scholarly journals Neural Collision Detection: an open source library to study the three-dimensional interactions of neurons and other tree-like structures

2021 ◽  
Author(s):  
Hagai Har-Gil ◽  
Yoav Jacobson ◽  
Alvar Proenneke ◽  
Jochen F Staiger ◽  
Omri Tomer ◽  
...  
Keyword(s):  
Collision Detection ◽  
Three Dimensional ◽  
Morphological Properties ◽  
Dimensional Structure ◽  
Neuronal Structure ◽  
3D Objects ◽  
As Graph ◽  
The Rich ◽  
High Level ◽  
Neuroscience Community

The analysis of neuronal structure and its relation to function has become a fundamental pillar in neuroscience since its earliest days, with the underlying premise that morphological properties can modulate neuronal computations. It is often the case that the rich three-dimensional structure of neurons is quantified by tools developed in other fields, such as graph theory and computational geometry; nevertheless, some of the more advanced tools developed in these fields have not yet been made accessible to the neuroscience community. Here we present Neural Collision Detection, a library providing high-level interfaces to collision-detection routines and alpha shape calculations, as well as statistical analysis and visualizations for 3D objects, with the aim to lower the entry gap for neuroscientists into these worlds. Our work here also demonstrates a variety of use cases for the library and exemplary analysis and visualizations that were carried out with it on real neuronal and vascular data.

An Assistant Interface to Design and Produce a Pop-Up Card

2010 ◽  
Vol 1 (2) ◽  
pp. 40-50
Author(s):  
Sosuke Okamura ◽  
Takeo Igarashi
Keyword(s):  
Real Time ◽  
Design Process ◽  
Collision Detection ◽  
User Study ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Design Activity ◽  
Three Dimensional Structure ◽  
Design And Production

This article describes an assistant interface to design and produce pop-up cards. A pop-up card is a piece of folded paper from which a three-dimensional structure pops up when opened. The authors propose an interface to assist the user in the design and production of a pop-up card. During the design process, the system examines whether the parts protrude from the card or whether the parts collide with one another when the card is closed. The user can concentrate on the design activity because the error occurrence and the error resolution are continuously fed to the user in real time. The authors demonstrate the features of their system by creating two pop-up card examples and perform an informal preliminary user study, showing that automatic protrusion and collision detection are effective in the design process.

An Assistant Interface to Design and Produce a Pop-Up Card

2012 ◽  
pp. 119-130
Author(s):  
Sosuke Okamura ◽  
Takeo Igarashi
Keyword(s):  
Real Time ◽  
Design Process ◽  
Collision Detection ◽  
User Study ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Design Activity ◽  
Three Dimensional Structure ◽  
Design And Production

This article describes an assistant interface to design and produce pop-up cards. A pop-up card is a piece of folded paper from which a three-dimensional structure pops up when opened. The authors propose an interface to assist the user in the design and production of a pop-up card. During the design process, the system examines whether the parts protrude from the card or whether the parts collide with one another when the card is closed. The user can concentrate on the design activity because the error occurrence and the error resolution are continuously fed to the user in real time. The authors demonstrate the features of their system by creating two pop-up card examples and perform an informal preliminary user study, showing that automatic protrusion and collision detection are effective in the design process.

scholarly journals A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 33 ◽  
Author(s):  
Dmitrii M. Nikolaev ◽  
Anton Emelyanov ◽  
Vitaly M. Boitsov ◽  
Maxim S Panov ◽  
Mikhail N. Ryazantsev
Keyword(s):  
Optical Properties ◽  
Rational Design ◽  
Molecular Design ◽  
Hybrid Approach ◽  
Three Dimensional ◽  
Membrane Voltage ◽  
Dimensional Structure ◽  
Fluorescent Indicators ◽  
Voltage Dependent ◽  
High Level

It was demonstrated in recent studies that some rhodopsins can be used in optogenetics as fluorescent indicators of membrane voltage. One of the promising candidates for these applications is archaerhodopsin-3. However, the fluorescent signal for wild-type achaerhodopsin-3 is not strong enough for real applications. Rational design of mutants with an improved signal is an important task, which requires both experimental and theoretical studies. Herein, we used a homology-based computational approach to predict the three-dimensional structure of archaerhodopsin-3, and a Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid approach with high-level multireference ab initio methodology (SORCI+Q/AMBER) to model optical properties of this protein. We demonstrated that this methodology allows for reliable prediction of structure and spectral properties of archaerhodopsin-3. The results of this study can be utilized for computational molecular design of efficient fluorescent indicators of membrane voltage for modern optogenetics on the basis of archaerhodopsin-3.

Structure of recombinant human lactoferrin expressed in Aspergillus awamori

1999 ◽  
Vol 55 (2) ◽  
pp. 403-407 ◽  
Author(s):  
Xiao-Lin Sun ◽  
Heather M. Baker ◽  
Steven C. Shewry ◽  
Geoffrey B. Jameson ◽  
Edward N. Baker
Keyword(s):  
Dynamic Properties ◽  
Release Kinetics ◽  
Three Dimensional ◽  
Strain Improvement ◽  
Human Lactoferrin ◽  
Aspergillus Awamori ◽  
Dimensional Structure ◽  
Iron Release ◽  
High Level ◽  
Chain Conformations

Human lactoferrin (hLf) has considerable potential as a therapeutic agent. Overexpression of hLf in the fungus Aspergillus awamori has resulted in the availability of very large quantities of this protein. Here, the three-dimensional structure of the recombinant hLf has been determined by X-ray crystallography at a resolution of 2.2 Å. The final model, comprising 5339 protein atoms (residues 1–691, 294 solvent molecules, two Fe3+and two CO_3^{2-} ions), gives an R factor of 0.181 (free R = 0.274) after refinement against 32231 reflections in the resolution range 10–2.2 Å. Superposition of the recombinant hLf structure onto the native milk hLf structure shows a very high level of correspondence; the main-chain atoms for the entire polypeptide can be superimposed with an r.m.s. deviation of only 0.3 Å and there are no significant differences in side-chain conformations or in the iron-binding sites. Dynamic properties, as measured by B-value distributions or iron-release kinetics, also agree closely. This shows that the structure of the protein is not affected by the mode of expression, the use of strain-improvement procedures or the changes in glycosylation due to the fungal system.

scholarly journals Interactions between Biocide Cationic Agents and Bacterial Biofilms

2002 ◽  
Vol 46 (5) ◽  
pp. 1469-1474 ◽  
Author(s):  
C. Campanac ◽  
L. Pineau ◽  
A. Payard ◽  
G. Baziard-Mouysset ◽  
C. Roques
Keyword(s):  
Quaternary Ammonium ◽  
Three Dimensional ◽  
Quaternary Ammonium Compounds ◽  
Dimensional Structure ◽  
Bacterial Biofilms ◽  
Physiological Changes ◽  
Essential Point ◽  
Three Dimensional Structure ◽  
High Level ◽  
Ammonium Compounds

ABSTRACT The resistance of bacterial biofilms to physical and chemical agents is attributed in the literature to various interconnected processes. The limitation of mass transfer alters the growth rate, and physiological changes in the bacteria in the film also appear. The present work describes an approach to determination of the mechanisms involved in the resistance of bacteria to quaternary ammonium compounds (benzalkonium chloride) according to the C-chain lengths of those compounds. For Pseudomonas aeruginosa CIP A 22, the level of resistance of the bacteria in the biofilm relative to that of planktonic bacteria increased with the C-chain length. For cells within the biofilm, the exopolysaccharide induced a characteristic increase in surface hydrophilicity. However, this hydrophilicity was eliminated by simple resuspension and washing. The sensitivity to quaternary ammonium compounds was restored to over 90%. Staphylococcus aureus CIP 53 154 had a very high level of resistance when it was in the biofilm form. A characteristic of bacteria from the biofilm was a reduction in the percent hydrophobicity, but the essential point is that this hydrophobicity was retained after the biofilm bacteria were resuspended and washed. The recovery of sensitivity was thus only partial. These results indicate that the factors involved in biofilm resistance to quaternary ammonium compounds vary according to the bacterial modifications induced by the formation of a biofilm. In the case of P. aeruginosa, we have underlined the involvement of the exopolysaccharide and particularly the three-dimensional structure (water channels). In the case of S. aureus, the role of the three-dimensional structure is limited and drastic physiological changes in the biofilm cells are more highly implicated in resistance.

scholarly journals The Brain, Seizures and Epilepsy Throughout Life: Understanding a Moving Target

2012 ◽  
Vol 12 (4_suppl) ◽  
pp. 7-12 ◽  
Author(s):  
Tallie Z. Baram
Keyword(s):  
Temporal Evolution ◽  
Three Dimensional ◽  
Epileptic Activity ◽  
Dimensional Structure ◽  
Moving Target ◽  
Neuronal Structure ◽  
Health And Disease ◽  
Dimension One ◽  
And Behavior ◽  
The Brain

The human brain is a tremendously complex and still enigmatic three-dimensional structure, composed of countless interconnected neurons and glia. The temporal evolution of the brain throughout life provides a fourth dimension, one that influences every element of the brain's function in health and disease. This temporal evolution contributes to the probability of seizure generation and to the type and the nature of these seizures. The age-specific properties of the brain also influence the consequences of seizures on neuronal structure and behavior. These, in turn, govern epileptic activity and cognitive and emotional functions, contributing to the diverse consequences of seizures and epilepsy throughout life.

scholarly journals A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 33
Author(s):  
Dmitrii M. Nikolaev ◽  
Anton Emelyanov ◽  
Vitaly M. Boitsov ◽  
Maxim S Panov ◽  
Mikhail N. Ryazantsev
Keyword(s):  
Optical Properties ◽  
Rational Design ◽  
Molecular Design ◽  
Hybrid Approach ◽  
Three Dimensional ◽  
Membrane Voltage ◽  
Dimensional Structure ◽  
Fluorescent Indicators ◽  
Voltage Dependent ◽  
High Level

It was demonstrated in recent studies that some rhodopsins can be used in optogenetics as fluorescent indicators of membrane voltage. One of the promising candidates for these applications is archaerhodopsin-3. However, the fluorescent signal for wild-type achaerhodopsin-3 is not strong enough for real applications. Rational design of mutants with an improved signal is an important task, which requires both experimental and theoretical studies. Herein, we used a homology-based computational approach to predict the three-dimensional structure of archaerhodopsin-3, and a Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid approach with high-level multireference ab initio methodology (SORCI+Q/AMBER) to model optical properties of this protein. We demonstrated that this methodology allows for reliable prediction of structure and spectral properties of archaerhodopsin-3. The results of this study can be utilized for computational molecular design of efficient fluorescent indicators of membrane voltage for modern optogenetics on the basis of archaerhodopsin-3.

scholarly journals A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 33 ◽  
Author(s):  
Dmitrii M. Nikolaev ◽  
Anton Emelyanov ◽  
Vitaly M. Boitsov ◽  
Maxim S Panov ◽  
Mikhail N. Ryazantsev
Keyword(s):  
Optical Properties ◽  
Rational Design ◽  
Molecular Design ◽  
Hybrid Approach ◽  
Three Dimensional ◽  
Membrane Voltage ◽  
Dimensional Structure ◽  
Fluorescent Indicators ◽  
Voltage Dependent ◽  
High Level

It was demonstrated in recent studies that some rhodopsins can be used in optogenetics as fluorescent indicators of membrane voltage. One of the promising candidates for these applications is archaerhodopsin-3. While it has already shown encouraging results, there is still a large room for improvement. One of possible directions is increasing the intensity of the protein's fluorescent signal. Rational design of mutants with an improved signal is an important task, which requires both experimental and theoretical studies. Herein, we used a homology-based computational approach to predict the three-dimensional structure of archaerhodopsin-3, and a Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid approach with high-level multireference ab initio methodology (SORCI+Q/AMBER) to model optical properties of this protein. We demonstrated that this methodology allows for reliable prediction of structure and spectral properties of archaerhodopsin-3. The results of this study can be utilized for computational molecular design of efficient fluorescent indicators of membrane voltage for modern optogenetics on the basis of archaerhodopsin-3.

Characteristics and Bioactivity of CaP Porous Coating with Bio-Inspired Dopamine

2012 ◽  
Vol 529-530 ◽  
pp. 233-236
Author(s):  
Yen Ting Liu ◽  
Kuan Chen Kung ◽  
Tzer Min Lee ◽  
Truan Sheng Lui
Keyword(s):  
Photoelectron Spectroscopy ◽  
Three Dimensional ◽  
Morphological Properties ◽  
Dimensional Structure ◽  
Porous Coating ◽  
Cell Behavior ◽  
Osteoblastic Cell ◽  
Biological Responses ◽  
Porous Architecture ◽  
Micro Arc Oxidation

mplants made of titanium and its alloys are widely used in dental and orthopedic fields due to their excellent chemical stability and mechanical properties. However, due to the bio-inert properties of titanium and its alloys, it is difficult to achieve a chemical bond with bone tissue and to form a new bond on the surface. To improve biocompatibility, surface treatments are often used to modify the chemical and morphological properties. Besides, the mussel-inspired molecule of 3,4-dihydroxy-L-phenylalanine (dopamine) shows excellent biological responses. The aim of this study is to investigate the physicochemical and biomedical properties of CaP porous coating with dopamine. The CaP porous coating was prepared on titanium by micro-arc oxidation, and then bio-inspired molecular of dopamine modified surface to improve the cell behavior. Characteristics of the morphology, chemical composition, and interfacial properties of dopamine-functionalized CaP porous architecture was performed by scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS). The osteoblastic cell behaviour, such as differentiation and morphology is evaluated. The nitrogen signal in XPS spectrum was indicated that the dopamine existed in the porous coating. The anatase and rutile phases of porous coating with dopamine were identified. Morphologies of porous coating with dopamine showed the uniform and three-dimensional structure. Cell culture experiments demonstrate that the porous coating with dopamine would improve cell behavior. All findings in this study indicated that CaP porous coating with dopamine have good bioactivity for clinical applications.

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

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