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Keywords = Couette flow cell

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15 pages, 3651 KiB  
Article
Upregulation of DJ-1 in Dopaminergic Neurons by a Physically-Modified Saline: Implications for Parkinson’s Disease
by Malabendu Jana, Sridevi Dasarathy, Supurna Ghosh and Kalipada Pahan
Int. J. Mol. Sci. 2023, 24(5), 4652; https://doi.org/10.3390/ijms24054652 - 28 Feb 2023
Cited by 3 | Viewed by 2408
Abstract
Parkinson’s disease (PD) is the second most common neurodegenerative disorder in human and loss-of-functions DJ-1 mutations are associated with a familial form of early onset PD. Functionally, DJ-1 (PARK7), a neuroprotective protein, is known to support mitochondria and protect cells from oxidative stress. [...] Read more.
Parkinson’s disease (PD) is the second most common neurodegenerative disorder in human and loss-of-functions DJ-1 mutations are associated with a familial form of early onset PD. Functionally, DJ-1 (PARK7), a neuroprotective protein, is known to support mitochondria and protect cells from oxidative stress. Mechanisms and agents by which the level of DJ-1 could be increased in the CNS are poorly described. RNS60 is a bioactive aqueous solution created by exposing normal saline to Taylor-Couette-Poiseuille flow under high oxygen pressure. Recently we have described neuroprotective, immunomodulatory and promyelinogenic properties of RNS60. Here we delineate that RNS60 is also capable of increasing the level of DJ-1 in mouse MN9D neuronal cells and primary dopaminergic neurons, highlighting another new neuroprotective effect of RNS60. While investigating the mechanism we found the presence of cAMP response element (CRE) in DJ-1 gene promoter and stimulation of CREB activation in neuronal cells by RNS60. Accordingly, RNS60 treatment increased the recruitment of CREB to the DJ-1 gene promoter in neuronal cells. Interestingly, RNS60 treatment also induced the enrollment of CREB-binding protein (CBP), but not the other histone acetyl transferase p300, to the promoter of DJ-1 gene. Moreover, knockdown of CREB by siRNA led to the inhibition of RNS60-mediated DJ-1 upregulation, indicating an important role of CREB in DJ-1 upregulation by RNS60. Together, these results indicate that RNS60 upregulates DJ-1 in neuronal cells via CREB–CBP pathway. It may be of benefit for PD and other neurodegenerative disorders. Full article
(This article belongs to the Special Issue Development of Dopaminergic Neurons 2.0)
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21 pages, 5206 KiB  
Article
Interplay of Active Stress and Driven Flow in Self-Assembled, Tumbling Active Nematics
by Weiqiang Wang and Rui Zhang
Crystals 2021, 11(9), 1071; https://doi.org/10.3390/cryst11091071 - 4 Sep 2021
Cited by 12 | Viewed by 3266
Abstract
Lyotropic chromonic liquid crystals (LCLCs) are a special type of hierarchical material in which self-assembled molecular aggregates are responsible for the formation of liquid crystal phases. Thanks to its unusual material properties and bio compatibility, it has found wide applications including the formation [...] Read more.
Lyotropic chromonic liquid crystals (LCLCs) are a special type of hierarchical material in which self-assembled molecular aggregates are responsible for the formation of liquid crystal phases. Thanks to its unusual material properties and bio compatibility, it has found wide applications including the formation of active nematic liquid crystals. Recent experiments have uncovered tumbling character of certain LCLCs. However, how tumbling behavior modifies structure and flow in driven and active nematics is poorly understood. Here, we rely on continuum simulation to study the interplay of extensile active stress and externally driven flow in a flow-tumbling nematic with a low twist modulus to mimic nematic LCLCs. We find that a spontaneous transverse flow can be developed in a flow-tumbling active nematic confined to a hybrid alignment cell when it is in log-rolling mode at sufficiently high activities. The orientation of the total spontaneous flow is tunable by tuning the active stress. We further show that activity can suppress pressure-driven flow of a flow-tumbling nematic in a planar-anchoring cell but can also promote a transition of the director field under a pressure gradient in a homeotropic-anchoring cell. Remarkably, we demonstrate that the frequency of unsteady director dynamics in a tumbling nematic under Couette flow is invariant against active stress when below a threshold activity but exhibits a discontinuous increase when above the threshold at which a complex, periodic spatiotemporal director pattern emerges. Taken together, our simulations reveal qualitative differences between flow-tumbling and flow-aligning active nematics and suggest potential applications of tumbling nematics in microfluidics. Full article
(This article belongs to the Special Issue Self-Assembly in Liquid Crystalline Materials)
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20 pages, 2847 KiB  
Article
Rotational Particle Separation in Solutions: Micropolar Fluid Theory Approach
by Vladimir Shelukhin
Polymers 2021, 13(7), 1072; https://doi.org/10.3390/polym13071072 - 29 Mar 2021
Cited by 6 | Viewed by 2388
Abstract
We develop a new mathematical model for rotational sedimentation of particles for steady flows of a viscoplastic granular fluid in a concentric-cylinder Couette geometry when rotation of the Couette cell inner cylinder is prescribed. We treat the suspension as a micro-polar fluid. The [...] Read more.
We develop a new mathematical model for rotational sedimentation of particles for steady flows of a viscoplastic granular fluid in a concentric-cylinder Couette geometry when rotation of the Couette cell inner cylinder is prescribed. We treat the suspension as a micro-polar fluid. The model is validated by comparison with known data of measurement. Within the proposed theory, we prove that sedimentation occurs due to particles’ rotation and rotational diffusion. Full article
(This article belongs to the Special Issue Advanced Polymer Simulation and Processing)
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12 pages, 2490 KiB  
Article
The Bacterial Amyloid-Like Hfq Promotes In Vitro DNA Alignment
by Frank Wien, Denis Martinez, Etienne Le Brun, Nykola C. Jones, Søren Vrønning Hoffmann, Jehan Waeytens, Melanie Berbon, Birgit Habenstein and Véronique Arluison
Microorganisms 2019, 7(12), 639; https://doi.org/10.3390/microorganisms7120639 - 3 Dec 2019
Cited by 20 | Viewed by 4641
Abstract
The Hfq protein is reported to be involved in environmental adaptation and virulence of several bacteria. In Gram-negative bacteria, Hfq mediates the interaction between regulatory noncoding RNAs and their target mRNAs. Besides these RNA-related functions, Hfq is also associated with DNA and is [...] Read more.
The Hfq protein is reported to be involved in environmental adaptation and virulence of several bacteria. In Gram-negative bacteria, Hfq mediates the interaction between regulatory noncoding RNAs and their target mRNAs. Besides these RNA-related functions, Hfq is also associated with DNA and is a part of the bacterial chromatin. Its precise role in DNA structuration is, however, unclear and whether Hfq plays a direct role in DNA-related processes such as replication or recombination is controversial. In previous works, we showed that Escherichia coli Hfq, or more precisely its amyloid-like C-terminal region (CTR), induces DNA compaction into a condensed form. In this paper, we evidence a new property for Hfq; precisely we show that its CTR influences double helix structure and base tilting, resulting in a strong local alignment of nucleoprotein Hfq:DNA fibers. The significance of this alignment is discussed in terms of chromatin structuration and possible functional consequences on evolutionary processes and adaptation to environment. Full article
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12 pages, 3968 KiB  
Article
Virtual-Wall Model for Molecular Dynamics Simulation
by Lijuan Qian, Chengxu Tu, Fubing Bao and Yonghao Zhang
Molecules 2016, 21(12), 1678; https://doi.org/10.3390/molecules21121678 - 9 Dec 2016
Cited by 8 | Viewed by 5562
Abstract
A large number of molecules are usually required to model atomic walls in molecular dynamics simulations. A virtual-wall model is proposed in this study to describe fluid-wall molecular interactions, for reducing the computational time. The infinite repetition of unit cell structures within the [...] Read more.
A large number of molecules are usually required to model atomic walls in molecular dynamics simulations. A virtual-wall model is proposed in this study to describe fluid-wall molecular interactions, for reducing the computational time. The infinite repetition of unit cell structures within the atomic wall causes the periodicity of the force acting on a fluid molecule from the wall molecules. This force is first calculated and then stored in the memory. A fluid molecule appearing in the wall force field is subjected to the force from the wall molecules. The force can then be determined by the position of the molecule relative to the wall. This model avoids excessive calculations of fluid-wall interactions and reduces the computational time drastically. The time reduction is significant for small fluid density and channel height. The virtual-wall model is applied to Poiseuille and Couette flows, and to a flow in a channel with a rough surface. Results of the virtual and atomic wall simulations agree well with each other, thereby indicating the usefulness of the virtual-wall model. The appropriate bin size and cut-off radius in the virtual-wall model are also discussed. Full article
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