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https://www.readbyqxmd.com/read/28327660/quantitative-volumetric-raman-imaging-of-three-dimensional-cell-cultures
#1
Charalambos Kallepitis, Mads S Bergholt, Manuel M Mazo, Vincent Leonardo, Stacey C Skaalure, Stephanie A Maynard, Molly M Stevens
The ability to simultaneously image multiple biomolecules in biologically relevant three-dimensional (3D) cell culture environments would contribute greatly to the understanding of complex cellular mechanisms and cell-material interactions. Here, we present a computational framework for label-free quantitative volumetric Raman imaging (qVRI). We apply qVRI to a selection of biological systems: human pluripotent stem cells with their cardiac derivatives, monocytes and monocyte-derived macrophages in conventional cell culture systems and mesenchymal stem cells inside biomimetic hydrogels that supplied a 3D cell culture environment...
March 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28326772/illuminating-the-reaction-pathways-of-viromimetic-assembly
#2
Hande E Cingil, Emre B Boz, Giovanni Biondaro, Renko de Vries, Martien A Cohen Stuart, Daniela J Kraft, Paul van der Schoot, Joris Sprakel
The co-assembly of well-defined biological nanostructures relies on a delicate balance between attractive and repulsive interactions between biomolecular building blocks. Viral capsids are a prototypical example, where coat proteins exhibit not only self-interactions but also interact with the cargo they encapsulate. In Nature the balance between antagonistic and synergistic interactions is evolved to avoid kinetic trapping and polymorphism. To date it has remained a major challenge to experimentally disentangle the complex kinetic reaction pathways that underlie successful co-assembly of biomolecular building blocks in a non-invasive approach with high temporal resolution...
March 22, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28321191/palmitoylethanolamide-reduces-neuropsychiatric-behaviors-by-restoring-cortical-electrophysiological-activity-in-a-mouse-model-of-mild-traumatic-brain-injury
#3
Francesca Guida, Serena Boccella, Monica Iannotta, Danilo De Gregorio, Catia Giordano, Carmela Belardo, Rosaria Romano, Enza Palazzo, Maria A Scafuro, Nicola Serra, Vito de Novellis, Francesco Rossi, Sabatino Maione, Livio Luongo
Traumatic brain injury (TBI) represents a major public health problem, which is associated with neurological dysfunction. In severe or moderate cases of TBI, in addition to its high mortality rate, subjects may encounter diverse behavioral dysfunctions. Previous reports suggest that an association between TBI and chronic pain syndromes tends to be more common in patients with mild forms of brain injury. Despite causing minimal brain damage, mild TBI (mTBI) often leads to persistent psychologically debilitating symptoms, which can include anxiety, various forms of memory and learning deficits, and depression...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28318014/-solvent-hydrogen-bond-occlusion-a-new-model-of-polar-desolvation-for-biomolecular-energetics
#4
Andrea Bazzoli, John Karanicolas
Water engages in two important types of interactions near biomolecules: it forms ordered "cages" around exposed hydrophobic regions, and it participates in hydrogen bonds with surface polar groups. Both types of interaction are critical to biomolecular structure and function, but explicitly including an appropriate number of solvent molecules makes many applications computationally intractable. A number of implicit solvent models have been developed to address this problem, many of which treat these two solvation effects separately...
March 20, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28314769/infrared-spectroscopic-characterization-of-monocytic-microvesicles-microparticles-released-upon-lipopolysaccharide-stimulation
#5
Joonsup Lee, Beryl Wen, Elizabeth A Carter, Valery Combes, Georges E R Grau, Peter A Lay
Microvesicles (MVs) are involved in cell-cell interactions, including disease pathogenesis. Nondestructive Fourier-transform infrared (FTIR) spectra from MVs were assessed as a technique to provide new biochemical insights into a LPS-induced monocyte model of septic shock. FTIR spectroscopy provided a quick method to investigate relative differences in biomolecular content of different MV populations that was complementary to traditional semiquantitative omics approaches, with which it is difficult to provide information on relative changes between classes (proteins, lipids, nucleic acids, carbohydrates) or protein conformations...
March 17, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28306271/switching-the-structural-force-in-ionic-liquid-solvent-mixtures-by-varying-composition
#6
Alexander M Smith, Alpha A Lee, Susan Perkin
The structure and interactions in electrolytes at high concentration have implications from energy storage to biomolecular interactions. However, many experimental observations are yet to be explained in these mixtures, which are far beyond the regime of validity of mean-field models. Here, we study the structural forces in a mixture of ionic liquid and solvent that is miscible in all proportions at room temperature. Using the surface force balance to measure the force between macroscopic smooth surfaces across the liquid mixtures, we uncover an abrupt increase in the wavelength above a threshold ion concentration...
March 3, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28306237/the-glycan-microarray-story-from-construction-to-applications
#7
Ji Young Hyun, Jaeyoung Pai, Injae Shin
Not only are glycan-mediated binding processes in cells and organisms essential for a wide range of physiological processes, but they are also implicated in various pathological processes. As a result, elucidation of glycan-associated biomolecular interactions and their consequences is of great importance in basic biological research and biomedical applications. In 2002, we and others were the first to utilize glycan microarrays in efforts aimed at the rapid analysis of glycan-associated recognition events...
March 17, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28301745/applications-of-surface-second-harmonic-generation-in-biological-sensing
#8
Renee J Tran, Krystal L Sly, John C Conboy
Surface second harmonic generation (SHG) is a coherent, nonlinear optical technique that is well suited for investigations of biomolecular interactions at interfaces. SHG is surface specific due to the intrinsic symmetry constraints on the nonlinear process, providing a distinct analytical advantage over linear spectroscopic methods, such as fluorescence and UV-Visible absorbance spectroscopies. SHG has the ability to detect low concentrations of analytes, such as proteins, peptides, and small molecules, due to its high sensitivity, and the second harmonic response can be enhanced through the use of target molecules that are resonant with the incident (ω) and/or second harmonic (2ω) frequencies...
March 16, 2017: Annual Review of Analytical Chemistry
https://www.readbyqxmd.com/read/28299694/electrochemical-quartz-crystal-nanobalance-eqcn-based-biosensor-for-sensitive-detection-of-antibiotic-residues-in-milk
#9
Sunil Bhand, Geetesh K Mishra
An electrochemical quartz crystal nanobalance (EQCN), which provides real-time analysis of dynamic surface events, is a valuable tool for analyzing biomolecular interactions. EQCN biosensors are based on mass-sensitive measurements that can detect small mass changes caused by chemical binding to small piezoelectric crystals. Among the various biosensors, the piezoelectric biosensor is considered one of the most sensitive analytical techniques, capable of detecting antigens at picogram levels. EQCN is an effective monitoring technique for regulation of the antibiotics below the maximum residual limit (MRL)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28295888/regimes-of-biomolecular-ultrasmall-nanoparticle-interactions
#10
Luca Boselli, Ester Polo, Valentina Castagnola, Kenneth A Dawson
Ultrasmall nanoparticles (USNPs), usually defined as NPs with core in the size range 1-3 nm, are a class of nanomaterials which show unique physicochemical properties, often different from larger NPs of the same material. Moreover, there are also indications that USNPs might have distinct properties in their biological interactions. For example, recent in vivo experiments suggest that some USNPs escape the liver, spleen, and kidney, in contrast to larger NPs that are strongly accumulated in the liver. Here, we present a simple approach to study the biomolecular interactions at the USNPs bio-nanointerface, opening up the possibility to systematically link these observations to microscopic molecular principles...
March 15, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28294600/histo-blood-group-antigen-presentation-is-critical-for-norovirus-vlp-binding-to-glycosphingolipids-in-model-membranes
#11
Waqas Nasir, Martin Frank, Angelika Kunze, Marta Bally, Francisco Parra, Per-Georg Nyholm, Fredrik Höök, Göran Larson
Virus entry depends on biomolecular recognition at the surface of cell membranes. In case of glycolipid receptors, these events are expected to be influenced by how the glycan epitope close to the membrane is presented to the virus. This presentation of membrane associated glycans is more restricted as compared to glycans in solution, particularly because of orientational constraints imposed on the glycolipid through its lateral interactions with other membrane lipids and proteins. We have developed and employed total internal reflection fluorescence microscopy (TIRFM) based binding assay and a scheme for molecular dynamics (MD) membrane simulations to investigate the consequences of various glycan presentation effects...
March 15, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28287704/orientational-binding-of-dna-guided-by-the-c2n-template
#12
Zonglin Gu, Lin Zhao, Weifeng Li, Shengtang Liu, Guangxin Duan, Jose Manuel Perez-Aguilar, Judong Luo, Ruhong Zhou
A detailed understanding of the interactions between biomolecules and nanomaterial surfaces is critical for the development of biomedical applications of these novel nanomaterials. Here, we characterized the binding patterns and dynamics of a double stranded DNA (dsDNA) segment on the recently synthesized nitrogenized graphene (C2N) with both theoretical (including classical and quantum calculations) and experimental approaches. Our results show that the dsDNA repeatedly exhibits a strong preference in its binding mode on the C2N substrate, displaying an upright orientation that is independent of its initial configurations...
March 13, 2017: ACS Nano
https://www.readbyqxmd.com/read/28281256/label-free-biosensors-based-on-bimodal-waveguide-bimw-interferometers
#13
Sonia Herranz, Adrián Fernández Gavela, Laura M Lechuga
The bimodal waveguide (BiMW) sensor is a novel common path interferometric transducer based on the evanescent field detection principle, which in combination with a bio-recognition element allows the direct detection of biomolecular interactions in a label-free scheme. Due to its inherent high sensitivity it has great potential to become a powerful analytical tool for monitoring substances of interest in areas such as environmental control, medical diagnostics and food safety, among others. The BiMW sensor is fabricated using standard silicon-based technology allowing cost-effective production, and meeting the requirements of portability and disposability necessary for implementation in a point-of-care (POC) setting...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28281253/microrna-biosensing-with-two-dimensional-surface-plasmon-resonance-imaging
#14
Ho Pui Ho, Fong Chuen Loo, Shu Yuen Wu, Dayong Gu, Ken-Tye Yong, Siu Kai Kong
Two-dimensional surface plasmon resonance (2D-SPR) imaging, which provides a real-time, sensitive, and high-throughput analysis of surface events in a two dimensional manner, is a valuable tool for studying biomolecular interactions and biochemical reactions without using any tag labels. The sensing principle of 2D-SPR includes angular, wavelength, and phase interrogation. In this chapter, the 2D-SPR imaging technique is applied for sensing a target microRNA by its corresponding oligonucleotide probes, with sequence complementarity, immobilized on the gold SPR sensing surface...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28280367/clarifying-the-molecular-mechanism-associated-with-carfilzomib-resistance-in-human-multiple-myeloma-using-microarray-gene-expression-profile-and-genetic-interaction-network
#15
Zhihong Zheng, Tingbo Liu, Jing Zheng, Jianda Hu
Carfilzomib is a Food and Drug Administration-approved selective proteasome inhibitor for patients with multiple myeloma (MM). However, recent studies indicate that MM cells still develop resistance to carfilzomib, and the molecular mechanisms associated with carfilzomib resistance have not been studied in detail. In this study, to better understand its potential resistant effect and its underlying mechanisms in MM, microarray gene expression profile associated with carfilzomib-resistant KMS-11 and its parental cell line was downloaded from Gene Expression Omnibus database...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28271485/d-glyceraldehyde-3-phosphate-dehydrogenase-structure-and-function
#16
Michael R White, Elsa D Garcin
Aside from its well-established role in glycolysis, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has been shown to possess many key functions in cells. These functions are regulated by protein oligomerization , biomolecular interactions, post-translational modifications , and variations in subcellular localization . Several GAPDH functions and regulatory mechanisms overlap with one another and converge around its role in intermediary metabolism. Several structural determinants of the protein dictate its function and regulation...
2017: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/28271461/new-approaches-for-the-reliable-in-vitro-assessment-of-binding-affinity-based-on-high-resolution-real-time-data-acquisition-of-radioligand-receptor-binding-kinetics
#17
Markus Zeilinger, Florian Pichler, Lukas Nics, Wolfgang Wadsak, Helmut Spreitzer, Marcus Hacker, Markus Mitterhauser
BACKGROUND: Resolving the kinetic mechanisms of biomolecular interactions have become increasingly important in early-phase drug development. Since traditional in vitro methods belong to dose-dependent assessments, binding kinetics is usually overlooked. The present study aimed at the establishment of two novel experimental approaches for the assessment of binding affinity of both, radiolabelled and non-labelled compounds targeting the A3R, based on high-resolution real-time data acquisition of radioligand-receptor binding kinetics...
December 2017: EJNMMI Research
https://www.readbyqxmd.com/read/28257994/towards-understanding-cellular-structure-biology-in-cell-nmr
#18
REVIEW
Safikur Rahman, Younhwa Byun, Md Imtaiyaz Hassan, Jihoe Kim, Vijay Kumar
To watch biological macromolecules perform their functions inside the living cells is the dream of any biologists. In-cell nuclear magnetic resonance is a branch of biomolecular NMR spectroscopy that can be used to observe the structures, interactions and dynamics of these molecules in the living cells at atomic level. In principle, in-cell NMR can be applied to different cellular systems to achieve biologically relevant structural and functional information. In this review, we summarize the existing approaches in this field and discuss its applications in protein interactions, folding, stability and post-translational modifications...
March 1, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28256228/phase-transitions-in-biological-systems-with-many-components
#19
William M Jacobs, Daan Frenkel
Biological mixtures such as the cytosol may consist of thousands of distinct components. There is now a substantial body of evidence showing that, under physiological conditions, intracellular mixtures can phase separate into spatially distinct regions with differing compositions. In this article we present numerical evidence indicating that such spontaneous compartmentalization exploits general features of the phase diagram of a multicomponent biomolecular mixture. In particular, we show that demixed domains are likely to segregate when the variance in the intermolecular interaction strengths exceeds a well-defined threshold...
February 28, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28245356/intuitive-density-functional-theory-based-energy-decomposition-analysis-for-protein-ligand-interactions
#20
M J S Phipps, T Fox, C S Tautermann, C-K Skylaris
First-principles quantum mechanical calculations with methods such as density functional theory (DFT) allow the accurate calculation of interaction energies between molecules. These interaction energies can be dissected into chemically relevant components such as electrostatics, polarization, and charge transfer using energy decomposition analysis (EDA) approaches. Typically EDA has been used to study interactions between small molecules; however, it has great potential to be applied to large biomolecular assemblies such as protein-protein and protein-ligand interactions...
March 8, 2017: Journal of Chemical Theory and Computation
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