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https://www.readbyqxmd.com/read/28640821/noise-reduction-in-single-time-frame-optical-dna-maps
#1
Paola C Torche, Vilhelm Müller, Fredrik Westerlund, Tobias Ambjörnsson
In optical DNA mapping technologies sequence-specific intensity variations (DNA barcodes) along stretched and stained DNA molecules are produced. These "fingerprints" of the underlying DNA sequence have a resolution of the order one kilobasepairs and the stretching of the DNA molecules are performed by surface adsorption or nano-channel setups. A post-processing challenge for nano-channel based methods, due to local and global random movement of the DNA molecule during imaging, is how to align different time frames in order to produce reproducible time-averaged DNA barcodes...
2017: PloS One
https://www.readbyqxmd.com/read/28634828/donation-and-back-donation-analyzed-through-a-charge-transfer-model-based-on-density-functional-theory
#2
Ulises Orozco-Valencia, José L Gázquez, Alberto Vela
The net charge transfer process that occurs between two species, A and B, interacting with each other, may be decomposed into two processes: one in which A receives charge from B, which can be identified as the electrophilic channel for A or the nucleophilic channel for B, and a second in which A donates charge to B, which can be identified as the nucleophilic channel for A or the electrophilic channel for B. By determining the amount of charge associated with both processes through the minimization of the interaction energy associated with each case, the expressions for the amount of charge involved in each case can be expressed in terms of the directional chemical potentials and the hardnesses of the interacting species...
July 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28629718/changes-in-podocyte-trpc-channels-evoked-by-plasma-and-sera-from-patients-with-recurrent-fsgs-and-by-putative-glomerular-permeability-factors
#3
Eun Young Kim, Hila Roshanravan, Stuart E Dryer
Primary forms of focal and segmental glomeruloslerosis (FSGS) are driven by circulating factors that cause dysfunction or loss podocytes. Rare genetic forms of FSGS can be caused by mutations in TRPC6, which encodes a Ca(2+)-permeable cationic channel expressed in mesangial cells and podocytes; and NPHS2, which encodes podocin, a TRPC6-binding protein expressed in podocyte slit diaphragm domains. Here we observed that exposing immortalized mouse podocytes to serum or plasma from recurrent FSGS patients for 24h increased the steady-state cell-surface abundance of TRPC6, accompanied by an increase in currents through endogenous TRPC6 channels evoked by a hypoosmotic stretch stimulus...
June 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28616984/oh-stretching-overtone-induced-dynamics-in-hso3f-from-reactive-molecular-dynamics-simulations
#4
Sebastian Brickel, Markus Meuwly
The OH-stretch induced dynamics in fluorosulfonic acid (HSO$_3$F) is characterized from a statistically significant number of trajectories using Multi-Surface Adiabatic Reactive Molecular Dynamics (MS-ARMD) simulations. The global reactive potential energy surface, which describes H-transfer and HF-elimination, is parametrized at the MP2/6-311G++(2p,2d) level of theory with an accuracy of better than 1 kcal/mol. Excitation along the OH-local mode leads to H-transfer dynamics but elimination of HF is only observed for excitations with $\nu \geq 6$ for 1 out of 5000 trajectories...
June 15, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28612144/fast-calcium-transients-translate-the-distribution-and-conduction-of-neural-activity-in-different-regions-of-a-single-sensory-neuron
#5
Nuhan Purali
In the present study, cytosolic calcium concentration changes were recorded in response to various forms of excitations, using the fluorescent calcium indicator dye OG-BAPTA1 together with the current or voltage clamp methods in stretch receptor neurons of crayfish. A single action potential evoked a rise in the resting calcium level in the axon and axonal hillock, whereas an impulse train or a large saturating current injection would be required to evoke an equivalent response in the dendrite region. Under voltage clamp conditions, amplitude differences between axon and dendrite responses vanished completely...
September 2017: Invertebrate Neuroscience: IN
https://www.readbyqxmd.com/read/28586686/vision-and-lack-of-vision-in-the-ocean
#6
Justin Marshall
As land-locked animals, when we visualise the ocean our mind's eye may see crashing waves or a vast blue expanse stretching to the horizon, a raft of torpedoing penguins, a glimpse of colourful coral reef fish from the shark-free safety of a sandy beach. Underwater, the crystal-clear, and in fact not at all silent, world of Jacques Cousteau, or more recently David Attenborough, is a wonderland that some cannot wait to witness first hand as divers, while others are content to see it on a screen. Spend a bit of time underwater, in the English Channel for example, and a few facts emerge...
June 5, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28583325/neuroprotective-effect-of-low-intensity-pulsed-ultrasound-against-mpp-induced-neurotoxicity-in-pc12-cells-involvement-of-k2p-channels-and-stretch-activated-ion-channels
#7
Lu Zhao, Yi Feng, Aiwei Shi, Lei Zhang, Shifang Guo, Mingxi Wan
Parkinson's disease is the second most common neurodegenerative disease. It is characterized by the loss of dopaminergic neurons in the substantia nigra pars compacta. 1-Methyl-4-phenylpyridinium (MPP(+)) is a dopaminergic neuronal toxin that is widely used in constructing Parkinson's disease models in vitro. Low-intensity pulsed ultrasound (LIPUS) is a non-invasive therapeutic approach that has neuromodulation and neuroprotective effects in the central neural system; however, whether LIPUS can provide protection for dopaminergic neurons against MPP(+)-induced neurocytotoxicity remains unknown...
June 2, 2017: Ultrasound in Medicine & Biology
https://www.readbyqxmd.com/read/28559335/spontaneous-formation-of-aligned-dna-nanowires-by-capillarity-induced-skin-folding
#8
So Nagashima, Hyun Dong Ha, Do Hyun Kim, Andrej Košmrlj, Howard A Stone, Myoung-Woon Moon
Although DNA nanowires have proven useful as a template for fabricating functional nanomaterials and a platform for genetic analysis, their widespread use is still hindered because of limited control over the size, geometry, and alignment of the nanowires. Here, we document the capillarity-induced folding of an initially wrinkled surface and present an approach to the spontaneous formation of aligned DNA nanowires using a template whose surface morphology dynamically changes in response to liquid. In particular, we exploit the familiar wrinkling phenomenon that results from compression of a thin skin on a soft substrate...
June 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28546458/proteoglycans-ion-channels-and-cell-matrix-adhesion
#9
REVIEW
Ioli Mitsou, Hinke A B Multhaupt, John R Couchman
Cell surface proteoglycans comprise a transmembrane or membrane-associated core protein to which one or more glycosaminoglycan chains are covalently attached. They are ubiquitous receptors on nearly all animal cell surfaces. In mammals, the cell surface proteoglycans include the six glypicans, CD44, NG2 (CSPG4), neuropilin-1 and four syndecans. A single syndecan is present in invertebrates such as nematodes and insects. Uniquely, syndecans are receptors for many classes of proteins that can bind to the heparan sulphate chains present on syndecan core proteins...
May 25, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28546113/stretch-activated-trpv2-channels-role-in-mediating-cardiopathies
#10
REVIEW
Elizabeth Aguettaz, Patrick Bois, Christian Cognard, Stéphane Sebille
Transient receptor potential vanilloid type 2, TRPV2, is a calcium-permeable cation channel belonging to the TRPV channel family. Although this channel has been first characterized as a noxious heat sensor, its mechanosensor property recently gained importance in various physiological functions. TRPV2 has been described as a stretch-mediated channel and a regulator of calcium homeostasis in several cell types and has been shown to be involved in the stretch-dependent responses in cardiomyocytes. Hence, several studies in the last years support the idea that TRPV2 play a key role in the function and structure of the heart, being involved in the cardiac compensatory mechanisms in response to pathologic or exercise-induced stress...
May 22, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28539337/altered-expression-and-modulation-of-the-two-pore-domain-k2p-mechano-gated-potassium-channel-trek-1-in-overactive-human-detrusor
#11
Ricardo H Pineda, Balachandar Nedumaran, Joseph A Hypolite, Xiao-Qing Pan, Shandra Wilson, Randall B Meacham, Anna P Malykhina
Background Detrusor overactivity (DO) is the abnormal response of the urinary bladder to physiological stretch during the filling phase of the micturition cycle. The mechanisms of bladder smooth muscle compliance upon the wall stretch are poorly understood. We previously reported that the function of normal detrusor is regulated by TREK-1, a member of the mechano-gated subfamily of two-pore domain potassium (K2P) channels. In the present study, we aimed to identify the changes in expression and function of TREK-1 channels under pathological conditions associated with DO, evaluate the potential relationship between TREK-1 channels and cytoskeletal proteins in the human bladder, and test the possibility of modulation of TREK-1 channel expression by small RNAs...
May 24, 2017: American Journal of Physiology. Renal Physiology
https://www.readbyqxmd.com/read/28538153/new-continuum-approaches-for-determining-protein-induced-membrane-deformations
#12
David Argudo, Neville P Bethel, Frank V Marcoline, Charles W Wolgemuth, Michael Grabe
The influence of the membrane on transmembrane proteins is central to a number of biological phenomena, notably the gating of stretch activated ion channels. Conversely, membrane proteins can influence the bilayer, leading to the stabilization of particular membrane shapes, topological changes that occur during vesicle fission and fusion, and shape-dependent protein aggregation. Continuum elastic models of the membrane have been widely used to study protein-membrane interactions. These mathematical approaches produce physically interpretable membrane shapes, energy estimates for the cost of deformation, and a snapshot of the equilibrium configuration...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28528666/role-of-nonneuronal-trpv4-signaling-in-inflammatory-processes
#13
Pradeep Rajasekhar, Daniel P Poole, Nicholas A Veldhuis
Transient receptor potential (TRP) ion channels are important signaling components in nociceptive and inflammatory pathways. This is attributed to their ability to function as polymodal sensors of environmental stimuli (chemical and mechanical) and as effector molecules in receptor signaling pathways. TRP vanilloid 4 (TRPV4) is a nonselective cation channel that is activated by multiple endogenous stimuli including shear stress, membrane stretch, and arachidonic acid metabolites. TRPV4 contributes to many important physiological processes and dysregulation of its activity is associated with chronic conditions of metabolism, inflammation, peripheral neuropathies, musculoskeletal development, and cardiovascular regulation...
2017: Advances in Pharmacology
https://www.readbyqxmd.com/read/28526353/stretch-activated-two-pore-domain-k2p-potassium-channels-in-the-heart-focus-on-atrial-fibrillation-and-heart-failure
#14
Constanze Schmidt, Felix Wiedmann, Stefan M Kallenberger, Antonius Ratte, Jan S Schulte, Beatrix Scholz, Frank Ulrich Müller, Niels Voigt, Maria-Patapia Zafeiriou, Joachim R Ehrlich, Ursula Tochtermann, Gábor Veres, Arjang Ruhparwar, Matthias Karck, Hugo A Katus, Dierk Thomas
Two-pore-domain potassium (K2P) channels modulate cellular excitability. The significance of stretch-activated cardiac K2P channels (K2P2.1, TREK-1, KCNK2; K2P4.1, TRAAK, KCNK4; K2P10.1, TREK-2, KCNK10) in heart disease has not been elucidated in detail. The aim of this work was to assess expression and remodeling of mechanosensitive K2P channels in atrial fibrillation (AF) and heart failure (HF) patients in comparison to murine models. Cardiac K2P channel levels were quantified in atrial (A) and ventricular (V) tissue obtained from patients undergoing open heart surgery...
May 16, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28526352/stretch-activated-potassium-currents-in-the-heart-focus-on-trek-1-and-arrhythmias
#15
REVIEW
Niels Decher, Aytug K Kiper, Susanne Rinné
This review focuses on the role and the molecular candidates of the cardiac stretch-activated potassium current (SAK). The functional properties of the two-pore domain potassium (K2P) channel TREK-1, a major candidate for the cardiac SAK, are analyzed and the molecular mechanism of stretch-activation in K2P potassium channels is discussed. Furthermore, the functional modulation of TREK-1 by different cardiac interaction partners, as well as evidence for the functional role of the stretch-dependent TREK-1 and its putative subunits in the heart is reviewed...
May 16, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28523001/the-role-of-transient-receptor-potential-vanilloid-4-in-pulmonary-inflammatory-diseases
#16
REVIEW
Rachel G Scheraga, Brian D Southern, Lisa M Grove, Mitchell A Olman
Ion channels/pumps are essential regulators of organ homeostasis and disease. In the present review, we discuss the role of the mechanosensitive cation channel, transient receptor potential vanilloid 4 (TRPV4), in cytokine secretion and pulmonary inflammatory diseases such as asthma, cystic fibrosis (CF), and acute lung injury/acute respiratory distress syndrome (ARDS). TRPV4 has been shown to play a role in lung diseases associated with lung parenchymal stretch or stiffness. TRPV4 indirectly mediates hypotonicity-induced smooth muscle contraction and airway remodeling in asthma...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28510575/electro-mechanical-dynamics-of-spiral-waves-in-a-discrete-2d-model-of-human-atrial-tissue
#17
Paul Brocklehurst, Haibo Ni, Henggui Zhang, Jianqiao Ye
We investigate the effect of mechano-electrical feedback and atrial fibrillation induced electrical remodelling (AFER) of cellular ion channel properties on the dynamics of spiral waves in a discrete 2D model of human atrial tissue. The tissue electro-mechanics are modelled using the discrete element method (DEM). Millions of bonded DEM particles form a network of coupled atrial cells representing 2D cardiac tissue, allowing simulations of the dynamic behaviour of electrical excitation waves and mechanical contraction in the tissue...
2017: PloS One
https://www.readbyqxmd.com/read/28502667/mechanosensitivity-from-aristotle-s-sense-of-touch-to-cardiac-mechano-electric-coupling
#18
REVIEW
Johann P Kuhtz-Buschbeck, Jochen Schaefer, Nicolaus Wilder
Scientific interest in mechanosensation likely commenced with Aristotle's description of the sense of touch in his treatise de Anima [On the Soul]. Considering touch as a vital sense distributed over the whole body, the philosopher outlined a "physiological concept" at the macro-level already 2400 years ago. From this starting point, we outline the onset of modern sensory physiology during the early 19th century. Physiologists distinguished between outer and inner senses at that time, without, however, referring to specific receptors or nerves...
May 11, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28499095/trpm7-is-involved-in-volume-regulation-in-salivary-glands
#19
J M Kim, S Choi, K Park
Under hypotonic conditions, the regulatory volume decrease (RVD) is essential to maintain physiological homeostasis and functions in diverse biological systems. Intracellular Ca(2+) has been reported as an important mediator of this response, but the underlying Ca(2+) mechanism responsible for RVD is still controversial. Here we investigate the role of Ca(2+) in the RVD response using live-cell imaging, microspectrofluorimetry, and a patch-clamp technique. A typical RVD was observed in submandibular gland acinar cells after swelling in a hypotonic solution, whereas intracellular Ca(2+) chelation completely inhibited the RVD response...
May 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28495756/cystic-fibrosis-transmembrane-conductance-regulator-mediates-tenogenic-differentiation-of-tendon-derived-stem-cells-and-tendon-repair-accelerating-tendon-injury-healing-by-intervening-in-its-downstream-signaling
#20
Yang Liu, Jia Xu, Liangliang Xu, Tianyi Wu, Yuxin Sun, Yuk-Wai Lee, Bin Wang, Hsiao-Chang Chan, Xiaohua Jiang, Jinfang Zhang, Gang Li
Tendons are a mechanosensitive tissue, which enables them to transmit to bone forces that are derived from muscle. Patients with tendon injuries, such as tendinopathy or tendon rupture, were often observed with matrix degeneration, and the healing of tendon injuries remains a challenge as a result of the limited understanding of tendon biology. Our study demonstrates that the stretch-mediated activation channel, cystic fibrosis transmembrane conductance regulator (CFTR), was up-regulated in tendon-derived stem cells (TDSCs) during tenogenic differentiation under mechanical stretching...
May 11, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
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