Surface attachment of protein fibrils via covalent modification strategies.

Chemical control of surface functionality and topography is an essential requirement for many technological purposes. In particular, the covalent attachment of monomeric proteins to surfaces has been the object of intense studies in recent years, for applications as varied as electrochemistry, immuno-sensing, and the production of biocompatible coatings. Little is known, however, about the characteristics and requirements underlying surface attachment of supramolecular protein nanostructures. Amyloid fibrils formed by the self-assembly of peptide and protein molecules represent one important class of such structures. These highly organized beta-sheet-rich assemblies are a hallmark of a range of neurodegenerative disorders, including Alzheimer's disease and type II diabetes, but recent findings suggest that they have much broader significance, potentially representing the global free energy minima of the energy landscapes of proteins and having potential applications in material science. In this paper, we describe strategies for attaching amyloid fibrils formed from different proteins to gold surfaces under different solution conditions. Our methods involve the reaction of sulfur containing small molecules (cystamine and 2-iminothiolane) with the amyloid fibrils, enabling their covalent linkage to gold surfaces. We demonstrate that irreversible attachment using these approaches makes possible quantitative analysis of experiments using biosensor techniques, such as quartz crystal microbalance (QCM) assays that are revolutionizing our understanding of the mechanisms of amyloid growth and the factors that determine its kinetic behavior. Moreover, our results shed light on the nature and relative importance of covalent versus noncovalent forces acting on protein superstructures at metal surfaces.

Atomic force microscopy observations of the topography of regenerated silk fibroin aggregations

How fibroin molecules fold themselves and further self-assemble into aggregations with specific structures when the solution concentration increases is the key to understanding the natural silk-forming process of the silkworm. A regenerated Bombyx mori silk fibroin solution was prepared, and serially diluted solutions were coated on aminated coverslips. Atomic force microscopy (AFM) observations of the topography of fibroin molecules revealed a transformation from rodlike aggregations 100-200 nm long to small globules 50 mn in diameter with decreasing concentrations. When the incubation duration increased, the aggregations of fibroin molecules showed a self-assembling process, which was measured with AFM. In particular, after the molecules were incubated for more than 20 min, rodlike micelles formed and were distributed evenly on the surface of the aminated slides. Flow chamber technology was used to study the effect of the shear loading on the topography of the fibroin molecular aggregations. After a shear loading was applied, larger rodlike particles formed at a higher incubation concentration in comparison with those at a lower concentration and were obviously oriented along the direction of fluid flow.

Thermocline topography, horizontal currents and “ridging” in the Eastern Tropical Pacific

ENGLISH: A primary objective of the Inter-American Tropical Tuna Commission is a knowledge of the ecology of tunas which inhabit the Eastern Tropical Pacific. This paper presents some results of the work in physical oceanography, which, it is hoped, will be useful to the biological work and at the same time of interest to physical oceanographers. The work presented here was begun in connection with simple observable facts; the thermocline is very close to the sea surface in a region off Costa Rica (Wooster and Cromwell, 1958), and this region is biologically productive (Holmes, et al. 1957; Brandhorst, 1958). It is the main object of this study to describe and explain these facts, insofar as possible. SPANISH: Uno de los principales objetivos de la Comisión Interamericana del Atún Tropical es el conocimiento de la ecología de los atunes que viven en el Pacífico Oriental Tropical. Este informe presenta algunos de los resultados del estudio en oceanografía física, los cuales se espera que serán útiles en la investigación biológica y, al mismo tiempo, de interés para los oceanógrafos físicos. El trabajo presentado aquí se inició en conexión con sencillos hechos observables; mar afuera de Costa Rica, la termoclina queda muy cerca de la superficie del mar (Wooster y Cromwell, 1958) y esta región es biológicamente productiva (Holmes, el al., 1957; Brandhorst, 1958). El objeto principal de este estudio es describir y explicar estos hechos, hasta donde sea posible. (PDF contains 32 pages.)

Expression of eph-family receptor tyrosine kinases and ephrins in the tadpole of the frog Xenopus laevis, and possible roles in the development of retinotectal topography

Assembling a nervous system requires exquisite specificity in the construction of neuronal connectivity. One method by which such specificity is implemented is the presence of chemical cues within the tissues, differentiating one region from another, and the presence of receptors for those cues on the surface of neurons and their axons that are navigating within this cellular environment.

Connections from one part of the nervous system to another often take the form of a topographic mapping. One widely studied model system that involves such a mapping is the vertebrate retinotectal projection-the set of connections between the eye and the optic tectum of the midbrain, which is the primary visual center in non-mammals and is homologous to the superior colliculus in mammals. In this projection the two-dimensional surface of the retina is mapped smoothly onto the two-dimensional surface of the tectum, such that light from neighboring points in visual space excites neighboring cells in the brain. This mapping is implemented at least in part via differential chemical cues in different regions of the tectum.

The Eph family of receptor tyrosine kinases and their cell-surface ligands, the ephrins, have been implicated in a wide variety of processes, generally involving cellular movement in response to extracellular cues. In particular, they possess expression patterns-i.e., complementary gradients of receptor in retina and ligand in tectum- and in vitro and in vivo activities and phenotypes-i.e., repulsive guidance of axons and defective mapping in mutants, respectively-consistent with the long-sought retinotectal chemical mapping cues.

The tadpole of Xenopus laevis, the South African clawed frog, is advantageous for in vivo retinotectal studies because of its transparency and manipulability. However, neither the expression patterns nor the retinotectal roles of these proteins have been well characterized in this system. We report here comprehensive descriptions in swimming stage tadpoles of the messenger RNA expression patterns of eleven known Xenopus Eph and ephrin genes, including xephrin-A3, which is novel, and xEphB2, whose expression pattern has not previously been published in detail. We also report the results of in vivo protein injection perturbation studies on Xenopus retinotectal topography, which were negative, and of in vitro axonal guidance assays, which suggest a previously unrecognized attractive activity of ephrins at low concentrations on retinal ganglion cell axons. This raises the possibility that these axons find their correct targets in part by seeking out a preferred concentration of ligands appropriate to their individual receptor expression levels, rather than by being repelled to greater or lesser degrees by the ephrins but attracted by some as-yet-unknown cue(s).

Rapid patterning of 1-D collagenous topography as an ECM protein fibril platform for image cytometry.

Cellular behavior is strongly influenced by the architecture and pattern of its interfacing extracellular matrix (ECM). For an artificial culture system which could eventually benefit the translation of scientific findings into therapeutic development, the system should capture the key characteristics of a physiological microenvironment. At the same time, it should also enable standardized, high throughput data acquisition. Since an ECM is composed of different fibrous proteins, studying cellular interaction with individual fibrils will be of physiological relevance. In this study, we employ near-field electrospinning to create ordered patterns of collagenous fibrils of gelatin, based on an acetic acid and ethyl acetate aqueous co-solvent system. Tunable conformations of micro-fibrils were directly deposited onto soft polymeric substrates in a single step. We observe that global topographical features of straight lines, beads-on-strings, and curls are dictated by solution conductivity; whereas the finer details such as the fiber cross-sectional profile are tuned by solution viscosity. Using these fibril constructs as cellular assays, we study EA.hy926 endothelial cells' response to ROCK inhibition, because of ROCK's key role in the regulation of cell shape. The fibril array was shown to modulate the cellular morphology towards a pre-capillary cord-like phenotype, which was otherwise not observed on a flat 2-D substrate. Further facilitated by quantitative analysis of morphological parameters, the fibril platform also provides better dissection in the cells' response to a H1152 ROCK inhibitor. In conclusion, the near-field electrospun fibril constructs provide a more physiologically-relevant platform compared to a featureless 2-D surface, and simultaneously permit statistical single-cell image cytometry using conventional microscopy systems. The patterning approach described here is also expected to form the basics for depositing other protein fibrils, seen among potential applications as culture platforms for drug screening.

Design of surface emitting distributed feedback quantum cascade laser with single-lobe far-field pattern and high outcoupling efficiency

A 7.8-mu m surface emitting second-order distributed feedback quantum cascade laser (DFB QCL) structure with metallized surface grating is studied. The modal property of this structure is described by utilizing coupled-mode theory where the coupling coefficients are derived from exact Floquet-Bloch solutions of infinite periodic structure. Based on this theory, the influence of waveguide structure and grating topography as well as device length on the laser performance is numerically investigated. The optimized surface emitting second-order DFB QCL structure design exhibits a high surface outcoupling efficiency of 22% and a low threshold gain of 10 cm(-1). Using a pi phase-shift in the centre of the grating, a high-quality single-lobe far-field radiation pattern is obtained.

Study of Radiolaria in the surface sediments from the area east of Taiwan Island

The species and characteristics of Radiolaria in the surface sediments were systematcally investigated in the sea east of Taiwan Island. One hundred and seventy-eight species of Radiolaria (including 21 unidentified species) have been identified in the surface sediments, and they belong to 2 orders, 34 families and 101 genera. Among them there are 19 families, 70 genera, 134 species of Spumellaria and 15 families, 31 genera, 44 species of Nassellaria. Of the 178 species of Radiolaria, the individual number of Spumellaria amounts to 88.1% of the total individual number, and that of Nassellaria amounts to 11.9% of the total individual number. It is shown that most of the dominant species belong to the tropical and subtropical dominant species and are brought into the area mainly by the Kuroshio, and some affecting factors including the submarine topography, submarine sediments, upwelling current east of Taiwan Island and carbonate dissolution play a secondary role in forming the Radiolaria distributions.

Variability of surface circulation in the South China Sea from satellite altimeter data

11-year satellite altimeter sea surface height (SSH) anomaly data from January 1993 to December 2003 are used to present the dominant spatial patterns and temporal variations of the South China Sea (SCS) surface circulation through Empirical Orthogonal Function (EOF) analysis. The first three EOF modes show the obvious seasonal variations of SSH in the SCS. EOF mode one is generally characterized by a basin-wide circulation. Mode two describes the double-cell basin scale circulation structure. The two cells were located off west of the Luzon Island and southeast of Vietnam, respectively. EOF mode three presents the mesoscale eddy structure in the western SCS, which develops into a strong cyclonic eddy rapidly from July to September. EOF mode one and mode three are also embedded with interannual signals, indicating that the SCS surface circulation variation is influenced by El Nino events prominently. The strong El Nino of 1997/98 obviously changed the SCS circulation structure. This study also shows that there existed a series of mesoscale eddies in the western SCS, and their temporal variation indicates intra-seasonal and interannual signals.

Dental topography and molar wear in Alouatta palliata from Costa Rica.

Paleoprimatologists depend on relationships between form and function of teeth to reconstruct the diets of fossil species. Most of this work has been limited to studies of unworn teeth. A new approach, dental topographic analysis, allows the characterization and comparison of worn primate teeth. Variably worn museum specimens have been used to construct species-specific wear sequences so that measurements can be compared by wear stage among taxa with known differences in diet. This assumes that individuals in a species tend to wear their molar teeth in similar ways, a supposition that has yet to be tested. Here we evaluate this assumption with a longitudinal study of changes in tooth form over time in primates. Fourteen individual mantled howling monkeys (Alouatta palliata) were captured and then recaptured after 2, 4, and 7 years when possible at Hacienda La Pacifica in Costa Rica between 1989-1999. Dental impressions were taken each time, and molar casts were produced and analyzed using dental topographic analysis. Results showed consistent decreases in crown slope and occlusal relief. In contrast, crown angularity, a measure of surface jaggedness, remained fairly constant except with extreme wear. There were no evident differences between specimens collected in different microhabitats. These results suggest that different individual mantled howling monkeys wear their teeth down in similar ways, evidently following a species-specific wear sequence. Dental topographic analysis may therefore be used to compare morphology among similarly worn individuals from different species.

Using the surface profiles of modern ice masses to inform palaeo-glacier reconstructions

Morphometric study of modern ice masses is useful because many reconstructions of glaciers traditionally draw on their shape for guidance Here we analyse data derived from the surface profiles of 200 modern ice masses-valley glaciers icefields ice caps and ice sheets with length scales from 10º to 10³ km-from different parts of the world Four profile attributes are investigated relief span and two parameters C* and C that result from using Nye s (1952) theoretical parabola as a profile descriptor C* and C respectively measure each profile s aspect ratio and steepness and are found to decrease in size and variability with span This dependence quantifies the competing influences of unconstrained spreading behaviour of ice flow and bed topography on the profile shape of ice masses which becomes more parabolic as span Increases (with C* and C tending to low values of 2.5-3.3 m ½) The same data reveal coherent minimum bounds in C* and C for modern ice masses that we develop into two new methods of palaeo glacier reconstruction In the first method glacial limits are known from moraines and the bounds are used to constrain the lowest palaeo ice surface consistent with modern profiles We give an example of applying this method over a three-dimensional glacial landscape in Kamchatka In the second method we test the plausibility of existing reconstructions by comparing their C* and C against the modern minimum bounds Of the 86 published palaeo ice masses that we put to this test 88% are found to be plausible The search for other morphometric constraints will help us formalise glacier reconstructions and reduce their uncertainty and subjectiveness

Surface deformations as a necessary requirement for resistance switching at the surface of SrTiO3:N

Atomic force microscopy (AFM), conductive AFM and electrochemical strain microscopy were used to study the topography change at the defect surface of SrTiO3:N, breakdown in the electrical conduction of the tip/sample/electrode system and ionic motion. The IV curves show resistance switching behavior in a voltage range ±6 V < U <± 10 V and a current of maximum ±10 nA. A series of sweeping IV curves resulted in an increase in ionically polarized states (surface charging), electrochemical volume (surface deformations) and sequential formations of stable surface protrusions. The surface deformations are reversible (U <± 5 V) without IVpinched hysteresis and remained stable during the resistance switching (U >± 6 V), revealing the additional necessity (albeit insufficient due to 50% yield of working cells) of surface protrusion formation for resistance switching memory.

Quantifying Submerged Fluvial Topography Using Hyperspatial Resolution UAS Imagery and Structure From Motion Photogrammetry.

Quantifying the topography of rivers and their associated bedforms has been a fundamental concern of fluvial geomorphology for decades. Such data, acquired at high temporal and spatial resolutions, are increasingly in demand for process-oriented investigations of flow hydraulics, sediment dynamics and in-stream habitat. In these riverine environments, the most challenging region for topographic measurement is the wetted, submerged channel. Generally, dry bed topography and submerged bathymetry are measured using different methods and technology. This adds to the costs, logistical challenges and data processing requirements of comprehensive river surveys. However, some technologies are capable of measuring the submerged topography. Through-water photogrammetry and bathymetric LiDAR are capable of reasonably accurate measurements of channel beds in clear water. Whilst the cost of bathymetric LiDAR remains high and its resolution relatively coarse, the recent developments in photogrammetry using Structure from Motion (SfM) algorithms promise a fundamental shift in the accessibility of topographic data for a wide range of settings. Here we present results demonstrating the potential of so called SfM-photogrammetry for quantifying both exposed and submerged fluvial topography at the mesohabitat scale. We show that imagery acquired from a rotary-winged Unmanned Aerial System (UAS) can be processed in order to produce digital elevation models (DEMs) with hyperspatial resolutions (c. 0.02 m) for two different river systems over channel lengths of 50-100 m. Errors in submerged areas range from 0.016 m to 0.089 m, which can be reduced to between 0.008 m and 0.053 m with the application of a simple refraction correction. This work therefore demonstrates the potential of UAS platforms and SfM-photogrammetry as a single technique for surveying fluvial topography at the mesoscale (defined as lengths of channel from c.10 m to a few hundred metres). This article is protected by copyright. All rights reserved.

Spatial variability in surface sediment organic carbon structure in Barkley Sound, Vancouver Island, Canada

Senior thesis written for Oceanography 445

QUANTIFICATION AND EXTRACTION OF SURFACE FEATURES FROM DIGITAL TERRAIN MODELS

Digital Terrain Models (DTMs) are important in geology and geomorphology, since elevation data contains a lot of information pertaining to geomorphological processes that influence the topography. The first derivative of topography is attitude; the second is curvature. GIS tools were developed for derivation of strike, dip, curvature and curvature orientation from Digital Elevation Models (DEMs). A method for displaying both strike and dip simultaneously as colour-coded visualization (AVA) was implemented. A plug-in for calculating strike and dip via Least Squares Regression was created first using VB.NET. Further research produced a more computationally efficient solution, convolution filtering, which was implemented as Python scripts. These scripts were also used for calculation of curvature and curvature orientation. The application of these tools was demonstrated by performing morphometric studies on datasets from Earth and Mars. The tools show promise, however more work is needed to explore their full potential and possible uses.

Influence of substrate topography on the growth and magnetic properties of obliquely deposited amorphous nanocolumns of Fe–Ni

We investigated the influence of substrate surface roughness on the structural and magnetic properties of obliquely deposited amorphous nanocolumns of Fe–Ni. Experiments showed that the surface roughness of the substrate greatly determines the morphology of the columnar structures and this in turn has a profound influence on the magnetic properties. Nucleation of Fe–Ni nanocolumns on a smooth silicon substrate was at random, while that on a rough glass substrate was defined by the irregularities on the substrate surface. It has been found that magnetic interaction between the nanocolumns prepared on a silicon substrate was due to their small inter-column separation. Well separated nanocolumns on a glass substrate resulted in exchange isolated magnetic domains. The size, shape and the distribution of nanocolumns can be tailored by appropriately choosing the surface roughness of the substrate. This will find potential applications in thin film magnetism.