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Gordon X Wang, Stephen J Smith, Philippe Mourrain
The distribution of proteins within sub-synaptic compartments is an essential aspect of their neurological function. Current methodology such as electron microscopy (EM) and super-resolution imaging techniques can provide precise localization of proteins, but are often limited to a small number of one-time observations with narrow spatial and molecular coverage. The diversity of synaptic proteins and synapse types demands synapse analysis on a scale that is prohibitive with current methods. Here, we demonstrate SubSynMAP, a fast, multiplexed sub-synaptic protein analysis method using wide-field data from deconvolution array tomography (ATD)...
October 22, 2016: ELife
Purva P Bhojane, Michael R Duff, Khushboo Bafna, Gabriella P Rimmer, Pratul K Agarwal, Elizabeth E Howell
Folate, or vitamin B9, is an important compound in one carbon metabolism. Previous studies have found weaker binding of dihydrofolate to dihydrofolate reductase in the presence of osmolytes. In other words, osmolytes are more difficult to remove from the dihydrofolate solvation shell than water; this shifts the equilibrium towards the free ligand and protein species. This study uses vapor pressure osmometry to explore the interaction of folate with the model osmolyte, glycine betaine. This method yields a preferential interaction potential (μ23/RT value)...
October 21, 2016: Biochemistry
Edmund R Glass, Mikhail G Dozmorov
BACKGROUND: The goal of many human disease-oriented studies is to detect molecular mechanisms different between healthy controls and patients. Yet, commonly used gene expression measurements from blood samples suffer from variability of cell composition. This variability hinders the detection of differentially expressed genes and is often ignored. Combined with cell counts, heterogeneous gene expression may provide deeper insights into the gene expression differences on the cell type-specific level...
October 6, 2016: BMC Bioinformatics
Boru Chen, Leping Dang, Xiao Zhang, Wenzhi Fang, Mengna Hou, Tiankuo Liu, Zhanzhong Wang
Kudzu starch was cross-linked with sodium trimetaphosphate (STMP) at different temperatures, time and of STMP concentrations in this work. The cross-linked starches (CLSs) were fractionated further into cross-linked amylose and amylopectin in order to compare the effect of cross-linking on the microstructure. According to scanning electron microscope (SEM), CLSs displayed the resemble appearance of spherical and polygonal shapes like NS. X-ray diffraction (XRD) revealed that amylose of native starch (A), NS and CLS displayed a combination of A-type and B-type structure, while that was not found in amylose of cross-linked starch (CLA)...
March 15, 2017: Food Chemistry
Noelle Merchak, Virginie Silvestre, Denis Loquet, Toufic Rizk, Serge Akoka, Joseph Bejjani
Triacylglycerols, which are quasi-universal components of food matrices, consist of complex mixtures of molecules. Their site-specific (13)C content, their fatty acid profile, and their position on the glycerol moiety may significantly vary with the geographical, botanical, or animal origin of the sample. Such variables are valuable tracers for food authentication issues. The main objective of this work was to develop a new method based on a rapid and precise (13)C-NMR spectroscopy (using a polarization transfer technique) coupled with multivariate linear regression analyses in order to quantify the whole set of individual fatty acids within triacylglycerols...
October 19, 2016: Analytical and Bioanalytical Chemistry
Kohei Ohashi, Takayuki Ishida
In radiography, when a blurred image caused by patient motion was acquired, radiologists retake an image as needed. However, retaking an image leads to extra radiation exposure to patients and reducing work efficiency. This study proposes the deblurring algorithm for blurred images caused by patient motion in radiography. In the proposed algorithm, we first take a video using an optical device during radiography. Second, we calculate the optical flow between each frame, and estimate a point spread function (PSF) based on the optical flows...
2016: Nihon Hoshasen Gijutsu Gakkai Zasshi
Sonia Fernández-Menéndez, María L Fernández-Sánchez, Héctor González-Iglesias, Belén Fernández-Colomer, José López-Sastre, Alfredo Sanz-Medel
PURPOSE: In this work, the absorption and/or bioavailability of iron from two chemical species, (57)Fe-Lf (apo-lactoferrin) complex and (57)FeSO4 at low and high dose, and in Lf excess were investigated in lactating wistar rats. METHODS: The methodology used is based on the use of stable isotopes in combination with the approach "isotope pattern deconvolution" and ICP-MS for detection. This approach provides quantitative information about exogenous ((57)Fe) and endogenous iron ((nat)Fe) distribution in fluids and tissues in the iron-supplemented rat groups...
October 18, 2016: European Journal of Nutrition
Christian Brinch Mollerup, Petur Weihe Dalsgaard, Marie Mardal, Kristian Linnet
High-resolution mass spectrometry (HRMS) is widely used for the drug screening of biological samples in clinical and forensic laboratories. With the continuous addition of new psychoactive substances (NPS), keeping such methods updated is challenging. HRMS allows for combined targeted and non-targeted screening; first, peaks are identified by software algorithms, and identifications are based on reference standard data. Remaining unknown peaks are attempted identified with in silico and literature data. However, several thousand peaks remain where most are unidentifiable or uninteresting in drug screening...
October 17, 2016: Drug Testing and Analysis
Lucia Geis-Asteggiante, Suzanne Ostrand-Rosenberg, Catherine Fenselau, Nathan J Edwards
Spectral counting is a straightforward label-free quantitation strategy used in bottom-up proteomics workflows. The application of spectral counting in label-free top-down proteomics workflows can be similarly straightforward, but has not been applied as widely as quantitation by chromatographic peak areas or peak intensities. In this study, we evaluate spectral counting for quantitative comparisons in label-free top-down proteomics workflows by comparison with chromatographic peak areas and intensities. We tested these quantitation approaches by spiking standard proteins into a complex protein background and comparing relative quantitation by spectral counts with normalized chromatographic peak areas and peak intensities from deconvoluted extracted ion chromatograms of the spiked proteins...
October 17, 2016: Analytical Chemistry
Phillip Walsh, Manuel Garbalena, Kevin A Schug
A time interval deconvolution (TID) method was devised to integrate a gas chromatography - vacuum ultraviolet (GC-VUV) data set in order to provide bulk characterization and speciation of finished gasoline samples. The method was demonstrated using a commercially available standard and tested on a series of ASTM gasoline proficiency samples. Very good correlation (R2 ~0.97-0.99) between GC-VUV and measurements using various ASTM methods was achieved. A key advantage of the TID method applied to GC-VUV datasets is that a large number of coelution events can be tolerated, resulting in significantly easier and faster separations, approximately 30 minutes in the case of gasoline...
October 17, 2016: Analytical Chemistry
Fausto Carnevale Neto, Alan C Pilon, Denise M Selegato, Rafael T Freire, Haiwei Gu, Daniel Raftery, Norberto P Lopes, Ian Castro-Gamboa
Dereplication based on hyphenated techniques has been extensively applied in plant metabolomics, thereby avoiding re-isolation of known natural products. However, due to the complex nature of biological samples and their large concentration range, dereplication requires the use of chemometric tools to comprehensively extract information from the acquired data. In this work we developed a reliable GC-MS-based method for the identification of non-targeted plant metabolites by combining the Ratio Analysis of Mass Spectrometry deconvolution tool (RAMSY) with Automated Mass Spectral Deconvolution and Identification System software (AMDIS)...
2016: Frontiers in Molecular Biosciences
Carl Brunius, Lin Shi, Rikard Landberg
INTRODUCTION: Liquid chromatography-mass spectrometry (LC-MS) is a commonly used technique in untargeted metabolomics owing to broad coverage of metabolites, high sensitivity and simple sample preparation. However, data generated from multiple batches are affected by measurement errors inherent to alterations in signal intensity, drift in mass accuracy and retention times between samples both within and between batches. These measurement errors reduce repeatability and reproducibility and may thus decrease the power to detect biological responses and obscure interpretation...
2016: Metabolomics: Official Journal of the Metabolomic Society
Meng Zhang, Lijuan Wang, Shi Shu, Aziz Sancar, Dongping Zhong
Photolyase is a blue-light-activated enzyme that repairs ultraviolet-induced DNA damage that occurs in the form of cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone (6-4) photoproducts. Previous studies on microbial photolyases have revealed an electron-tunneling pathway that is critical for the repair mechanism. In this study, we used femtosecond spectroscopy to deconvolute seven electron-transfer reactions in 10 elementary steps in all classes of CPD photolyases. We report a unified electron-transfer pathway through a conserved structural configuration that bifurcates to favor direct tunneling in prokaryotes and a two-step hopping mechanism in eukaryotes...
October 14, 2016: Science
A Mercuri, S Wu, S Stranzinger, S Mohr, S Salar-Behzadi, M Bresciani, E Fröhlich
This work aims to better understand the in vivo behaviour of modified release (MR) formulations (Envarsus(®) tablets and Advagraf(®) capsules) using in vitro properties of tacrolimus and in silico simulations. The in silico concentration profiles of tacrolimus released from the MR formulations were predicted after building a three compartments PK model with GastroPlus™, and using the experimentally determined in vitro physico-chemical properties as input parameters. In vitro-in vivo correlations (IVIVC) were obtained after deconvolution of in vivo data from a clinical trial...
October 11, 2016: International Journal of Pharmaceutics
Griselda Hernández, David M LeMaster
Both (15)N chemical shift anisotropy (CSA) and sufficiently rapid exchange linebroadening transitions exhibit relaxation contributions that are proportional to the square of the magnetic field. Deconvoluting these contributions is further complicated by residue-dependent variations in protein amide (15)N CSA values which have proven difficult to accurately measure. Exploiting recently reported improvements for the implementation of T1 and T1ρ experiments, field strength-dependent studies have been carried out on the B3 domain of protein G (GB3) as well as on the immunophilin FKBP12 and a H87V variant of that protein in which the major conformational exchange linebroadening transition is suppressed...
October 12, 2016: Journal of Biomolecular NMR
C García-Garrido, P E Sánchez-Jiménez, L A Pérez-Maqueda, A Perejón, José M Criado
The polymer-to-ceramic transformation kinetics of two widely employed ceramic precursors, 1,3,5,7-tetramethyl-1,3,5,7-tetravinylcyclotetrasiloxane (TTCS) and polyureamethylvinylsilazane (CERASET), have been investigated using coupled thermogravimetry and mass spectrometry (TG-MS), Raman, XRD and FTIR. The thermally induced decomposition of the pre-ceramic polymer is the critical step in the synthesis of polymer derived ceramics (PDCs) and accurate kinetic modeling is key to attaining a complete understanding of the underlying process and to attempt any behavior predictions...
October 13, 2016: Physical Chemistry Chemical Physics: PCCP
Andrew G Stack, Jose M Borreguero, Timothy R Prisk, Eugene Mamontov, Hsiu-Wen Wang, Lukas Vlcek, David J Wesolowski
Solvent exchanges on solid surfaces and dissolved ions are a fundamental property important for understanding chemical reactions, but the rates of fast exchanges are poorly constrained. We probed the diffusional motions of water adsorbed onto nanoparticles of the mineral barite (BaSO4) using quasi-elastic neutron scattering (QENS) and classical molecular dynamics (MD) to reveal the complex dynamics of water exchange along mineral surfaces. QENS data as a function of temperature and momentum transfer (Q) were fit using scattering functions derived from MD trajectories...
October 10, 2016: Physical Chemistry Chemical Physics: PCCP
Shuntaro Arase, Kanta Horie, Takashi Kato, Akira Noda, Yasuhiro Mito, Masatoshi Takahashi, Toshinobu Yanagisawa
Multivariate curve resolution-alternating least squares (MCR-ALS) method was investigated for its potential to accelerate pharmaceutical research and development. The fast and efficient separation of complex mixtures consisting of multiple components, including impurities as well as major drug substances, remains a challenging application for liquid chromatography in the field of pharmaceutical analysis. In this paper we suggest an integrated analysis algorithm functioning on a matrix of data generated from HPLC coupled with photo-diode array detector (HPLC-PDA) and consisting of the mathematical program for the developed multivariate curve resolution method using an expectation maximization (EM) algorithm with a bidirectional exponentially modified Gaussian (BEMG) model function as a constraint for chromatograms and numerous PDA spectra aligned with time axis...
October 21, 2016: Journal of Chromatography. A
H F M C Martiniano, N Galamba
We study, through molecular dynamics simulations, the structure and orientational dynamics of water next to a blocked hydrophobic amino acid, valine (Val), above and below the freezing point of water. The structure and the orientational dynamics of waters with four water neighbors (4WN) and less than four water neighbors (L4WN) in the Val's coordination sphere are deconvoluted. We find that in spite of the excluded volume effects waters with L4WN have faster librational dynamics than bulk water, reminiscent of water at the liquid-vapor interface, and faster orientational dynamics than waters with 4WN, at every temperature...
October 5, 2016: Physical Chemistry Chemical Physics: PCCP
Russell W Driver, Timothy D W Claridge, Steve Scheiner, Martin D Smith
The precise role of non-conventional hydrogen bonds such as the C-H⋅⋅⋅O interaction in influencing the conformation of small molecules remains unresolved. Here we survey a series of β-turn mimetics using X-ray crystallography and NMR spectroscopy in conjunction with quantum calculation, and conclude that favourable torsional and electronic effects are important for the population of states with conformationally influential C-H⋅⋅⋅O interactions. Our results also highlight the challenge in attempting to deconvolute a myriad of interdependent noncovalent interactions in order to focus on the contribution of a single one...
October 6, 2016: Chemistry: a European Journal
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