scholarly journals EVR: reconstruction of bacterial chromosome 3D structure models using error-vector resultant algorithm

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Kang-Jian Hua ◽  
Bin-Guang Ma
Keyword(s):  
Parallel Implementation ◽  
3D Structure ◽  
Software Tool ◽  
Structural Features ◽  
Bacterial Chromosome ◽  
Modeling Tools ◽  
Computing Power ◽  
Error Vector ◽  
Contact Frequency ◽  
Simple Error

Abstract Background More and more 3C/Hi-C experiments on prokaryotes have been published. However, most of the published modeling tools for chromosome 3D structures are targeting at eukaryotes. How to transform prokaryotic experimental chromosome interaction data into spatial structure models is an important task and in great need. Results We have developed a new reconstruction program for bacterial chromosome 3D structure models called EVR that exploits a simple Error-Vector Resultant (EVR) algorithm. This software tool is particularly optimized for the closed-loop structural features of prokaryotic chromosomes. The parallel implementation of the program can utilize the computing power of both multi-core CPUs and GPUs. Conclusions EVR can be used to reconstruct the bacterial 3D chromosome structure based on the contact frequency matrix derived from 3C/Hi-C experimental data quickly and precisely.

scholarly journals EVR: Reconstruction of Bacterial Chromosome 3D Structure Using Error-Vector Resultant Algorithm

2018 ◽  
Author(s):  
Kang-Jian Hua ◽  
Bin-Guang Ma
Keyword(s):  
Closed Loop ◽  
3D Structure ◽  
Software Tool ◽  
Structural Features ◽  
Bacterial Chromosome ◽  
Modeling Tools ◽  
Error Vector ◽  
3D Structures ◽  
Contact Frequency ◽  
Simple Error

ABSTRACTMore and more 3C/Hi-C experiments on prokaryotes have been published. However, most of the published modeling tools for chromosome 3D structures are targeting at eukaryotes. How to transform prokaryotic experimental chromosome interaction data into spatial structures is an important task and in great need. We have developed a new reconstruction program for bacterial chromosome 3D structures called EVR that exploits a simple Error-Vector Resultant (EVR) algorithm. This software tool is particularly optimized for the closed-loop structural features of prokaryotic chromosomes. EVR can be used to reconstruct the bacterial 3D chromosome structure based on the contact frequency matrix derived from 3C/Hi-C experimental data quickly and precisely.

Detection, Averaging, and 3D Reconstruction of Biological Specimens on Hypercubes (Transputer-based) Computers

1990 ◽  
Vol 48 (1) ◽  
pp. 454-455
Author(s):  
Jose-Maria Carazo ◽  
I. Benavides ◽  
S. Marco ◽  
J.L. Carrascosa ◽  
E.L. Zapata
Keyword(s):  
3D Reconstruction ◽  
3D Structure ◽  
Three Dimensional ◽  
Software Tools ◽  
Mapping Method ◽  
Computer Architectures ◽  
Parallel Computer ◽  
Reconstruction Process ◽  
Computing Power ◽  
Order Of Magnitude

Obtaining the three-dimensional (3D) structure of negatively stained biological specimens at a resolution of, typically, 2 - 4 nm is becoming a relatively common practice in an increasing number of laboratories. A combination of new conceptual approaches, new software tools, and faster computers have made this situation possible. However, all these 3D reconstruction processes are quite computer intensive, and the middle term future is full of suggestions entailing an even greater need of computing power. Up to now all published 3D reconstructions in this field have been performed on conventional (sequential) computers, but it is a fact that new parallel computer architectures represent the potential of order-of-magnitude increases in computing power and should, therefore, be considered for their possible application in the most computing intensive tasks.We have studied both shared-memory-based computer architectures, like the BBN Butterfly, and local-memory-based architectures, mainly hypercubes implemented on transputers, where we have used the algorithmic mapping method proposed by Zapata el at. In this work we have developed the basic software tools needed to obtain a 3D reconstruction from non-crystalline specimens (“single particles”) using the so-called Random Conical Tilt Series Method. We start from a pair of images presenting the same field, first tilted (by ≃55°) and then untilted. It is then assumed that we can supply the system with the image of the particle we are looking for (ideally, a 2D average from a previous study) and with a matrix describing the geometrical relationships between the tilted and untilted fields (this step is now accomplished by interactively marking a few pairs of corresponding features in the two fields). From here on the 3D reconstruction process may be run automatically.

Automated and Adaptive Geometry Preparation for AR/VR-Applications

2021 ◽  
Author(s):  
Maximilian Peter Dammann ◽  
Wolfgang Steger ◽  
Ralph Stelzer
Keyword(s):  
Software Tool ◽  
Product Structure ◽  
Preparation Process ◽  
Data Preparation ◽  
Batch Mode ◽  
Computing Power ◽  
Time Savings ◽  
Automatic Preparation ◽  
Target Platform ◽  
Selection Of

Abstract Product visualization in AR/VR applications requires a largely manual process of data preparation. Previous publications focus on error-free triangulation or transformation of product structure data and display attributes for AR/VR applications. This paper focuses on the preparation of the required geometry data. In this context, a significant reduction in effort can be achieved through automation. The steps of geometry preparation are identified and examined with respect to their automation potential. In addition, possible couplings of sub-steps are discussed. Based on these explanations, a structure for the geometry preparation process is proposed. With this structured preparation process it becomes possible to consider the available computing power of the target platform during the geometry preparation. The number of objects to be rendered, the tessellation quality and the level of detail can be controlled by the automated choice of transformation parameters. We present a software tool in which partial steps of the automatic preparation are already implemented. After an analysis of the product structure of a CAD file, the transformation is executed for each component. Functions implemented so far allow, for example, the selection of assemblies and parts based on filter options, the transformation of geometries in batch mode, the removal of certain details and the creation of UV maps. Flexibility, transformation quality and time savings are described and discussed.

Automated and adaptive geometry preparation for ar/vr-applications

2021 ◽  
pp. 1-26
Author(s):  
Maximilian Peter Dammann ◽  
Wolfgang Steger ◽  
Ralph Stelzer
Keyword(s):  
Performance Optimization ◽  
Software Tool ◽  
Product Structure ◽  
Preparation Process ◽  
Data Preparation ◽  
Batch Mode ◽  
Computing Power ◽  
Automatic Preparation ◽  
Target Platform ◽  
Selection Of

Abstract Product visualization in AR/VR applications requires a largely manual process of data preparation. Previous publications focus on error-free triangulation or transformation of product structure data and display attributes for AR/VR applications. This paper focuses on the preparation of the required geometry data. In this context, a significant reduction in effort can be achieved through automation. The steps of geometry preparation are identified and examined concerning their automation potential. In addition, possible couplings of sub-steps are discussed. Based on these explanations, a structure for the geometry preparation process is proposed. With this structured preparation process, it becomes possible to consider the available computing power of the target platform during the geometry preparation. The number of objects to be rendered, the tessellation quality, and the level of detail can be controlled by the automated choice of transformation parameters. Through this approach, tedious preparation tasks and iterative performance optimization can be avoided in the future, which also simplifies the integration of AR/VR applications into product development and use. A software tool is presented in which partial steps of the automatic preparation are already implemented. After an analysis of the product structure of a CAD file, the transformation is executed for each component. Functions implemented so far allow, for example, the selection of assemblies and parts based on filter options, the transformation of geometries in batch mode, the removal of certain details, and the creation of UV maps. Flexibility, transformation quality, and timesavings are described and discussed.

The function analysis diagram: Intended benefits and coexistence with other functional models

2013 ◽  
Vol 27 (3) ◽  
pp. 249-257 ◽  
Author(s):  
Marco Aurisicchio ◽  
Rob Bracewell ◽  
Gareth Armstrong
Keyword(s):  
Adaptive Design ◽  
Research Collaboration ◽  
Function Analysis ◽  
Software Tool ◽  
Major Power ◽  
Modeling Tools ◽  
Diagram Method ◽  
Functional Models ◽  
Simple Notation

AbstractUnderstanding product functions is a key aspect of the work undertaken by engineers involved in complex system design. The support offered to these engineers by existing modeling tools such as the function tree and the function structure is limited because they are not intuitive and do not scale well to deal with real-world engineering problems. A research collaboration between two universities and a major power system company in the aerospace domain has allowed the authors to further develop a method for function analysis known as function analysis diagram that was already in use by line engineers. The capability to generate and edit these diagrams was implemented in the Decision Rationale editor, a software tool for capturing design rationale. This article presents the intended benefits of the method and justifies them using an engineering case study. The results of the research have shown that the function analysis diagram method has a simple notation, permits the modeling of product functions together with structure, allows the generation of rich and accurate descriptions of product functionality, is useful to work with variant and adaptive design tasks, and can coexist with other functional modeling methods.

scholarly journals Cryo-electron Microscopy Structures of Novel Viruses from Mud Crab Scylla paramamosain with Multiple Infections

2019 ◽  
Vol 93 (7) ◽  
Author(s):  
Yuanzhu Gao ◽  
Shanshan Liu ◽  
Jiamiao Huang ◽  
Qianqian Wang ◽  
Kunpeng Li ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
3D Structure ◽  
Structural Features ◽  
Economic Losses ◽  
Scylla Paramamosain ◽  
Multiple Infections ◽  
Mud Crab ◽  
Cryo Electron Microscopy ◽  
Novel Virus ◽  
Icosahedral Capsid

ABSTRACT Viruses associated with sleeping disease (SD) in crabs cause great economic losses to aquaculture, and no effective measures are available for their prevention. In this study, to help develop novel antiviral strategies, single-particle cryo-electron microscopy was applied to investigate viruses associated with SD. The results not only revealed the structure of mud crab dicistrovirus (MCDV) but also identified a novel mud crab tombus-like virus (MCTV) not previously detected using molecular biology methods. The structure of MCDV at a 3.5-Å resolution reveals three major capsid proteins (VP1 to VP3) organized into a pseudo-T=3 icosahedral capsid, and affirms the existence of VP4. Unusually, MCDV VP3 contains a long C-terminal region and forms a novel protrusion that has not been observed in other dicistrovirus. Our results also reveal that MCDV can release its genome via conformation changes of the protrusions when viral mixtures are heated. The structure of MCTV at a 3.3-Å resolution reveals a T= 3 icosahedral capsid with common features of both tombusviruses and nodaviruses. Furthermore, MCTV has a novel hydrophobic tunnel beneath the 5-fold vertex and 30 dimeric protrusions composed of the P-domains of the capsid protein at the 2-fold axes that are exposed on the virion surface. The structural features of MCTV are consistent with a novel type of virus. IMPORTANCE Pathogen identification is vital for unknown infectious outbreaks, especially for dual or multiple infections. Sleeping disease (SD) in crabs causes great economic losses to aquaculture worldwide. Here we report the discovery and identification of a novel virus in mud crabs with multiple infections that was not previously detected by molecular, immune, or traditional electron microscopy (EM) methods. High-resolution structures of pathogenic viruses are essential for a molecular understanding and developing new disease prevention methods. The three-dimensional (3D) structure of the mud crab tombus-like virus (MCTV) and mud crab dicistrovirus (MCDV) determined in this study could assist the development of antiviral inhibitors. The identification of a novel virus in multiple infections previously missed using other methods demonstrates the usefulness of this strategy for investigating multiple infectious outbreaks, even in humans and other animals.

The Function Analysis Diagram

2012 ◽  
Author(s):  
Marco Aurisicchio ◽  
Rob Bracewell ◽  
Gareth Armstrong
Keyword(s):  
Complex System ◽  
Research Collaboration ◽  
Function Analysis ◽  
Software Tool ◽  
Design Rationale ◽  
Major Power ◽  
Modeling Tools ◽  
Engineering Problems ◽  
Simple Notation ◽  
Complex System Design

Understanding product functions is a key aspect of the work undertaken by engineers involved in complex system design. The support offered to these engineers by existing modeling tools such as the Function Tree and the Function Structure is limited as they are not intuitive and do not scale well to deal with real world engineering problems. A research collaboration between two universities and a major power system company in the aerospace domain has allowed the authors to further develop a method for function analysis known as Function Analysis Diagram (FAD) which was already in use by line engineers. The capability to generate and edit these diagrams was implemented in the Decision Rationale editor (DRed) a software tool for capturing design rationale. This article presents the main beneficial characteristics of the method and justifies them using two engineering case studies. The results of the research have shown that the FAD method has a simple notation, permits the modeling of product functions together with structure, allows the production of rich and accurate descriptions of product functionality and is suitable to represent complex problems.

Molecular Cloning and Structural Insights into pectin lyase proteins from different strains of Fusarium

2020 ◽  
Vol 17 ◽  
Author(s):  
Sangeeta Yadav ◽  
Gautam Anand ◽  
Vinay K Singh ◽  
Dinesh Yadav
Keyword(s):  
Structure Prediction ◽  
Disulfide Bonds ◽  
3D Structure ◽  
Chemical Characterization ◽  
Structural Features ◽  
Docking Studies ◽  
Biochemical Properties ◽  
Pectin Lyase ◽  
Homology Search ◽  
Multiple Sequence

: Pectin lyaseis an industrially important enzymeof pectinase group that degrade pectin polymers forming 4,5-unsaturated oligogalacturonides. Several fugal pectin lyase genes predominately from Aspergillus and Penicillium genera have been reported in the literature. Five pectin lyase genes were cloned from FusariumoxysporumMTCC1755, F.monoliforme var. subglutinansMTCC2015, FusariumavneceumMTCC10572, and FusariumsolaniMTCC3004 using PCR approach. Pectin lyase genes and proteins were subjected to homology search, multiple sequence alignment, motif search, physio-chemical characterization, phylogenetic tree construction, 3D structure prediction and molecular docking. Many conserved amino acids were found at several positions in all the pectin lyase proteins. Phylogenetic analysis of these proteins alongwith other pectinases revealed two major clusters representing members of lyases and hydrolases. In-silico characterization revealed pectin lyase proteins to be highly stable owing to the presence of disulfide bonds in their structure. Molecular weight and pI of these proteins were in the range 14.4 to 25.1 kDa and 4.47-9.39 respectively. Pectin lyase proteins from different Fusariumstrains were very much similar in their structural features and biochemical properties which might be due to their similarity on the primary sequence. Docking studies revealed that electrostatic forces, vander Waal and hydrogen bonds are the major interacting forces between the ligands and the enzyme. This might be accountable for comparatively higher and better activity of pectin lyase against galacturonic acid as compared to α-D-galactopyranuronic acid, galactofuranuronicacid and galactopyranuronate. Aspartate, tyrosine and tryptophan residues in the active site of the enzyme are responsible for ligand binding.

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