scholarly journals RNA promotes the formation of spatial compartments in the nucleus

2020 ◽  
Author(s):  
Sofia A. Quinodoz ◽  
Prashant Bhat ◽  
Noah Ollikainen ◽  
Joanna W. Jachowicz ◽  
Abhik K. Banerjee ◽  
...  
Keyword(s):  
Nuclear Structure ◽  
Ribosome Biogenesis ◽  
Three Dimensional ◽  
Spatial Proximity ◽  
High Concentration ◽  
3D Structures ◽  
Nuclear Compartments ◽  
Regulatory Processes ◽  
Wide Range ◽  
Heterochromatin Assembly

SUMMARYThe nucleus is a highly organized arrangement of RNA, DNA, and protein molecules that are compartmentalized within three-dimensional (3D) structures involved in shared functional and regulatory processes. Although RNA has long been proposed to play a global role in organizing nuclear structure, exploring the role of RNA in shaping nuclear structure has remained a challenge because no existing methods can simultaneously measure RNA-RNA, RNA-DNA, and DNA-DNA contacts within 3D structures. To address this, we developed RNA & DNA SPRITE (RD-SPRITE) to comprehensively map the location of all RNAs relative to DNA and other RNAs. Using this approach, we identify many RNAs that are localized near their transcriptional loci (RNA-DNA) together with other diffusible ncRNAs (RNA-RNA) within higher-order DNA structures (DNA-DNA). These RNA-chromatin compartments span three major classes of nuclear functions: RNA processing (including ribosome biogenesis, mRNA splicing, snRNA biogenesis, and histone mRNA processing), heterochromatin assembly, and gene regulation. More generally, we identify hundreds of ncRNAs that form stable nuclear compartments in spatial proximity to their transcriptional loci. We find that dozens of nuclear compartments require RNA to guide protein regulators into these 3D structures, and focusing on several ncRNAs, we show that these ncRNAs specifically regulate heterochromatin assembly and the expression of genes contained within these compartments. Together, our results demonstrate a unique mechanism by which RNA acts to shape nuclear structure by forming high concentration territories immediately upon transcription, binding to diffusible regulators, and guiding them into spatial compartments to regulate a wide range of essential nuclear functions.

scholarly journals Viscoelastic Characteristics of Mechanically Assembled Three-Dimensional Structures Formed by Compressive Buckling

2018 ◽  
Vol 85 (12) ◽  
Author(s):  
Haibo Li ◽  
Xi Wang ◽  
Feng Zhu ◽  
Xin Ning ◽  
Heling Wang ◽  
...  
Keyword(s):  
Compressive Strain ◽  
Scaling Law ◽  
Three Dimensional ◽  
Band Width ◽  
Viscoelastic Damping ◽  
Clear Understanding ◽  
3D Structures ◽  
Damping Effect ◽  
Wide Range ◽  
Compressive Buckling

Vibrational microplatforms that exploit complex three-dimensional (3D) architectures assembled via the controlled compressive buckling technique represent promising candidates in 3D micro-electromechanical systems (MEMS), with a wide range of applications such as oscillators, actuators, energy harvesters, etc. However, the accuracy and efficiency of such 3D MEMS might be significantly reduced by the viscoelastic damping effect that arises from material viscosity. Therefore, a clear understanding and characterization of such effects are essential to progress in this area. Here, we present a study on the viscoelastic damping effect in complex 3D structures via an analytical model and finite element analysis (FEA). By adopting the Kelvin–Voigt model to characterize the material viscoelasticity, an analytical solution is derived for the vibration of a buckled ribbon. This solution then yields a scaling law for the half-band width or the quality factor of vibration that can be extended to other classes of complex 3D structures, as validated by FEA. The scaling law reveals the dependence of the half-band width on the geometries of 3D structures and the compressive strain. The results could serve as guidelines to design novel 3D vibrational microplatforms for applications in MEMS and other areas of technology.

scholarly journals Modeling structure, stability and flexibility of double-stranded RNAs in salt solutions

2018 ◽  
Author(s):  
L. Jin ◽  
Y.Z. Shi ◽  
C.J. Feng ◽  
Y.L. Tan ◽  
Z.J. Tan
Keyword(s):  
Electrostatic Potential ◽  
Cell Metabolism ◽  
3D Structure ◽  
Three Dimensional ◽  
Coarse Grained ◽  
Structure Stability ◽  
Salt Solutions ◽  
3D Structures ◽  
Coarse Grained Model ◽  
Wide Range

AbstractDouble-stranded (ds) RNAs play essential roles in many processes of cell metabolism. The knowledge of three-dimensional (3D) structure, stability and flexibility of dsRNAs in salt solutions is important for understanding their biological functions. In this work, we further developed our previously proposed coarse-grained model to predict 3D structure, stability and flexibility for dsRNAs in monovalent and divalent ion solutions through involving an implicit structure-based electrostatic potential. The model can make reliable predictions for 3D structures of extensive dsRNAs with/without bulge/internal loops from their sequences, and the involvement of the structure-based electrostatic potential and corresponding ion condition can improve the predictions on 3D structures of dsRNAs in ion solutions. Furthermore, the model can make good predictions on thermal stability for extensive dsRNAs over the wide range of monovalent/divalent ion concentrations, and our analyses show that thermally unfolding pathway of a dsRNA is generally dependent on its length as well as its sequence. In addition, the model was employed to examine the salt-dependent flexibility of a dsRNA helix and the calculated salt-dependent persistence lengths are in good accordance with experiments.

From Levinthal’s Paradox to the Effects of Cell Environmental Perturbation on Protein Folding

2020 ◽  
Vol 26 (42) ◽  
pp. 7537-7554 ◽  
Author(s):  
Juan Zeng ◽  
Zunnan Huang
Keyword(s):  
Protein Folding ◽  
Posttranslational Modifications ◽  
Three Dimensional ◽  
Rational Drug Design ◽  
Basic Knowledge ◽  
Sequence Evolution ◽  
3D Structures ◽  
Folding Mechanism ◽  
Cellular Environment ◽  
Environment Temperature

Background: The rapidly increasing number of known protein sequences calls for more efficient methods to predict the Three-Dimensional (3D) structures of proteins, thus providing basic knowledge for rational drug design. Understanding the folding mechanism of proteins is valuable for predicting their 3D structures and for designing proteins with new functions and medicinal applications. Levinthal’s paradox is that although the astronomical number of conformations possible even for proteins as small as 100 residues cannot be fully sampled, proteins in nature normally fold into the native state within timescales ranging from microseconds to hours. These conflicting results reveal that there are factors in organisms that can assist in protein folding. Methods: In this paper, we selected a crowded cell-like environment and temperature, and the top three Posttranslational Modifications (PTMs) as examples to show that Levinthal’s paradox does not reflect the folding mechanism of proteins. We then revealed the effects of these factors on protein folding. Results: The results summarized in this review indicate that a crowded cell-like environment, temperature, and the top three PTMs reshape the Free Energy Landscapes (FELs) of proteins, thereby regulating the folding process. The balance between entropy and enthalpy is the key to understanding the effect of the crowded cell-like environment and PTMs on protein folding. In addition, the stability/flexibility of proteins is regulated by temperature. Conclusion: This paper concludes that the cellular environment could directly intervene in protein folding. The long-term interactions of the cellular environment and sequence evolution may enable proteins to fold efficiently. Therefore, to correctly understand the folding mechanism of proteins, the effect of the cellular environment on protein folding should be considered.

Turbulent three-dimensional dielectric electrohydrodynamic convection between two plates

2012 ◽  
Vol 696 ◽  
pp. 228-262 ◽  
Author(s):  
A. Kourmatzis ◽  
J. S. Shrimpton
Keyword(s):  
Spatial Data ◽  
Three Dimensional ◽  
Reynolds Numbers ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Energy Budgets ◽  
Turbulent Regime ◽  
Scalar Flux ◽  
Wide Range ◽  
Scalar Variance

AbstractThe fundamental mechanisms responsible for the creation of electrohydrodynamically driven roll structures in free electroconvection between two plates are analysed with reference to traditional Rayleigh–Bénard convection (RBC). Previously available knowledge limited to two dimensions is extended to three-dimensions, and a wide range of electric Reynolds numbers is analysed, extending into a fully inherently three-dimensional turbulent regime. Results reveal that structures appearing in three-dimensional electrohydrodynamics (EHD) are similar to those observed for RBC, and while two-dimensional EHD results bear some similarities with the three-dimensional results there are distinct differences. Analysis of two-point correlations and integral length scales show that full three-dimensional electroconvection is more chaotic than in two dimensions and this is also noted by qualitatively observing the roll structures that arise for both low (${\mathit{Re}}_{E} = 1$) and high electric Reynolds numbers (up to ${\mathit{Re}}_{E} = 120$). Furthermore, calculations of mean profiles and second-order moments along with energy budgets and spectra have examined the validity of neglecting the fluctuating electric field ${ E}_{i}^{\ensuremath{\prime} } $ in the Reynolds-averaged EHD equations and provide insight into the generation and transport mechanisms of turbulent EHD. Spectral and spatial data clearly indicate how fluctuating energy is transferred from electrical to hydrodynamic forms, on moving through the domain away from the charging electrode. It is shown that ${ E}_{i}^{\ensuremath{\prime} } $ is not negligible close to the walls and terms acting as sources and sinks in the turbulent kinetic energy, turbulent scalar flux and turbulent scalar variance equations are examined. Profiles of hydrodynamic terms in the budgets resemble those in the literature for RBC; however there are terms specific to EHD that are significant, indicating that the transfer of energy in EHD is also attributed to further electrodynamic terms and a strong coupling exists between the charge flux and variance, due to the ionic drift term.

scholarly journals Application of Dendrimers for Treating Parasitic Diseases

Pharmaceutics ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 343
Author(s):  
Veronica Folliero ◽  
Carla Zannella ◽  
Annalisa Chianese ◽  
Debora Stelitano ◽  
Annalisa Ambrosino ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Water Solubility ◽  
Parasitic Infection ◽  
Three Dimensional ◽  
Medical Knowledge ◽  
High Ratio ◽  
Molecular Volume ◽  
Parasitic Infections ◽  
Parasitic Diseases ◽  
Wide Range

Despite advances in medical knowledge, parasitic diseases remain a significant global health burden and their pharmacological treatment is often hampered by drug toxicity. Therefore, drug delivery systems may provide useful advantages when used in combination with conventional therapeutic compounds. Dendrimers are three-dimensional polymeric structures, characterized by a central core, branches and terminal functional groups. These nanostructures are known for their defined structure, great water solubility, biocompatibility and high encapsulation ability against a wide range of molecules. Furthermore, the high ratio between terminal groups and molecular volume render them a hopeful vector for drug delivery. These nanostructures offer several advantages compared to conventional drugs for the treatment of parasitic infection. Dendrimers deliver drugs to target sites with reduced dosage, solving side effects that occur with accepted marketed drugs. In recent years, extensive progress has been made towards the use of dendrimers for therapeutic, prophylactic and diagnostic purposes for the management of parasitic infections. The present review highlights the potential of several dendrimers in the management of parasitic diseases.

scholarly journals An Overview on the Rheology, Mechanical Properties, Durability, 3D Printing, and Microstructural Performance of Nanomaterials in Cementitious Composites

Materials ◽  
2021 ◽  
Vol 14 (11) ◽  
pp. 2950
Author(s):  
Hongwei Song ◽  
Xinle Li
Keyword(s):  
Mechanical Properties ◽  
3D Printing ◽  
Three Dimensional ◽  
Cementitious Materials ◽  
Research Area ◽  
Cementitious Composites ◽  
Split Tensile Strength ◽  
Contour Crafting ◽  
Wide Range ◽  
Active Research

The most active research area is nanotechnology in cementitious composites, which has a wide range of applications and has achieved popularity over the last three decades. Nanoparticles (NPs) have emerged as possible materials to be used in the field of civil engineering. Previous research has concentrated on evaluating the effect of different NPs in cementitious materials to alter material characteristics. In order to provide a broad understanding of how nanomaterials (NMs) can be used, this paper critically evaluates previous research on the influence of rheology, mechanical properties, durability, 3D printing, and microstructural performance on cementitious materials. The flow properties of fresh cementitious composites can be measured using rheology and slump. Mechanical properties such as compressive, flexural, and split tensile strength reveal hardened properties. The necessary tests for determining a NM’s durability in concrete are shrinkage, pore structure and porosity, and permeability. The advent of modern 3D printing technologies is suitable for structural printing, such as contour crafting and binder jetting. Three-dimensional (3D) printing has opened up new avenues for the building and construction industry to become more digital. Regardless of the material science, a range of problems must be tackled, including developing smart cementitious composites suitable for 3D structural printing. According to the scanning electron microscopy results, the addition of NMs to cementitious materials results in a denser and improved microstructure with more hydration products. This paper provides valuable information and details about the rheology, mechanical properties, durability, 3D printing, and microstructural performance of cementitious materials with NMs and encourages further research.

scholarly journals Polymer cyclization for the emergence of hierarchical nanostructures

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chaojian Chen ◽  
Manjesh Kumar Singh ◽  
Katrin Wunderlich ◽  
Sean Harvey ◽  
Colette J. Whitfield ◽  
...  
Keyword(s):  
Self Assembly ◽  
Three Dimensional ◽  
Hierarchical Structures ◽  
Structural Similarity ◽  
Vital Role ◽  
Nanomaterial Synthesis ◽  
Wide Range ◽  
Linear Poly ◽  
Polymer Folding ◽  
Dynamics Simulations

AbstractThe creation of synthetic polymer nanoobjects with well-defined hierarchical structures is important for a wide range of applications such as nanomaterial synthesis, catalysis, and therapeutics. Inspired by the programmability and precise three-dimensional architectures of biomolecules, here we demonstrate the strategy of fabricating controlled hierarchical structures through self-assembly of folded synthetic polymers. Linear poly(2-hydroxyethyl methacrylate) of different lengths are folded into cyclic polymers and their self-assembly into hierarchical structures is elucidated by various experimental techniques and molecular dynamics simulations. Based on their structural similarity, macrocyclic brush polymers with amphiphilic block side chains are synthesized, which can self-assemble into wormlike and higher-ordered structures. Our work points out the vital role of polymer folding in macromolecular self-assembly and establishes a versatile approach for constructing biomimetic hierarchical assemblies.

scholarly journals A developmentally descriptive method for quantifying shape in gastropod shells

2020 ◽  
Vol 17 (163) ◽  
pp. 20190721
Author(s):  
J. Larsson ◽  
A. M. Westram ◽  
S. Bengmark ◽  
T. Lundh ◽  
R. K. Butlin
Keyword(s):  
Empirical Studies ◽  
Three Dimensional ◽  
Shell Shape ◽  
Large Set ◽  
Littorina Saxatilis ◽  
Shape Variation ◽  
Gastropod Shell ◽  
Geometric Morphometric ◽  
Wide Range ◽  
Descriptive Method

The growth of snail shells can be described by simple mathematical rules. Variation in a few parameters can explain much of the diversity of shell shapes seen in nature. However, empirical studies of gastropod shell shape variation typically use geometric morphometric approaches, which do not capture this growth pattern. We have developed a way to infer a set of developmentally descriptive shape parameters based on three-dimensional logarithmic helicospiral growth and using landmarks from two-dimensional shell images as input. We demonstrate the utility of this approach, and compare it to the geometric morphometric approach, using a large set of Littorina saxatilis shells in which locally adapted populations differ in shape. Our method can be modified easily to make it applicable to a wide range of shell forms, which would allow for investigations of the similarities and differences between and within many different species of gastropods.

scholarly journals A Review on Biosensors and Recent Development of Nanostructured Materials-Enabled Biosensors

Sensors ◽  
2021 ◽  
Vol 21 (4) ◽  
pp. 1109
Author(s):  
Varnakavi. Naresh ◽  
Nohyun Lee
Keyword(s):  
High Surface ◽  
Three Dimensional ◽  
Biological Response ◽  
Volume Ratio ◽  
Recent Decade ◽  
Disease Diagnosis ◽  
Electrical Signal ◽  
Detection Sensitivity ◽  
Wide Range ◽  
Color Tunability

A biosensor is an integrated receptor-transducer device, which can convert a biological response into an electrical signal. The design and development of biosensors have taken a center stage for researchers or scientists in the recent decade owing to the wide range of biosensor applications, such as health care and disease diagnosis, environmental monitoring, water and food quality monitoring, and drug delivery. The main challenges involved in the biosensor progress are (i) the efficient capturing of biorecognition signals and the transformation of these signals into electrochemical, electrical, optical, gravimetric, or acoustic signals (transduction process), (ii) enhancing transducer performance i.e., increasing sensitivity, shorter response time, reproducibility, and low detection limits even to detect individual molecules, and (iii) miniaturization of the biosensing devices using micro-and nano-fabrication technologies. Those challenges can be met through the integration of sensing technology with nanomaterials, which range from zero- to three-dimensional, possessing a high surface-to-volume ratio, good conductivities, shock-bearing abilities, and color tunability. Nanomaterials (NMs) employed in the fabrication and nanobiosensors include nanoparticles (NPs) (high stability and high carrier capacity), nanowires (NWs) and nanorods (NRs) (capable of high detection sensitivity), carbon nanotubes (CNTs) (large surface area, high electrical and thermal conductivity), and quantum dots (QDs) (color tunability). Furthermore, these nanomaterials can themselves act as transduction elements. This review summarizes the evolution of biosensors, the types of biosensors based on their receptors, transducers, and modern approaches employed in biosensors using nanomaterials such as NPs (e.g., noble metal NPs and metal oxide NPs), NWs, NRs, CNTs, QDs, and dendrimers and their recent advancement in biosensing technology with the expansion of nanotechnology.

scholarly journals Pulsed Electromagnetic Cross-Well Exploration for Monitoring Permafrost and Examining the Processes of Its Geocryological Changes

Geosciences ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 60
Author(s):  
Viacheslav Glinskikh ◽  
Oleg Nechaev ◽  
Igor Mikhaylov ◽  
Kirill Danilovskiy ◽  
Vladimir Olenchenko
Keyword(s):  
High Performance ◽  
Geophysical Methods ◽  
Three Dimensional ◽  
High Sensitivity ◽  
Data Interpretation ◽  
Industrial Facilities ◽  
Wide Range ◽  
Vector Finite Element ◽  
A New Technique ◽  
Pulsed Electromagnetic

This paper is dedicated to the topical problem of examining permafrost’s state and the processes of its geocryological changes by means of geophysical methods. To monitor the cryolithozone, we proposed and scientifically substantiated a new technique of pulsed electromagnetic cross-well sounding. Based on the vector finite-element method, we created a mathematical model of the cross-well sounding process with a pulsed source in a three-dimensional spatially heterogeneous medium. A high-performance parallel computing algorithm was developed and verified. Through realistic geoelectric models of permafrost with a talik under a highway, constructed following the results of electrotomography field data interpretation, we numerically simulated the pulsed sounding on the computing resources of the Siberian Supercomputer Center of SB RAS. The simulation results suggest the proposed system of pulsed electromagnetic cross-well monitoring to be characterized by a high sensitivity to the presence and dimensions of the talik. The devised approach can be oriented to addressing a wide range of issues related to monitoring permafrost rocks under civil and industrial facilities, buildings, and constructions.

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