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Kevin A Welle, Tian Zhang, Jennifer R Hyrohorenko, Shichen Shen, Jun Qu, Sina Ghaemmaghami
Recent advances in mass spectrometry have enabled system-wide analyses of protein turnover. By globally quantifying the kinetics of protein clearance and synthesis, these methodologies can provide important insights into the regulation of the proteome under varying cellular and environmental conditions. To facilitate such analyses, we have employed a methodology that combines metabolic isotopic labeling (Stable Isotope Labeling in Cell Culture - SILAC) with isobaric tagging (Tandem Mass Tags - TMT) for analysis of multiplexed samples...
October 20, 2016: Molecular & Cellular Proteomics: MCP
Lorenzo Cecchi, Marzia Innocenti, Fabrizio Melani, Marzia Migliorini, Lanfranco Conte, Nadia Mulinacci
Herein we describe the influence of olive oil refining processes on the lignan profile. The detection of new isobaric lignans is suggested to reveal frauds in commercial extra-Virgin Olive Oils. We analyzed five commercial olive oils by HPLC-DAD-TOF/MS to evaluate their lignan content and detected, for the first time, some isobaric forms of natural (+)-pinoresinol and (+)-1-acetoxypinoresinol. Then we analyzed partially and fully-refined oils from Italy, Tunisia and Spain. The isobaric forms occur only during the bleaching step of the refining process and remain unaltered after the final deodorizing step...
March 15, 2017: Food Chemistry
Yan Xiong, Xiangfang Tang, Qingshi Meng, Hongfu Zhang
Ammonia has been considered the contaminant primarily responsible for respiratory disease in poultry. Even though it can cause tracheal lesions, its adverse effects on the trachea have not been sufficiently studied. The present study investigated tracheal changes in Arbor Acres broilers (Gallus gallus) induced by high concentration of ammonia using isobaric tag for relative and absolute quantification (iTRAQ)-based proteome analysis. In total, 3,706 proteins within false discovery rate of 1% were identified, including 119 significantly differentially expressed proteins...
October 17, 2016: Science China. Life Sciences
Daniel P Pike, Celine L Hartman, Gregory J Weissler, Elisa N D Palladino, Carolyn J Albert, David A Ford
Platelet-activating factor (PAF) is a potent biologically active phospholipid that mediates human physiological and pathophysiologic responses. PAF levels increase transiently and are typically assessed by techniques with limitations related to expense, sensitivity, pre-analysis derivatization and interference with isobaric molecules. This study elucidates a facile, accurate liquid chromatography-mass spectrometry analytical method for PAF. In negative ion mode using electrospray ionization, collisionally-activated dissociation analysis showed a unique product ion for acetate adducts of PAF molecular species representing the loss of methyl acetate from the polar head group and loss of a part of the acetate group from the sn-2 position...
October 18, 2016: Lipids
Liza J Burton, Mariela Rivera, Ohuod Hawsawi, Jin Zou, Tamaro Hudson, Guangdi Wang, Qiang Zhang, Luis Cubano, Nawal Boukli, Valerie Odero-Marah
Muscadine grape skin extract (MSKE) is derived from muscadine grape (Vitis rotundifolia), a common red grape used to produce red wine. Endoplasmic reticulum (ER) stress activates the unfolded protein response (UPR) that serves as a survival mechanism to relieve ER stress and restore ER homeostasis. However, when persistent, ER stress can alter the cytoprotective functions of the UPR to promote autophagy and cell death. Although MSKE has been documented to induce apoptosis, it has not been linked to ER stress/UPR/autophagy...
2016: PloS One
Radhe Sharan, Rajan Verma, Akshay Dhawan, Jugal Kumar
BACKGROUND: Ropivacaine, a newer local anesthetic, is gaining increased acceptance due to its improved safety profile over bupivacaine and lignocaine. Analgesic adjuvants have proved to be valuable in improving the quality of anesthesia and duration of analgesia. AIM: To compare the efficacy of clonidine and fentanyl as adjuvants to ropivacaine in spinal anesthesia in lower abdominal surgeries. MATERIALS AND METHODS: A randomized, double-blind control study was carried out in 100 patients who were randomly divided into two groups...
September 2016: Anesthesia, Essays and Researches
Alba Hykollari, Katharina Paschinger, Barbara Eckmair, Iain B H Wilson
N-glycans from invertebrates and protists have often unusual structures which present analytical challenges. Both core and antennal modifications can be quite different from the more familiar vertebrate glycan motifs; thereby, contrary to the concept that "simple" organisms have "simple" N-glycans, rather complex oligosaccharides structures, including zwitterionic and anionic ones, have been found in a range of species. Thus, to facilitate the optimized elucidation of the maximal possible range of structures, the analytical workflow for glycomics of these organisms should include sequential release and fractionation steps...
2017: Methods in Molecular Biology
Yachun Su, Liping Xu, Zhuqing Wang, Qiong Peng, Yuting Yang, Yun Chen, Youxiong Que
BACKGROUND: Sugarcane smut, which is caused by Sporisorium scitamineum, has been threatening global sugarcane production. Breeding smut resistant sugarcane varieties has been proven to be the most effective method of controlling this particular disease. However, a lack of genome information of sugarcane has hindered the development of genome-assisted resistance breeding programs. Furthermore, the molecular basis of sugarcane response to S. scitamineum infection at the proteome level was incomplete and combining proteomic and transcriptional analysis has not yet been conducted...
October 12, 2016: BMC Genomics
Xin-Yu Yuan, Rui-Heng Wang, Xiao-Dan Zhao, Yun-Bo Luo, Da-Qi Fu
Natural mutants of the Non-ripening (Nor) gene repress the normal ripening of tomato fruit. The molecular mechanism of fruit ripening regulation by the Nor gene is unclear. To elucidate how the Nor gene can affect ripening and fruit quality at the protein level, we used the fruits of Nor mutants and wild-type Ailsa Craig (AC) to perform iTRAQ (isobaric tags for relative and absolute quantitation) analysis. The Nor mutation altered tomato fruit ripening and affected quality in various respects, including ethylene biosynthesis by down-regulating the abundance of 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), pigment biosynthesis by repressing phytoene synthase 1 (PSY1), ζ-carotene isomerase (Z-ISO), chalcone synthase 1 (CHS1) and other proteins, enhancing fruit firmness by increasing the abundance of cellulose synthase protein, while reducing those of polygalacturonase 2 (PG2) and pectate lyase (PL), altering biosynthesis of nutrients such as carbohydrates, amino acids, and anthocyanins...
2016: PloS One
Sibylle Pfammatter, Eric Bonneil, Pierre Thibault
Quantitative proteomics using isobaric reagents tandem mass tags (TMT) or isobaric tags for relative and absolute quantitation (iTRAQ) provide a convenient approach to compare changes in protein abundances across multiple samples. However, the analysis of complex protein digests by isobaric labeling can be undermined by the relative large proportion of co-selected peptide ions that lead to distorted reporter ion ratios and affect the accuracy and precision of quantitative measurements. Here, we investigated the use of high-field asymmetric waveform ion mobility spectrometry (FAIMS) in proteomic experiments to reduce sample complexity and improve protein quantification using TMT isobaric labeling...
October 10, 2016: Journal of Proteome Research
Tatsuya Joutsuka, Akihiro Morita
Difference spectroscopy between two close systems is widely used to augment its selectivity to the different part of the observed system, though the molecular dynamics calculation of tiny difference spectra would be computationally extraordinary demanding by subtraction of two spectra. Therefore, we have proposed an efficient computational algorithm of difference spectra without resorting to the subtraction. The present paper reports our extension of the theoretical method in the isothermal-isobaric (NPT) ensemble...
October 10, 2016: Journal of Physical Chemistry. B
Bingbing Wang, Daniel A Knopf, Swarup China, Bruce W Arey, Tristan H Harder, Mary K Gilles, Alexander Laskin
Heterogeneous ice nucleation is a physical chemistry process of critical relevance to a range of topics in the fundamental and applied sciences and technologies. Heterogeneous ice nucleation remains insufficiently understood, partially due to the lack of experimental methods capable of obtaining in situ microscopic details of ice formation over nucleating substrates or particles. We present microscopic observations of ice nucleation events on kaolinite particles at the nanoscale and demonstrate the capability of direct tracking and micro-spectroscopic characterization of individual ice nucleating particles (INPs) in an authentic atmospheric sample...
September 21, 2016: Physical Chemistry Chemical Physics: PCCP
Praveen Mannam, Navin Rauniyar, TuKiet T Lam, Ruiyan Luo, Patty J Lee, Anup Srivastava
Cigarette smoking is the primary risk factor for COPD which is characterized by excessive inflammation and airflow obstruction of the lung. While inflammation is causally related to initiation and progression of COPD, the mitochondrial mechanisms that underlie the associated inflammatory responses are poorly understood. In this context, we have studied the role played by Mitogen activated protein (MAP) kinase kinase 3 (MKK3), a dual-specificity protein kinase, in cigarette smoke induced-inflammation and mitochondrial dysfunction...
October 4, 2016: Free Radical Biology & Medicine
Jidong Chen, Xiaolei Cui, Zhengjiang Qian, Yanjiao Li, Kang Kang, Junle Qu, Li Li, Deming Gou
BACKGROUND: Pulmonary arterial hypertension (PAH) is a lethal disease with pronounced narrowing of pulmonary vessels due to abnormal cell proliferation. The platelet-derived growth factor BB (PDGF-BB) is well known as a potent mitogen for smooth muscle cell proliferation. To better understand how this growth factor regulates pulmonary arterial smooth muscle cells (PASMCs) proliferation, we sought to characterize the response to PDGF-BB stimulation at system-wide levels, including the transcriptome and proteome...
October 6, 2016: BMC Genomics
Spiros Manolakos, Francy Sinatra, Leila Nikkhouy Albers, Kevin Hufford, James Alberti, Erkinjon G Nazarov, Theresa Evans-Nguyen
Differential mobility spectrometry (DMS) is applied to the analysis of inorganic mixtures relevant to nuclear forensics. Three primary components of potential radiological dispersal devices (RDDs): cobalt, cesium, and strontium, were studied by DMS to demonstrate rapid sample clean-up when coupled to mass spectrometry. Nanosprayed salt solutions comprised of stable analogs, as proxies to these radioisotopes, and isobaric interferents were introduced to DMS. The DMS effluent was directly coupled to a mass spectrometer to confirm the elemental identity of the separated clusters...
October 7, 2016: Analytical Chemistry
Tong Ren, Shide Lin, Zhongfeng Wang, Aijia Shang
Astrocytoma is one of the most common types of brain tumor, which is histologically and clinically classified into four grades (I-IV): I (pilocytic astrocytoma), II (diffuse astrocytoma), III (anaplastic astrocytoma), and IV (glioblastoma multiforme). A higher grade astrocytoma represents a worse prognosis and is more aggressive. In this study, we compared the differential proteome profile of astrocytoma from grades I to IV. The protein samples from clinical specimens of grades I, II, III, and IV astrocytoma were analyzed by two-dimensional liquid chromatography-tandem mass spectrometry and isobaric tags for relative and absolute quantitation and quantification...
2016: OncoTargets and Therapy
Tsan-Wan Chiu, Ying-Lun Chen, Chien-Yi Wu, Pei-Ling Yu, Ying-Hua Shieh, Bin Huang
BACKGROUND: Hydrogen sulfide (H2S) is one of the endogenous gaseous molecules promoting the production of nitric oxide (NO) which has cardioprotective functions. However, the role of the H2S-mediated protein S-nitrosoproteome and its subsequent physiological response remains unclear. METHODS: Endothelial cells EAhy 926 were treated with 50 μM of H2S for 2 hours. The NO bound S-nitrosoproteins were purified by a biotin-switch and then digested by trypsin. Resulting peptides from control and H2S treatment were separately labeled by isobaric tag for relative and absolute quantitation 114/115, quantified by liquid chromatography tandem-mass spectrometry and analyzed by ingenuity pathway analysis (IPA) software...
September 2016: Acta Cardiol Sin
X L Ren, L Q Li, L Xu, Y S Guo, L M Lu
Potassium is one of the three main mineral nutrients, and is vital for leaf growth and the quality of tobacco (Nicotiana tabacum) plants. In recent years, the isobaric tags for relative and absolute quantitation (iTRAQ) method has been one of the most popular techniques for quantitative proteomic analysis. In this study, we used iTRAQ to compare protein abundances in the roots of control and low potassium-treated tobacco seedlings, and found that 108 proteins were differentially expressed between the two treatments...
August 29, 2016: Genetics and Molecular Research: GMR
Anna Maria A P Fernandes, Pedro H Vendramini, Renan Galaverna, Nicolas V Schwab, Luciane C Alberici, Rodinei Augusti, Roger F Castilho, Marcos N Eberlin
Mass spectrometry imaging (MSI) of neurotransmitters has so far been mainly performed by matrix-assisted laser desorption/ionization (MALDI) where derivatization reagents, deuterated matrix and/or high resolution, or tandem MS have been applied to circumvent problems with interfering ion peaks from matrix and from isobaric species. We herein describe the application of desorption electrospray ionization mass spectrometry imaging (DESI)-MSI in rat brain coronal and sagittal slices for direct spatial monitoring of neurotransmitters and choline with no need of derivatization reagents and/or deuterated materials...
October 4, 2016: Journal of the American Society for Mass Spectrometry
Qian-Feng Li, Min Xiong, Peng Xu, Li-Chun Huang, Chang-Quan Zhang, Qiao-Quan Liu
Brassinosteroids (BRs), essential plant-specific steroidal hormones, function in a wide spectrum of plant growth and development events, including seed germination. Rice is not only a monocotyledonous model plant but also one of the most important staple food crops of human beings. Rice seed germination is a decisive event for the next-generation of plant growth and successful seed germination is critical for rice yield. However, little is known about the molecular mechanisms on how BR modulates seed germination in rice...
October 5, 2016: Scientific Reports
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