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https://www.readbyqxmd.com/read/29116757/-esi-cad-msn-procedure-for-sequencing-lignin-oligomers-based-on-a-study-of-synthetic-model-compounds-with-%C3%AE-o-4-and-5-5-linkages
#1
Huaming Sheng, Weijuan Tang, Jinshan Gao, James Steven Riedeman, Guannan Li, Tiffany Mae Jarrell, Matthew R Hurt, Linan Yang, Priya Murria, Xin Ma, John Joseph Nash, Hilkka I Kenttamaa
Seven synthesized G-lignin oligomer model compounds (ranging in size from dimers to an octamer) with 5-5 and/or β-O-4 linkag-es, and three synthesized S-lignin model compounds (a dimer, trimer and tetramer) with β-O-4 linkages, were evaporated and deprotonated using negative-ion mode ESI in a linear quadrupole ion trap/Fourier transform ion cyclotron resonance mass spec-trometer. The collision-activated dissociation (CAD) fragmentation patterns (obtained in MS2 and MS3 experiments, respectively) for the negative ions were studied in order to develop a procedure for sequencing unknown lignin oligomers...
November 8, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29063733/design-synthesis-of-9h-fluorenone-based-1-2-3-triazole-analogues-as-mycobacterium-tuberculosis-inha-inhibitors
#2
Suresh Amaroju, Singireddi Srinivasarao, Agnieszka Napiórkowska, Ewa Augustynowicz-Kopeć, Mallika Alvala, Christian Lherbet, Kondapalli Venkata Gowri Chandra Sekhar
We prepared fifty various 9H-fluorenone based 1,2,3-triazole analogues varied with NH, -S- and -SO2- groups using click chemistry. The target compounds were characterized by routine analytical techniques, (1) H, (13) CNMR, Mass, Elemental, single crystal XRD (8a) and screened for in vitro antitubercular activity against Mycobacterium tuberculosis (MTB) H37Rv strain and two 'wild' strains Spec. 210 and Spec. 192 and MIC50 was determined. Further, the compounds were evaluated for MTB InhA inhibition study as well...
October 24, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28970861/prostate-cancer-recognition-based-on-mass-spectrometry-sensing-data-and-data-fingerprint-recovery
#3
Khalfalla Awedat, Ikhlas Abdel-Qader, James R Springstead
The high dimensionality and noisy spectra of Mass Spectrometry (MS) data are two of the main challenges to achieving high accuracy recognition. The objective of this work is to produce an accurate prediction of class content by employing compressive sensing (CS). Not only can CS significantly reduce MS data dimensionality, but it will also allow for full reconstruction of original data. We are proposing a weighted mixing of L1- and L2-norms via a regularization term as a classifier within compressive sensing framework...
March 2017: Biomedical Signal Processing and Control
https://www.readbyqxmd.com/read/28955476/periaortic-lymphoma-in-a-cat
#4
Laura Bree, Chiara Bergamino, Ronan Mullins, Pamela Kelly, Robert Shiel
CASE SUMMARY: A 14-year-old neutered male Siamese cat was presented with a 3 month history of lethargy, inappetence, dehydration, hindlimb ataxia and intermittent proprioceptive deficits in the hindlimbs. Physical examination revealed low body condition score (1.75/5), pallor and bilateral basilar grade II/VI systolic heart murmur. Neurological examination revealed hindlimb ataxia, severe atrophy of the hindlimb musculature, intermittent hindlimb proprioceptive deficits and normoreflexia...
July 2017: JFMS open reports
https://www.readbyqxmd.com/read/28738591/procedures-for-precise-measurements-of-135-cs-137-cs-atom-ratios-in-environmental-samples-at-extreme-dynamic-ranges-and-ultra-trace-levels-by-thermal-ionization-mass-spectrometry
#5
James A Dunne, David A Richards, Hsin-Wei Chen
Determination of (135)Cs/(137)Cs atom ratios has the potential to be a powerful tool for nuclear forensics and monitoring environmental processes. We present optimized chemical separation techniques and thermal ionization mass spectrometry (TIMS) protocols to obtain precise (135)Cs/(137)Cs atom ratios for a range of environmental sample types. We use a combination of double AMP-PAN separation and Sr-spec resin column purification to yield excellent separation from the alkali metals (Rb separation factor > 600), which normally suppress ionization of Cs...
November 1, 2017: Talanta
https://www.readbyqxmd.com/read/28537067/multifunctional-triple-decker-inverse-12-metallacrown-4-sandwiching-halides
#6
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
#7
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...
September 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28498477/identification-of-candidate-substrates-of-ubiquitin-specific-protease-13-using-2d-dige
#8
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...
July 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
#9
Tesla Yudhistira, Sandip V Mulay, Kyung Jin Lee, Youngsam Kim, Hee-Sung Park, David G Churchill
The role of fluorescent molecules in diagnosis, treatment as well as in biomedical research has great current medicinal significance and is the focus of concentrated effort across the scientific research spectrum. Related research continues to reveal new practical sensing systems that bear 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...
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
#10
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
#11
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
#12
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
#13
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
#14
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...
March 2017: Proteomics
https://www.readbyqxmd.com/read/27922621/sharing-brain-mapping-statistical-results-with-the-neuroimaging-data-model
#15
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
#16
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
#17
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
#18
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
#19
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
#20
REVIEW
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)...
September 2017: Mass Spectrometry Reviews
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