Relevant bibliographies by topics / Proteomic studie

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Academic literature on the topic 'Proteomic studie'

Author: Grafiati
Published: 11 March 2023

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Journal articles on the topic "Proteomic studie"

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Sadeesh, Nithin, Mauro Scaravilli, and Leena Latonen. "Proteomic Landscape of Prostate Cancer: The View Provided by Quantitative Proteomics, Integrative Analyses, and Protein Interactomes." Cancers 13, no. 19 (September 27, 2021): 4829. http://dx.doi.org/10.3390/cancers13194829.

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Prostate cancer is the second most frequent cancer of men worldwide. While the genetic landscapes and heterogeneity of prostate cancer are relatively well-known already, methodological developments now allow for studying basic and dynamic proteomes on a large scale and in a quantitative fashion. This aids in revealing the functional output of cancer genomes. It has become evident that not all aberrations at the genetic and transcriptional level are translated to the proteome. In addition, the proteomic level contains heterogeneity, which increases as the cancer progresses from primary prostate cancer (PCa) to metastatic and castration-resistant prostate cancer (CRPC). While multiple aspects of prostate adenocarcinoma proteomes have been studied, less is known about proteomes of neuroendocrine prostate cancer (NEPC). In this review, we summarize recent developments in prostate cancer proteomics, concentrating on the proteomic landscapes of clinical prostate cancer, cell line and mouse model proteomes interrogating prostate cancer-relevant signaling and alterations, and key prostate cancer regulator interactomes, such as those of the androgen receptor (AR). Compared to genomic and transcriptomic analyses, the view provided by proteomics brings forward changes in prostate cancer metabolism, post-transcriptional RNA regulation, and post-translational protein regulatory pathways, requiring the full attention of studies in the future.
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Masood, Afshan, Hicham Benabdelkamel, and Assim Alfadda. "Obesity Proteomics: An Update on the Strategies and Tools Employed in the Study of Human Obesity." High-Throughput 7, no. 3 (September 12, 2018): 27. http://dx.doi.org/10.3390/ht7030027.

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Proteomics has become one of the most important disciplines for characterizing cellular protein composition, building functional linkages between protein molecules, and providing insight into the mechanisms of biological processes in a high-throughput manner. Mass spectrometry-based proteomic advances have made it possible to study human diseases, including obesity, through the identification and biochemical characterization of alterations in proteins that are associated with it and its comorbidities. A sizeable number of proteomic studies have used the combination of large-scale separation techniques, such as high-resolution two-dimensional gel electrophoresis or liquid chromatography in combination with mass spectrometry, for high-throughput protein identification. These studies have applied proteomics to comprehensive biochemical profiling and comparison studies while using different tissues and biological fluids from patients to demonstrate the physiological or pathological adaptations within their proteomes. Further investigations into these proteome-wide alterations will enable us to not only understand the disease pathophysiology, but also to determine signature proteins that can serve as biomarkers for obesity and related diseases. This review examines the different proteomic techniques used to study human obesity and discusses its successful applications along with its technical limitations.
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Stubbs, Keith A., and David J. Vocadlo. "Affinity-Based Proteomics Probes; Tools for Studying Carbohydrate-Processing Enzymes." Australian Journal of Chemistry 62, no. 6 (2009): 521. http://dx.doi.org/10.1071/ch09140.

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As more information becomes available through the efforts of high-throughput screens, there is increasing pressure on the three main ‘omic’ fields, genomics, proteomics, and metabolomics, to organize this material into useful libraries that enable further understanding of biological systems. Proteomics especially is faced with two highly challenging tasks. The first is assigning the activity of thousands of putative proteins, the existence of which has been suggested by genomics studies. The second is to serve as a link between genomics and metabolomics by demonstrating which enzymes play roles in specific metabolic pathways. Underscoring these challenges in one area are the thousands of putative carbohydrate-processing enzymes that have been bioinformatically identified, mostly in prokaryotes, but that have unknown or unverified activities. Using two brief examples, we illustrate how biochemical pathways within bacteria that involve carbohydrate-processing enzymes present interesting potential antimicrobial targets, offering a clear motivation for gaining a functional understanding of biological proteomes. One method for studying proteomes that has been developed recently is to use synthetic compounds termed activity-based proteomics probes. Activity-based proteomic profiling using such probes facilitates rapid identification of enzyme activities within proteomes and assignment of function to putative enzymes. Here we discuss the general design principles for these probes with particular reference to carbohydrate-processing enzymes and give an example of using such a probe for the profiling of a bacterial proteome.
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Solovyeva, Elizaveta M., Julia A. Bubis, Irina A. Tarasova, Anna A. Lobas, Mark V. Ivanov, Alexey A. Nazarov, Ilya A. Shutkov, and Mikhail V. Gorshkov. "On the Feasibility of Using an Ultra-Fast DirectMS1 Method of Proteome-Wide Analysis for Searching Drug Targets in Chemical Proteomics." Biochemistry (Moscow) 87, no. 11 (November 2022): 1342–53. http://dx.doi.org/10.1134/s000629792211013x.

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Abstract Protein quantitation in tissue cells or physiological fluids based on liquid chromatography/mass spectrometry is one of the key sources of information on the mechanisms of cell functioning during chemotherapeutic treatment. Information on significant changes in protein expression upon treatment can be obtained by chemical proteomics and requires analysis of the cellular proteomes, as well as development of experimental and bioinformatic methods for identification of the drug targets. Low throughput of whole proteome analysis based on liquid chromatography and tandem mass spectrometry is one of the main factors limiting the scale of these studies. The method of direct mass spectrometric identification of proteins, DirectMS1, is one of the approaches developed in recent years allowing ultrafast proteome-wide analyses employing minute-scale gradients for separation of proteolytic mixtures. Aim of this work was evaluation of both possibilities and limitations of the method for identification of drug targets at the level of whole proteome and for revealing cellular processes activated by the treatment. Particularly, the available literature data on chemical proteomics obtained earlier for a large set of onco-pharmaceuticals using multiplex quantitative proteome profiling were analyzed. The results obtained were further compared with the proteome-wide data acquired by the DirectMS1 method using ultrashort separation gradients to evaluate efficiency of the method in identifying known drug targets. Using ovarian cancer cell line A2780 as an example, a whole-proteome comparison of two cell lysis techniques was performed, including the freeze-thaw lysis commonly employed in chemical proteomics and the one based on ultrasonication for cell disruption, which is the widely accepted as a standard in proteomic studies. Also, the proteome-wide profiling was performed using ultrafast DirectMS1 method for A2780 cell line treated with lonidamine, followed by gene ontology analyses to evaluate capabilities of the method in revealing regulation of proteins in the cellular processes associated with drug treatment.
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Agarwal, Ashok, Manesh Kumar Panner Selvam, and Saradha Baskaran. "Proteomic Analyses of Human Sperm Cells: Understanding the Role of Proteins and Molecular Pathways Affecting Male Reproductive Health." International Journal of Molecular Sciences 21, no. 5 (February 27, 2020): 1621. http://dx.doi.org/10.3390/ijms21051621.

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Human sperm proteomics research has gained increasing attention lately, which provides complete information about the functional state of the spermatozoa. Changes in the sperm proteome are evident in several male infertility associated conditions. Global proteomic tools, such as liquid chromatography tandem mass spectrometry and matrix-assisted laser desorption/ionization time-of-flight, are used to profile the sperm proteins to identify the molecular pathways that are defective in infertile men. This review discusses the use of proteomic techniques to analyze the spermatozoa proteome. It also highlights the general steps involved in global proteomic approaches including bioinformatic analysis of the sperm proteomic data. Also, we have presented the findings of major proteomic studies and possible biomarkers in the diagnosis and therapeutics of male infertility. Extensive research on sperm proteome will help in understanding the role of fertility associated sperm proteins. Validation of the sperm proteins as biomarkers in different male infertility conditions may aid the physician in better clinical management.
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Burat, Bastien, Audrey Reynaerts, Dominique Baiwir, Maximilien Fléron, Gauthier Eppe, Teresinha Leal, and Gabriel Mazzucchelli. "Characterization of the Human Eccrine Sweat Proteome—A Focus on the Biological Variability of Individual Sweat Protein Profiles." International Journal of Molecular Sciences 22, no. 19 (October 8, 2021): 10871. http://dx.doi.org/10.3390/ijms221910871.

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The potential of eccrine sweat as a bio-fluid of interest for diagnosis and personalized therapy has not yet been fully evaluated, due to the lack of in-depth sweat characterization studies. Thanks to recent developments in omics, together with the availability of accredited sweat collection methods, the analysis of human sweat may now be envisioned as a standardized, non-invasive test for individualized monitoring and personalized medicine. Here, we characterized individual sweat samples, collected from 28 healthy adult volunteers under the most standardized sampling methodology, by applying optimized shotgun proteomics. The thorough characterization of the sweat proteome allowed the identification of 983 unique proteins from which 344 were identified across all samples. Annotation-wise, the study of the sweat proteome unveiled the over-representation of newly addressed actin dynamics, oxidative stress and proteasome-related functions, in addition to well-described proteolysis and anti-microbial immunity. The sweat proteome composition correlated with the inter-individual variability of sweat secretion parameters. In addition, both gender-exclusive proteins and gender-specific protein abundances were highlighted, despite the high similarity between human female and male sweat proteomes. In conclusion, standardized sample collection coupled with optimized shotgun proteomics significantly improved the depth of sweat proteome coverage, far beyond previous similar studies. The identified proteins were involved in many diverse biological processes and molecular functions, indicating the potential of this bio-fluid as a valuable biological matrix for further studies. Addressing sweat variability, our results prove the proteomic profiling of sweat to be a promising bio-fluid analysis for individualized, non-invasive monitoring and personalized medicine.
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Han, Mee-Jung, and Sang Yup Lee. "The Escherichia coli Proteome: Past, Present, and Future Prospects." Microbiology and Molecular Biology Reviews 70, no. 2 (June 2006): 362–439. http://dx.doi.org/10.1128/mmbr.00036-05.

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SUMMARY Proteomics has emerged as an indispensable methodology for large-scale protein analysis in functional genomics. The Escherichia coli proteome has been extensively studied and is well defined in terms of biochemical, biological, and biotechnological data. Even before the entire E. coli proteome was fully elucidated, the largest available data set had been integrated to decipher regulatory circuits and metabolic pathways, providing valuable insights into global cellular physiology and the development of metabolic and cellular engineering strategies. With the recent advent of advanced proteomic technologies, the E. coli proteome has been used for the validation of new technologies and methodologies such as sample prefractionation, protein enrichment, two-dimensional gel electrophoresis, protein detection, mass spectrometry (MS), combinatorial assays with n-dimensional chromatographies and MS, and image analysis software. These important technologies will not only provide a great amount of additional information on the E. coli proteome but also synergistically contribute to other proteomic studies. Here, we review the past development and current status of E. coli proteome research in terms of its biological, biotechnological, and methodological significance and suggest future prospects.
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Sobolev, Vladimir V., Anna G. Soboleva, Elena V. Denisova, Eva A. Pechatnikova, Eugenia Dvoryankova, Irina M. Korsunskaya, and Alexandre Mezentsev. "Proteomic Studies of Psoriasis." Biomedicines 10, no. 3 (March 7, 2022): 619. http://dx.doi.org/10.3390/biomedicines10030619.

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In this review paper, we discuss the contribution of proteomic studies to the discovery of disease-specific biomarkers to monitor the disease and evaluate available treatment options for psoriasis. Psoriasis is one of the most prevalent skin disorders driven by a Th17-specific immune response. Although potential patients have a genetic predisposition to psoriasis, the etiology of the disease remains unknown. During the last two decades, proteomics became deeply integrated with psoriatic research. The data obtained in proteomic studies facilitated the discovery of novel mechanisms and the verification of many experimental hypotheses of the disease pathogenesis. The detailed data analysis revealed multiple differentially expressed proteins and significant changes in proteome associated with the disease and drug efficacy. In this respect, there is a need for proteomic studies to characterize the role of the disease-specific biomarkers in the pathogenesis of psoriasis, develop clinical applications to choose the most efficient treatment options and monitor the therapeutic response.
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Campanati, Anna, Emanuela Martina, Federico Diotallevi, Giulia Radi, Andrea Marani, Davide Sartini, Monica Emanuelli, et al. "Saliva Proteomics as Fluid Signature of Inflammatory and Immune-Mediated Skin Diseases." International Journal of Molecular Sciences 22, no. 13 (June 29, 2021): 7018. http://dx.doi.org/10.3390/ijms22137018.

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Saliva is easy to access, non-invasive and a useful source of information useful for the diagnosis of serval inflammatory and immune-mediated diseases. Following the advent of genomic technologies and -omic research, studies based on saliva testing have rapidly increased and human salivary proteome has been partially characterized. As a proteomic protocol to analyze the whole saliva proteome is not currently available, the most common aim of the proteomic analysis is to discriminate between physiological and pathological conditions. The salivary proteome has been initially investigated in several diseases: oral squamous cell carcinoma and oral leukoplakia, chronic graft-versus-host disease, and Sjögren’s syndrome. Otherwise, salivary proteomics studies in the dermatological field are still in the initial phase, thus the aim of this review is to collect the best research evidence on the role of saliva proteomics analysis in immune-mediated skin diseases to understand the direction of research in this field. The results of PRISMA analysis reported herein suggest that human saliva analysis could provide significant data for the diagnosis and prognosis of several immune-mediated and inflammatory skin diseases in the next future.
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Bespyatykh, Ju A., E. A. Shitikov, and E. N. Ilina. "Proteomics for the Investigation of Mycobacteria." Acta Naturae 9, no. 1 (March 15, 2017): 15–25. http://dx.doi.org/10.32607/20758251-2017-9-1-15-25.

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The physiology of Mycobacterium tuberculosis, the causative agent of tuberculosis, is being studied with intensity. However, despite the genomic and transcriptomic data available today, the pathogenic potential of these bacteria remains poorly understood. Therefore, proteomic approaches seem relevant in studying mycobacteria. This review covers the main stages in the proteomic analysis methods used to study mycobacteria. The main achievements in the area of M. tuberculosis proteomics are described in general. Special attention is paid to the proteomic features of the Beijing family, which is widespread in Russia. Considering that the proteome is a set of all the proteins in the cell, post-translational modifications of mycobacterium proteins are also described.
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Dissertations / Theses on the topic "Proteomic studie"

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Benkovská, Dagmar. "Proteomické studie ječmene související s výrobou piva." Doctoral thesis, Vysoké učení technické v Brně. Fakulta chemická, 2013. http://www.nusl.cz/ntk/nusl-233378.

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Tato práce se zabývá proteomickými studiemi ječmene v souvislosti s výrobou piva. Ječmen patří mezi nejvýznamnější plodiny na světě a je využíván hlavně pro sladovnické účely, nejčastěji pro pivovarnictví. Studium proteinů ječmene během sladování a výroby piva poskytuje informace o změnách v proteinovém složení nebo jejich posttranslačních modifikacích. Jelikož jsou proteiny v ječmeni a jejich změny zásadní pro kvalitu sladu a piva, proteomické studie ječmene mají potenciál pro zlepšení procesu sladování a pivovarnictví. Hlavním cílem této práce je studium ve vodě rozpustných proteinů ječmene a jejich změn, ke kterým dochází během sladování a výroby piva. Rozdíly v proteinovém složení byly sledovány pomocí gelové elektroforézy, kapalinové chromatografie na reverzní fázi, gelové chromatografie a MALDI-TOF hmotnostní spektrometrie. Během sladování se vlivem klíčení zrna zvyšuje množství některých proteinů a také jsou tvořeny nové proteiny. V průběhu vaření piva se naopak v důsledku vysoké teploty a enzymatické aktivity proteáz mnoho proteinů rozkládá. Těmto drsným podmínkám odolají jen některé proteiny, které přechází až do piva a mohou ovlivnit jeho kvalitu. Dále byly zkoumány různé odrůdy ječmene a jejich rozdíly. Byly porovnány odrůdy povolené pro výrobu certifikovaného Českého piva s jednou osvědčenou sladovnickou odrůdou a jednou nesladovnickou odrůdou ječmene. Kromě toho byly studovány v alkoholu rozpustné proteiny ječmene a jejich změny v průběhu sladování. Zvláštní pozornost byla věnována vybrané skupině posttranslačních modifikací proteinů: glykosylacím. Neenzymaticky glykosylované proteiny ječmene (neboli glykované proteiny) jsou tvořeny v průběhu sladování kvůli přítomnosti velkého množství glukózy uvolněné z rozkladu škrobu. Glykované proteiny ovlivňují stabilitu proteinů a kvalitu piva, obzvlášť pěnotvorný účinek. Enzymatické N-glykosylace představují nejčastěji studované posttranslační modifikace u rostlin, protože glykoproteiny hrají klíčovou roli v různých biologických funkcích. Glykoproteiny jsou často přítomny v malém množství, a proto je pro jejich analýzu potřebné obohacení glykoproteinů z komplexní směsi. Pro studium glykoproteinů byla využita afinitní chromatografie s lektinem concanavalin A. Kromě toho byla také optimalizována analýza sacharidové části glykoproteinů. Tato disertační práce přináší důležité informace o proteinech ječmene, jejich změnách a analýze, které budou užitečné pro další studium.
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Alvarez, de Eulate Diaz de San Martin Eva Maria. "Electrochemical studies toward proteomic analysis." Thesis, Curtin University, 2014. http://hdl.handle.net/20.500.11937/702.

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This thesis provides the basis for a label-free bioanalytical platform using electrochemical analysis at liquid –liquid interfaces. The possibility to detect biomolecules such as proteins in a label-free manner via adsorption and ion-transfer was achieved. Several pre-treatment steps used in proteome analysis, such as protein pre-concentration and digestion, were studied. The results demonstrate the promise of this strategy for the detection and identification of proteins.
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VACCHINI, MATTIA. "DESIGN, SYNTHESIS AND DEVELOPMENT OF GLYCOTOOLS FOR NEUROCHEMISTRY STUDIES." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2020. http://hdl.handle.net/10281/262350.

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Contesto scientifico. I glicani rivestono un ruolo cruciale nel sistema nervoso centrale (SNC) e il loro studio è fondamentale per un'accurata comprensione della neurochimica, ma la conoscenza scientifica riguardo ai glicani presenti nel SNC è ancora limitata. Lo scopo di questa tesi è fornire nuovi strumenti al glicochimico e al glicoanalista per condurre studi di neurochimica, funzionali all'esplorazione del ruolo dei glicani nel SNC. Questa tesi presenta un nuovo metodo analitico per lo studio degli N-glicani da tessuti cerebrali (LSD); lo stato dell'arte di un lavoro in corso riguardante l'investigazione di N-glicani e N-glicoproteine differentemente espresse in tessuti cerebrali appartenenti a diverse specie; un efficiente metodo di marcatura chimica per (glico)proteine, applicato con successo a una N-glicoproteina, Neuroserpina (NS), che polimerizza nel SNC con conseguenze patologiche; e le sintesi di glicosidi e glicodendrimeri con potenziali applicazioni in studi neurochimici. Metodi. LSD si sviluppa a partire dalla lisi chimica di tessuti cerebrali (tc), con conseguente precipitazione del proteoma (i.e., metanolo/cloroformio), deglicosilazione enzimatica (i.e., PNGase F), purificazione degli N-glicani, marcatura chimica (i.e., amminazione riduttiva su N-acetilglucosammina terminale) e analisi tramite approcci LC-MS. LSD è stato ottimizzato su campioni di tc e accuratamente validato (i.e., sensibilità, precisione, linearità, range dinamico, selettività, robustezza). L'analisi degli N-glicani è stata anche effettuata tramite deglicosilazione enzimatica in-gel da elettroforesi di proteine, mentre un protocollo di digestione con Tripsina in-gel è stato usato per l'identificazione di N-glicoproteine e siti di N-glicosilazione tramite approcci LC-MS su peptidi. NS è stata dimetilata chimicamente (i.e., amminazione riduttiva su lisina), nella sua forma monomerica (mhNS) e polimerica (phNS) e l'esito della reazione è stato valutato tramite MS, per l'investigazione dei determinanti molecolari coinvolti nel meccanismo di polimerizzazione. I glicosidi sono stati sintetizzati usando una reazione di glicosilazione di tipo Fischer, condotta su monosaccaridi deprotetti, usando alcol allilico e decenolo come accettori glicosidici, mentre i glicodendrimeri sono stati ottenuti sfruttando la chimica delle ossime per la decorazione con gruppi maltosilici di dendrimeri sintetizzati tramite metatesi delle olefine. Risultati. LSD presenta il più basso limite di rivelabilità (1 mg di tc) rispetto a molti altri lavori riportati in letteratura ed è attualmente il metodo di neuro-N-glicomica più accuratamente validato. La deglicosilazione in-gel per l'analisi degli N-glicani cerebrali ha prodotto cromatogrammi informativi per ogni frazione del proteoma con elevata risoluzione (e.g., sensibilità fino a 100 EU da una singola banda di gel), permettendo l'analisi dei peptidi deglicosilati dallo stesso campione (i.e., un totale di 1200 peptidi, 570 proteine, 57 N-glicoproteine, e nuovi siti di N-glicosilazione identificati). La marcatura chimica di NS si è dimostrata efficiente (i.e., 80-90% di resa), compatibile con la struttura nativa della proteina, e funzionale all'uso designato, in quanto capace di evidenziare differenze statisticamente significative nel profilo di marcatura di mhNS e phNS (i.e., 9 lisine). La sintesi di glicosidi ha fornito prodotti con buona resa (e.g., 70%) e alfa-stereoselettività, mentre quella dei glicodendrimeri ha generato molecole esponenti gruppi maltosilici, utilizzabili nel contesto di studi di neurochimica. Conclusioni. I metodi e le molecole contenuti in questa tesi apporteranno beneficio alla comunità scientifica glicochimica, incrementando il numero di strumenti che il glicochimico e il glicoanalista possono utilizzare per portare avanti lo studio degli effetti dei glicani in contesto neurologico e neuromedico.
Background. Glycans play crucial roles within the central nervous system (CNS) and their study is essential for a thorough comprehension of neurochemistry, but the scientific knowledge about CNS glycans remains scarce. The aim of this thesis is to provide the glycochemist and glycoanalyst with novel tools for neurochemistry studies, towards the exploration of glycan roles in the CNS. This thesis presents a novel analytical method for brain N-glycans investigation (LSD); the state of the art of an ongoing work for the investigation of N-glycans and N-glycoproteins differentially expressed in brain tissues of different species; an efficient chemical labelling method for (glyco)proteins, successfully applied on Neuroserpin (NS), a pathologically-polymerising CNS N-glycoprotein; and the syntheses of glycosides and glycodendrimers with potential room for neuromedical studies. Methods. LSD comprised brain tissue (bt) chemical lysis, proteome precipitation (i.e., methanol/chloroform), enzymatic deglycosylation (i.e., PNGase F), N-glycans purification, chemical labelling (i.e., reductive amination on terminal N-acetylglucosamine), and LC-MS bioanalysis. The method has been optimised on bt and thoroughly validated (i.e., sensitivity, precision, linearity, range, selectivity, robustness). N-glycans analysis has also been carried out through protein electrophoresis in-gel deglycosylation, while in-gel trypsinisation was used for the LC-MS identification of N-glycoproteins and N-glycosylation sites. NS has been dimethylated (i.e., reductive amination on lysine) in its monomeric (mhNS) and polymeric (phNS) forms, and the reaction outcome has been evaluated using MS, towards the investigation of NS polymerisation-driving molecular features. Glycosides were synthesised with a Fischer- type glycosylation reaction on unprotected monosaccharides using either allyl alcohol or decenol as glycosyl acceptors, while glycodendrimers were obtained decorating olefin-metathesis-synthesised dendrimers with maltose moieties, exploiting oxime chemistry. Results. LSD displayed the lowest detection limit (1 mg of bt) in comparison to many other works reported in the literature and is the most thoroughly validated neuro-N-glycomic method reported to date. In-gel deglycosylation for brain N-glycans analysis furnished informative chromatograms for every proteome fraction with high resolution (e.g., sensitivity up to 100 EU from a single gel band), permitting the analysis of deglycosylated peptides from the same sample (i.e., a total of 1200 peptides, 570 proteins, 57 N-glycoproteins, and novel N-glycosylation sites identified). NS chemical labelling displayed high efficiency (i.e., 80-90% yield), compatibility with the protein folding, and suitability towards the intended purpose, being able to highlight statistically significant differences in mhNS and phNS labelling patterns (i.e., 9 lysines). The syntheses of glycosides furnished products with good yield (i.e., 70%) and a- stereoselectivity, while that of glycodendrimers afforded molecules exposing several maltose moieties, employable in the context of neurochemistry studies. Conclusions. Methods and molecules delivered within this thesis will benefit the glycochemistry community, by enlarging the glycochemist and glycoanalyst toolkits to carry on the investigation of glycans- related effects in neurological and neuromedical context.
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Mzoughet, Kouassi ahou Judith Elisabeth Patricia. "Physiochemical and proteomic studies on azaspiracid contaminated mussels." Thesis, Queen's University Belfast, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.517086.

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Sridhar, Varshini. "Proteomic studies of grape xylem tissue and sap." Thesis, Florida Agricultural and Mechanical University, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=1594029.

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Pierce’s disease (PD), caused by bacterium Xylella fastidiosa, seriously hampers the cultivation of Vitis vinifera also known as bunch grapes, in different parts of the world. The bacterium clogs xylem vessels and forms a biofilm, resulting in the wilting of the plant. Bunch grape cultivars exhibit certain degree of tolerance to PD, however most commercial cultivars suffer heavy loss due to this devastating disease. Therefore, studies on genetic variation for disease tolerance will assist in identification of key molecular components that confer tolerance to PD. Vitis species, such as, Florida hybrid bunch (FH) and muscadine grape ( Vitis rotundifolia) are widely cultivated in southeastern United States, and are known for their tolerance to PD. A detailed proteomic profile study of contrasting grape species is vital to understand the biological molecules associated with the PD tolerance. However information on total protein composition of Vitis xylem and sap is limited. The overall goals of this study are to determine the signal sequences associated with xylem and sap for the delivery of therapeutic proteins to control Xylella fastidiosa. The specific objectives of this research project are: 1) to compare the proteome profiles of xylem tissue and xylem sap from PD tolerant and -susceptible grapevine cultivars, and 2) to determine the role of proteins in the tissue and sap associated with PD tolerance mechanism. In this study, we used Bunch, FH, and Muscadine grape cultivars to characterize differentially expressed and unique proteins. Differentially expressed proteins were identified using LC MS/MS spectrometry searched against Vitis database. A total of 2519 and 402 proteins were identified in xylem and sap respectively, of which 151 proteins were common to both tissues. Bunch, FH, and muscadine sap showed 52, 53, and 30 unique proteins respectively. The cluster dendrogram analysis of the sap proteome showed that all of the Vitis species are bifolious. Based on the aforementioned, Florida hybrid bunch and muscadines are more closely related to each other than to bunch grape. Functional analysis and gene ontology revealed that proteins involved in carbohydrate metabolic process are more abundant in bunch grape, while FH and muscadine grape have more defense related proteins. Therefore, it is plausible to conclude that major functions of sap proteins in Bunch, FH, and Muscadine grapes are carbohydrate metabolic process and proteolysis (23%), protein phosphorylation (38%), and oxidation and reduction process (16%), respectively. Proteins involved in the defense and peroxidase activity are abundantly present in xylem and sap of FH and muscadine, and these proteins are relatively in reduced levels in bunch xylem and sap. Together, our findings highlight the possible roles of the identified unique proteins towards PD tolerance to Florida hybrid bunch and muscadine cultivars.

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Mansor, Rozaihan. "Proteomic and metabolomic studies on milk during bovine mastitis." Thesis, University of Glasgow, 2012. http://theses.gla.ac.uk/3207/.

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The principal objectives of the study presented in this thesis were to study the changes of milk proteomes, peptidomes and metabolomes during the course of bovine mastitis in comparison with normal milk samples and to discover new bovine mastitis biomarkers using various modern and up-to-date methodologies such as proteomics, peptidomics and metabolomics. Bovine mastitis caused by bacterial infection of the mammary gland of dairy cows is often associated with loss of milk production due to a reduction in milk composition and quality which in turns, lead to negative economic impact on dairy industry. Two important acute phase proteins (APPs) which serve as valuable biomarkers in bovine mastitis were investigated in every chapter using developed and validated enzyme linked immunosorbent assay (ELISA) for bovine milk haptoglobin and commercially available ELISA for bovine milk serum amyloid A3 (M-SAA3). These APPs were quantified alongside somatic cell counts (SCC) and California Mastitis Test (CMT) to confirm the disease status of each animal used in this study. Proteomic methodologies were applied including 1D gel electrophoresis, 2D gel electrophoresis, MALDI-TOF analysis and difference gel electrophoresis to investigate the changes of milk proteome in both subclinical and clinical mastitic milk samples in comparison with healthy milk samples. However these investigations did not reveal novel biomarkers for mastitis. Next, peptidomic methodologies were used to study the changes in milk peptidome and to detect the presence of any significant disease biomarkers in the presence of bovine mastitis by using CE-MS and LC-MS/MS. A total of 31 and 14 polypeptides can be used to discriminate control from infected groups and E. coli from S. aureus infected groups respectively. Lastly, metabolomic methodology was applied with an intention to study the changes in milk metabolome and ultimately to detect the presence of novel biomarkers in bovine mastitis. Di- and tri-peptides were found higher in S. aureus than in E. coli infected groups and based on metabolic pathways, arachidonic, arginine and galactose metabolites were seen increased in mastitic milk samples in comparison to healthy milk samples. Overall, the findings detailed in this thesis indicate that the use of advanced proteomic and metabolomic methodologies could deliver on their promise of the discovery of potential significant bovine mastitis biomarkers. Further studies are needed for validation of these proposed biomarkers and it was hoped that better prevention and treatment methods for bovine mastitis can be achieved in the future.
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Patel, V. "Proteomic studies into the pathogenesis of Enamel Renal Syndrome." Thesis, University College London (University of London), 2018. http://discovery.ucl.ac.uk/10044766/.

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Background: Enamel Renal Syndrome is an autosomal recessive disorder that is characterised by nephrocalcinosis and amelogenesis imperfecta where the causative gene is FAM20A. Unlike most cases of nephrocalcinosis where hypercalciuria is its instrumental cause, patients with ERS have normocalciuria, suggesting an atypical mechanism in calcium handling by the kidneys. Methods: Detection of recombinant FAM20A was performed on HeLa cells and its culture media by Western analysis. Plasma and gingival fibroblasts were used for the detection of FAM20A in control and ERS samples by two-dimensional gel electrophoresis. Human milk was utilised for the quantitation of FAM20A using both shotgun and targeted proteomics approach. Mouse kidneys were used for differential protein expression and functional proteomic analysis to help understand how the absence of FAM20A can severely impact calcium homeostasis. Results: A low amount of FAM20A was detected in human milk. Results from plasma samples and gingival fibroblasts were inconclusive. Differential protein expression profiling of kidneys revealed S100 calcium-binding protein A9 to be 2.9 fold up-regulated in the Fam20a knockout mouse. This protein is a major determinant of arterial calcification. Functional analysis indicated disturbed calcium-regulation mediated by mitochondria and peroxisomes in the absence of Fam20a. Conclusion: The removal of FAM20A triggers a disruptive ripple in the finely tuned intricate pathway of proteins all entangled to regulate calcium homeostasis; a consequence of which leads to ectopic calcification within the interstitium.
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Kang, Huan. "Mass Spectrometry Based Proteomics and Lipidomics Studies." BYU ScholarsArchive, 2015. https://scholarsarchive.byu.edu/etd/6161.

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Mass spectrometry has emerged as having a vital role in various applications to biochemical fields. In this thesis, we have utilized a variety of mass spectrometry techniques for both bacteriophage proteomics and colostrum and milk lipidomics studies. Our first study was the proteome characterization of Great Salt Lake bacteriophage NS01 with SDS-PAGE GEL to separate the viral proteins and high performance liquid chromatography (HPLC) coupled with an LTQ Orbitrap to identify the proteins after in-gel digestion. In this project, we have successfully identified 11 proteins with high confidence, p-values < 0.01, including coat protein gp88 with a coverage of 91% and tail protein gp86 with a coverage of 40.96%, which facilitated the classification of NS01 as a T7-like phage. Our second study was the discovery of colostrum and milk biomarkers that can be used to predict the likelihood of development of production-related metabolic diseases (PRMDs) in dairy cows through a lipidomics approach. In this study, an electrospray ionization, time-of-flight mass spectrometer was applied to lipid profiling, quantification and significant biomolecule selection. A Q-Star quadrupole, orthogonal time-of-flight mass spectrometer and an Agilent 6530 accurate-mass quadrupole/time-of flight mass spectrometer were both used for lipid biomarker fragmentation and identification. According to linear discriminative statistical modeling, three panels of biomarkers were defined. A combination of 2 milk lipid predictors, including DG18:0/18:0 and TG 18:0/18:0/18:1, provided PRMD predictions with 75.0% sensitivity at 90.0% specificity. A combination of 3 colostrum lipid predictors, including TG16:0/18:1/18:3, DG16:0/16:0 and C40H60NO, provided PRMD prediction with 90.0% sensitivity at 86.4% specificity. Furthermore, a combination of 7 colostrum and milk biomarkers, including calculated differences between 'shared' markers found to be significantly different in both colostrum and milk, provided a predictive sensitivity of 87.5% at a specificity of 100%. Thus, three panels of lipid biomarkers have been discovered in 1-4 day postparturient dairy cow colostrum and milk that can be used to predict resistance or susceptibility prior to onset of clinically apparent PRMDs. These novel lipids could be used as important diagnostic predictors in the future. Therefore, mass spectrometry based proteomics and lipidomics approaches have been efficient tools in the biochemical research described in this thesis.
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Peng, Ivory Xingyu. "Electrospray-assisted laser desorption ionization mass spectrometry for proteomic studies." Diss., Restricted to subscribing institutions, 2009. http://proquest.umi.com/pqdweb?did=1997571271&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.

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Harasaki, Kouki Daniel. "Proteomic identification and functional studies of clathrin-coated vesicle components." Thesis, University of Cambridge, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.613727.

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Books on the topic "Proteomic studie"

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Bridge, Paul, David Smith, and Erko Stackebrandt, eds. Trends in the systematics of bacteria and fungi. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789244984.0000.

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Abstract There are fundamental differences between the current levels of genomic and proteomic knowledge for bacteria and fungi. With multiple growth forms and over 100,000 known species, the fungi probably present a more complex situation, but genomic studies are hindered by the lack of reliable reference data for many species. As activities such as environmental sampling, and genomic and proteomic profiling, become more important in extending our understanding of ecosystems, there is an increasing imperative for researchers in microbial systematics to develop the methods and concepts required to interpret the information being generated. This volume presents a collection of chapters that provide some insights into how current methods and resources are being used in microbial systematics, together with some thoughts and suggestions about how both methodologies and concepts may develop in the future.
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Design of human nutrigenomics studies. Wageningen, the Netherlands: Wageningen Academic Publishers, 2009.

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Kwok, Hang Fai. Proteomic and genomic studies on the venom of Gila monster and Mexican beaded lizard. [S.l: The Author], 2003.

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Fantl, Wendy. Revealing Uncharted Biology with Single Cells Proteomic Technologies: Case Studies. Elsevier Science & Technology Books, 2022.

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Divan, Aysha, and Janice A. Royds. 4. Proteins. Oxford University Press, 2016. http://dx.doi.org/10.1093/actrade/9780198723882.003.0004.

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Biological functions require protein and the protein makeup of a cell determines its behaviour and identity. Proteins, therefore, are the most abundant molecules in the body except for water. The approximately 20,000 protein coding genes in the human genome can, by alternative splicing, multiple translation starts, and post-translational modifications, produce over 1,000,000 different proteins, collectively called ‘the proteome’. It is the size of the proteome and not the genome that defines the complexity of an organism. ‘Proteins’ describes the composition and structure of proteins and how they are studied. What information is required in order to understand how proteins work and what happens when this function is impaired in disease?
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Barnes, Rosemary A., and Matthijs Backx. Fungal infections in intensive therapy units. Edited by Christopher C. Kibbler, Richard Barton, Neil A. R. Gow, Susan Howell, Donna M. MacCallum, and Rohini J. Manuel. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780198755388.003.0036.

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Invasive candidiasis remains the main cause of invasive fungal disease in the intensive care unit. The risk of infection is often overestimated and most units will have incidences of 1–2% or lower. Units with higher incidences may have specific geographical and epidemiological factors, or may need to address infection control issues contributing to transmission. Routine use of prophylaxis or empiric therapy is not warranted at this level of disease. Discriminatory risk factors for this low incidence of disease are poorly defined and Candida specific biomarkers have not been validated for pre-emptive therapy. Insights into human response to invasive fungal disease gained from proteomic and genomic studies will increase our understanding, enabling us to target fungal diagnostics and antifungal treatments more accurately.
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Case Studies of Existing Human Tissue Repositories: "Best Practices" for a Biospecimen Resource for the Genomic and Proteomic Era. RAND Corporation, 2004.

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Vermeulen, Roel, Douglas A. Bell, Dean P. Jones, Montserrat Garcia-Closas, Avrum Spira, Teresa W. Wang, Martyn T. Smith, Qing Lan, and Nathaniel Rothman. Application of Biomarkers in Cancer Epidemiology. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780190238667.003.0006.

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Advancements in OMICs are now enabling investigators to explore comprehensively the biological consequences of exogenous and endogenous exposures by detecting molecular signatures of exposure, early signs of adverse biological effects, preclinical disease, and molecularly defined cancer subtypes. These new technologies have proven invaluable for assembling a comprehensive portrait of human exposure, health, and disease. This includes hypothesis-driven biomarkers, as well as platforms that can agnostically analyze entire biologic processes and “compartments,” including the measurement of small molecules (metabolomics), DNA polymorphisms and rarer inherited variants (genomics), methylation and microRNA (epigenomics), chromosome-wide alterations, mRNA (transcriptomics), proteins (proteomics), and the microbiome (microbiomics). Although the implementation of these technologies in epidemiologic studies has already shown great promise, some challenges of particular importance must be addressed. Non-genetic OMIC markers vary over time due to both random variation and physiologic changes. Therefore, there is an urgent need for cohorts to collect repeat biological samples over time.
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Suffredini, Anthony F., and J. Perren Cobb. Genetic and molecular expression patterns in critical illness. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780199600830.003.0031.

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Investigators who study RNA, proteins, or metabolites use analytic platforms that simultaneously measure changes in the relative abundance of thousands of molecules in a single biological sample. Over the last decade, the application of these high-throughput, genome-wide platforms to study critical illness and injury has generated huge quantities of data that require specialized computational skills for analysis. These investigations hold promise for improving our understanding of the host response, thereby transforming the practice of intensive care. This chapter summarizes recent technological and computational approaches used in genomics, proteomics, and metabolomics. While major advances have been made with these approaches when applied to chronic diseases, the acute nature of critical illness and injury has unique challenges. The rapidity of initiating events, the trajectory of inflammation that follows injury or infection and the interplay of host responses to a replicating infection, all have major effects on changes in gene and molecular expression. This complexity is further accentuated by measurement that may vary with the timing and type of tissue sampled after the critical event. In addition, the hunt for novel molecular markers holds promise for identifying patients at risk for severe illness and for enabling more individualized therapy.
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Sklar, Larry A., ed. Flow Cytometry for Biotechnology. Oxford University Press, 2005. http://dx.doi.org/10.1093/oso/9780195183146.001.0001.

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Flow cytometry is a sensitive and quantitative platform for the measurement of particle fluorescence. In flow cytometry, the particles in a sample flow in single file through a focused laser beam at rates of hundreds to thousands of particles per second. During the time each particle is in the laser beam, on the order of ten microseconds, one or more fluorescent dyes associated with that particle are excited. The fluorescence emitted from each particle is collected through a microscope objective, spectrally filtered, and detected with photomultiplier tubes. Flow cytometry is uniquely capable of the precise and quantitative molecular analysis of genomic sequence information, interactions between purified biomolecules and cellular function. Combined with automated sample handling for increased sample throughput, these features make flow cytometry a versatile platform with applications at many stages of drug discovery. Traditionally, the particles studied are cells, especially blood cells; flow cytometry is used extensively in immunology. This volume shows how flow cytometry is integrated into modern biotechnology, dealing with issues of throughput, content, sensitivity, and high throughput informatics with applications in genomics, proteomics and protein-protein interactions, drug discovery, vaccine development, plant and reproductive biology, pharmacology and toxicology, cell-cell interactions and protein engineering.
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Book chapters on the topic "Proteomic studie"

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Sénécaut, Nicolas, Pierre Poulain, Laurent Lignières, Samuel Terrier, Véronique Legros, Guillaume Chevreux, Gaëlle Lelandais, and Jean-Michel Camadro. "Quantitative Proteomics in Yeast: From bSLIM and Proteome Discoverer Outputs to Graphical Assessment of the Significance of Protein Quantification Scores." In Methods in Molecular Biology, 275–92. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2257-5_16.

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AbstractSimple light isotope metabolic labeling (bSLIM) is an innovative method to accurately quantify differences in protein abundance at the proteome level in standard bottom-up experiments. The quantification process requires computation of the ratio of intensity of several isotopologs in the isotopic cluster of every identified peptide. Thus, appropriate bioinformatic workflows are required to extract the signals from the instrument files and calculate the required ratio to infer peptide/protein abundance. In a previous study (Sénécaut et al., J Proteome Res 20:1476–1487, 2021), we developed original open-source workflows based on OpenMS nodes implemented in a KNIME working environment. Here, we extend the use of the bSLIM labeling strategy in quantitative proteomics by presenting an alternative procedure to extract isotopolog intensities and process them by taking advantage of new functionalities integrated into the Minora node of Proteome Discoverer 2.4 software. We also present a graphical strategy to evaluate the statistical robustness of protein quantification scores and calculate the associated false discovery rates (FDR). We validated these approaches in a case study in which we compared the differences between the proteomes of two closely related yeast strains.
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Dannenmaier, Stefan, Silke Oeljeklaus, and Bettina Warscheid. "2nSILAC for Quantitative of Prototrophic Baker’s Yeast." In Methods in Molecular Biology, 253–70. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1024-4_18.

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AbstractStable isotope labeling by amino acids in cell culture (SILAC) combined with high-resolution mass spectrometry is a quantitative strategy for the comparative analysis of (sub)proteomes. It is based on the metabolicincorporation of stable isotope-coded amino acids during growth of cells or organisms. Here, complete labeling of proteins with the amino acid(s) selected for incorporation needs to be guaranteed to enable accurate quantification on a proteomic scale. Wild-type strains of baker’s yeast (Saccharomyces cerevisiae), which is a widely accepted and well-studied eukaryotic model organism, are generally able to synthesize all amino acids on their own (i.e., prototrophic). To render them amenable to SILAC, auxotrophies are introduced by genetic manipulations. We addressed this limitation by developing a generic strategy for complete “native” labeling of prototrophic S. cerevisiae with isotope-coded arginine and lysine, referred to as “2nSILAC”. It allows for directly using and screening several genome-wide yeast mutant collections that are easily accessible to the scientific community for functional proteomic studies but are based on prototrophic variants of S. cerevisiae.
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Elagamey, Eman, Kanika Narula, Niranjan Chakraborty, and Subhra Chakraborty. "Extracellular Matrix Proteome: Isolation of ECM Proteins for Proteomics Studies." In Nitrogen Metabolism in Plants, 155–72. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9790-9_14.

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Guest, Paul C. "Proteomic Studies of Psychiatric Disorders." In Methods in Molecular Biology, 59–89. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7614-0_4.

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Kurihara, Tatsuo, and Nobuyoshi Esaki. "Proteomic Studies of Psychrophilic Microorganisms." In Psychrophiles: from Biodiversity to Biotechnology, 333–44. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-74335-4_19.

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Ferguson, R. E., P. J. Selby, and R. E. Banks. "Proteomic Studies in Urological Malignancies." In Proteomics in Nephrology, 257–79. Basel: KARGER, 2003. http://dx.doi.org/10.1159/000074603.

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Graham, David R. M. "Proteomic Studies of HIV-1." In HIV-1 Proteomics, 39–58. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6542-7_4.

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Schober, Florian A., Ilian Atanassov, Christoph Freyer, and Anna Wredenberg. "Quantitative Proteomics in Drosophila with Holidic Stable-Isotope Labeling of Amino Acids in Fruit Flies (SILAF)." In Methods in Molecular Biology, 75–87. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0834-0_7.

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AbstractProtein-focused research has been challenging in Drosophila melanogaster due to few specific antibodies for Western blotting and the lack of effective labeling methods for quantitative proteomics. Herein, we describe the preparation of a holidic medium that allows stable-isotope labeling of amino acids in fruit flies (SILAF). Furthermore, in this chapter, we provide a protocol for mitochondrial enrichments from Drosophila larvae and flies together with a procedure to generate high-quality peptides for further analysis by mass spectrometry. Samples obtained following this protocol can be used for various functional studies such as comprehensive proteome profiling or quantitative analysis of posttranslational modifications upon enrichment. SILAF is based on standard fly routines in a basic wet lab environment and provides a flexible and cost-effective tool for quantitative protein expression analysis.
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Dias-Neto, Emmanuel, Daniel Martins-de-Souza, Elida P. B. Ojopi, and Wagner F. Gattaz. "Genetic and Proteomic Studies in Schizophrenia." In Advances in Schizophrenia Research 2009, 193–218. New York, NY: Springer New York, 2009. http://dx.doi.org/10.1007/978-1-4419-0913-8_10.

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Ferguson, Roisean E., and Rosamonde E. Banks. "Preanalytical Issues in Clinical Proteomic Studies." In Clinical Proteomics, 1–12. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2008. http://dx.doi.org/10.1002/9783527622153.ch1.

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Conference papers on the topic "Proteomic studie"

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Hashim, O. "Proteomics Approach To Cancer Studies." 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.e7-41.

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Martens, William L., Philip Poronnik, and Darren Saunders. "Hypothesis-Driven Sonification of Proteomic Data Distributions Indicating Neurodegredation in Amyotrophic Lateral Sclerosis." In The 22nd International Conference on Auditory Display. Arlington, Virginia: The International Community for Auditory Display, 2016. http://dx.doi.org/10.21785/icad2016.024.

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Three alternative sonifications of proteomic data distributions were compared as a means to indicate the neuropathology associated with Amyotrophic Lateral Sclerosis (ALS) via auditory display (through exploration of the differentiation of induced pluripotent stem cell derived neurons). Pure visual displays of proteomic data often result in ”visual overload” such that detailed or subtle data important to describe ALS neurodegradation may be glossed over, and so three competing approaches to the sonification of proteomic data were designed to capitalize upon human auditory capacities that complement the visual capacities engaged by more conventional graphic representations. The auditory displays resulting from hypothesis-driven design of three alternative sonifications were evaluated by naïve listeners, who were instructed to listen for differences between the sonifications produce from proteomic data associated with three different types of cells. One of the sonifications was based upon the hypothesis that auditory sensitivity to regularities and irregularities in spatio-temporal patterns in the data could be heard through spatial distribution of sonification components. The design of a second sonification was based upon the hypothesis that variation in timbral components might create a distinguishable sound for each of three types of cells. A third sonification was based upon the hypothesis that redundant variation in both spatial and timbral components would be even more powerful as a means for identifying spatio-temporal patterns in the dynamic, multidimensional data generated in current proteomic studies of ALS.
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Remih, Katharina, Valerie Durkalski-Mauldin, WilliamM Lee, Zemin Su, Laura Krieg, Isabel Karkossa, Kristin Schubert, Martin von Bergen, RobertJohn Fontana, and Pavel Strnad. "Serum proteomic characterisation in acute liver failure." In 38. Jahrestagung der Deutsche Arbeitsgemeinschaft zum Studium der Leber. Georg Thieme Verlag, 2022. http://dx.doi.org/10.1055/s-0041-1740709.

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Anathapadmanabhan, Varsha, Selene Swanson, Siddharth Saini, Vijay Menon, and Larisa Litovchick. "Abstract 343: Proteomic and functional studies identify DCAF7 as major partner of DYRK1A." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-343.

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Kim, Byeoung C., Jin H. Jeong, Dong S. Jeong, Eui Y. Choi, Jae H. Kim, and Kie B. Nahm. "Simplified laser fluorescence scanner for proteomics studies and early cancer diagnosis." In Photonics Asia 2002, edited by Britton Chance, Mingzhe Chen, and Gilwon Yoon. SPIE, 2002. http://dx.doi.org/10.1117/12.482938.

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Townsend, Reid R., Henry Rohrs, Richard LeDuc, James P. Malone, Petra Erdman-Gilmore, Donald L. Hill, Clinton J. Grubbs, Ming You, and Ronald A. Lubet. "Abstract 3700: Proteomic credentialing in a model for chemoprevention studies of urinary bladder cancer." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-3700.

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Truckenmueller, F., B. Goeppert, S. Pusch, I. Heinze, J. Kirkpatrick, P. Schirmacher, A. Ori, and S. Roessler. "Quantitative LC-MS-based shot gun proteomics identifies deregulated proteins in gallbladder carcinoma." In 36. Jahrestagung der Deutschen Arbeitsgemeinschaft zum Studium der Leber. Georg Thieme Verlag KG, 2020. http://dx.doi.org/10.1055/s-0039-3402207.

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Schumacher, A., C. Metzendorf, S. Ribback, and F. Dombrowski. "Investigation of the glycogen-associated proteome via proximity-biotinylation." In 36. Jahrestagung der Deutschen Arbeitsgemeinschaft zum Studium der Leber. Georg Thieme Verlag KG, 2020. http://dx.doi.org/10.1055/s-0039-3402193.

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Jeong, Jieun, and Jake Y. Chen. "RIC: Ranking with Interaction Chains and Its Application in Computational Clinical Proteomics Studies." In 2009 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2009. http://dx.doi.org/10.1109/bibm.2009.58.

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Chen, Jake Yue, Sarah L. Pinkerton, Changyu Shen, and Mu Wang. "An integrated computational proteomics method to extract protein targets for Fanconi Anemia studies." In the 2006 ACM symposium. New York, New York, USA: ACM Press, 2006. http://dx.doi.org/10.1145/1141277.1141316.

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Reports on the topic "Proteomic studie"

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Wang, Zhiyong, and Alma Burlingame. Final Report: Proteomic study of brassinosteroid responses in Arabidopsis. Office of Scientific and Technical Information (OSTI), November 2017. http://dx.doi.org/10.2172/1410667.

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Rohan, Thomas E. Proteomic Prediction of Breast Cancer Risk: A Cohort Study. Fort Belvoir, VA: Defense Technical Information Center, March 2009. http://dx.doi.org/10.21236/ada506647.

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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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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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Zhu, Haining. 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/ada581392.

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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 2010. http://dx.doi.org/10.21236/ada545702.

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Bebarta, Vikhyat. Characterization of the Human Proteomic Response to Hydrocodone: A Preliminary Study. Fort Belvoir, VA: Defense Technical Information Center, May 2014. http://dx.doi.org/10.21236/ada613490.

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Bebarta, Vikhyat. Characterization of the Human Proteomic Response to Hydrocodone: A Preliminary Study. Fort Belvoir, VA: Defense Technical Information Center, March 2013. http://dx.doi.org/10.21236/ada578490.

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