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Three-dimensional Modeling (three-dimensional + modeling)
Selected AbstractsA three-dimensional model of the U1 small nuclear ribonucleoprotein particleENTOMOLOGICAL RESEARCH, Issue 2 2010Jason A. SOMARELLI Abstract Most of the pre-mRNAs in the eukaryotic cell are comprised of protein-coding exons and non-protein-coding introns. The introns are removed and the exons are ligated together, or spliced, by a large, macromolecular complex known as the spliceosome. This RNA-protein assembly is made up of five uridine-rich small nuclear RNAs (U1-, U2-, U4-, U5- and U6-snRNA) as well over 300 proteins, which form small nuclear ribonucleoprotein particles (snRNPs). Initial recognition of the 5, exon/intron splice site is mediated by the U1 snRNP, which is composed of the U1 snRNA as well as at least ten proteins. By combining structural informatics tools with the available biochemical and crystallographic data, we attempted to simulate a complete, three dimensional U1 snRNP from the silk moth, Bombyx mori. Comparison of our model with empirically derived crystal structures and electron micrographs pinpoints both the strengths and weaknesses in the in silico determination of macromolecular complexes. One of the most striking differences between our model and experimentally generated structures is in the positioning of the U1 snRNA stem-loops. This highlights the continuing difficulties in generating reliable, complex RNA structures; however, three-dimensional modeling of individual protein subunits by threading provided models of biological significance and the use of both automated and manual docking strategies generated a complex that closely reflects the assembly found in nature. Yet, without utilizing experimentally-derived contacts to select the most likely docking scenario, ab initio docking would fall short of providing a reliable model. Our work shows that the combination of experimental data with structural informatics tools can result in generation of near-native macromolecular complexes. [source] A reduced integration solid-shell finite element based on the EAS and the ANS concept,Geometrically linear problemsINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 10 2009Marco Schwarze Abstract In this paper a new reduced integration eight-node solid-shell finite element is presented. The enhanced assumed strain (EAS) concept based on the Hu,Washizu variational principle requires only one EAS degree-of-freedom to cure volumetric and Poisson thickness locking. One key point of the derivation is the Taylor expansion of the inverse Jacobian with respect to the element center, which closely approximates the element shape and allows us to implement the assumed natural strain (ANS) concept to eliminate the curvature thickness and the transverse shear locking. The second crucial point is a combined Taylor expansion of the compatible strain with respect to the center of the element and the normal through the element center leading to an efficient and locking-free hourglass stabilization without rank deficiency. Hence, the element requires only a single integration point in the shell plane and at least two integration points in thickness direction. The formulation fulfills both the membrane and the bending patch test exactly, which has, to the authors' knowledge, not yet been achieved for reduced integration eight-node solid-shell elements in the literature. Owing to the three-dimensional modeling of the structure, fully three-dimensional material models can be implemented without additional assumptions. Copyright © 2009 John Wiley & Sons, Ltd. [source] Image reconstructions from two orthogonal projectionsINTERNATIONAL JOURNAL OF IMAGING SYSTEMS AND TECHNOLOGY, Issue 2 2003Yuanmei Wang Abstract A vector entropy optimization-based neural network approach is presented to handle image reconstructions from two orthogonal projections. An accurate and parallel reconstruction is attained with this method allowing parallel implementation. This is an attempt to extract the image information from two projections. It is especially meaningful for clinical applications and three-dimensional modeling of the coronary arteries. © 2003 Wiley Periodicals, Inc. Int J Imaging Syst Technol 13, 141,145, 2003; Published online in Wiley Inter-Science (www.interscience.wiley.com). DOI 10.1002/ima.10036 [source] View planning and automated data acquisition for three-dimensional modeling of complex sitesJOURNAL OF FIELD ROBOTICS (FORMERLY JOURNAL OF ROBOTIC SYSTEMS), Issue 11-12 2009Paul S. Blaer Constructing highly detailed three-dimensional (3-D) models of large complex sites using range scanners can be a time-consuming manual process. One of the main drawbacks is determining where to place the scanner to obtain complete coverage of a site. We have developed a system for automatic view planning called VuePlan. When combined with our mobile robot, AVENUE, we have a system that is capable of modeling large-scale environments with minimal human intervention throughout both the planning and acquisition phases. The system proceeds in two distinct stages. In the initial phase, the system is given a two-dimensional site footprint with which it plans a minimal set of sufficient and properly constrained covering views. We then use a 3-D laser scanner to take scans at each of these views. When this planning system is combined with our mobile robot it automatically computes and executes a tour of these viewing locations and acquires them with the robot's onboard laser scanner. These initial scans serve as an approximate 3-D model of the site. The planning software then enters a second phase in which it updates this model by using a voxel-based occupancy procedure to plan the next best view (NBV). This NBV is acquired, and further NBVs are sequentially computed and acquired until an accurate and complete 3-D model is obtained. A simulator tool that we developed has allowed us to test our entire view planning algorithm on simulated sites. We have also successfully used our two-phase system to construct precise 3-D models of real-world sites located in New York City: Uris Hall on the campus of Columbia University and Fort Jay on Governors Island. © 2009 Wiley Periodicals, Inc. [source] A single-amino acid substitution in the sixth leucine-rich repeat of barley MLA6 and MLA13 alleviates dependence on RAR1 for disease resistance signalingTHE PLANT JOURNAL, Issue 2 2004Dennis A. Halterman Summary Interactions between barley and the powdery mildew pathogen, Blumeria graminis f. sp. hordei, (Bgh) are determined by unique combinations of host resistance genes, designated Mildew-resistance locus (Ml), and cognate pathogen avirulence genes. These interactions occur both dependent and independent of Rar1 (required for Mla12 resistance) and Sgt1 (Suppressor of G-two allele of skp1), which are differentially required for diverse plant disease-resistance pathways. We have isolated two new functional Mla alleles, Rar1 -independent Mla7 and Rar1 -dependent Mla10, as well as the Mla paralogs, Mla6-2 and Mla13-2. Utilizing the inherent diversity amongst Mla -encoded proteins, we identified the only two amino acids exclusively conserved in RAR1-dependent MLA6, MLA10, MLA12, and MLA13 that differ at the corresponding position in RAR1-independent MLA1 and MLA7. Two- and three-dimensional modeling places these residues on a predicted surface of the sixth leucine-rich repeat (LRR) domain at positions distinct from those within the ,-sheets hypothesized to determine resistance specificity. Site-directed mutagenesis of these residues indicates that RAR1 independence requires the presence of an aspartate at position 721, as mutation of this residue to a structurally similar, but uncharged, asparagine did not alter RAR1 dependence. These results demonstrate that a single-amino acid substitution in the sixth MLA LRR can alter host signaling but not resistance specificity to B. graminis. [source] | |||||||||||||