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https://www.readbyqxmd.com/read/28537067/multifunctional-triple-decker-inverse-12-metallacrown-4-sandwiching-halides
#1
Ling-Yu Guo, Hai-Feng Su, Mohamedally Kurmoo, Xing-Po Wang, Quan-Qin Zhao, Shui-Chao Lin, Chen-Ho Tung, Di Sun, Lan-Sun Zheng
A family of six triple-decker complexes, {(MX)2[(pz)4]3} (Hpz = 4-nitropyrazole, MX = NaCl, 1; NaBr, 2; NaI, 3; KCl, 4; KBr, 5, and KI, 6), exhibiting inclusion of halides into inverse 12-metallacrown-4 [inv-(12-MCCu(I),pz-4)] array has been realized. Single-crystal X-ray crystallography of each compound reveals a common structural feature consisting of four Cu(I) ions bonded by four pz to form a square metallomacrocycle comprising four metal centers and eight N atoms, thus giving an inv-[12-MCCu(I),pz-4] motif...
June 1, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28505286/pixie-an-algorithm-for-automated-ion-mobility-arrival-time-extraction-and-collision-cross-section-calculation-using-global-data-association
#2
Jian Ma, Cameron P Casey, Xueyun Zheng, Yehia M Ibrahim, Christopher S Wilkins, Ryan S Renslow, Dennis G Thomas, Samuel H Payne, Matthew E Monroe, Richard D Smith, Justin G Teeguarden, Erin S Baker, Thomas O Metz
Motivation: Drift tube ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS) is increasingly implemented in high throughput omics workflows, and new informatics approaches are necessary for processing the associated data. To automatically extract arrival times for molecules measured by DTIMS at multiple electric fields and compute their associated collisional cross sections (CCS), we created the PNNL Ion Mobility Cross Section Extractor (PIXiE). The primary application presented for this algorithm is the extraction of data that can then be used to create a reference library of experimental CCS values for use in high throughput omics analyses...
May 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28498477/identification-of-candidate-substrates-of-ubiquitin-specific-protease-13-using-2d-dige
#3
Jianmin Wang, Yingli Liu, Lijuan Tang, Sufen Qi, Yingjun Mi, Dianwu Liu, Qingbao Tian
The present study aimed to identify candidate substrates of ubiquitin-specific protease (USP)13 using two-dimensional fluorescence difference gel electrophoresis (2D-DIGE). USP13 is a well-characterized member of the USP family, which regulates diverse cellular functions by cleaving ubiquitin from ubiquitinated protein substrates. However, existing studies indicate that USP13 has no detectable hydrolytic activity in vitro. This finding implies that USP13 likely has different substrate specificity. In this study, a USP cleavage assay was performed using two different types of model substrates (glutathione S-transferase-Ub52 and ubiquitin-β-galactosidase) to detect the deubiquitinating enzyme (DUB) activity of USP13...
May 10, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28493382/thiomaleimide-functionalization-for-selective-biological-fluorescence-detection-of-peroxynitrite-as-tested-in-hela-and-raw-264-7-cells
#4
Tesla Yudhistira, Sandip V Mulay, Kyungjin Lee, Youngsam Kim, Hee-Sung Park, David G Churchill
The role of fluorescent molecules in diagnosis, treatments as well as in biomedical research has great current medicinal significance; related research continues to reveal new practical systems with enhanced features for interfacing of substituted molecules with biological systems. As part of an effort to better understand chalcogenide systems, a new dithiomaleimide BODIPY (BDP-NGM) probe has been designed, synthesized and characterized. The fluorescence of BDP-NGM was quenched by the incorporation of [3,4-bis(phenylthio)] on the maleimide-4-phenyl moiety which is in turn placed at the meso-position of the BODIPY system...
May 11, 2017: Chemistry, An Asian Journal
https://www.readbyqxmd.com/read/28299940/epsilon-q-an-automated-analyzer-interface-for-mass-spectral-library-search-and-label-free-protein-quantification
#5
Jin-Young Cho, Hyoung-Joo Lee, Seul-Ki Jeong, Young-Ki Paik
Mass spectrometry (MS) is a widely used proteome analysis tool for biomedical science. In an MS-based bottom-up proteomic approach to protein identification, sequence database (DB) searching has been routinely used because of its simplicity and convenience. However, searching a sequence DB with multiple variables and modification options can increase processing time and false-positive errors in large and complicated MS datasets. Spectral library searching is an alternative solution, avoiding the limitations of sequence DB searching and allowing the detection of more peptides with high sensitivity...
March 16, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28154187/decreased-mitochondrial-pyruvate-transport-activity-in-the-diabetic-heart-role-of-mitochondrial-pyruvate-carrier-2-mpc2-acetylation
#6
Shraddha S Vadvalkar, Satoshi Matsuzaki, Craig A Eyster, Jennifer R Giorgione, Lee B Bockus, Caroline S Kinter, Michael Kinter, Kenneth M Humphries
Alterations in mitochondrial function contribute to diabetic cardiomyopathy. We have previously shown that heart mitochondrial proteins are hyperacetylated in OVE26 mice, a transgenic model of type 1 diabetes. However, the universality of this modification and its functional consequences are not well established. In this study, we demonstrate that Akita type 1 diabetic mice exhibit hyperacetylation. Functionally, isolated Akita heart mitochondria have significantly impaired maximal (state 3) respiration with physiological pyruvate (0...
March 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28087276/drosophila-argonaute2-turnover-is-regulated-by-the-ubiquitin-proteasome-pathway
#7
Madoka Chinen, Elissa P Lei
Argonaute (AGO) proteins play a central role in the RNA interference (RNAi) pathway, which is a cytoplasmic mechanism important for post-transcriptional regulation of gene expression. In Drosophila, AGO2 also functions in the nucleus to regulate chromatin insulator activity and transcription. Although there are a number of studies focused on AGO2 function, the regulation of AGO2 turnover is not well understood. We found that mutation of T1149 or R1158 in the conserved PIWI domain causes AGO2 protein instability, but only T1149 affects RNAi activity...
February 12, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28029043/critical-conditions-for-liquid-chromatography-of-statistical-copolymers-functionality-type-and-composition-distribution-characterization-by-up-lccc-esi-ms
#8
Ruben Epping, Ulrich Panne, Jana Falkenhagen
Statistical ethylene oxide (EO) and propylene oxide (PO) copolymers of different monomer compositions and different average molar masses additionally containing two kinds of end groups (FTD) were investigated by ultra high pressure liquid chromatography under critical conditions (UP-LCCC) combined with electrospray ionization time-of flight mass spectrometry (ESI-TOF-MS). Theoretical predictions of the existence of a critical adsorption point (CPA) for statistical copolymers with a given chemical and sequence distribution1 could be studied and confirmed...
February 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/27991726/an-optimised-version-of-the-secretome-protein-enrichment-with-click-sugars-specs-method-leads-to-enhanced-coverage-of-the-secretome
#9
Alperen Serdaroglu, Stephan A Müller, Ute Schepers, Stefan Bräse, Wilko Weichert, Stefan F Lichtenthaler, Peer-Hendrik Kuhn
The secretome, the entirety of all soluble proteins either being secreted or proteolytically released by a cell, plays a key role in inter-cellular communication of multi-cellular organisms. Pathological alterations contribute to diseases such as hypertension, cancer, autoimmune disorders or neurodegenerative diseases. Hence, studying disease-related perturbations of the secretome and the secretome itself covers an important aspect of cellular physiology. We recently developed the secretome protein enrichment with click sugars (SPECS) method that enables the analysis of secretomes of in vitro cell cultures even in the presence of FCS with MS...
December 19, 2016: Proteomics
https://www.readbyqxmd.com/read/27922621/sharing-brain-mapping-statistical-results-with-the-neuroimaging-data-model
#10
Camille Maumet, Tibor Auer, Alexander Bowring, Gang Chen, Samir Das, Guillaume Flandin, Satrajit Ghosh, Tristan Glatard, Krzysztof J Gorgolewski, Karl G Helmer, Mark Jenkinson, David B Keator, B Nolan Nichols, Jean-Baptiste Poline, Richard Reynolds, Vanessa Sochat, Jessica Turner, Thomas E Nichols
Only a tiny fraction of the data and metadata produced by an fMRI study is finally conveyed to the community. This lack of transparency not only hinders the reproducibility of neuroimaging results but also impairs future meta-analyses. In this work we introduce NIDM-Results, a format specification providing a machine-readable description of neuroimaging statistical results along with key image data summarising the experiment. NIDM-Results provides a unified representation of mass univariate analyses including a level of detail consistent with available best practices...
December 6, 2016: Scientific Data
https://www.readbyqxmd.com/read/27862147/signal-preprocessing-multivariate-analysis-and-software-tools-for-ma-ldi-tof-mass-spectrometry-imaging-for-biological-applications
#11
REVIEW
Pere Ràfols, Dídac Vilalta, Jesús Brezmes, Nicolau Cañellas, Esteban Del Castillo, Oscar Yanes, Noelia Ramírez, Xavier Correig
Mass spectrometry imaging (MSI) is a label-free analytical technique capable of molecularly characterizing biological samples, including tissues and cell lines. The constant development of analytical instrumentation and strategies over the previous decade makes MSI a key tool in clinical research. Nevertheless, most MSI studies are limited to targeted analysis or the mere visualization of a few molecular species (proteins, peptides, metabolites, or lipids) in a region of interest without fully exploiting the possibilities inherent in the MSI technique, such as tissue classification and segmentation or the identification of relevant biomarkers from an untargeted approach...
November 9, 2016: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27859457/time-of-flight-mass-spectrometry-introduction-to-the-basics
#12
REVIEW
Ulrich Boesl
The intention of this tutorial is to introduce into the basic concepts of time-of-flight mass spectrometry, beginning with the most simple single-stage ion source with linear field-free drift region and continuing with two-stage ion sources combined with field-free drift regions and ion reflectors-the so-called reflectrons. Basic formulas are presented and discussed with the focus on understanding the physical relations of geometric and electric parameters, initial distribution of ionic parameters, ion flight times, and ion flight time incertitude...
January 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27780848/sucrose-nonfermenting-related-kinase-enzyme-mediated-rho-associated-kinase-signaling-is-responsible-for-cardiac-function
#13
Stephanie M Cossette, Vijesh J Bhute, Xiaoping Bao, Leanne M Harmann, Mark A Horswill, Indranil Sinha, Adam Gastonguay, Shabnam Pooya, Michelle Bordas, Suresh N Kumar, Shama P Mirza, Sean P Palecek, Jennifer L Strande, Ramani Ramchandran
BACKGROUND: Cardiac metabolism is critical for the functioning of the heart, and disturbance in this homeostasis is likely to influence cardiac disorders or cardiomyopathy. Our laboratory has previously shown that SNRK (sucrose nonfermenting related kinase) enzyme, which belongs to the AMPK (adenosine monophosphate-activated kinase) family, was essential for cardiac metabolism in mammals. Snrk global homozygous knockout (KO) mice die at postnatal day 0, and conditional deletion of Snrk in cardiomyocytes (Snrk cmcKO) leads to cardiac failure and death by 8 to 10 months...
December 2016: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/27750373/mass-spectrometric-strategies-for-the-investigation-of-biomarkers-of-illicit-drug-use-in-wastewater
#14
Félix Hernández, Sara Castiglioni, Adrian Covaci, Pim de Voogt, Erik Emke, Barbara Kasprzyk-Hordern, Christoph Ort, Malcolm Reid, Juan V Sancho, Kevin V Thomas, Alexander L N van Nuijs, Ettore Zuccato, Lubertus Bijlsma
The analysis of illicit drugs in urban wastewater is the basis of wastewater-based epidemiology (WBE), and has received much scientific attention because the concentrations measured can be used as a new non-intrusive tool to provide evidence-based and real-time estimates of community-wide drug consumption. Moreover, WBE allows monitoring patterns and spatial and temporal trends of drug use. Although information and expertise from other disciplines is required to refine and effectively apply WBE, analytical chemistry is the fundamental driver in this field...
October 17, 2016: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27741559/the-arc-of-mass-spectrometry-exchange-formats-is-long-but-it-bends-toward-hdf5
#15
Manor Askenazi, Hisham Ben Hamidane, Johannes Graumann
The evolution of data exchange in Mass Spectrometry spans decades and has ranged from human-readable text files representing individual scans or collections thereof (McDonald et al., 2004) through the official standard XML-based (Harold, Means, & Udemadu, 2005) data interchange standard (Deutsch, 2012), to increasingly compressed (Teleman et al., 2014) variants of this standard sometimes requiring purely binary adjunct files (Römpp et al., 2011). While the desire to maintain even partial human readability is understandable, the inherent mismatch between XML's textual and irregular format relative to the numeric and highly regular nature of actual spectral data, along with the explosive growth in dataset scales and the resulting need for efficient (binary and indexed) access has led to a phenomenon referred to as "technical drift" (Davis, 2013)...
October 14, 2016: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27611504/marine-environment-pollution-the-contribution-of-mass-spectrometry-to-the-study-of-seawater
#16
Emanuele Magi, Marina Di Carro
The study of marine pollution has been traditionally addressed to persistent chemicals, generally known as priority pollutants; a current trend in environmental analysis is a shift toward "emerging pollutants," defined as newly identified or previously unrecognized contaminants. The present review is focused on the peculiar contribution of mass spectrometry (MS) to the study of pollutants in the seawater compartment. The work is organized in five paragraphs where the most relevant groups of pollutants, both "classical" and "emerging," are presented and discussed, highlighting the relative data obtained by the means of different MS techniques...
September 9, 2016: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27602546/computational-methods-and-challenges-in-hydrogen-deuterium-exchange-mass-spectrometry
#17
Jürgen Claesen, Tomasz Burzykowski
Hydrogen/Deuterium exchange (HDX) has been applied, since the 1930s, as an analytical tool to study the structure and dynamics of (small) biomolecules. The popularity of using HDX to study proteins increased drastically in the last two decades due to the successful combination with mass spectrometry (MS). Together with this growth in popularity, several technological advances have been made, such as improved quenching and fragmentation. As a consequence of these experimental improvements and the increased use of protein-HDXMS, large amounts of complex data are generated, which require appropriate analysis...
September 7, 2016: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27593344/precise-analysis-of-gallium-isotopic-composition-by-mc-icp-ms
#18
Wei Yuan, Jiu Bin Chen, Jean-Louis Birck, Zuo Ying Yin, Sheng Liu Yuan, Hong Ming Cai, Zhong Wei Wang, Qiang Huang, Zhu Hong Wang
Though an isotope approach could be beneficial for better understanding the biogeochemical cycle of gallium (Ga), an analogue of the monoisotopic element aluminum (Al), the geochemistry of Ga isotopes has not been widely elaborated. We developed a two-step method for purifying Ga from geological (biological) samples for precise measurement of Ga isotope ratio using multicollector inductively coupled plasma mass spectrometry (MC-ICP-MS). Ga was thoroughly separated from other matrix elements using two chromatographic columns loaded with AG 1-X4 and Ln-spec resin, respectively...
October 4, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27580014/mass-spectral-fragmentation-of-trimethylsilylated-small-molecules
#19
REVIEW
Zijuan Lai, Oliver Fiehn
Mass spectrometry-based untargeted metabolomics detects many peaks that cannot be identified. While advances have been made for automatic structure annotations in LC-electrospray-MS/MS, no open source solutions are available for hard electron ionization used in GC-MS. In metabolomics, most compounds bear moieties with acidic protons, for example, amino, hydroxyl, or carboxyl groups. Such functional groups increase the boiling points of metabolites too much for use in GC-MS. Hence, in GC-MS-focused metabolomics, derivatization of these groups is essential and has been employed since the 1960s...
August 31, 2016: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27579891/mass-spectrometry-derived-systems-biology-technologies-delineate-the-system-s-biochemical-applications-of-siderophores
#20
Qiao Su, Guang Xu, Tianbing Guan, Yumei Que, Haitao Lu
Siderophores are chemically diverse secondary metabolites that primarily assist the host organisms to chelate iron. Siderophores are biosynthesized by many biological organisms, including bacteria, fungi, and plants and they are responsible for a variety of biological functions beyond capture iron. Thus, they could provide a novel understanding of host-pathogen interactions, plant physiology, disease pathogenesis, and drug development. However, knowledge gaps in analytical technologies, chemistry, and biology have severely impeded the applications of siderophores, and a new strategy is urgently needed to bridge these gaps...
August 31, 2016: Mass Spectrometry Reviews
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