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https://www.readbyqxmd.com/read/28550165/the-clasp2-protein-interaction-network-in-adipocytes-links-clip2-to-agap3-clasp2-to-g2l1-mark2-and-soga1-and-identifies-soga1-as-a-microtubule-associated-protein
#1
Rikke Kruse, James Krantz, Natalie Barker, Richard Coletta, Ruslan Rafikov, Moulun Luo, Kurt Hoejlund, Lawrence J Mandarino, Paul R Langlais
CLASP2 is a microtubule-associated protein that undergoes insulin-stimulated phosphorylation and co-localization with reorganized actin and GLUT4 at the plasma membrane. To gain insight to the role of CLASP2 in this system, we developed and successfully executed a streamlined interactome approach and built a CLASP2 protein network in 3T3-L1 adipocytes. Using two different commercially available antibodies for CLASP2 and an antibody for epitope-tagged, overexpressed CLASP2, we performed multiple affinity purification coupled with mass spectrometry (AP-MS) experiments in combination with label-free quantitative proteomics and analyzed the data with the bioinformatics tool Significance Analysis of Interactome (SAINT)...
May 26, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28541380/a-fully-bayesian-latent-variable-model-for-integrative-clustering-analysis-of-multi-type-omics-data
#2
Qianxing Mo, Ronglai Shen, Cui Guo, Marina Vannucci, Keith S Chan, Susan G Hilsenbeck
Identification of clinically relevant tumor subtypes and omics signatures is an important task in cancer translational research for precision medicine. Large-scale genomic profiling studies such as The Cancer Genome Atlas (TCGA) Research Network have generated vast amounts of genomic, transcriptomic, epigenomic, and proteomic data. While these studies have provided great resources for researchers to discover clinically relevant tumor subtypes and driver molecular alterations, there are few computationally efficient methods and tools for integrative clustering analysis of these multi-type omics data...
May 24, 2017: Biostatistics
https://www.readbyqxmd.com/read/28541047/multitargeted-flavonoid-inhibition-of-the-pathogenic-bacterium-staphylococcus-aureus-a-proteomic-characterization
#3
Wael A Elmasri, Rui Zhu, Wenjing Peng, Moustafa Al-Hariri, Firas Kobeissy, Phat Tran, Abdul N Hamood, Mohamed F Hegazy, Paul W Paré, Yehia Mechref
Growth inhibition of the pathogen Staphylococcus aureus with currently available antibiotics is problematic in part due to bacterial biofilm protection. Although recently characterized natural products, including 3',4',5-trihydroxy-6,7-dimethoxy-flavone [1], 3',4',5,6,7-pentahydroxy-flavone [2], and 5-hydroxy-4',7-dimethoxy-flavone [3], exhibit both antibiotic and biofilm inhibitory activities, the mode of action of such hydroxylated flavonoids with respect to S. aureus inhibition is yet to be characterized...
May 25, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28536832/proteomic-profiling-reveals-crucial-retinal-protein-alterations-in-the-early-phase-of-an-experimental-glaucoma-model
#4
Fabian Anders, Julia Teister, Sebstian Funke, Norbert Pfeiffer, Franz Grus, Thanos Solon, Verena Prokosch
PURPOSE: Clinical glaucoma is difficult to assess in terms of molecular pathophysiology, prompting studies in experimental models of glaucoma. The purpose of this study was to investigate quantitative changes in retinal protein expression at the onset of experimental glaucoma in rats. Analyzing the proteome provides a suitable tool to decipher the pathophysiological processes in glaucomatous degeneration. METHODS: Thermic cauterization of episcleral veins was utilized to elevate the intraocular pressure in Sprague Dawley rats...
May 24, 2017: Graefe's Archive for Clinical and Experimental Ophthalmology
https://www.readbyqxmd.com/read/28534676/applications-of-raman-spectroscopy-in-biopharmaceutical-manufacturing-a-short-review
#5
Kevin Buckley, Alan G Ryder
The production of active pharmaceutical ingredients (APIs) is currently undergoing its biggest transformation in a century. The changes are based on the rapid and dramatic introduction of protein- and macromolecule-based drugs (collectively known as biopharmaceuticals) and can be traced back to the huge investment in biomedical science (in particular in genomics and proteomics) that has been ongoing since the 1970s. Biopharmaceuticals (or biologics) are manufactured using biological-expression systems (such as mammalian, bacterial, insect cells, etc...
June 2017: Applied Spectroscopy
https://www.readbyqxmd.com/read/28529348/different-stationary-phase-selectivities-and-morphologies-for-intact-protein-separations
#6
REVIEW
A Astefanei, I Dapic, M Camenzuli
The central dogma of biology proposed that one gene encodes for one protein. We now know that this does not reflect reality. The human body has approximately 20,000 protein-encoding genes; each of these genes can encode more than one protein. Proteins expressed from a single gene can vary in terms of their post-translational modifications, which often regulate their function within the body. Understanding the proteins within our bodies is a key step in understanding the cause, and perhaps the solution, to disease...
2017: Chromatographia
https://www.readbyqxmd.com/read/28526530/insights-into-the-early-stage-of-pinus-nigra-arn-somatic-embryogenesis-using-discovery-proteomics
#7
Katarína Klubicová, Lubica Uvácková, Maksym Danchenko, Peter Nemecek, Ludovít Skultéty, Ján Salaj, Terézia Salaj
The somatic embryogenesis in conifers represents a suitable model of plant regeneration system facilitating studies of fundamental aspects of an early development as well as in vitro micropropagation. The aim of our study was to deeper understand the somatic embryogenesis in the conifer tree Pinus nigra Arn. Comparative proteomic analysis based on 2D-PAGE in 1) proliferating embryogenic tissues (E) initiated from immature zygotic embryos, 2) non-embryogenic calli (NEC) initiated from cotyledons of somatic seedlings of the same genotypes, 3) embryogenic tissues that lost the maturation capacity (E-L) of two cell lines (E362, E366)...
May 16, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28522940/potential-urine-proteomics-biomarkers-for-primary-nephrotic-syndrome
#8
Young Wook Choi, Yang Gyun Kim, Min-Young Song, Ju-Young Moon, Kyung-Hwan Jeong, Tae-Won Lee, Chun-Gyoo Ihm, Kang-Sik Park, Sang-Ho Lee
BACKGROUND: Nephrotic syndrome (NS) is a nonspecific kidney disorder, commonly caused by minimal change disease (MCD), focal segmental glomerulosclerosis (FSGS), and membranous nephropathy (MN). Here we analyzed urinary protein profiles, aiming to discover disease-specific biomarkers of these three common diseases in NS. METHODS: Sixteen urine samples were collected from patients with biopsy-proven NS and healthy controls. After removal of high-abundance proteins, the urinary protein profile was analyzed by LC-MS/MS to generate a discovery set...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28522339/proteomics-analysis-of-fusarium-proliferatum-under-various-initial-ph-during-fumonisin-production
#9
Taotao Li, Liang Gong, Yong Wang, Feng Chen, Vijai Kumar Gupta, Qijie Jian, Xuewu Duan, Yueming Jiang
Fusarium proliferatum as a fungal pathogen can produce fumonisin which causes a great threat to animal and human health. Proteomic approach was a useful tool for investigation into mycotoxin biosynthesis in fungal pathogens. In this study, we analyzed the fumonisin content and mycelium proteins of Fusarium proliferatum cultivated under the initial pH5 and 10. Fumonisin production after 10days was significantly induced in culture condition at pH10 than pH5. Ninety nine significantly differently accumulated protein spots under the two pH conditions were detected using two dimensional polyacrylamide gel electrophoresis and 89 of these proteins were successfully identified by MALDI-TOF/TOF and LC-ESI-MS/MS analysis...
May 15, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28520987/proteosign-an-end-user-online-differential-proteomics-statistical-analysis-platform
#10
Georgios Efstathiou, Andreas N Antonakis, Georgios A Pavlopoulos, Theodosios Theodosiou, Peter Divanach, David C Trudgian, Benjamin Thomas, Nikolas Papanikolaou, Michalis Aivaliotis, Oreste Acuto, Ioannis Iliopoulos
Profiling of proteome dynamics is crucial for understanding cellular behavior in response to intrinsic and extrinsic stimuli and maintenance of homeostasis. Over the last 20 years, mass spectrometry (MS) has emerged as the most powerful tool for large-scale identification and characterization of proteins. Bottom-up proteomics, the most common MS-based proteomics approach, has always been challenging in terms of data management, processing, analysis and visualization, with modern instruments capable of producing several gigabytes of data out of a single experiment...
May 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28517930/middle-down-193-nm-ultraviolet-photodissociation-for-unambiguous-antibody-identification-and-its-implications-for-immunoproteomic-analysis
#11
Victoria C Cotham, Andrew P Horton, Jiwon Lee, George Georgiou, Jennifer S Brodbelt
Mass spectrometry (MS) has emerged as a powerful tool within the growing field of immunoproteomics, which aims to understand antibody-mediated immunity at the molecular-level based on the direct determination of serological antibody repertoire. To date, these methods have relied on the use of high-resolution bottom-up proteomic strategies that require effective sampling and characterization of low abundance peptides derived from the antigen-binding domains of polyclonal antibody mixtures. Herein, we describe a method that uses restricted Lys-C enzymatic digestion to increase the average mass of proteolytic IgG peptides (≥4...
May 26, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28516777/improvements-in-mass-spectrometry-assay-library-generation-for-targeted-proteomics
#12
Johan Teleman, Simon Hauri, Johan Malmström
In data independent acquisition mass spectrometry (DIA-MS), targeted extraction of peptide signals in silico using mass spectrometry assay libraries is a successful method for the identification and quantification of proteins. Still, it remains unclear if high quality assay libraries with more accurate peptide ion coordinates can improve peptide target identification rates in DIA analysis. In this study, we systematically improved and evaluated the common algorithmic steps for assay library generation and demonstrate that increased assay quality results in substantially higher identification rates of peptide targets from mouse organ protein lysates measured by DIA-MS...
May 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28515134/identification-of-novel-seroreactive-antigens-in-johne-s-disease-cattle-using-the-mycobacterium-tuberculosis-protein-array
#13
John P Bannantine, Joseph J Campo, Lingling Li, Arlo Randall, Jozelyn Pablo, Craig A Praul, Juan Antonio Raygoza Garay, Judith R Stabel, Vivek Kapur
Johne's Disease, a chronic gastrointestinal inflammatory disease caused by Mycobacterium avium subspecies paratuberculosis (Map), is endemic in dairy cattle and other ruminants worldwide and remains a challenge to diagnose using traditional serological methods. Given the close phylogenetic relationship between Map and the human pathogen, Mycobacterium tuberculosis (Mtb), we here applied a whole proteome Mtb protein array to identify seroreactive and diagnostic Map antigens. A genome-scale pairwise analysis of amino acid identity between orthologous proteins in Map and Mtb showed an average of 62% identity, with more than half the orthologous proteins sharing > 75% identity...
May 17, 2017: Clinical and Vaccine Immunology: CVI
https://www.readbyqxmd.com/read/28510335/proteoforms-in-peripheral-blood-mononuclear-cells-as-novel-rejection-biomarkers-in-liver-transplant-recipients
#14
T K Toby, M Abecassis, K Kim, P M Thomas, R T Fellers, R D LeDuc, N L Kelleher, J Demetris, J Levitsky
Biomarker profiles of acute rejection in liver transplant recipients could enhance the diagnosis and management of recipients. Our aim was to identify diagnostic proteoform signatures of acute rejection in circulating immune cells, using an emergent "top down" proteomics methodology. We prepared differentially processed and cryopreserved cell lysates from 26 non-viral liver transplant recipients by molecular weight-based fractionation and analyzed them by mass spectrometry of whole proteins in three steps: 1) Nanocapillary liquid chromatography coupled with high-resolution tandem mass spectrometry; 2) database searching to identify and characterize intact proteoforms; 3) data processing through a hierarchical linear model matching the study design to quantify proteoform fold changes in patients with rejection vs...
May 16, 2017: American Journal of Transplantation
https://www.readbyqxmd.com/read/28509388/proteomic-explorations-of-autism-spectrum-disorder
#15
Nicholas Szoko, Adam J McShane, Marvin R Natowicz
Proteomics, the large-scale study of protein expression in cells and tissues, is a powerful tool to study the biology of clinical conditions and has provided significant insights in many experimental systems. Herein, we review the basics of proteomic methodology and discuss challenges in using proteomic approaches to study autism. Unlike other experimental approaches, such as genomic approaches, there have been few large-scale studies of proteins in tissues from persons with autism. Most of the proteomic studies on autism used blood or other peripheral tissues; few studies used brain tissue...
May 16, 2017: Autism Research: Official Journal of the International Society for Autism Research
https://www.readbyqxmd.com/read/28503667/neopeptide-analyser-a-software-tool-for-neopeptide-discovery-in-proteomics-data
#16
Mandy Peffers, Andrew R Jones, Antony McCabe, James Anderson
Experiments involving mass spectrometry (MS)-based proteomics are widely used for analyses of connective tissues. Common examples include the use of relative quantification to identify differentially expressed peptides and proteins in cartilage and tendon. We are working on characterising so-called 'neopeptides', i.e. peptides formed due to native cleavage of proteins, for example under pathological conditions. Unlike peptides typically quantified in MS workflows due to the in vitro use of an enzyme such as trypsin, a neopeptide has at least one terminus that was not due to the use of trypsin in the workflow...
April 7, 2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28502000/reverse-phase-protein-microarrays
#17
Elisa Baldelli, Valerie Calvert, Alex Hodge, Amy VanMeter, Emanuel F Petricoin, Mariaelena Pierobon
While genes and RNA encode information about cellular status, proteins are considered the engine of the cellular machine, as they are the effective elements that drive all cellular functions including proliferation, migration, differentiation, and apoptosis. Consequently, investigations of the cellular protein network are considered a fundamental tool for understanding cellular functions.Alteration of the cellular homeostasis driven by elaborate intra- and extracellular interactions has become one of the most studied fields in the era of personalized medicine and targeted therapy...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28501205/an-integrated-strategy-for-the-quantitative-analysis-of-endogenous-proteins-a-case-of-gender-dependent-expression-of-p450-enzymes-in-rat-liver-microsome
#18
Yuhao Shao, Xiaoxi Yin, Dian Kang, Boyu Shen, Zhangpei Zhu, Xinuo Li, Haofeng Li, Lin Xie, Guangji Wang, Yan Liang
Liquid chromatography mass spectrometry based methods provide powerful tools for protein analysis. Cytochromes P450 (CYPs), the most important drug metabolic enzymes, always exhibit sex-dependent expression patterns and metabolic activities. To date, analysis of CYPs based on mass spectrometry is still facing critical technical challenges due to the complexity and diversity of CYP isoforms besides lack of corresponding standards. The aim of present work consisted in developing a label-free qualitative and quantitative strategy for endogenous proteins, and then applying to the gender-difference study for CYPs in rat liver microsomes (RLMs)...
August 1, 2017: Talanta
https://www.readbyqxmd.com/read/28495502/multipronged-quantitative-proteomics-reveals-serum-proteome-alterations-in-breast-cancer-intrinsic-subtypes
#19
Akshada Gajbhiye, Raju Dabhi, Khushman Taunk, Mashanipalya G Jagadeeshaprasad, Sourav RoyChoudhury, Anupama Mane, Santhakumari Bayatigeri, Koel Chaudhury, Manas K Santra, Srikanth Rapole
Being molecularly heterogeneous, breast cancer tends to be a complicated oncological disease with high incidence rates throughout the world. The primary aim of this study was to identify the set of serum proteins with discriminatory capabilities towards the four major subtypes of breast cancer. We employed multipronged quantitative proteomic approaches like 2D-DIGE, iTRAQ and SWATH-MS and identified 307 differentially regulated proteins. Luminal A subtype consisted of 24, Luminal B subtype 38, HER2 Enriched subtype 17 and Triple negative breast cancer subtype 10 differentially regulated subtype specific proteins...
May 8, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28483925/msstatsqc-longitudinal-system-suitability-monitoring-and-quality-control-for-targeted-proteomic-experiments
#20
Eralp Dogu, Sara Mohammad-Taheri, Susan E Abbatiello, Michael S Bereman, Brendan MacLean, Birgit Schilling, Olga Vitek
Selected Reaction Monitoring (SRM) is a powerful tool for targeted detection and quantification of peptides in complex matrices. An important objective of SRM is to obtain peptide quantifications that are (1) suitable for the purpose of the investigation, and (2) reproducible across laboratories and runs. The first objective is achieved by system suitability tests (SST), which verify that mass spectrometric instrumentation performs as specified. The second objective is achieved by quality control (QC), which provides in-process quality assurance of the sample profile...
May 8, 2017: Molecular & Cellular Proteomics: MCP
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