journal
MENU ▼
Read by QxMD icon Read
search

Molecular & Cellular Proteomics: MCP

journal
https://www.readbyqxmd.com/read/28935716/proteomic-analysis-of-phytophthora-infestans-reveals-the-importance-of-cell-wall-proteins-in-pathogenicity
#1
Svante Resjö, Maja Brus, Ashfaq Ali, Harold J G Meijer, Marianne Sandin, Francine Govers, Fredrik Levander, Laura Grenville-Briggs, Erik Andreasson
The oomycete Phytophthora infestans is the most harmful pathogen of potato. It causes the disease late blight, which generates increased yearly costs of up to one billion euro in the EU alone and is difficult to control. We have performed a large-scale quantitative proteomics study of six P. infestans life stages with the aim to identify proteins that change in abundance during development, with a focus on pre-infectious life stages. Over 10 000 peptides from 2061 proteins were analysed. We identified a number of abundance profiles of proteins that were up- or downregulated in different combinations of life stages...
September 21, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28887382/identification-of-a-novel-salmonella-type-iii-effector-by-quantitative-secretome-profiling
#2
Sen Cheng, Lu Wang, Qian Liu, Linlu Qi, Kaiwen Yu, Zhen Wang, Mei Wu, Yanhua Liu, Jiaqi Fu, Mo Hu, Min Li, Daoguo Zhou, Xiaoyun Liu
Salmonellaenterica serovar Typhimurium is arguably one of the most studied bacterial pathogens and successful infection requires the delivery of its virulence factors (effectors) directly into host cells via the type III secretion systems (T3SSs). Central to Salmonella pathogenesis, these effector proteins have been subjected to extensive studies over the years. Nevertheless, whether additional effectors exist remains unclear. Here we report the identification of a novel Salmonella T3SS effector STM1239 (which we renamed SopF) via quantitative secretome profiling...
September 8, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28887381/global-analysis-of-membrane-associated-protein-oligomerization-using-protein-correlation-profiling
#3
Zachary McBride, Donglai Chen, Christy Reick, Jun Xie, Daniel B Szymanski
Membrane-associated proteins are required for essential processes like transport, organelle biogenesis, and signaling. Many are expected to function as part of an oligomeric protein complex. However, membrane-associated proteins are challenging to work with, and large-scale datasets on the oligomerization state of this important class of proteins is missing. Here we combined cell fractionation of Arabidopsis leaves with nondenaturing detergent solubilization and LC/MS-based profiling of size exclusion chromatography fractions to measure the apparent masses of >1350 membrane-associated proteins...
September 8, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28887380/proteomic-signature-reveals-modulation-of-human-macrophage-polarization-and-functions-under-differing-environmental-oxygen-conditions
#4
Magali Court, Graciane Petre, Michèle El-Atifi, Arnaud Millet
Macrophages are innate immune cells which can react to a large number of environmental stimuli thanks to a high degree of plasticity. These cells are involved in a variety of tissue functions in homeostasis, and they play essential roles in pathological contexts. Macrophages’ activation state, which determines their functional orientation, is strongly influenced by the cellular environment. A large body of macrophage literature is devoted to better defining polarizations from a molecular viewpoint. It is now accepted that a multidimensional model of polarization is needed to grasp the broad phenotype repertoire controlled by environmental signals...
September 8, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28887379/a-comprehensive-open-source-platform-for-mass-spectrometry-based-glycoproteomics-data-analysis
#5
Gang Liu, Kai Cheng, Chi Y Lo, Jun Li, Jun Qu, Sriram Neelamegham
Glycosylation is among the most abundant and diverse protein post-translational modifications (PTMs) identified to date. The structural analysis of this PTM is challenging due to the diverse monosaccharides which are not conserved among organisms, the branched nature of glycans, their isomeric structures, and heterogeneity in the glycan distribution at a given site. Glycoproteomics experiments have adopted the traditional high-throughput LC-MS(n) proteomics workflow to analyze site-specific glycosylation. However, comprehensive computational platforms for data analyses are scarce...
September 8, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28874504/proteome-analysis-of-hypoxic-glioblastoma-cells-reveals-sequential-metabolic-adaptation-nbsp-of-one-carbon-metabolic-pathways
#6
Kangling Zhang, Pei Xu, James L Sowers, Daniel F Machuca, Barsam Mirfattah, Jason Herring, Hui Tang, Yan Chen, Bing Tian, Allan R Brasier, Lawrence C Sowers
Rapidly proliferating tumors are exposed to a hypoxic microenvironment due to their density, high metabolic consumption, and interruptions in blood flow due to immature angiogenesis. Cellular responses to hypoxia promote highly malignant and metastatic behavior, as well as a chemotherapy-resistant state. In order to better understand the complex relationships between hypoxic adaptations and cancer progression, we studied the dynamic proteome responses of glioblastoma cells exposed to hypoxia via an innovative approach: quantification of newly synthesized proteins using heavy stable-isotope arginine labeling combined with accurate assessment of cell replication by quantification of the light/heavy arginine ratio of peptides in histone H4...
September 5, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28867676/a-varroa-destructor-protein-atlas-reveals-molecular-underpinnings-of-developmental-transitions-and-sexual-differentiation
#7
Alison McAfee, Queenie Chan, Jay Evans, Leonard J Foster
Varroa destructor is the most economically damaging honey bee pest, weakening colonies by simultaneously parasitizing bees and transmitting harmful viruses. Despite these impacts on honey bee health, surprisingly little is known about its fundamental molecular biology. Here we present a Varroa protein atlas crossing all major developmental stages (egg, protonymph, deutonymph and adult) for both male and female mites as a web-based interactive tool (http://foster.nce.ubc.ca/varroa/index.html). We used intensity-based label-free quantitation to find 1,433 differentially expressed proteins across developmental stages...
September 3, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28864778/quantitative-mass-spectrometry-reveals-food-intake-induced-neuropeptide-level-changes-in-rat-brain-functional-assessment-of-selected-neuropeptides-as-feeding-regulators
#8
Hui Ye, Jingxin Wang, Zichuan Tian, Fengfei Ma, James A Dowell, Quentin Bremer, Gaoyuan Lu, Brian Baldo, Lingjun Li
Endogenous neuropeptides are important signaling molecules that function as regulators of food intake and body weight. Previous work has shown that neuropeptide gene expression levels in a forebrain reward site, the nucleus accumbens (NAc), were changed by feeding. In order to directly monitor feeding-induced changes in neuropeptide expression levels within the NAc, we employed a combination of cryostat dissection, heat stabilization, neuropeptide extraction and label-free quantitative neuropeptidomics via a liquid chromatography-high resolution mass spectrometry platform...
September 1, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28860124/quantitative-analysis-of-the-proteome-response-to-the-histone-deacetylase-inhibitor-hdaci-vorinostat-in-niemann-pick-type-c1-disease
#9
Kanagaraj Subramanian, Navin Rauniyar, Mathieu Lavalleé-Adam, John R Yates, William E Balch
Niemann-Pick type C (NPC) disease is an inherited, progressive neurodegenerative disorder principally caused by mutations in the NPC1 gene. NPC disease is characterized by the accumulation of unesterified cholesterol in the late endosomes (LE) and lysosomes (LE) (LE/Ly). Vorinostat, a histone deacetylase inhibitor (HDACi), restores cholesterol homeostasis in fibroblasts derived from NPC patients; however, the exact mechanism by which Vorinostat restores cholesterol level is not known yet. In this study, we performed comparative proteomic profiling of the response of NPC1I1061T fibroblasts to Vorinostat...
August 31, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28851738/phosphoproteomic-analysis-reveals-the-importance-of-kinase-regulation-during-orbivirus-infection
#10
Bjorn-Patrick Mohl, Edward Emmott, Polly Roy
Bluetongue virus (BTV) causes infections in wild and domesticated ruminants with high morbidity and mortality and is responsible for significant economic losses in both developing and developed countries. BTV serves as a model for the study of other members of the Orbivirus genus. Previously, the importance of casein kinase 2 for BTV replication was demonstrated. To identify intracellular signalling pathways and novel host-cell kinases involved during BTV infection, the phosphoproteome of BTV infected cells was analysed...
August 29, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28827280/systematic-and-quantitative-assessment-of-hydrogen-peroxide-reactivity-with-cysteines-across-human-proteomes
#11
Ling Fu, Ke-Ke Liu, Ming-An Sun, Cai-Ping Tian, Rui Sun, Carlos Morales Betanzos, Keri A Tallman, Ned A Porter, Yong Yang, Dian-Jing Guo, Daniel C Liebler, Jing Yang
Protein cysteinyl residues are the mediators of hydrogen peroxide (H2O2)-dependent redox signaling. However, site-specific mapping of the selectivity and dynamics of these redox reactions in cells poses a major analytical challenge. Here we describe a chemoproteomic platform to systematically and quantitatively analyze the reactivity of thousands of cysteines toward H2O2 in human cells. We identified >900 H2O2-sensitive cysteines, which are defined as the H2O2-dependent redoxome. Although redox sites associated with antioxidative and metabolic functions are consistent, most of the H2O2-dependent redoxome varies dramatically between different cells...
August 21, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28821604/development-of-a-multiplexed-assay-for-oral-cancer-candidate-biomarkers-using-peptide-immunoaffinity-enrichment-and-targeted-mass-spectrometry
#12
Yung-Chin Hsiao, Lang-Ming Chi, Kun-Yi Chien, Wei-Fan Chiang, Szu-Fan Chen, Yao-Ning Chuang, Shih-Yu Lin, Chia-Chun Wu, Ya-Ting Chang, Lichieh Julie Chu, Yi-Ting Chen, Shu-Li Chia, Chih-Yen Chien, Kai-Ping Chang, Yu-Sun Chang, Jau-Song Yu
Oral cancer is one of the most common cancers worldwide, and there are currently no biomarkers approved for aiding its management. Although many potential oral cancer biomarkers have been discovered, very few have been verified in body fluid specimens in parallel to evaluate their clinical utility. The lack of appropriate multiplexed assays for chosen targets represents one of the bottlenecks to achieving this goal. In the present study, we develop a peptide immunoaffinity enrichment-coupled multiple reaction monitoring-mass spectrometry (SISCAPA-MRM) assay for verifying multiple reported oral cancer biomarkers in saliva...
August 18, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28821603/a-simple-light-isotope-metabolic-labeling-slim-labeling-strategy-a-powerful-tool-to-address-the-dynamics-of-proteome-variations-in-vivo
#13
Thibaut Léger, Camille Garcia, Laetitia Collomb, Jean-Michel Camadro
Many quantitative proteomics strategies rely on in vivo metabolic incorporation of amino acids with modified stable isotope profiles into proteins. These methods give rise to multiple ions for each peptide, with possible distortion of the isotopolog distribution, making the overall analytical process complex. We validated an alternative strategy, simple light isotope metabolic labeling (SLIM-labeling), which alleviates many of these problems. SLIM-labeling is based on the in vivo reduction of the isotopic composition of proteins using metabolic precursors with a unique light isotope composition to label all amino acids...
August 18, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28821602/large-scale-proteomics-combined-with-transgenic-experiments-demonstrates-an-important-role-of-jasmonic-acid-nbsp-in-potassium-nbsp-deficiency-response-in-wheat-and-rice
#14
Gezi Li, Yufang Wu, Guoyu Liu, Xianghong Xiao, Pengfei Wang, Tian Gao, Mengjun Xu, Qiaoxia Han, Yonghua Wang, Tiancai Guo, Guozhang Kang
Potassium (K+) is the most abundant inorganic cation in plants, and molecular dissection of K+ deficiency has received considerable interest in order to minimize K+ fertilizer input and develop high quality K+-efficient crops. However, the molecular mechanism of plant responses to K+ deficiency is still poorly understood. In this study, two-week-old bread wheat seedlings grown hydroponically in Hoagland solution were transferred to K+-free conditions for 8 d, and their root and leaf proteome profiles were assessed using the iTRAQ proteome method...
August 18, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28821601/high-sensitivity-quantitative-proteomics-using-automated-multidimensional-nano-flow-chromatography-and-accumulated-ion-monitoring-on-quadrupole-orbitrap-linear-ion-trap-mass-spectrometer
#15
Paolo Cifani, Alex Kentsis
Quantitative proteomics using high-resolution and accuracy mass spectrometry promises to transform our understanding of biological systems and disease. Recent development of parallel reaction monitoring (PRM) using hybrid instruments substantially improved the specificity of targeted mass spectrometry. Combined with high-efficiency ion trapping, this approach also provided significant improvements in sensitivity. Here, we investigated the effects of ion isolation and accumulation on the sensitivity and quantitative accuracy of targeted proteomics using the recently developed hybrid quadrupole-Orbitrap-linear ion trap mass spectrometer...
August 18, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28814509/chemoproteomics-reveals-chemical-diversity-and-dynamics-of-4-oxo-2-nonenal-modifications-in-cells
#16
Rui Sun, Ling Fu, Ke-Ke Liu, Cai-Ping Tian, Yong Yang, Keri A Tallman, Ned A Porter, Daniel C Liebler, Jing Yang
4-Oxo-2-nonenal (ONE) derived from lipid peroxidation modifies nucleophiles and transduces redox signaling by its reactions with proteins. However, the molecular interactions between ONE and complex proteomes and their dynamics in situ remain largely unknown. Here we describe a quantitative chemoproteomic analysis of protein adduction by ONE in cells, in which the cellular target profile of ONE is mimicked by its alkynyl surrogate. The analyses reveal four types of ONE-derived modifications in cells, including ketoamide and Schiff-base adducts to lysine, Michael adducts to cysteine, and a novel pyrrole adducts to cysteine...
August 16, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28798222/an-integrated-approach-to-explore-composition-and-dynamics-of-cholesterol-rich-membrane-microdomains-in-sexual-stages-of-malaria-parasite
#17
Federica Fratini, Carla Raggi, Gabriella Sferra, Cecilia Birago, Anna Sansone, Felicia Grasso, Chiara Currà, Anna Olivieri, Tomasino Pace, Stefania Mochi, Leonardo Picci, Carla Ferreri, Antonella Di Biase, Elisabetta Pizzi, Marta Ponzi
Membrane microdomains that include lipid rafts, are involved in key physiological and pathological processes and participate in the entry of endocellular pathogens. These assemblies, enriched in cholesterol and sphingolipids, form highly dynamic, liquid-ordered phases that can be separated from the bulk membranes thanks to their resistance to solubilization by non-ionic detergents. To characterize complexity and dynamics of detergent-resistant membranes of sexual stages of the rodent malaria parasite Plasmodium berghei, here we propose an integrated study of raft components based on proteomics, lipid analysis and bioinformatics...
August 10, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28794006/identification-of-the-sox2-interactome-by-bioid-reveals-ep300-as-a-mediator-of-sox2-dependent-squamous-differentiation-and-lung-squamous-cell-carcinoma-growth
#18
Bo Ram Kim, Etienne Coyaud, Estelle Laurent, Jonathan St-Germain, Emily Van de Laar, Ming Sound Tsao, Brian Raught, Nadeem Moghal
Lung cancer is the leading cause of cancer mortality worldwide, with squamous cell carcinoma (SQCC) being the second most common form. SQCCs are thought to originate in bronchial basal cells through an injury response to smoking, which results in this stem cell population committing to hyperplastic squamous rather than mucinous and ciliated fates. Copy number gains in SOX2 in the region of 3q26-28 occur in 94% of SQCCs, and appear to act both early and late in disease progression by stabilizing the initial squamous injury response in stem cells and promoting growth of invasive carcinoma...
August 9, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28747380/identification-of-differentially-expressed-splice-variants-by-the-proteogenomic-pipeline-splicify
#19
Malgorzata A Komor, Thang Pham, Annemieke C Hiemstra, Sander R Piersma, Anne S Bolijn, Tim Schelfhorst, Pien M Delis-van Diemen, Marianne Tijssen, Robert P Sebra, Meredith Ashby, Gerrit A Meijer, Connie R Jimenez, Remond J A Fijneman
Proteogenomics, i.e. comprehensive integration of genomics and proteomics data, is a powerful approach identifying novel protein biomarkers. This is especially the case for proteins that differ structurally between disease and control conditions. As tumor development is associated with aberrant splicing, we focus on this rich source of cancer specific biomarkers. To this end, we developed a proteogenomic pipeline, Splicify, which is able to detect differentially expressed protein isoforms. Splicify is based on integrating RNA massive parallel sequencing data and tandem mass spectrometry proteomics data to identify protein isoforms resulting from differential splicing between two conditions...
July 26, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28729386/dormancy-in-embryos-insight-from-hydrated-encysted-embryos-of-an-aquatic-invertebrate
#20
Tamar Ziv, Vered Chalifa-Caspi, Nadav Denekamp, Inbar Plaschkes, Sylwiya Sylwia Kierszniowska, Idit Blais, Arie Admon, Esther Lubzens
Numerous aquatic invertebrates remain dormant for decades in a hydrated state as encysted embryos. In search for functional pathways associated with this form of dormancy, we used label-free quantitative proteomics to compare the proteomes of hydrated encysted dormant embryos (resting eggs; RE) with non-dormant embryos (amictic eggs; AM) of the rotifer Brachionus plicatilis</p> <p>A total of 2,631 proteins were identified in rotifer eggs. About 62% proteins showed higher abundance in AM relative to RE (Fold Change>3; p=0...
July 20, 2017: Molecular & Cellular Proteomics: MCP
journal
journal
39834
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"