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Progress in Biophysics and Molecular Biology

Kaveh Rayani, Eric Lin, Calvin Craig, Marcel Lamothe, Sanam Shafaattalab, Marvin Gunawan, Alison Yueh Li, Leif Hove-Madsen, Glen F Tibbits
The zebrafish (Danio rerio) heart is a viable model of mammalian cardiovascular function due to similarities in heart rate, ultrastructure, and action potential morphology. Zebrafish are able to tolerate a wide range of naturally occurring temperatures through altering chronotropic and inotropic properties of the heart. Optical mapping of cannulated zebrafish hearts can be used to assess the effect of temperature on excitation-contraction (EC) coupling and to explore the mechanisms underlying voltage (Vm ) and calcium (Ca2+ ) transients...
July 11, 2018: Progress in Biophysics and Molecular Biology
Ayachi Fakher, Eder C Lima, Abdellatif Sakly, Houcine Mejri, Abdelmottaleb Ben Lamine
In this study, the formalism of statistical physics is used to describe and interpret the adsorption mechanism by applying the law of real gas which takes into account the interaction between the reactive red 120 dye (RR-120) molecules due to its very large size (approximately 2.11 nm). Modeling of the RR-120 dye adsorption isotherms on Spirulina platensis sp. is performed. Five models based on statistical physics formalism are developed: Hill model with one adsorbed site energy, Hill model with two energies, Hill model with three energies, double layer model with one energy and double layer model with two energies...
July 7, 2018: Progress in Biophysics and Molecular Biology
Yun Qiao, Quan Dong, Baichen Li, Sofian Obaid, Christian Miccile, Rose T Yin, Trisha Talapatra, Zexu Lin, Sihui Li, Zhenyu Li, Igor R Efimov
Human cardiac slices have emerged as a promising model of the human heart for scientific research and drug testing. Retaining the normal tissue architecture, a multi-cell type environment, and the native extracellular matrix, human cardiac slices faithfully replicate organ-level adult cardiac physiology. Previously, we demonstrated that human cardiac tissue slices cultured for 24 h maintained normal electrophysiology. In this project, we further optimized the organotypic culture condition to maintain normal electrophysiology of the human cardiac slices for 4 days...
June 27, 2018: Progress in Biophysics and Molecular Biology
Nikhil Pillai, Morgan Craig, Aristeidis Dokoumetzidis, Sorell L Schwartz, Robert Bies, Immanuel Freedman
In mathematical pharmacology, models are constructed to confer a robust method for optimizing treatment. The predictive capability of pharmacological models depends heavily on the ability to track the system and to accurately determine parameters with reference to the sensitivity in projected outcomes. To closely track chaotic systems, one may choose to apply chaos synchronization. An advantageous byproduct of this methodology is the ability to quantify model parameters. In this paper, we illustrate the use of chaos synchronization combined with Nelder-Mead search to estimate parameters of the well-known Kirschner-Panetta model of IL-2 immunotherapy from noisy data...
June 18, 2018: Progress in Biophysics and Molecular Biology
Jan-David Nicolas, Marten Bernhardt, Susanne F Schlick, Malte Tiburcy, Wolfram-Hubertus Zimmermann, Amara Khan, Andrea Markus, Frauke Alves, Karl Toischer, Tim Salditt
With the development of advanced focusing optics for x-rays, we can now use x-ray beams with spot sizes in the micro- or nanometer range to scan cells and large areas of tissues and continuously record the diffraction signals. From this data, x-ray scattering maps or so-called x-ray darkfield images are computed showing how different types of cells or regions of tissues differ in their diffraction intensity. At the same time a diffraction pattern is available for each scan point which encodes the local nanostructure, averaged over many contributing constituents illuminated by the beam...
June 15, 2018: Progress in Biophysics and Molecular Biology
Ursula Ravens
Zebrafish heart has evolved as an intensely studied model for cardiac development, physiology and pathophysiology. A particular advantage is its morphological and functional similarity to mammalian, especially human heart. Zebrafish are simple to breed, uncomplicated to handle and easy to modify genetically. Because of the transparency of the early embryo, drug effects on heart rate and rhythm can be observed directly. Here we will compare the ionic basis of the electrophysiological properties of the zebrafish to those of other mammalian hearts and discuss the suitability of zebrafish as a model organism for human electrophysiology...
June 15, 2018: Progress in Biophysics and Molecular Biology
Matiyo Ojehomon, Sarah L Alderman, Love Sandhu, Sierra Sutcliffe, Terry Van Raay, Todd E Gillis, John F Dawson
Zebrafish is rapidly becoming a key model organism for studying a variety of biological processes from molecules to organisms. Interactions involving actin, a contractile protein and part of the cytoskeleton, are regulated by actin binding proteins in the majority of physiological processes in eukaryotic cells. To understand the contribution of actin proteins to the physiological processes of zebrafish, it is important to identify the diverse isoforms of actin encoded by its genome; however, significant sequence identity complicates isoform assignments...
June 15, 2018: Progress in Biophysics and Molecular Biology
Theodore R Rieger, Richard J Allen, Lukas Bystricky, Yuzhou Chen, Glen Wright Colopy, Yifan Cui, Angelica Gonzalez, Yifei Liu, R D White, R A Everett, H T Banks, Cynthia J Musante
Quantitative systems pharmacology (QSP) models aim to describe mechanistically the pathophysiology of disease and predict the effects of therapies on that disease. For most drug development applications, it is important to predict not only the mean response to an intervention but also the distribution of responses, due to inter-patient variability. Given the necessary complexity of QSP models, and the sparsity of relevant human data, the parameters of QSP models are often not well determined. One approach to overcome these limitations is to develop alternative virtual patients (VPs) and virtual populations (Vpops), which allow for the exploration of parametric uncertainty and reproduce inter-patient variability in response to perturbation...
June 15, 2018: Progress in Biophysics and Molecular Biology
Armando Aranda-Anzaldo, Myrna A R Dent
Waddington's epigenetic landscape was introduced in biology for understanding the complex process of metazoan development in an accessible fashion. The epigenetic landscape concept implies the coupling of cell differentiation and tissue/organ morphogenesis under a simple visual metaphor or analogy with significant heuristic value. Yet in recent times the epigenetic landscape has been reduced to an illustration device just for cell differentiation thus diminishing its explanatory power and heuristic value. On the other hand, the current mainstream in cancer research is concentrated on the search for proximate causes but not on achieving a deeper understanding of the phenomenon...
June 8, 2018: Progress in Biophysics and Molecular Biology
Mohamed M M Elnasharty, Ahmed M Ghoneim, Azhar M Elwan
This work has a major interest of the use of Moringa oleifera leaves extract as protective and protective-therapeutic natural supplement helping the biosystem to stand against irradiation induced damage. Rats were orally administered with Moringa oleifera leaves extract by two modalities. The dielectric properties were measured over the frequency range 106 - 2 × 108  Hz and in the temperature window 283-313 K. The dielectric parameters were used to estimate some thermodynamic state functions and evaluate the energy within the Hb molecule...
June 6, 2018: Progress in Biophysics and Molecular Biology
Azhar M Elwan, Aida A Salama, Abdelbaset M Sayed, Ahmed M Ghoneim, Aziza A Elsaied, Fatma A Ibrahim, Mohamed M M Elnasharty
It has been found that medicinal plants have chemical and/or therapeutic effects on different diseases related to oxidative damage. This work investigates the use of ethanolic Moringa oleifera leaves extract; as a protective and/or therapeutic agent against damage induced by high acute dose of ionizing radiation. Also, this study aims to explore the associations of electrical properties (relaxation time and DC conductivity of bone marrow) with biochemical markers (SOD, CAT and GSH) to detect and prognosticate radiation effects...
June 6, 2018: Progress in Biophysics and Molecular Biology
Yanis R Espinosa, Raúl J Grigera, C Gastón Ferrara
We used simulations by Molecular Dynamics to characterize the mechanism whereby the variations in the urea concentration modifies the micellar structure of sodium dodecyl sulfate monomers in water. From a self-assembled micellar system, we observed that increasing urea concentration leads to a decrease in aggregation number. Likewise, when increasing urea concentration, the micelles increase their nonpolar surface exposed to solvent, while the polar surface exposed to solvent decreases. This rearrangement process of SDS micelles in presence of urea is mainly due to the fact that the ions of Na+ that stabilize the micellar structure increase its interaction with urea...
June 4, 2018: Progress in Biophysics and Molecular Biology
Alexey V Dvornikov, Pieter P de Tombe, Xiaolei Xu
Hypertrophic cardiomyopathy (HCM) is usually manifested by increased myofilament Ca2+ sensitivity, excessive contractility, and impaired relaxation. In contrast, dilated cardiomyopathy (DCM) originates from insufficient sarcomere contractility and reduced cardiac pump function, subsequently resulting in heart failure. The zebrafish has emerged as a new model of human cardiomyopathy with high-throughput screening, which will facilitate the discovery of novel genetic factors and the development of new therapies...
May 30, 2018: Progress in Biophysics and Molecular Biology
A C Aristotelous, J M Crawford, G S Edwards, D P Kiehart, S Venakides
Dorsal closure is a model cell sheet movement that occurs midway through Drosophila embryogenesis. A dorsal hole, filled with amnioserosa, closes through the dorsalward elongation of lateral epidermal cell sheets. Closure requires contributions from 5 distinct tissues and well over 140 genes (see Mortensen et al., 2018, reviewed in Kiehart et al., 2017 and Hayes and Solon, 2017). In spite of this biological complexity, the movements (kinematics) of closure are geometrically simple at tissue, and in certain cases, at cellular scales...
May 29, 2018: Progress in Biophysics and Molecular Biology
Aishwarya K Paknikar, Benjamin Eltzner, Sarah Köster
Blood platelets are the key cellular players in blood clotting and thus of great biomedical importance. While spreading at the site of injury, they reorganize their cytoskeleton within minutes and assume a flat appearance. As platelets possess no nucleus, many standard methods for visualizing cytoskeletal components by means of fluorescence tags fail. Here we employ silicon-rhodamine actin and tubulin probes for imaging these important proteins in a time-resolved manner. We find two distinct timescales for platelet spread area development and for cytoskeletal reorganization, indicating that although cell spreading is most likely associated with actin polymerization at the cell edges, distinct, stress-fiber-like actin structures within the cell, which may be involved in the generation of contractile forces, form on their own timescale...
May 26, 2018: Progress in Biophysics and Molecular Biology
Aidan C Daly, Michael Clerx, Kylie A Beattie, Jonathan Cooper, David J Gavaghan, Gary R Mirams
The modelling of the electrophysiology of cardiac cells is one of the most mature areas of systems biology. This extended concentration of research effort brings with it new challenges, foremost among which is that of choosing which of these models is most suitable for addressing a particular scientific question. In a previous paper, we presented our initial work in developing an online resource for the characterisation and comparison of electrophysiological cell models in a wide range of experimental scenarios...
May 26, 2018: Progress in Biophysics and Molecular Biology
Arturo Tozzi, James F Peters, Andrew A Fingelkurts, Alexander A Fingelkurts, Leonid Perlovsky
The discrepancy between syntax and semantics is a painstaking issue that hinders a better comprehension of the underlying neuronal processes in the human brain. In order to tackle the issue, we at first describe a striking correlation between Wittgenstein's Tractatus, that assesses the syntactic relationships between language and world, and Perlovsky's joint language-cognitive computational model, that assesses the semantic relationships between emotions and "knowledge instinct". Once established a correlation between a purely logical approach to the language and computable psychological activities, we aim to find the neural correlates of syntax and semantics in the human brain...
May 24, 2018: Progress in Biophysics and Molecular Biology
Katherine Courchaine, Graham Rykiel, Sandra Rugonyi
The role of hemodynamics in cardiovascular development is not well understood. Indeed, it would be remarkable if it were, given the dauntingly complex array of intricately synchronized genetic, molecular, mechanical, and environmental factors at play. However, with congenital heart defects affecting around 1 in 100 human births, and numerous studies pointing to hemodynamics as a factor in cardiovascular morphogenesis, this is not an area in which we can afford to remain in the dark. This review seeks to present the case for the importance of research into the biomechanics of the developing cardiovascular system...
May 23, 2018: Progress in Biophysics and Molecular Biology
Y Z B Xue, Y M Niu, B Tang, C M Wang
Osteoarthritis (OA) is a prevalent joint disorder worldwide. Recent studies suggested that macrophages play an important role in the progression of OA. However, the detailed pathology related to macrophages is still ambiguous, especially those related to mechanotransduction. In this study, PCL/EUG composite scaffolds were first fabricated by electrospinning. The stiffness of as-fabricated scaffolds was controlled by adjusting the PCL-versus-EUG ratio. The mechanical properties, structural characterics and chemical composition of the scaffolds were investigated using various materials characterization techniques...
May 21, 2018: Progress in Biophysics and Molecular Biology
Azhar M Elwan, Aida A Salama, Abdelbaset M Sayed, Ahmad M Ghoneim, Aziza A Assaied, Fatma A Ibrahim, Hany A Shousha, Mohamed M M Elnasharty
The response of adult Wistar albino female rats toward two dose rates of gamma radiation delivered as acute dose of 7 Gy is investigated using classical methodologies as chemical, hematological and histological parameters in comparison with newly introduced dielectric parameters. Two groups of rats were exposed to γ ray with dose rates 533.35 mGy/min and 325.89 mGy/min. Then the irradiated groups were followed up for two weeks after irradiation. In case of higher dose rate, high percentage of animals was lost and there were substantial alterations in the dielectric parameters in addition to massive damage in liver and bone marrow cells...
May 10, 2018: Progress in Biophysics and Molecular Biology
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