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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 14, 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...
May 11, 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
Kyung In Baek, Yichen Ding, Chih-Chiang Chang, Megan Chang, René R Sevag Packard, Jeffrey J Hsu, Peng Fei, Tzung K Hsiai
The advent of 4-dimensional (4D) light-sheet fluorescence microscopy (LSFM) has provided an entry point for rapid image acquisition to uncover real-time cardiovascular structure and function with high axial resolution and minimal photo-bleaching/-toxicity. We hereby review the fundamental principles of our LSFM system to investigate cardiovascular morphogenesis and regeneration after injury. LSFM enables us to reveal the micro-circulation of blood cells in the zebrafish embryo and assess cardiac ventricular remodeling in response to chemotherapy-induced injury using an automated segmentation approach...
May 9, 2018: Progress in Biophysics and Molecular Biology
Bala Divya M, Maniharika Vemula, Kannan Balakrishnan, Sharmistha Banerjee, Lalitha Guruprasad
The distinctive PE and PPE families of proteins in Mycobacterium tuberculosis (M.tb), the tuberculosis (TB) causing bacteria, have been associated primarily with antigenicity, immune-modulation and virulence. Earlier, using structure-based sequence annotation, we identified a 225 amino acid conserved PE-PPE domain (Pfam: PF08237) commonly present in some PE and PPE proteins which was observed to comprise α/β-serine hydrolase fold. The prediction was supported by experimental validations of PE16 that was shown to exhibit esterase activity...
May 8, 2018: Progress in Biophysics and Molecular Biology
Pratichi Singh, J Febin Prabhu Dass
IFNL3 gene plays a crucial role in immune defense against viruses. It induces the interferon stimulated genes (ISGs) with antiviral properties by activating the JAK-STAT pathway. In this study, we investigated the evolutionary force involved in shaping the IFNL3 gene to perform its downstream function as a regulatory gene in HCV clearance. We have selected 25 IFNL3 coding sequences with human gene as a reference sequence and constructed a phylogeny. Furthermore, rate of variation, substitution saturation test, phylogenetic informativeness and differential selection were also analysed...
May 7, 2018: Progress in Biophysics and Molecular Biology
Chantal J M van Opbergen, Stephanie M van der Voorn, Marc A Vos, Teun P de Boer, Toon A B van Veen
Sudden cardiac death is a leading cause of death worldwide, mainly caused by highly disturbed electrical activation patterns in the heart. Currently, murine models are the most popular model to study underlying molecular mechanisms of inherited or acquired cardiac electrical abnormalities, although the numerous electrophysiological discrepancies between mouse and human raise the question whether mice are the optimal model to study cardiac rhythm disorders. Recently it has been uncovered that the zebrafish cardiac electrophysiology seems surprisingly similar to the human heart, mainly because the zebrafish AP contains a clear plateau phase and ECG characteristics show alignment with the human ECG...
May 7, 2018: Progress in Biophysics and Molecular Biology
John S Torday
Biology has remained descriptive since its formalization by Linnaeus in the 18th Century. Dobzhansky has challenged us to think mechanistically by stating that 'Nothing in Biology makes sense except in the light of evolution', but NeoDarwinian evolution remains untestable or refutable. The physicist Bohm has encouraged us to recognize that our perception of 'reality' is mediated by our evolved, subjective senses, though there is a coherent Implicate Order just out of reach. Only recently has a novel understanding of physiologic evolution based on cell-cell communication for embryonic development and phylogeny offered the opportunity to mechanistically merge Quantum Mechanics with Evolutionary Biology...
May 2, 2018: Progress in Biophysics and Molecular Biology
Mohamed M M Elnasharty, Hany A Shousha, Azhar M Elwan
In this paper we'll shed some light on well-known physical parameters to introduce them as new tools, biophysical markers, for diagnosis and prognosis of the molecular, cellular, tissue and organ biosystems such as Haemoglobin representing the macromolecules' category. Where the data reveal a lot of information about the effect of radiation dose rate on the macromolecule that are not discovered by conventional ways. Also, data put forward the dielectric and thermodynamical parameters and classify them as premiers and superiors for the detection of any disturbance that occurs in the electrical homogeneity of the macromolecule...
May 2, 2018: Progress in Biophysics and Molecular Biology
Waqar Ali, Shagufta Shafique, Sajid Rashid
Emerging implications of probable ATP-dependent RNA helicase p68 in tumorigenesis and progression makes it a discerning target for cancer therapy. Recently it has been reported that tyrosyl-phosphorylation of p68 promotes β-catenin nuclear translocation and cancer metastasis through elevating the epithelial-mesenchymal transition. Despite recent advances, the structural characterization of this interaction, mode of action and induced conformational changes remain elusive. Here, through comparative structure analysis and molecular dynamics simulation assays, we explored comparative binding pattern of phospho-p68 against β-catenin...
May 2, 2018: Progress in Biophysics and Molecular Biology
Patricia Hodgson, Jake Ireland, Bianka Grunow
The zebrafish (ZF) has become an essential model for biomedical, pharmacological and eco-toxicological heart research. Despite the anatomical differences between fish and human hearts, similarities in cellular structure and conservation of genes as well as pathways across vertebrates have led to an increase in the popularity of ZF as a model for human cardiac research. ZF research benefits from an entirely sequenced genome, which allows us to establish and study cardiovascular mutants to better understand cardiovascular diseases...
May 2, 2018: Progress in Biophysics and Molecular Biology
H Frederik Nijhout, Kenneth Z McKenna
The wings of Lepidoptera develop from imaginal disks that are made up of a simple two-layered epithelium whose structure is always congruent with the final adult wing. It is therefore possible to map every point on the imaginal disk to a location on the adult wing throughout the period of growth and morphogenesis. The wings of different species of Lepidoptera differ greatly in both size and shape, yet it is possible to fate-map homologous locations on the developing wing disks and explicitly monitor the growth, size, and shape of the wing, or any of its regions, throughout the entire ontogeny of the wing...
April 26, 2018: Progress in Biophysics and Molecular Biology
Axel Lange, Hans L Nemeschkal, Gerd B Müller
We present a cellular automaton-based model for threshold behaviors in vertebrate digit patterning and polydactyly formation. The rules of the model follow classical reactor-diffusion algorithms. Yet it is not physical diffusion that is taken as the required natural agent but the propagation of cellular states, which can be represented by the same differential equations. The bistable cellular states in the model correspond to mesenchymal limb bud cells that can be either "on" or "off" for the cartilage differentiation pathway...
April 25, 2018: Progress in Biophysics and Molecular Biology
Tomas Tomka, Dagmar Iber, Marcelo Boareto
The sculpturing of the vertebrate body plan into segments begins with the sequential formation of somites in the presomitic mesoderm (PSM). The rhythmicity of this process is controlled by travelling waves of gene expression. These kinetic waves emerge from coupled cellular oscillators and sweep across the PSM. In zebrafish, the oscillations are driven by autorepression of her genes and are synchronized via Notch signalling. Mathematical modelling has played an important role in explaining how collective properties emerge from the molecular interactions...
April 24, 2018: Progress in Biophysics and Molecular Biology
John S Torday, William B Miller
Reduction of developmental biology to self-referential cell-cell communication offers a portal for understanding fundamental mechanisms of physiology as derived from physics through quantum mechanics. It is argued that self-referential organization is implicit to the Big Bang and its further expression is a recoil reaction to that Singularity. When such a frame is considered, in combination with experimental evidence for the importance of epigenetic inheritance, the unicellular state can be reappraised as the primary object of selection...
April 13, 2018: Progress in Biophysics and Molecular Biology
William B Miller, John S Torday
Contemporary research supports the viewpoint that self-referential cognition is the proper definition of life. From that initiating platform, a cohesive alternative evolutionary narrative distinct from standard Neodarwinism can be presented. Cognition-Based Evolution contends that biological variation is a product of a self-reinforcing information cycle that derives from self-referential attachment to biological information space-time with its attendant ambiguities. That information cycle is embodied through obligatory linkages among energy, biological information, and communication...
April 13, 2018: Progress in Biophysics and Molecular Biology
Jaakko Haverinen, Minna Hassinen, Hanna Korajoki, Matti Vornanen
Na+ channel α-subunit composition of the zebrafish heart and electrophysiological properties of Na+ current (INa ) of zebrafish ventricular myocytes were examined. Eight Na+ channel α-subunits were expressed in both atrium and ventricle of the zebrafish heart. Nav 1.5Lb, an orthologue to the human Nav 1.5, was clearly the predominant isoform in both chambers representing 65.2 ± 4.1% and 83.1 ± 2.1% of all Na+ channel transcripts in atrium and ventricle, respectively. Nav 1.4b, an orthologue to human Nav 1...
April 12, 2018: Progress in Biophysics and Molecular Biology
Paul N Adler
The frizzled pathway regulates the planar polarity of epithelial cells. In insects this is manifested by the polarity of cuticular structures such as hairs (trichomes) and sensory bristles. A variety of evidence has established that this is achieved by regulating the subcellular location for activating the cytoskeleton in the epithelial cells. How this is accomplished is still poorly understood. In the best-studied tissue, the Drosophila pupal wing two important cytoskeletal regulators have been identified...
April 9, 2018: Progress in Biophysics and Molecular Biology
Alexis Pietak, Michael Levin
Positional information describes pre-patterns of morphogenetic substances that alter spatio-temporal gene expression to instruct development of growth and form. A wealth of recent data indicate bioelectrical properties, such as the transmembrane potential (Vmem ), are involved as instructive signals in the spatiotemporal regulation of morphogenesis. However, the mechanistic relationships between Vmem and molecular positional information are only beginning to be understood. Recent advances in computational modeling are assisting in the development of comprehensive frameworks for mechanistically understanding how endogenous bioelectricity can guide anatomy in a broad range of systems...
April 4, 2018: Progress in Biophysics and Molecular Biology
Zhongyu Liu, Manting Au, Xuan Wang, Pok-Man Boris Chan, Puxiang Lai, Lei Sun, Yongping Zheng, Limin Rong, Chunyi Wen
OBJECTIVES: This pilot study aimed to investigate the feasibility of non-invasively assessing synovial tissue hypoxia in vivo using photoacoustic (PA) imaging in a post-traumatic osteoarthritis model and explore its correlation with OA severity. METHODS: The three-dimensional vasculature structure and oxygenation level of synovial tissues of destabilization of the medial meniscus (DMM)-induced osteoarthritis (OA) mice were longitudinally monitored using PA imaging...
March 27, 2018: Progress in Biophysics and Molecular Biology
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