A Conceptual Cortical Surface Atlas

Volumetric, slice-based, 3-D atlases are invaluable tools for understanding complex cortical convolutions. We present a simple scheme to convert a slice-based atlas to a conceptual surface atlas that is easier to visualize and understand. The key idea is to unfold each slice into a one-dimensional vector, and concatenate a succession of these vectors – while maintaining as much spatial contiguity as possible – into a 2-D matrix. We illustrate our methodology using a coronal slice-based atlas of the Rhesus Monkey cortex. The conceptual surface-based atlases provide a useful complement to slice-based atlases for the purposes of indexing and browsing.     

A Mass Spectrometric-Derived Cell Surface Protein Atlas

Cell surface proteins are major targets of biomedical research due to their utility as cellular markers and their extracellular accessibility for pharmacological intervention. However, information about the cell surface protein repertoire (the surfaceome) of individual cells is only sparsely available. Here, we applied the Cell Surface Capture (CSC) technology to 41 human and 31 mouse cell types to generate a mass-spectrometry derived Cell Surface Protein Atlas (CSPA) providing cellular surfaceome snapshots at high resolution. The CSPA is presented in form of an easy-to-navigate interactive database, a downloadable data matrix and with tools for targeted surfaceome rediscovery (http://wlab.ethz.ch/cspa). The cellular surfaceome snapshots of different cell types, including cancer cells, resulted in a combined dataset of 1492 human and 1296 mouse cell surface glycoproteins, providing experimental evidence for their cell surface expression on different cell types, including 136 G-protein coupled receptors and 75 membrane receptor tyrosine-protein kinases. Integrated analysis of the CSPA reveals that the concerted biological function of individual cell types is mainly guided by quantitative rather than qualitative surfaceome differences. The CSPA will be useful for the evaluation of drug targets, for the improved classification of cell types and for a better understanding of the surfaceome and its concerted biological functions in complex signaling microenvironments.     

Topography of murine leukemia virus envelope proteins: characterization of transmembrane components

Trypsinization of intact Moloney murine leukemia virus resulted in cleavage of p15(E) and Pr15(E) at a site near the middle of the molecule, producing a 9,000-dalton amino-terminal fragment which contains the disulfide linkage site to gp70 and which carries p15(E) epitopes b and c, but not epitope a. After solubilization of the viral membrane, trypsinization occurred at a second site within 1,000 daltons of the carboxy end of p15(E). This site is not exposed in intact virions, indicating that p15(E) and Pr15(E) are transmembrane proteins.     

Fine Structural Analysis of Animal Cell Surfaces: Membranes and Cell Surface Topography

Current research on the mechanism of transmembrane regulationof topographic modulation at the cell surface is described forthe sea urchin egg and Sarcoma 180 ascites tumor cells of SwissWebster white mice. The transmembrane system is characterizedin terms of three components: glycocalyx, membrane, and cytofibrillarstructures. The importance of membrane molecular architectureper se relative to the other surface components is assessedin terms of freeze fracture analysis of both cell types as wellas concanavalin A (ConA)-mediated long term agglutination, cytochalasinB effects, and other drug-induced changes at Sarcoma 180 cellsurfaces. A quantitative and qualitative assessment of intramembranousparticle (IMP) sizes and density distributions reveals intrinsicstructural changes of the fusing membranes at cortical reactionduring sea urchin egg fertilization and also with the post-fertilizedaccumulation of surface microvilli. Comparable changes in IMPare noted for microvillus retraction and membrane smoothingin Sarcoma 180 cells under a variety of experimental conditions.On the other hand, chemical perturbation of S-180 cell surfacesreveals a rather non-ubiquitous, though identifiable, involvementof microfilaments and no microtubule involvement in these topographicchanges. These observations suggest that the plasma membraneis a dynamic structure poised between "restrictive" and "lessrestrictive" states of fluidity or deformability and, hence,is a determinant component in topographic change.     

Larval Settlement: The Role of Surface Topography for Sessile Coral Reef Invertebrates

For sessile marine invertebrates with complex life cycles, habitat choice is directed by the larval phase. Defining which habitat-linked cues are implicated in sessile invertebrate larval settlement has largely concentrated on chemical cues which are thought to signal optimal habitat. There has been less effort establishing physical settlement cues, including the role of surface microtopography. This laboratory based study tested whether surface microtopography alone (without chemical cues) plays an important contributing role in the settlement of larvae of coral reef sessile invertebrates. We measured settlement to tiles, engineered with surface microtopography (holes) that closely matched the sizes (width) of larvae of a range of corals and sponges, in addition to surfaces with holes that were markedly larger than larvae. Larvae from two species of scleractinian corals (Acropora millepora and Ctenactis crassa) and three species of coral reef sponges (Luffariella variabilis, Carteriospongia foliascens and Ircinia sp.,) were used in experiments. L. variabilis, A. millepora and C. crassa showed markedly higher settlement to surface microtopography that closely matched their larval width. C. foliascens and Ircinia sp., showed no specificity to surface microtopography, settling just as often to microtopography as to flat surfaces. The findings of this study question the sole reliance on chemical based larval settlement cues, previously established for some coral and sponge species, and demonstrate that specific physical cues (surface complexity) can also play an important role in larval settlement of coral reef sessile invertebrates.     

Influence of the Surface Topography of Stainless Steel on Bacterial Adhesion

Bacterial adhesion on stainless steel may cause problems such as microbially induced corrosion or represent a chronic source of microbial contamination. The investigation focussed on how the extent and patterns of four bacterial species comprising three different phyla and a broad variety of physicochemical characteristics was influenced by the surface topography of AISI 304 stainless steel. Five types of surface finish corresponding to roughness values R a between 0.03 and 0.89 w m were produced. Adhesion of all four bacteria was minimal at R a =0.16 w m, whereas smoother and rougher surfaces gave rise to more adhesion. This surface exhibited parallel scratches of 0.7 w m, in which a high proportion of bacteria of three of the strains aligned. Reduced overall adhesion was attributed to unfavorable interactions between this surface and bacteria oriented other than parallel to the scratches. Interaction energy calculations and considerations of micro-geometry confirmed this mechanism. Rougher surfaces exhibiting wider scratches allowed a higher fraction of bacteria to adhere in other orientations, whereas the orientation of cells adhered to the smoothest surface was completely random.     

Surface Topography and Cytomatrix Elements in Protoplasts from Plant Cells

We studied the surface topography of protoplasts from callus of Daucus sativus(Hofm.) Roehl. and from mesophyll cells of Nicotiana tabacumL. We also followed the distribution of actin elements of the cytomatrix in the subcortical cytoplasm layer. Protoplasts were prepared for scanning electron microscopy by a modified method without drying in the critical point apparatus. After postfixation with OsO₄, carrot and tobacco protoplasts had a similar topography of the surface: it was rough and had few pores. When carrot protoplasts were not postfixed with OsO₄, their surface looked different: it was folded and had 1.5-m pores, which sometimes were bordered with globules 0.3 m in diameter, or it consisted of conical cells varying in depth and size of their bases. We believe that, when protoplasts were not fixed with OsO₄, they lost lipid-containing structures from their surface, and what remained was the protein carcass of the plasmalemma and the underlying layer of the cytoplasm. The inner surface of opened carrot protoplasts had elaborate topography, apparently produced by the elements of the cytomatrix, that is, a relatively thick layer of the cortical cytoplasm, where, using phalloidin–colloidal gold and transmission electron microscopy, we could observe a dense network of actin filaments.     

Topography and dynamics of synthesis of structural proteins of Newcastle disease virus

Zhdanov, Victor M. (The D. I. Ivanovsky Institute of Virology, Moscow, USSR), Nonna B. Azadova, and Leonid V. Uryvayev. Topography and dynamics of synthesis of structural proteins of Newcastle disease virus. J. Bacteriol. 91:1902-1906. 1966.-Newcastle disease virus S and V antigens are synthesized in the cytoplasm, as revealed by the immunofluorescence method. In some experiments, S antigen was found also in the nucleoli. Actinomycin D moderately decreased the titer of infectious virus and V antigen and accelerated the time of appearance of mature virus. Proflavine sharply decreased the synthesis of both antigens and the release of mature virus.     

Surface activity in vitro: role of surfactant proteins

Pattle, who provided some of the initial direct evidence for the presence of pulmonary surfactant in the lung, was also the first to show surfactant was susceptible to proteases such as trypsin. Pattle concluded surfactant was a lipoprotein. Our group has investigated the roles of the surfactant proteins (SP-) SP-A, SP-B, and SP-C using a captive bubble tensiometer. These studies show that SP-C>SP-B>SP-A in enhancing surfactant lipid adsorption (film formation) to the equilibrium surface tension of approximately 22-25 mN/m from the 70 mN/m of saline at 37 degrees C. In addition to enhancing adsorption, surfactant proteins can stabilize surfactant films so that lateral compression induced through surface area reduction results in the lowering of surface tension (gamma) from approximately 25 mN/m (equilibrium) to values near 0 mN/m. These low tensions, which are required to stabilize alveoli during expiration, are thought to arise through exclusion of fluid phospholipids from the surface monolayer, resulting in an enrichment in the gel phase component dipalmitoylphosphatidylcholine (DPPC). The results are consistent with DPPC enrichment occurring through two mechanisms, selective DPPC adsorption and preferential squeeze-out of fluid components such as unsaturated phosphatidylcholine (PC) and phosphatidylglycerol (PG) from the monolayer. Evidence for selective DPPC adsorption arises from experiments showing that the surface area reductions required to achieve gamma near 0 mN/m with DPPC/PG samples containing SP-B or SP-A plus SP-B films were less than those predicted for a pure squeeze-out mechanism. Surface activity improves during quasi-static or dynamic compression-expansion cycles, indicating the squeeze-out mechanism also occurs. Although SP-C was not as effective as SP-B in promoting selective DPPC adsorption, this protein is more effective in promoting the reinsertion of lipids forced out of the surface monolayer following overcompression at low gamma values. Addition of SP-A to samples containing SP-B but not SP-C limits the increase in gamma(max) during expansion. It is concluded that the surfactant apoproteins possess distinct overlapping functions. SP-B is effective in selective DPPC insertion during monolayer formation and in PG squeeze-out during monolayer compression. SP-A can promote adsorption during film formation, particularly in the presence of SP-B. SP-C appears to have a superior role to SP-B in formation of the surfactant reservoir and in reinsertion of collapse phase lipids.     

Cell Surface Topography Is a Regulator of Molecular Interactions during Chemokine-Induced Neutrophil Spreading

Adhesive interactions between neutrophils and endothelium involve chemokine-induced neutrophil spreading and subsequent crawling on the endothelium to sites of transmigration. We investigated the importance of cell topography in this process using immunofluorescence, scanning electron microscopy, and live-cell imaging using total internal reflectance microscopy to observe redistribution of key membrane proteins, both laterally and relative to surface topography, during neutrophil spreading onto glass coated with interleukin 8. During formation of the lamellipod, L-selectin is distributed on microvilli tips along the top of the lamellipodium, whereas the interleukin 8 receptors CXCR1 and CXCR2 and the integrin LFA-1 (α_Lβ₂) were present at the interface between the lamellipodium and the substrate. Total internal reflection fluorescence imaging indicated that LFA-1 and both chemokine receptors redistributed into closer contact with the substrate as the cells spread onto the surface and remodeled their topography. A geometric model of the surface remodeling with nonuniform distribution of molecules and a realistic distribution of microvilli heights was matched to the data, and the fits indicated a 1000-fold increase in the concentration of chemokine receptors and integrins available for bond formation at the interface. These observations imply that topographical remodeling is a key mechanism for regulating cell adhesion and surface-induced activation of cells.     

Land Surface Phenology in the Tropics: The Role of Climate and Topography in a Snow-Free Mountain

Leaf phenology represents a major temporal component of ecosystem functioning, and understanding the drivers of seasonal variation in phenology is essential to understand plant responses to climate change. We assessed the patterns and drivers of land surface phenology, a proxy for leafing phenology, for the meridional Espinhaço Range, a South American tropical mountain comprising a mosaic of savannas, dry woodlands, montane vegetation and moist forests. We used a 14-year time series of MODIS/NDVI satellite images, acquired between 2001 and 2015, and extracted phenological indicators using the TIMESAT algorithm. We obtained precipitation data from the Tropical Rainfall Measuring Mission, land surface temperature from the MODIS MOD11A2 product, and cloud cover frequency from the MODIS MOD09GA product. We also calculated the topographic wetness index and simulated clear-sky radiation budgets based on the SRTM elevation model. The relationship between phenology and environmental drivers was assessed using general linear models. Temporal displacement in the start date of the annual growth season was more evident than variations in season length among vegetation types, indicating a possible temporal separation in the use of resources. Season length was inversely proportional to elevation, decreasing 1.58 days per 100 m. Green-up and senescence rates were faster where annual temperature amplitude was higher. We found that water and light availability, modulated by topography, are the most likely drivers of land surface phenology in the region, determining the start, end and length of the growing season. Temperature had an important role in determining the rates of leaf development and the strength of vegetation seasonality, suggesting that tropical vegetation is also sensitive to latitudinal temperature changes, regardless of the elevational gradient. Our work improves the current understanding of phenological strategies in the seasonal tropics and emphasizes the importance of topography in shaping light and water availability for leaf development in snow-free mountains.     

Cell Adhesion Molecule Distribution Relative to Neutrophil Surface Topography Assessed by TIRFM

The positioning of adhesion molecules relative to the microtopography of the cell surface has a significant influence on the molecule's availability to form adhesive contacts. Measurements of the ratio of fluorescence intensity per unit area in epi-fluorescence images versus total internal reflection fluorescence images provides a means to assess the relative accessibility for bond formation of different fluorescently labeled molecules in cells pressed against a flat substrate. Measurements of the four principal adhesion molecules on human neutrophils reveal that L-selectin has the highest ratio of total internal reflection fluorescence/epi intensity, and that P-selectin glycoprotein ligand-1 (PSGL-1) and the integrins α_Lβ₂ (LFA-1) and α_Mβ₂ (Mac-1) have ratios similar to each other but lower than for L-selectin. All of the ratios increased with increasing impingement, indicating an alteration of surface topography with increasing surface compression. These results are consistent with model predictions for molecules concentrated near the tips of microvilli in the case of L-selectin, and sequestered away from the microvillus tips in the case of LFA-1, Mac-1, and PSGL-1. The results confirm differences among adhesion molecules in their surface distribution and reveal how the availability of specific adhesion molecules is altered by mechanical compression of the surface in live cells.     

Cell Surface Topography Is a Regulator of Molecular Interactions during Chemokine-Induced Neutrophil Spreading

Adhesive interactions between neutrophils and endothelium involve chemokine-induced neutrophil spreading and subsequent crawling on the endothelium to sites of transmigration. We investigated the importance of cell topography in this process using immunofluorescence, scanning electron microscopy, and live-cell imaging using total internal reflectance microscopy to observe redistribution of key membrane proteins, both laterally and relative to surface topography, during neutrophil spreading onto glass coated with interleukin 8. During formation of the lamellipod, L-selectin is distributed on microvilli tips along the top of the lamellipodium, whereas the interleukin 8 receptors CXCR1 and CXCR2 and the integrin LFA-1 (α_Lβ₂) were present at the interface between the lamellipodium and the substrate. Total internal reflection fluorescence imaging indicated that LFA-1 and both chemokine receptors redistributed into closer contact with the substrate as the cells spread onto the surface and remodeled their topography. A geometric model of the surface remodeling with nonuniform distribution of molecules and a realistic distribution of microvilli heights was matched to the data, and the fits indicated a 1000-fold increase in the concentration of chemokine receptors and integrins available for bond formation at the interface. These observations imply that topographical remodeling is a key mechanism for regulating cell adhesion and surface-induced activation of cells.     

Surface map comparison: studying function diversity of homologous proteins

A simplified protein surface cartography approach has been developed to assist in the analysis of surface features in homologous families, and thus to predict conservation or divergence of protein functions and protein-protein interaction patterns. A spherical approximation of protein surface was used, with a focus on charged and hydrophobic residues. The resulting surface map allows for qualitative analysis and comparison of surfaces of proteins, but can also be used to define a simple numerical measure of map similarity between two or more proteins. The latter was shown to be useful for function based classifications within large protein families.Surface map analysis was tested on several test cases: haemoglobins, death domains and TRAF domains. It was shown that surface map comparison allows a better function prediction than general sequence analysis methods and can reproduce known examples of functional variation within a divergent group of proteins. In another example, we predict novel, unexpected sets of common functional properties for seemingly distant members of a large group of divergent proteins. The method was also shown to be robust enough to allow using protein models from comparative modelling instead of experimental structures.