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Lauren E Marshall, Roy Koomullil, Andra R Frost, Joel L Berry
A preclinical testing model for cancer therapeutics that replicates in vivo physiology is needed to accurately describe drug delivery and efficacy prior to clinical trials. To develop an in vitro model of breast cancer that mimics in vivo drug/nutrient delivery as well as physiological size and bio-composition, it is essential to describe the mass transport quantitatively. The objective of the present study was to develop in vitro and computational models to measure mass transport from a perfusion system into a 3D extracellular matrix (ECM)...
October 21, 2016: Annals of Biomedical Engineering
Ting Hu, Qilin Huang, Kahing Wong, Hong Yang
Four polysaccharide fractions, LRP-1, LRP-2, LRP-3 and LRP-4 were extracted stepwise from Lignosus rhinocerotis sclerotia with distilled water at 25, 95, 120°C and 1.0M NaOH solution at 4°C. Their structure, molecular size and chain conformation were clarified using SEC-MALLS-RI, GC, FT-IR and UV-VIS. Furthermore, their immunomodulatory activities were evaluated by the model of cyclophosphamide (Cy)-induced immunosuppression. The LRP-1 and LRP-2 were polysaccharide-protein complexes (46-68% β-D-glucan and 27-48% protein), while LRP-3 and LRP-4 were absolutely composed of β-D-glucose...
October 18, 2016: International Journal of Biological Macromolecules
Virve Sihvola, Anna-Liisa Levonen
Reactive oxygen species (ROS) and products of their reactions with cellular macromolecules such as unsaturated fatty acids have been implicated to be important regulators of signalling processes via oxidation or alkylation of redox active thiol residues in target proteins. One of key redox-sensitive signalling proteins mediating the response to oxidant stress is Keap1 (Kelch-like erythroid cell-derived protein with CNC homology [ECH]-associated protein 1), which is a negative regulator of transcription factor Nuclear factor-erythroid 2 p45-related factor 2 (Nrf2) and the central hub for sensing endogenous and environmental oxidative and electrophilic stress...
October 18, 2016: Archives of Biochemistry and Biophysics
J L Vilas, J Navas, J Gómez-Blanco, J M de la Rosa-Trevín, R Melero, I Peschiera, I Ferlenghi, J Cuenca, R Marabini, J M Carazo, J Vargas, C O S Sorzano
Random conical tilt (RCT) and orthogonal tilt reconstruction (OTR) are two remarkable methods for reconstructing the three-dimensional structure of macromolecules at low resolution. These techniques use two images at two different sample tilts. One of the most demanding steps in these methods at the image processing level is to identify corresponding particles on both micrographs, and manual or semiautomatic matching methods are usually used. Here we present an approach to solve this bottleneck with a fully automatic method for assigning particle tilt pairs...
October 18, 2016: Journal of Structural Biology
Bavand Keshavarz, Eric C Houze, John R Moore, Michael R Koerner, Gareth H McKinley
The breakup and atomization of complex fluids can be markedly different than the analogous processes in a simple Newtonian fluid. Atomization of paint, combustion of fuels containing antimisting agents, as well as physiological processes such as sneezing are common examples in which the atomized liquid contains synthetic or biological macromolecules that result in viscoelastic fluid characteristics. Here, we investigate the ligament-mediated fragmentation dynamics of viscoelastic fluids in three different canonical flows...
October 7, 2016: Physical Review Letters
Hahnbeom Park, Philip Bradley, Per Greisen, Yuan Liu, Vikram Khipple Mulligan, David E Kim, David Baker, Frank DiMaio
Most biomolecular modeling energy functions for structure prediction, sequence design, and molecular docking, have been parameterized using existing macromolecular structural data; this contrasts molecular mechanics force fields which are largely optimized using small-molecule data. In this study, we describe an integrated method that enables optimization of a biomolecular modeling energy function simultaneously against small-molecule thermodynamic data and high-resolution macromolecular structural data. We use this approach to develop a next-generation Rosetta energy function that utilizes a new anisotropic implicit solvation model, and an improved electrostatics and Lennard-Jones model, illustrating how energy functions can be considerably improved in their ability to describe large-scale energy landscapes by incorporating both small-molecule and macromolecule data...
October 21, 2016: Journal of Chemical Theory and Computation
Sang-Ho Kwon, Sekyung Oh, Marisa Nacke, Keith E Mostov, Joshua H Lipschutz
Exosomes, 40-150 nm extracellular vesicles, transport biological macromolecules that mediate intercellular communications. While exosomes are known to originate from maturation of endosomes into multivesicular endosomes (MVEs; also known as multivesicular bodies, MVBs) with subsequent fusion of the MVEs with the plasma membrane, it remains unclear how cargos are selected for exosomal release. Using an inducible expression system for the exosome cargo protein GPRC5B and following its trafficking trajectory, we show here that newly synthesized GPRC5B protein accumulates in the Golgi complex prior to its release into exosomes...
October 20, 2016: Journal of Biological Chemistry
Shu Yang, Anne Rosenwald
Macroautophagy, a highly conserved process in eukaryotic cells, is initiated in response to stress, especially nutrient starvation. Macroautophagy helps cells survive by engulfing proteins and organelles into an unusual double-membraned structure called the autophagosome, which then fuses with the lysosome. Upon degradation of the engulfed contents, the building blocks are recycled for synthesis of new macromolecules. Recent work has demonstrated that construction of the autophagosome requires a variety of small GTPases in variations of their normal roles in membrane traffic...
October 20, 2016: Small GTPases
Agnieszka Mierczynska-Vasilev, Paul A Smith
The adsorption of macromolecules on solid surfaces is of great importance in the field of nanotechnology, biomaterials, biotechnological, and food processes. In the field of oenology adsorption of wine macromolecules such as polyphenols, polysaccharides, and proteins is much less desirable on membrane materials because of fouling and reduced filtering performance. On the other hand, adsorption of these molecules on processing aids is very beneficial for achieving wine clarity and stability. In this article, the effect of surface chemical functionalities on the adsorption of white, rosé, and red wine constituents was evaluated...
October 18, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Joana Roßberg, Falko O Rottke, Burkhard Schulz, Andreas Lendlein
The influence of terminal functionalization of oligo(ε-caprolactone)s (OCL) with phenylboronic acid pinacol ester or phenylboronic acid on the enzymatic degradation behavior at the air-water interface is investigated by the Langmuir monolayer degradation technique. While the unsubstituted OCL immediately degrades after injection of the enzyme lipase from Pseudomonas cepacia, enzyme molecules are incorporated into the films based on end-capped OCL before degradation. This incorporation of enzymes does not inhibit or suppress the film degradation, but retards it significantly...
October 20, 2016: Macromolecular Rapid Communications
Mordjane Boukhet, Fabien Piguet, Hadjer Ouldali, Manuela Pastoriza-Gallego, Juan Pelta, Abdelghani Oukhaled
The transport of macromolecules through nanopores is involved in many biological functions and is today at the basis of promising technological applications. Nevertheless the interpretation of the dynamics of the macromolecule/nanopore interaction is still misunderstood and under debate. At the nanoscale, inside biomimetic channels under an external applied voltage, electrophoresis, which is the electric force acting on electrically charged molecules, and electroosmotic flow (EOF), which is the fluid transport associated with ions, contribute to the direction and magnitude of the molecular transport...
October 20, 2016: Nanoscale
James M Cash, Mathew R Heal, Ben Langford, Julia Drewer
The atmospheric reactions leading to the generation of secondary organic aerosol (SOA) from the oxidation of isoprene are generally assumed to produce only racemic mixtures, but aspects of the chemical reactions suggest this may not be the case. In this review, the stereochemical outcomes of published isoprene-degradation mechanisms contributing to high amounts of SOA are evaluated. Despite evidence suggesting isoprene first-generation oxidation products do not contribute to SOA directly, this review suggests the stereochemistry of first-generation products may be important because their stereochemical configurations may be retained through to the second-generation products which form SOA...
October 20, 2016: Environmental Science. Processes & Impacts
Renata Kurtyka, Wojciech Pokora, Zbigniew Tukaj, Waldemar Karcz
Naphthoquinones are secondary metabolites widely distributed in nature and produced by bacteria, fungi and higher plants. Their biological activity may result from induction of oxidative stress, caused by redox cycling, or direct interaction with cellular macromolecules, in which quinones act as electrophiles. The redox homeostasis is known as one of factors involved in auxin-mediated plant growth regulation. To date, however, little is known about the crosstalk between reactive oxygen species (ROS) produced by quinones and the plant growth hormone auxin (IAA)...
October 19, 2016: AoB Plants
Koen E Merkus, Menno W J Prins, Cornelis Storm
Tethered particle motion (TPM), the motion of a micro- or nanoparticle tethered to a substrate by a macromolecule, is a system that has proven to be extremely useful for its ability to reveal physical features of the tether, because the thermal motion of the bound particle reports sensitively on parameters like the length, the rigidity, or the folding state of its tether. In this article, we survey the applicability of TPM to probe the kinetics of single secondary bonds, bonds that form and break between the tethered particle and a substrate due, for instance, to receptor/ligand pairs on particle and substrate...
October 18, 2016: Biophysical Journal
Han Wang, Xingyu Gao, Jun Fang
The smooth particle mesh Ewald (SPME) method is the standard method for computing the electrostatic interactions in the molecular simulations. In this work, we develop the multiple staggered mesh Ewald (MSME) method, which averages the SPME forces computed on, e.g. M, staggered meshes. We prove, from a theoretical perspective, that the MSME is as accurate as the SPME, but uses M(2) times less mesh points in a certain parameter range. In the complementary parameter range, the MSME is as accurate as the SPME with twice of the interpolation order...
October 19, 2016: Journal of Chemical Theory and Computation
Xiang Liu, Danijela Gregurec, Joseba Irigoyen, Angel Martinez, Sergio Moya, Roberto Ciganda, Philippe Hermange, Jaime Ruiz, Didier Astruc
Understanding the relationship between the location of nanoparticles (NPs) in an organic matrix and their catalytic performances is essential for catalyst design. Here we show that catalytic activities of Au, Ag and CuNPs stabilized by dendrimers using coordination to intradendritic triazoles, galvanic replacement or stabilization outside dendrimers strongly depends on their location. AgNPs are found at the inner click dendrimer periphery, whereas CuNPs and AuNPs are encapsulated in click dendrimer nanosnakes...
October 19, 2016: Nature Communications
Mariana Pavel, David C Rubinsztein
Autophagy (literally "self-eating") is an evolutionarily conserved degradation process where cytoplasmic components are engulfed by vesicles called autophagosomes, which are then delivered to lysosomes, where their contents are degraded. Under stress conditions, such as starvation or oxidative stress, autophagy is upregulated in order to degrade macromolecules and restore the nutrient balance. The source of membranes that participate in the initial formation of phagophores is still incompletely understood and many intracellular structures have been shown to act as lipid donors, including the endoplasmic reticulum, Golgi, nucleus, mitochondria and the plasma membrane...
October 18, 2016: FEBS Journal
Horrolein Arab, Soleiman Mahjoub, Karimollah Hajian-Tilaki, Mehdi Moghadasi
BACKGROUND: Alzheimer's disease (AD) is the most prevalent degenerative disorder of the brain among elderly individuals. Many studies indicate that oxidative stress is an important pathogenic factor which involves oxidizing macromolecules such as DNA, lipids, and proteins in AD. Green tea is a rich source of antioxidant compounds that can remove radical oxygen species. The purpose of this study was to investigate the influence of green tea consumption on markers of oxidative stress in AD...
2016: Caspian Journal of Internal Medicine
Jiyoul Lee, Jong Won Chung, Gyubok Yoon, Moo Hyung Lee, Do Hwan Kim, Jozeph Park, Jin-Kyun Lee, Moon Sung Kang
Field-effect mobility of a polymer semiconductor film is known to be enhanced when the gate dielectric interfacing with the film is weakly polarizable. Accordingly, gate dielectrics with lower dielectric constant (k) are preferred for attaining polymer field-effect transistors (PFETs) with larger mobilities. At the same time, it is also known that inducing more charge carriers into the polymer semiconductor films helps enhancing their field-effect mobility, because large number of traps presented in such a disorder system can be compensated substantially...
October 18, 2016: ACS Applied Materials & Interfaces
Victoria C Foletta, Michelle Palmieri, Joachim Kloehn, Shaun Mason, Stephen F Previs, Malcolm J McConville, Oliver M Sieber, Clinton R Bruce, Greg M Kowalski
Deuterated water (²H₂O), a stable isotopic tracer, provides a convenient and reliable way to label multiple cellular biomass components (macromolecules), thus permitting the calculation of their synthesis rates. Here, we have combined ²H₂O labelling, GC-MS analysis and a novel cell fractionation method to extract multiple biomass components (DNA, protein and lipids) from the one biological sample, thus permitting the simultaneous measurement of DNA (cell proliferation), protein and lipid synthesis rates...
October 13, 2016: Metabolites
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