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Progress in Biophysics and Molecular Biology

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https://www.readbyqxmd.com/read/28527890/mechano-electric-coupling-heterogeneity-in-repolarization-and-the-electrocardiographic-t-wave
#1
REVIEW
V M F Meijborg, C N W Belterman Va, J M T de Bakker, R Coronel, C E Conrath
Stretch influences repolarization by mechano-electric coupling (MEC) and contributes to arrhythmogenesis. Although there is an abundance of research on electrophysiological effects of MEC, it is still unclear how MEC translates to the ECG. We aim to provide an overview of the MEC research focused on the ECG and the underlying changes in electrophysiology. In addition, we present new data on the effect of left ventricular pressure on the electrocardiographic T-wave. We show that an increase in left ventricular pressure leads to prolonged QT-intervals with increased amplitudes of the STT-segment...
May 17, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28526354/outline-of-a-unified-darwinian-evolutionary-theory-for-physical-and-biological-systems
#2
REVIEW
Carlos Baladrón, Andrei Khrennikov
The scheme of a unified Darwinian evolutionary theory for physical and biological systems is described. Every physical system is methodologically endowed with a classical information processor what turns every system into an agent being also susceptible to evolution. Biological systems retain this structure as natural extensions of physical systems from which they are built up. Optimization of information flows turns out to be the key element to study the possible emergence of quantum behavior and the unified Darwinian description of physical and biological systems...
May 16, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28526353/stretch-activated-two-pore-domain-k2p-potassium-channels-in-the-heart-focus-on-atrial-fibrillation-and-heart-failure
#3
REVIEW
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
#4
REVIEW
Niels Decher, Aytug K Kiper, Susanne Rinné
This review focuses on the role and the molecular candidates for the cardiac stretch-activated potassium current (SAK). The functional properties of 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/28506694/optogenetics-gets-to-the-heart-a-guiding-light-beyond-defibrillation
#5
REVIEW
Claudia Crocini, Cecilia Ferrantini, Francesco S Pavone, Leonardo Sacconi
Optogenetics provides a tool for controlling the electrical activity of excitable cells by means of the interaction of light with light-gated ion channels. Despite the fact that optogenetics has been intensively utilized in the neurosciences, it has been more rarely employed as an instrument for studying cardiac pathophysiology. However, the advantages of optical approaches to perturb cardiac electrical activity are numerous, especially when the spatio-temporal qualities of light are utterly exploited. Here, we review the main breakthroughs employing optogenetics to perturb cardiac pathophysiology and attempt a comparison of methods and procedures that have employed optogenetics in the heart...
May 12, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28502667/mechanosensitivity-from-aristotle-s-sense-of-touch-to-cardiac-mechano-electric-coupling
#6
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/28487218/neural-implementation-of-operations-used-in-quantum-cognition
#7
REVIEW
Jerome R Busemeyer, Pegah Fakhari, Peter Kvam
Quantum probability theory has been successfully applied outside of physics to account for numerous findings from psychology regarding human judgement and decision making behavior. However, the researchers who have made these applications do not rely on the hypothesis that the brain is some type of quantum computer. This raises the question of how could the brain implement quantum algorithms other than quantum physical operations. This article outlines one way that a neural based system could perform the computations required by applications of quantum probability to human behavior...
May 6, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28483446/molecular-recognition-of-the-environment-and-mechanisms-of-the-origin-of-species-in-quantum-like-modeling-of-evolution
#8
REVIEW
Alexey V Melkikh, Andrei Khrennikov
A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown that these mechanisms, at the molecular level, cannot work steadily in terms of classical mechanics. Quantum mechanisms of changes in the genome, based on the long-range interaction potential between biologically important molecules, are proposed as one of possible explanation...
May 5, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28479315/quantum-field-theory-and-coalgebraic-logic-in-theoretical-computer-science
#9
REVIEW
Gianfranco Basti, Antonio Capolupo, Giuseppe Vitiello
We suggest that in the framework of the Category Theory it is possible to demonstrate the mathematical and logical dual equivalence between the category of the q-deformed Hopf Coalgebras and the category of the q-deformed Hopf Algebras in quantum field theory (QFT), interpreted as a thermal field theory. Each pair algebra-coalgebra characterizes a QFT system and its mirroring thermal bath, respectively, so to model dissipative quantum systems in far-from-equilibrium conditions, with an evident significance also for biological sciences...
May 4, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28450155/ionised-concentrations-in-calcium-and-magnesium-buffers-standards-and-precise-measurement-are-mandatory
#10
John A S McGuigan, James W Kay, Hugh Y Elder
In Ca(2+) and Mg(2+) buffer solutions the ionised concentrations ([X(2+)]) are either calculated or measured. Calculated values vary by up to a factor of seven due to the following four problems: The calculated [X(2+)] in buffers are so inconsistent that calculation is not an option. Until standards are available, the [X(2+)] in the buffers must be measured. The Ligand Optimisation Method is an accurate and independently verified method of doing this (McGuigan & Stumpff, Anal. Biochem. 436, 29, 2013). Lack of standards means it is not possible to compare the published [Ca(2+)] in the nmolar range, and the apparent constant (K(/)) values for Ca(2+) and Mg(2+) binding to intracellular ligands amongst different laboratories...
April 24, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28442432/fibre-diffraction-studies-of-biological-macromolecules
#11
REVIEW
D A Marvin
Two fundamental structures in molecular biology, DNA and the α-helix, were determined using X-ray fibre diffraction data, and yet fibre diffraction occupies an obscure niche in structural biology. Relatively few structures are appropriate for the technique, and it seldom supplies data of the quality common in protein crystallography; however, it has proven indispensable in some cases. Here we outline some aspects of helix diffraction mathematics, and then illustrate the application of fibre diffraction by three case studies: DNA, filamentous bacterial viruses, and bacterial pili...
April 24, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28427899/energy-and-information-flows-in-biological-systems-bioenergy-transduction-of-v1-atpase-rotary-motor-and-dynamics-of-thermodynamic-entropy-in-information-flows
#12
REVIEW
Ichiro Yamato, Takeshi Murata, Andrei Khrennikov
We classify research fields in biology with respect to flows of materials, energy, and information. We investigate energy transducing mechanisms in biology, using as a representative the typical molecular rotary motor V1-ATPase from a bacterium Enterococcus hirae. The structures of several intermediates of the rotary motor are described and the molecular mechanism of the motor converting chemical energy into mechanical energy is discussed. Comments and considerations on the information flows in biology, especially on the thermodynamic entropy in quantum physical and biological systems, are presented in section 3 in a biologist friendly manner...
April 17, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28412397/caveat-on-the-boltzmann-distribution-function-use-in-biology
#13
REVIEW
Carlos Sevcik
Sigmoid semilogarithmic functions with shape of Boltzmann equations, have become extremely popular to describe diverse biological situations. Part of the popularity is due to the easy availability of software which fits Boltzmann functions to data, without much knowledge of the fitting procedure or the statistical properties of the parameters derived from the procedure. The purpose of this paper is to explore the plasticity of the Boltzmann function to fit data, some aspects of the optimization procedure to fit the function to data and how to use this plastic function to differentiate the effect of treatment on data and to attest the statistical significance of treatment effect on the data...
April 13, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28392224/the-non-equilibrium-basis-of-turing-instability-and-localised-biological-work
#14
REVIEW
Yoram Schiffmann
Turing's theory for biological pattern formation is based on the instability of the homogeneous state, which occurs if certain key criteria are met. The problem of how chemical energy is converted to localised biological work requires one to understand not only the basis of localised power generation, but also the age-old puzzle of how organisms decrease their entropy; these problems can only be solved by the identification of the Turing Instability. At the heart of this is how natural selection, not chemistry, has fashioned the large non-equilibrium overall affinity (ΔG is a large negative quantity) for the oxidation of the fuel molecules...
April 6, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28389261/an-engineering-paradigm-in-the-biomedical-sciences-knowledge-as-epistemic-tool
#15
REVIEW
Mieke Boon
In order to deal with the complexity of biological systems and attempts to generate applicable results, current biomedical sciences are adopting concepts and methods from the engineering sciences. Philosophers of science have interpreted this as the emergence of an engineering paradigm, in particular in systems biology and synthetic biology. This article aims at the articulation of the supposed engineering paradigm by contrast with the physics paradigm that supported the rise of biochemistry and molecular biology...
April 4, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28363422/the-triangle-inequality-constraint-in-similarity-judgments
#16
REVIEW
James M Yearsley, Albert Barque-Duran, Elisa Scerrati, James A Hampton, Emmanuel M Pothos
Since Tversky's (1977) seminal investigation, the triangle inequality, along with symmetry and minimality, have had a central role in investigations of the fundamental constraints on human similarity judgments. The meaning of minimality and symmetry in similarity judgments has been straightforward, but this is not the case for the triangle inequality. Expressed in terms of dissimilarities, and assuming a simple, linear function between dissimilarities and distances, the triangle inequality constraint implies that human behaviour should be consistent with Dissimilarity (A,B) + Dissimilarity (B,C) ≥ Dissimilarity (A,C), where A, B, and C are any three stimuli...
March 28, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28342743/measurement-of-ion-fluxes-across-epithelia
#17
REVIEW
Miroslaw Zajac, Krzysztof Dolowy
Epithelial tissues line all wet surfaces of vertebrate bodies. Their major function is directional transport of ions and water. Cells forming an epithelial layer are bound together by a tight junction that forms a barrier to ion flux. Ions and water are transported via specialized molecules. The presence of a defect in a single ion channel molecule leads to cystic fibrosis - the most common, fatal, human genetic disease. The paper describes ion transport data obtained by means of different experimental techniques...
March 22, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28341288/establishing-the-structures-within-populations-of-models
#18
REVIEW
Philip M Gemmell
As computational biology matures as a field, increasing attention is being paid to the relation of computational models to their target. One aspect of this is addressing how computational models can appropriately reproduce the variation seen in experimental data, with one solution being to use populations of models united by a common set of equations (the framework), with each individual member of the population (each model) possessing its own unique set of equation parameters. These model populations are then calibrated and validated against experimental data, and as a whole reproduce the experimentally observed variation...
March 21, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28315699/the-neglected-functions-of-intrinsically-disordered-proteins-and-the-origin-of-life
#19
REVIEW
Laurent Jaeken
The example of gelatine shows that extended proteins behave quite differently than globular ones: with water they form a gel. Historically the colloid view of protoplasm was discredited in favour of membrane-(pump)-theory (MPT), but unjustified. In his association-induction hypothesis Ling demonstrates that MPT is full of contradictions and that the colloid view has to be re-considered. In that case IDP's play a crucial role in this. What Ling calls the 'living state' consists of the unitary protoplasmic structure from which it was experimentally demonstrated that it can survive and keep Na(+) and K(+) concentrations without a delineating membrane...
March 15, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28286052/a-systems-biology-approach-to-overcome-trail-resistance-in-cancer-treatment
#20
REVIEW
Kumar Selvarajoo
Over the last decade, our research team has investigated the dynamic responses and global properties of living cells using systems biology approaches. More specifically, we have developed computational models and statistical techniques to interpret instructive cell signaling and high-throughput transcriptome-wide behaviors of immune, cancer, and embryonic development cells. Here, I will focus on our recent works in overcoming cancer resistance. TRAIL (tumor necrosis factor related apoptosis-inducing ligand), a proinflammatory cytokine, has shown promising success in controlling cancer threat due to its ability to induce apoptosis in cancers specifically, while having limited effect on normal cells...
March 9, 2017: Progress in Biophysics and Molecular Biology
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