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European Biophysics Journal: EBJ

Rudolf Rigler, Jerker Widengren
In this review, we give a historical view of how our research in the development and use of fluorescence correlation spectroscopy (FCS) and related techniques has its roots and how it originally evolved from the pioneering work of Manfred Eigen, his colleagues, and coworkers. Work on temperature-jump (T-jump) experiments, conducted almost 50 years ago, led on to the development of the FCS technique. The pioneering work in the 1970s, introducing and demonstrating the concept for FCS, in turn formed the basis for the breakthrough use of FCS more than 15 years later...
December 19, 2017: European Biophysics Journal: EBJ
Jonathan A Fauerbach, Thomas M Jovin
The defining feature of the extensive family of amyloid diseases is the formation of networks of entangled elongated protein fibrils and amorphous aggregates exhibiting crossed β-sheet secondary structure. The time course of amyloid conversion has been studied extensively in vitro with the proteins involved in the neurodegenerative pathology of Parkinson's disease (α-synuclein), Alzheimer's disease (Tau) and Huntington's disease (Huntingtin). Although much is known about the thermodynamics and kinetics of the transition from a soluble, intrinsically disordered monomer to the fibrillar end state, the putative oligomeric intermediates, currently considered to be the major initiators of cellular toxicity, are as yet poorly defined...
December 18, 2017: European Biophysics Journal: EBJ
Julian Victor, Gerhard Steger, Detlev Riesner
Sequence specific cleavage of RNA can be achieved by hammerhead ribozymes as well as DNAzymes. They comprise a catalytic core sequence flanked by regions that form double strands with complementary RNA. While different types of ribozymes have been discovered in natural organisms, DNAzymes derive from in vitro selection. Both have been used for therapeutic down-regulation of harmful proteins by reducing drastically the corresponding mRNA concentration. A priori DNAzymes appear advantageous because of the higher haemolytic stability and better cost effectiveness when compared to RNA...
December 16, 2017: European Biophysics Journal: EBJ
Herbert Jäckle, Carmen Rotte, Peter Gruss
Manfred Eigen turned 90 on May 9th, 2017. He celebrated with a small group of colleagues and friends on behalf of the many inspired by him over his lifetime-whether scientists, artists, or philosophers. A small group of friends, because many-who by their breakthroughs have changed the face of science in different research areas-have already died. But it was a special day, devoted to the many genius facets of Manfred Eigen's oeuvre, and a day to highlight the way in which he continues to exude a great, vital and unbroken passion for science as well as an insatiable curiosity beyond his own scientific interests...
December 11, 2017: European Biophysics Journal: EBJ
Edward Bormashenko, Alexander Voronel
Physical (thermodynamic and kinetic), chemical, and biological reasoning restrict the spatial dimensions of living cells (prokaryotic and eukaryotic) and confine them to between 1 and 100 µm. Cells should necessarily be macroscopic, dissipative objects, resisting thermal fluctuations and providing sufficient informational capacity. The upper limit of the spatial dimensions of cells is supplied by their ability to withstand gravity and inertia forces under reasonable deformations. The upper limit of cell dimensions is also governed by the hierarchy of characteristic time scales, inherent for mass and heat transport...
December 4, 2017: European Biophysics Journal: EBJ
H Moysés Nussenzveig
Membrane elastic properties play important roles in regulating cell shape, motility, division and differentiation. Here I review optical tweezer (OT) investigations of membrane surface tension and bending modulus, emphasizing didactic aspects and insights provided for cell biology. OT measurements employ membrane-attached microspheres to extract long cylindrical nanotubes named tethers. The Helfrich-Canham theory yields elastic parameters in terms of tether radius and equilibrium extraction force. It assumes initial point-like microsphere attachment and no cytoskeleton content within tethers...
November 21, 2017: European Biophysics Journal: EBJ
Shusuke Oura, Masahiro Ito, Yoshikazu Homma, Kazuo Umemura
In this study, we investigated the interaction of base sequence-assigned single-stranded DNA (ssDNA) molecules with the surfaces of single-walled carbon nanotube (SWNT)-thymine (T30)/cytosine (C30) hybrids (T30/C30-SWNT), by measuring the modulation of near-infrared (NIR) photoluminescence (PL). Significant PL shifts were observed when T30/C30-SWNTs were reacted with 30-mers of adenine (A30)/guanine (G30). In contrast, when non-complementary ssDNA was used, no significant energy shift was observed in the PL modulation except when T30-SWNTs were reacted with G30...
November 20, 2017: European Biophysics Journal: EBJ
Lech Gmachowski
Lateral movement of a molecule in a biomembrane containing small compartments (0.23-μm diameter) and large ones (0.75 μm) is analyzed using a fractal description of its walk. The early time dependence of the mean square displacement varies from linear due to the contribution of ballistic motion. In small compartments, walking molecules do not have sufficient time or space to develop an asymptotic relation and the diffusion coefficient deduced from the experimental records is lower than that measured without restrictions...
November 2, 2017: European Biophysics Journal: EBJ
Mahdi Muhammad Moosa, Asha Z Goodman, Josephine C Ferreon, Chul Won Lee, Allan Chris M Ferreon, Ashok A Deniz
Protein thermodynamic stability is intricately linked to cellular function, and altered stability can lead to dysfunction and disease. The linear extrapolation model (LEM) is commonly used to obtain protein unfolding free energies ([Formula: see text]) by extrapolation of solvent denaturation data to zero denaturant concentration. However, for some proteins, different denaturants result in non-coincident LEM-derived [Formula: see text] values, raising questions about the inherent assumption that the obtained [Formula: see text] values are intrinsic to the protein...
October 27, 2017: European Biophysics Journal: EBJ
A A Anosov, A A Sharakshane, E Yu Smirnova, O Yu Nemchenko
The Smoluchowski equation with an energy profile of a special type and an assumed hydrophobic ("half") pore source term is used to describe the process of hydrophilic pore formation in a lipid bilayer at the gel-liquid phase transition. The source term reflects the occurrence of molecule packing defects in a lipid bilayer at phase transition. The time sequences of the pore formation and closure events are treated as non-stationary, second-order Erlang flows whose characteristics depend on the equation solution...
October 25, 2017: European Biophysics Journal: EBJ
Mauro Dalla Serra, Alessandro Tossi
No abstract text is available yet for this article.
December 2017: European Biophysics Journal: EBJ
Viktorija Radotić, Dries Braeken, Damir Kovačić
Many studies have shown that the topography of the substrate on which neurons are cultured can promote neuronal adhesion and guide neurite outgrowth in the same direction as the underlying topography. To investigate this effect, isotropic substrate-complementary metal-oxide-semiconductor (CMOS) chips were used as one example of microelectrode arrays (MEAs) for directing neurite growth of spiral ganglion neurons. Neurons were isolated from 5 to 7-day-old rat pups, cultured 1 day in vitro (DIV) and 4 DIV, and then fixed with 4% paraformaldehyde...
December 2017: European Biophysics Journal: EBJ
C Potrich, L Lunelli, V Vaghi, L Pasquardini, C Pederzolli
A new communication route among cells was reported in recent years, via extracellular vesicles and their cargo. Exosomes in particular are attracting increasing interest as privileged mediators of this cell communication route. The exosome-mediated transfer of nucleic acids, especially of microRNAs, is particularly promising for their use both as biomarkers of pathologies and as a therapeutic tool. Here, a simplified model of interaction among cells, microRNAs and vesicles is studied using a biophysical approach...
December 2017: European Biophysics Journal: EBJ
Saša Svetina
Here we discuss cell-to-cell variability in isogenic cell populations on the basis of an analogy between the processes of vesicle self-reproduction and cell self-replication. A short review of the theoretical analysis of vesicle self-reproduction is presented to indicate that this process only occurs under the fulfillment of specific criteria: causal relations between the values of vesicle variables involved in its growth and division, and the parameters of the environment. It is shown that when division is asymmetric, both vesicle birth size and interdivision times are variable...
December 2017: European Biophysics Journal: EBJ
Aleksandra Pavićević, Jinghui Luo, Ana Popović-Bijelić, Miloš Mojović
Albumin is the most abundant plasma protein and as such has been the subject of many studies using a variety of techniques. One of them, capable of monitoring the conformational changes and the binding capacity of proteins, is electron paramagnetic resonance spectroscopy (EPR) spin labeling. To date, albumin has been investigated using a number of different spin labels, mostly spin-labeled fatty acids (SLFAs). However, albumin can bind up to seven equivalents of fatty acids, making it difficult to determine which parts of the molecule undergo conformational changes...
December 2017: European Biophysics Journal: EBJ
Katarina Macková, Alexandra Zahradníková, Matej Hoťka, Barbora Hoffmannová, Ivan Zahradník, Alexandra Zahradníková
Developing cardiac myocytes undergo substantial structural and functional changes transforming the mechanism of excitation-contraction coupling from the embryonic form, based on calcium influx through sarcolemmal DHPR calcium channels, to the adult form, relying on local calcium release through RYR calcium channels of sarcoplasmic reticulum stimulated by calcium influx. We characterized day-by-day the postnatal development of the structure of sarcolemma, using techniques of confocal fluorescence microscopy, and the development of the calcium current, measured by the whole-cell patch-clamp in isolated rat ventricular myocytes...
December 2017: European Biophysics Journal: EBJ
Julija Zavadlav, Staš Bevc, Matej Praprotnik
In this review article, we discuss and analyze some recently developed hybrid atomistic-mesoscopic solvent models for multiscale biomolecular simulations. We focus on the biomolecular applications of the adaptive resolution scheme (AdResS), which allows solvent molecules to change their resolution back and forth between atomistic and coarse-grained representations according to their positions in the system. First, we discuss coupling of atomistic and coarse-grained models of salt solution using a 1-to-1 molecular mapping-i...
December 2017: European Biophysics Journal: EBJ
P Parisse, I Rago, L Ulloa Severino, F Perissinotto, E Ambrosetti, P Paoletti, M Ricci, A P Beltrami, D Cesselli, L Casalis
Extracellular vesicles (EVs) are small vesicles ensuring transport of molecules between cells and throughout the body. EVs contain cell type-specific signatures and have been proposed as biomarkers in a variety of diseases. Their small size (<1 μm) and biological and physical functions make them obvious candidates for therapeutic agents in immune therapy, vaccination, regenerative medicine and drug delivery. However, due to the complexity and heterogeneity of their origin and composition, the actual mechanism through which these vesicles exert their functions is still unknown and represents a great biomedical challenge...
December 2017: European Biophysics Journal: EBJ
Thi-Huong Nguyen, Andreas Greinacher
Antibodies against the chemokine platelet factor 4 (PF4) in complex with heparin cause the prothrombotic adverse drug reaction heparin-induced thrombocytopenia (HIT). The current dilemma for laboratory diagnosis of HIT is that only about 50% of these antibodies are pathogenic, but the widely available enzyme immunosorbent assays (EIA), used for diagnosis in the clinical laboratory cannot differentiate between non-pathogenic- and pathogenic (platelet activating) antibodies. It would be highly desirable to improve diagnosis for HIT...
December 2017: European Biophysics Journal: EBJ
Luka Mesarec, Wojciech Góźdź, Samo Kralj, Miha Fošnarič, Samo Penič, Veronika Kralj-Iglič, Aleš Iglič
Biological membranes are composed of different components and there is no a priori reason to assume that all components are isotropic. It was previously shown that the anisotropic properties of membrane components may explain the stability of membrane tubular protrusions even without the application of external force. Our theoretical study focuses on the role of anisotropic membrane components in the stability of membrane tubular structures generated or stabilized by actin filaments. We show that the growth of the actin cytoskeleton inside the vesicle can induce the partial lateral segregation of different membrane components...
December 2017: European Biophysics Journal: EBJ
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