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proteomics and visualization

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https://www.readbyqxmd.com/read/29344869/isolation-of-amyloid-plaques-and-neurofibrillary-tangles-from-archived-alzheimer-s-disease-tissue-using-laser-capture-microdissection-for-downstream-proteomics
#1
Eleanor Drummond, Shruti Nayak, Geoffrey Pires, Beatrix Ueberheide, Thomas Wisniewski
Here, we describe a new method that allows localized proteomics of amyloid plaques and neurofibrillary tangles (NFTs), which are the two pathological hallmarks of Alzheimer's disease (AD). Amyloid plaques and NFTs are visualized using immunohistochemistry and microdissected from archived, formalin-fixed paraffin-embedded (FFPE) human tissue samples using laser-capture microdissection. The majority of human tissue specimens are FFPE; hence the use of this type of tissue is a particular advantage of this technique...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344855/protocol-for-the-analysis-of-laser-capture-microdissected-fresh-frozen-tissue-homogenates-by-silver-stained-1d-sds-page
#2
DaRue A Prieto, Gordon Whitely, Donald J Johann, Josip Blonder
The heterogeneity present in solid tumors adds significant difficulty to scientific analysis and improved understanding. Fundamentally, solid tumor formation consists of cancer cells proper along with stromal elements. The burgeoning malignant process is dependent upon modified stromal elements. Collectively, the stroma forms an essential microenvironment, which is indispensable for the survival and growth of the malignant neoplasm. This cellular heterogeneity makes molecular profiling of solid tumors via mass spectrometry (MS)-based proteomics a daunting task...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29324038/the-evolution-and-metamorphosis-of-arthropod-proteomics-and-genomics
#3
Judith H Willis
This article presents an overview of the development of techniques for analyzing cuticular proteins (CPs), their transcripts, and their genes over the past 50 years based primarily on experience in the laboratory of J.H. Willis. It emphasizes changes in the kind of data that can be gathered and how such data provided insights into the molecular underpinnings of insect metamorphosis and cuticle structure. It describes the techniques that allowed visualization of the location of CPs at both the anatomical and intracuticular levels and measurement of the appearance and deployment of transcripts from CP genes as well as what was learned from genomic and transcriptomic data...
January 7, 2018: Annual Review of Entomology
https://www.readbyqxmd.com/read/29322920/investigation-and-identification-of-functional-post-translational-modification-sites-associated-with-drug-binding-and-protein-protein-interactions
#4
Min-Gang Su, Julia Tzu-Ya Weng, Justin Bo-Kai Hsu, Kai-Yao Huang, Yu-Hsiang Chi, Tzong-Yi Lee
BACKGROUND: Protein post-translational modification (PTM) plays an essential role in various cellular processes that modulates the physical and chemical properties, folding, conformation, stability and activity of proteins, thereby modifying the functions of proteins. The improved throughput of mass spectrometry (MS) or MS/MS technology has not only brought about a surge in proteome-scale studies, but also contributed to a fruitful list of identified PTMs. However, with the increase in the number of identified PTMs, perhaps the more crucial question is what kind of biological mechanisms these PTMs are involved in...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29321522/accelerated-proteomic-visualization-of-individual-predatory-venoms-of-conus-purpurascens-reveals-separately-evolved-predation-evoked-venom-cabals
#5
S W A Himaya, Frank Marí, Richard J Lewis
Cone snail venoms have separately evolved for predation and defense. Despite remarkable inter- and intra-species variability, defined sets of synergistic venom peptides (cabals) are considered essential for prey capture by cone snails. To better understand the role of predatory cabals in cone snails, we used a high-throughput proteomic data mining and visualisation approach. Using this approach, the relationship between the predatory venom peptides from nine C. purpurascens was systematically analysed. Surprisingly, potentially synergistic levels of κ-PVIIA and δ-PVIA were only identified in five of nine specimens...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29317273/mitochondrial-network-responses-in-oxidative-physiology-and-disease
#6
REVIEW
Young-Mi Go, Jolyn Fernandes, Xin Hu, Karan Uppal, Dean P Jones
Mitochondrial activities are linked directly or indirectly to all cellular functions in aerobic eukaryotes. Omics methods enable new approaches to study functional organization of mitochondria and their adaptive and maladaptive network responses to bioenergetic fuels, physiologic demands, environmental challenges and aging. In this review, we consider mitochondria collectively within a multicellular organism as a macroscale "mitochondriome", functioning to organize bioenergetics and metabolism as an organism utilizes environmental resources and protects against environmental threats...
January 6, 2018: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/29306441/liposome-assisted-metabolic-glycan-labeling-with-cell-and-tissue-selectivity
#7
Yifei Du, Ran Xie, Yuting Sun, Xinqi Fan, Xing Chen
Metabolic labeling of glycans with sugar chemical reporters (i.e., unnatural sugars bearing a bioorthogonal group), followed by bioorthogonal reaction with imaging probes or affinity tags, has enabled visualization and proteomic analysis of glycosylation in live cells and in living animals. This two-step metabolic glycan labeling strategy has emerged as a powerful tool for probing glycosylation, but suffers from a lack of cell-type selectivity. Here we describe liposome-assisted bioorthogonal reporter (LABOR), a liposome-assisted format of metabolic glycan labeling that allows for cell-selective and tissue-specific glycan imaging and glycoproteomic profiling...
2018: Methods in Enzymology
https://www.readbyqxmd.com/read/29280960/metagomics-a-web-based-tool-for-peptide-centric-functional-and-taxonomic-analysis-of-metaproteomics-data
#8
Michael Riffle, Damon H May, Emma Timmins-Schiffman, Molly P Mikan, Daniel Jaschob, William Stafford Noble, Brook L Nunn
Metaproteomics is the characterization of all proteins being expressed by a community of organisms in a complex biological sample at a single point in time. Applications of metaproteomics range from the comparative analysis of environmental samples (such as ocean water and soil) to microbiome data from multicellular organisms (such as the human gut). Metaproteomics research is often focused on the quantitative functional makeup of the metaproteome and which organisms are making those proteins. That is: What are the functions of the currently expressed proteins? How much of the metaproteome is associated with those functions? And, which microorganisms are expressing the proteins that perform those functions? However, traditional protein-centric functional analysis is greatly complicated by the large size, redundancy, and lack of biological annotations for the protein sequences in the database used to search the data...
December 27, 2017: Proteomes
https://www.readbyqxmd.com/read/29227670/expanding-proteoform-identifications-in-top-down-proteomic-analyses-by-constructing-proteoform-families
#9
Leah V Schaffer, Michael R Shortreed, Anthony J Cesnik, Brian L Frey, Stefan K Solntsev, Mark Scalf, Lloyd M Smith
In top-down proteomics, intact proteins are analyzed by tandem mass spectrometry, and proteoforms, which are defined forms of a protein with specific sequences of amino acids and localized post-translational modifications, are identified using precursor mass and fragmentation data. Many proteoforms that are detected in the precursor scan (MS1) are not selected for fragmentation by the instrument, and therefore remain unidentified in typical top-down proteomic workflows. Our laboratory has developed the open source software program Proteoform Suite to analyze MS1-only intact proteoform data...
December 11, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29213065/modulation-of-microtubule-acetylation-by-the-interplay-of-tppp-p25-sirt2-and-new-anticancer-agents-with-anti-sirt2-potency
#10
Adél Szabó, Judit Oláh, Sándor Szunyogh, Attila Lehotzky, Tibor Szénási, Marianna Csaplár, Matthias Schiedel, Péter Lőw, Manfred Jung, Judit Ovádi
The microtubule network exerts multifarious functions controlled by its decoration with various proteins and post-translational modifications. The disordered microtubule associated Tubulin Polymerization Promoting Protein (TPPP/p25) and the NAD+-dependent tubulin deacetylase sirtuin-2 (SIRT2) play key roles in oligodendrocyte differentiation by acting as dominant factors in the organization of myelin proteome. Herein, we show that SIRT2 impedes the TPPP/p25-promoted microtubule assembly independently of NAD+; however, the TPPP/p25-assembled tubulin ultrastructures were resistant against SIRT2 activity...
December 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29209003/prostate-cancer-diagnosis-and-characterization-with-mass-spectrometry-imaging
#11
REVIEW
Annika Kurreck, Lindsey A Vandergrift, Taylor L Fuss, Piet Habbel, Nathalie Y R Agar, Leo L Cheng
BACKGROUND: Prostate cancer (PCa), the most common cancer and second leading cause of cancer death in American men, presents the clinical challenge of distinguishing between indolent and aggressive tumors for proper treatment. PCa presents significant alterations in metabolic pathways that can potentially be measured using techniques like mass spectrometry (MS) or MS imaging (MSI) and used to characterize PCa aggressiveness. MS quantifies metabolomic, proteomic, and lipidomic profiles of biological systems that can be further visualized for their spatial distributions through MSI...
December 5, 2017: Prostate Cancer and Prostatic Diseases
https://www.readbyqxmd.com/read/29203214/unravelling-the-differences-comparative-proteomic-analysis-of-a-clonal-virulent-and-an-attenuated-histomonas-meleagridis-strain
#12
Andreas Monoyios, Martina Patzl, Sarah Schlosser, Michael Hess, Ivana Bilic
The current study focused on Histomonas meleagridis, a unicellular protozoan, responsible for histomonosis in poultry. Recently, the occurrence of the disease increased due to the ban of effective chemotherapeutic drugs. Basic questions regarding the molecular biology, virulence mechanisms or even life cycle of the flagellate are still puzzling. In order to address some of these issues, we conducted a comparative proteomic analysis of a virulent and an attenuated H. meleagridis strain traced back to a single cell and propagated in vitro as monoxenic mono-eukaryotic cultures...
December 1, 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/29188495/protein-biomarkers-and-neuroproteomics-characterization-of-microvesicles-exosomes-from-human-cerebrospinal-fluid-following-traumatic-brain-injury
#13
Rachna Manek, Ahmed Moghieb, Zhihui Yang, Dhwani Kumar, Firas Kobessiy, George Anis Sarkis, Vijaya Raghavan, Kevin K W Wang
Recently, there have been emerging interests in the area of microvesicles and exosome (MV/E) released from brain cells in relation to neurodegenerative diseases. However, only limited studies focused on MV/E released post-traumatic brain injury (TBI) as they highlight on the mechanistic roles of released proteins. This study sought to examine if CSF samples from severe TBI patients contain MV/E with unique protein contents. First, nanoparticle tracking analysis determined MV/E from TBI have a mode of 74-98 nm in diameter, while control CSF MV/E have a mode of 99-104 nm...
November 29, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/29170418/gene-therapy-restores-mfrp-and-corrects-axial-eye-length
#14
Gabriel Velez, Stephen H Tsang, Yi-Ting Tsai, Chun-Wei Hsu, Anuradha Gore, Aliaa H Abdelhakim, MaryAnn Mahajan, Ronald H Silverman, Janet R Sparrow, Alexander G Bassuk, Vinit B Mahajan
Hyperopia (farsightedness) is a common and significant cause of visual impairment, and extreme hyperopia (nanophthalmos) is a consequence of loss-of-function MFRP mutations. MFRP deficiency causes abnormal eye growth along the visual axis and significant visual comorbidities, such as angle closure glaucoma, cystic macular edema, and exudative retinal detachment. The Mfrp rd6 /Mfrp rd6 mouse is used as a pre-clinical animal model of retinal degeneration, and we found it was also hyperopic. To test the effect of restoring Mfrp expression, we delivered a wild-type Mfrp to the retinal pigmented epithelium (RPE) of Mfrp rd6 /Mfrp rd6 mice via adeno-associated viral (AAV) gene therapy...
November 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29158881/serum-proteomic-profiling-of-obsessive-compulsive-disorder-washing-subtype-a-preliminary-study
#15
Mona Zamanian-Azodi, Mostafa Rezaei-Tavirani, Naser Nejadi, Afsaneh Arefi Oskouie, Faird Zayeri, Mostafa Hamdieh, Akram Safaei, Majid Rezaei-Tavirani, Alireza Ahmadzadeh, Alireza Amouzandeh-Nobaveh, Farshad Okhovatian
Introduction: Obsessive-Compulsive Disorder (OCD) is a disabling mental condition that its proteomic profiling is not yet investigated. Proteomics is a valuable tool to discover biomarker approaches. It can be helpful to detect protein expression changes in complex disorders such as OCD. Methods: Here, by the application of 2D gel electrophoresis (2DE), a pilot study of serum proteome profile of females with washing subtype of OCD was performed. Serum samples were obtained from females with washing subtype of OCD...
July 2017: Basic and Clinical Neuroscience
https://www.readbyqxmd.com/read/29158489/yeast-display-biopanning-identifies-human-antibodies-targeting-glioblastoma-stem-like-cells
#16
Michael Zorniak, Paul A Clark, Benjamin J Umlauf, Yongku Cho, Eric V Shusta, John S Kuo
Glioblastoma stem-like cells (GSC) are hypothesized to evade current therapies and cause tumor recurrence, contributing to poor patient survival. Existing cell surface markers for GSC are developed from embryonic or neural stem cell systems; however, currently available GSC markers are suboptimal in sensitivity and specificity. We hypothesized that the GSC cell surface proteome could be mined with a yeast display antibody library to reveal novel immunophenotypes. We isolated an extensive collection of antibodies that were differentially selective for GSC...
November 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29157295/single-cell-multiplexed-cytokine-profiling-of-cd19-car-t-cells-reveals-a-diverse-landscape-of-polyfunctional-antigen-specific-response
#17
Qiong Xue, Emily Bettini, Patrick Paczkowski, Colin Ng, Alaina Kaiser, Timothy McConnell, Olja Kodrasi, Máire F Quigley, James Heath, Rong Fan, Sean Mackay, Mark E Dudley, Sadik H Kassim, Jing Zhou
BACKGROUND: It remains challenging to characterize the functional attributes of chimeric antigen receptor (CAR)-engineered T cell product targeting CD19 related to potency and immunotoxicity ex vivo, despite promising in vivo efficacy in patients with B cell malignancies. METHODS: We employed a single-cell, 16-plex cytokine microfluidics device and new analysis techniques to evaluate the functional profile of CD19 CAR-T cells upon antigen-specific stimulation. CAR-T cells were manufactured from human PBMCs transfected with the lentivirus encoding the CD19-BB-z transgene and expanded with anti-CD3/anti-CD28 coated beads...
November 21, 2017: Journal for Immunotherapy of Cancer
https://www.readbyqxmd.com/read/29140531/an-update-on-sorfs-org-a-repository-of-small-orfs-identified-by-ribosome-profiling
#18
Volodimir Olexiouk, Wim Van Criekinge, Gerben Menschaert
sORFs.org (http://www.sorfs.org) is a public repository of small open reading frames (sORFs) identified by ribosome profiling (RIBO-seq). This update elaborates on the major improvements implemented since its initial release. sORFs.org now additionally supports three more species (zebrafish, rat and Caenorhabditis elegans) and currently includes 78 RIBO-seq datasets, a vast increase compared to the three that were processed in the initial release. Therefore, a novel pipeline was constructed that also enables sORF detection in RIBO-seq datasets comprising solely elongating RIBO-seq data while previously, matching initiating RIBO-seq data was necessary to delineate the sORFs...
November 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29136207/linkedomics-analyzing-multi-omics-data-within-and-across-32-cancer-types
#19
Suhas V Vasaikar, Peter Straub, Jing Wang, Bing Zhang
The LinkedOmics database contains multi-omics data and clinical data for 32 cancer types and a total of 11 158 patients from The Cancer Genome Atlas (TCGA) project. It is also the first multi-omics database that integrates mass spectrometry (MS)-based global proteomics data generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) on selected TCGA tumor samples. In total, LinkedOmics has more than a billion data points. To allow comprehensive analysis of these data, we developed three analysis modules in the LinkedOmics web application...
November 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29118029/giapronto-a-one-click-graph-visualization-software-for-proteomics-datasets
#20
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
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