scholarly journals 6-Bromo-7-hydroxy-3-methylcoumarin (mBhc) is an efficient multi-photon labile protecting group for thiol caging and three-dimensional chemical patterning

2016 ◽  
Vol 14 (35) ◽  
pp. 8289-8300 ◽  
Author(s):  
M. Mohsen Mahmoodi ◽  
Stephanie A. Fisher ◽  
Roger Y. Tam ◽  
Philip C. Goff ◽  
Reid B. Anderson ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Biological Processes ◽  
Protecting Group ◽  
Thiol Groups ◽  
Temporal Control ◽  
Chemical Patterning ◽  
Spatio Temporal

Photochemical release of thiol groups allows spatio-temporal control of biological processes.

scholarly journals Directing multicellular organization by varying the aspect ratio of soft hydrogel microwells

2021 ◽  
Author(s):  
Gayatri Jayant Pahapale ◽  
Jiaxiang Tao ◽  
Milos Nikolic ◽  
Sammy Gao ◽  
Giuliano Scarcelli ◽  
...  
Keyword(s):  
Aspect Ratio ◽  
Three Dimensional ◽  
Force Balance ◽  
Substrate Stiffness ◽  
Self Organization ◽  
Balance Model ◽  
Physical Factors ◽  
Biological Processes ◽  
Chemical Patterning ◽  
Wide Range

Multicellular organization with precise spatial definition is an essential step in a wide range of biological processes, including morphogenesis, development, and healing. Gradients and patterns of chemoattractants are well-described guides of multicellular organization, but the influences of three-dimensional geometry of soft hydrogels on multicellular organization are less well defined. Here, we report the discovery of a new mode of self-organization of endothelial cells in ring-like patterns on the perimeters of hydrogel microwells that is independent of protein or chemical patterning and is driven only by geometry and substrate stiffness. We observe quantitatively striking influences of both the microwell aspect ratio (ε = perimeter/depth) and the hydrogel modulus. We systematically investigate the physical factors of cells and substrates that drive this multicellular behavior and present a mathematical model that explains the multicellular organization based upon balancing extracellular and cytoskeletal forces. These forces are determined in part by substrate stiffness, geometry, and cell density. The force balance model predicts the direction and distance of translational cell migration based on the dynamic interaction between tangential cytoskeletal tension and cell-cell and cell-substrate adhesion. We further show that the experimental observations can be leveraged to drive customized multicellular self-organization. Our observation of this multicellular behavior demonstrates the importance of the combinatorial effects of geometry and stiffness in complex biological processes. It also provides a new methodology for direction of cell organization that may facilitate the engineering of bionics and integrated model organoid systems.

scholarly journals Theory of mechano-chemical patterning and optimal migration in cell monolayers

2020 ◽  
Author(s):  
Daniel Boocock ◽  
Naoya Hino ◽  
Natalia Ruzickova ◽  
Tsuyoshi Hirashima ◽  
Edouard Hannezo
Keyword(s):  
Cell Migration ◽  
Mapk Pathway ◽  
Three Dimensional ◽  
Collective Cell Migration ◽  
Chemical Patterning ◽  
Collective Behaviors ◽  
Erk Mapk ◽  
Spatio Temporal

AbstractCollective cell migration offers a rich field of study for non-equilibrium physics and cellular biology, revealing phenomena such as glassy dynamics [1], pattern formation [2] and active turbulence [3]. However, how mechanical and chemical signaling are integrated at the cellular level to give rise to such collective behaviors remains unclear. We address this by focusing on the highly conserved phenomenon of spatio-temporal waves of density [2, 4–8] and ERK/MAPK activation [9–11], which appear both in vitro and in vivo during collective cell migration and wound healing. First, we propose a biophysical theory, backed by mechanical and optogenetic perturbation experiments, showing that patterns can be quantitatively explained by a mechano-chemical coupling between three-dimensional active cellular tensions and the mechano-sensitive ERK/MAPK pathway. Next, we demonstrate how this biophysical mechanism can robustly induce migration in a desired orientation, and we determine a theoretically optimal pattern for inducing efficient collective migration fitting well with experimentally observed dynamics. We thereby provide a bridge between the biophysical origin of spatio-temporal instabilities and the design principles of robust and efficient long-ranged migration.

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 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 The Spatio-temporal Control of the Expression of Glutamine Synthetase in the Liver Is Mediated by Its 5′-Enhancer

1995 ◽  
Vol 270 (47) ◽  
pp. 28251-28256 ◽  
Author(s):  
Heleen Lie-Venema ◽  
T. Labruyère Wil ◽  
A. van Roon Marian ◽  
A. J. de Boer Piet ◽  
Antoon F.M. Moorman ◽  
...  
Keyword(s):  
Glutamine Synthetase ◽  
Temporal Control ◽  
Spatio Temporal
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