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https://www.readbyqxmd.com/read/28092459/toward-high-throughput-and-multiplexed-imaging-of-genome-organization
#1
Eric F Joyce
Dr. Eric Joyce from the Department of Genetics at the University of Pennsylvania was awarded The President's Innovation award at the annual Society of Biomolecular Imaging and Informatics meeting held in Boston, September 2016. Chromosome interactions are a fundamental aspect of nuclear organization that can activate and silence genes or even direct chromosome rearrangements. However, the molecular mechanisms underlying how chromosomal segments find each other and form stable interactions within cells remain unknown...
January 2017: Assay and Drug Development Technologies
https://www.readbyqxmd.com/read/28088101/sequenced-defined-biomolecules-for-nanomaterial-synthesis-functionalization-and-assembly
#2
REVIEW
Joseph M Slocik, Rajesh R Naik
Biomolecules represent an invaluable resource to nanotechnology by providing a large diversity of highly functional biomolecular templates. As a result, these have been extensively used for controlling the synthesis, functionalization, and assembly of nanomaterials, while also creating materials with new properties and structures. In the following, we focus on the use of peptides to achieve these goals and describe their general utility, sequence programmability, and use as templates. Also, we highlight several recent advances in the identification and selection of high affinity nanomaterial-binding peptides, provide a few examples of peptide functionalized surfaces and peptide templated materials, and describe how simple modifications to well characterized nanomaterial-binding peptides can be used to manipulate interactions and physiochemical properties...
January 11, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28068769/high-resolution-coarse-grained-model-of-hydrated-anion-exchange-membranes-that-accounts-for-hydrophobic-and-ionic-interactions-through-short-ranged-potentials
#3
Jibao Lu, Liam C Jacobson, Yamila A Perez Sirkin, Valeria Molinero
Molecular simulations provide a versatile tool to study the structure, anion conductivity, and stability of anion-exchange membrane (AEM) materials and can provide a fundamental understanding of the relation between structure and property of membranes that is key for their use in fuel cells and other applications. The quest for large spatial and temporal scales required to model the multiscale structure and transport processes in the polymer electrolyte membranes, however, cannot be met with fully atomistic models, and the available coarse-grained (CG) models suffer from several challenges associated with their low-resolution...
January 10, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28068057/topological-control-of-extracellular-matrix-growth-a-native-like-model-for-cell-morphodynamics-studies
#4
David Caballero, Josep Samitier
The interaction of cells with their natural environment influences a large variety of cellular phenomena, including cell adhesion, proliferation, and migration. The complex extracellular matrix network has challenged the attempts to replicate in vitro the heterogeneity of the cell environment and has threatened, in general, the relevance of in vitro studies. In this work, we describe a new and extremely versatile approach to generate native-like extracellular matrices with controlled morphologies for the in vitro study of cellular processes...
January 9, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28067766/wavelength-scanning-spr-imaging-sensors-based-on-an-acousto-optic-tunable-filter-and-a-white-light-laser
#5
Youjun Zeng, Lei Wang, Shu-Yuen Wu, Jianan He, Junle Qu, Xuejin Li, Ho-Pui Ho, Dayong Gu, Bruce Zhi Gao, Yonghong Shao
A fast surface plasmon resonance (SPR) imaging biosensor system based on wavelength interrogation using an acousto-optic tunable filter (AOTF) and a white light laser is presented. The system combines the merits of a wide-dynamic detection range and high sensitivity offered by the spectral approach with multiplexed high-throughput data collection and a two-dimensional (2D) biosensor array. The key feature is the use of AOTF to realize wavelength scan from a white laser source and thus to achieve fast tracking of the SPR dip movement caused by target molecules binding to the sensor surface...
January 5, 2017: Sensors
https://www.readbyqxmd.com/read/28067047/solvatochromic-and-fluorogenic-dyes-as-environment-sensitive-probes-design-and-biological-applications
#6
Andrey S Klymchenko
Fluorescent environment-sensitive probes are specially designed dyes that change their fluorescence intensity (fluorogenic dyes) or color (e.g., solvatochromic dyes) in response to change in their microenvironment polarity, viscosity, and molecular order. The studies of the past decade, including those of our group, have shown that these molecules become universal tools in fluorescence sensing and imaging. In fact, any biomolecular interaction or change in biomolecular organization results in modification of the local microenvironment, which can be directly monitored by these types of probes...
January 9, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28064429/structural-insight-into-the-gene-expression-profiling-of-the-hcn-operon-in-pseudomonas-aeruginosa
#7
Nilkanta Chowdhury, Angshuman Bagchi
Pseudomonas aeruginosa is a common opportunistic human pathogen. It generally attacks immunosuppressed patients like AIDS, cancer, cystic fibrosis, etc. The virulence of P. aeruginosa is mediated by various virulence factors. One of such potential virulence factors is HCN synthesized by HCN synthase enzyme, which is encoded by the hcnABC operon. The expressions of the genes of this operon are regulated by three transcriptional regulators, viz., LasR, ANR, and RhlR. In our previous work, we analyzed the molecular details of the functionalities of LasR...
January 7, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28062046/recent-advances-in-biological-single-molecule-applications-of-optical-tweezers-and-fluorescence-microscopy
#8
M Hashemi Shabestari, A E C Meijering, W H Roos, G J L Wuite, E J G Peterman
Over the past two decades, single-molecule techniques have evolved into robust tools to study many fundamental biological processes. The combination of optical tweezers with fluorescence microscopy and microfluidics provides a powerful single-molecule manipulation and visualization technique that has found widespread application in biology. In this combined approach, the spatial (~nm) and temporal (~ms) resolution, as well as the force scale (~pN) accessible to optical tweezers is complemented with the power of fluorescence microscopy...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28062039/measuring-force-induced-dissociation-kinetics-of-protein-complexes-using-single-molecule-atomic-force-microscopy
#9
K Manibog, C F Yen, S Sivasankar
Proteins respond to mechanical force by undergoing conformational changes and altering the kinetics of their interactions. However, the biophysical relationship between mechanical force and the lifetime of protein complexes is not completely understood. In this chapter, we provide a step-by-step tutorial on characterizing the force-dependent regulation of protein interactions using in vitro and in vivo single-molecule force clamp measurements with an atomic force microscope (AFM). While we focus on the force-induced dissociation of E-cadherins, a critical cell-cell adhesion protein, the approaches described here can be readily adapted to study other protein complexes...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28054357/linking-amyotrophic-lateral-sclerosis-and-spinal-muscular-atrophy-through-rna-transcriptome-homeostasis-a-genomics-perspective
#10
REVIEW
Margarida Gama-Carvalho, Marina L Garcia-Vaquero, Francisco R Pinto, Florence Besse, Joachim Weis, Aaron Voigt, Jörg B Schulz, Javier De Las Rivas
In this review we present our most recent understanding of key biomolecular processes that underlie two motor neuron degenerative disorders, Amyotrophic Lateral Sclerosis (ALS) and Spinal Muscular Atrophy (SMA). We focus on the role of four multifunctional proteins involved in RNA metabolism (TDP-43, FUS, SMN and Senataxin) that play a causal role in these diseases. Recent results have led to a novel scenario of intricate connections between these four proteins, bringing transcriptome homeostasis into the spotlight as a common theme in motor neuron degeneration...
January 5, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28052351/smpbs-web-server-for-computing-biomolecular-electrostatics-using-finite-element-solvers-of-size-modified-poisson-boltzmann-equation
#11
Yang Xie, Jinyong Ying, Dexuan Xie
SMPBS (Size Modified Poisson-Boltzmann Solvers) is a web server for computing biomolecular electrostatics using finite element solvers of the size modified Poisson-Boltzmann equation (SMPBE). SMPBE not only reflects ionic size effects but also includes the classic Poisson-Boltzmann equation (PBE) as a special case. Thus, its web server is expected to have a broader range of applications than a PBE web server. SMPBS is designed with a dynamic, mobile-friendly user interface, and features easily accessible help text, asynchronous data submission, and an interactive, hardware-accelerated molecular visualization viewer based on the 3Dmol...
January 4, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28042932/novel-adomet-analogues-as-tools-for-enzymatic-transfer-of-photo-crosslinkers-and-capturing-rna-protein-interactions
#12
Fabian Muttach, Florain Mäsing, Armido Studer, Andrea Rentmeister
Elucidation of biomolecular interactions is of utmost importance in biochemistry. Photo-crosslinking offers the possibility to precisely determine RNA-protein interactions. However, despite the inherent specificity of enzymes, approaches for site-specific introduction of photo-crosslinking moieties into nucleic acids are scarce. Methyltransferases in combination with synthetic analogues of their natural cosubstrate S-adenosyl-L-methionine (AdoMet) allow for the post-synthetic site-specific modification of biomolecules...
January 2, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28042821/integration-of-curved-d-type-optical-fiber-sensor-with-microfluidic-chip
#13
Yung-Shin Sun, Chang-Jyun Li, Jin-Cherng Hsu
A curved D-type optical fiber sensor (OFS) combined with a microfluidic chip is proposed. This OFS, based on surface plasmon resonance (SPR) of the Kretchmann's configuration, is applied as a biosensor to measure the concentrations of different bio-liquids such as ethanol, methanol, and glucose solutions. The SPR phenomenon is attained by using the optical fiber to guide the light source to reach the side-polished, gold-coated region. Integrating this OFS with a polymethylmethacrylate (PMMA)-based microfluidic chip, the SPR spectra for liquids with different refractive indices are recorded...
December 30, 2016: Sensors
https://www.readbyqxmd.com/read/28035651/high-quality-nmr-structures-a-new-force-field-with-implicit-water-and-membrane-solvation-for-xplor-nih
#14
Ye Tian, Charles D Schwieters, Stanley J Opella, Francesca M Marassi
Structure determination of proteins by NMR is unique in its ability to measure restraints, very accurately, in environments and under conditions that closely mimic those encountered in vivo. For example, advances in solid-state NMR methods enable structure determination of membrane proteins in detergent-free lipid bilayers, and of large soluble proteins prepared by sedimentation, while parallel advances in solution NMR methods and optimization of detergent-free lipid nanodiscs are rapidly pushing the envelope of the size limit for both soluble and membrane proteins...
December 29, 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28034959/counting-the-ions-surrounding-nucleic-acids
#15
David R Jacobson, Omar A Saleh
Nucleic acids are strongly negatively charged, and thus electrostatic interactions-screened by ions in solution-play an important role in governing their ability to fold and participate in biomolecular interactions. The negative charge creates a region, known as the ion atmosphere, in which cation and anion concentrations are perturbed from their bulk values. Ion counting experiments quantify the ion atmosphere by measuring the preferential ion interaction coefficient: the net total number of excess ions above, or below, the number expected due to the bulk concentration...
December 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/28028744/bacterial-production-of-site-specific-13-c-labeled-phenylalanine-and-methodology-for-high-level-incorporation-into-bacterially-expressed-recombinant-proteins
#16
Bhargavi Ramaraju, Hana McFeeters, Bernhard Vogler, Robert L McFeeters
Nuclear magnetic resonance spectroscopy studies of ever larger systems have benefited from many different forms of isotope labeling, in particular, site specific isotopic labeling. Site specific (13)C labeling of methyl groups has become an established means of probing systems not amenable to traditional methodology. However useful, methyl reporter sites can be limited in number and/or location. Therefore, new complementary site specific isotope labeling strategies are valuable. Aromatic amino acids make excellent probes since they are often found at important interaction interfaces and play significant structural roles...
December 27, 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28026944/mdanse-an-interactive-analysis-environment-for-molecular-dynamics-simulations
#17
G Goret, B Aoun, E Pellegrini
The MDANSE software-Molecular Dynamics Analysis of Neutron Scattering Experiments-is presented. It is an interactive application for postprocessing molecular dynamics (MD) simulations. Given the widespread use of MD simulations in material and biomolecular sciences to get a better insight for experimental techniques such as thermal neutron scattering (TNS), the development of MDANSE has focused on providing a user-friendly, interactive, graphical user interface for analyzing many trajectories in the same session and running several analyses simultaneously independently of the interface...
January 6, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28006716/biomolecular-aspects-of-depression-a-retrospective-analysis
#18
Brandon N Peacock, David J Scheiderer, Gottfried H Kellermann
OBJECTIVE: The effects of psychological stress, oxidative stress, and chronic low grade inflammation on the neuro-immune connection have been implicated in the pathogenesis of depression. Thus, in the recent past, there has been a growing effort in determining the mechanism of this pathogenesis. While attempting to map out, this mechanism researchers and clinicians have searched for clinically relevant biomarkers for use in the diagnosis and for the assessment of those suffering from depression...
November 10, 2016: Comprehensive Psychiatry
https://www.readbyqxmd.com/read/28001394/predicting-the-kinetics-of-rna-oligonucleotides-using-markov-state-models
#19
Giovanni Pinamonti, Jianbo Zhao, David E Condon, Fabian Paul, Frank Noè, Douglas H Turner, Giovanni Bussi
Nowadays different experimental techniques, such as single molecule or relaxation experiments, can provide dynamic properties of biomolecular systems, but the amount of detail obtainable with these methods is often limited in terms of time or spatial resolution. Here we use state-of-the-art computational techniques, namely, atomistic molecular dynamics and Markov state models, to provide insight into the rapid dynamics of short RNA oligonucleotides, to elucidate the kinetics of stacking interactions. Analysis of multiple microsecond-long simulations indicates that the main relaxation modes of such molecules can consist of transitions between alternative folded states, rather than between random coils and native structures...
January 5, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/27998086/dna-accelerated-copper-catalysis-of-friedel-crafts-conjugate-addition-enantioselective-protonation-reactions-in-water
#20
Almudena García-Fernández, Rik P Megens, Lara Villarino, Gerard Roelfes
DNA-induced rate acceleration has been identified as one of the key elements for the success of the DNA-based catalysis concept. Here we report on a novel DNA-based catalytic Friedel-Crafts conjugate addition/enantioselective protonation reaction in water, which represents the first example of a reaction that critically depends on the >700- to 990-fold rate acceleration caused by the presence of a DNA scaffold. The DNA-induced rate acceleration observed is the highest reported due to the environment presented by a biomolecular scaffold for any hybrid catalyst, to date...
December 21, 2016: Journal of the American Chemical Society
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