules kept their direction in the parent granule, but took an orthogonal direction in the protuberance. The occurrence of these morphological and structural features is tentatively correlated with the mode of growth of these granules.

Hard X-ray beams with beam sizes in the sub-micrometre range are frequently available at third-generation synchrotron radiation sources, enabling new insights into the structure of materials at different levels of hierarchy by applying novel techniques such as scanning microbeam diffraction or scanning small-angle scattering. The high brilliance of the radiation from wiggler and undulator sources allows in situ experiments such as mechanical testing of single fibres to be performed, and even the combination of microbeam scanning with in situ testing is feasible. Three different experiments on single carbon fibres are presented: an in situ tensile test using a 10 microm collimated beam, a scanning experiment applying a 3 microm beam from a tapered glass capillary, and a scanning experiment with simultaneous in situ bending with a 0.1 microm beam provided by a waveguide structure.

Highly oriented native cellulose fibres (flax) and softwood (pine) have been investigated by means of X-ray diffraction. Local structural information was obtained by using X-ray microbeams. Tensile tests were performed in situ, revealing a change of orientation of cellulose microfibrils in materials with tensile strain. In flax fibres, the microfibrils rotate during the first percent of stretching, into a more parallel orientation with respect to the fibre axis. For wood, a decrease of orientation with the onset of strain hardening is found for the first time.

Microbeam grazing-incidence small-angle X-ray scattering (microGISAXS) has been used and the technique has been improved in order to investigate protein nucleation and crystal growth, assisted by a protein nanotemplate. The aim is to understand the protein nanotemplate method in detail, as this method has been proved capable of accelerating and increasing crystal size and quality as well as inducing crystallization of proteins that are not crystallizable by classical methods. The nanotemplate experimental setup was used for drops containing growing lysozyme crystals at three different stages of growth.

Waveguide and glass capillary optics have been used to study morphological variations across single as-spun poly(p-phenylene benzobisoxazole) (PBO) fibres. The waveguide provides a beam with a submicrometre dimension perpendicular to the fibre axis. The glass capillary optics provide a beam of a few micrometres in diameter. By directly comparing results obtained with both optics it is possible to assess the influence of beam size on experimental observations. The study demonstrates that submicrometre beams are invaluable for detailed morphological studies across single fibres. The greater morphological averaging inherent to data collected using glass capillary optics reduces the variation between skin and core measurements, as well as obscuring other important features. Crystalline domain orientation, (200) crystal plane spacings and reflection intensities can be determined from data generated using a submicrometre beam. All parameters are found to vary significantly across the diameter of single PBO fibres. In terms of orientation, both skin and core regions exhibit a lower degree of crystalline domain orientation than an intermediate zone. In terms of (200) crystal plane spacing, the observed variations suggest residual stresses within the fibre structure following manufacture.

Three natural pyrrolizidines, (+)-amphorogynines A and D and (+)-retronecine, have been prepared from a common lactam intermediate. This central compound, in turn, was synthesized in diastereomerically enriched form through a highly selective [2 + 2]-cycloaddition of dichloroketene with a chiral enol ether, followed by Beckmann ring expansion and reduction. Subsequent stereocenters were then cleanly introduced through internal induction.

Protein microdiffraction using monochromatic beams is becoming a routine tool at third-generation synchrotron radiation sources. Beam sizes have reached the scale of about 5 microm, with illuminated crystal volumes of approximately 500 microm3, as shown for the case of bovine rhodopsin, which was refined to a resolution of 2.6 A. Progress in X-ray optical systems and instrumentation will enable the method to be extended to smaller beams and smaller crystal volumes.

We have determined the structure of bovine rhodopsin at 2.65 A resolution using untwinned native crystals in the space group P3(1), by molecular replacement from the 2.8 A model (1F88) solved in space group P4(1). The new structure reveals mechanistically important details unresolved previously, which are considered in the membrane context by docking the structure into a cryo-electron microscopy map of 2D crystals. Kinks in the transmembrane helices facilitate inter-helical polar interactions. Ordered water molecules extend the hydrogen bonding networks, linking Trp265 in the retinal binding pocket to the NPxxY motif near the cytoplasmic boundary, and the Glu113 counterion for the protonated Schiff base to the extracellular surface. Glu113 forms a complex with a water molecule hydrogen bonded between its main chain and side-chain oxygen atoms. This can be expected to stabilise the salt-bridge with the protonated Schiff base linking the 11-cis-retinal to Lys296. The cytoplasmic ends of helices H5 and H6 have been extended by one turn. The G-protein interaction sites mapped to the cytoplasmic ends of H5 and H6 and a spiral extension of H5 are elevated above the bilayer. There is a surface cavity next to the conserved Glu134-Arg135 ion pair. The cytoplasmic loops have the highest temperature factors in the structure, indicative of their flexibility when not interacting with G protein or regulatory proteins. An ordered detergent molecule is seen wrapped around the kink in H6, stabilising the structure around the potential hinge in H6. These findings provide further explanation for the stability of the dark state structure. They support a mechanism for the activation, initiated by photo-isomerisation of the chromophore to its all-trans form, that involves pivoting movements of kinked helices, which, while maintaining hydrophobic contacts in the membrane interior, can be coupled to amplified translation of the helix ends near the membrane surfaces.

Rhodopsin, the pigment protein responsible for dim-light vision, is a G protein-coupled receptor that converts light absorption into the activation of a G protein, transducin, to initiate the visual response. We have crystallised detergent-solubilised bovine rhodopsin in the native form and after chemical modifications as needles 10-40 microm in cross-section. The crystals belong to the trigonal space group P3(1), with two molecules of rhodopsin per asymmetric unit, related by a non-crystallographic 2-fold axis parallel with the crystallographic screw axis along c (needle axis). The unit cell dimensions are a=103.8 A, c=76.6 A for native rhodopsin, but vary over a wide range after heavy atom derivatisation, with a between 101.5 A and 113.9 A, and c between 76.6 A and 79.2 A. Rhodopsin molecules are packed with the bundle of transmembrane helices tilted from the c-axis by about 100 degrees . The two molecules in the asymmetric unit form contacts along the entire length of their transmembrane helices 5 in an antiparallel orientation, and they are stacked along the needle axis according to the 3-fold screw symmetry. Hence hydrophobic contacts are prominent at protein interfaces both along and normal to the needle axis. The best crystals of native rhodopsin in this crystal form diffracted X-rays from a microfocused synchrotron source to 2.55 A maximum resolution. We describe steps taken to extend the diffraction limit from about 10 A to 2.6 A.

The remarkable mechanical properties of biological materials reside in their complex hierarchical architecture and in specific molecular mechanistic phenomena. The fundamental importance of molecular interactions and bond recovery has been suggested by studies on deformation and fracture of bone and nacre. Like these mineral-based materials, wood also represents a complex nanocomposite with excellent mechanical performance, despite the fact that it is mainly based on polymers. In wood, however, the mechanistic contribution of processes in the cell wall is not fully understood. Here we have combined tensile tests on individual wood cells and on wood foils with simultaneous synchrotron X-ray diffraction analysis in order to separate deformation mechanisms inside the cell wall from those mediated by cell-cell interactions. We show that tensile deformation beyond the yield point does not deteriorate the stiffness of either individual cells or foils. This indicates that there is a dominant recovery mechanism that re-forms the amorphous matrix between the cellulose microfibrils within the cell wall, maintaining its mechanical properties. This stick-slip mechanism, rather like Velcro operating at the nanometre level, provides a 'plastic response' similar to that effected by moving dislocations in metals. We suggest that the molecular recovery mechanism in the cell matrix is a universal phenomenon dominating the tensile deformation of different wood tissue types.

The stone-like otoliths from the ears of teleost fishes are involved in balance and hearing and consist of calcium carbonate crystallites embedded in a protein framework. We report that a previously unknown gene, starmaker, is required in zebrafish for otolith morphogenesis. Reduction of starmaker activity by injection of modified antisense oligonucleotides causes a change in the crystal lattice structure and thus a change in otolith morphology. The expression pattern of starmaker, along with the presence of the protein on the growing otolith, suggest that the expression levels of starmaker control the shape of the otoliths.

Water microdrops of about 50 microm in diameter, generated by an ink-jet system, have been used to hydrate fragments of Pogonophora tubes. In situ X-ray microdiffraction with a beam size of 10 microm was used to follow the structural transformations that affected the crystalline beta-chitin part of the specimens. Starting from anhydrous chitin, the formation of a full beta-chitin dihydrate was observed within about 90 s. A disordered intermediate phase with variable d-spacing that could be due to a mixture of anhydrous and hydrated beta-chitin layers was also detected.

The retinoblastoma tumor suppressor protein (pRb) regulates the cell cycle, facilitates differentiation, and restrains apoptosis. Furthermore, dysfunctional pRb is thought to be involved in the development of most human malignancies. Many of the functions of pRb are mediated by its regulation of the E2F transcription factors. To understand the structural basis for this regulation, we have determined the crystal structure of a fragment of E2F in complex with the pocket domain of the tumor suppressor protein. The pRb pocket, comprising the A and B cyclin-like domains, is the major focus of tumourigenic mutations in the protein. The fragment of E2F used in our structural studies, residues 409-426 of E2F-1, represents the core of the pRb-binding region of the transcription factor. The structure shows that E2F binds at the interface of the A and B domains of the pocket making extensive interactions with conserved residues from both. We show by solution studies that a second site, probably contained within the "marked box" region of E2F, is responsible for additional interactions with the pRb pocket but is insufficient for complex formation on its own. In addition, we show that the interaction of the core binding fragment of E2F with pRb is inhibited by phosphorylation of the tumor suppressor protein by CDK2cyclin DE. Finally, our data reveal that the tight binding of the human papillomavirus E7 oncoprotein to pRb prevents subsequent interactions with the marked box region of E2F but not with its core binding region.

This investigation presents new insights into the structure of human secondary lamellae. Lamellar specimens that appear dark and bright on alternate osteon transverse sections under circularly polarizing light were isolated using a new technique, and examined by polarizing light microscopy, synchrotron X-ray diffraction, and confocal microscopy. A distribution of unidirectional collagen bundles and of two overlapping oblique bundles appears on circularly polarizing light microscopy images in relation to the angle between the specimen and the crossed Nicols' planes. The unidirectional collagen bundles observed at 45 degrees run parallel to the osteon axis in the dark lamellar specimens and perpendicular to it in the bright ones. Small and wide-angle micro-focus X-ray diffraction indicates that the dark lamellae are structurally quite homogeneous, with collagen fibers and apatite crystals preferentially oriented parallel to the osteon axis. Bright lamellar specimens exhibit different orientation patterns with the dominant ones bidirectional at +/-45 degrees with respect to the osteon axis. Accordingly, confocal microscopy evidences the presence of longitudinal bundles in dark lamellar specimens and oblique bundles in the bright ones. Radial bundles are evidenced in both lamellar types. The alternate osteon structure is described by a rather continuous multidirectional pattern, in which dark and bright lamellae display different mechanical and possibly biological functions.