1,721,089 research outputs found
Preface
No full textThis thorough book collects methods and strategies to analyze proteomics data. It is intended to describe how data obtained by gel-based or gel-free proteomics approaches can be inspected, organized, and interpreted to extrapolate biological information. Organized into four sections, the volume explores strategies to analyze proteomics data obtained by gel-based approaches, different data analysis approaches for gel-free proteomics experiments, bioinformatic tools for the interpretation of proteomics data to obtain biological significant information, as well as methods to integrate proteomics data with other omics datasets including genomics, transcriptomics, metabolomics, and other types of data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detailed implementation advice that will ensure high quality results in the lab. Authoritative and practical, Proteomics Data Analysis serves as an ideal guide to introduce researchers, both experienced and novice, to new tools and approaches for data analysis to encourage the further study of proteomics
Protein Secretion Prediction Tools and Extracellular Vesicles Databases
No full textSecreted proteins play important roles in several biological processes such as growth, proliferation differentiation, cell-cell communication, migration, and apoptosis; moreover, these extracellular molecules mediate homeostasis by influencing the cross-talking within the surrounding tissues. Currently, the research area of cell secretome has become of great interest since the profiling of secreted proteins could be essential for the biomarker discovery and for the identification of new therapeutic strategies. Several bioinformatic platforms have been implemented for the in silico characterization of secreted proteins: this chapter describes a typical workflow for the analysis of proteins secreted by cultured cells through bioinformatic approaches. Central issue is related to discrimination between proteins secreted by classical and non-classical pathways. Therefore, specific prediction tools for the classification of candidate secreted proteins are here presented
Proteomic analysis of lymphoid and haematopoietic neoplasms: There's more than biomarker discovery
No full textLymphoid and haematopoietic neoplasms comprise a broad spectrum of different tumours, classified by the World Health Organization (WHO) on the basis of a combination of morphology, immunophenotypic, genetic and clinical features. Up to date for many of these neoplasms no single feature is regarded as a diagnostic gold standard. The application of proteomics to the study of neoplastic haematological diseases could help in the search for new diagnostic and prognostic markers, as well as in the development of new therapeutic strategies. In this review, we focus on the actual role of proteomics technologies in the study of neoplastic haematology. In particular, we analyse the results obtained in the field of body fluid, cell lines, and tissues proteomics, and discuss the improvement allowed by the new developed proteomic strategies, such as nanofluidic systems, analysis of formalin-fixed tissues, and quantitative high throughput techniques (SILAC, ICAT, iTRAQ)
Comparative Evaluation of Software Features and Performances
No full textAnalysis of two-dimensional gel images is a crucial step for the determination of changes inthe protein expression, but at present, it still represents one of the bottlenecks in 2-DE studies. Over the years, different commercial and academic software packages have been developed for the analysis of 2-DE images. Each of these shows different advantageous characteristics in terms of quality of analysis. In this chapter, the characteristics of the different commercial software packages are compared in order to evaluate their main features and performances
Pancreatic cancer stem cells: Perspectives on potential therapeutic approaches of pancreatic ductal adenocarcinoma
No full textPancreatic ductal adenocarcinoma is one of the most aggressive solid tumours of the pancreas, characterised by a five-year survival rate less than 8%. Recent reports that pancreatic cancer stem cells (PCSCs) contribute to the tumorigenesis, progression, and chemoresistance of pancreatic cancer have prompted the investigation of new therapeutic approaches able to directly target PCSCs. In the present paper the non-cancer related drugs that have been proposed to target CSCs that could potentially combat pancreatic cancer are reviewed and evaluated. The role of some pathways and deregulated proteins in PCSCs as new therapeutic targets are also discussed with a focus on selected specific inhibitors. Finally, advances in the development of nanoparticles for targeting PCSCs and site-specific drug delivery are highlighted, and their limitations considered
Proteomics of human cancer tissues and cells
No full textProteomic analysis of cancer tissues and cells provides valuable information to identify promising targets for cancer diagnosis, prognosis and therapy. Novel strategies have emerged to optimize the workflow of tissue procurement, and tissue and cell selection, and to improve protocols for the extraction of protein from fresh, frozen and paraffin-embedded tissue. Moreover, in the context of advanced approaches to proteomics, mass spectrometry and array-based technologies strongly contribute to protein profiling of cancer tissues and cells.
The focus of this review is the methods by which all the steps of a proteomic investigation on human-cancer tissue (from choice of the experimental model to validation of candidate biomarkers) should be performed, paying particular attention to recently developed strategies. The review also presents an overview of the most recent high-throughput proteomic studies in cancer research. (c) 2010 Elsevier Ltd. All rights reserved
A proteomic approach to study the autoregulation of nodulation in Medicago truncatula.
No full textPlant belonging to Leguminosae family can establish a symbiotic relationship with nitrogen-fixing bacteria, termed rhizobia, that lead to the formation of a new organ, the root nodule. This organogenetic pathway starts as a consequence of a molecular cross-talk between plants and bacteria. The systemic pathway, also termed Autoregulation Of Nodulation (AON), is a mechanism by which a plant controls the number of nodules inhibiting further nodule formation after the first few nodules have been formed, as a consequence of a molecular communication between root and shoot.With the aim of gaining a deeper insight in the signalling cascade of AON, we compared the root and shoot proteomes of Medicago truncatula plants inoculated with the symbiotic rhizobium, Sinorhizobium meliloti, with those of uninoculated plants
Local and Systemic Proteomic Changes in Medicago truncatula at an Early Phase of Sinorhizobium meliloti Infection.
No full textThe symbiotic association with N-fixing bacteria facilitates the growth of leguminous plants under nitrogen-limiting conditions. The establishment of the symbiosis requires signal exchange between the host and the bacterium, which leads to the formation of root nodules, inside which bacteria are hosted. The formation of nodules is controlled through local and systemic mechanisms which involves root-shoot communication. Our study was aimed at investigating the proteomic changes occurring in shoots and concomitantly in roots of Medicago truncatula at an early stage of Sinorhizobium meliloti infection. The principal systemic effects consisted in alteration of chloroplast proteins, induction of proteins responsive to biotic stress and changes in proteins involved in hormonal signaling and metabolism. The most relevant local effect was the induction of proteins involved in the utilization of photosynthates and C-consuming processes (such as sucrose synthase and fructose-bisphosphate aldolase). In addition, some redox enzymes such as peroxiredoxin and ascorbate peroxydase showed an altered abundance. The analysis of local and systemic proteome changes suggests the occurrence of a stress response in the shoots and the precocious alteration of energy metabolism in roots and shoots. Furthermore, our data support the hypothesis that ABA and ethylene participate in the communicative network between root and shoot in the control of rhizobial infection
Post-harvest proteomics of grapes infected by Penicillium during withering to produce Amarone wine
No full textThe study of withered grape infection by Penicillium, a potentially toxigenic fungus, is relevant topreserve grape quality during the post-harvest dehydration process. This report describes the firstproteomic analysis of Amarone wine grapes, infected by two strains of P. expansum (Pe1) and P.crustosum (Pc4). Protein identification by MS analysis allowed a better understanding ofphysiological mechanisms underlying the pathogen attack. The Pe1 strain had a major impact on V.vinifera protein expression inducing pathogenesis-related proteins and other protein speciesinvolved in energy metabolism. A greater expression of new Penicillium proteins involved inenergy metabolism and some protein species related to redox homeostasis has been observed ongrapes infected by Pc4 strain. Moreover, the new induced proteins in infected grapes couldrepresent potential markers in withered grapes, thus creating the chance to develop case-sensitiveprevention strategies to inhibit fungal growth
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