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Expert Review of Proteomics

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https://www.readbyqxmd.com/read/29757692/integrative-omics-from-data-to-biology
#1
Hassan Dihazi, Abdul R Asif, Tim Beißbarth, Rainer Bohrer, Kirstin Feussner, Ivo Feussner, Olaf Jahn, Christof Lenz, Andrzej Majcherczyk, Bernhard Schmidt, Kerstin Schmitt, Henning Urlaub, Oliver Valerius
Multi-omic approaches are promising a broader view on cellular processes and a deeper understanding of biological systems. With strongly improved high-throughput methods the amounts of data generated have become huge, and their handling challenging. New bioinformatic tools and pipelines for the integration of data from different omics disciplines continue to emerge, and will support scientists to reliably interpret data in the context of biological processes. Comprehensive data integration strategies will fundamentally improve systems biology and systems medicine...
May 14, 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29724137/pursuit-of-proteomic-excellence-and-the-excitement-in-ko%C3%A5-ice-slovakia-at-the-11th-central-and-eastern-european-proteomic-conference-ceepc
#2
Suresh Gadher, Mangesh Bhide, Hana Kovarova
The Central and Eastern European Proteomic Conference (CEEPC) successfully launched its second decade of proteomics in Košice, Slovakia with a program of systems biology, cellular, clinical, veterinary and sports proteomics. Whilst many conferences are struggling to attract participants, CEEPC with its outstanding track record and unique 'family - feel' packaged with excellent ambiance is thriving and bringing together proteomics experts from academia, industry, scientific specialties, clinics and precision medicine communities interested in resolving mysteries about protein functionalities in health and disease...
May 4, 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29717934/understanding-leishmania-parasites-through-proteomics-and-implications-for-the-clinic
#3
Shyam Sundar, Bhawana Singh
Leishmania spp. are causative agents of leishmaniasis, a broad-spectrum neglected vector-borne disease. Genomic and transcriptional studies are not capable of solving intricate biological mysteries, leading to the emergence of proteomics, which can provide insights into the field of parasite biology and its interactions with the host. Areas covered: The combination of genomics and informatics with high throughput proteomics may improve our understanding of parasite biology and pathogenesis. This review analyses the roles of diverse proteomic technologies that facilitate our understanding of global protein profiles and definition of parasite development, survival, virulence and drug resistance mechanisms for disease intervention...
May 2, 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29707974/mass-spectrometric-analysis-of-glycosylated-viral-proteins
#4
David J Harvey
Viral diseases contribute much to human and animal suffering and enormous efforts are directed at developing appropriate vaccines for protection. Glycoproteins constitute much of the viral surfaces and are obvious targets for such vaccine development. This review describes mass spectrometric methods used for the structural determination of these compounds. Areas covered: The review describes the structures of the N- and O-linked glycans found on glycoproteins and mass spectrometric methods for their ionization and fragmentation...
April 30, 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29694790/the-role-of-mass-spectrometry-in-the-characterization-of-biologic-protein-products
#5
Deepali Rathore, Anneliese Faustino, John Schiel, Eric Pang, Michael Boyne, Sarah Rogstad
Mass spectrometry (MS) is widely used in the characterization of biomolecules including peptide and protein therapeutics. These biotechnology products have seen rapid growth over the past few decades and continue to dominate the global pharmaceutical market. Advances in MS instrumentation and techniques have enhanced protein characterization capabilities and supported an increased development of biopharmaceutical products. Areas covered: This review describes recent developments in MS-based biotherapeutic analysis including sequence determination, post-translational modifications (PTMs) and higher order structure (HOS) analysis along with improvements in ionization and dissociation methods...
April 25, 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29683367/insights-into-apoptotic-proteins-in-chemotherapy-quantification-techniques-and-informing-therapy-choice
#6
Janine Naß, Thomas Efferth
INTRODUCTION: Cancer is one of the leading causes of morbidity and mortality worldwide. A hallmark of cancer is evasion of apoptosis leading to tumor progression and drug resistance. Biomarker research has become a sign of the times, and proteins involved in apoptosis may be used for clinical diagnostic or prognostic purposes in cancer treatment. The recent progress in proteomic technology has triggered an emerging number of researchers to study the molecular mechanisms that regulate the apoptotic signal transduction pathways in cancer...
April 23, 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29671356/extracellular-vesicles-pathogenetic-diagnostic-and-therapeutic-value-in-traumatic-brain-injury
#7
Stefania Mondello, Eric P Thelin, Gerry Shaw, Michelle Salzet, Carmela Visalli, Dasa Cizkova, Firas Kobeissy, Andras Buki
Traumatic brain injury (TBI) is a leading cause of death and disability worldwide. Accurate classification according to injury-specific and patient-specific characteristics is critical to help informed clinical decision-making and to the pursuit of precision medicine in TBI. Reliable biomarker signatures for improved TBI diagnostics are required but still an unmet need. Areas covered: Extracellular vesicles (EVs) represent a new class of biomarker candidates in TBI. These nano-sized vesicles have key roles in cell signaling profoundly impacting pathogenic pathways, progression and long-term sequelae of TBI...
April 19, 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29648896/does-the-dysregulation-of-matrix-metalloproteinases-contribute-to-recurrent-implantation-failure
#8
Mustapha Benkhalifa, Yosra Zayani, Véronique Bach, Henri Copin, Moncef Feki, Moncef Benkhalifa, Monia Allal-Elasmi
The progress in in vitro fertilization (IVF) techniques for infertility management has led to the investigation of embryo implantation site proteins such as Matrix metalloproteinases (MMPs), which may have a key role in embryo-endometrium crosstalk and in the molecular mechanisms of the embryo implantation. Areas covered: Numerous studies have generated much information concerning the relation between the different proteins at the site of implantation such as cytokines, growth factors, adhesion molecules and MMPs...
April 12, 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29542338/affinity-enrichment-for-mass-spectrometry-improving-the-yield-of-low-abundance-biomarkers
#9
Brianna Kim, Robyn Araujo, Marissa Howard, Ruben Magni, Lance A Liotta, Alessandra Luchini
Mass spectrometry (MS) is the premier tool for discovering novel disease-associated protein biomarkers. Unfortunately, when applied to complex body fluid samples, MS has poor sensitivity for the detection of low abundance biomarkers (≪10 ng/mL), derived directly from the diseased tissue cells or pathogens. Areas covered: Herein we discuss the strengths and drawbacks of technologies used to concentrate low abundance analytes in body fluids, with the aim to improve the effective sensitivity for MS discovery...
March 22, 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29540077/when-nature-s-robots-go-rogue-exploring-protein-homeostasis-dysfunction-and-the-implications-for-understanding-human-aging-disease-pathologies
#10
Julie A Reisz, Alexander S Barrett, Travis Nemkov, Kirk C Hansen, Angelo D'Alessandro
Proteins have been historically regarded as "nature's robots": Molecular machines that are essential to cellular/extracellular physical mechanical properties and catalyze key reactions for cell/system viability. However, these robots are kept in check by other protein-based machinery to preserve proteome integrity and stability. During aging, protein homeostasis is challenged by oxidation, decreased synthesis, and increasingly inefficient mechanisms responsible for repairing or degrading damaged proteins...
March 14, 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29521143/human-disease-glycomics-technology-advances-enabling-protein-glycosylation-analysis-part-2
#11
Arun V Everest-Dass, Edward S X Moh, Christopher Ashwood, Abdulrahman M M Shathili, Nicolle H Packer
The changes in glycan structures have been attributed to disease states for several decades. The surface glycosylation pattern is a signature of physiological state of a cell. In this review we provide a link between observed substructural glycan changes and a range of diseases. Areas covered: We highlight biologically relevant glycan substructure expression in cancer, inflammation, neuronal diseases and diabetes. Furthermore, the alterations in antibody glycosylation in a disease context are described. Expert commentary: Advances in technologies, as described in Part 1 of this review have now enabled the characterization of specific glycan structural markers of a range of disease states...
April 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29466886/proteomic-approaches-to-identify-blood-based-biomarkers-for-depression-and-bipolar-disorders
#12
Rhian Lauren Preece, Sung Yeon Sarah Han, Sabine Bahn
Major depressive disorder (MDD) and bipolar disorder (BD) are leading causes of disability worldwide, yet many people remain undiagnosed, are misdiagnosed, and/or ineffectively treated. Diagnosis relies on the clinical assessment of symptoms, and there is currently no molecular or brain-imaging diagnostic test available. Identifying and validating protein biomarkers could provide a more accurate and objective means of diagnosis. Areas covered: Proteomics is a powerful tool that enables the identification and quantification of novel candidate biomarkers of disease...
April 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29471684/the-future-role-of-proteomics-in-the-understanding-of-acute-kidney-injury
#13
Michael R Bennett, Prasad Devarajan
No abstract text is available yet for this article.
March 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29411645/application-of-the-maldi-biotyper-to-clinical-microbiology-progress-and-potential
#14
Markus Kostrzewa
The introduction of the MALDI Biotyper in laboratories substantially changed microbiology practice, this has been called a revolution. The system accelerated diagnostic while costs were reduced and accuracy was increased. In just a few years MALDI-TOF MS became the first-line identification tool for microorganisms. Ten years after its introduction, more than 2000 MALDI Biotyper systems are installed in laboratories which are performing routine diagnostic, and the number is still increasing. Areas covered: This article summarises changes in clinical microbiology introduced by the MALDI Biotyper and its effects, as it has been published in peer reviewed articles found in PubMed...
March 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29400572/characterizing-bacterial-glycoproteins-with-lc-ms
#15
Kelly M Fulton, Jianjun Li, Juan M Tomas, Jeffrey C Smith, Susan M Twine
Though eukaryotic glycoproteins have been studied since their discovery in the 1930s, the first bacterial glycoprotein was not identified until the 1970s. As a result, their role in bacterial pathogenesis is still not well understood and they remain an understudied component of bacterial virulence. In recent years, mass spectrometry has emerged as a leading technology for the study of bacterial glycoproteins, largely due to its sensitivity and versatility. Areas covered: Identification and comprehensive characterization of bacterial glycoproteins usually requires multiple complementary mass spectrometry approaches, including intact protein analysis, top-down analysis, and bottom-up methods used in combination with specialized liquid chromatography...
March 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29376447/characterizing-disease-associated-changes-in-post-translational-modifications-by-mass-spectrometry
#16
Camilla Thygesen, Inga Boll, Bente Finsen, Maciej Modzel, Martin R Larsen
Exploring post-translational modifications (PTMs) with the use of mass spectrometry (PTMomics) is a rapidly developing area, with methods for discovery/quantification being developed and advanced on a regular basis. PTMs are highly important for the regulation of protein function, interaction and activity, both in physiological and disease states. Changes in PTMs can either cause, or be the result of a disease, making them central for biomarker studies and studies of disease pathogenesis. Recently, it became possible to study multiple PTMs simultaneously from low amount of sample material, thereby increasing coverage of the PTMome obtainable from a single sample...
March 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29338453/proteomic-serum-biomarkers-for-neuromuscular-diseases
#17
Sandra Murphy, Margit Zweyer, Rustam R Mundegar, Dieter Swandulla, Kay Ohlendieck
The clinical evaluation of neuromuscular symptoms often includes the assessment of altered blood proteins or changed enzyme activities. However, the blood concentration of many muscle-derived serum markers is not specific for different neuromuscular disorders and also shows alterations in the course of these diseases. Thus, the establishment of more reliable biomarker signatures for improved muscle diagnostics is required. Areas covered: To address the lack of muscle disease-specific marker molecules, mass spectrometry-based proteomics was applied to the systematic identification and biochemical characterization of new serum biomarker candidates...
March 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29336192/how-mass-spectrometric-approaches-applied-to-bacterial-identification-have-revolutionized-the-study-of-human-gut-microbiota
#18
Dubourg Grégory, Hervé Chaudet, Jean-Christophe Lagier, Didier Raoult
Describing the human hut gut microbiota is one the most exciting challenges of the 21st century. Currently, high-throughput sequencing methods are considered as the gold standard for this purpose, however, they suffer from several drawbacks, including their inability to detect minority populations. The advent of mass-spectrometric (MS) approaches to identify cultured bacteria in clinical microbiology enabled the creation of the culturomics approach, which aims to establish a comprehensive repertoire of cultured prokaryotes from human specimens using extensive culture conditions...
March 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29310484/pathology-proteomics-and-the-pathway-to-personalised-medicine
#19
Ping Jin, Jiang Lan, Kui Wang, Mark S Baker, Canhua Huang, Edouard C Nice
As we move from a discovery to a translational phase in proteomics, with a focus on developing validated clinical assays to assist personalized medicine, there is a growing need for strong bidirectional interactions with the clinical pathology community. Thus, while on one hand the proteomics community will provide candidate biomarkers to assist in diagnosis, prognosis, surveillance, identification of individualized patient medication, and development and validation of new assays for diagnostic use, on the other the pathology community will assist with specific tissue identification and selection (e...
March 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29285957/human-disease-glycomics-technology-advances-enabling-protein-glycosylation-analysis-part-1
#20
Arun V Everest-Dass, Edward S X Moh, Christopher Ashwood, Abdulrahman M M Shathili, Nicolle H Packer
Protein glycosylation is recognized as an important post-translational modification, with specific substructures having significant effects on protein folding, conformation, distribution, stability and activity. However, due to the structural complexity of glycans, elucidating glycan structure-function relationships is demanding. The fine detail of glycan structures attached to proteins (including sequence, branching, linkage and anomericity) is still best analysed after the glycans are released from the purified or mixture of glycoproteins (glycomics)...
February 2018: Expert Review of Proteomics
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