The emergence of cooperative dynamics in polymers as an effect of conformational restrictions: The case of crystallization and an example on heterogeneous confinement

2011 ◽  
Vol 522 (1-2) ◽  
pp. 135-143 ◽  
Author(s):  
Pietro Calandra ◽  
Marco Pieruccini ◽  
Simone Sturniolo
Keyword(s):  
Cooperative Dynamics ◽  
Conformational Restrictions

Cooperative dynamics and speciation in deep eutectic solvent + DMSO mixtures

2021 ◽  
pp. 115790
Author(s):  
Vira Agieienko ◽  
Ali Reza Harifi-Mood ◽  
Richard Buchner
Keyword(s):  
Deep Eutectic Solvent ◽  
Cooperative Dynamics

scholarly journals Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Puneet Sharma ◽  
Jie Wu ◽  
Benedikt S. Nilges ◽  
Sebastian A. Leidel
Keyword(s):  
Human Cells ◽  
Ribosome Profiling ◽  
Model Organisms ◽  
Treatment Conditions ◽  
Genome Wide ◽  
Optimized Protocol ◽  
Gene Level ◽  
Translation Inhibitor ◽  
Species Specific ◽  
Conformational Restrictions

AbstractRibosome profiling measures genome-wide translation dynamics at sub-codon resolution. Cycloheximide (CHX), a widely used translation inhibitor to arrest ribosomes in these experiments, has been shown to induce biases in yeast, questioning its use. However, whether such biases are present in datasets of other organisms including humans is unknown. Here we compare different CHX-treatment conditions in human cells and yeast in parallel experiments using an optimized protocol. We find that human ribosomes are not susceptible to conformational restrictions by CHX, nor does it distort gene-level measurements of ribosome occupancy, measured decoding speed or the translational ramp. Furthermore, CHX-induced codon-specific biases on ribosome occupancy are not detectable in human cells or other model organisms. This shows that reported biases of CHX are species-specific and that CHX does not affect the outcome of ribosome profiling experiments in most settings. Our findings provide a solid framework to conduct and analyze ribosome profiling experiments.

scholarly journals Cooperative Dynamics in Bidirectional Transport on Flexible Lattice

2021 ◽  
Vol 182 (1) ◽  
Author(s):  
Akriti Jindal ◽  
Atul Kumar Verma ◽  
Arvind Kumar Gupta
Keyword(s):  
Bidirectional Transport ◽  
Cooperative Dynamics

scholarly journals Synthetic protocell biology: from reproduction to computation

2007 ◽  
Vol 362 (1486) ◽  
pp. 1727-1739 ◽  
Author(s):  
Ricard V Solé ◽  
Andreea Munteanu ◽  
Carlos Rodriguez-Caso ◽  
Javier Macía
Keyword(s):  
Current Knowledge ◽  
Building Blocks ◽  
Biochemical Networks ◽  
Cellular Structures ◽  
Biological Complexity ◽  
Artificial Cell ◽  
Future Challenges ◽  
Cooperative Dynamics ◽  
The Origin Of Life ◽  
Review Current

Cells are the building blocks of biological complexity. They are complex systems sustained by the coordinated cooperative dynamics of several biochemical networks. Their replication, adaptation and computational features emerge as a consequence of appropriate molecular feedbacks that somehow define what life is. As the last decades have brought the transition from the description-driven biology to the synthesis-driven biology, one great challenge shared by both the fields of bioengineering and the origin of life is to find the appropriate conditions under which living cellular structures can effectively emerge and persist. Here, we review current knowledge (both theoretical and experimental) on possible scenarios of artificial cell design and their future challenges.

Cooperative dynamics

2011 ◽  
Vol 23 (37) ◽  
pp. 370301
Author(s):  
Nir Gov
Keyword(s):  
Cooperative Dynamics
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