Relevant bibliographies by topics / Proteomics approaches

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Proteomics approaches'

Author: Grafiati
Published: 6 September 2023

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Journal articles on the topic "Proteomics approaches"

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DePalma, Angelo. "Improving Proteomics Approaches." Genetic Engineering & Biotechnology News 33, no. 10 (May 15, 2013): 24–26. http://dx.doi.org/10.1089/gen.33.10.10.

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Kalvodova, Lucie. "Understanding the proteomes using non-proteomics approaches: Expanding the scope of PROTEOMICS." PROTEOMICS 17, no. 1-2 (January 2017): 1770013. http://dx.doi.org/10.1002/pmic.201770013.

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Mahajan, R., and P. Gupta. "Proteomics: taking over where genomics leaves off." Czech Journal of Genetics and Plant Breeding 46, No. 2 (June 29, 2010): 47–53. http://dx.doi.org/10.17221/34/2009-cjgpb.

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The proteomic studies are simultaneously developed in several directions and significantly influence our notions on the capabilities of biological sciences. The need for proteomics research is necessary as there are certain genes in a cell that encode proteins with specific functions. Using a variety of techniques, proteomics can be used to study how proteins interact within a system or how the protein expression changes in different parts of the body, in different stages of its life cycle and in different environmental conditions as every individual has one genome and many proteomes. Besides the qualitative and quantitative description of the expressed proteins, proteomics also deals with the analysis of mutual interactions of proteins. Thereby, candidate proteins can be identified which may be used as starting-points for diagnostic or even therapeutic approaches.
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Sokolowska, Izabela, Armand G. Ngounou Wetie, Alisa G. Woods, and Costel C. Darie. "Applications of Mass Spectrometry in Proteomics." Australian Journal of Chemistry 66, no. 7 (2013): 721. http://dx.doi.org/10.1071/ch13137.

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Characterisation of proteins and whole proteomes can provide a foundation to our understanding of physiological and pathological states and biological diseases or disorders. Constant development of more reliable and accurate mass spectrometry (MS) instruments and techniques has allowed for better identification and quantification of the thousands of proteins involved in basic physiological processes. Therefore, MS-based proteomics has been widely applied to the analysis of biological samples and has greatly contributed to our understanding of protein functions, interactions, and dynamics, advancing our knowledge of cellular processes as well as the physiology and pathology of the human body. This review will discuss current proteomic approaches for protein identification and characterisation, including post-translational modification (PTM) analysis and quantitative proteomics as well as investigation of protein–protein interactions (PPIs).
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Roeraade, Johan. "Nanotechnology Approaches to Proteomics." Biochemical Society Transactions 27, no. 3 (June 1, 1999): A69. http://dx.doi.org/10.1042/bst027a069a.

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Vahkal, Brett, Jamie Kraft, Emanuela Ferretti, Minyoung Chung, Jean-François Beaulieu, and Illimar Altosaar. "Review of Methodological Approaches to Human Milk Small Extracellular Vesicle Proteomics." Biomolecules 11, no. 6 (June 3, 2021): 833. http://dx.doi.org/10.3390/biom11060833.

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Proteomics can map extracellular vesicles (EVs), including exosomes, across disease states between organisms and cell types. Due to the diverse origin and cargo of EVs, tailoring methodological and analytical techniques can support the reproducibility of results. Proteomics scans are sensitive to in-sample contaminants, which can be retained during EV isolation procedures. Contaminants can also arise from the biological origin of exosomes, such as the lipid-rich environment in human milk. Human milk (HM) EVs and exosomes are emerging as a research interest in health and disease, though the experimental characterization and functional assays remain varied. Past studies of HM EV proteomes have used data-dependent acquisition methods for protein detection, however, improvements in data independent acquisition could allow for previously undetected EV proteins to be identified by mass spectrometry. Depending on the research question, only a specific population of proteins can be compared and measured using isotope and other labelling techniques. In this review, we summarize published HM EV proteomics protocols and suggest a methodological workflow with the end-goal of effective and reproducible analysis of human milk EV proteomes.
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Oikonomou, Panos, Roberto Salatino, and Saeed Tavazoie. "In vivo mRNA display enables large-scale proteomics by next generation sequencing." Proceedings of the National Academy of Sciences 117, no. 43 (October 9, 2020): 26710–18. http://dx.doi.org/10.1073/pnas.2002650117.

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Large-scale proteomic methods are essential for the functional characterization of proteins in their native cellular context. However, proteomics has lagged far behind genomic approaches in scalability, standardization, and cost. Here, we introduce in vivo mRNA display, a technology that converts a variety of proteomics applications into a DNA sequencing problem. In vivo-expressed proteins are coupled with their encoding messenger RNAs (mRNAs) via a high-affinity stem-loop RNA binding domain interaction, enabling high-throughput identification of proteins with high sensitivity and specificity by next generation DNA sequencing. We have generated a high-coverage in vivo mRNA display library of the Saccharomyces cerevisiae proteome and demonstrated its potential for characterizing subcellular localization and interactions of proteins expressed in their native cellular context. In vivo mRNA display libraries promise to circumvent the limitations of mass spectrometry-based proteomics and leverage the exponentially improving cost and throughput of DNA sequencing to systematically characterize native functional proteomes.
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FOSTER, LEONARD J. "MASS SPECTROMETRY OUTGROWS SIMPLE BIOCHEMISTRY: NEW APPROACHES TO ORGANELLE PROTEOMICS." Biophysical Reviews and Letters 01, no. 02 (April 2006): 209–21. http://dx.doi.org/10.1142/s1793048006000057.

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Organelles are subcellular compartments or structures that typically carry out a defined set of functions within the cell. The functions of many organelles are known or predicted, but without knowing all the components of any recognized organelle it is difficult to fully understand them. Mass spectrometry-based proteomics now allows for routine identification of several hundreds or thousands of proteins in very complex samples; for cell biologists, organelles represent perhaps the most interesting class of cellular components to apply this new technology to. However, in order to analyze the proteome of an organelle it first must be purified, and the limitations in purifying any biological sample to homogeneity quickly become apparent to the vigilant mass spectrometrist. At the end of an organelle proteomic investigation, investigators are left with a long list of proteins whose location needs to be verified by an orthogonal method, a daunting prospect; or, they must accept an unknown and possibly very high level of incorrect localizations. Some of these caveats can be partially overcome by incorporating quantitative aspects into organelle proteomic studies. This review discusses some alternative approaches to organelle proteomics where questions of specificity and/or functional relevance are addressed by incorporating a quantitative dimension into the experiment.
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Pino, Lindsay K., Jacob Rose, Amy O'Broin, Samah Shah, and Birgit Schilling. "Emerging mass spectrometry-based proteomics methodologies for novel biomedical applications." Biochemical Society Transactions 48, no. 5 (October 20, 2020): 1953–66. http://dx.doi.org/10.1042/bst20191091.

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Research into the basic biology of human health and disease, as well as translational human research and clinical applications, all benefit from the growing accessibility and versatility of mass spectrometry (MS)-based proteomics. Although once limited in throughput and sensitivity, proteomic studies have quickly grown in scope and scale over the last decade due to significant advances in instrumentation, computational approaches, and bio-sample preparation. Here, we review these latest developments in MS and highlight how these techniques are used to study the mechanisms, diagnosis, and treatment of human diseases. We first describe recent groundbreaking technological advancements for MS-based proteomics, including novel data acquisition techniques and protein quantification approaches. Next, we describe innovations that enable the unprecedented depth of coverage in protein signaling and spatiotemporal protein distributions, including studies of post-translational modifications, protein turnover, and single-cell proteomics. Finally, we explore new workflows to investigate protein complexes and structures, and we present new approaches for protein–protein interaction studies and intact protein or top-down MS. While these approaches are only recently incipient, we anticipate that their use in biomedical MS proteomics research will offer actionable discoveries for the improvement of human health.
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Gnatenko, Dmitri V., Peter L. Perrotta, and Wadie F. Bahou. "Proteomic approaches to dissect platelet function: half the story." Blood 108, no. 13 (December 15, 2006): 3983–91. http://dx.doi.org/10.1182/blood-2006-06-026518.

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AbstractPlatelets play critical roles in diverse hemostatic and pathologic disorders and are broadly implicated in various biological processes that include inflammation, wound healing, and thrombosis. Recent progress in high-throughput mRNA and protein profiling techniques has advanced our understanding of the biological functions of platelets. Platelet proteomics has been adopted to decode the complex processes that underlie platelet function by identifying novel platelet-expressed proteins, dissecting mechanisms of signal or metabolic pathways, and analyzing functional changes of the platelet proteome in normal and pathologic states. The integration of transcriptomics and proteomics, coupled with progress in bioinformatics, provides novel tools for dissecting platelet biology. In this review, we focus on current advances in platelet proteomic studies, with emphasis on the importance of parallel transcriptomic studies to optimally dissect platelet function. Applications of these global profiling approaches to investigate platelet genetic diseases and platelet-related disorders are also addressed.
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Dissertations / Theses on the topic "Proteomics approaches"

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Johnson, Hannah. "New Approaches to Quantitative Proteomics." Thesis, University of Manchester, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.492739.

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Absolute quantitative proteomics typically relies on the use of stable isotope labelled internal standards introduced in a known amount. Comparative signal intensities of the labelled and unlabelled peptides allow the inference of protein concentration.
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Jiang, Yanjie. "Approaches for Improved Positional Proteomics." ScholarWorks@UNO, 2013. http://scholarworks.uno.edu/td/1715.

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Positional proteomics is emerging as an attractive technique to characterize protein termini, which play important biological roles in cells. Even with the advances in past decades, there still are areas for improvement. This thesis focuses on improving data quality and assignment confidence in positional proteomics. A novel workflow was designed for the large-scale identification of protein N-terminal sequences. 4-sulfophenyl isothiocyanate (SPITC) is used for N-termini sulfonation; Upon higher energy collisional dissociation (HCD), SPITC peptides in electrospray ionization ESI generate predominately y-type ion series; such simplification of spectra enables the identification of N-termini with high fidelity. The presence of b1 + SPITC product ions upon HCD furthers the confidence for N-terminal identifications. Secondly, sulfonated N-terminal peptides possess one negative charge site at low pH, which was exploited to enrich the SPITC modified N-terminal peptides by electrostatic repulsion hydrophilic interaction (ERLIC) chromatography. Such enrichment process allows both N-termini enriched and N-termini deficient fractions to be collected and analyzed by LC-MS/MS. This method was applied to an E. coli cell lysate, identifying approximately 350 N-terminal peptides (85% represented neo-N-termini from protein degradation and 15% from leading methionine excision). These N-terminal peptides represented 274 distinct E.coli proteins, 224 of which were also identified in the analysis of flow-through fractions from internal peptides. Another approach we took to boost the identification confidence is by exploiting iTRAQ (isobaric tag for relative and absolute quantitation) in the positional proteomics workflow. This approach allows for multiplexed comparison between different samples, and thus is well-suited for degradadomics analyses where degraded samples are compared to control samples. Both control and protease treated sample are labeled by different tags which allows direct comparison of protein N-termini with neo-N-termini. In addition, samples are analyzed duplicate by labeling with two tags, aiming for quick validation of peptides by internal replicates. In this study, Asp-N digested E.coli cell lysate is taken as a model system. A total of 500 N-terminal peptides, corresponding to 370 proteins, were identified with high confidence in one experiment, with 87% of those proteolytic products matching the expected protease digestion specificity, validating the assignment accuracy of this approach.
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Getao, Shi. "DEVELOPMENT OF FUNCTIONAL PROTEOMICS APPROACHES FOR STUDYING RETROGRADE TRANSPORT." Phd thesis, Ecole Normale Supérieure de Paris - ENS Paris, 2011. http://tel.archives-ouvertes.fr/tel-00635924.

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Le trafic rétrograde permet le transport des protéines de la membrane plasmique vers le réticulum endoplasmique, via l'appareil de Golgi, évité la dégradation des lysosomes. Des études antérieures ont montré que le transport rétrograde est crucial pour les fonctions cellulaires telles que la signalisation, l'homéostasie ionique, et l'établissement de gradients du morphogène Wnt. Par ailleurs, le transport rétrograde joue un rôle essentiel dans l'internalisation cellulaire des facteurs pathogènes comme les toxines protéiques et les protéines de virus. Toutefois, la liste actuelle des protéines cargos est limitée, et il est probable que de nombreuses fonctions cellulaires du transport rétrograde restent encore à découvrir. De toute évidence, un fort besoin existe pour une caractérisation plus poussée de cette voie de transport. Dans cette étude, quatre différentes approches protéomiques ont été développées visant à identifier les protéines membranaires prenant la route du transport rétrograde: SNAP-tag, sulfatation, la FKBP, et la streptavidine. Parmi ceux-ci, l'approche SNAP-tag s'est avéré être la stratégie la plus efficace pour identifier les candidats du fret de la voie rétrograde. Cette stratégie est basée sur la modification covalente du protéome de la membrane plasmique avec un benzylguanine (BG) dérivés. Seules les protéines membranaires BG-taggées qui sont ensuite transportés par voie rétrograde peuvent coupler covalentement à une protéine de fusion de SNAP-tag localisée dans la TGN. L'approche a été validée, étape par étape, en utilisant une protéine cargo rétrograde bien étudiée, toxine Shiga sous-unité B (STxB). Nous avons pu montrer que les STxB peuvent être capturés et identifiées par l'approche SNAP-tag. Par ailleurs, couplé à la LC-MS, les candidats des nouvelle protéines de la voie rétrograde ont été identifiés. Les trois autres approches ont guidé notre choix vers la stratégie la plus efficace en protéomique, en apportant des possibilités d'expérimentation et de défauts dans les domaines de la chimie organique et en biologie cellulaire. Généralement, ce travail de thèse a permis de développer une nouvelle stratégie protéomique qui pourraient être appliquée pour identifier les nouvelles candidats de la route rétrograde. Nous avons mis au point une approche dynamique en protéomique qui complète la protéomique traditionnelle. Par ailleurs, le concept d'utiliser des outils chimiques pour étudier le transport rétrograde peut également être appliqué à d'autres voies d'endocytose.
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Barberis, Elettra. "New non-invasive approaches for proteomics and metabolomics analyses." Doctoral thesis, Università del Piemonte Orientale, 2020. http://hdl.handle.net/11579/115041.

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Recent technological developments in analytical chemistry spurred the analysis of historical, archaeological and paleontological objects. The Identification of proteins and small molecules from cultural heritage objects is crucial to characterize the materials used by the artists and it can provide invaluable information for designing restoration interventions. All most the developed analytical procedures require at least a micro sampling from the object. However, non-invasive techniques are always preferred for the analysis of precious and unique objects. A part of this PhD research focused on the development and application of new non-invasive methods for the analysis of cultural heritage. A new method for the non-invasive analysis of proteins and small molecules with mass spectrometry from cultural heritage objects was discussed; the results obtained using a non-invasive imaging instrument on ancient Egyptian mural paintings were also presented; the development and application of non-invasive methods that use portable infrared spectroscopy instrumentation were shown. The recent revolution in mass spectrometry technology with the introduction of high throughput instruments and techniques has led to the widespread expansion of advanced analytical methods in health science. But today, the main target of modern mass spectrometry analysis in biomedical research can be summarize as the development of effective and reliable approaches able of discriminating diseased conditions at their earliest stage, in a non or minimally-invasive manner. The aim of the second part of this PhD research was the development and application of non-invasive methods for the analysis of biological materials. A new method for the non-invasive analysis and characterization of adenoma in colon rectal cancer was presented and a combined bi and mono-dimensional gas chromatography mass spectrometry approach for the identification of new biomarkers for prostate cancer in serum was discussed.
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Yang, Xu. "Quantitative Approaches for Protein Differential Expression Analysis." Thesis, Virginia Tech, 2009. http://hdl.handle.net/10919/36172.

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In this work, tandem mass spectrometry (MS/MS)-based quantitative protocols were developed to facilitate differential protein expression analysis and biomarker discovery via a two-step sample interrogation strategy: (a) global protein profiling and differential expression analysis by spectral counting; and, (b) biomarker candidate validation by targeted screening, i.e., multiple reaction monitoring (MRM). Preliminary experiments were performed to evaluate the performance of the spectral counting method. The method proved to be applicable for proteins with spectral counts⠥2, and a close-to-linear relationship between protein concentration and spectral count data was achievable at protein concentration levels <0.1 μM. The detection limit was 40-800 fmol. A protein/peptide library containing ~10,000 peptide entries that facilitates the development of future MRM experiments, was developed. For each protein, the library provides the number and sequence of detectable peptides, the charge state, the spectral count, the molecular weight, the parameters that characterize the quality of the tandem mass spectrum, the peptide retention time, and the top 10 most intense product ions that correspond to a given parent peptide. Only proteins identified by at least two spectral counts are listed. An MRM experiment was performed to demonstrate the successful applicability of this peptide library for the identification of putative biomarkers in proteomic samples.
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Gauthier, Daniel. "Design, development and application of new technological approaches in subcellular proteomics." Thesis, McGill University, 2008. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=18721.

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The field of subcellular proteomics aims to describe and analyze all the proteins present in a precise subcellular compartment at a given time. In contrast to whole-cell or whole-organism proteomics, the analysis of individual organelles has provided simpler proteomes from which relevant biological information could be more easily derived. To date, the protein complement of several subcellular structures, including the mitochondria, lysosome, peroxysome, phagosome and nucleus has been described. The powerful and rapidly evolving instrumentation as well as the development of biochemical and bioinformatics tools now allow scientists to derive whole organelle models based on the proteomic data generated. This field however still faces numerous challenges. Among those is the analysis of membrane-associated proteins, whose large and hydrophobic character complicate their extraction, subsequent separation and analysis by mass spectrometry. Another emerging limitation in subcellular proteomic resides in the difficulty in collecting enough material of a very pure preparation of the organelle of interest, which still depend on lengthy and labor-intensive density-based centrifugation as the method of choice for subcellular fractionation. The work presented in this thesis describes the development of new methods for subcellular proteomics that address the above-mentioned limitations, and their application to relevant biological models. In chapter 2, we present the design of a non-discriminatory investigative approach to study membrane proteins. Relying on detergent-free and gel-free procedures, this strategy allowed identification of hundreds of cell surface-exposed proteins from freshly ejaculated bovine spermatozoa, as presented in chapter 3. Diverging from traditional cell fractionation protocols, we have refined in chapter 4 a fluorescence-assisted organelle sorting method and have employed it to acquire the proteome of corticotropes-derived secretory granules. Our proc
Le domaine de la protéomique subcellulaire vise à décrire et analyser toutes les protéines présentes dans un compartiment subcellulaire précis à un temps donné. Contrastant avec la protéomique des cellules ou d'organismes complets, l'analyse d'organelles individuelles a généré des protéomes plus simples desquels l'information biologique pertinente peut être plus facilement extraite. À ce jour, le complément de protéines de plusieurs structures subcellulaires, incluant la mitochondrie, le lysosome, le peroxysome, le phagosome et le noyau a été décrit. L'évolution rapide et la puissance de l'instrumentation disponible couplées au développement d'outils biochimiques et bioinformatiques permettent maintenant aux scientifiques de générer des modèles d'organelles complets basés sur les données générées par la protéomique. Ce domaine, cependant, fait toujours face à plusieurs défis. Parmi ceux-ci, on doit mentionner l'analyse des protéines associées à la membrane dont la taille et l'hydrophobicité compliquent l'extraction, la séparation subséquente et l'analyse par spectrométrie de masse. Une autre limitation émergeante en protéomique subcellulaire est l'obtention d'une préparation très pure d'organelles d'intérêt et ce, en quantité suffisante, qui dépend toujours de longues et laborieuses centrifugations basées sur la densité comme méthode de choix pour la fractionnement subcellulaire. Le travail présenté dans cette thèse décrit le développement de nouvelles méthodes en protéomique subcellulaire qui s'adressent aux défis mentionnés précédemment, et leur application à des modèles biologiques pertinents. Dans le chapitre 2, nous présentons l'élaboration et la mise au point d'une approche investigatrice non discriminatoire pour étudier les protéines de membrane. Basée essentiellement sur des procédures sans détergent et sans gel de séparation, cette stratégie a permis l'identification de centaines$
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Wang, Linan. "Proteomic Based Approaches for Differentiating Tumor Subtypes." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1482248318956052.

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Pancotti, A. "PROTEOMIC APPROACHES IN DRUGS AND BIOMARKERS DISCOVERY." Doctoral thesis, Università degli Studi di Milano, 2013. http://hdl.handle.net/2434/217538.

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DOTTORATO DI RICERCA IN CHIMICA DEL FARMACO (XXV CICLO) Proteomic approaches in Drugs and Biomarkers Discovery Dott. Andrea Pancotti Tutor: Prof. Marina Carini Co-tutor: Prof. Sergio Romeo Abstract My thesis project is focused on development and application of proteomic approaches in two fundamental research areas: the drug discovery process and the discovery of disease biomarkers. In particular, new and reliable strategies by mass spectrometry for the fast identification and validation of drug targets, lead compounds and disease biomarkers have been considered. Proteomic Approaches in Drug Discovery In Prof. Romeo’s group new compounds have been identified with high in vitro efficacy against the intraerythrocytic stages of Plasmodium falciparum (P.f.) (IC50 <10 nM),1 but the molecular target is unknown and preliminary results indicate that these compounds may exerts their activity against P.f. through multiple targets. Proteomics offers a unique tool for target identification2 and several proteomic approaches are available, one of the most interesting is the so called chemical proteomics, which couple affinity purification methods with mass spectrometry and therefore permits to increase selectivity and sensitivity.3 In order to facilitate the mass spectrometric analysis, it would be necessary to know the target localization into P.f. of our compounds. Therefore last year, fluorescence compounds, as analytical tools for preliminary target identification, were designed. These compounds have been tested in the Prof. Taramelli’s laboratory against D10 and W2 strains, but only few compounds resulted to be active, and activities were elicited only in a micromolar range. These activities were not sufficient to conduct fluorescent studies, therefore further optimizations were undertaken. Considering the recent SAR obtained in our laboratory, compound 1 has been synthesized characterized by the presence of coumarin and a propylendiamine linker between leucine and the fluorescent group. This compound was active against P.f (IC50 D10 and W2= 13 nM) and fluorescent studies are being performed. In the meanwhile we are focusing our attention on the target identification. The adopted chemical proteomics approach requires the preparation of an alkyne derivate of the lead compound that will be incubated in a Pf lysate. Then trough click chemistry the protein bound alkyne derivative will be reacted with an azide containing a cleavable linker and a terminal biotin unit (compound 3). The lysate will be purified by affinity based chromatography using streptavidin beads. Then the cleavable linker will be cleaved and the protein-compound complex analyzed using HPLC-MS analysis. Thus propargylic derivative 2 was synthesized. It was tested in the Professor Taramelli’s laboratory and resulted to be very active against Pf. (IC50 D10= 8nM/ IC50 W2= 12nM). Compound 3 has been synthesized and it is characterized by a biotin unit, an acylhydrazone cleavable linker, a poliethylenglicol spacer and a terminal azide. In order to verify if compound 2 and 3 were useful tools to perform the procedure that we aimed to follow, the optimized click chemistry reaction was performed between the two compounds obtaining compound 4. In order to test the whole proteomics procedure, compound 4 was immobilized on agarose streptavidin beads and after the selective cleavage of the acylhydrazone cleavable linker and reduction of intermediate, compound 5 was obtained and characterized through direct infusion ESI-MS spectrum. After this successful result the final proteomics analysis is being conducted in collaboration with Professor Taramelli’s laboratory. Proteomic Approaches in Biomarkers Discovery One of the most exciting areas of proteomic research is the identification and validation of disease biomarkers which can be used as measurements within clinical studies and for the purpose of predictive diagnosis. The study of proteomics is considered to be a key for the characterization of human diseases and disease states, and mass spectrometry technology plays a crucial role in this disease research. We will focus in particular on detection and quantization of post-translational modifications of proteins caused by oxidative and carbonyl stress. While the development of specific antibodies against modified proteins has made it possible to confirm the occurrence of oxidative stress in vivo and its involvement in several physio-pathological conditions, the resultant chemical modifications of proteins has not yet been explored. Hence we need proteomic tools, which can sensitively detect oxidative damage on peptides and proteins: these tools would be helpful to understand exactly when, how, and where the damage occurs, and to gain a deeper insights into the mechanism of onset, progression, and/or complication of the diseases. Proteomics approaches have led to the identification of the protein/s showing high sensitivity to oxidation/carbonylation, and among them human serum albumin (HSA) was found to be the main target in the circulation.4-6 During the first year we demonstrated covalent modification of HSA-Cys34 by acrolein in patients undergoing hepatectomy surgery by using a mass spectrometric approach based on a triple quadruple mass spectrometer in precursor ion scan mode, able to identify unknown modifications of Cys34 by reactive carbonyl species (RCS) generated by lipid peroxidation. However, parallel studies performed in our laboratories demonstrated that in some pathologic conditions (i.e. uremic subjects), Cys34 undergoes disulfide formation by cysteinylation, thus limiting its availability for reaction with RCS. Hence, Cys 34-adducts couldn’t always be useful as carbonylation biomarkers. Therefore, I focused my attention on another HSA nucleophilic site (His-146), previously recognized as a potential oxidation/carbonylation target7. Digesting HSA with tripsin or tripsin+chimotripsin, two different peptides containing His-146 have been obtained: H*PYFYAPELLFFAK and H*PY, respectively. Anyway, analysis of tripsin or tripsin+chimotripsin digested HNE-HSA adduct did not lead to identification of any covalent modifications on His 146. Using an high-resolution, high mass accuracy mass spectrometer (LTQ-Orbitrap), performing a full scan analysis in data-dependent mode followed by data analysis with the SEQUEST algorithm it was possible to explain that the absence of any signals relative to RCS-H*PYFYAPELLFFAK adducts was due to different missed cleavages. The analyses relative to the H*PY peptide indicated the formation of one adduct only, H(HNE)PYF, but no significant fragmentation of the corresponding [M+H]+ was observed in MS/MS experiments, even working at high collision energy (40eV). Maybe the reason could be that the peptide is too short for an optimal fragmentation. Taking into account these observations, we have considered as alternative approach the application of a new HSA digestion strategy, based on the use of chimotripsin only. In silico studies indicated the EIARRH*PY peptide as a new tag containing the target residue His 146 in the middle, exactly like Cys-34 in the LQQC*PF peptide, previously analyzed with satisfactory results. This new peptide has also the appropriate length to be analyzed by HPLC-MS/MS. Hence, the EIARRH*PY peptide seemed to possess the optimal characteristics to start a new MS strategy involving His-146 as a carbonyl adduction site on HSA. Thus, HSA was isolated from human plasma by affinity chromatography, reduced with NaBH4 and digested with chimotripsin only in order to obtain the expected peptide. The peptide mixture was analyzed by LTQ-Orbitrap in data dependent scan mode and afterwards by the SEQUEST algorithm, comparing the obtained data with the primary sequence of the protein. The results of the analysis confirmed the formation of the expected peptide. In this way we created the bases for the future studies on the EIARRH*PY peptide, in order to identify any covalent modifications of His146 induced by RCS. References 1. Vaiana, N.; Marzahn, M.; Parapini, S.; Liu, P.; DelAgli, M.; Pancotti, A.; Sangiovanni, E.; Basilico, N.; Bosisio, E.; Dunn, B. M.; Taramelli, D.; Romeo, S. Bioorganic & Medicinal Chemistry Letters 2012, 22, 5915. 2. Brown, D.; Superti-Furga, G. Drug Discov Today 2003, 8, 1067. 3. Godl, K.; Wissing, J.; Kurtenbach, A.; Habenberger, P.; Blencke, S.; Gutbrod, H.; Salassidis, K.; Stein-gerlach, M.; Missio, A.; Cotten, M.; Daub, H. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 15434. 4. Mera, K.; Anraku, M.; Kitamura, K.; Nakajou, K.; Maruyama, T.; Otagiri, M. Biochem. Biophys. Res. Commun. 2005, 334, 1322. 5. Anraku, M.; Kitamura, K.; Shinohara, A.; Adachi, M.; Suenaga, A.; Maruyama, T.; Miyanaka, K.; Miyoshi, T.; Shiraishi, N.; Nonoguchi, H.; Otagiri, M.; Tomita, K. Kidney Int. 2004, 66, 841. 6. Aldini, G.; Vistoli, G.; Regazzoni, L.; Gamberoni, L.; Facino, R. M.; Yamaguchi, S.; Uchida, K.; Carini, M. Chem. Res. Toxicol. 2008, 21, 824. 7. Aldini, G.; Gamberoni, L.; Orioli, M.; Beretta, G.; Regazzoni, L.; Facino, R. M.; Carini, M. J. Mass Spectrom. 2006, 41, 1149.
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Liao, Peter Lee Ming Liao. "Bioinformatics approaches to cancer biomarker discovery and characterization." Case Western Reserve University School of Graduate Studies / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=case1525694252170957.

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Strbenac, Dario. "Novel Preprocessing Approaches for Omics Data Types and Their Performance Evaluation." Thesis, The University of Sydney, 2016. http://hdl.handle.net/2123/16007.

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A diverse range of high-dimensional datasets has recently become available to help elucidate the functioning of biological systems and defects within those systems leading to disease. All of these new technologies come with the challenges of determining how the raw data should be efficiently processed or normalised and, subsequently, how can the data best be summarised for more complex downstream analysis. There are many approaches to summarising and normalising omics data, with new methods frequently being developed. To date, there has not been a comprehensive evaluation of existing methods for many omics data types. This thesis focusses on systematically evaluating existing methods for three different types of omics data and, having identified limitations in the current methods, also proposes new approaches to improve their quality. Firstly, CAGE-seq data are considered. A two-stage method based on a novel region-finding algorithm followed by a classifier that integrates sequence patterns surrounding the identified regions is shown to possess superior performance to two existing methods. Similarly, a novel data summarisation approach to gene expression data, which integrates changes in location and scale into a unified metric, demonstrates benefits in two-class classification problems. The error rates are found to be competitive with existing methods, and the feature selection has higher stability and increased biological relevance. Finally, in the proteomics setting, there are many choices for how to summarise peptides to proteins, as well as issues relating to batch effects and whether internal controls are necessary. By developing a broad variety of performance metrics, and an accompanying web-based framework, novel recommendations about peptide to protein summaries and batch correction algorithms are made, and a surprising result regarding the necessity of internal standards is revealed.
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Books on the topic "Proteomics approaches"

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Santamaría, Enrique, and Joaquín Fernández-Irigoyen, eds. Current Proteomic Approaches Applied to Brain Function. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7119-0.

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Mauro, Fasano, ed. The proteomic approach in neurodegenerative disease research. Trivandrum, Kerala, India: Research Signpost, 2007.

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Mauro, Fasano, ed. The proteomic approach in neurodegenerative disease research. Trivandrum, Kerala, India: Research Signpost, 2007.

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Gil, Alterovitz, Benson Roseann, and Ramoni Marco F, eds. Automation in proteomics and genomics: An engineering case-based approach. Chichester, West Sussex, U.K: John Wiley, 2008.

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Ye, Shui Qing. Bioinformatics: A practical approach. Boca Raton: Chapman & Hall/CRC, 2008.

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Proteomics Approaches to Unravel Virus - Vertebrate Host Interactions. Elsevier, 2021. http://dx.doi.org/10.1016/s0065-3527(21)x0002-4.

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Gerold, Gisa. Proteomics Approaches to Unravel Virus - Vertebrate Host Interactions. Elsevier Science & Technology, 2021.

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Gerold, Gisa. Proteomics Approaches to Unravel Virus- Vertebrate Host Interactions. Elsevier Science & Technology Books, 2021.

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Stoyanov, Alexandre. Separation Science and Proteomics: Current Trends and New Approaches. Elsevier Science & Technology Books, 2017.

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Stoyanov, Alexandre. Separation Science and Proteomics: Current Trends and New Approaches. Elsevier Science & Technology Books, 2018.

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Book chapters on the topic "Proteomics approaches"

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Vaz, Candida, and Vivek Tanavde. "Proteomics." In Omics Approaches, Technologies And Applications, 57–73. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-13-2925-8_4.

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Craven, Rachel A., Peter J. Selby, and Rosamonde E. Banks. "Proteomics-Based Approaches." In Principles of Molecular Oncology, 247–64. Totowa, NJ: Humana Press, 2004. http://dx.doi.org/10.1007/978-1-59259-664-5_8.

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Pucci-Minafra, Ida. "Breast Cancer Proteomics." In Omics Approaches in Breast Cancer, 183–209. New Delhi: Springer India, 2014. http://dx.doi.org/10.1007/978-81-322-0843-3_9.

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Rees, Johanna S., and Kathryn S. Lilley. "Comparative Proteomic Approaches." In Methods in Animal Proteomics, 121–58. Oxford, UK: Wiley-Blackwell, 2011. http://dx.doi.org/10.1002/9780470960660.ch6.

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Latosinska, Agnieszka, Antonia Vlahou, and Manousos Makridakis. "Tissue Proteomics." In Integration of Omics Approaches and Systems Biology for Clinical Applications, 129–55. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2018. http://dx.doi.org/10.1002/9781119183952.ch8.

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Astle, John M., and Thomas Kodadek. "Microarray Approaches to Autoantibody Profiling." In Clinical Proteomics, 511–32. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2008. http://dx.doi.org/10.1002/9783527622153.ch28.

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Krüger, Beate, and Thomas Dandekar. "Bioinformatical Approaches to Detect and Analyze Protein Interactions." In Proteomics, 401–31. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60761-157-8_23.

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Sechi, S. "Mass Spectrometric Approaches to Quantitative Proteomics." In Proteomics in Nephrology, 59–78. Basel: KARGER, 2003. http://dx.doi.org/10.1159/000074590.

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Thakur, Meenakshi, Krishan D. Sharma, and Madan L. Verma. "Advances in Proteomics Approaches for Food Authentication." In Biotechnological Approaches in Food Adulterants, 154–79. First edition. | Boca Raton, FL : CRC Press/Taylor & Francis Group, 2020.: CRC Press, 2020. http://dx.doi.org/10.1201/9780429354557-7.

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Filip, Szymon, and Jerome Zoidakis. "Proteomics of Body Fluids." In Integration of Omics Approaches and Systems Biology for Clinical Applications, 93–112. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2018. http://dx.doi.org/10.1002/9781119183952.ch6.

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Conference papers on the topic "Proteomics approaches"

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Zhang, Bing, Jing Li, David L. Tabb, and Byung-Hoon Park. "Network Approaches for Shotgun Proteomics Data Analysis." In 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing. IEEE, 2009. http://dx.doi.org/10.1109/ijcbs.2009.74.

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He, S. R., E. J. Breen, and S. M. N. Hunt. "Proteomics: approaches and image analysis tools for drug discovery." In 2003 International Conference on Multimedia and Expo. ICME '03. Proceedings (Cat. No.03TH8698). IEEE, 2003. http://dx.doi.org/10.1109/icme.2003.1221347.

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Li, KC. "New Clinical Approaches Combining Genomics And Proteomics With Imaging." In 2nd International University of Malaya Research Imaging Symposium (UMRIS) 2005: Fundamentals of Molecular Imaging. Kuala Lumpur, Malaysia: Department of Biomedical Imaging, University of Malaya, 2005. http://dx.doi.org/10.2349/biij.1.1.e7-54.

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VON DER LIETH, C. W. "EXPANDING PROTEOMICS TO GLYCOBIOLOGY: BIOCOMPUTING APPROACHES UNDERSTANDING THE FUNCTION OF SUGAR." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2001. http://dx.doi.org/10.1142/9789812799623_0026.

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King Wai Lau and J. Siepen. "Bioinformatic approaches to improve the identification of peptides from proteomics experiments." In IET Seminar on Signal Processing for Genomics. IEE, 2006. http://dx.doi.org/10.1049/ic:20060370.

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Stringer, Kathleen A., Jennifer Racz, Gerta Mane, Michael Ford, Lindsay Schmidt, Kurt Schumacher, Carlen Fifer, and Regine Caruthers. "Complementary Approaches Of Proteomics And Immunophenotyping Provide Insight Into The Pathogenesis Of Plastic Bronchitis." In American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California. American Thoracic Society, 2012. http://dx.doi.org/10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a2489.

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Beliavskaya, K., K. Bulanаva, and V. Syakhovich. "DEVELOPMENT OF APPROACHES TO THE ANALYSIS OF HUMAN CONFORMATIONAL FUNCTIONS USING TOP-DOWN PROTEOMICS." In SAKHAROV READINGS 2020: ENVIRONMENTAL PROBLEMS OF THE XXI CENTURY. Minsk, ICC of Minfin, 2020. http://dx.doi.org/10.46646/sakh-2020-2-26-30.

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Harjanto, Dewi, Jennifer G. Abelin, Matthew Malloy, Prerna Suri, Tyler Colson, Scott P. Goulding, Amanda L. Creech, et al. "Abstract B23: Enhanced HLA-II epitope prediction for immunotherapy with novel proteomics and genomics approaches." In Abstracts: AACR Special Conference on Tumor Immunology and Immunotherapy; November 17-20, 2019; Boston, MA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/2326-6074.tumimm19-b23.

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Li, Yingxi, Nico Hüttmann, Zoran Minic, and Maxim V. Berezovski. "Proteomics Approaches for the Discovery of Potential Enzymatic Biomarkers for Early Diagnosis of Breast Cancer." In International Electronic Conference on Biomedicines. Basel Switzerland: MDPI, 2023. http://dx.doi.org/10.3390/ecb2023-14099.

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Bebek, Gurkan, Giridharan Gokulrangan, Hua Xu, and Mark R. Chance. "Abstract 3217: Identification of mutated peptides/proteins driving cancer phenotype utilizing improved shotgun proteomics and data analysis approaches." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-3217.

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Reports on the topic "Proteomics approaches"

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Davidson, George S. High-throughput proteomics : optical approaches. Office of Scientific and Technical Information (OSTI), September 2008. http://dx.doi.org/10.2172/945920.

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Heifetz, Yael, and Michael Bender. Success and failure in insect fertilization and reproduction - the role of the female accessory glands. United States Department of Agriculture, December 2006. http://dx.doi.org/10.32747/2006.7695586.bard.

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The research problem. Understanding of insect reproduction has been critical to the design of insect pest control strategies including disruptions of mate-finding, courtship and sperm transfer by male insects. It is well known that males transfer proteins to females during mating that profoundly affect female reproductive physiology, but little is known about the molecular basis of female mating response and no attempts have yet been made to interfere with female post-mating responses that directly bear on the efficacy of fertilization. The female reproductive tract provides a crucial environment for the events of fertilization yet thus far those events and the role of the female tract in influencing them are poorly understood. For this project, we have chosen to focus on the lower reproductive tract because it is the site of two processes critical to reproduction: sperm management (storage, maintenance, and release from storage) and fertilization. E,fforts during this project period centered on the elucidation of mating responses in the female lower reproductive tract The central goals of this project were: 1. To identify mating-responsive genes in the female lower reproductive tract using DNA microarray technology. 2. In parallel, to identify mating-responsive genes in these tissues using proteomic assays (2D gels and LC-MS/MS techniques). 3. To integrate proteomic and genomic analyses of reproductive tract gene expression to identify significant genes for functional analysis. Our main achievements were: 1. Identification of mating-responsive genes in the female lower reproductive tract. We identified 539 mating-responsive genes using genomic and proteomic approaches. This analysis revealed a shift from gene silencing to gene activation soon after mating and a peak in differential gene expression at 6 hours post-mating. In addition, comparison of the two datasets revealed an expression pattern consistent with the model that important reproductive proteins are pre-programmed for synthesis prior to mating. This work was published in Mack et al. (2006). Validation experiments using real-time PCR techniques suggest that microarray assays provide a conservativestimate of the true transcriptional activity in reproductive tissues. 2.lntegration of proteomics and genomics data sets. We compared the expression profiles from DNA microarray data with the proteins identified in our proteomic experiments. Although comparing the two data sets poses analyical challenges, it provides a more complete view of gene expression as well as insights into how specific genes may be regulated. This work was published in Mack et al. (2006). 3. Development of primary reproductive tract cell cultures. We developed primary cell cultures of dispersed reproductive tract cell types and determined conditions for organ culture of the entire reproductive tract. This work will allow us to rapidly screen mating-responsive genes for a variety of reproductive-tract specifi c functions. Scientific and agricultural significance. Together, these studies have defined the genetic response to mating in a part of the female reproductive tract that is critical for successful fertllization and have identified alarge set of mating-responsive genes. This work is the first to combine both genomic and proteomic approaches in determining female mating response in these tissues and has provided important insights into insect reproductive behavior.
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Avni, Adi, and Gitta L. Coaker. Proteomic investigation of a tomato receptor like protein recognizing fungal pathogens. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7600030.bard.

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Maximizing food production with minimal negative effects on the environment remains a long-term challenge for sustainable food production. Microbial pathogens cause devastating diseases, minimizing crop losses by controlling plant diseases can contribute significantly to this goal. All plants possess an innate immune system that is activated after recognition of microbial-derived molecules. The fungal protein Eix induces defense responses in tomato and tobacco. Plants recognize Eix through a leucine-rich-repeat receptor- like-protein (LRR-RLP) termed LeEix. Despite the knowledge obtained from studies on tomato, relatively little is known about signaling initiated by RLP-type immune receptors. The focus of this grant proposal is to generate a foundational understanding of how the tomato xylanase receptor LeEix2 signals to confer defense responses. LeEix2 recognition results in pattern triggered immunity (PTI). The grant has two main aims: (1) Isolate the LeEix2 protein complex in an active and resting state; (2) Examine the biological function of the identified proteins in relation to LeEix2 signaling upon perception of the xylanase elicitor Eix. We used two separate approaches to isolate receptor interacting proteins. Transgenic tomato plants expressing LeEix2 fused to the GFP tag were used to identify complex components at a resting and activated state. LeEix2 complexes were purified by mass spectrometry and associated proteins identified by mass spectrometry. We identified novel proteins that interact with LeEix receptor by proteomics analysis. We identified two dynamin related proteins (DRPs), a coiled coil – nucleotide binding site leucine rich repeat (SlNRC4a) protein. In the second approach we used the split ubiquitin yeast two hybrid (Y2H) screen system to identified receptor-like protein kinase At5g24010-like (SlRLK-like) (Solyc01g094920.2.1) as an interactor of LeEIX2. We examined the role of SlNRC4a in plant immunity. Co-immunoprecipitation demonstrates that SlNRC4a is able to associate with different PRRs. Physiological assays with specific elicitors revealed that SlNRC4a generally alters PRR-mediated responses. SlNRC4a overexpression enhances defense responses while silencing SlNRC4 reduces plant immunity. We propose that SlNRC4a acts as a non-canonical positive regulator of immunity mediated by diverse PRRs. Thus, SlNRC4a could link both intracellular and extracellular immune perception. SlDRP2A localizes at the plasma membrane. Overexpression of SlDRP2A increases the sub-population of LeEIX2 inVHAa1 endosomes, and enhances LeEIX2- and FLS2-mediated defense. The effect of SlDRP2A on induction of plant immunity highlights the importance of endomembrane components and endocytosis in signal propagation during plant immune . The interaction of LeEIX2 with SlRLK-like was verified using co- immunoprecipitation and a bimolecular fluorescence complementation assay. The defence responses induced by EIX were markedly reduced when SlRLK-like was over-expressed, and mutation of slrlk-likeusing CRISPR/Cas9 increased EIX- induced ethylene production and SlACSgene expression in tomato. Co-expression of SlRLK-like with different RLPs and RLKs led to their degradation, apparently through an endoplasmic reticulum-associated degradation process. We provided new knowledge and expertise relevant to expression of specific be exploited to enhance immunity in crops enabling the development of novel environmentally friendly disease control strategies.
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Hayes, Ronald L. Biochemical Markers of Brain Injury: An Integrated Proteomics-Based Approach. Fort Belvoir, VA: Defense Technical Information Center, February 2005. http://dx.doi.org/10.21236/ada437666.

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Hayes, Ronald L. Biochemical Markers of Brain Injury: An Integrated Proteomics Based Approach. Fort Belvoir, VA: Defense Technical Information Center, February 2004. http://dx.doi.org/10.21236/ada425658.

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Hayes, Ronald L. Biochemical Markers of Brain Injury: An Integrated Proteomics-Based Approach. Fort Belvoir, VA: Defense Technical Information Center, December 2011. http://dx.doi.org/10.21236/ada561092.

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Hayes, Ronald L. Biochemical Markers of Brain Injury: An Integrated Proteomics-Based Approach. Fort Belvoir, VA: Defense Technical Information Center, February 2007. http://dx.doi.org/10.21236/ada474912.

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Ghanim, Murad, Joe Cicero, Judith K. Brown, and Henryk Czosnek. Dissection of Whitefly-geminivirus Interactions at the Transcriptomic, Proteomic and Cellular Levels. United States Department of Agriculture, February 2010. http://dx.doi.org/10.32747/2010.7592654.bard.

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Our project focuses on gene expression and proteomics of the whitefly Bemisia tabaci (Gennadius) species complex in relation to the internal anatomy and localization of expressed genes and virions in the whitefly vector, which poses a major constraint to vegetable and fiber production in Israel and the USA. While many biological parameters are known for begomovirus transmission, nothing is known about vector proteins involved in the specific interactions between begomoviruses and their whitefly vectors. Identifying such proteins is expected to lead to the design of novel control methods that interfere with whitefly-mediated begomovirus transmission. The project objectives were to: 1) Perform gene expression analyses using microarrays to study the response of whiteflies (B, Q and A biotypes) to the acquisition of begomoviruses (Tomato yellow leaf curl (TYLCV) and Squash leaf curl (SLCV). 2) Construct a whitefly proteome from whole whiteflies and dissected organs after begomovirus acquisition. 3) Validate gene expression by q-RTPCR and sub-cellular localization of candidate ESTs identified in microarray and proteomic analyses. 4) Verify functionality of candidate ESTs using an RNAi approach, and to link these datasets to overall functional whitefly anatomical studies. During the first and second years biological experiments with TYLCV and SLCV acquisition and transmission were completed to verify the suitable parameters for sample collection for microarray experiments. The parameters were generally found to be similar to previously published results by our groups and others. Samples from whole whiteflies and midguts of the B, A and Q biotypes that acquired TYLCV and SLCV were collected in both the US and Israel and hybridized to B. tabaci microarray. The data we analyzed, candidate genes that respond to both viruses in the three tested biotypes were identified and their expression that included quantitative real-time PCR and co-localization was verified for HSP70 by the Israeli group. In addition, experiments were undertaken to employ in situ hybridization to localize several candidate genes (in progress) using an oligonucleotide probe to the primary endosymbiont as a positive control. A proteome and corresponding transcriptome to enable more effective protein identification of adult whiteflies was constructed by the US group. Further validation of the transmission route of begomoviruses, mainly SLCV and the involvement of the digestive and salivary systems was investigated (Cicero and Brown). Due to time and budget constraints the RNAi-mediated silencing objective to verify gene function was not accomplished as anticipated. HSP70, a strong candidate protein that showed over-expression after TYLCV and SLCV acquisition and retention by B. tabaci, and co-localization with TYLCV in the midgut, was further studies. Besides this protein, our joint research resulted in the identification of many intriguing candidate genes and proteins that will be followed up by additional experiments during our future research. To identify these proteins it was necessary to increase the number and breadth of whitefly ESTs substantially and so whitefly cDNAs from various libraries made during the project were sequenced (Sanger, 454). As a result, the proteome annotation (ID) was far more successful than in the initial attempt to identify proteins using Uniprot or translated insect ESTs from public databases. The extent of homology shared by insects in different orders was surprisingly low, underscoring the imperative need for genome and transcriptome sequencing of homopteran insects. Having increased the number of EST from the original usable 5500 generated several years ago to >600,000 (this project+NCBI data mining), we have identified about one fifth of the whitefly proteome using these new resources. Also we have created a database that links all identified whitefly proteins to the PAVEdb-ESTs in the database, resulting in a useful dataset to which additional ESTS will be added. We are optimistic about the prospect of linking the proteome ID results to the transcriptome database to enable our own and other labs the opportunity to functionally annotate not only genes and proteins involved in our area of interest (whitefly mediated transmission) but for the plethora of other functionalities that will emerge from mining and functionally annotating other key genes and gene families in whitefly metabolism, development, among others. This joint grant has resulted in the identification of numerous candidate proteins involved in begomovirus transmission by B. tabaci. A next major step will be to capitalize on validated genes/proteins to develop approaches to interfere with the virus transmission.
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Kyprianou, Natasha, and Haining Zhu. Biomarker Discovery and Mechanistic Studies of Prostate Cancer Using Targeted Proteomic Approaches. Fort Belvoir, VA: Defense Technical Information Center, July 2011. http://dx.doi.org/10.21236/ada561372.

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Kyprianou, Natasha. Biomarker Discovery and Mechanistic Studies of Prostate Cancer Using Targeted Proteomic Approaches. Fort Belvoir, VA: Defense Technical Information Center, July 2012. http://dx.doi.org/10.21236/ada581284.

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