scholarly journals Digital, Three-Dimensional Visualization of Root Systems in Peat

Soil Systems ◽  
2020 ◽  
Vol 4 (1) ◽  
pp. 13 ◽  
Author(s):  
Stella Gribbe ◽  
Gesche Blume-Werry ◽  
John Couwenberg
Keyword(s):  
Root System ◽  
3D Visualization ◽  
Large Diameter ◽  
3D Structure ◽  
Three Dimensional ◽  
Plant Morphology ◽  
Dimensional Structure ◽  
Valuable Insight ◽  
Similar Data ◽  
Soil Matrix

Belowground plant structures are inherently difficult to observe in the field. Sedge peat that mainly consists of partly decayed roots and rhizomes offers a particularly challenging soil matrix to study (live) plant roots. To obtain information on belowground plant morphology, research commonly relies on rhizotrons, excavations, or computerized tomography scans (CT). However, all of these methods have certain limitations. For example, CT scans of peat cores cannot sharply distinguish between plant material and water, and rhizotrons do not provide a 3D structure of the root system. Here, we developed a low-cost approach for 3D visualization of the root system in peat monoliths. Two large diameter (20 cm) peat cores were extracted, frozen and two smaller peat monoliths (47 × 6.5 × 13 cm) were taken from each core. Slices of 0.5 mm or 1 mm were cut from one of the frozen monoliths, respectively, using a paper block cutter and the freshly cut surface of the monolith was photographed after each cut. A 3D model of the fresh (live) roots and rhizomes was reconstructed from the resulting images of the thinner slices based on computerized image analysis, including preprocessing, filtering, segmentation and 3D visualization using the open-source software Fiji, Drishti, and Ilastik. Digital volume measurements on the models produced similar data as manual washing out of roots from the adjacent peat monoliths. The constructed 3D models provide valuable insight into the three-dimensional structure of the root system in the peat matrix.

3D Structure of Striations in the North Pacific

2021 ◽  
Author(s):  
YU ZHANG ◽  
YU PING GUAN ◽  
RUI XIN HUANG
Keyword(s):  
North Pacific ◽  
3D Structure ◽  
Three Dimensional ◽  
Vertical Plane ◽  
Dimensional Structure ◽  
The North ◽  
Layer Analysis ◽  
Fluid Potential ◽  
The North Pacific

AbstractOcean striations are composed of alternating quasi-zonal band-like flows; this kind of organized structure of currents be found in all world’s oceans and seas. Previous studies have mainly been focused on the mechanisms of their generation and propagation. This study uses the spatial high-pass filtering to obtain the three-dimensional structure of ocean striations in the North Pacific in both the z-coordinate and σ-coordinate based on 10-yr averaged SODA3 data. First, we identify an ideal-fluid potential density domain where the striations are undisturbed by the surface forcing and boundary effects. Second, using the isopycnal layer analysis, we show that on isopycnal surfaces the orientations of striations nearly follow the potential vorticity (PV) contours, while in the meridional-vertical plane the central positions of striations are generally aligned with the latitude of zero gradient of the relative PV. Our analysis provides a simple dynamical interpretation and better understanding for the role of ocean striations.

scholarly journals Analysis of the three dimensional structure of the kidney glomerulus capillary network

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Mark Terasaki ◽  
Jason Cory Brunson ◽  
Justin Sardi
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
The Body ◽  
Capillary Network ◽  
Dimensional Structure ◽  
Pixel Resolution ◽  
Longitudinal Splitting ◽  
Kidney Glomerulus ◽  
Minimum Number ◽  
Glomerular Size

AbstractThe capillary network of the kidney glomerulus filters small molecules from the blood. The glomerular 3D structure should help to understand its function, but it is poorly characterized. We therefore devised a new approach in which an automated tape collecting microtome (ATUM) was used to collect 0.5 μm thick serial sections from fixed mouse kidneys. The sections were imaged by scanning electron microscopy at ~ 50 nm/pixel resolution. With this approach, 12 glomeruli were reconstructed at an x–y–z resolution ~ 10 × higher than that of paraffin sections. We found a previously undescribed no-cross zone between afferent and efferent branches on the vascular pole side; connections here would allow blood to exit without being adequately filtered. The capillary diameters throughout the glomerulus appeared to correspond with the amount of blood flow within them. The shortest path (minimum number of branches to travel from afferent to efferent arterioles) is relatively independent of glomerular size and is present primarily on the vascular pole size. This suggests that new branches and longer paths form on the urinary pole side. Network analysis indicates that the glomerular network does not form by repetitive longitudinal splitting of capillaries. Thus the 3D structure of the glomerular capillary network provides useful information with which to understand glomerular function. Other tissue structures in the body may benefit from this new three dimensional approach.

scholarly journals Molecular Cloning, Modeling, and Characterization of Type 2 Metallothionein from Plantago ovata Forsk

Sequencing ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Amitava Moulick ◽  
Debashis Mukhopadhyay ◽  
Shonima Talapatra ◽  
Nirmalya Ghoshal ◽  
Sarmistha Sen Raychaudhuri
Keyword(s):  
Molecular Cloning ◽  
Structure Prediction ◽  
3D Structure ◽  
Three Dimensional ◽  
Transcript Level ◽  
Copper Stress ◽  
Dimensional Structure ◽  
Functional Study ◽  
Plantago Ovata

Plantago ovata Forsk is a medicinally important plant. Metallothioneins are cysteine rich proteins involved in the detoxification of heavy metals. Molecular cloning and modeling of MT from P. ovata is not reported yet. The present investigation will describe the isolation, structure prediction, characterization, and expression under copper stress of type 2 metallothionein (MT2) from this species. The gene of the protein comprises three exons and two introns. The deduced protein sequence contains 81 amino acids with a calculated molecular weight of about 8.1 kDa and a theoretical pI value of 4.77. The transcript level of this protein was increased in response to copper stress. Homology modeling was used to construct a three-dimensional structure of P. ovata MT2. The 3D structure model of P. ovata MT2 will provide a significant clue for further structural and functional study of this protein.

scholarly journals 3D Structure of VP1 Structural Protein on Enterovirus A71 Using Swiss-Model

BIOEDUSCIENCE ◽  
2020 ◽  
Vol 4 (1) ◽  
pp. 37-47
Author(s):  
Suprianto ◽  
Made Budiarsa ◽  
Fatmah Dhafir
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Stable Structure ◽  
Target Protein ◽  
Dimensional Structure ◽  
Structural Protein ◽  
Three Dimensional Structure ◽  
Enterovirus A71 ◽  
And Function ◽  
Ramachandran Plots

Background: VP1 structural protein plays a role as a key player in the pathogenesis, has a uniqueness that is interesting enough to be studied by studying the nature and function of structural proteins VP1. This study aims to predict the three-dimensional structure of proteins VP1 on EV-A71. Methods: The target protein is obtained from UniProt server with an access code A0A097EV89using templates 4cey.1.A (PDB ID) were analyzed in silico by homology method using SWISS-MODEL server. Results: Analysis showed the target protein and the template has 95.29% identity and is composed of 297 amino acids with a value of -2.15 QMEAN. Structural protein VP1 in Ramachandran Plots have a stable structure, non-glycine residue in the outlier regions only around 0.34% (A53 ALA) Rated rotamer outliers 1.61%.    Conclusion: The three-dimensional structure model of the protein studied has a stable structure and the information obtained is useful for further research in developing vaccines for diseases caused by EV-A71.  

scholarly journals A New Bioreactor to Promote Follicular Growth With or Without Activin A

2021 ◽  
Author(s):  
Cynthia Jovet ◽  
Eloise Fraison ◽  
Jacqueline Lornage ◽  
Nicolas Morel-journel ◽  
Antoine Gavoille ◽  
...  
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Activin A ◽  
Structure Group ◽  
Dimensional Structure ◽  
Follicular Growth ◽  
Primordial Follicles ◽  
Estradiol Secretion ◽  
Follicular Density

Abstract Background: The aim of the present study was to evaluate the effect of Activin A on the activation of in vitro folliculogenesis of human ovarian tissues with or without our new three-dimensional structure (3D-structure). Methods: Five fresh ovarian human tissues were cultured in vitro in 4 groups with 100ng/mL Activin A or without Activine A and within or without a 3D-structure for 20 or 22 days of in vitro culture. Follicular density and quality were evaluated, and follicular diameters were measured. Estradiol secretion was quantified. Proliferation and apoptosis through immunostaining were performed.Results: The proportion of primordial follicles was significantly reduced, and the proportion of primary and secondary follicles was significantly increased in all four groups (p<0.001). Antral cavities were observed in the four culture groups. Activin A supplementation did not significantly affect the follicular density, follicular quality, follicular growth, or estradiol secretion (p>0.05). The 3D-structure increased the density of primary follicles and decreased the estradiol secretion (p<0.001). Tissular proliferation was significantly lower in the 3D-structure group compared to the non-3D-structure group (p=0.008). Regarding tissular apoptosis, it was significantly higher in the Activin group compared to the non-Activin group (0.006). Conclusion: The presence of Activin A did not seem to play a key role in in vitro folliculogenesis activation. However, the results may indicate that the 3D-structure could be more physiological and could prevent a pejorative in vitro folliculogenesis flare-up.

scholarly journals Analysis of the Thermostability Determinants of Hyperthermophilic Esterase EstE1 Based on Its Predicted Three-Dimensional Structure

2006 ◽  
Vol 72 (4) ◽  
pp. 3021-3025 ◽  
Author(s):  
Jin-Kyu Rhee ◽  
Do-Yun Kim ◽  
Dae-Gyun Ahn ◽  
Jung-Hyuk Yun ◽  
Seung-Hwan Jang ◽  
...  
Keyword(s):  
Homology Modeling ◽  
Hydrophobic Interactions ◽  
3D Structure ◽  
Three Dimensional ◽  
Ion Pair ◽  
Archaeoglobus Fulgidus ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Structure Relationship

ABSTRACT The three-dimensional (3D) structure of the hyperthermophilic esterase EstE1 was constructed by homology modeling using Archaeoglobus fulgidus esterase as a reference, and the thermostability-structure relationship was analyzed. Our results verified the predicted 3D structure of EstE1 and identified the ion pair networks and hydrophobic interactions that are critical determinants for the thermostability of EstE1.

Three-dimensional visualization of top-down superimposed thrust sheets in the SW Grenville Province, Ontario

2019 ◽  
Vol 157 (2) ◽  
pp. 149-159
Author(s):  
Jacob W.D. Strong ◽  
Alan P. Dickin
Keyword(s):  
Large Scale ◽  
3D Visualization ◽  
3D Structure ◽  
Three Dimensional ◽  
Grenville Province ◽  
Tectonic History ◽  
Thrust Sheets ◽  
History Of ◽  
Seismic Sections ◽  
Back Arc

AbstractTo properly understand the tectonic history of the Grenville Province it is necessary to have a reliable, scientifically based understanding of the present-day three-dimensional (3D) structure of the orogen. Based on detailed Nd isotope mapping of surface boundaries and Lithoprobe seismic sections, this study provides the first detailed visualization of the 3D structure of the Grenville gneiss belt in Ontario using the SketchUp software package. The 3D visualization supports a model in which thrust geometry was imposed from the top downwards, controlled by the NW boundary of the Central Metasedimentary Belt that originated as a failed back-arc rift zone. The Central Metasedimentary Belt boundary controlled the trajectory of the Allochthon Boundary Thrust, its underlying tectonic duplex and, ultimately, the Grenville Front. This process of superimposed thrusting explains the large-scale change in the trajectory of the Grenville Front north of Georgian Bay that has been called the ‘Big Bend’. To assist in visualizing the 3D model, a fly-through animation is provided in the supplementary material.

scholarly journals Three-dimensional structure of the basketweave Z-band in midshipman fish sonic muscle

2019 ◽  
Vol 116 (31) ◽  
pp. 15534-15539 ◽  
Author(s):  
Thomas Burgoyne ◽  
John M. Heumann ◽  
Edward P. Morris ◽  
Carlo Knupp ◽  
Jun Liu ◽  
...  
Keyword(s):  
Actin Filaments ◽  
Striated Muscle ◽  
Electron Tomography ◽  
3D Structure ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Band Model ◽  
Type I ◽  
Sonic Muscle ◽  
Subtomogram Averaging

Striated muscle enables movement in all animals by the contraction of myriads of sarcomeres joined end to end by the Z-bands. The contraction is due to tension generated in each sarcomere between overlapping arrays of actin and myosin filaments. At the Z-band, actin filaments from adjoining sarcomeres overlap and are cross-linked in a regular pattern mainly by the protein α-actinin. The Z-band is dynamic, reflected by the 2 regular patterns seen in transverse section electron micrographs; the so-called small-square and basketweave forms. Although these forms are attributed, respectively, to relaxed and actively contracting muscles, the basketweave form occurs in certain relaxed muscles as in the muscle studied here. We used electron tomography and subtomogram averaging to derive the 3D structure of the Z-band in the swimbladder sonic muscle of type I male plainfin midshipman fish (Porichthys notatus), into which we docked the crystallographic structures of actin and α-actinin. The α-actinin links run diagonally between connected pairs of antiparallel actin filaments and are oriented at an angle of about 25° away from the actin filament axes. The slightly curved and flattened structure of the α-actinin rod has a distinct fit into the map. The Z-band model provides a detailed understanding of the role of α-actinin in transmitting tension between actin filaments in adjoining sarcomeres.

scholarly journals Identification and “in silico” Structural Analysis of the Glutamine-rich Protein Qrp (YheA) in Staphylococcus Aureus

2019 ◽  
Vol 12 (1) ◽  
pp. 18-29
Author(s):  
Javier Escobar-Perez ◽  
Katterine Ospina-Garcia ◽  
Zayda Lorena Corredor Rozo ◽  
Ricaurte Alejandro Marquez-Ortiz ◽  
Jaime E Castellanos ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Structural Analysis ◽  
Protein Function ◽  
In Silico ◽  
3D Structure ◽  
Three Dimensional ◽  
3D Models ◽  
Protein Domain ◽  
Dimensional Structure ◽  
Biofilm Growth

Background: YlbF and YmcA are two essential proteins for the formation of biofilm, sporulation, and competence in Bacillus subtilis. In these two proteins, a new protein domain called com_ylbF was recently discovered, but its role and protein function has not yet been established. Objective: In this study, we identified and performed an “in silico” structural analysis of the YheA protein, another com_ylbF-containing protein, in the opportunistic pathogen Staphylococcus aureus. Methods: The search of the yheA gene was performed using BLAST-P and tBLASn algorithms. The three-dimensional (3D) models of YheA, as well as YlbF and YmcA proteins, were built using the I-TASSER and Quark programs. The identification of the native YheA in Staphylococcus aureus was carried out through chromatography using the FPLC system. Results: We found that YheA protein is more widely distributed in Gram-positive bacteria than YlbF and YmcA. Two new and important characteristics for YheA and other com_ylbF-containing proteins were found: a highly conserved 3D structure and the presence of a putative conserved motif located in the central region of the domain, which could be involved in its function. Additionally, we established that Staphylococcus aureus expresses YheA protein in both planktonic growth and biofilm. Finally, we suggest renaming YheA as glutamine-rich protein (Qrp) in S. aureus. Conclusion: The Grp (YheA), YlbF, and YmcA proteins adopt a highly conserved three-dimensional structure, harboring a protein-specific putative motif within the com_ylbF domain, which possibly favors the interaction with their substrates. Finally, Staphylococcus aureus expresses the Grp (YheA) protein in both planktonic and biofilm growth.

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