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Crystal structure of an Eph receptor-ephrin complex.

The Eph family of receptor tyrosine kinases and their membrane-anchored ephrin ligands are important in regulating cell-cell interactions as they initiate a unique bidirectional signal transduction cascade whereby information is communicated into both the Eph-expressing and the ephrin-expressing cells. Initially identified as regulators of axon pathfinding and neuronal cell migration, Ephs and ephrins are now known to have roles in many other cell-cell interactions, including those of vascular endothelial cells and specialized epithelia. Here we report the crystal structure of the complex formed between EphB2 and ephrin-B2, determined at 2.7 A resolution. Each Eph receptor binds an ephrin ligand through an expansive dimerization interface dominated by the insertion of an extended ephrin loop into a channel at the surface of the receptor. Two Eph-Ephrin dimers then join to form a tetramer, in which each ligand interacts with two receptors and each receptor interacts with two ligands. The Eph and ephrin molecules are precisely positioned and orientated in these complexes, promoting higher-order clustering and the initiation of bidirectional signalling.

Amino Acid Sequence↗

Disruption of a salt bridge dramatically accelerates subunit exchange in duck delta2 crystallin.

Intragenic complementation is a unique property of oligomeric enzymes with which to study subunit-subunit interactions. Complementation occurs when different subunits, each possessing distinct mutations that render the individual homomutant proteins inactive, interact to form a heteromutant protein with partial recovery of activity. In this paper, complementation events between human argininosuccinate lyase (ASL) and its homolog, duck delta2 crystallin, were characterized. Different active site mutants in delta2 crystallin complement by the regeneration of native-like active sites as reported previously for ASL. The complementarity of the ASL and delta2 crystallin subunit interfaces was illustrated by the in vivo formation of active hybrid tetramers from inactive ASL and inactive delta2 crystallin mutants. Subunits of both ASL and delta2 crystallin do not dissociate and reassociate in vitro at room temperature, even after 6 days of incubation, indicating that the multimerization interface is very strong. However, disruption of a salt bridge network in the tetrameric interface of delta2 crystallin caused a drastic acceleration of subunit dissociation. Double mutants combining these interface mutants with active site mutants of delta2 crystallin were able to dissociate and reassociate to form active tetramers in vitro within hours. These results suggest that exchange of subunits may occur without unfolding of the monomer. Intragenic complementation in these interface mutants occurs by reintroducing the native salt bridge interaction upon hetero-oligomerization. Our studies demonstrate the value of intragenic complementation as a tool for investigating subunit-subunit interactions in oligomeric proteins.

Animals↗

Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase.

The structure of Bacillus subtilis TrmB (BsTrmB), the tRNA (m7G46) methyltransferase, was determined at a resolution of 2.1 A. This is the first structure of a member of the TrmB family to be determined by X-ray crystallography. It reveals a unique variant of the Rossmann-fold methyltransferase (RFM) structure, with the N-terminal helix folded on the opposite site of the catalytic domain. The architecture of the active site and a computational docking model of BsTrmB in complex with the methyl group donor S-adenosyl-L-methionine and the tRNA substrate provide an explanation for results from mutagenesis studies of an orthologous enzyme from Escherichia coli (EcTrmB). However, unlike EcTrmB, BsTrmB is shown here to be dimeric both in the crystal and in solution. The dimer interface has a hydrophobic core and buries a potassium ion and five water molecules. The evolutionary analysis of the putative interface residues in the TrmB family suggests that homodimerization may be a specific feature of TrmBs from Bacilli, which may represent an early stage of evolution to an obligatory dimer.

Bacillus subtilis↗

Generalizations regarding the process and phenomenon of osseointegration. Part II. In vitro studies.

In this review, the appropriate use of cell culture to evaluate substrate effects on osteoblast behavior during the process of osseointegration has been considered in the context of existing reports. The interactions of osteoblasts with different substrates can be measured in terms of cytotoxicity, attachment, proliferation, and differentiation. The osteoblast culture systems that produce an osteoblast matrix opposing implant material substrates provide one model for evaluating the implant-bone interface. Alterations in osteoblast behavior at different culture substrates may reflect clinical determinants of bone formation at these substrates in vivo; however, cell responses in vitro have not been compared or correlated with in vivo outcomes. Legitimate interpretations of in vitro experiments are discussed in terms of practical, technical, and biologic limitations presented by the cell culture approach. Cell culture provides access to molecular and cellular information that fosters nanostructural engineering approaches to implant design and significant hypotheses to be tested in vivo. In this way, cell culture offers unique insights into the process and phenomenon of osseointegration.

Animals↗

High-resolution simultaneous three-photon fluorescence and third-harmonic-generation microscopy.

In recent years, nonlinear laser scanning microscopy has gained much attention due to its unique ability of deep optical sectioning. Based on our previous studies, a 1,200-1,300-nm femtosecond laser can provide superior penetration capability with minimized photodamage possibility. However, with the longer wavelength excitation, three-photon-fluorescence (3PF) would be necessary for efficient use of intrinsic and extrinsic visible fluorophores. The three-photon process can provide much better spatial resolution than two-photon-fluorescence due to the cubic power dependency. On the other hand, third-harmonic-generation (THG), another intrinsic three-photon process, is interface-sensitive and can be used as a general structural imaging modality to show the exact location of cellular membranes. The virtual-transition characteristic of THG prevents any excess energy from releasing in bio-tissues and, thus, THG acts as a truly noninvasive imaging tool. Here we demonstrated the first combined 3PF and THG microscopy, which can provide three-dimensional high-resolution images with both functional molecule specificity and sub-micrometer structural mapping capability. The simultaneously acquired 3PF and THG images based on a 1,230-nm Cr:forsterite femtosecond laser are shown with a Hoechst-labeled hepatic cell sample. Strong 3PF around 450 nm from DNA-bounded Hoechst-33258 can be observed inside each nucleus while THG reveals the location of plasma membranes and other membrane-based organelles such as mitochondria. Considering that the maximum-allowable laser power in common nonlinear laser microscopy is less than 10 mW at 800 nm, it is remarkable that even with a 100-mW 1,230-nm incident power, there is no observable photo damage on the cells, demonstrating the noninvasiveness of this novel microscopy technique.

Bisbenzimidazole↗

Intermolecular interactions between cholecystokinin-8 and the third extracellular loop of the cholecystokinin A receptor.

The interaction of the C-terminal octapeptide of cholecystokinin, CCK-8, with the third extracellular loop of human cholecystokinin-A receptor, CCK(A)-R(329-357), has been probed by high-resolution NMR and extensive computer simulations. The structure of CCK(A)-R(329-357) in the presence of dodecylphosphocholine micelles consists of three alpha-helices, with the first and third corresponding to the extracellular ends of transmembrane (TM) helices 6 and 7. The central helix, residues W335-R345, is found to lie on the zwitterionic surface. Titration with CCK-8 produces a stable complex with a number of intermolecular NOEs between the C-terminus of the ligand (Trp(30), Met(31), Asp(32)) and the interface of TM6 and the third extracellular loop (N333, A334, Y338) of the receptor fragment. The mode of ligand binding based on these intermolecular NOEs is in agreement with a number of published findings from receptor mutagenesis and photoaffinity cross-linking. Utilizing these ligand/receptor points of interaction, the structural features of CCK(A)-R(329-357), and also the structures of CCK-8 and CCK(A)-R(1-47) previously determined, extensive molecular dynamics simulations of the CCK-8/CCK(A)-R complex were carried out. The results provide unique insight into the molecular interactions and forces important for the binding of CCK-8 to CCK(A)-R.

Amino Acid Sequence↗

Structural and functional studies of complement inhibitor C4b-binding protein.

C4b-binding protein (C4BP) is a potent inhibitor of the classical pathway of the complement system. This large plasma glycoprotein consists of seven identical alpha-chains and a unique beta-chain held together by disulphide bridges. Both types of subunits are composed almost exclusively of complement control protein domains (CCPs). Using homology-based computer modelling and mutagenesis of recombinant proteins we have localized binding sites for several ligands of C4BP: complement factor C4b, heparin and vitamin K-dependent anticoagulant protein S (PS). We found that C4b requires CCP1-3 of the alpha-chain for binding. The interaction is ionic in nature and mediated by a cluster of positively charged amino acids present on the interface between CCP1 and CCP2 of the alpha-chain. Loss of C4b-binding resulted in a loss of all inhibitory functions of C4BP within the classical pathway of complement. Binding of heparin required CCPs 1-3 of the alpha-chain, with CCP2 being the most important, as well as the cluster of positively charged amino acids involved in binding of C4b. The interaction between C4BP and PS is of very high affinity and conveyed by a cluster of surface exposed hydrophobic amino acids localized on CCP1 of the beta-chain. Furthermore, C4BP is captured on the surface of several pathogens, which may contribute to their serum resistance and pathogenicity. We have localized interaction of C4BP with Neisseria gonorrhoeae, Bordetella pertussis, Streptococcus pyogenes and Escherichia coli to various regions of the alpha-chain.

Animals↗

Autocalibration of a projector-camera system.

This paper presents a method for calibrating a projector-camera system that consists of multiple projectors (or multiple poses of a single projector), a camera, and a planar screen. We consider the problem of estimating the homography between the screen and the image plane of the camera or the screen-camera homography, in the case where there is no prior knowledge regarding the screen surface that enables the direct computation of the homography. It is assumed that the pose of each projector is unknown while its internal geometry is known. Subsequently, it is shown that the screen-camera homography can be determined from only the images projected by the projectors and then obtained by the camera, up to a transformation with four degrees of freedom. This transformation corresponds to arbitrariness in choosing a two-dimensional coordinate system on the screen surface and when this coordinate system is chosen in some manner, the screen-camera homography as well as the unknown poses of the projectors can be uniquely determined. A noniterative algorithm is presented, which computes the homography from three or more images. Several experimental results on synthetic as well as real images are shown to demonstrate the effectiveness of the method.

Algorithms↗

The Autoimmune Disease Database: a dynamically compiled literature-derived database.

BACKGROUND: Autoimmune diseases are disorders caused by an immune response directed against the body's own organs, tissues and cells. In practice more than 80 clinically distinct diseases, among them systemic lupus erythematosus and rheumatoid arthritis, are classified as autoimmune diseases. Although their etiology is unclear these diseases share certain similarities at the molecular level i.e. susceptibility regions on the chromosomes or the involvement of common genes. To gain an overview of these related diseases it is not feasible to do a literary review but it requires methods of automated analyses of the more than 500,000 Medline documents related to autoimmune disorders. RESULTS: In this paper we present the first version of the Autoimmune Disease Database which to our knowledge is the first comprehensive literature-based database covering all known or suspected autoimmune diseases. This dynamically compiled database allows researchers to link autoimmune diseases to the candidate genes or proteins through the use of named entity recognition which identifies genes/proteins in the corresponding Medline abstracts. The Autoimmune Disease Database covers 103 autoimmune disease concepts. This list was expanded to include synonyms and spelling variants yielding a list of over 1,200 disease names. The current version of the database provides links to 541,690 abstracts and over 5,000 unique genes/proteins. CONCLUSION: The Autoimmune Disease Database provides the researcher with a tool to navigate potential gene-disease relationships in Medline abstracts in the context of autoimmune diseases.

Autoimmune Diseases↗

Morphological characterisation of portal myofibroblasts and hepatic stellate cells in the normal dog liver.

BACKGROUND: Hepatic fibrosis is a common outcome of hepatic injury in both man and dog. Activated fibroblasts which develop myofibroblastic characteristics play an essential role in hepatic fibrogenesis, and are comprised of three subpopulations: 1) portal or septal myofibroblasts, 2) interface myofibroblasts and 3) the perisinusoidally located hepatic stellate cells (HSC). The present study was performed to investigate the immunohistochemical characteristics of canine portal myofibroblasts (MF) and HSC in the normal unaffected liver as a basis for further studies on fibrogenesis in canine liver disease. RESULTS: In the formalin-fixed and paraffin embedded normal canine liver vimentin showed staining of hepatic fibroblasts, probably including MF in portal areas and around hepatic veins; however, HSC were in general negative. Desmin proved to react with both portal MF and HSC. A unique feature of these HSC was the positive immunostaining for alpha-smooth muscle actin (alpha-SMA) and muscle-specific actin clone HHF35 (HHF35), also portal MF stained positive with these antibodies. Synaptophysin and glial fibrillary acidic protein (GFAP) were consistently negative in the normal canine liver. In a frozen chronic hepatitis case (with expected activated hepatic MF and HSC), HSC were negative to synaptophysin, GFAP and NCAM. Transmission electron microscopy (TEM) immunogold labelling for alpha-SMA and HHF35 recognized the positive cells as HSC situated in the space of Disse. CONCLUSION: In the normal formalin-fixed and paraffin embedded canine liver hepatic portal MF and HSC can be identified by alpha-SMA, HHF35 and to a lesser extent desmin immunostaining. These antibodies can thus be used in further studies on hepatic fibrosis. Synaptophysin, GFAP and NCAM do not seem suitable for marking of canine HSC. The positivity of HSC for alpha-SMA and HHF35 in the normal canine liver may eventually reflect a more active regulation of hepatic sinusoidal flow by these HSC compared to other species.

Journal Article↗

["You learn, we teach"? Questioning relations between education and health from the perspective of vulnerability].

This article explores the meanings associated with the motto used in a World No-Tobacco Day campaign to stimulate a discussion of the principal underlying messages in the field of health education in Brazil. The study focuses on the concept of vulnerability to contextualize and explore its interfaces with education in order to highlight the theoretical, practical, and political productivity of the link between health education and studies on vulnerability. In conclusion, the necessary renewal of health practices in general and health education practices in particular can benefit tremendously from the vulnerability reference, to the extent that it demarcates a new horizon for situating and linking risks, "causalities", and "determinations", drawing health--as well as the possibility of illness--into the field of real life, into the world of inter-subjective relations, where these processes gain unique meanings.

Communication↗

Structural and mechanistic mapping of a unique fumarate reductase.

The 1.8 A resolution crystal structure of the tetraheme flavocytochrome c3, Fcc3, provides the first mechanistic insight into respiratory fumarate reductases or succinate dehydrogenases. The multi-redox center, three-domain protein shows a 40 A long 'molecular wire' allowing rapid conduction of electrons through a new type of cytochrome domain onto the active site flavin, driving the reduction of fumarate to succinate. In this structure a malate-like molecule is trapped in the enzyme active site. The interactions between this molecule and the enzyme suggest a clear mechanism for fumarate reduction in which the substrate is polarized and twisted, facilitating hydride transfer from the reduced flavin and subsequent proton transfer. The enzyme active site in the oxidized form is completely buried at the interface between the flavin-binding and the clamp domains. Movement of the cytochrome and clamp domains is postulated to allow release of the product.

Amino Acid Sequence↗

Stabilization and remodeling of the membrane skeleton during lens fiber cell differentiation and maturation.

Actin filaments are integral components of the plasma membrane-associated cytoskeleton (membrane skeleton) and are believed to play important roles in the determination of cell polarity, shape, and membrane mechanical properties, however the roles of actin regulatory proteins in controlling the assembly, stability, and organization of actin filaments in the membrane skeleton are not well understood. Tropomodulin is a tropomyosin and actin-binding protein that stabilizes tropomyosin-actin filaments by capping their pointed ends and is associated with the spectrin-actin membrane skeleton in erythrocytes, skeletal muscle cells, and lens fiber cells, a specialized epithelial cell type. In this study, we have investigated the role of tropomodulin and other membrane skeleton components in lens fiber cell differentiation and maturation. Our results demonstrate that tropomodulin is expressed concomitantly with lens fiber cell differentiation and assembles onto the plasma membrane only after fiber cells have begun to elongate and form apical-apical contacts with the undifferentiated epithelium. In contrast, other membrane skeleton components, spectrin, actin, and tropomyosin, are constitutively expressed and assembled on the plasma membranes of both undifferentiated and differentiated fiber cells. Tropomodulin, but not other membrane skeleton components, is also enriched at a novel structure at the apical and basal ends of newly elongated fiber cells at the fiber cell-epithelium and fiber cell-capsule interface, respectively. Once assembled, tropomodulin and its binding partners, tropomyosin and actin, remain membrane-associated and are not proteolyzed during fiber cell maturation and aging, despite proteolysis of alpha-spectrin and other cytoskeletal filament systems such as microtubules and intermediate filaments. We propose that actin filament stabilization by tropomodulin, coupled with partial proteolysis of other cytoskeletal components, represents a programmed remodeling of the lens membrane skeleton that may be essential to maintain plasma membrane integrity and transparency of the extremely elongated, long-lived cells of the lens. The unique localization of tropomodulin at fiber cell tips further suggests a new role for tropomodulin at cell-cell and cell-substratum contacts; this may be important for cell migration and/or adhesion during differentiation and morphogenesis.

Actins↗

Developmental modification of the Drosophila cell cycle.

The cell cycle is subject to extrinsic regulation that coordinates cell division with developmental events. This important area at the interface of developmental biology and research into the cell cycle has yielded recent exciting advances. Developmental modification of the cell cycle is exemplified during Drosophila embryogenesis. Early in embryogenesis, regulation of the cell cycle becomes progressively more complex as a simple S-M cycle is altered to include gap phases. Later in embryogenesis, the cycle alters again, to include only an S and a gap phase. These developmental alterations are partly effected by regulating the expression of genes that control key transitions in the cell cycle. Certain controls that are unique to the variant cell cycles have also been defined. The field is now poised for the identification of the intervening steps between the developmental signals and their ultimate effects on known cell cycle regulators.

Animals↗

IgM secretion and absorption in the materno-fetal interface of a viviparous teleost, Neoditrema ransonneti (Perciformes; Embiotocidae).

We investigated maternal IgM secretion in the ovary and the absorption of IgM by fetuses in a viviparous fish, Neoditrema ransonneti (Embiotocidae). Serum IgM, whose molecular weight was approx. 820k, was purified by two steps of gel filtration chromatography. Immunohistochemistry and Western blotting revealed that IgM was secreted from the epithelia of the ovigerous lamellae of pregnant females into ovarian cavity fluid. The IgM-secreting activity of ovigerous folds showed notable changes according to the reproductive stage. In fetuses, IgM was absorbed as macromolecules by enterocytes of the hypertrophied hindgut. IgM in the fetal blood was also demonstrated, although its concentration remained low during gestation. These findings suggest that IgM was transported from the maternal tissues to embryos via a unique pathway in N. ransonneti.

Animals↗

Response mechanism of polymer membrane-based potentiometric polyion sensors.

The potentiometric response mechanism of a previously reported polymer membrane-based electrode sensitive to the polyanion heparin is established. Based on transport and extraction studies, the heparin response is attributed to a nonequilibrium change in the phase boundary potential at the sample/membrane interface. While true equilibrium polyion response, obtained for low heparin concentrations only after very long equilibration times (> 20 h), yields the expected Nernstian response slope of < 1 mV/decade, the observed large and reproducible EMF response to clinically relevant heparin concentrations (approximately 10(-7) M) during typical measurement periods (2-5 min) is ascribed to a steady-state kinetic process defined by the flux of the polyion both to the surface and into the bulk of the polymer membrane. A model describing this nonequilibrium response is presented. With this model, the uniqueness of the polymer membrane composition (e.g., very low plasticizer content, strictly controlled cationic site concentration, etc.) required to achieve analytically useful heparin response becomes clear. Practical working conditions and limitations of the sensor are discussed. To support the generality of the steady-state model proposed, corresponding EMF response data for a newly developed membrane electrode sensitive to a polycationic protein (protamine) are also presented. It is shown that the protamine-responsive membrane electrode appears to operate via the exact same kinetic mechanism as the heparin sensing system.

Biosensing Techniques↗

Photon absorption in resonant-cavity-enhanced gaas far-infrared detectors.

Interface reflection has been demonstrated to play an important role in GaAs multilayer homojunction far-infrared (FIR) detectors. A transfer matrix method that is able to provide a true optical field distribution within an FIR detector has been employed to optimize photon absorption and structure. The dependence of photon absorption on the reflectivity and the phase shift of the bottom mirror in a resonant-cavity-enhanced GaAs FIR detector has been investigated. Weak wavelength selectivity has been observed for both resonant and off-resonant FIR, which is a unique advantage for detector application. In comparison with the experimental result, a 20.8% increase in quantum efficiency was found in an optimized FIR detector.

Journal Article↗

View from the boundary.

Re-implementing biological mechanisms on robots not only has technological application but can provide a unique perspective on the nature of sensory processing in animals. To make a robot work, we need to understand the function as part of an embodied, behaving system. I argue that this perspective suggests that the terms "representation" and "information processing" can be misleading when we seek to understand how neurobiological mechanisms carry out perceptual processes. This argument is presented here with reference to a robot model of cricket behavior, which has demonstrated competence comparable to that of the insect, but utilizes surprisingly simple central processing. Instead it depends on sensory interfaces that are well matched to the task, and on the link between environment, action, and perception.

Animals↗