RNA pseudoknots and the regulation of protein synthesis

2008 ◽  
Vol 36 (4) ◽  
pp. 684-689 ◽  
Author(s):  
Ian Brierley ◽  
Robert J.C. Gilbert ◽  
Simon Pennell
Keyword(s):  
Protein Synthesis ◽  
Three Dimensional ◽  
Biological Processes ◽  
Structural Elements ◽  
Base Pairs ◽  
Internal Ribosome Entry ◽  
Diverse Range ◽  
Rna Pseudoknots ◽  
Single Stranded Region ◽  
Almost All

RNA pseudoknots are structural elements found in almost all classes of RNA. Pseudoknots form when a single-stranded region in the loop of a hairpin base-pairs with a stretch of complementary nucleotides elsewhere in the RNA chain. This simple folding strategy is capable of generating a large number of stable three-dimensional folds that display a diverse range of highly specific functions in a variety of biological processes. The present review focuses on pseudoknots that act in the regulation of protein synthesis using cellular and viral examples to illustrate their versatility. Emphasis is placed on structurally well-defined pseudoknots that play a role in internal ribosome entry, autoregulation of initiation, ribosomal frameshifting during elongation and trans-translation.

Designing TIMP (tissue inhibitor of metalloproteinases) variants that are selective metalloproteinase inhibitors

2003 ◽  
Vol 70 ◽  
pp. 201-212 ◽  
Author(s):  
Hideaki Nagase ◽  
Keith Brew
Keyword(s):  
Three Dimensional ◽  
Therapeutic Interventions ◽  
Tissue Inhibitors Of Metalloproteinases ◽  
Structural Basis ◽  
Structural Elements ◽  
Ridge Structure ◽  
Extracellular Matrix Components ◽  
Metalloproteinase Inhibitors ◽  
The Matrix ◽  
A Disintegrin And Metalloproteinase

The tissue inhibitors of metalloproteinases (TIMPs) are endogenous inhibitors of the matrix metalloproteinases (MMPs), enzymes that play central roles in the degradation of extracellular matrix components. The balance between MMPs and TIMPs is important in the maintenance of tissues, and its disruption affects tissue homoeostasis. Four related TIMPs (TIMP-1 to TIMP-4) can each form a complex with MMPs in a 1:1 stoichiometry with high affinity, but their inhibitory activities towards different MMPs are not particularly selective. The three-dimensional structures of TIMP-MMP complexes reveal that TIMPs have an extended ridge structure that slots into the active site of MMPs. Mutation of three separate residues in the ridge, at positions 2, 4 and 68 in the amino acid sequence of the N-terminal inhibitory domain of TIMP-1 (N-TIMP-1), separately and in combination has produced N-TIMP-1 variants with higher binding affinity and specificity for individual MMPs. TIMP-3 is unique in that it inhibits not only MMPs, but also several ADAM (a disintegrin and metalloproteinase) and ADAMTS (ADAM with thrombospondin motifs) metalloproteinases. Inhibition of the latter groups of metalloproteinases, as exemplified with ADAMTS-4 (aggrecanase 1), requires additional structural elements in TIMP-3 that have not yet been identified. Knowledge of the structural basis of the inhibitory action of TIMPs will facilitate the design of selective TIMP variants for investigating the biological roles of specific MMPs and for developing therapeutic interventions for MMP-associated diseases.

Electrical Capacitance Volume Tomography (ECVT) for industrial and medical applications-An Overview

2015 ◽  
Vol 11 (1) ◽  
pp. 2897-2908
Author(s):  
Mohammed S.Aljohani
Keyword(s):  
Imaging Technique ◽  
Three Dimensional ◽  
Biological Processes ◽  
Electrical Capacitance ◽  
Image Reconstruction Techniques ◽  
Phase Dynamics ◽  
Non Invasive ◽  
Electrical Capacitance Volume Tomography ◽  
And Performance ◽  
Optimization And Performance

Tomography is a non-invasive, non-intrusive imaging technique allowing the visualization of phase dynamics in industrial and biological processes. This article reviews progress in Electrical Capacitance Volume Tomography (ECVT). ECVT is a direct 3D visualizing technique, unlike three-dimensional imaging, which is based on stacking 2D images to obtain an interpolated 3D image. ECVT has recently matured for real time, non-invasive 3-D monitoring of processes involving materials with strong contrast in dielectric permittivity. In this article, ECVT sensor design, optimization and performance of various sensors seen in literature are summarized. Qualitative Analysis of ECVT image reconstruction techniques has also been presented.

scholarly journals Structural relation matching: an algorithm to identify structural patterns into RNAs and their interactions

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Michela Quadrini
Keyword(s):  
Hydrogen Bonding ◽  
Secondary Structure ◽  
Nucleotide Sequence ◽  
Thermus Thermophilus ◽  
Three Dimensional ◽  
Secondary Structures ◽  
Structural Effect ◽  
Biological Processes ◽  
Structural Pattern ◽  
Rna Molecules

Abstract RNA molecules play crucial roles in various biological processes. Their three-dimensional configurations determine the functions and, in turn, influences the interaction with other molecules. RNAs and their interaction structures, the so-called RNA–RNA interactions, can be abstracted in terms of secondary structures, i.e., a list of the nucleotide bases paired by hydrogen bonding within its nucleotide sequence. Each secondary structure, in turn, can be abstracted into cores and shadows. Both are determined by collapsing nucleotides and arcs properly. We formalize all of these abstractions as arc diagrams, whose arcs determine loops. A secondary structure, represented by an arc diagram, is pseudoknot-free if its arc diagram does not present any crossing among arcs otherwise, it is said pseudoknotted. In this study, we face the problem of identifying a given structural pattern into secondary structures or the associated cores or shadow of both RNAs and RNA–RNA interactions, characterized by arbitrary pseudoknots. These abstractions are mapped into a matrix, whose elements represent the relations among loops. Therefore, we face the problem of taking advantage of matrices and submatrices. The algorithms, implemented in Python, work in polynomial time. We test our approach on a set of 16S ribosomal RNAs with inhibitors of Thermus thermophilus, and we quantify the structural effect of the inhibitors.

scholarly journals 3D Reconstruction of Cultural Heritage Sites as an Educational Approach. The Sanctuary of Delphi

2021 ◽  
Vol 11 (8) ◽  
pp. 3635
Author(s):  
Ioannis Liritzis ◽  
Pantelis Volonakis ◽  
Spyros Vosinakis
Keyword(s):  
University Students ◽  
3D Reconstruction ◽  
Cultural Heritage ◽  
New Technology ◽  
Three Dimensional ◽  
Computer Gaming ◽  
Educational Approach ◽  
Heritage Sites ◽  
3D Environment ◽  
Almost All

In the field of cultural heritage, three-dimensional (3D) reconstruction of monuments is a usual activity for many professionals. The aim in this paper focuses on the new technology educational application combining science, history, and archaeology. Being involved in almost all stages of implementation steps and assessing the level of participation, university students use tools of computer gaming platform and participate in ways of planning the virtual environment which improves their education through e-Learning. The virtual 3D environment is made with different imaging methods (helium-filled balloon, Structure for motion, 3D repository models) and a developmental plan has been designed for use in many future applications. Digital tools were used with 3D reconstructed buildings from the museum archive to Unity 3D for the design. The pilot study of Information Technology work has been employed to introduce cultural heritage and archaeology to university syllabuses. It included students with a questionnaire which has been evaluated accordingly. As a result, the university students were inspired to immerse themselves into the virtual lab, aiming to increasing the level of interaction. The results show a satisfactory learning outcome by an easy to use and real 3D environment, a step forward to fill in needs of contemporary online sustainable learning demands.

scholarly journals Membrane fusion studied by colloidal probes

2021 ◽  
Vol 50 (2) ◽  
pp. 223-237 ◽  
Author(s):  
Hannes Witt ◽  
Filip Savić ◽  
Sarah Verbeek ◽  
Jörn Dietz ◽  
Gesa Tarantola ◽  
...  
Keyword(s):  
Membrane Fusion ◽  
Optical Tweezers ◽  
Three Dimensional ◽  
Biological Processes ◽  
Supported Membranes ◽  
Supported Bilayers ◽  
Force Microscopy ◽  
Advantages And Disadvantages ◽  
Atomic Force ◽  
Colloidal Probes

AbstractMembrane-coated colloidal probes combine the benefits of solid-supported membranes with a more complex three-dimensional geometry. This combination makes them a powerful model system that enables the visualization of dynamic biological processes with high throughput and minimal reliance on fluorescent labels. Here, we want to review recent applications of colloidal probes for the study of membrane fusion. After discussing the advantages and disadvantages of some classical vesicle-based fusion assays, we introduce an assay using optical detection of fusion between membrane-coated glass microspheres in a quasi two-dimensional assembly. Then, we discuss free energy considerations of membrane fusion between supported bilayers, and show how colloidal probes can be combined with atomic force microscopy or optical tweezers to access the fusion process with even greater detail.

scholarly journals Functional Assessment of 12 Rare Allelic CYP2C9 Variants Identified in a Population of 4773 Japanese Individuals

2021 ◽  
Vol 11 (2) ◽  
pp. 94
Author(s):  
Masaki Kumondai ◽  
Akio Ito ◽  
Evelyn Marie Gutiérrez Rico ◽  
Eiji Hishinuma ◽  
Akiko Ueda ◽  
...  
Keyword(s):  
Enzymatic Activity ◽  
Three Dimensional ◽  
Warfarin Dose ◽  
Catalytic Efficiency ◽  
Therapeutic Window ◽  
Wild Type ◽  
Drug Metabolizing Enzyme ◽  
Novel Variants ◽  
Metabolizing Enzyme ◽  
Almost All

Cytochrome P450 2C9 (CYP2C9) is an important drug-metabolizing enzyme that contributes to the metabolism of approximately 15% of clinically used drugs, including warfarin, which is known for its narrow therapeutic window. Interindividual differences in CYP2C9 enzymatic activity caused by CYP2C9 genetic polymorphisms lead to inconsistent treatment responses in patients. Thus, in this study, we characterized the functional differences in CYP2C9 wild-type (CYP2C9.1), CYP2C9.2, CYP2C9.3, and 12 rare novel variants identified in 4773 Japanese individuals. These CYP2C9 variants were heterologously expressed in 293FT cells, and the kinetic parameters (Km, kcat, Vmax, catalytic efficiency, and CLint) of (S)-warfarin 7-hydroxylation and tolbutamide 4-hydroxylation were estimated. From this analysis, almost all novel CYP2C9 variants showed significantly reduced or null enzymatic activity compared with that of the CYP2C9 wild-type. A strong correlation was found in catalytic efficiencies between (S)-warfarin 7-hydroxylation and tolbutamide 4-hydroxylation among all studied CYP2C9 variants. The causes of the observed perturbation in enzyme activity were evaluated by three-dimensional structural modeling. Our findings could clarify a part of discrepancies among genotype–phenotype associations based on the novel CYP2C9 rare allelic variants and could, therefore, improve personalized medicine, including the selection of the appropriate warfarin dose.

A test of airborne, side-looking synthetic-aperture radar in central Newfoundland for geological reconnaissance

1991 ◽  
Vol 28 (2) ◽  
pp. 257-265 ◽  
Author(s):  
D. F. Graham ◽  
D. R. Grant
Keyword(s):  
Surface Roughness ◽  
Synthetic Aperture Radar ◽  
Three Dimensional ◽  
Synthetic Aperture ◽  
Structural Elements ◽  
Terrain Classification ◽  
Regional Trends ◽  
Valuable Complement ◽  
Wide Swath ◽  
Aperture Radar

Side-looking, C-band synthetic-aperture radar (SAR) penetrates cloud and fog, and operates day or night, to produce pseudo-three-dimensional terrain images with enhanced topography and surface roughness. The images, which have a 20 m resolution and cover large areas, have been used to map the regional trends, patterns of lineaments, and terrain types over a 6200 km2 area of complex lithology, structure, and drift cover. Four lineament classes are differentiated. Glacial trends are clear, and bedrock structures (faults, fractures, joints, foliation, and folded bedding) with relief expression at the surface show through the drift as lineaments. They accurately reproduce most known features when compared with bedrock and Quatenary geology maps. Hitherto unrecognized structural elements are revealed. Tones and textures reflect minute surface roughness variations useful in terrain classification. SAR wide-swath-mode imagery is thus a valuable complement to aerial photography, and is superior in revealing hummocky moraine, ribbed moraine, boulder fields and stony till. Wider use of this imagery is encouraged.

scholarly journals Symmetric Boundary Condition for Laplacian on Net of Regular Hexagons

2017 ◽  
Vol 9 (3) ◽  
pp. 46
Author(s):  
Daniel Lee
Keyword(s):  
Boundary Condition ◽  
Matrix Theory ◽  
Three Dimensional ◽  
Cardiac Tissues ◽  
Energy Product ◽  
Symmetric Boundary Condition ◽  
Almost All ◽  
Wave Phenomena ◽  
Dimensional Cell ◽  
Theory Series

Hexagonal grid methods are found useful in many research works, including numerical modeling in spherical coordinates, in atmospheric and ocean models, and simulation of electrical wave phenomena in cardiac tissues. Almost all of these used standard Laplacian and mostly on one configuration of regular hexagons. In this work, discrete symmetric boundary condition and energy product for anisotropic Laplacian are investigated firstly on general net of regular hexagons, and then generalized to its most extent in two- or three-dimensional cell-center finite difference applications up to the usage of symmetric stencil in central differences. For analysis of Laplacian related applications, this provides with an approach in addition to the M-matrix theory, series method, functional interpolations and Fourier vectors.

Bioprinting in ophthalmology: current advances and future pathways

2019 ◽  
Vol 25 (3) ◽  
pp. 496-514 ◽  
Author(s):  
Nataraj Poomathi ◽  
Sunpreet Singh ◽  
Chander Prakash ◽  
Rajkumar V. Patil ◽  
P.T. Perumal ◽  
...  
Keyword(s):  
3D Printing ◽  
Cardiac Tissue ◽  
Human Life ◽  
Three Dimensional ◽  
3D Models ◽  
Eye Diseases ◽  
Biological Research ◽  
Content Type ◽  
Almost All ◽  
Time Of Operation

Purpose Bioprinting is a promising technology, which has gained a recent attention, for application in all aspects of human life and has specific advantages in different areas of medicines, especially in ophthalmology. The three-dimensional (3D) printing tools have been widely used in different applications, from surgical planning procedures to 3D models for certain highly delicate organs (such as: eye and heart). The purpose of this paper is to review the dedicated research efforts that so far have been made to highlight applications of 3D printing in the field of ophthalmology. Design/methodology/approach In this paper, the state-of-the-art review has been summarized for bioprinters, biomaterials and methodologies adopted to cure eye diseases. This paper starts with fundamental discussions and gradually leads toward the summary and future trends by covering almost all the research insights. For better understanding of the readers, various tables and figures have also been incorporated. Findings The usages of bioprinted surgical models have shown to be helpful in shortening the time of operation and decreasing the risk of donor, and hence, it could boost certain surgical effects. This demonstrates the wide use of bioprinting to design more precise biological research models for research in broader range of applications such as in generating blood vessels and cardiac tissue. Although bioprinting has not created a significant impact in ophthalmology, in recent times, these technologies could be helpful in treating several ocular disorders in the near future. Originality/value This review work emphasizes the understanding of 3D printing technologies, in the light of which these can be applied in ophthalmology to achieve successful treatment of eye diseases.

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