scholarly journals Virtual Stencil for Patterning and Modeling in a Quantitative Volume Using EWOD and DEP Devices for Microfluidics

Micromachines ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1104
Author(s):  
Yi-Wei Lin ◽  
Ying-Jhen Ciou ◽  
Da-Jeng Yao
Keyword(s):  
Propylene Carbonate ◽  
3D Structure ◽  
Three Dimensional ◽  
Electrode Array ◽  
Dimensional Structure ◽  
Electrowetting On Dielectric ◽  
System A ◽  
Photosensitive Polymer ◽  
Uv Lamp ◽  
Gap Height

Applying microfluidic patterning, droplets were precisely generated on an electrowetting-on-dielectric (EWOD) chip considering these parameters: number of generating electrodes, number of cutting electrodes, voltage, frequency and gap between upper and lower plates of the electrode array on the EWOD chip. In a subsequent patterning experiment, an environment with three generating electrodes, one cutting electrode and a gap height 10 μm, we obtained a quantitative volume for patterning. Propylene carbonate liquid and a mixed colloid of polyphthalate carbonate (PPC) and photosensitive polymer material were manipulated into varied patterns. With support from a Z-axis lifting platform and a UV lamp, a cured 3D structure was stacked. Using an EWOD system, a multi-layer three-dimensional structure was produced for the patterning. A two-plate EWOD system patterned propylene carbonate in a quantitative volume at 140 Vpp/20 kHz with automatic patterning.

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 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.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of a single variable domain of the immunoglobulin superfamily in amphioxus,Amphi-IgSF-V

2014 ◽  
Vol 70 (8) ◽  
pp. 1072-1075 ◽  
Author(s):  
Bo Jiang ◽  
Yanjie Liu ◽  
Rong Chen ◽  
Zhenbao Wang ◽  
Mansoor Tariq ◽  
...  
Keyword(s):  
Immune System ◽  
Structural Information ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Immunoglobulin Superfamily ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
System A ◽  
Human Immunoglobulins

Amphioxus is regarded as an essential animal model for the study of immune evolution. Discovery of new molecules with the immunoglobulin superfamily (IgSF) variable (V) domain in amphioxus would help in studying the evolution of IgSF V molecules in the immune system. A protein was found which just contains only one IgSF V domain in amphioxus, termedAmphi-IgSF-V; it has over 30% sequence identity to the V domains of human immunoglobulins and mammalian T-cell receptors. In order to clarify the three-dimensional structure of this new molecule in amphioxus,Amphi-IgSF-V was expressed, purified and crystallized, and diffraction data were collected to a resolution of 1.95 Å. The crystal belonged to space groupP3221, with unit-cell parametersa=b= 53.9,c= 135.5 Å. The Matthews coefficient and solvent content were calculated to be 2.58 Å3 Da−1and 52.38%, respectively. The results will provide structural information to study the evolution of IgSF V molecules in the immune system.

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 Effect of culture methods on cumulus and oocyte morphology and meiotic competence of bovine oocytes from early antral follicles

2005 ◽  
Vol 48 (6) ◽  
pp. 562-571
Author(s):  
L. Kątska-Książkiewicz ◽  
H. Alm
Keyword(s):  
Three Dimensional ◽  
Collagen Gel ◽  
Standard System ◽  
Dimensional Structure ◽  
Culture Methods ◽  
Normal Morphology ◽  
Antral Follicles ◽  
System A ◽  
Meiotic Competence

Abstract. The objective of the present study was to establish a culture system that would maintain the three-dimensional structure of bovine early antral follicles (EAF) or isolated cumulus-oocyte-granulosa complexes (COCGs) and increase the resulting portion of COCs with normal morphology for subsequent IVM. The morphological quality and meiotic competence of oocytes originating from early antral bovine ovarian follicles (0.2 to 0.7 mm and 0.4 to 0.7 mm diameter) were evaluated following culture in vitro for 14 and 7 d, respectively, and subsequent in vitro maturation. Growth culture modifications included culture in the well of the well (WOW) system; a microdroplet of collagen gel (2 x 5 μl vs. 2 x 400 μl; standard system) and culture of EAF in hanging drops of medium (inverted system). Significantly higher (P<0.01) proportions of COCs with normal morphology (60.4%) were obtained from COCGs compared to EAF (4.8%) grown in the WOW system. Embedding of COCGs in microdrops of collagen gel significantly increased proportion of COCs with normal morphology (63.2%) compared to those embedded in standard volume gels (35.3%). Recovery rate of COCs with normal morphology from cultured EAF was improved both by using microdrops of gel (44%) and by culture in the inverted system (39.3%) over that found for the standard system (8.5%).

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.

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