Visualization of the entire surface of a protein by cartographic projection

A minicomputer based system for the determination and schematicrepresentation of protein surfaces is described. The algorithmsare based on the atomic coordinates of globular protein moleculesof the Brookhaven Protein Data Bank. Using a cartographic projectiona normalized graphic representation is obtained of the aminoacid residues located on the surface of the considered protein.The programs are written in FORTRAN IV (surface determination)and BASIC (graphic representation). Received on April 28, 1986; accepted on July 17, 1986     

Visualization of the microwave beam generated by a plasma relativistic microwave amplifier

A method based on the detection of emission of a dielectric screen with metal microinclusions in open air is applied to visualize the transverse structure of a high-power microwave beam. In contrast to other visualization techniques, the results obtained in this work provide qualitative information not only on the electric field strength, but also on the structure of electric field lines in the microwave beam cross section. The interpretation of the results obtained with this method is confirmed by numerical simulations of the structure of electric field lines in the microwave beam cross section by means of the CARAT code.     

Visualization of the retino-hypothalamic projection in the rat by cobalt precipitation

Summary The technique of cobalt sulfide precipitation combined with Timm's sulfide-silver method for intensification of heavy metals was used to delineate the retino-hypothalamic projection of the rat. Freshly isolated rat brains were dissected and a solution of cobaltous chloride was applied to one of the cut optic nerves. Sixteen hours later, after cobalt ions had passed into the brain along the entire length of the optic fibers, the preparation was treated with ammonium sulfide to precipitate the cobalt as cobalt sulfide. In thick light microscopic sections, cobalt-filled axons were visualized as black fibers against a light gold background. Such fibers were observed to leave the posterior medial portion of the optic chiasm and, after arching dorsally, to project into the posterior fifth of the suprachiasmatic nucleus (SCN), as well as into the rostral part of the arcuate nucleus. Neither bifurcation of these axons nor looping of the axons back to the chiasm was seen. Most fibers projected to the SCN contralateral to the filled nerve, but the projection represented less than 0.1 % of the total number of fibers in one optic nerve. These observations are considered to be graphic evidence of a retino-hypothalamic projection. The interpretation of the cobalt method is discussed, as are the functions of the connections that have been observed.This work was supported by the Nuffield FoundationWe are grateful to Mr. Clifford Jeal of the Department of Pathology for excellent advice on photomicrography     

Visualization of exocytotic secretory processes of mast cells by fluorescence techniques

Secretory processes via exocytosis in rat peritoneal mast cells were visualized by two complementary fluorescence techniques; one staining pre-exocytotic granules with a basic probe and the other staining post-exocytotic granules with acidic probes. Granules within mast cells were selectively stained with acridine orange and emitted orange yellow fluorescence. Upon stimulation with compound 48/80, release of acridine orange from granules was observed both in population and single cell measurements. This release was seen in some localized area of mast cells. Opening of pores between plasma membranes and granule membranes was monitored using acidic fluorescence probes such as 6-carboxyfluorescein or lucifer yellow CH. Not only granules located at peripheral region, but also granules near the core region participated in exocytosis. The existence of junctions between these granules was suggested. TMA-DPH, a lipophilic membrane probe, which was localized at plasma membrane before stimulation, diffused into granule membranes after stimulation. This shows that after stimulation, some constituents of plasma and granule membranes were mixed. Even after extensive degranulation, mast cells extruded acidic probes, indicating the plasma membranes still play a role of barrier. Activation of lateral motion of granules preceding to exocytosis was not observed. It was concluded that the visualization of secretory processes by fluorescence and image processing techniques will be useful for the study of molecular mechanisms underlying exocytosis.     

Computerization of a population projection model based on generalized age-dependent branching processes: a connection with the Leslie matrix

The population projection model based on generalized age-dependent branching processes developed by Mode and Busby (1981) involves the solution of a large number of renewal type equations. It is shown that these equations may be solved recursively. Such a solution has two implications. One is that the projection model may be very efficiently computerized. Second, the recursive algorithm developed has striking similarities to two traditional methods of population projection used by demographers: the Leslie matrix and cohort component methods. The results presented here associate traditional projection techniques with the theory of age-dependent branching processes.     

Manipulation of living cells by using PC-controlled micro-pattern projection system

In order to meet the diversifying demand for the cell manipulation in the rapid progress of cell engineering, we developed a novel technique to capture the living cells on a culture substrate by irradiating light in a multiple manner. In clear contrast to the conventional cell patterning using the previously patterned substrate, the cell-retaining area can be defined even after cell seeding, and the captured cells can continue to grow freely beyond the defined area afterwards. After the light irradiation in arbitrary micropattern by using a newly developed apparatus and the process to remove non-captured cells including EDTA treatment, the highly contrasted cell patterns were formed with the precision of single cell size. Moreover, it was determined that the cell capturing arose just after light irradiation and diminished gradually in a time scale of 10h. It was confirmed that the cells maintained their viability well after the manipulation process including photo-induced cell capturing.     

Backwrd population projection by a generalized inverse

The Leslie population projection matrix may be used to project forward in time the age distribution or age-sex distribution of a population. As it is a singular matrix, it does not have an inverse, and so it is not clear that there is a corresponding procedure for backward projection. In terms of the eigenvalues and eigenvectors of the Leslie matrix, certain generalized inverses are constructed that can sometimes be used advantageously for backward projection.     

Visualization of excitation energy transfer processes in plants and algae

Development of the time-resolved fluorescence spectroscopy in the pico-second time range and its application to the energy transfer processes in many photosynthetic organisms is reviewed here. This method enabled visualization of energy transfer processes by three-dimensional expression of fluorescence spectra and discrimination of kinetic components and spectral components. The second generation of the ultrafast fluorescence spectroscopy is the femto-second (fs) fluorescence up-conversion, and this has enabled analyses of the transfer processes from carotenoids to chlorophylls with a resolution of less than 100 fs. For future progress, a further development of the spectroscopy is indispensable as well as structural data at atomic resolution. This revised version was published online in June 2006 with corrections to the Cover Date.     

Opto-electrical processes in a conducting polymer-bacteriorhodopsin system

In this report, we highlight the opto-electrical processes at a conducting polymer-bacteriorhodopsin (bR) interface in presence of a voltage bias. Oriented bR on a conducting polymer substrate forms a unique hybrid system where the oxidation state of the polymer controls the optically activated proton gradient in the bR side. The internal conversion of the intermediate deprotonated M-state and the proton transfer/transport of bR at the interface can be controlled by the electrostatic environment and leads to interesting device features in this process.     

Autowave processes in a distributed chemical system

The autowave processes with a characteristic wavelength and oscillation period may arise under some initial conditions in a uniform active medium. The wavelength and period depend on the chemical and physical parameters of the system and are independent of the initial and boundary conditions and of the system linear size. The processes occur in a homogeneous solution in the course of an oscillating chemical reaction. Similar processes may play an important role in the phenomena of short-term memory, cardiac arrhythmia, morphogenesis and prebiological evolution.Different types of structures are discussed, and experimental data and mathematical models are presented.     

Visualization of peptide-immunoreactive processes on serotonin-immunoreactive cells using two-color immunoperoxidase staining

The sequential application of the peroxidase-antiperoxidase (PAP) technique with nickel-intensified DAB and with DAB alone was used to visualize black peptide-immunoreactive endings on amber serotonin-immunoreactive cells in 1-2-micron paraffin sections of the hamster medulla. Met-enkephalin- and substance P-positive terminals were present on serotonin cells in the raphe nuclei, the ventral reticular formation, and in the nucleus interfascicularis hypoglossi. The presence of enkephalin-immunoreactive endings on medullary serotonin-immunoreactive cells correlates with the analgesia and autonomic changes that result from the application of morphine or met-enkephalin to the medulla.     

Temporal development of vegetation and geomorphology in a man-made beach-dune system by natural processes

Twenty-four yrs of primary succession in a man-made beach-dune system at the Baltic coast of Denmark, built of calcareous, marine sand and the dune planted with Ammophila arenaria , was studied by qualitative observations, quantitative records in permanent plots, levelling and soil analysis within a selected area of 0.75 ha. The aim of the study was to discuss whether human initiated and influenced beach and dune dynamics mimick natural beach and dune processes, and to discuss the relationship between succession and zonation. During the study period, which started in 1979, the man-made dune stabilized rather fast. In the stabilized dune, a sand-pararendzina with a thin A-horizon developed. The beach expanded by accretion of less calcareous, marine sand. On the beach new dunes, 3 m high, successively developed. The number of species in the study area increased from 16 to 55, accompanied by species and life form dynamics, characteristic for primary succession on sandy coasts. A gradual change in species composition of the permanent plots, which appeared by a DCA analysis, could by using TWINSPAN be structured into four groups or plant communities, which reflect succession as well as zonation. Two groups represent the vegetation of sandy beaches with annual dicotyledon species, and mobile dunes dominated by rhizomatous geophytes, especially A. arenaria. The two other groups represent stabilized, calcareous dune, dominated by hemicryptophytes, specially Festuca rubra , and less stabilized dune with F. rubra and the invasive alien Rosa rugosa. It was concluded, that the main trends in the geomorphological and vegetational development of the man-made beach-dune system is similar to the development in natural dunes. In the future, further accretion and seaward dune formation may be expected, but is it also expected, that larger parts of the area gradually will be covered by low scrubs of R. rugosa.     

Serins with intermediate brightness have a higher survival in the wild

More ornamented individuals are supposed to signal their superior quality and health, however the development of larger ornaments or brighter plumages can affect their survival probabilities. The survival of male serins Serinus serinus in relation to the color characteristics of carotenoid-derived breast coloration was analyzed in a six-year capture–recapture study in northeastern Spain. A total of 210 males were individually marked generating 340 captures, between 1997 and 2003. The model with the best fit indicated a quadratic relationship between brightness of carotenoid-derived coloration and survival, independent of time and age of the birds, so that individuals with intermediate plumage brightness survived longer. Hence, results stress that plumage color in male serins is under stabilizing natural selection, with reduced survival both in drabber and brighter individuals. While lower condition of drabber individuals can explain their lower survival, brighter birds can suffer more from predation risk or from a higher investment of resources into mate attraction and/or reproduction.     

Simulation of oscillatory processes in a beam-plasma system with a virtual cathode in gas-filled interaction space

Physical processes occurring in an intense electron beam with a virtual cathode in an interaction space filled with neutral gas are studied in a two-dimensional model. A mathematical model is proposed for investigating complicated self-consistent processes of neutral gas ionization by the beam electrons and the dynamics of an electron beam and heavy positive ions in the common space charge field with allowance for the two-dimensional motion of charged particles. Three characteristic dynamic regimes of the system are revealed: complete suppression of oscillations of the virtual cathode as a result of neutralizing its space charge by positive ions; the pulsed generation regime, in which the ions dynamics repeatedly suppresses and restores the virtual cathode oscillations; and the continuous generation regime with an anomalously high level of noisy oscillations.     

基于光投影数字化传感系统的飞蝗表面三维结构

本文基于结构光投影数字化传感系统构建东亚飞蝗Locusta migratoria manilensis表面的三维结构。首先得到其外形尺寸和肢体各部分拓扑结构,然后从被调制的条纹结构光中恢复出物体表面高度变化的相位信息,再通过相位和高度的对应关系重建出物体表面三维特征。此结果将为农药研制和施用设计提供科学依据,对促进蝗虫的防治以及虚拟昆虫研究起到积极作用。     

Axon guidance processes in the retinotectal and vomeronasal projection are controlled by Eph receptor tyrosine kinases and ephrins

The Eph family of receptor tyrosine kinases and their ‘ligands’, the ephrins, have been shown to play key roles in a number of different developmental processes such as cell migration, boundary formation, axon guidance, synapse formation and vasculogenesis. Here, we summarize recent findings derived from investigating the role of the EphA family during development of the retinotectal and vomeronasal projection uncovering a role of ephrin-A molecules as axon guidance receptors.     

Direct Visualization of a Transmembrane Channel Associated with Ribosomes

Examination of directly frozen rough endoplasmic reticulum (ER) of retinal pigment epithelial cells by freeze-fracture and freeze-substitution revealed distinct paired transmembrane proteins associated with membrane ribosomes. Ribosomal subunits on intact ER membrane are directly visualized for the first time, providing a global view of the structure of the ribosome and the corresponding structures on the ER membrane. The ribosomal intersubunit cleft appears to be continuous with a cleft between paired transmembrane proteins that extends into the lumen of the ER. This continuous cleft may be the path taken by nascent polypeptides.