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European Biophysics Journal: EBJ

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https://www.readbyqxmd.com/read/29159501/a-fundamental-study-of-photoluminescence-modulation-from-dna-wrapped-single-walled-carbon-nanotubes
#1
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
https://www.readbyqxmd.com/read/29094176/fractal-analysis-of-lateral-movement-in-biomembranes
#2
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
https://www.readbyqxmd.com/read/29080139/denaturant-specific-effects-on-the-structural-energetics-of-a-protein-denatured-ensemble
#3
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
https://www.readbyqxmd.com/read/29071369/erlang-flow-of-hydrophilic-pore-formation-and-closure-events-in-a-lipid-bilayer-during-phase-transition-resulting-from-diffusion-in-the-radius-space
#4
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
https://www.readbyqxmd.com/read/28980105/allowance-for-radial-dilution-in-evaluating-the-concentration-dependence-of-sedimentation-coefficients-for-globular-proteins
#5
Trushar R Patel, Donald J Winzor, David J Scott
The accuracy with which the concentration dependence of the sedimentation coefficient, s = s (0)(1 - kc), can be quantified for globular proteins by commonly used procedures has been examined by subjecting simulated sedimentation velocity distributions for ovalbumin to c(s)‒s analysis. Because this procedure, as well as its g(s)‒s counterpart, is based on assumed constancy of s over the time course of sedimentation coefficient measurement in a given experiment, the best definition of the concentration coefficient k is obtained by associating the measured s with the mean of plateau concentrations for the initial and final distributions used for its determination...
October 4, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28975383/intrinsic-thermodynamics-of-high-affinity-inhibitor-binding-to-recombinant-human-carbonic-anhydrase-iv
#6
Aurelija Mickevičiūtė, David D Timm, Marius Gedgaudas, Vaida Linkuvienė, Zhiwei Chen, Abdul Waheed, Vilma Michailovienė, Asta Zubrienė, Alexey Smirnov, Edita Čapkauskaitė, Lina Baranauskienė, Jelena Jachno, Jurgita Revuckienė, Elena Manakova, Saulius Gražulis, Jurgita Matulienė, Enrico Di Cera, William S Sly, Daumantas Matulis
Membrane-associated carbonic anhydrase (CA) isoform IV participates in carbon metabolism and pH homeostasis and is implicated in the development of eye diseases such as retinitis pigmentosa and glaucoma. A series of substituted benzenesulfonamides were designed and their binding affinity to CA IV was determined by fluorescent thermal shift assay and isothermal titration calorimetry (ITC). Compound [(4-chloro-2-phenylsulfanyl-5-sulfamoyl-benzoyl)amino]propyl acetate (19) bound CA IV with the K d of 1.0 nM and exhibited significant selectivity over the remaining 11 human CA isoforms...
October 3, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28929205/simulation-of-the-osmosis-based-drug-encapsulation-in-erythrocytes
#7
Duobiao Ge, Lili Zou, Chengpan Li, Sen Liu, Shibo Li, Sijie Sun, Weiping Ding
Drug-loaded erythrocytes have been proposed for the treatment of disease. A common way to load drugs into erythrocytes is to apply osmotic shock. Currently, osmosis-based drug encapsulation is studied mainly experimentally, whereas a related theoretical model is still incomplete. In this study, a set of equations is developed to simulate the osmosis-based drug-encapsulation process. First, the modeling is validated with hemolysis rates and the drug-loaded quantities to be found in the literature. Then, the variation of the erythrocyte volume, formation of the pore on the erythrocyte membrane, and quantities of drug loaded into and hemoglobin released from erythrocytes are studied...
September 20, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28916873/effects-of-methotrexate-on-the-quality-of-oocyte-maturation-in-vitro
#8
N Tian, J Yu, Sh Zhang, W Y Ma, T Wang, Y M Wang
Methotrexate (MTX), an antifolate drug, is widely used for clinical treatment of malignancies and ectopic pregnancy. Many studies have documented that MTX has strong side-effects on rapidly dividing somatic cells. However, its side-effects on female reproductive cells have not been widely reported. Combined with in vitro culture, two-photon fluorescence imaging and three-dimensional reconstruction, this study analyzed the effects of MTX on oocyte maturation time, chromosome arrangement, karyotype, spindle morphology, and the localization of microtubule organizing centers (MTOCs)...
September 15, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28889232/modulation-of-the-flavin-protein-interactions-in-nadh-peroxidase-and-mercuric-ion-reductase-a-resonance-raman-study
#9
Julie Keirsse-Haquin, Thierry Picaud, Luc Bordes, Adrienne Gomez de Gracia, Alain Desbois
NADH peroxidase (Npx) and mercuric ion reductase (MerA) are flavoproteins belonging to the pyridine nucleotide:disulfide oxidoreductases (PNDO) and catalyzing the reduction of toxic substrates, i.e., hydrogen peroxide and mercuric ion, respectively. To determine the role of the flavin adenine dinucleotide (FAD) in the detoxification mechanism, the resonance Raman (RR) spectra of these enzymes under various redox and ligation states have been investigated using blue and/or near-UV excitation(s). These data were compared to those previously obtained for glutathione reductase (GR), another enzyme of the PNDO family, but catalyzing the reduction of oxidized glutathione...
September 9, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28889176/proton-pump-inhibitors-have-ph-dependent-effects-on-the-thermostability-of-the-carboxyl-terminal-domain-of-voltage-gated-proton-channel-hv1
#10
Qing Zhao, Weiyan Zuo, Shangrong Zhang, Yongqiang Zhang, Chuanyong Li, Shu Jie Li
The voltage-gated proton channel Hv1 is highly selective for H(+) and is activated by membrane depolarization and pH gradient. An increased external and decreased internal pH opens the Hv1 channel. The intracellular C-terminal domain of Hv1 is responsible for channel dimerization, cooperative, and thermosensitive gating. Here, we found that proton pump inhibitors (PPIs) interact with the C-terminal domain of human Hv1. The interaction between PPIs and the C-terminal domain, which is pH-dependent, lowered the thermal and structural stability of the protein at pH 4, but enhanced the thermal and structural stability at pH 8...
September 9, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28875401/mechanism-of-salt-induced-activity-enhancement-of-a-marine-derived-laccase-lac15
#11
Jie Li, Yanan Xie, Rui Wang, Zemin Fang, Wei Fang, Xuecheng Zhang, Yazhong Xiao
Laccase (benzenediol: oxygen oxidoreductases, EC1.10.3.2) is a multi-copper oxidase capable of oxidizing a variety of phenolic and other aromatic organic compounds. The catalytic power of laccase makes it an attractive candidate for potential applications in many areas of industry including biodegradation of organic pollutants and synthesis of novel drugs. Most laccases are vulnerable to high salt and have limited applications. However, some laccases are not only tolerant to but also activated by certain concentrations of salt and thus have great application potential...
September 5, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28865004/gold-nanoparticles-with-patterned-surface-monolayers-for-nanomedicine-current-perspectives
#12
REVIEW
Paolo Pengo, Maria Şologan, Lucia Pasquato, Filomena Guida, Sabrina Pacor, Alessandro Tossi, Francesco Stellacci, Domenico Marson, Silvia Boccardo, Sabrina Pricl, Paola Posocco
Molecular self-assembly is a topic attracting intense scientific interest. Various strategies have been developed for construction of molecular aggregates with rationally designed properties, geometries, and dimensions that promise to provide solutions to both theoretical and practical problems in areas such as drug delivery, medical diagnostics, and biosensors, to name but a few. In this respect, gold nanoparticles covered with self-assembled monolayers presenting nanoscale surface patterns-typically patched, striped or Janus-like domains-represent an emerging field...
September 1, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29128893/regional-biophysics-conference-rbc2016
#13
Mauro Dalla Serra, Alessandro Tossi
No abstract text is available yet for this article.
December 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29075798/microelectrode-array-induced-neuronal-alignment-directs-neurite-outgrowth-analysis-using-a-fast-fourier-transform-fft
#14
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
https://www.readbyqxmd.com/read/29043382/cell-transfer-of-information-via-mir-loaded-exosomes-a-biophysical-approach
#15
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
https://www.readbyqxmd.com/read/28986665/investigating-cell-functioning-by-theoretical-analysis-of-cell-to-cell-variability
#16
REVIEW
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
https://www.readbyqxmd.com/read/28942583/maleimido-proxyl-as-an-epr-spin-label-for-the-evaluation-of-conformational-changes-of-albumin
#17
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
https://www.readbyqxmd.com/read/28913625/calcium-release-dependent-inactivation-precedes-formation-of-the-tubular-system-in-developing-rat-cardiac-myocytes
#18
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
https://www.readbyqxmd.com/read/28905203/adaptive-resolution-simulations-of-biomolecular-systems
#19
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
https://www.readbyqxmd.com/read/28866771/atomic-force-microscopy-analysis-of-extracellular-vesicles
#20
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
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