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https://www.readbyqxmd.com/read/27911411/preparation-and-in-vivo-use-of-an-activity-based-probe-for-n-acylethanolamine-acid-amidase
#1
Elisa Romeo, Silvia Pontis, Stefano Ponzano, Fabiola Bonezzi, Marco Migliore, Simona Di Martino, Maria Summa, Daniele Piomelli
Activity-based protein profiling (ABPP) is a method for the identification of an enzyme of interest in a complex proteome through the use of a chemical probe that targets the enzyme's active sites. A reporter tag introduced into the probe allows for the detection of the labeled enzyme by in-gel fluorescence scanning, protein blot, fluorescence microscopy, or liquid chromatography-mass spectrometry. Here, we describe the preparation and use of the compound ARN14686, a click chemistry activity-based probe (CC-ABP) that selectively recognizes the enzyme N-acylethanolamine acid amidase (NAAA)...
November 23, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27905125/gadd45%C3%AE-is-involved-in-the-apoptosis-of-lymphocytes-induced-by-riboflavin-and-ultraviolet-light
#2
Peng Yang, Huiqin Wen, Tao Zhong, Hailiang Hu, Bangqiang Zhu, Kang Xia, Mo Xu, Maohong Bian
BACKGROUND: Riboflavin plus ultraviolet (UV) pathogen reduction technology (RF-PRT) is an effective method for inactivating the residual white blood cells (WBCs) in blood components. The RF-PRT system for platelets is known to activate many signaling pathways, including p38 and NF-κB. Nevertheless, proteomic studies in WBCs after riboflavin plus UV treatment requires further analysis. STUDY DESIGN AND METHODS: ABO/D-matched lymphocytes were pooled, split, and treated with RF-PRT or UV light or left untreated...
December 1, 2016: Transfusion
https://www.readbyqxmd.com/read/27903962/targeted-proteomics-in-urinary-extracellular-vesicles-identifies-biomarkers-for-diagnosis-and-prognosis-of-prostate-cancer
#3
Tamara Sequeiros, Marina Rigau, Cristina Chiva, Melania Montes, Iolanda Garcia-Grau, Marta Garcia, Sherley Diaz, Ana Celma, Irene Bijnsdorp, Alex Campos, Primiano Di Mauro, Salvador Borrós, Jaume Reventós, Andreas Doll, Rosanna Paciucci, Michiel Pegtel, Inés de Torres, Eduard Sabidó, Juan Morote, Mireia Olivan
Rapid and reliable diagnosis of prostate cancer (PCa) is highly desirable as current used methods lack specificity. In addition, identification of PCa biomarkers that can classify patients into high- and low-risk groups for disease progression at early stage will improve treatment decision-making. Here, we describe a set of protein-combination panels in urinary extracellular vesicles (EVs), defined by targeted proteomics and immunoblotting techniques that improve early non-invasive detection and stratification of PCa patients...
November 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/27903464/a-peptide-retrieval-strategy-enables-significant-improvement-of-quantitative-performance-without-compromising-confidence-of-identification
#4
Chengjian Tu, Shichen Shen, Quanhu Sheng, Yu Shyr, Jun Qu
: Reliable quantification of low-abundance proteins in complex proteomes is challenging largely owing to the limited number of spectra/peptides identified. In this study we developed a straightforward method to improve the quantitative accuracy and precision of proteins by strategically retrieving the less confident peptides that were previously filtered out using the standard target-decoy search strategy. The filtered-out MS/MS spectra matched to confidently-identified proteins were recovered, and the peptide-spectrum-match FDR were re-calculated and controlled at a confident level of FDR≤1%, while protein FDR maintained at ~1%...
November 26, 2016: Journal of Proteomics
https://www.readbyqxmd.com/read/27901089/a-silac-based-method-for-quantitative-proteomic-analysis-of-intestinal-organoids
#5
Alexis Gonneaud, Christine Jones, Naomie Turgeon, Dominique Lévesque, Claude Asselin, François Boudreau, François-Michel Boisvert
Organoids have the potential to bridge 3D cell culture to tissue physiology by providing a model resembling in vivo organs. Long-term growing organoids were first isolated from intestinal crypt cells and recreated the renewing intestinal epithelial niche. Since then, this technical breakthrough was applied to many other organs, including prostate, liver, kidney and pancreas. We describe here how to apply a SILAC-based quantitative proteomic approach to measure protein expression changes in intestinal organoids under different experimental conditions...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27899155/comparative-sequence-analysis-of-cyclospora-cayetanensis-apicoplast-genomes-originating-from-diverse-geographical-regions
#6
Hediye Nese Cinar, Yvonne Qvarnstrom, Yuping Wei-Pridgeon, Wen Li, Fernanda S Nascimento, Michael J Arrowood, Helen R Murphy, AhYoung Jang, Eunje Kim, RaeYoung Kim, Alexandre da Silva, Gopal R Gopinath
BACKGROUND: Cyclospora cayetanensis is an emerging coccidian parasite that causes endemic and epidemic diarrheal disease called cyclosporiasis, and this infection is associated with consumption of contaminated produce or water in developed and developing regions. Food-borne outbreaks of cyclosporiasis have occurred almost every year in the USA since the 1990s. Investigations of these outbreaks are currently hampered due to lack of molecular epidemiological tools for trace back analysis...
November 29, 2016: Parasites & Vectors
https://www.readbyqxmd.com/read/27897006/session-introduction
#7
Nikolay Samusik, Nima Aghaeepour, Sean Bendall
Recent technological developments allow gathering single-cell measurements across different domains (genomic, transcriptomics, proteomics, imaging etc). Sophisticated computational algorithms are required in order to harness the power of single-cell data. This session is dedicated to computational methods for single-cell analysis in various biological domains, modelling of population heterogeneity, as well as translational applications of single cell data.
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896771/selective-reaction-monitoring-for-quantitation-of-cellular-proteins
#8
Vitor M Faça
Proteins and proteomes are dynamic and complex. The accurate identification and measurement of their properties such as abundance, location, and turnover are challenging tasks. Even though high-throughput proteomics has significantly evolved, the technique still lacks fully quantitative and reproducible qualities. A mass spectrometry-based targeted proteomic strategy called selective reaction monitoring (SRM) has emerged in recent years as an important multiplex platform to precisely quantify sets of proteins in multiple samples...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896769/depletion-of-highly-abundant-proteins-of-the-human-blood-plasma-applications-in-proteomics-studies-of-psychiatric-disorders
#9
Sheila Garcia, Paulo A Baldasso, Paul C Guest, Daniel Martins-de-Souza
Psychiatric disorders are complex diseases involving exogenous and endogenous factors. Biomarkers for diagnosis or prediction of successful treatment are not existent. In addition, the molecular basis of these diseases is still poorly understood. Blood plasma represents the most complex proteome as it contains subproteomes from several body tissues. However, the high abundance of some little proteins can obscure the analysis of hundreds of low abundance proteins, which are potential biomarkers. Therefore, removal of these high abundance proteins is pivotal in any proteomic study of plasma...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896757/lc-ms-e-multiplex-ms-ms-ion-mobility-and-label-free-quantitation-in-clinical-proteomics
#10
Gustavo Henrique Martins Ferreira Souza, Paul C Guest, Daniel Martins-de-Souza
Proteomic tools can only be implemented in clinical settings if high-throughput, automated, sensitive, and accurate methods are developed. This has driven researchers to the edge of mass spectrometry (MS)-based proteomics capacity. Here we provide an overview of recent achievements in mass spectrometric technologies and instruments. This includes development of high and ultra definition-MS(E) (HDMS(E) and UDMS(E)) through implementation of ion mobility (IM) MS towards sensitive and accurate label-free proteomics using ultra performance liquid chromatography (UPLC)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896756/multiplex-biomarker-approaches-in-type-2-diabetes-mellitus-research
#11
Susan E Ozanne, Hassan Rahmoune, Paul C Guest
Type 2 diabetes mellitus is a multifactorial condition resulting in high fasting blood glucose levels. Although its diagnosis is straightforward, there is not one set of biomarkers or drug targets that can be used for classification or personalized treatment of individuals who suffer from this condition. Instead, the application of multiplex methods incorporating a systems biology approach is essential in order to increase our understanding of this disease. This chapter reviews the state of the art in biomarker studies of human type 2 diabetes from a proteomic and metabolomic perspective...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896750/inference-method-for-developing-mathematical-models-of-cell-signaling-pathways-using-proteomic-datasets
#12
Tianhai Tian, Jiangning Song
The progress in proteomics technologies has led to a rapid accumulation of large-scale proteomic datasets in recent years, which provides an unprecedented opportunity and valuable resources to understand how living organisms perform necessary functions at systems levels. This work presents a computational method for designing mathematical models based on proteomic datasets. Using the mitogen-activated protein (MAP) kinase pathway as the test system, we first develop a mathematical model including the cytosolic and nuclear subsystems...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27895910/proteomic-identification-of-cryostress-in-epididymal-spermatozoa
#13
Sung Jae Yoon, Md Saidur Rahman, Woo Sung Kwon, Do Yeal Ryu, Yoo Jin Park, Myung Geol Pang
BACKGROUND: Cryopreservation of epididymal spermatozoa is important in cases in which it is not possible to collect semen using normal methods, as the sudden death of an animal or a catastrophic injury. However, the freezing and thawing processes cause stress to spermatozoa, including cold shock, osmotic damage, and ice crystal formation, thereby reducing sperm quality. We assessed the motility (%), motion kinematics, capacitation status, and viability of spermatozoa using computer-assisted sperm analysis and Hoechst 33258/chlortetracycline fluorescence staining...
2016: Journal of Animal Science and Biotechnology
https://www.readbyqxmd.com/read/27895852/protein-protein-interaction-network-of-celiac-disease
#14
Mona Zamanian Azodi, Hassan Peyvandi, Mohammad Rostami-Nejad, Akram Safaei, Kamran Rostami, Reza Vafaee, Mohammadhossein Heidari, Mostafa Hosseini, Mohammad Reza Zali
AIM: The aim of this study is to investigate the Protein-Protein Interaction Network of Celiac Disease. BACKGROUND: Celiac disease (CD) is an autoimmune disease with susceptibility of individuals to gluten of wheat, rye and barley. Understanding the molecular mechanisms and involved pathway may lead to the development of drug target discovery. The protein interaction network is one of the supportive fields to discover the pathogenesis biomarkers for celiac disease...
2016: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/27894104/proteomic-profiling-of-nci-60-extracellular-vesicles-uncovers-common-protein-cargo-and-cancer-type-specific-biomarkers
#15
Stephanie N Hurwitz, Mark A Rider, Joseph L Bundy, Xia Liu, Rakesh K Singh, David G Meckes
Packed with biological information, extracellular vesicles (EVs) offer exciting promise for biomarker discovery and applications in therapeutics and non-invasive diagnostics. Currently, our understanding of EV contents is confined by the limited cells from which vesicles have been characterized utilizing the same enrichment method. Using sixty cell lines from the National Cancer Institute (NCI-60), here we provide the largest proteomic profile of EVs in a single study, identifying 6,071 proteins with 213 common to all isolates...
November 24, 2016: Oncotarget
https://www.readbyqxmd.com/read/27894102/comparative-proteomics-of-a-model-mcf10a-krasg12v-cell-line-reveals-a-distinct-molecular-signature-of-the-krasg12v-cell-surface
#16
Xiaoying Ye, King C Chan, Andrew M Waters, Matthew Bess, Adam Harned, Bih-Rong Wei, Jadranka Loncarek, Brian T Luke, Benjamin C Orsburn, Bradley D Hollinger, Robert M Stephens, Rachel Bagni, Alex Martinko, James A Wells, Dwight V Nissley, Frank McCormick, Gordon Whiteley, Josip Blonder
Oncogenic Ras mutants play a major role in the etiology of most aggressive and deadly carcinomas in humans. In spite of continuous efforts, effective pharmacological treatments targeting oncogenic Ras isoforms have not been developed. Cell-surface proteins represent top therapeutic targets primarily due to their accessibility and susceptibility to different modes of cancer therapy. To expand the treatment options of cancers driven by oncogenic Ras, new targets need to be identified and characterized at the surface of cancer cells expressing oncogenic Ras mutants...
November 24, 2016: Oncotarget
https://www.readbyqxmd.com/read/27892491/selected-biomarkers-revealed-potential-skin-toxicity-caused-by-certain-copper-compounds
#17
Hairui Li, Pei Zhen Toh, Jia Yao Tan, Melvin T Zin, Chi-Ying Lee, Bo Li, Melvina Leolukman, Hongqian Bao, Lifeng Kang
Copper is an essential mineral and plays important roles in skin growth and activity. Copper delivery through skin can provide beneficial effects but its potential to induce skin irritation reactions is often overlooked. Data on dermal toxicity caused by copper compounds is scant. Some recognized in vitro skin toxicity methods are unsuitable for all metal compounds. Here, we employ a keratinocyte-based model and evaluated the skin irritation potential of copper compounds at cellular, genomic and proteomic levels...
November 28, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27891302/epidemiology-of-sj%C3%A3-gren-s-syndrome-from-an-oral-perspective
#18
REVIEW
Anne Isine Bolstad, Kathrine Skarstein
Oral symptoms are among the most distressing manifestations for patients with Sjögren's syndrome (SS). The feeling of dry mouth is unpleasant, and hyposalivation may contribute to difficulty in speaking, chewing and swallowing and reduced quality of life. Reduced salivary flow increases the risk for dental caries and problems with prosthetic replacement. It seems that SS is not as frequently occurring as previously anticipated. Population-based prevalence studies on primary SS in Europe, conducted on large background populations and in accordance with the AECG criteria, reported of a prevalence of 1-9 cases per 10,000 people...
2016: Current Oral Health Reports
https://www.readbyqxmd.com/read/27891114/comparative-analysis-of-two-helicobacter-pylori-strains-using-genomics-and-mass-spectrometry-based-proteomics
#19
Roger Karlsson, Kaisa Thorell, Shaghayegh Hosseini, Diarmuid Kenny, Carina Sihlbom, Åsa Sjöling, Anders Karlsson, Intawat Nookaew
Helicobacter pylori, a gastroenteric pathogen believed to have co-evolved with humans over 100,000 years, shows significant genetic variability. This motivates the study of different H. pylori strains and the diseases they cause in order to identify determinants for disease evolution. In this study, we used proteomics tools to compare two H. pylori strains. Nic25_A was isolated in Nicaragua from a patient with intestinal metaplasia, and P12 was isolated in Europe from a patient with duodenal ulcers. Differences in the abundance of surface proteins between the two strains were determined with two mass spectrometry-based methods, label-free quantification (MaxQuant) or the use of tandem mass tags (TMT)...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27890915/pharmacological-evidence-a-new-therapeutic-approach-to-the-treatment-of-chronic-heart-failure-through-sur2b-kir6-1-channel-in-endothelial-cells
#20
Shang Wang, Chao-Liang Long, Jun Chen, Wen-Yu Cui, Yan-Fang Zhang, Hao Zhang, Hai Wang
Both iptakalim (Ipt) and natakalim (Nat) activate the SUR2B/Kir6.1 channel, an ATP-sensitive potassium channel (KATP) subtype, with high selectivity. In this study we investigated the therapeutic effects of Ipt and Nat against isoproterenol-induced chronic heart failure (ISO-CHF) in rats, and demonstrated a new therapeutic approach to the treatment of CHF through activation of the SUR2B/Kir6.1 channel in endothelial cells. In ISO-CHF rats, oral administration of Nat (1, 3, 9 mg·kg(-1)·d(-1)) or Ipt (3 mg·kg(-1)·d(-1)) for 60 days significantly improved cardiac dysfunction, reversed cardiac remodeling, significantly attenuated the pathological increases in BNP levels, and improved endothelial dysfunction by adjusting the balance between endothelin and NO systems...
November 28, 2016: Acta Pharmacologica Sinica
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