journal
MENU ▼
Read by QxMD icon Read
search

Molecular & Cellular Proteomics: MCP

journal
https://www.readbyqxmd.com/read/29141914/proteotranscriptomics-reveal-signaling-networks-in-the-ovarian-cancer-microenvironment
#1
Thomas Worzfeld, Florian Finkernagel, Silke Reinartz, Anne Konzer, Till Adhikary, Andrea Nist, Thorsten Stiewe, Uwe Wagner, Mario Looso, Johannes Graumann, Rolf Müller
Ovarian cancer is characterized by early transcoelomic metastatic spread via the peritoneal fluid, where tumor cell spheroids (TU), tumor-associated T cells (TAT), and macrophages (TAM) create a unique microenvironment promoting cancer progression, chemoresistance and immuno-suppression. However, the underlying signaling mechanisms remain largely obscure.  To chart these signaling networks, we performed comprehensive proteomic and transcriptomic analyses of TU, TAT and TAM from ascites of ovarian cancer patients...
November 15, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29141913/multiplexed-biomarker-panels-discriminate-zika-and-dengue-virus-infection-in-humans
#2
Guang Song, Hee-Sool Rho, Jianbo Pan, Pedro Ramos, Ki-Jun Yoon, Freddy A Medina, Emily M Lee, Daniel J Eichinger, Guo-Li Ming, Jorge L Muñoz-Jordan, Hengli Tang, Ignacio Pino, Hongjun Song, Jiang Qian, Heng Zhu
Zika virus (ZIKV) and dengue virus (DENV) are closely related flaviviruses that cause widespread, acute febrile illnesses, notably microcephaly for fetuses of infected pregnant women. Detecting the viral cause of these illnesses is paramount to determine risks to patients, counsel pregnant women, and help fight outbreaks. A combined diagnostic algorithm for ZIKV and DENV requires Reverse transcription polymerase chain reaction (RT-PCR) and IgM antibody detection. RT-PCR differentiates between DENV and ZIKV infections during the acute phases of infection, but differentiation based on IgM antibodies is currently nearly impossible in endemic areas...
November 15, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29133510/single-cell-immuno-laser-microdissection-coupled-to-label-free-proteomics-to-reveal-the-proteotypes-of-human-brain-cells-after-ischemia
#3
Teresa García-Berrocoso, Víctor Llombart, Laura Colàs-Campàs, Alexandre Hainard, Virginie Licker, Anna Penalba, Laura Ramiro, Alba Simats, Alejandro Bustamante, Elena Martínez-Saez, Francesc Canals, Jean-Charles Sanchez, Joan Montaner
Cerebral ischemia entails rapid tissue damage in the affected brain area causing devastating neurological dysfunction. How each component of the neurovascular unit contributes or responds to the ischemic insult in the context of the human brain has not been solved yet. Thus, the analysis of the proteome is a straightforward approach to unraveling these cell proteotypes.In this study, post-mortem brain slices from ischemic stroke patients were obtained corresponding to infarcted (IC) and contralateral (CL) areas...
November 13, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29122912/top-down-microproteomics-bridged-to-maldi-ms-imaging-reveals-the-molecular-physiome-of-brain-regions
#4
Vivian Delcourt, Julien Franck, Jusal Quanico, Jean-Pascal Gimeno, Maxence Wisztorski, Antonella Raffo Romero, Firas Kobeissy, Xavier Roucou, Michel Salzet, Isabelle Fournier
Tissue top-down microproteomics was performed on 3 brain regions, leading to the characterization of 123 reference proteins. Moreover, 8 alternative proteins from alternative open reading frames (AltORF) were identified. Some proteins display specific post-translational modification profiles or truncation linked to the brain regions and their functions. Systems biology analysis performed on the microproteome identified in each region allowed to associate sub-networks with the functional physiology of each brain region...
November 9, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29118029/giapronto-a-one-click-graph-visualization-software-for-proteomics-datasets
#5
Amber Kathryn Weiner, Simone Sidoli, Sharon J Diskin, Ben Garcia
Here we present a free interactive web tool to process and visualize proteomics datasets with a single click. GiaPronto can process all proteomics quantification methods, i.e. label-free, SILAC and isobaric labeling, and analyze post-translational modifications (PTMs). The software performs normalization and statistics, assists determination of regulated proteins, biomarkers and Gene Ontology (GO) enrichment, and provides high resolution images and tables for further data analysis. We foresee that GiaPronto will become the most rapid and simple tool for assessing data quality and determining most relevant features of proteomic datasets...
November 8, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29113996/characterization-of-the-molecular-mechanisms-underlying-glucose-stimulated-insulin-secretion-from-isolated-pancreatic-%C3%AE-cells-using-ptmomics
#6
Taewook Kang, Pia Jensen, Honggang Huang, Gitte Lund Christensen, Nils Billestrup, Martin R Larsen
Normal pancreatic islet β-cells (PBCs) abundantly secrete insulin in response to elevated blood glucose levels, in order to maintain an adequate control of energy balance and glucose homeostasis. However, the molecular mechanisms underlying the insulin secretion are unclear. Improving our understanding of glucose-stimulated insulin secretion (GSIS) mechanisms under normal conditions is a prerequisite for developing better interventions against diabetes. Here, we aimed at identifying novel signaling pathways involved in the initial release of insulin from PBCs after glucose stimulation using quantitative strategies for the assessment of phosphorylated proteins and sialylated N-linked (SA) glycoproteins...
November 7, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29093020/acetylome-profiling-reveals-extensive-lysine-acetylation-of-the-fatty-acid-metabolism-pathway-in-the-diatom-phaeodactylum-tricornutum
#7
Zhuo Chen, Ling Luo, Runfa Chen, Hanhua Hu, Yufang Pan, Haibo Jiang, Xia Wan, Hu Jin, Yangmin Gong
N(ε) -lysine acetylation represents a highly dynamic and reversibly regulated post-translational modification widespread in almost all organisms, and plays important roles for regulation of protein function in diverse metabolic pathways. However, little is known about the role of lysine acetylation in photosynthetic eukaryotic microalgae. We integrated proteomic approaches to comprehensively characterize the lysine acetylome in the model diatom Phaeodactylum tricornutum. In total, 2324 acetylation sites from 1220 acetylated proteins were identified, representing the largest dataset of the lysine acetylome in plants to date...
November 1, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29089373/functional-characterization-and-comparison-of-plasmodium-falciparum-proteins-as-targets-of-transmission-blocking-antibodies
#8
Daria Nikolaeva, Joseph J Illingworth, Kazutoyo Miura, Daniel Gw Alanine, Iona J Brian, Yuanyuan Li, Alex J Fyfe, Dari F Da, Anna Cohuet, Carole A Long, Simon J Draper, Sumi Biswas
Plasmodium falciparum malaria continues to evade control efforts, utilizing highly specialized sexual-stages to transmit infection between the human host and mosquito vector. In a vaccination model, antibodies directed to sexual-stage antigens, when ingested in the mosquito blood meal, can inhibit parasite growth in the midgut and consequently arrest transmission. Despite multiple datasets for the Plasmodium sexual-stage transcriptome and proteome, there have been no rational screens to identify candidate antigens for transmission-blocking vaccine (TBV) development...
October 31, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29079721/diverse-peptide-hormones-affecting-root-growth-identified-in-the-medicago-truncatula-secreted-peptidome
#9
Neha Patel, Nadiatul A Mohd-Radzman, Leo Corcilius, Ben Crossett, Angela Connolly, Stuart J Cordwell, Ariel Ivanovici, Katia Taylor, James Wlilliams, Steve Binos, Michael Mariani, Richard J Payne, Michael A Djordjevic
Multigene families encoding diverse secreted peptide hormones play important roles in plant development. A need exists to efficiently elucidate the structures and post-translational modifications of these difficult-to-isolate peptide hormones in planta so that their biological functions can be determined. A mass spectrometry and bioinformatics approach was developed to comprehensively analyse the secreted peptidome of Medicago hairy root cultures and xylem sap. We identified 759 spectra corresponding to the secreted products of twelve peptide hormones including four CEP (C-TERMINALLY ENCODED PEPTIDE), two CLE (CLV3/ENDOSPERM SURROUNDING REGION RELATED) and six XAP (XYLEM SAP ASSOCIATED PEPTIDE) peptides...
October 27, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29079720/a-global-survey-of-atpase-activity-in-plasmodium-falciparum-asexual-blood-stages-and-gametocytes
#10
Corrie Ortega, Andrew Frando, Bobbie-Jo Webb-Robertson, Lindsey N Anderson, Neil D Fleck, Erika L Flannery, Matthew Fishbaugher, Taylor A Murphree, Joshua R Hansen, Richard D Smith, Stefan Hi Kappe, Aaron Wright, Christoph Grundner
Effective malaria control and elimination in hyperendemic areas of the world will require treatment of the Plasmodium falciparum (Pf) blood stage that causes disease as well as the gametocyte stage that is required for transmission from humans to the mosquito vector. Most currently used therapies do not kill gametocytes, a highly specialized, non-replicating sexual parasite stage. Further confounding next generation drug development against Pf is the unknown metabolic state of the gametocyte and the lack of known biochemical activity for most parasite gene products in general...
October 27, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29079719/integrated-proteomic-and-transcriptomic-analysis-revealslong-noncoding-rna-hotair-promotes-hepatocellular-carcinoma-cell-proliferation-by-regulating-opioid-growth-factor-receptor-ogfr
#11
Ying Wu, Qian Xiong, Siting Li, Xue Yang, Feng Ge
Long non-coding RNA HOX transcript antisense RNA (HOTAIR) is involved in human tumorigenesis and is dysregulated in hepatocellular carcinoma (HCC). However, the molecular mechanisms underlying HOTAIR functions in HCC are largely unknown. Here, we employed an integrated transcriptomic and quantitative proteomic analysis to systematically explore the regulatory role of HOTAIR in HCC. A total of 673 transcripts and 293 proteins were found to be dysregulated after HOTAIR inhibition. Bioinformatics studies indicated that differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) are involved in many biological processes, especially cancer-related signaling pathways...
October 27, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29070702/optimization-of-experimental-parameters-in-data-independent-mass-spectrometry-significantly-increases-depth-and-reproducibility-of-results
#12
Roland Bruderer, Oliver M Bernhardt, Tejas Gandhi, Yue Xuan, Julia Sondermann, Manuela Schmidt, David Gomez-Varela, Lukas Reiter
Comprehensive, reproducible and precise analysis of large sample cohorts is one of the key objectives of quantitative proteomics. Here, we present an implementation of data-independent acquisition using its parallel acquisition nature that surpasses the limitation of serial MS2 acquisition of data-dependent acquisition on a quadrupole ultra-high field Orbitrap mass spectrometer. In deep single shot data-independent acquisition, we identified and quantified 6,383 proteins in human cell lines using 2-or-more peptides/protein and over 7,100 proteins when including the 717 proteins that were identified on the basis of a single peptide sequence...
October 25, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29066631/advancing-a-high-throughput-glycotope-centric-glycomics-workflow-based-on-nanolc-ms-2-product-dependent-ms-3-analysis-of-permethylated-glycans
#13
Cheng-Te Hsiao, Po-Wei Wang, Hua-Chien Chang, Yen-Ying Chen, Shui-Hua Wang, Yijuang Chern, Kay-Hooi Khoo
The intrinsic nature of glycosylation, namely non-template encoded, stepwise elongation and termination with a diverse range of isomeric glyco-epitopes (glycotopes), translates into ambiguity in most cases of mass spectrometry (MS)-based glycomic mapping. It is arguable that whether one needs to delineate every single glycomic entity, which may be counterproductive. Instead, one should focus on identifying as many structural features as possible that would collectively define the glycomic characteristics of a cell or tissue, and how these may change in response to self-programmed development, immuno-activation, and malignant transformation...
October 24, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29055021/meercat-multiplexed-efficient-cell-free-expression-of-recombinant-qconcats-for-large-scale-absolute-proteome-quantification
#14
Nobuaki Takemori, Ayako Takemori, Yuki Tanaka, Yaeta Endo, Jane L Hurst, Guadalupe Gómez-Baena, Victoria M Harman, Robert J Beynon
A major challenge in proteomics is the absolute accurate quantification of large numbers of proteins. QconCATs, artificial proteins that are concatenations of multiple standard peptides, are well established as an efficient means to generate standards for proteome quantification. Previously, QconCATs have been expressed in bacteria, but we now describe QconCAT expression in a robust, cell-free system. The new expression approach rescues QconCATs that previously were unable to be expressed in bacteria and can reduce the incidence of proteolytic damage to QconCATs...
October 20, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29046390/novel-sarcopenia-related-alterations-in-sarcomeric-protein-post-translational-modifications-in-skeletal-muscles-identified-by-top-down-proteomics
#15
Liming Wei, Zachery R Gregorich, Ziqing Lin, Wenxuan Cai, Yutong Jin, Susan H McKiernan, Sean McIlwain, Judd M Aiken, Richard L Moss, Gary M Diffee, Ying Ge
Sarcopenia, the age-related loss of skeletal muscle mass and strength, is a significant cause of morbidity in the elderly and is a major burden on health care systems. Unfortunately, the underlying molecular mechanisms in sarcopenia remain poorly understood. Herein, we utilized top-down proteomics to elucidate sarcopenia-related changes in the fast- and slow-twitch skeletal muscles of aging rats with a focus on the sarcomeric proteome, which includes both myofilament and Z-disc proteins-the proteins that constitute the contractile apparatuses...
October 18, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29046389/the-antibody-repertoire-of-colorectal-cancer
#16
Seong Won Cha, Stefano Bonissone, Seungjin Na, Pavel A Pevzner, Vineet Bafna
Immunotherapy is becoming increasingly important in the fight against cancers, utilizing and manipulating the body's immune response to treat tumors. Understanding the immune repertoire - the collection of immunological proteins - of treated and untreated cells is possible at the genomic, but technically difficult at the protein level. Standard protein databases do not include the highly divergent sequences of somatic rearranged immunoglobulin genes, and may lead to missed identifications in a mass spectrometry search...
October 18, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29046388/the-early-dendritic-cell-signaling-induced-by-virulent-francisellatularensis-strain-occurs-in-phases-and-involves-the-activation-of-erks-and-p38-in-the-later-stage
#17
Ivo Fabrik, Marek Link, Daniela Putzova, Lenka Plzakova, Zuzana Lubovska, Vlada Philimonenko, Ivona Pavkova, Pavel Rehulka, Zuzana Krocova, Pavel Hozak, Marina Santic, Jiri Stulik
Dendritic cells (DCs) infected by Francisella tularensis are poorly activated and do not undergo classical maturation process. While reasons of such unresponsiveness are not fully understood, their impact on the priming of immunity is well appreciated. Previous attempts to explain the behavior of Francisella-infected DCs were hypothesis-driven and focused on events at later stages of infection. Here, we took an alternative unbiased approach by applying methods of global phosphoproteomics to analyze the dynamics of cell signaling in primary DCs during the first hour of infection by Francisella tularensis...
October 18, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29042480/prediction-of-protein-complexes-in-trypanosoma-brucei-by-protein-correlation-profiling-mass-spectrometry-and-machine-learning
#18
Thomas W M Crozier, Michele Tinti, Mark Larance, Angus I Lamond, Michael A J Ferguson
A disproportionate number of predicted proteins from the genome sequence of the protozoan parasite Trypanosoma brucei, an important human and animal pathogen, are hypothetical proteins of unknown function. This paper describes a protein correlation profiling mass spectrometry approach, using two size exclusion and one ion exchange chromatography systems, to derive sets of predicted protein complexes in this organism by hierarchical clustering and machine learning methods. These hypothesis-generating proteomic data are provided in an open access online data visualisation environment (http://134...
October 17, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29021294/identification-of-serological-biomarkers-for-early-diagnosis-of-lung-cancer-using-a-protein-array-based-approach
#19
Jianbo Pan, Guang Song, Dunyan Chen, Yadong Li, Shuang Liu, Shaohui Hu, Christian Rosa, Daniel J Eichinger, Ignacio Pino, Heng Zhu, Jiang Qian, Yi Huang
Lung cancer (LC) remains the leading cause of mortality from malignant tumors worldwide. Currently, a lack of serological biomarkers for early LC diagnosis is a major roadblock for early intervention and prevention of LC. To undertake this challenge, we employed a two-phase strategy to discover and validate a biomarker panel using a protein array-based approach. In Phase I, we obtained serological autoimmune profiles of 80 LC patients and 20 healthy subjects on HuProt arrays, and identified 170 candidate proteins significantly associated with LC...
October 11, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29018126/systematic-identification-of-mycobacterium-tuberculosis%C3%A2-effectors-reveals-that-bfrb-suppresses-innate-immunity
#20
Xiang He, He-Wei Jiang, Hong Chen, Hainan Zhang, Yin Liu, Zhao-Wei Xu, Fanlin Wu, Shu-Juan Guo, Jing-Li Hou, Mingkun Yang, Wei Yan, Jiaoyu Deng, Lijun Bi, Xian-En Zhang, Sheng-Ce Tao
Mycobacterium tuberculosis (Mtb) has evolved multiple strategies to counter the human immune system. The effectors of Mtb play important roles in the interactions with the host. However, due to the lack of highly efficient strategies, there are only a handful of known Mtb effectors, thus hampering our understanding of Mtb pathogenesis. In this study, we probed Mtb proteome microarray with biotinylated whole-cell lysates of human macrophages, identifying 27 Mtb membrane proteins and secreted proteins that bind to macrophage proteins...
October 10, 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"