scholarly journals Identification of Rhythmically Expressed LncRNAs in the Zebrafish Pineal Gland and Testis

2021 ◽  
Vol 22 (15) ◽  
pp. 7810
Author(s):  
Shital Kumar Mishra ◽  
Taole Liu ◽  
Han Wang
Keyword(s):  
Pineal Gland ◽  
Noncoding Rna ◽  
Time Course ◽  
Kegg Pathway ◽  
Experimental Studies ◽  
Three Dimensional ◽  
Bioinformatic Analysis ◽  
Computational Techniques ◽  
Near Future ◽  
Coding Potential

Noncoding RNAs have been known to contribute to a variety of fundamental life processes, such as development, metabolism, and circadian rhythms. However, much remains unrevealed in the huge noncoding RNA datasets, which require further bioinformatic analysis and experimental investigation—and in particular, the coding potential of lncRNAs and the functions of lncRNA-encoded peptides have not been comprehensively studied to date. Through integrating the time-course experimentation with state-of-the-art computational techniques, we studied tens of thousands of zebrafish lncRNAs from our own experiments and from a published study including time-series transcriptome analyses of the testis and the pineal gland. Rhythmicity analysis of these data revealed approximately 700 rhythmically expressed lncRNAs from the pineal gland and the testis, and their GO, COG, and KEGG pathway functions were analyzed. Comparative and conservative analyses determined 14 rhythmically expressed lncRNAs shared between both the pineal gland and the testis, and 15 pineal gland lncRNAs as well as 3 testis lncRNAs conserved among zebrafish, mice, and humans. Further, we computationally analyzed the conserved lncRNA-encoded peptides, and revealed three pineal gland and one testis lncRNA-encoded peptides conserved among these three species, which were further investigated for their three-dimensional (3D) structures and potential functions. Our computational findings provided novel annotations and regulatory mechanisms for hundreds of rhythmically expressed pineal gland and testis lncRNAs in zebrafish, and set the stage for their experimental studies in the near future.

Time Series Analysis of Transmesothelial Invasion by Endometrial Stromal and Epithelial Cells Using Three-dimensional Confocal Microscopy

2001 ◽  
Vol 7 (S2) ◽  
pp. 580-581
Author(s):  
CA Witz ◽  
S Cho ◽  
VE Centonze ◽  
IA Montoya-Rodriguez ◽  
RS Schenken
Keyword(s):  
Epithelial Cells ◽  
Stromal Cells ◽  
Time Course ◽  
Three Dimensional ◽  
Collagen Iv ◽  
Mesothelial Cells ◽  
Endometrial Stromal Cells ◽  
Human Collagen ◽  
Endometrial Epithelial Cells

Using human peritoneal explants, we have previously demonstrated that endometrial stromal cells (ESCs) and endometrial epithelial cells (EECs) attach to intact mesothelium. Attachment occurs within one hour and mesothelial invasion occurs within 18 hours (Figure 1). We have also demonstrated that, in vivo, the mesothelium overlies a continuous layer of collagen IV (Col IV).More recently we have used CLSM, to study the mechanism and time course of ESC and EEC attachment and invasion through mesothelial monolayers. in these studies, CellTracker® dyes were used to label cells. Mesothelial cells were labeled with chloromethylbenzoylaminotetramethylrhodamine (CellTracker Orange). Mesothelial cells were then plated on human collagen IV coated, laser etched coverslips. Mesothelial cells were cultured to subconfluence. ESCs and EECs, labeled with chloromethylfluorscein diacetate (CellTracker Green) were plated on the mesothelial monolayers. Cultures were examined at 1, 6, 12 and 24 hours with simultaneous differential interference contrast and CLSM.

scholarly journals Research on the Computed Tomography Pebble Flow Detecting System for HTR-PM

2017 ◽  
Vol 2017 ◽  
pp. 1-13
Author(s):  
Xin Wan ◽  
Ximing Liu ◽  
Jichen Miao ◽  
Peng Cong ◽  
Yuai Zhang ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Three Dimensional ◽  
Helical Ct ◽  
Design Parameters ◽  
Three Dimensional Model ◽  
Safe Operation ◽  
Cross Sectional ◽  
Ct System ◽  
Near Future ◽  
Pebble Flow

Pebble dynamics is important for the safe operation of pebble-bed high temperature gas-cooled reactors and is a complicated problem of great concern. To investigate it more authentically, a computed tomography pebble flow detecting (CT-PFD) system has been constructed, in which a three-dimensional model is simulated according to the ratio of 1 : 5 with the core of HTR-PM. A multislice helical CT is utilized to acquire the reconstructed cross-sectional images of simulated pebbles, among which special tracer pebbles are designed to indicate pebble flow. Tracer pebbles can be recognized from many other background pebbles because of their heavy kernels that can be resolved in CT images. The detecting principle and design parameters of the system were demonstrated by a verification experiment on an existing CT system in this paper. Algorithms to automatically locate the three-dimensional coordinates of tracer pebbles and to rebuild the trajectory of each tracer pebble were presented and verified. The proposed pebble-detecting and tracking technique described in this paper will be implemented in the near future.

scholarly journals Pineal gland transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in STH sheep with two FecB genotypes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Chunyan Li ◽  
Xiaoyun He ◽  
Zijun Zhang ◽  
Chunhuan Ren ◽  
Mingxing Chu
Keyword(s):  
Pineal Gland ◽  
Expression Pattern ◽  
Noncoding Rna ◽  
Target Genes ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Rna Seq ◽  
Important Regulator ◽  
Gsh Metabolism ◽  
Transcriptome Expression

Abstract Background Long noncoding RNA (lncRNA) has been identified as important regulator in hypothalamic-pituitary-ovarian axis associated with sheep prolificacy. However, little is known of their expression pattern and potential roles in the pineal gland of sheep. Herein, RNA-Seq was used to detect transcriptome expression pattern in pineal gland between follicular phase (FP) and luteal phase (LP) in FecBBB (MM) and FecB++ (ww) STH sheep, respectively, and differentially expressed (DE) lncRNAs and mRNAs associated with reproduction were identified. Results Overall, 135 DE lncRNAs and 1360 DE mRNAs in pineal gland between MM and ww sheep were screened. Wherein, 39 DE lncRNAs and 764 DE mRNAs were identified (FP vs LP) in MM sheep, 96 DE lncRNAs and 596 DE mRNAs were identified (FP vs LP) in ww sheep. Moreover, GO and KEGG enrichment analysis indicated that the targets of DE lncRNAs and DE mRNAs were annotated to multiple biological processes such as phototransduction, circadian rhythm, melanogenesis, GSH metabolism and steroid biosynthesis, which directly or indirectly participate in hormone activities to affect sheep reproductive performance. Additionally, co-expression of lncRNAs-mRNAs and the network construction were performed based on correlation analysis, DE lncRNAs can modulate target genes involved in related pathways to affect sheep fecundity. Specifically, XLOC_466330, XLOC_532771, XLOC_028449 targeting RRM2B and GSTK1, XLOC_391199 targeting STMN1, XLOC_503926 targeting RAG2, XLOC_187711 targeting DLG4 were included. Conclusion All of these differential lncRNAs and mRNAs expression profiles in pineal gland provide a novel resource for elucidating regulatory mechanism underlying STH sheep prolificacy.

scholarly journals Targeting hepatocyte growth factor in epithelial–stromal interactions in an in vitro experimental model of human periodontitis

Odontology ◽  
2021 ◽  
Author(s):  
Yoko Yamaguchi ◽  
Akira Saito ◽  
Masafumi Horie ◽  
Akira Aoki ◽  
Patrick Micke ◽  
...  
Keyword(s):  
Growth Factor ◽  
Hepatocyte Growth Factor ◽  
Experimental Studies ◽  
Three Dimensional ◽  
Collagen Gel ◽  
Neutralizing Antibody ◽  
Chronic Inflammatory Disease ◽  
Collagen Degradation ◽  
Hepatocyte Growth

AbstractPeriodontitis is a chronic inflammatory disease leading to progressive connective tissue degradation and loss of the tooth-supporting bone. Clinical and experimental studies suggest that hepatocyte growth factor (HGF) is involved in the dysregulated fibroblast–epithelial cell interactions in periodontitis. The aim of this study was to explore effects of HGF to impact fibroblast-induced collagen degradation. A patient-derived experimental cell culture model of periodontitis was applied. Primary human epithelial cells and fibroblasts isolated from periodontitis-affected gingiva were co-cultured in a three-dimensional collagen gel. The effects of HGF neutralizing antibody on collagen gel degradation were tested and transcriptome analyses were performed. HGF neutralizing antibody attenuated collagen degradation and elicited expression changes of genes related to extracellular matrix (ECM) and cell adhesion, indicating that HGF signaling inhibition leads to extensive impact on cell–cell and cell–ECM interactions. Our study highlights a potential role of HGF in periodontitis. Antagonizing HGF signaling by a neutralizing antibody may represent a novel approach for periodontitis treatment.

Use of ionic currents to identify and estimate parameters in models of channel blockade

1990 ◽  
Vol 259 (2) ◽  
pp. H626-H634
Author(s):  
C. F. Starmer ◽  
V. V. Nesterenko ◽  
F. R. Gilliam ◽  
A. O. Grant
Keyword(s):  
Time Course ◽  
Experimental Studies ◽  
Ionic Currents ◽  
Blocking Agent ◽  
Model Parameters ◽  
Protein Conformations ◽  
Channel Blockade ◽  
Channel Blocking ◽  
Individual Contributions ◽  
Modulated Receptor

Models of ion channel blockade are frequently validated with observations of ionic currents resulting from electrical or chemical stimulation. Model parameters for some models (modulated receptor hypothesis) cannot be uniquely determined from ionic currents. The time course of ionic currents reflects the activation (fraction of available channels that conduct in the presence of excitation) and availability of channels (the ability of the protein to make a transition to a conducting conformation and where this conformation is not complexed with a drug). In the presence of a channel blocking agent, the voltage dependence of availability appears modified and has been interpreted as evidence that drug-complexed channels exhibit modified transition rates between channel protein conformations. Because blockade and availability both modify ionic currents, their individual contributions to macroscopic conductance cannot be resolved from ionic currents except when constant affinity binding to a bindable site is assumed. Experimental studies of nimodipine block of calcium channels and lidocaine block of sodium channels illustrate these concepts.

scholarly journals Numerical and Experimental Studies on a Three-Dimensional Numerical Wave Tank

IEEE Access ◽  
2018 ◽  
Vol 6 ◽  
pp. 6585-6593 ◽  
Author(s):  
Xiaojie Tian ◽  
Qingyang Wang ◽  
Guijie Liu ◽  
Wei Deng ◽  
Zhiming Gao
Keyword(s):  
Experimental Studies ◽  
Three Dimensional ◽  
Numerical Wave Tank ◽  
Wave Tank ◽  
Numerical Wave

Numerical Modeling of Tube Hydropiercing Using Phenomenological and Micro-Mechanical Damage Criteria

2013 ◽  
Vol 549 ◽  
pp. 172-179 ◽  
Author(s):  
Amir Hassannejadasl ◽  
Daniel E. Green
Keyword(s):  
Experimental Studies ◽  
Three Dimensional ◽  
Equivalent Plastic Strain ◽  
Mechanical Damage ◽  
High Strength ◽  
Dimensional Finite Element ◽  
Steel Dp600 ◽  
Three Dimensional Finite Element ◽  
Jc Model ◽  
Damage Criteria

Hydropiercing is an efficient way of piercing holes in mass produced hydroformed parts with complex geometries. By driving piercing punches radially into a hydroformed and fully pressurized tube, holes will be pierced and extruded into the tube-wall. Recent experimental studies have shown that the formability of advanced high strength steel (AHSS) tubes can be increased with the application of internal pressure. In this study, three-dimensional finite element simulations of a tube hydropiercing process of a dual phase steel (DP600) were performed in LS-DYNA, using phenomenological, micromechanical and combined damage criteria. Damage was included in the numerical analysis by applying constant equivalent plastic strain (CEPS), the Gurson-Tvergaard-Needleman (GTN), and the Extended GTN (GTN+JC) model. In order to calibrate the parameters in each model, a specialized hole-piercing fixture was designed and piercing tests were carried out on non-pressurized tube specimens. Of the various ductile fracture criteria, the results predicted with the GTN+JC model, such as the punch load-displacement, the roll-over depth, and the quality of the clearance zone correlated the best with the experimental data.

Fracture Mechanics of Thin Plates and Shells Under Combined Membrane, Bending, and Twisting Loads

2005 ◽  
Vol 58 (1) ◽  
pp. 37-48 ◽  
Author(s):  
Alan T. Zehnder ◽  
Mark J. Viz
Keyword(s):  
Fracture Mechanics ◽  
Plate Theory ◽  
Experimental Studies ◽  
Three Dimensional ◽  
Crack Tip ◽  
Thin Plates ◽  
Element Analysis ◽  
Crack Tip Fields ◽  
Plates And Shells ◽  
Membrane Bending

The fracture mechanics of plates and shells under membrane, bending, twisting, and shearing loads are reviewed, starting with the crack tip fields for plane stress, Kirchhoff, and Reissner theories. The energy release rate for each of these theories is calculated and is used to determine the relation between the Kirchhoff and Reissner theories for thin plates. For thicker plates, this relationship is explored using three-dimensional finite element analysis. The validity of the application of two-dimensional (plate theory) solutions to actual three-dimensional objects is analyzed and discussed. Crack tip fields in plates undergoing large deflection are analyzed using von Ka´rma´n theory. Solutions for cracked shells are discussed as well. A number of computational methods for determining stress intensity factors in plates and shells are discussed. Applications of these computational approaches to aircraft structures are examined. The relatively few experimental studies of fracture in plates under bending and twisting loads are also reviewed. There are 101 references cited in this article.

Noninvasive three-dimensional electrocardiographic imaging of ventricular activation sequence

2005 ◽  
Vol 289 (6) ◽  
pp. H2724-H2732 ◽  
Author(s):  
Xin Zhang ◽  
Indiresha Ramachandra ◽  
Zhongming Liu ◽  
Basharat Muneer ◽  
Steven M. Pogwizd ◽  
...  
Keyword(s):  
Surface Potential ◽  
Body Surface ◽  
Cardiac Arrhythmias ◽  
Experimental Studies ◽  
Three Dimensional ◽  
Electrocardiographic Imaging ◽  
Ventricular Activation ◽  
Body Surface Potential ◽  
Life Threatening ◽  
Activation Sequence

Imaging the myocardial activation sequence is critical for improved diagnosis and treatment of life-threatening cardiac arrhythmias. It is desirable to reveal the underlying cardiac electrical activity throughout the three-dimensional (3-D) myocardium (rather than just the endocardial or epicardial surface) from noninvasive body surface potential measurements. A new 3-D electrocardiographic imaging technique (3-DEIT) based on the boundary element method (BEM) and multiobjective nonlinear optimization has been applied to reconstruct the cardiac activation sequences from body surface potential maps. Ultrafast computerized tomography scanning was performed for subsequent construction of the torso and heart models. Experimental studies were then conducted, during left and right ventricular pacing, in which noninvasive assessment of ventricular activation sequence by means of 3-DEIT was performed simultaneously with 3-D intracardiac mapping (up to 200 intramural sites) using specially designed plunge-needle electrodes in closed-chest rabbits. Estimated activation sequences from 3-DEIT were in good agreement with those constructed from simultaneously recorded intracardiac electrograms in the same animals. Averaged over 100 paced beats (from a total of 10 pacing sites), total activation times were comparable (53.3 ± 8.1 vs. 49.8 ± 5.2 ms), the localization error of site of initiation of activation was 5.73 ± 1.77 mm, and the relative error between the estimated and measured activation sequences was 0.32 ± 0.06. The present experimental results demonstrate that the 3-D paced ventricular activation sequence can be reconstructed by using noninvasive multisite body surface electrocardiographic measurements and imaging of heart-torso geometry. This new 3-D electrocardiographic imaging modality has the potential to guide catheter-based ablative interventions for the treatment of life-threatening cardiac arrhythmias.

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