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Expert Review of Proteomics

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https://www.readbyqxmd.com/read/27885863/progress-and-pitfalls-in-finding-the-missing-proteins-from-the-human-proteome-map
#1
Victor Segura, Alba Garin-Muga, Elizabeth Guruceaga, Fernando J Corrales
The Human Proteome Project was launched with two main goals: the comprehensive and systematic definition of the human proteome map and the development of ready to use analytical tools to measure relevant proteins in their biological context in health and disease. Despite the great progress in this endeavour, there is still a group of reluctant proteins with no, or scarce, experimental evidence supporting their existence. These are called the 'missing proteins' and represent one of the biggest challenges to complete the human proteome map...
December 2, 2016: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27892738/methodological-approaches-and-insights-on-protein-aggregation-in-biological-systems
#2
Paulo Bastos, Fábio Trindade, Adelino Leite-Moreira, Inês Falcão-Pires, Rita Ferreira, Rui Vitorino
The proper folding of native proteins is critical and dynamic, but inherently unstable. Therefore, proteins eventually end up adopting misfolded conformations which compromise their function and may even trigger aggregation. Risk factors for neurodegenerative, metabolic and heart diseases compromise cellular protein quality-control systems, promoting protein aggregation. Multiple protein post-translational modifications dynamically regulate protein aggregation and disaggregation in a very complex, intricate and delicate balance...
November 28, 2016: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27817217/spaceflight-induced-changes-in-the-human-proteome
#3
Alexey S Kononikhin, Natalia L Starodubtseva, Lyudmila Kh Pastushkova, Daria N Kashirina, Kristina Yu Fedorchenko, Alexander G Brhozovsky, Igor A Popov, Irina M Larina, Evgeny N Nikolaev
Spaceflight is one of the most extreme conditions encountered by humans: Individuals are exposed to radiation, microgravity, hypodynamia, and will experience isolation. A better understanding of the molecular processes induced by these factors may allow us to develop personalized countermeasures to minimize risks to astronauts. Areas covered: This review is a summary of literature searches from PubMed, NASA, Roskosmos and the authors' research experiences and opinions. The review covers the available proteomic data on the effects of spaceflight factors on the human body, including both real space missions and ground-based model experiments...
November 21, 2016: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27791437/urinary-biomarkers-for-renal-tract-malformations
#4
Pedro Magalhães, Joost P Schanstra, Emma Carrick, Harald Mischak, Petra Zürbig
Renal tract malformations (RTMs) are congenital anomalies of the kidneys and urinary tract, which are the major cause of end-stage renal disease in children. Using immunoassay-based approaches (ELISA, western blot), individual urinary proteins including transforming growth factor β, tumor necrosis factor and monocyte attractant proteins 1 were found to be associated to RTMs. However, only mass spectrometry (MS) based methods leading to the identification of panels of protein-based markers composed of fragments of the extracellular matrix allowed the prediction of progression of RTMs and its complications...
November 15, 2016: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27838931/proteomic-insights-into-extracellular-vesicle-biology-defining-exosomes-and-shed-microvesicles
#5
David W Greening, Rong Xu, Shashi Gopal, Alin Rai, Richard J Simpson
Extracellular vesicles (EVs) are critical mediators of intercellular communication, capable of regulating the transcriptional landscape of target cells through horizontal transmission of biological information, such as proteins, lipids, and RNA species. This capability highlights their potential as novel targets for disease intervention. Areas covered: This review focuses on the emerging importance of discovery proteomics (high-throughput, unbiased quantitative protein identification) and targeted proteomics (hypothesis-driven quantitative protein subset analysis) mass spectrometry (MS)-based strategies in EV biology, especially exosomes and shed microvesicles...
November 12, 2016: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27838927/unlocking-the-proteomic-information-encoded-in-maldi-tof-ms-data-used-for-microbial-identification-and-characterization
#6
Clifton K Fagerquist
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) is increasingly utilized as a rapid technique to identify microorganisms including pathogenic bacteria. However, little attention has been paid to the significant proteomic information encoded in the MS peaks that collectively constitute the MS "fingerprint". This review/perspective is intended to explore this topic in greater detail in the hopes that it may spur interest and further research in this area. Areas covered: This paper examines the recent literature on utilizing MALDI-TOF for bacterial identification...
November 12, 2016: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27813434/toxicoproteomics-in-human-health-and-disease-an-update
#7
Shankar Suman, Sanjay Mishra, Yogeshwer Shukla
Toxicoproteomics is an emerging area of omics, intended to explore the changes in protein expression and modifications in biological samples exposed to toxicants. The development of techniques that utilize sophisticated instruments in proteomics has facilitated the exploration of a wide-range of protein coverage and assisted the quantitative and qualitative evaluation of protein changes as a result of the toxic effects of toxic substances. Areas covered: Studies on toxicoproteomics have an immense potential to explore the molecular mechanism of action of a variety of toxic substances through deciphering the proteomic map altered as a result of toxicant exposure...
November 11, 2016: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27771981/blood-biomarker-discovery-in-drug-free-schizophrenia-the-contribution-of-proteomics-and-multiplex-immunoassays
#8
Sophie Sabherwal, Jane A English, Melanie Föcking, Gerard Cagney, David R Cotter
Recent evidence supports an association between systemic abnormalities and the pathology of psychotic disorders which has led to the search for peripheral blood-based biomarkers. Areas covered: Here, we summarize blood biomarker findings in schizophrenia from the literature identified by two methods currently driving biomarker discovery in the human proteome; mass spectrometry and multiplex immunoassay. From a total of 14 studies in the serum or plasma of drug-free schizophrenia patients; 47 proteins were found to be significantly altered twice or more, in the same direction...
November 11, 2016: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27798968/prospective-applications-of-ultrahigh-resolution-proteomics-in-clinical-mass-spectrometry
#9
L Renee Ruhaak, Yuri E M van der Burgt, Christa M Cobbaert
Advances in mass spectrometry (MS)-based proteomic strategies have resulted in robust protein biomarker discovery studies often performed on high resolution accurate mass (HRAM) platforms. For successful translation of promising protein biomarkers into useful clinical tests, trans-sector networks and collaboration among stakeholders involved in the biomarker pipeline are urgently needed. Areas covered: In this perspective, literature- and empirical evidence is combined with author's opinions to discuss the progress of ultrahigh resolution MS and provide insight in its potential for validation and development of clinical tests...
November 7, 2016: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27774815/immunomic-approaches-for-antigen-discovery-of-human-parasites
#10
Kokouvi Kassegne, Eniola Michael Abe, Jun-Hu Chen, Xiao-Nong Zhou
Genetics combined with proteomics allows for a better understanding of parasite-host interactions and host immune responses. Immunomics elucidates that antigens are targets of induced or naturally acquired immunity (NAI), a promising solution to the challenge of eradicating human infections. High-throughput protein microarrays enhance rapid antigen discovery for the development of serodiagnostic tests/vaccines. Areas covered: This review systematically analyzes the emergence of protein microarrays as a powerful technology for parasite antigen discovery and subsequently summarizes some of the attributes and disadvantages of these approaches...
November 7, 2016: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27813428/how-may-targeted-proteomics-complement-genomic-data-in-breast-cancer
#11
Mathilde Guerin, Anthony Gonçalves, Yves Toiron, Emilie Baudelet, Stéphane Audebert, Jean-Baptiste Boyer, Jean-Paul Borg, Luc Camoin
Breast cancer (BC) is the most common female cancer in the world and was recently deconstructed in different molecular entities. Although most of the recent assays to characterize tumors at the molecular level are genomic-based, proteins are the actual executors of cellular functions and represent the vast majority of targets for anticancer drugs. Accumulated data has demonstrated an important level of quantitative and qualitative discrepancies between genomic/transcriptomic alterations and their protein counterparts, mostly related to the large number of post-translational modifications...
November 4, 2016: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27807991/mass-spectrometry-protein-tests-ready-for-prime-time-or-not
#12
Dobrin Nedelkov
Mass spectrometry has played an important role in protein biomarker discovery. Yet, very few of the candidate biomarkers have been validated, and mass spectrometry-based protein tests have not made a significant inroad into clinical laboratories. Areas covered: Offered here is a unique perspective on the future of mass spectrometry protein tests, in view of the following determinants: the true demand for such clinical tests, end-users requirements, platforms and systems design, sample preparation bottlenecks, analytical and clinical validation, and regulatory approval...
November 3, 2016: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27744719/progress-and-prospects-for-the-discovery-of-biomarkers-for-gastric-cancer-a-focus-on-proteomics
#13
Yasuhiko Mohri, Yuji Toiyama, Masato Kusunoki
Patient outcomes from gastric cancer vary due to the complexity of stomach carcinogenesis. Recent research using proteomic technologies has targeted components of all of these systems in order to develop biomarkers to aid the early diagnosis of gastric cancer and to assist in prognostic stratification. Areas covered: This review is comprised of evidence obtained from literature searches from PubMed. It covers the evidence of diagnostic, prognostic, and predictive biomarkers for gastric cancer using proteomic technologies, and provides up-to-date references...
October 31, 2016: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27748142/the-proteomic-landscape-of-renal-tumors
#14
Clizia Chinello, Vincenzo L'imperio, Martina Stella, Andrew James Smith, Giorgio Bovo, Angelica Grasso, Marco Grasso, Francesca Raimondo, Marina Pitto, Fabio Pagni, Fulvio Magni
Renal cell carcinoma (RCC) is the most fatal of the common urologic cancers, with approximately 35% of patients dying within 5 years following diagnosis. Therefore, there is a need for non-invasive markers that are capable of detecting and determining the severity of small renal masses at an early stage in order to tailor treatment and follow-up. Proteomic studies have proved to be very useful in the study of tumors. Areas covered: In this review, we will detail the current knowledge obtained by the different proteomic approaches, focusing on MS-based strategies, used to investigate RCC biology in order to identify diagnostic, prognostic and predictive biomarkers on tissue, cultured cells and biological fluids...
October 28, 2016: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27718753/proteomics-approach-to-identify-biomarkers-for-upper-gastrointestinal-cancer
#15
Kazuto Harada, Dilsa Mizrak Kaya, Yusuke Shimodaira, Shumei Song, Hideo Baba, Jaffer A Ajani
The prognosis for patients with upper gastrointestinal cancers remains dismal despite the development of multimodality therapies that incorporate surgery, chemotherapy, and radiotherapy. Early diagnosis and personalized treatment should lead to better prognosis. Given the advances in proteomic technologies over the past decades, proteomics promises to be the most effective technique to identify novel diagnostics and therapeutic targets. Areas covered: For this review, keywords were searched in combination with "proteomics" and "gastric cancer" or "esophageal cancer" in PubMed...
October 10, 2016: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27718750/platelet-proteomics-applied-to-the-search-for-novel-antiplatelet-therapeutic-targets
#16
Irene Izquierdo, Ángel García
Unwanted platelet activation is associated with numerous diseases, mainly thrombosis-related. In this context, proteomics has emerged as a novel tool with potential for drug target discovery and to scrutinize the effects of antiplatelet drugs. Areas covered: The present review presents the main findings of platelet proteomic studies to date in the context of drug target discovery and perspectives for the future ahead. It includes data and evidences obtained from literature searches on PubMed as well as commentaries derived from the authors' experience and opinions...
October 8, 2016: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27678273/current-status-of-proteomics-of-esophageal-carcinoma
#17
Norihisa Uemura, Tadashi Kondo
Esophageal cancer (EC) is one of the most common causes of cancer-related death worldwide. Identifying suitable biomarkers for early diagnosis as well as predicting lymph node metastasis, prognosis and the therapeutic response of EC is essential for the effective and efficient management for EC. There is an urgent need to develop effective, novel approaches for patients who do not respond to conventional treatment. Areas covered: EC is characterized by the presence of two main histological types such as squamous cell carcinoma and adenocarcinoma, which differ in their response to treatments and prognosis...
October 8, 2016: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27678017/the-challenge-of-integrating-proximate-and-ultimate-causes-to-reconstruct-the-natural-histories-of-venoms-the-evolutionary-link
#18
Juan J Calvete
No abstract text is available yet for this article.
October 8, 2016: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27650042/deciphering-bioactive-peptides-and-their-action-mechanisms-through-proteomics
#19
Osmel Fleitas Martinez, Caleb Mawuli Agbale, Fernanda Nomiyama, Octávio Luiz Franco
Bioactive peptides such as antimicrobial peptides (AMPs), ribosomally synthesized and post translationally modified peptides (RiPPs) and the non-ribosomal peptides (NRPs) have emerged with promising applications in medicine, agriculture and industry. However, their development has been limited by several difficulties making it necessary to search for novel discovery methods. In this context, proteomics has been considered a reliable tool. Areas covered: This review highlights recent developments in proteomic tools that facilitate the discovery of AMPs, RiPPs and NRPs as well as the elucidation of action mechanisms of AMPs and resistance mechanisms of pathogens to them...
October 8, 2016: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27661264/protein-based-therapeutic-for-anemia-caused-by-dyserythropoiesis
#20
Jean-Benoît Arlet, Flavia Guillem, Mathilde Lamarque, Michael Dussiot, Thiago Maciel, Ivan Moura, Olivier Hermine, Geneviève Courtois
Major advances have been recently made in understanding the molecular determinants of dyserythropoiesis, particularly due to recent works in β-thalassemia. The purpose of this review is devoted to underline the role of some proteins recently evidenced in the field, that may be new alternative therapeutic targets in the near future to alleviate different types of anemia. Areas covered: This review covers the contemporary aspects of some proteins involved in various types of dyserythropoiesis, including the transcriptional factor GATA-1 and its protective chaperone HSP70, but also cytokines of the transforming growth factor beta (TFG-β) family, TGF-β1 and GDF-11, and hormones as erythroferrone...
October 6, 2016: Expert Review of Proteomics
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