Conserved structural features of the synaptic fusion complex: SNARE proteins reclassified as Q- and R-SNAREs

SNARE [soluble NSF (N-ethylmaleimide-sensitive fusion protein) attachment protein receptor] proteins are essential for membrane fusion and are conserved from yeast to humans. Sequence alignments of the most conserved regions were mapped onto the recently solved crystal structure of the heterotrimeric synaptic fusion complex. The association of the four α-helices in the synaptic fusion complex structure produces highly conserved layers of interacting amino acid side chains in the center of the four-helix bundle. Mutations in these layers reduce complex stability and cause defects in membrane traffic even in distantly related SNAREs. When syntaxin-4 is modeled into the synaptic fusion complex as a replacement of syntaxin-1A, no major steric clashes arise and the most variable amino acids localize to the outer surface of the complex. We conclude that the main structural features of the neuronal complex are highly conserved during evolution. On the basis of these features we have reclassified SNARE proteins into Q-SNAREs and R-SNAREs, and we propose that fusion-competent SNARE complexes generally consist of four-helix bundles composed of three Q-SNAREs and one R-SNARE.

An in vitro study of the dynamic features of the major histocompatibility complex class I complex relevant to its role as a versatile peptide-receptive molecule

The major histocompatibility complex class I complex consists of a heavy chain and a light chain (β2-microglobulin, β2m), which assemble with a short endogenously derived peptide in the endoplasmic reticulum. The class I peptide can be directly exchanged, either at the cell surface or, as recently described, in vesicles of the endocytic compartments, thus allowing exogenous peptides to enter the class I presentation pathway. To probe the interactions between the components of the class I molecule, we analyzed the exchange of peptide and β2m by using purified, recombinant H2-Kb/peptide complexes in a cell-free in vitro system. The exchange of competitor peptide was primarily dependent on the off-rate of the original peptide in the class I binding groove. Peptide exchange was not enhanced by the presence of exogenous β2m, as exchange occurred to the same extent in its absence. Thus, the exchange of peptide and β2m are independent events. The exchange rate of β2m also was not affected by the dissociation rates of the original peptides. Furthermore, peptides could substantially exchange into class I molecules over a pH range of 5.5 to 7.5, conditions prevalent in certain endocytic compartments. We conclude that the dynamic properties of the components of class I molecules explain its function as a highly peptide-receptive molecule. The major histocompatibility complex class I can readily receive peptides independent of the presence of exogenous β2m, even at a low pH. Such properties are relevant to class I peptide acquisition, which can occur at the cell surface, as well as in specialized endosomes.

Altering dimerization specificity by changes in surface electrostatics

Arc repressor forms a homodimer in which the subunits intertwine to create a single globular domain. To obtain Arc sequences that fold preferentially as heterodimers, variants with surface patches of excess positive or negative charge were designed. Several but not all oppositely charged sequence pairs showed preferential heterodimer formation. In the most successful design pair, α helix B of one subunit contained glutamic acids at positions 43, 46, 47, 48, and 50, whereas the other subunit contained lysines or arginines at these positions. A continuum electrostatic model captures many features of the experimental results and suggests that the most successful designs include elements of both positive and negative design.

Surface signaling in pathogenesis.

Surface signaling plays a major role in fungal infection. Topographical features of the plant surface and chemicals on the surface can trigger germination of fungal spores and differentiation of the germ tubes into appressoria. Ethylene, the fruit-ripening hormone, triggers germination of conidia, branching of hyphae, and multiple appressoria formation in Colletotrichum, thus allowing fungi to time their infection to coincide with ripening of the host. Genes uniquely expressed during appressoria formation induced by topography and surface chemicals have been isolated. Disruption of some of them has been shown to decrease virulence on the hosts. Penetration of the cuticle by the fungus is assisted by fungal cutinase secreted at the penetration structure of the fungus. Disruption of cutinase gene in Fusarium solani pisi drastically decreased its virulence. Small amounts of cutinase carried by spores of virulent pathogens, upon contact with plant surface, release small amounts of cutin monomers that trigger cutinase gene expression. The promoter elements involved in this process in F. solani pisi were identified, and transcription factors that bind these elements were cloned. One of them, cutinase transcription factor 1, expressed in Escherichia coli, is phosphorylated. Several protein kinases from F. solani pisi were cloned. The kinase involved in phosphorylation of specific transcription factors and the precise role of phosphorylation in regulating cutinase gene transcription remain to be elucidated.

Real-time 3D semi-local surface patch extraction using GPGPU

Feature vectors can be anything from simple surface normals to more complex feature descriptors. Feature extraction is important to solve various computer vision problems: e.g. registration, object recognition and scene understanding. Most of these techniques cannot be computed online due to their complexity and the context where they are applied. Therefore, computing these features in real-time for many points in the scene is impossible. In this work, a hardware-based implementation of 3D feature extraction and 3D object recognition is proposed to accelerate these methods and therefore the entire pipeline of RGBD based computer vision systems where such features are typically used. The use of a GPU as a general purpose processor can achieve considerable speed-ups compared with a CPU implementation. In this work, advantageous results are obtained using the GPU to accelerate the computation of a 3D descriptor based on the calculation of 3D semi-local surface patches of partial views. This allows descriptor computation at several points of a scene in real-time. Benefits of the accelerated descriptor have been demonstrated in object recognition tasks. Source code will be made publicly available as contribution to the Open Source Point Cloud Library.

Electrocardiographic features of disease progression in arrhythmogenic right ventricular cardiomyopathy/dysplasia.

BACKGROUND Arrhythmogenic right ventricular cardiomyopathy/dysplasia (ARVC/D) is considered a progressive cardiomyopathy. However, data on the clinical features of disease progression are limited. The aim of this study was to assess 12-lead surface electrocardiographic (ECG) changes during long-term follow-up, and to compare these findings with echocardiographic data in our large cohort of patients with ARVC/D. METHODS Baseline and follow-up ECGs of 111 patients from three tertiary care centers in Switzerland were systematically analyzed with digital calipers by two blinded observers, and correlated with findings from transthoracic echocardiography. RESULTS The median follow-up was 4 years (IQR 1.9-9.2 years). ECG progression was significant for epsilon waves (baseline 14% vs. follow-up 31%, p = 0.01) and QRS duration (111 ms vs. 114 ms, p = 0.04). Six patients with repolarization abnormalities according to the 2010 Task Force Criteria at baseline did not display these criteria at follow-up, whereas in all patients with epsilon waves at baseline these depolarization abnormalities also remained at follow-up. T wave inversions in inferior leads were common (36% of patients at baseline), and were significantly associated with major repolarization abnormalities (p = 0.02), extensive echocardiographic right ventricular involvement (p = 0.04), T wave inversions in lateral precordial leads (p = 0.05), and definite ARVC/D (p = 0.05). CONCLUSIONS Our data supports the concept that ARVC/D is generally progressive, which can be detected by 12-lead surface ECG. Repolarization abnormalities may disappear during the course of the disease. Furthermore, the presence of T wave inversions in inferior leads is common in ARVC/D.

(Table 1) Concentration and geological parameters of n-alkanes and n-alkenes in surface sediments from the Gulf of Gabes, Tunisia

Abstract Hydrocarbons in surface sediments were studied quantitatively and qualitatively in 18 stations along the coastline of Gabes Gulf in Tunisia. The results show that the total hydrocarbon levels vary along a wide range from 90 to 1,800 ppm. The GC-MS profiles of aliphatic hydrocarbons vary according to the stations and show that the hydrocarbons were derived from various sources. A special feature prevalent in several stations was identified: aliphatic hydrocarbons with distinctive chemical features. This includes a high abundance of even-numbered n-alkanes (n-C14 - n-C26, maximizing at n-C18, n-C20 and n-C22) and n-alk-1-enes (n-C14:1 - n-C24:1, maximizing at n-C16:1, n-C18:1, n-C20:1 and n-C22:1). This unusual predominance of even-numbered n-alkanes/alkenes is reported for the first time in the Gulf of Gabes and it thus contributes to the information on the rare occurrence of such distributions in the geosphere.

Morphology and surface texture of quartz grains from ODP Site 105-645

The shapes and surface textures of sand-sized quartz grains from the sediments cored at Site 645 in southern Baffin Bay during ODP Leg 105 were studied to characterize the terrigenous materials and the settling processes involved in the deposition of these sediments. Here, we show a homogeneous sand fraction that results from mixing grains from various provenances. The characteristics inherited from terrestrial processes (varying degrees of wear; fluviatile, aeolian, and diagenetic features) dominate the characteristics that result from evolution in a high-energy marine environment. Thus, the influence of the last stage of sedimentation in a deep-marine environment was difficult to distinguish. However, fluctuations in the relative proportions of particular features reveal that the terrigenous material derived from sedimentary formations of Baffin Island and East Greenland or from direct abrasion of the crystalline shield, which changed through time as the dominant settling processes evolved. In particular, this study confirms the onset of major ice rafting as old as late Miocene.

Constraining storm-scale forecasts of deep convective initiation with surface weather observations

Thesis (Ph.D.)--University of Washington, 2016-06

Features of nitrogen adsorption on nonporous carbon and silica surfaces in the framework of classical density functional theory

Equilibrium adsorption data of nitrogen on a series of nongraphitized carbon blacks and nonporous silica at 77 K were analyzed by means of classical density functional theory to determine the solid-fluid potential. The behavior of this potential profile at large distance is particularly considered. The analysis of nitrogen adsorption isotherms seems to indicate that the adsorption in the first molecular layer is localized and controlled mainly by short-range forces due to the surface roughness, crystalline defects, and functional groups. At distances larger than approximately 1.3-1.5 molecular diameters, the adsorption is nonlocalized and appears as a thickening of the adsorbed film with increasing bulk pressure in a relatively weak adsorption potential field. It has been found that the asymptotic decay of the potential obeys the power law with the exponent being -3 for carbon blacks and -4 for silica surface, which signifies that in the latter case the adsorption potential is mainly exerted by surface oxygen atoms. In all cases, the absolute value of the solid-fluid potential is much smaller than that predicted by the Lennard-Jones pair potential with commonly used solid-fluid molecular parameters. The effect of surface heterogeneity on the heat of adsorption is also discussed.

Application of edge-to-edge matching model to understand the in-plane texture of TiSi2 (C49) thin films on (001)(Si) surface

The edge-to-edge matching model, which was originally developed for predicting crystallographic features in diffusional phase transformations in solids, has been used to understand the formation of in-plane textures in TiSi2 (C49) thin films on Si single crystal (001)si surface. The model predicts all the four previously reported orientation relationships between C49 and Si substrate based on the actual atom matching across the interface and the basic crystallographic data only. The model has strong potential to be used to develop new thin film materials. (c) 2006 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Genes for the majority of group A streptococcal virulence factors and extracellular surface proteins do not confer an increased propensity to cause invasive disease

Background. The factors behind the reemergence of severe, invasive group A streptococcal (GAS) diseases are unclear, but it could be caused by altered genetic endowment in these organisms. However, data from previous studies assessing the association between single genetic factors and invasive disease are often conflicting, suggesting that other, as-yet unidentified factors are necessary for the development of this class of disease. Methods. In this study, we used a targeted GAS virulence microarray containing 226 GAS genes to determine the virulence gene repertoires of 68 GAS isolates (42 associated with invasive disease and 28 associated with noninvasive disease) collected in a defined geographic location during a contiguous time period. We then employed 3 advanced machine learning methods (genetic algorithm neural network, support vector machines, and classification trees) to identify genes with an increased association with invasive disease. Results. Virulence gene profiles of individual GAS isolates varied extensively among these geographically and temporally related strains. Using genetic algorithm neural network analysis, we identified 3 genes with a marginal overrepresentation in invasive disease isolates. Significantly, 2 of these genes, ssa and mf4, encoded superantigens but were only present in a restricted set of GAS M-types. The third gene, spa, was found in variable distributions in all M-types in the study. Conclusions. Our comprehensive analysis of GAS virulence profiles provides strong evidence for the incongruent relationships among any of the 226 genes represented on the array and the overall propensity of GAS to cause invasive disease, underscoring the pathogenic complexity of these diseases, as well as the importance of multiple bacteria and/ or host factors.

Solution structure and characterization of the LGR8 receptor binding surface of insulin-like peptide 3

Insulin-like peptide 3 (INSL3), a member of the relaxin peptide family, is produced in testicular Leydig cells and ovarian thecal cells. Gene knock-out experiments have identified a key biological role in initiating testes descent during fetal development. Additionally, INSL3 has an important function in mediating male and female germ cell function. These actions are elicited via its recently identified receptor, LGR8, a member of the leucine-rich repeat-containing G-protein- coupled receptor family. To identify the structural features that are responsible for the interaction of INSL3 with its receptor, its solution structure was determined by NMR spectroscopy together with in vitro assays of a series of B-chain alanine-substituted analogs. Synthetic human INSL3 was found to adopt a characteristic relaxin/ insulin-like fold in solution but is a highly dynamic molecule. The four termini of this two-chain peptide are disordered, and additional conformational exchange is evident in the molecular core. Alanine-substituted analogs were used to identify the key residues of INSL3 that are responsible for the interaction with the ectodomain of LGR8. These include Arg(B16) and Val(B19), with His(B12) and Arg(B20) playing a secondary role, as evident from the synergistic effect on the activity in double and triple mutants involving these residues. Together, these amino acids combine with the previously identified critical residue, Trp(B27), to form the receptor binding surface. The current results provide clear direction for the design of novel specific agonists and antagonists of this receptor.

Surface wind fields (on Earth)

This document sets out to clarify the role of fronts and other atmospheric features on the form of surface wind fields. This is intended as a basic meteorological review of the typical features we will encounter in wind fields. Thus there is a strong emphasis on description at a fairly rudimentary level. The document should prove useful as we think about different models we could adopt for wind fields.