scholarly journals Multidimensional Scaling Applied to Histogram-Based DNA Analysis

2012 ◽  
Vol 2012 ◽  
pp. 1-11
Author(s):  
António C. Costa ◽  
J. A. Tenreiro Machado ◽  
Maria Dulce Quelhas
Keyword(s):  
Dna Sequences ◽  
Dna Analysis ◽  
Structural Information ◽  
Three Dimensional ◽  
Correlation Method ◽  
Stream Data ◽  
Chromosomal Dna ◽  
Statistical Measures ◽  
Level Information ◽  
High Level

This paper aims to study the relationships between chromosomal DNA sequences of twenty species. We propose a methodology combining DNA-based word frequency histograms, correlation methods, and an MDS technique to visualize structural information underlying chromosomes (CRs) and species. Four statistical measures are tested (Minkowski, Cosine, Pearson product-moment, and Kendallτrank correlations) to analyze the information content of 421 nuclear CRs from twenty species. The proposed methodology is built on mathematical tools and allows the analysis and visualization of very large amounts of stream data, like DNA sequences, with almost no assumptions other than the predefined DNA “word length.” This methodology is able to produce comprehensible three-dimensional visualizations of CR clustering and related spatial and structural patterns. The results of the four test correlation scenarios show that the high-level information clusterings produced by the MDS tool are qualitatively similar, with small variations due to each correlation method characteristics, and that the clusterings are a consequence of the input data and not method’s artifacts.

scholarly journals DNA sequence encodes the position of DNA supercoils

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Sung Hyun Kim ◽  
Mahipal Ganji ◽  
Eugene Kim ◽  
Jaco van der Torre ◽  
Elio Abbondanzieri ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Structural Information ◽  
Three Dimensional ◽  
Decisive Role ◽  
Chromosomal Dna ◽  
Dna Structures ◽  
Cellular Processes ◽  
Specific Sequences ◽  
Good Agreement

The three-dimensional organization of DNA is increasingly understood to play a decisive role in vital cellular processes. Many studies focus on the role of DNA-packaging proteins, crowding, and confinement in arranging chromatin, but structural information might also be directly encoded in bare DNA itself. Here, we visualize plectonemes (extended intertwined DNA structures formed upon supercoiling) on individual DNA molecules. Remarkably, our experiments show that the DNA sequence directly encodes the structure of supercoiled DNA by pinning plectonemes at specific sequences. We develop a physical model that predicts that sequence-dependent intrinsic curvature is the key determinant of pinning strength and demonstrate this simple model provides very good agreement with the data. Analysis of several prokaryotic genomes indicates that plectonemes localize directly upstream of promoters, which we experimentally confirm for selected promotor sequences. Our findings reveal a hidden code in the genome that helps to spatially organize the chromosomal DNA.

Multi-Temporal Correlation Method for Damage Assessment of Buildings from High-Resolution SAR Images of the 2013 Typhoon Haiyan

2016 ◽  
Vol 11 (3) ◽  
pp. 577-592 ◽  
Author(s):  
Pisut Nakmuenwai ◽  
◽  
Fumio Yamazaki ◽  
Wen Liu ◽  
Keyword(s):  
Three Dimensional ◽  
Correlation Method ◽  
Correlation Coefficients ◽  
Temporal Correlation ◽  
Fish Traps ◽  
Multi Temporal ◽  
Potential Damage ◽  
Cartesian Coordinate ◽  
Color Composite ◽  
High Level

In this study, damage caused by Typhoon Haiyan in the city of Tacloban, Philippines is extracted from COSMO-SkyMed imagery data. A multitemporal correlation map, i.e., a color composite of the backscattering coefficients obtained on different days and their correlation coefficients, is used to indicate changes. The Hyperboloid Change Index is proposed as a measure of the level of destruction. The method is demonstrated in a three-dimensional Cartesian coordinate system to elaborate the relationships among the aforementioned parameters. Compared to other candidate methods, a hyperboloid equation is found to be the most suitable for change detection, and its resulting positive value indicates that the typhoon had a high level of impact on the area. Potential damage areas are extracted using a thresholding operation, and the results are compared to two WorldView-2 satellite images to specifically assess coastal erosion and damage to buildings and offshore fish traps.

scholarly journals Three-Dimensional Visualization System with Spatial Information for Navigation of Tele-Operated Robots

Sensors ◽  
2019 ◽  
Vol 19 (3) ◽  
pp. 746 ◽  
Author(s):  
Seung-Hun Kim ◽  
Chansung Jung ◽  
Jaeheung Park
Keyword(s):  
Real Time ◽  
Spatial Information ◽  
Three Dimensional ◽  
Laser Scanner ◽  
Effective Control ◽  
Visualization System ◽  
Level Information ◽  
Surrounding Space ◽  
The Right ◽  
High Level

This study describes a three-dimensional visualization system with spatial information for the effective control of a tele-operated robot. The environmental visualization system for operating the robot is very important. The tele-operated robot performs tasks in a disaster area that is not accessible to humans. The visualization system should perform in real-time to cope with rapidly changing situations. The visualization system should also provide accurate and high-level information so that the tele-operator can make the right decisions. The proposed system consists of four fisheye cameras and a 360° laser scanner. When the robot moves to the unknown space, a spatial model is created using the spatial information data of the laser scanner, and a single-stitched image is created using four images from cameras and mapped in real-time. The visualized image contains the surrounding spatial information; hence, the tele-operator can not only grasp the surrounding space easily, but also knows the relative position of the robot in space. In addition, it provides various angles of view without moving the robot or sensor, thereby coping with various situations. The experimental results show that the proposed method has a more natural appearance than the conventional methods.

scholarly journals Cuttlefish see shape from shading, fine-tuning coloration in response to pictorial depth cues and directional illumination

2016 ◽  
Vol 283 (1826) ◽  
pp. 20160062 ◽  
Author(s):  
Sarah Zylinski ◽  
D. Osorio ◽  
Sonke Johnsen
Keyword(s):  
Three Dimensional ◽  
Shape From Shading ◽  
Surface Curvature ◽  
Fine Tuning ◽  
Human Observer ◽  
Lateral Asymmetry ◽  
Depth Cues ◽  
Level Information ◽  
High Level ◽  
Light And Shadow

Humans use shading as a cue to three-dimensional form by combining low-level information about light intensity with high-level knowledge about objects and the environment. Here, we examine how cuttlefish Sepia officinalis respond to light and shadow to shade the white square (WS) feature in their body pattern. Cuttlefish display the WS in the presence of pebble-like objects, and they can shade it to render the appearance of surface curvature to a human observer, which might benefit camouflage. Here we test how they colour the WS on visual backgrounds containing two-dimensional circular stimuli, some of which were shaded to suggest surface curvature, whereas others were uniformly coloured or divided into dark and light semicircles. WS shading, measured by lateral asymmetry, was greatest when the animal rested on a background of shaded circles and three-dimensional hemispheres, and less on plain white circles or black/white semicircles. In addition, shading was enhanced when light fell from the lighter side of the shaded stimulus, as expected for real convex surfaces. Thus, the cuttlefish acts as if it perceives surface curvature from shading, and takes account of the direction of illumination. However, the direction of WS shading is insensitive to the directions of background shading and illumination; instead the cuttlefish tend to turn to face the light source.

scholarly journals DNA sequence encodes the position of DNA supercoils

2017 ◽  
Author(s):  
Sung Hyun Kim ◽  
Mahipal Ganji ◽  
Jaco van der Torre ◽  
Elio Abbondanzieri ◽  
Cees Dekker
Keyword(s):  
Dna Sequence ◽  
Single Molecule ◽  
Dna Sequences ◽  
Structural Information ◽  
Three Dimensional ◽  
Decisive Role ◽  
Dimensional Structure ◽  
Transcription Start Sites ◽  
Cellular Processes

AbstractThe three-dimensional structure of DNA is increasingly understood to play a decisive role in gene regulation and other vital cellular processes, which has triggered an explosive growth of research on the spatial architecture of the genome. Many studies focus on the role of various DNA-packaging proteins, crowding, and confinement in organizing chromatin, but structural information might also be directly encoded in bare DNA itself. Here, we use a fluorescence-based single-molecule technique to visualize plectonemes, the extended intertwined DNA loops that form upon twisting DNA. Remarkably, we find that the underlying DNA sequence directly encodes the structure of supercoiled DNA by pinning plectonemes at specific positions. We explore a variety of DNA sequences to determine what features influence pinning, and we develop a physical model that predicts the level of plectoneme pinning in excellent agreement with the data. The intrinsic curvature measured over a range of ~70 base pairs is found to be the key property governing the supercoiled structure of DNA. Our model predicts that plectonemes are likely to localize directly upstream of prokaryotic transcription start sites, and this prediction is experimentally verifiedin vitro.Our results reveal a hidden code in DNA that helps to spatially organize the genome.

Transcription factor/DNA interactions visualized by electron spectroscopic imaging

1992 ◽  
Vol 50 (1) ◽  
pp. 450-451
Author(s):  
David P. Bazett-Jones ◽  
Mark L. Brown
Keyword(s):  
Transcription Factor ◽  
Dna Sequences ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Phosphorus Content ◽  
Spectroscopic Imaging ◽  
Electron Spectroscopic Imaging ◽  
Dna Backbone ◽  
Two Parameters ◽  
High Level

A multisubunit RNA polymerase enzyme is ultimately responsible for transcription initiation and elongation of RNA, but recognition of the proper start site by the enzyme is regulated by general, temporal and gene-specific trans-factors interacting at promoter and enhancer DNA sequences. To understand the molecular mechanisms which precisely regulate the transcription initiation event, it is crucial to elucidate the structure of the transcription factor/DNA complexes involved. Electron spectroscopic imaging (ESI) provides the opportunity to visualize individual DNA molecules. Enhancement of DNA contrast with ESI is accomplished by imaging with electrons that have interacted with inner shell electrons of phosphorus in the DNA backbone. Phosphorus detection at this intermediately high level of resolution (≈lnm) permits selective imaging of the DNA, to determine whether the protein factors compact, bend or wrap the DNA. Simultaneously, mass analysis and phosphorus content can be measured quantitatively, using adjacent DNA or tobacco mosaic virus (TMV) as mass and phosphorus standards. These two parameters provide stoichiometric information relating the ratios of protein:DNA content.

Two-Dimensional Crystallization of Tetanus Toxin

1985 ◽  
Vol 43 ◽  
pp. 528-529
Author(s):  
Jeffry A. Reidler ◽  
John P. Robinson
Keyword(s):  
Electron Microscopy ◽  
Tetanus Toxin ◽  
Structural Information ◽  
Three Dimensional ◽  
Two Dimensional ◽  
Membrane Interface ◽  
3D Reconstructions ◽  
Cellular Receptors ◽  
Computer Reconstruction ◽  
2D Crystals

We have prepared two-dimensional (2D) crystals of tetanus toxin using procedures developed by Uzgiris and Kornberg for the directed production of 2D crystals of monoclonal antibodies at an antigen-phospholipid monolayer interface. The tetanus toxin crystals were formed using a small mole fraction of the natural receptor, GT1, incorporated into phosphatidyl choline monolayers. The crystals formed at low concentration overnight. Two dimensional crystals of this type are particularly useful for structure determination using electron microscopy and computer image refinement. Three dimensional (3D) structural information can be derived from these crystals by computer reconstruction of photographs of toxin crystals taken at different tilt angles. Such 3D reconstructions may help elucidate the mechanism of entry of the enzymatic subunit of toxins into cells, particularly since these crystals form directly on a membrane interface at similar concentrations of ganglioside GT1 to the natural cellular receptors.

EMCAT: An automatic image-processing system for electron-microscopic tomography

1994 ◽  
Vol 52 ◽  
pp. 418-419
Author(s):  
Weiping Liu ◽  
John W. Sedat ◽  
David A. Agard
Keyword(s):  
Image Processing ◽  
Structural Information ◽  
Imaging Technique ◽  
Three Dimensional ◽  
Processing System ◽  
Electron Microscopic ◽  
Data Set ◽  
Ordered Structures ◽  
Automatic Image Processing ◽  
Em Tomography

Any real world object is three-dimensional. The principle of tomography, which reconstructs the 3-D structure of an object from its 2-D projections of different view angles has found application in many disciplines. Electron Microscopic (EM) tomography on non-ordered structures (e.g., subcellular structures in biology and non-crystalline structures in material science) has been exercised sporadically in the last twenty years or so. As vital as is the 3-D structural information and with no existing alternative 3-D imaging technique to compete in its high resolution range, the technique to date remains the kingdom of a brave few. Its tedious tasks have been preventing it from being a routine tool. One keyword in promoting its popularity is automation: The data collection has been automated in our lab, which can routinely yield a data set of over 100 projections in the matter of a few hours. Now the image processing part is also automated. Such automations finish the job easier, faster and better.

Three-Dimensional Structure of Cloned T3 Connector Protein at 1.6nm Resolution

1990 ◽  
Vol 48 (1) ◽  
pp. 282-283
Author(s):  
José L. Carrascosa ◽  
José M. Valpuesta ◽  
Hisao Fujisawa
Keyword(s):  
Dna Sequences ◽  
Expression Vector ◽  
Three Dimensional ◽  
Deae Cellulose ◽  
Dna Packaging ◽  
Dimensional Structure ◽  
Two Dimensional ◽  
Freezing And Thawing ◽  
Three Dimensional Structure ◽  
Dimensional Reconstruction

The head to tail connector of bacteriophages plays a fundamental role in the assembly of viral heads and DNA packaging. In spite of the absence of sequence homology, the structure of connectors from different viruses (T4, Ø29, T3, P22, etc) share common morphological features, that are most clearly revealed in their three-dimensional structure. We have studied the three-dimensional reconstruction of the connector protein from phage T3 (gp 8) from tilted view of two dimensional crystals obtained from this protein after cloning and purification.DNA sequences including gene 8 from phage T3 were cloned, into Bam Hl-Eco Rl sites down stream of lambda promotor PL, in the expression vector pNT45 under the control of cI857. E R204 (pNT89) cells were incubated at 42°C for 2h, harvested and resuspended in 20 mM Tris HC1 (pH 7.4), 7mM 2 mercaptoethanol, ImM EDTA. The cells were lysed by freezing and thawing in the presence of lysozyme (lmg/ml) and ligthly sonicated. The low speed supernatant was precipitated by ammonium sulfate (60% saturated) and dissolved in the original buffer to be subjected to gel nitration through Sepharose 6B, followed by phosphocellulose colum (Pll) and DEAE cellulose colum (DE52). Purified gp8 appeared at 0.3M NaCl and formed crystals when its concentration increased above 1.5 mg/ml.

Guided surgery with 3D printed device: a case report

2020 ◽  
Author(s):  
Michelle Carvalho de Sales ◽  
Rafael Maluza Flores ◽  
Julianny da Silva Guimaraes ◽  
Gustavo Vargas da Silva Salomao ◽  
Tamara Kerber Tedesco ◽  
...  
Keyword(s):  
Operating Time ◽  
Three Dimensional ◽  
Conventional Technique ◽  
Cervical Region ◽  
Mean Deviation ◽  
Apical Region ◽  
Virtual Planning ◽  
Surgical Guide ◽  
Surgical Guides ◽  
High Level

Dental surgeons need in-depth knowledge of the bone tissue status and gingival morphology of atrophic maxillae. The aim of this study is to describe preoperative virtual planning of placement of five implants and to compare the plan with the actual surgical results. Three-dimensional planning of rehabilitation using software programs enables surgical guides to be specially designed for the implant site and manufactured using 3D printing. A patient with five teeth missing was selected for this study. The patient’s maxillary region was scanned with CBCT and a cast model was produced. After virtual planning using ImplantViewer, five implants were placed using a printed surgical guide. Two weeks after the surgical procedure, the patient underwent another CBCT scan of the maxilla. Statistically significant differences were detected between the virtually planned positions and the actual positions of the implants, with a mean deviation of 0.36 mm in the cervical region and 0.7 mm in the apical region. The surgical technique used enables more accurate procedures when compared to the conventional technique. Implants can be better positioned, with a high level of predictability, reducing both operating time and patient discomfort.

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