scholarly journals Estimation of three-dimensional structure of forest and development of roots of trees using LiDAR data

2019 ◽  
Vol 1 ◽  
pp. 1-1
Author(s):  
Mamoru Koarai ◽  
Akane Narikiyo ◽  
Wataru Murakami
Keyword(s):  
Root System ◽  
System Development ◽  
Three Dimensional ◽  
Tree Height ◽  
Deterrent Effect ◽  
Dimensional Structure ◽  
Lidar Data ◽  
Three Dimensional Structure ◽  
Root System Development ◽  
The Stability

<p><strong>Abstract.</strong> There is deterrent effect to the slope collapse for development of the root of the tree. However, it's difficult to know the development situation of the roots of the forest. On the other hand, they're becoming able to estimate the forest three-dimensional structure such as the tree height, the tree number and diameter breast height, etc. by LiDAR data. Because tree height and diameter are related to development of roots of trees, the authors try to estimate the root system development situation of the forest by LiDAR data to presume indirectly the stability of slope. The authors surveyed the diameters and root system development of about one hundred trees in the cut forest of cedar woods in the weathered granite Abukuma Mountains, Fukushima Prefecture. The three-dimensional structure of the cut forest was presumed from LiDAR data before felling. As the results of consideration, this report show that the three-dimensional structure of the forest is presumed from LiDAR data, and the development situation of the roots of the forest was estimated for slope stability analysis.</p>

Using high-resolution LiDAR data to quantify the three-dimensional structure of vegetation in urban green space

2016 ◽  
Vol 19 (4) ◽  
pp. 1749-1765 ◽  
Author(s):  
Rhiannon J. C. Caynes ◽  
Matthew G. E. Mitchell ◽  
Dan Sabrina Wu ◽  
Kasper Johansen ◽  
Jonathan R. Rhodes
Keyword(s):  
High Resolution ◽  
Green Space ◽  
Three Dimensional ◽  
Urban Green Space ◽  
Dimensional Structure ◽  
Lidar Data ◽  
Urban Green ◽  
Three Dimensional Structure

scholarly journals Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0251751
Author(s):  
Siti Nor Hasmah Ishak ◽  
Nor Hafizah Ahmad Kamarudin ◽  
Mohd Shukuri Mohamad Ali ◽  
Adam Thean Chor Leow ◽  
Fairolniza Mohd Shariff ◽  
...  
Keyword(s):  
Amino Acids ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Substrate Preference ◽  
Dynamics Simulation ◽  
Dimensional Structure ◽  
Docking Analysis ◽  
Three Dimensional Structure ◽  
Ion Interactions ◽  
The Stability

5M mutant lipase was derived through cumulative mutagenesis of amino acid residues (D43E/T118N/E226D/E250L/N304E) of T1 lipase from Geobacillus zalihae. A previous study revealed that cumulative mutations in 5M mutant lipase resulted in decreased thermostability compared to wild-type T1 lipase. Multiple amino acids substitution might cause structural destabilization due to negative cooperation. Hence, the three-dimensional structure of 5M mutant lipase was elucidated to determine the evolution in structural elements caused by amino acids substitution. A suitable crystal for X-ray diffraction was obtained from an optimized formulation containing 0.5 M sodium cacodylate trihydrate, 0.4 M sodium citrate tribasic pH 6.4 and 0.2 M sodium chloride with 2.5 mg/mL protein concentration. The three-dimensional structure of 5M mutant lipase was solved at 2.64 Å with two molecules per asymmetric unit. The detailed analysis of the structure revealed that there was a decrease in the number of molecular interactions, including hydrogen bonds and ion interactions, which are important in maintaining the stability of lipase. This study facilitates understanding of and highlights the importance of hydrogen bonds and ion interactions towards protein stability. Substrate specificity and docking analysis on the open structure of 5M mutant lipase revealed changes in substrate preference. The molecular dynamics simulation of 5M-substrates complexes validated the substrate preference of 5M lipase towards long-chain p-nitrophenyl–esters.

Modeling the impact of point mutations on the stability of proteins

2020 ◽  
Vol 18 (04) ◽  
pp. 2050019
Author(s):  
K. G. Kulikov ◽  
T. V. Koshlan
Keyword(s):  
Protein Interactions ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Point Mutations ◽  
Dimensional Structure ◽  
Amino Acid Residues ◽  
Three Dimensional Structure ◽  
The Stability ◽  
The Impact ◽  
Proven Theorem

A new method has been introduced which allows us to determine the stability of protein complexes with point changes of amino acid residues that also take into account the three-dimensional structure of the complex. This formulated and proven theorem is aimed at determining the criterion for the stability of protein molecules. The algorithm and software package were developed for analyzing protein interactions, taking into account their three-dimensional structure from the PDB database.

Laser scanning as a tool for the analysis of the greenery on the example of Poremba district in Lublin

2015 ◽  
Vol 26 (3-4) ◽  
pp. 132-140
Author(s):  
P. G. Kotsyuba ◽  
I. D. Semko ◽  
I. I. Kozak ◽  
T. V. Parpan ◽  
G. G. Kozak ◽  
...  
Keyword(s):  
Laser Scanning ◽  
Green Space ◽  
Three Dimensional ◽  
Tree Height ◽  
Field Measurements ◽  
Airborne Lidar ◽  
Dimensional Structure ◽  
Lidar Data ◽  
Definition Of ◽  
Airborne Lidar Data

World experience shows that the survey of green spaces by traditional methods is very time consuming, costly and does not always get all the information you need to make of adequate management decisions by municipal authorities. The aim of this article was to show the main stages of analysis and prospects of urban green space using aerial lidar data and submit the effect of three-dimensional visualization of the study area. There were presented the possibilities and perspectives of using the data obtained from airborne laser scanning (ALS) for the analysis of greenery on the example of Poremba district in Lublin (Poland). Research conducted in Poremba district in the Polish city of Lublin (district was built from 1988 to 2005 and is located in the western part of the city). Analysis of green space conducted using quantitative analytical methods. By detailed analysis of the study area were used aerial lidar data from the year 2015. To classify aerial lidar data such software were used: LP360, ArcMap 10.3, Toolbox LAStools. The process of analysis begins with the definition of points, belonging to ground (Ground - GR), and the classification was realized using «lasground» with tools LAStools. The article is dedicated to development the method of estimation the tree height based on airborne LiDAR data. Method applies more information about the three-dimensional structure of natural objects derived from the processing of airborne LiDAR data compared with known methods. Furthermore, the method is adapted to determine and calculate characteristics of stand which using for tree inventory in cities. Methodological and algorithmic instructions to determine the tree parameters in city were proposed. These instructions allow automatically calculating the characteristics of the tree parameters, such as the allocation of each tree and tree height. The study area was analyzed in terms of the distribution of vegetation (separately individual growing trees and groups of trees). For that purpose there was applied an available ALS data. Based on the ALS data there were separated the tops of the trees and their height. In order to verify the ALS data there were used the results of field measurements (coordinates for the tree trunks, the diameter at breast height of trees, their height, crown projection). The analysis of the greenery within the Poremba district using the ALS data after verification with the field measurements proved to be an effective tool for the characterization of the greenery areas in particular city. This research may be important in terms of planning the planting of greenery areas and spatial development of the Lublin.

The Three-dimensional structure of frozen-hydrated nudaurelia capensis β virus

1987 ◽  
Vol 45 ◽  
pp. 650-651
Author(s):  
N. H. Olson ◽  
T. S. Baker ◽  
Wu Bo Mu ◽  
J. E. Johnson ◽  
D. A. Hendry
Keyword(s):  
South African ◽  
Rna Virus ◽  
Carbon Film ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Electron Dose ◽  
Total Electron ◽  
Three Dimensional Structure ◽  
Negative Stain ◽  
Dimensional Reconstruction

Nudaurelia capensis β virus (NβV) is an RNA virus of the South African Pine Emperor moth, Nudaurelia cytherea capensis (Lepidoptera: Saturniidae). The NβV capsid is a T = 4 icosahedron that contains 60T = 240 subunits of the coat protein (Mr = 61,000). A three-dimensional reconstruction of the NβV capsid was previously computed from visions embedded in negative stain suspended over holes in a carbon film. We have re-examined the three-dimensional structure of NβV, using cryo-microscopy to examine the native, unstained structure of the virion and to provide a initial phasing model for high-resolution x-ray crystallographic studiesNβV was purified and prepared for cryo-microscopy as described. Micrographs were recorded ∼1 - 2 μm underfocus at a magnification of 49,000X with a total electron dose of about 1800 e-/nm2.

Three Dimensional structure and organization of diploid chromosomes by optical section microscopy

1987 ◽  
Vol 45 ◽  
pp. 633-635
Author(s):  
David A. Agard ◽  
Yasushi Hiraoka ◽  
John W. Sedat
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Developmental State ◽  
Mitotic Cell ◽  
Biological Properties ◽  
Dimensional Structure ◽  
Specific Gene ◽  
Three Dimensional Structure ◽  
Complementary Techniques ◽  
Dynamic Structures

In an effort to understand the complex relationship between structure and biological function within the nucleus, we have embarked on a program to examine the three-dimensional structure and organization of Drosophila melanogaster embryonic chromosomes. Our overall goal is to determine how DNA and proteins are organized into complex and highly dynamic structures (chromosomes) and how these chromosomes are arranged in three dimensional space within the cell nucleus. Futher, we hope to be able to correlate structual data with such fundamental biological properties as stage in the mitotic cell cycle, developmental state and transcription at specific gene loci.Towards this end, we have been developing methodologies for the three-dimensional analysis of non-crystalline biological specimens using optical and electron microscopy. We feel that the combination of these two complementary techniques allows an unprecedented look at the structural organization of cellular components ranging in size from 100A to 100 microns.

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.

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