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https://www.readbyqxmd.com/read/28922574/super-resolution-microscopy-unveils-dynamic-heterogeneities-in-nanoparticle-protein-corona
#1
Natalia Feiner-Gracia, Michaela Beck, Sílvia Pujals, Sébastien Tosi, Tamoghna Mandal, Christian Buske, Mika Linden, Lorenzo Albertazzi
The adsorption of serum proteins, leading to the formation of a biomolecular corona, is a key determinant of the biological identity of nanoparticles in vivo. Therefore, gaining knowledge on the formation, composition, and temporal evolution of the corona is of utmost importance for the development of nanoparticle-based therapies. Here, it is shown that the use of super-resolution optical microscopy enables the imaging of the protein corona on mesoporous silica nanoparticles with single protein sensitivity...
September 18, 2017: Small
https://www.readbyqxmd.com/read/28921967/quantifying-secondary-structure-changes-in-calmodulin-using-2d-ir-spectroscopy
#2
Lucy Minnes, Daniel John Shaw, Benjamin P Cossins, Paul M Donaldson, Gregory M Greetham, Michael Towrie, Anthony Parker, Matthew James Baker, Alistair J Henry, Richard J Taylor, Neil T Hunt
Revealing the details of biomolecular processes in solution needs tools that can monitor structural dynamics over a range of time and length scales. We assess the ability of 2D-IR spectroscopy in combination with multivariate data analysis to quantify changes in secondary structure of the multifunctional calcium-binding messenger protein Calmodulin (CaM) as a function of temperature and Ca2+ concentration. Our approach produced quantitative agreement with circular dichroism (CD) spectroscopy in detecting the domain melting transitions of Ca2+-free (apo) CaM (reduction in α-helix structure by 13% (CD) and 15% (2D))...
September 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28921497/quantitative-analysis-of-nucleic-acid-stability-with-ligands-under-high-pressure-to-design-novel-drugs-targeting-g-quadruplexes
#3
Shuntaro Takahashi, Naoki Sugimoto
Nucleic acids (DNA and RNA) can form various non-canonical structures. Because some serious diseases are caused by the conformational change of G-quadruplex DNA structures, the development of ligands that bind and stabilize G-quadruplex DNA is of interest to the field of nucleic acid chemistry. Volumetric changes (ΔV) in the biomolecular reaction include the structural change of biomolecules and hydration behaviors, which provide information about the tertiary interaction between G-quadruplex DNA and ligands...
September 18, 2017: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/28921104/development-of-constant-ph-simulation-methods-in-implicit-solvent-and-applications-in-biomolecular-systems
#4
REVIEW
Fernando Luís Barroso daSilva, Luis Gustavo Dias
pH is a critical parameter for biological and technological systems directly related with electrical charges. It can give rise to peculiar electrostatic phenomena, which also makes them more challenging. Due to the quantum nature of the process, involving the forming and breaking of chemical bonds, quantum methods should ideally by employed. Nevertheless, due to the very large number of ionizable sites, different macromolecular conformations, salt conditions, and all other charged species, the CPU time cost simply becomes prohibitive for computer simulations, making this a quite complex problem...
September 18, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28920908/a-cmos-front-end-with-integrated-magnetoresistive-sensors-for-biomolecular-recognition-detection-applications
#5
Tiago Costa, Filipe A Cardoso, Jose Germano, Paulo P Freitas, Moises S Piedade
The development of giant magnetoresistive (GMR) sensors has demonstrated significant advantages in nanomedicine, particularly for ultrasensitive point-of-care diagnostics. To this end, the detection system is required to be compact, portable, and low power consuming at the same time that a maximum signal to noise ratio is maintained. This paper reports a CMOS front-end with integrated magnetoresistive sensors for biomolecular recognition detection applications. Based on the characterization of the GMR sensor's signal and noise, CMOS building blocks (i...
September 14, 2017: IEEE Transactions on Biomedical Circuits and Systems
https://www.readbyqxmd.com/read/28920687/manipulating-protein-protein-interactions-in-nrps-type-ii-pcps
#6
Matt J Jaremko, D John Lee, Ashay Patel, Victoria Winslow, Stanley J Opella, J Andrew McCammon, Michael D Burkart
In an effort to elucidate and engineer interactions in type II nonribosomal peptide synthetases, we analyzed biomolecular recognition between the essential peptidyl carrier proteins and adenylation domains using NMR spectroscopy, molecular dynamics, and mutational studies. Three peptidyl carrier proteins, PigG, PltL, and RedO, in addition to their cognate adenylation domains, PigI, PltF, and RedM, were investigated for their cross species activity. Of the three peptidyl carrier proteins, only PigG, showed substantial cross-pathway activity...
September 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28920117/hiv-haart-associated-oxidative-stress-is-detectable-by-metabonomics
#7
REVIEW
Aurelia A Williams, Lungile J Sitole, Debra Meyer
Chronic human immunodeficiency virus (HIV) infection, separately and in combination with highly active antiretroviral therapy (HAART) is closely associated with oxidative stress (OS). Most studies demonstrating redox imbalances in HIV-infected individuals have done so using conventional biochemical methodologies. The limited simultaneous detection of multiple OS markers within one sample is a major drawback of these methodologies and can be addressed through the use of metabonomics. HIV-metabonomic studies utilizing biofluids from HAART cohorts as the investigative source, are on the increase...
September 18, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28916835/plasmon-coupled-whispering-gallery-modes-on-nanodisk-arrays-for-signal-enhancements
#8
Tae Young Kang, Wonju Lee, Heesang Ahn, Dong-Myeong Shin, Chang-Seok Kim, Jin-Woo Oh, Donghyun Kim, Kyujung Kim
Metallic nanostructures including single and double nanodisks are successfully used to enhance the localized electric field in vicinity of microcavity in whispering gallery mode (WGM) sensor. We demonstrate numerical calculations of plasmonic coupling of WGMs to single and double nanodisk arrays on a planar substrate. We then experimentally confirmed that the resonance wavelength of WGM sensor was dramatically shifted by adoption of single and double nanodisks on the surface of microcavity in the WGM sensor...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28916781/6-bromo-indirubin-3-oxime-6bio-a-glycogen-synthase-kinase-3%C3%AE-inhibitor-activates-cytoprotective-cellular-modules-and-suppresses-cellular-senescence-mediated-biomolecular-damage-in-human-fibroblasts
#9
Aimilia D Sklirou, Nicolas Gaboriaud-Kolar, Issidora Papassideri, Alexios-Leandros Skaltsounis, Ioannis P Trougakos
As genetic interventions or extended caloric restriction cannot be applied in humans, many studies have been devoted to the identification of natural products that can prolong healthspan. 6-bromoindirubin-3'-oxime (6BIO), a hemi-synthetic derivative of indirubins found in edible mollusks and plants, is a potent inhibitor of Glycogen synthase kinase 3β (Gsk-3β). This pleiotropic kinase has been implicated in various age-related diseases including tumorigenesis, neurodegeneration and diabetes. Accordingly, 6BIO has shown anti-tumor and anti-neurodegenerative activities; nevertheless, the potential role of 6BIO in normal human cells senescence remains largely unknown...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28916759/influenza-d-in-italy-towards-a-better-understanding-of-an-emerging-viral-infection-in-swine
#10
Emanuela Foni, Chiara Chiapponi, Laura Baioni, Irene Zanni, Marianna Merenda, Carlo Rosignoli, Constantinos S Kyriakis, Mario Vittorio Luini, Maria Lucia Mandola, Luca Bolzoni, Arrigo Daniele Nigrelli, Silvia Faccini
Influenza D virus (IDV), a new member of the Orthomyxoviridae family, was first reported in 2011 in swine in Oklahoma, and consequently found in cattle across North America and Eurasia. To investigate the circulation of IDV among pigs in Italy, in the period between June 2015 and May 2016, biomolecular and virological tests were performed on 845 clinical samples collected from 448 pig farms affected by respiratory distress located in the Po Valley. Serological tests were conducted on 3698 swine sera, including archive sera collected in 2009, as well as samples collected in 2015 from the same region...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28913758/a-review-of-hydrogen-production-by-photosynthetic-organisms-using-whole-cell-and-cell-free-systems
#11
Baker A Martin, Paul D Frymier
Molecular hydrogen is a promising currency in the future energy economy due to the uncertain availability of finite fossil fuel resources and environmental effects from their combustion. It also has important uses in the production of fertilizers and platform chemicals as well as in upgrading conventional fuels. Conventional methods for producing molecular hydrogen from natural gas produce carbon dioxide and use a finite resource as feedstock. However, these issues can be overcome by using light energy from the Sun combined with microorganisms and their molecular machinery capable of photosynthesis...
September 14, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28910857/a-guide-to-quantitative-biomarker-assay-development-using-whispering-gallery-mode-biosensors
#12
Heather M Robison, Ryan C Bailey
Whispering gallery mode (WGM) sensors are a class of powerful analytical techniques defined by the measurement of changes in the local refractive index at or near the sensor surface. When functionalized with target-specific capture agents, analyte binding can be measured with very low limits of detection. There are many geometric manifestations of WGM sensors, with chip-integrated silicon photonic devices first commercialized because of the robust, wafer-scale device fabrication, facile optical interrogation, and amenability to the creation of multiplexed sensor arrays...
September 14, 2017: Current Protocols in Chemical Biology
https://www.readbyqxmd.com/read/28910854/characterizing-the-nano-bio-interface-using-microscopic-techniques-imaging-the-cell-system-is-just-as-important-as-imaging-the-nanoparticle-system
#13
Christie M Sayes, Henry Lujan
The rapid growth of nanotechnology and its industries has elevated the need to understand the risks associated with handling, using, and disposing of nanomaterials. These risks can be assessed through exposure measurement and hazard identification. One of the common challenges associated with quantifying nanomaterials in products, waste, humans, or the environment is the lack of tools available to measure concentration. The ability of refined tools and techniques to qualitatively detect nanoparticles in complex matrices has been demonstrated...
September 14, 2017: Current Protocols in Chemical Biology
https://www.readbyqxmd.com/read/28910082/macromolecular-profiling-of-organelles-in-normal-diploid-and-cancer-cells
#14
Svitlana M Levchenko, Andrey N Kuzmin, Artem Pliss, Junle Qu, Paras N Prasad
To advance an understanding of cellular regulation and function it is crucial to identify molecular contents in cellular organelles, which accommodate specific biochemical processes. Towards achievement of this goal, we applied micro-Raman-Biomolecular Component Analysis assay for molecular profiling of major organelles in live cells. We used this assay for comparative analysis of proteins 3D conformation and quantification of proteins, RNA and lipids concentrations in nucleoli, endoplasmic reticulum and mitochondria of WI-38 diploid lung fibroblasts and HeLa cancer cells...
September 14, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28905203/adaptive-resolution-simulations-of-biomolecular-systems
#15
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...
September 13, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28903006/constructing-a-multiplexed-dna-pattern-by-combining-precise-magnetic-manipulation-and-dna-driven-assembly
#16
Yingwei Zhang, Mengjiao Cheng, Yue Wang, Feng Shi
There is an urgent demand to construct multiplexed biomolecular patterns to obtain more biological information from a single experiment. However, with only limited reports focusing on defective top-down approaches, challenges remain to develop a bottom-up strategy for multiplexed patterning. To this end, a novel strategy has been proposed to fabricate multiplexed DNA patterns via macroscopic assembly through combined precise magnetic manipulation and DNA hybridization-driven self-assembly. Therefore, a multiplexed DNA pattern composed of glass fibers loaded with multiple specific strands of DNA was constructed, and its potential application in simultaneous detection of multiplex target DNA was demonstrated...
September 13, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28901745/terminating-dna-tile-assembly-with-nanostructured-caps
#17
Deepak K Agrawal, Ruoyu Jiang, Seth Reinhart, Abdul M Mohammed, Tyler D Jorgenson, Rebecca Schulman
Precise control over the nucleation, growth, and termination of self-assembly processes is a fundamental tool for controlling product yield and assembly dynamics. Mechanisms for altering these processes programmatically could allow the use of simple components to self-assemble complex final products or to design processes allowing for dynamic assembly or reconfiguration. Here we use DNA tile self-assembly to develop general design principles for building complexes that can bind to a growing biomolecular assembly and terminate its growth by systematically characterizing how different DNA origami nanostructures interact with the growing ends of DNA tile nanotubes...
September 18, 2017: ACS Nano
https://www.readbyqxmd.com/read/28901258/from-biology-to-therapy-improvements-of-therapeutic-options-in-lung-cancer
#18
Luigi Formisano, Valerie M Jansen, Roberta Marciano, Roberto Bianco
Lung cancer is the leading cause of cancer-related mortality around the world, despite effective chemotherapeutic agents, the prognosis has remained poor for a long time. The discovery of molecular changes that drive lung cancer has led to a dramatic shift in the therapeutic landscape of this disease. In "in vitro" and "in vivo" models of NSCLC (non-small cell lung cancer), angiogenesis blockade has demonstrated an excellent anti-tumor activity, thus, a number of anti-angiogenic drugs have been approved by regulatory authorities for use in clinical practice...
September 12, 2017: Anti-cancer Agents in Medicinal Chemistry
https://www.readbyqxmd.com/read/28898077/simulation-of-reversible-protein-protein-binding-and-calculation-of-binding-free-energies-using-perturbed-distance-restraints
#19
Jan Walther Perthold, Chris Oostenbrink
Virtually all biological processes depend on the interaction between proteins at some point. The correct prediction of biomolecular binding free-energies has many interesting applications in both basic and applied pharmaceutical research. While recent advances in the field of molecular dynamics (MD) simulations have proven the feasibility of the calculation of protein-protein binding free energies, the large conformational freedom of proteins and complex free energy landscapes of binding processes make such calculations a difficult task...
September 12, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28895970/mechanisms-and-applications-of-terahertz-metamaterial-sensing-a-review
#20
REVIEW
Wendao Xu, Lijuan Xie, Yibin Ying
Terahertz (THz) technology has attracted great worldwide interest and novel high-intensity THz sources and plasmonics are two of the most active fields of recent research. Being situated between infrared light and microwave radiation, the absorption of THz rays in molecular and biomolecular systems is dominated by the excitation of intramolecular and intermolecular vibrations. This indicates that THz technology is an effective tool for sensing applications. However, the low sensitivity of free-space THz detection limits the sensing applications, which gives a great opportunity to metamaterials...
September 12, 2017: Nanoscale
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