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Progress in Biophysics and Molecular Biology

Sepanta Hosseinpour, Reza Fekrazad, Praveen R Arany, Qingsong Ye
Photobiomodulation (PBM) encompasses a light application aimed to increase healing process, tissue regeneration, and reducing inflammation and pain. PBM is specifically aimed to modify the expression of cellular molecules; however, PBM impacts on cellular and molecular pathways especially in bone regenerative medicine have been investigated in scattered different studies. The purpose of the current study is to systematically review evidence on molecular impact of PBM on bone regeneration. A comprehensive electronic search in Medline, Scopus, EMBASE, EBSCO, Cochrane library, web of science, and google scholar was conducted from January 1975 to October 2018 limited to English language publications on administrations of photobiomodulation for bone regeneration which evaluated biological factors...
April 16, 2019: Progress in Biophysics and Molecular Biology
Maxim P Evstigneev, Anatoly S Buchelnikov, Vladislav P Evstigneev
The review discusses the theory of interceptor-protector action (the IPA theory) as the new self-consistent biophysical theory establishing a quantitative interrelation between parameters measured in independent physico-chemical experiment and in vitro biological experiment for the class of DNA binding drugs. The elements of the theory provide complete algorithm of analysis, which may potentially be applied to any system of DNA targeting aromatic drugs. Such analytical schemes, apart from extension of current scientific knowledge, are important in the context of rational drug design for managing drug's response by changing the physico-chemical parameters of molecular complexation...
April 13, 2019: Progress in Biophysics and Molecular Biology
Bin Tang
No abstract text is available yet for this article.
April 13, 2019: Progress in Biophysics and Molecular Biology
Noa Lamm, Samuel Rogers, Anthony J Cesare
DNA replication plays a central role in genome health. Deleterious alteration of replication dynamics, or "replication stress", is a key driver of genome instability and oncogenesis. The replication stress response is regulated by the ATR kinase, which functions to mitigate replication abnormalities through coordinated efforts that arrest the cell cycle and repair damaged replication forks. mTOR kinase regulates signaling networks that control cell growth and metabolism in response to environmental cues and cell stress...
April 13, 2019: Progress in Biophysics and Molecular Biology
Marco Tarantola, Tim Meyer, Christoph F Schmidt, Wolfram Hubertus Zimmermann
No abstract text is available yet for this article.
April 10, 2019: Progress in Biophysics and Molecular Biology
V V Matveev
Cell theory, as formulated by Theodor Schwann in 1839, introduced the idea that the cell is the main structural unit of living nature. Later, in solving the problem of cell multiplication, Rudolf Virchow expanded the cell theory with a postulate: all cells only arise from pre-existing cells. But what did the very first cell arise from? This paper proposes extending the Virchow's law by the assumption that between the nonliving protocell and the first living cell the continuity of fundamental physical properties (the principle of invariance of physical properties) is preserved...
April 6, 2019: Progress in Biophysics and Molecular Biology
Paul T Matsudaira, Chandra S Verma
No abstract text is available yet for this article.
April 2, 2019: Progress in Biophysics and Molecular Biology
Gilza Barcelos de Souza, Tiago Antônio de Oliveira Mendes, Patrícia Pereira Fontes, Vanessa de Almeida Barros, Amanda Bonoto Gonçalves, Thiago de Freitas Ferreira, Maximiller Dal-Bianco Lamas Costa, Murilo Siqueira Alves, Luciano Gomes Fietto
Dormancy-Associated gene 1/Auxin Repressed protein (DRM1/ARP) genes are responsive to hormones involved in defense response to biotic stress, such as salicylic acid (SA) and methyl jasmonate (MeJA), as well as to hormones that regulate plant growth and development, including auxins. These characteristics suggest that this gene family may be an important link between the response to pathogens and plant growth and development. In this investigation, the DRM1/ARP genes were identified in the genome of four legume species...
March 23, 2019: Progress in Biophysics and Molecular Biology
Brian J Caldwell, Charles E Bell
While much of this volume focuses on mammalian DNA repair systems that are directly involved in genome instability and cancer, it is important to still be mindful of model systems from prokaryotes. Herein we review the Red recombination system of bacteriophage λ, which consists of an exonuclease for resecting dsDNA ends, and a single-strand annealing protein (SSAP) for binding the resulting 3'-overhang and annealing it to a complementary strand. The genetics and biochemistry of Red have been studied for over 50 years, in work that has laid much of the foundation for understanding DNA recombination in higher eukaryotes...
March 20, 2019: Progress in Biophysics and Molecular Biology
Albino Bacolla, Zu Ye, Zamal Ahmed, John A Tainer
A hallmark of cancer is genomic instability, which can enable cancer cells to evade therapeutic strategies. Here we employed a computational approach to uncover mechanisms underlying cancer mutational burden by focusing upon relationships between 1) translocation breakpoints and the thousands of G4 DNA-forming sequences within retrotransposons impacting transcription and exemplifying probable non-B DNA structures and 2) transcriptome profiling and cancer mutations. We determined the location and number of G4 DNA-forming sequences in the Genome Reference Consortium Human Build 38 and found a total of 358,605 covering ~13...
March 14, 2019: Progress in Biophysics and Molecular Biology
Neha Kumari, Savita Yadav
A large section of cellular proteins in both prokaryotic and eukaryotic systems have oligomeric property. Intently, oligomerization of protein is an invaluable phenomenon from the point of view of protein evolution. This review comprises an overview on modulation of protein oligomerization. The comprehensive modulation of protein oligomerization can be supportive for effective drug designing in future. Most common mechanisms of protein oligomerization are domain swapping and ligand induced dimerization. Infrequent mechanism of protein oligomerization involves point mutations at dimer interface, post-translational modification and insertion/deletion at interface...
March 11, 2019: Progress in Biophysics and Molecular Biology
Philippe Frit, Virginie Ropars, Mauro Modesti, Jean-Baptiste Charbonnier, Patrick Calsou
In vertebrates, double-strand breaks in DNA are primarily repaired by Non-Homologous End-Joining (NHEJ). The ring-shaped Ku heterodimer rapidly senses and threads onto broken DNA ends forming a recruiting hub. Through protein-protein contacts eventually reinforced by protein-DNA interactions, the Ku-DNA hub attracts a series of specialized proteins with scaffolding and/or enzymatic properties. To shed light on these dynamic interplays, we review here current knowledge on proteins directly interacting with Ku and on the contact points involved, with a particular accent on the different classes of Ku-binding motifs identified in several Ku partners...
March 6, 2019: Progress in Biophysics and Molecular Biology
Aleksandra Klimas, Gloria Ortiz, Steven C Boggess, Evan W Miller, Emilia Entcheva
Combined optogenetic stimulation and optical imaging permit scalable, contact-free high-throughput probing of cellular electrophysiology and optimization of stem-cell derived excitable cells, such as neurons and muscle cells. We report a new "on-axis" configuration (combined single optical path for stimulation and for multiparameter imaging) of OptoDyCE, our all-optical platform for studying human induced pluripotent stem-cell-derived cardiomyocytes (hiPSC-CMs) and other cell types, optically driven by Channelrhodopsin2 (ChR2)...
March 5, 2019: Progress in Biophysics and Molecular Biology
Fatih Deniz
Water pollution and diminishing fossil based fuel reserves with their deleterious exhaust gases are worldwide major environmental and economic problems. Datura stramonium L. species greatly grows wild in the most parts of temperate regions of the world. The biodiesel production from the seed oil of D. stramonium L. have been reported in literature. However, no study has been found regarding the use of defatted residual seed biomass of D. stramonium L. for the wastewater treatment. An integrated approach towards sustainable wastewater treatment and biofuel production using D...
March 1, 2019: Progress in Biophysics and Molecular Biology
Marc-Williams Debono, Gustavo Maia Souza
In this manuscript we propose the working hypothesis of plants as eco-plastic and electromic interfaces able to drive emergent intelligent behaviors from synchronized electrical networks. Behind the semantic and anthropocentric problems related by many authors to the extensive use of the terms cognition, intelligence or even 'consciousness' for plants, we preconize a more pragmatic point of view considering the vegetal world as a complex biosystemic entity able to co-build the world or a form of world or of significant reality via a set of reciprocal, emerging and confluent interactions...
February 28, 2019: Progress in Biophysics and Molecular Biology
Birgit Goversen, Malin Kb Jonsson, Nikki Hl van den Heuvel, Rianne Rijken, Marc A Vos, Toon Ab van Veen, Teun P de Boer
The human Ether-à-go-go Related Gene (hERG) encodes the pore forming subunit of the channel that conducts the rapid delayed rectifier potassium current IKr . IKr drives repolarization in the heart and when IKr is dysfunctional, cardiac repolarization delays, the QT interval on the electrocardiogram (ECG) prolongs and the risk of developing lethal arrhythmias such as Torsade de Pointes (TdP) increases. TdP risk is incorporated in drug safety screening for cardiotoxicity where hERG is the main target since the IKr channels appear highly sensitive to blockage...
February 27, 2019: Progress in Biophysics and Molecular Biology
Chelsea E Cunningham, Mackenzie J MacAuley, Garima Yadav, Frederick S Vizeacoumar, Andrew Freywald, Franco J Vizeacoumar
Genomic instability, and more specifically chromosomal instability (CIN), arises from a number of processes that are defective in cancer, such as aberrant mitotic cell division, replication stress, defective DNA damage repair, and ineffective telomere maintenance. CIN is an emerging hallmark of cancer that contributes to tumor heterogeneity through increased rates of genetic alterations. As genetic heterogeneity within a single tumor and between tumors is a key challenge leading to treatment failures, this brings to question, whether therapeutic approaches should aim at the genetic diversity or a specific mutation present within these tumors...
February 25, 2019: Progress in Biophysics and Molecular Biology
Ahmad Tahmasebi, Elham Ashrafi-Dehkordi, Amir Ghaffar Shahriari, Seyed Mohammad Mazloomi, Esmaeil Ebrahimie
Abiotic environmental stresses are important factors that limit the growth, fiber yield, and quality of cotton. In this study, an integrative meta-analysis and a system-biology analysis were performed to explore the underlying transcriptomic mechanisms that are critical for response to stresses. From the meta-analysis, it was observed that a total of 1465 differentially expressed genes (DEGs) between normal and stress conditions. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that DEGs were significantly enriched in the ubiquitin-dependent process, biosynthesis of secondary metabolites, plant hormone, and signaled transduction...
February 22, 2019: Progress in Biophysics and Molecular Biology
Andrej Korenić, Slobodan Perović, Milan M Ćirković, Paul-Antoine Miquel
Symmetry-based explanations using symmetry breaking (SB) as the key explanatory tool have complemented and replaced traditional causal explanations in various domains of physics. The process of spontaneous SB is now a mainstay of contemporary explanatory accounts of large chunks of condensed-matter physics, quantum field theory, nonlinear dynamics, cosmology, and other disciplines. A wide range of empirical research into various phenomena related to symmetries and SB across biological scales has accumulated as well...
February 15, 2019: Progress in Biophysics and Molecular Biology
Fatih Deniz
A combinatorial study integrating synthetic dye bioremediation and biodiesel production using discarded pepper seed biomass was performed for a cleaner and more sustainable environment/energy in the present work. The vegetal oil was extracted from the pepper seed biomass and the defatted residual biomass was mainly investigated as a sustainable green generation alternative biosorbent source for the treatment of colored aqueous effluents. To test the wastewater cleaning ability of biosorbent, basic red 46 was selected as a common harmful model synthetic dye...
January 21, 2019: Progress in Biophysics and Molecular Biology
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