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Volume 1, June

Biophysica, Volume 1, Issue 1 (March 2021) – 6 articles

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Editorial
Biophysica—A New International Open Access Journal to Integrate Across the Modern Biophysical Sciences and Engineering
Biophysica 2021, 1(1), 73-75; https://0-doi-org.brum.beds.ac.uk/10.3390/biophysica1010006 - 22 Mar 2021
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Abstract
“What do Biophysicists talk about [...] Full article
Review
Recent Advances in Plasma-Based Cancer Treatments: Approaching Clinical Translation through an Intracellular View
Biophysica 2021, 1(1), 48-72; https://0-doi-org.brum.beds.ac.uk/10.3390/biophysica1010005 - 06 Mar 2021
Cited by 1 | Viewed by 604
Abstract
Plasma medicine is a multidisciplinary field of research which is combining plasma physics and chemistry with biology and clinical medicine to launch a new cancer treatment modality. It mainly relies on utilizing low temperature plasmas in atmospheric pressure to generate and instill a [...] Read more.
Plasma medicine is a multidisciplinary field of research which is combining plasma physics and chemistry with biology and clinical medicine to launch a new cancer treatment modality. It mainly relies on utilizing low temperature plasmas in atmospheric pressure to generate and instill a cocktail of reactive species to selectively target malignant cells for inhibition the cell proliferation and tumor progression. Following a summarized review of primary in vitro and in vivo studies on the antitumor effects of low temperature plasmas, this article briefly outlines the plasma sources which have been developed for cancer therapeutic purposes. Intracellular mechanisms of action and significant pathways behind the anticancer effects of plasma and selectivity toward cancer cells are comprehensively discussed. A thorough understanding of involved mechanisms helps investigators to explicate many disputes including optimal plasma parameters to control the reactive species combination and concentration, transferring plasma to the tumors located in deep, and determining the optimal dose of plasma for specific outcomes in clinical translation. As a novel strategy for cancer therapy in clinical trials, designing low temperature plasma sources which meet the technical requirements of medical devices still needs to improve in efficacy and safety. Full article
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Article
Nervous Activity of the Brain in Five Dimensions
Biophysica 2021, 1(1), 38-47; https://0-doi-org.brum.beds.ac.uk/10.3390/biophysica1010004 - 22 Feb 2021
Cited by 1 | Viewed by 810
Abstract
The nervous activity of the brain takes place in higher-dimensional functional spaces. It has been proposed that the brain might be equipped with phase spaces characterized by four spatial dimensions plus time, instead of the classical three plus time. This suggests that global [...] Read more.
The nervous activity of the brain takes place in higher-dimensional functional spaces. It has been proposed that the brain might be equipped with phase spaces characterized by four spatial dimensions plus time, instead of the classical three plus time. This suggests that global visualization methods for exploiting four-dimensional maps of three-dimensional experimental data sets might be used in neuroscience. We asked whether it is feasible to describe the four-dimensional trajectories (plus time) of two-dimensional (plus time) electroencephalographic traces (EEG). We made use of quaternion orthographic projections to map to the surface of four-dimensional hyperspheres EEG signal patches treated with Fourier analysis. Once achieved the proper quaternion maps, we show that this multi-dimensional procedure brings undoubted benefits. The treatment of EEG traces with Fourier analysis allows the investigation the scale-free activity of the brain in terms of trajectories on hyperspheres and quaternionic networks. Repetitive spatial and temporal patterns undetectable in three dimensions (plus time) are easily enlightened in four dimensions (plus time). Further, a quaternionic approach makes it feasible to identify spatially far apart and temporally distant periodic trajectories with the same features, such as, e.g., the same oscillatory frequency or amplitude. This leads to an incisive operational assessment of global or broken symmetries, domains of attraction inside three-dimensional projections and matching descriptions between the apparently random paths hidden in the very structure of nervous fractal signals. Full article
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Review
Chiral Dualism as a Unifying Principle in Molecular Biophysics
Biophysica 2021, 1(1), 22-37; https://0-doi-org.brum.beds.ac.uk/10.3390/biophysica1010003 - 08 Feb 2021
Viewed by 670
Abstract
The origin and potential role of chiral asymmetry remain one of the most exciting issues in biology. In this paper we review the chirality of biological macromolecules, starting at the level of single molecules and continuing to the level of supramolecular assemblies. We [...] Read more.
The origin and potential role of chiral asymmetry remain one of the most exciting issues in biology. In this paper we review the chirality of biological macromolecules, starting at the level of single molecules and continuing to the level of supramolecular assemblies. We discuss the physical and chemical consequences of the presence of chirality and their role in the self-organization and formation of structural hierarchies in cells. Homochirality may serve as an essential factor that invokes mechanisms required to control the formation of discrete structural hierarchies in macromolecules and macromolecular assemblies. Symmetry is of fundamental importance not only for all molecular biology as a systemic factor of its organization but also for pharmacology, as well as a systemic factor of drug stereospecificity. Full article
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Communication
A Protein Assembly Hypothesis for Population-Specific Decrease in Dementia with Time
Biophysica 2021, 1(1), 15-21; https://0-doi-org.brum.beds.ac.uk/10.3390/biophysica1010002 - 07 Feb 2021
Viewed by 492
Abstract
A recent report in the journal, Neurology, documents age-normalized, nation-specific (e.g., United States and Western Europe), progressive decrease of dementia, beginning about 25 years ago. This observation has, thus far, not had explanation. We begin our proposed explanation with the following previous [...] Read more.
A recent report in the journal, Neurology, documents age-normalized, nation-specific (e.g., United States and Western Europe), progressive decrease of dementia, beginning about 25 years ago. This observation has, thus far, not had explanation. We begin our proposed explanation with the following previous disease construct. (1) Some dementia is caused by innate immune over-response to infections. (2) The innate immune over-response occurs via excessive conversion of amyloid protein to α-sheet conformation. (3) This conversion evolved to inhibit invading microbes by binding microbe-associated α-sheet, e.g., in hyper-expanded capsid intermediates of some viruses. The rarity of human α-sheet makes this inhibition specific for microbial invaders. As foundation, here we observe directly, for the first time, extreme, sheet-like outer shell thinness in a hyper-expanded capsid of phage T3. Based on phage/herpesvirus homology, we propose the following. The above decrease in dementia is caused by varicella-zoster virus (VZV) vaccination, USFDA-approved about 25 years ago; VZV is a herpesvirus and causes chickenpox and shingles. In China and Japan, a cotemporaneous non-decrease is explained by lower anti-VZV vaccination. Co-assembly extension of α-sheet is relatively independent of amino acid sequence. Thus, we project that additional dementia is suppressible by vaccination against other viruses, including other herpesviruses. Full article
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Article
Molecular Forces Governing the Biological Function of Per-Arnt-Sim-B (PAS-B) Domains: A Comparative Computational Study
Biophysica 2021, 1(1), 1-14; https://0-doi-org.brum.beds.ac.uk/10.3390/biophysica1010001 - 05 Feb 2021
Viewed by 516
Abstract
Per-Arnt-Sim (PAS) domains are evolutionarily-conserved regions found in proteins in all living systems, involved in transcriptional regulation and the response to hypoxic and xenobiotic stress. Despite having low primary sequence similarity, they show an impressively high structural conservation. Nonetheless, understanding the underlying mechanisms [...] Read more.
Per-Arnt-Sim (PAS) domains are evolutionarily-conserved regions found in proteins in all living systems, involved in transcriptional regulation and the response to hypoxic and xenobiotic stress. Despite having low primary sequence similarity, they show an impressively high structural conservation. Nonetheless, understanding the underlying mechanisms that drive the biological function of the PAS domains remains elusive. In this work, we used molecular dynamics simulations and bioinformatics tools in order the investigate the molecular characteristics that govern the intrinsic dynamics of five PAS-B domains (human AhR receptor, NCOA1, HIF1α, and HIF2α transcription factors, and Drosophila Suzukii (D. Suzukii) juvenile hormone receptor JHR). First, we investigated the effects of different length of N and C terminal regions of the AhR PAS-B domain, showing that truncation of those segments directly affects structural stability and aggregation propensity of the domain. Secondly, using the recently annotated PAS-B located in the methoprene-tolerant protein/juvenile hormone receptor (JHR) from D. Suzukii, we have shown that the mutation of the highly conserved “gatekeeper” tyrosine to phenylalanine (Y322F) does not affect the stability of the domain. Finally, we investigated possible redox-regulation of the AhR PAS-B domain by focusing on the cysteinome residues within PAS-B domains. The cysteines in AhR PAS-B are directly regulating the dynamics of the small molecule ligand-gating loop (residues 305 to 326). In conclusion, we comprehensibly described several molecular features governing the behaviour of PAS-B domains in solution, which may lead to a better understanding of the forces driving their biological functions. Full article
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