Dissertations / Theses on the topic 'Label-free quantitative proteomic'
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Cummings, Rebecca. "Development and application of label free quantitative proteomic methods." Thesis, University of Liverpool, 2012. http://livrepository.liverpool.ac.uk/8313/.
Full textPaiva, Ana Luiza Sobral. "Biochemical responses of bean-to-string [Vigna unguiculata L. (Walp.)] to salt stress and infection by severe mosaic of cowpea (CPSMV) revealed by quantitative proteomics dial free." Universidade Federal do CearÃ, 2015. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=13591.
Full textAs sessile organisms, plants are exposed to a plethora of environmental stresses to which they must respond to maintain efficient growth and survival. Therefore, in order to improve our understanding on the complex mechanisms involved in the cowpea response to salt stress and to a compatible interaction with the cowpea severe mosaic virus (CPSMV), we used a label-free quantitative proteomic approach to identify the salt and virus responsive proteins in the leaves of the Pitiuba (CE-31) cultivar. The proteins extracted from the leaves (control and treated) 2 and 6 days post-treatment only with salt (DPS), only infected with CPSMV (DPV) or both of them (DPSV) were analyzed using mass spectrometry. At 2 DPS, 350 proteins with at least two-fold differences in abundance, in comparison with controls, were differentially accumulated in the leaves of the salt-treated (80% up and 20% down-accumulated), 281 at 2DPV (25% up and 75% down-accumulated) and 321 at 2 DPSV (45% up and 55% down-accumulated) plants. At 6 DPS, 350 proteins were differentially accumulated in the leaves of the salt-treated (90% up and 10% down-accumulated), 225 at 6 DPV (80% up and 20% down-accumulated) and 315 at 6 DPSV (94% up and 6% down-accumulated) plants. The qualitative analysis showed biochemical differences when the cowpea plants were challenged concurrently with both stresses. To cope with salinity, cowpea increased the abundance of proteins directly involved with the salt tolerance mechanisms. The results indicated that the CPSMV induce the down-accumulating of several proteins to invade and spread in host at early infection period (2 DPV), but at 6 DPV plant can induce accumulation of diverse proteins related with defense, although these strategies canât avoid the negatives effects of disease. When exposed simultaneously to salt/CPSMV stresses, a balance in protein accumulation involved in many biological process. This is the first work employing this approach in cowpea and providing evidences of the plant biochemical mechanisms involved in the responses of cowpea to these stresses.
Como organismos sÃsseis, as plantas sÃo expostas a uma variedade de estresses ambientais aos quais devem responder para sobreviverem e se desenvolverem. A fim de melhorar a nossa compreensÃo sobre os mecanismos complexos envolvidos na resposta do feijÃo-de-corda ao estresse salino e na interaÃÃo compatÃvel com o vÃrus do mosaico severo do caupi (CPSMV), foi utilizada uma abordagem proteÃmica quantitativa, livre de marcaÃÃo, para identificar proteÃnas, responsivas a essess estresses em folhas de feijÃo-de-corda, cv. CE-31. As proteÃnas extraÃdas a partir de folhas primÃrias, 2 e 6 dias apÃs o tratamento sà com o sal (DPS), somente infectadas (DPV), ou sob aÃÃo combinada dos dois (DPSV) foram analisadas, usando espectrometria de massas e comparadas com grupo controle. No 2 DPS, foram identificadas 350 proteÃnas diferencialmente acumuladas (80% aumentaram em abundÃncia e 20% diminuÃram), no 2 DPV 281 (25% aumentaram em abundÃncia e 75% diminuÃram) e no 2 DPSV 321 (45% aumentaram em abundÃncia e 55% diminuÃram). Jà no 6 DPS, foram identificadas 350 proteÃnas diferencialmente acumuladas (90% mostraram aumento em abundÃncia e 10% diminuiÃÃo), no 6 DPV 225 (80% aumentaram em abundÃncia e 20% diminuÃram) e no 6 DPSV 315 proteÃnas(94% aumentaram em abundÃncia e 6% diminuÃram). Para lidar com a salinidade, o cv. CE-31 aumentou a abundÃncia de proteÃnas envolvidas diretamente com os mecanismos de tolerÃncia ao sal. Em relaÃÃo à infecÃÃo da planta pelo CPSMV, os resultados obtidos indicaram que o vÃrus induz reduÃÃo na abundÃncia de vÃrias proteÃnas nos tempos iniciais de infecÃÃo, provavelmente favorecendo a invasÃo e propagaÃÃo na planta, mas, no 6 DPSV, a planta recupera sua capacidade de acionar mecanismos de defesa, embora esses jà nÃo sejam mais efetivos para evitar o estabelecimento da doenÃa viral. Durante exposiÃÃo simultÃnea da planta ao sal e ao vÃrus, ocorreu um equilÃbrio entre o aumento e diminuiÃÃo em abundÃncia de proteÃnas envolvidas em diversos processos metabÃlicos. Esse trabalho à pioneiro nessa abordagem em feijÃo-de-corda e fornece evidÃncias dos mecanismos bioquÃmicos envolvidos nas resposta da planta a esses estresses.
Bertaccini, Diego. "Advances in analytical methodologies for the characterization and quantification in proteomic analysis." Thesis, Strasbourg, 2014. http://www.theses.fr/2014STRAF043/document.
Full textThe objective of this Ph.D. thesis was to develop and optimize new methodologies and analytical approaches to improve the potential of the mass spectrometry based proteomics.The first part of this work focused on the development of the N-Termini proteomics. This topic was addressed with a specific N-Termini chemical derivatization based on TMPP. We have shown that our method allowed both specific N-Terminomics and classical proteomics studies in the same experiment.This N-Terminus methodology was applied to study the proteolytic cleavages of the exported proteins in P. falciparum, a parasite responsible for the malaria.In order to automatize the complex and tedious informatics processsing of the MS/SM data of ourTMPP based N-Terminomics method, we have introduced a new approach (named dN-TOP), based on the use of a stable isotope labeled TMPP which made now N-Terminome proteomics compatible with high throughput studies.The second part addresses quantitative aspects of proteomics. It describes the optimization of quantitative methods at the peptide level or at the protein level for five different proteomic studies in the context of protein complex subunits, targeted SRM based prion, quantification of monoclonal antibodies glycation and hemoglobin HbA2 for reference measurement methods standardization
Zaccarin, Mattia. "Setting up of an innovative procedure for redox proteomics: and its application for definition of the redox status of cells with high metastatic potential." Doctoral thesis, Università degli studi di Padova, 2013. http://hdl.handle.net/11577/3423382.
Full textSTATO DELL’ARTE: Il proteoma include 214.000 cisteine in forma di gruppi tiolici liberi od altra forma. Di queste, solamente un insieme relativamente ristretto ha un ruolo nella mediazione di segnali cellulari. Tali cisteine, attive dal punto di vista dell’ossido-riduzione, sono più sensibili all’ossidazione e la loro forma ossidata è più facilmente riducibile. Sono dunque necessarie specifiche tecniche di proteomica, globalmente indicate con il termine proteomica delle ossido-riduzioni, per identificare tali modifiche e studiarne la regolazione in diversi processi cellulari. Risulta quindi determinante la capacità di identificare sia le proteine che i residui coinvolti e di quantificarne il grado di modificazione. E proprio la quantificazione delle differenze tra due o più stati di un sistema biologico, si colloca tra gli obiettivi tecnicamente più sfidanti della proteomica: nel corso degli ultimi cinque anni, tecniche basate sulla spettrometria di massa associata a cromatografia in fase liquida hanno progressivamente guadagnato affidabilità e robustezza. Molti autori condividono tuttora una visione delle ossido-riduzioni nella mediazione del segnale in cui il destino cellulare dipende principalmente dall’intensità e dalla durata degli stimoli ossidanti: nel presente lavoro si vuole invece sostenere il coinvolgimento di un equilibrio che includa l’azione concomitante sia di specie nucleofile sia di specie elettrofile. OBIETTIVO: Il duplice obiettivo del mio lavoro di Dottorato è stato sia lo sviluppo di una metodologia idonea all’identificazione e quantificazione di proteine, attive dal punto di vista delle ossido-riduzioni, in campioni complessi, sia l’applicazione di tale metodologia allo studio di un sistema cellulare ingegnerizzato di carcinoma mammario (MCF10A) caratterizzato da diversi gradi di malignità. METODI: Al fine di perseguire tale obiettivo ho tratto vantaggio da un approccio che integra la marcatura chimica differenziale (non-isotopica) per mezzo di sonde reattive con i residui di cisteina (NEM, IAM, HPDP) e la purificazione cromatografica delle proteine attive dal punto di vista ossido-riduttivo, alla successiva analisi LC-MS/MS ed elaborazione informatizzata dei dati mediante OpenMS per una quantificazione label-free. Tutti i passaggi di tale metodologia sono quindi stati messi a punto e validati in stretta collaborazione con esperti biochimici e bioinformatici. RISULTATI: E’ stato sviluppato un metodo efficiente ed economico, non basato sull’utilizzo di marcatori isotopici, per la caratterizzazione delle proteine attive dal punto di vista ossido-riduttivo in campioni proteici complessi. L’applicazione del protocollo di quantificazione ad un campione test ha dato il 100% di stime corrette di sovra/sotto-espressione della miscela proteica. L’applicazione del metodo allo studio del modello cellulare di carcinoma mammario ha portato all’identificazione di più di 300 proteine ed ha permesso il raggruppamento di quelle sensibili dal punto di vista ossido-riduttivo in gruppi non differenziali e sovra- o sotto-ossidate nelle cellule più maligne rispetto alla loro controparte meno aggressiva. CONCLUSIONI: Nonostante sia comunemente riconosciuta l’associazione tra fenomeni neoplastici ed uno stress ossidativo, questo studio collega la maggiore malignità di un modello cellulare di carcinoma mammario ad un complesso equilibrio ossido-riduttivo. In questo contesto, specifici bersagli proteici sono ossidati mentre viene mantenuto un ambiente cellulare complessivamente ridotto. Risultati preliminari evidenziano poi l’enzima G6PDH come possibile elemento chiave nella regolazione di tale equilibrio.
Muller, Leslie. "Développements de méthodes de préparation d’échantillons pour l’analyse protéomique quantitative : application à la recherche de biomarqueurs de pathologies." Thesis, Strasbourg, 2017. http://www.theses.fr/2017STRAF067/document.
Full textLabel-free quantitative proteomics strategies are very attractive for diseases biomarkers researches. These approaches require the full control and the repeatability of the analytical workflow. In particular, the sample preparation has to be repeatable enough to ensure the quality and reliability of the results. Objectives of this work were to optimize and develop analytical methods for quantitative proteomics, with a special focus on the sample preparation step. Thus, an innovative, easy and fast protocol allowing the analysis of high sample numbers with high repeatability was developed and further optimized: the “Tube-Gel” protocol. Besides,sample preparations adapted to a variety of biological matrices were developed for the search of biomarkers. The developed methods and their application allowed the identification of potential biomarkers for a variety of diseases: glioblastoma, diffuse large B-cell lymphomas and renal transplants failures
NUKALA, SARATH BABU. "BIOANALYTICAL AND PROTEOMIC APPROACHES IN THE STUDY OF PATHOLOGIC ECS DYSFUNCTIONALITY, OXIDATIVE STRESS AND THE EFFECTS OF PFKFB3 MODULATORS." Doctoral thesis, Università degli Studi di Milano, 2019. http://hdl.handle.net/2434/644236.
Full textBranson, Owen E. "Improved tag-count approaches for label-free quantitation of proteome differences in bottom-up proteomic experiments." The Ohio State University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=osu1471553685.
Full textMackay, Katherine. "A comparative study of analysis methods in quantitative label free proteomics." Thesis, University of Liverpool, 2015. http://livrepository.liverpool.ac.uk/2050359/.
Full textJarnuczak, Andrew. "Mass spectrometry-based quantitative proteomics applied to the analysis of Saccharomyces cerevisiae heat stress response and chaperone deletion strains." Thesis, University of Manchester, 2015. https://www.research.manchester.ac.uk/portal/en/theses/mass-spectrometrybased-quantitative-proteomics-applied-to-the-analysis-of-saccharomyces-cerevisiae-heat-stress-response-and-chaperone-deletion-strains(c653915b-70fa-44d7-9bb7-6e7965349ff0).html.
Full textHaddad, Iman. "Caractérisation protéomique du matrisome des maladies des petits vaisseaux cérébraux par spectrométrie de masse." Thesis, Université Paris sciences et lettres, 2020. http://www.theses.fr/2020UPSLS026.
Full textDiseases of the small vessels of the brain are responsible for damage to the white matter of the brain and multiple deep braininfarctions. They are the cause of more than 25% of strokes and are the second cause of dementia after Alzheimer's dementia. It is aset of pathological processes, which affect small arteries, arterioles, cerebral venule or capillary of less than 400µm. Thecerebrovascular matrisome seems to be a converging pathological pathway between the various diseases of the small vessels of thegenetic type and of the sporadic type. The matrisome is the set of proteins constituting the extracellular matrix (ECM) as well as theassociated proteins, their roles consist not only in the support and the anchoring of the cells but also in various fundamental processessuch as differentiation, proliferation, Survival or migration of cells. The structural and physico-chemical diversity of these proteins,however, makes their analysis particularly delicate. Within the framework of this thesis we propose to characterize in a quantitativeand qualitative way the microvascular matrisome in the diseases of the small vessels, as well as to identify commonabnormalities orspecific to each disease. For this we have developed a label-free quantitative proteomic approach on cerebral and peripheral vesselsisolated from three preclinical genetic murine models and two murine models for the sporadic character. We have developed andvalidated a new robust and sensitive method for the quantitative non-labeling analysis of changes in the matrisome of mouse cerebralarteries and the application of our method on the arteries of the different mouse models studied has allowed us to identify someavenues. Interesting for each disease independently but also highlighted some common signatures between the different studies
Miraee-Nedjad, Samaneh. "Early events in the onset of type II diabetes : effects of aggregated amylin (IAPP) on the islet proteome and metabolic pathways." Thesis, University of Manchester, 2013. https://www.research.manchester.ac.uk/portal/en/theses/early-events-in-the-onset-of-type-ii-diabetes-effects-of-aggregated-amylin-iapp-on-the-isletproteome-and-metabolic-pathways(55b2f0a5-f312-4276-8dfd-d94a0ee04232).html.
Full textResende, Virginia Maria Ferreira. "Análise proteônica de venenos de Apis mellifera baseada em espectrometria de massas: abordagem quantitativa label-free e identificação de fosforilação." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/5/5146/tde-12062013-115302/.
Full textHoneybee venom toxins disturb the activity of critical cellular processes, triggering immunological, physiological, and neurological responses within victims. Studies on venom toxins have provided invaluable knowledge towards elucidating the molecular and functional details of their biological targets, yet there has been no report of a full proteome/phosphoproteome profile of honeybee venom. In this study, we focused on Apis mellifera honeybee venom characterization, including proteins identification, label-free quantitative analysis and phosphorylation identification. Making use of a MS-based proteomic approach, consisting on in-solution digestion followed by LC-MS/MS analysis, we were able to compare the effect of the liquid chromatography gradient length on the sample coverage, consequently, to identify a higher number of proteins using longer separation gradient of the tryptic peptides. Favorable identification of phosphorylations was achieved by the application of a long separation gradient combined with CID fragmentation and high accuracy mass measurement using an LTQ Orbitrap Velos. Here we report on the comparative shotgun proteomics study of the venoms of two Apis mellifera subspecies, A. m. carnica and A. m. ligustica, and the hybrid known as Africanized honey bee (AHB). We identified 51 proteins in total, with 42 of them being common among the three venoms, including many previously unidentified entries. Performing label-free quantification, we observed that few proteins were found with different relative amounts. Additionally, we revealed the phosphorylation of two proteins in all the samples, with two of them being HBV toxins/allergens: melittin and icarapin. Icarapin was identified as phosphorylated at 205Ser. Melittin was identified as phosphorylated at the 18Ser and 10Thr positions in all venoms, as well. Given these novel findings, we then chose to compare the toxicity of the phosphorylated/unphosphorylated forms of the major venom toxin, melittin, considering the most prominent phosphorylation event, the phosphorylated 18Ser position. We showed that the toxicity is in fact decreased when the peptide is phosphorylated. Based on a combination of efficient methodology and state-of-the-art instrumentation, delineated by our Shotgun-NanoESI-Long Gradient-LTQ Orbitrap Velos analysis, we achieved proteomic coverage far surpassing any previous report. Together, these discoveries pave the way for future phosphovenomic studies
Paiva, Ana Luiza Sobral. "Respostas bioquímicas do feijão-de-corda [Vigna unguiculata L. (Walp.)] ao estresse salino e infecção pelo vírus do mosaico severo do caupi (CPSMV) reveladas pela proteômica quantitativa livre de marcação." reponame:Repositório Institucional da UFC, 2015. http://www.repositorio.ufc.br/handle/riufc/18855.
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As sessile organisms, plants are exposed to a plethora of environmental stresses to which they must respond to maintain efficient growth and survival. Therefore, in order to improve our understanding on the complex mechanisms involved in the cowpea response to salt stress and to a compatible interaction with the cowpea severe mosaic virus (CPSMV), we used a label-free quantitative proteomic approach to identify the salt and virus responsive proteins in the leaves of the Pitiuba (CE-31) cultivar. The proteins extracted from the leaves (control and treated) 2 and 6 days post-treatment only with salt (DPS), only infected with CPSMV (DPV) or both of them (DPSV) were analyzed using mass spectrometry. At 2 DPS, 350 proteins with at least two-fold differences in abundance, in comparison with controls, were differentially accumulated in the leaves of the salt-treated (80% up and 20% down-accumulated), 281 at 2DPV (25% up and 75% down-accumulated) and 321 at 2 DPSV (45% up and 55% down-accumulated) plants. At 6 DPS, 350 proteins were differentially accumulated in the leaves of the salt-treated (90% up and 10% down-accumulated), 225 at 6 DPV (80% up and 20% down-accumulated) and 315 at 6 DPSV (94% up and 6% down-accumulated) plants. The qualitative analysis showed biochemical differences when the cowpea plants were challenged concurrently with both stresses. To cope with salinity, cowpea increased the abundance of proteins directly involved with the salt tolerance mechanisms. The results indicated that the CPSMV induce the down-accumulating of several proteins to invade and spread in host at early infection period (2 DPV), but at 6 DPV plant can induce accumulation of diverse proteins related with defense, although these strategies can’t avoid the negatives effects of disease. When exposed simultaneously to salt/CPSMV stresses, a balance in protein accumulation involved in many biological process. This is the first work employing this approach in cowpea and providing evidences of the plant biochemical mechanisms involved in the responses of cowpea to these stresses.
Como organismos sésseis, as plantas são expostas a uma variedade de estresses ambientais aos quais devem responder para sobreviverem e se desenvolverem. A fim de melhorar a nossa compreensão sobre os mecanismos complexos envolvidos na resposta do feijão-de-corda ao estresse salino e na interação compatível com o vírus do mosaico severo do caupi (CPSMV), foi utilizada uma abordagem proteômica quantitativa, livre de marcação, para identificar proteínas, responsivas a essess estresses em folhas de feijão-de-corda, cv. CE-31. As proteínas extraídas a partir de folhas primárias, 2 e 6 dias após o tratamento só com o sal (DPS), somente infectadas (DPV), ou sob ação combinada dos dois (DPSV) foram analisadas, usando espectrometria de massas e comparadas com grupo controle. No 2° DPS, foram identificadas 350 proteínas diferencialmente acumuladas (80% aumentaram em abundância e 20% diminuíram), no 2° DPV 281 (25% aumentaram em abundância e 75% diminuíram) e no 2° DPSV 321 (45% aumentaram em abundância e 55% diminuíram). Já no 6° DPS, foram identificadas 350 proteínas diferencialmente acumuladas (90% mostraram aumento em abundância e 10% diminuição), no 6° DPV 225 (80% aumentaram em abundância e 20% diminuíram) e no 6° DPSV 315 proteínas(94% aumentaram em abundância e 6% diminuíram). Para lidar com a salinidade, o cv. CE-31 aumentou a abundância de proteínas envolvidas diretamente com os mecanismos de tolerância ao sal. Em relação à infecção da planta pelo CPSMV, os resultados obtidos indicaram que o vírus induz redução na abundância de várias proteínas nos tempos iniciais de infecção, provavelmente favorecendo a invasão e propagação na planta, mas, no 6° DPSV, a planta recupera sua capacidade de acionar mecanismos de defesa, embora esses já não sejam mais efetivos para evitar o estabelecimento da doença viral. Durante exposição simultânea da planta ao sal e ao vírus, ocorreu um equilíbrio entre o aumento e diminuição em abundância de proteínas envolvidas em diversos processos metabólicos. Esse trabalho é pioneiro nessa abordagem em feijão-de-corda e fornece evidências dos mecanismos bioquímicos envolvidos nas resposta da planta a esses estresses.
Denecker, Thomas. "Bioinformatique et analyse de données multiomiques : principes et applications chez les levures pathogènes Candida glabrata et Candida albicans Functional networks of co-expressed genes to explore iron homeostasis processes in the pathogenic yeast Candida glabrata Efficient, quick and easy-to-use DNA replication timing analysis with START-R suite FAIR_Bioinfo: a turnkey training course and protocol for reproducible computational biology Label-free quantitative proteomics in Candida yeast species: technical and biological replicates to assess data reproducibility Rendre ses projets R plus accessibles grâce à Shiny Pixel: a content management platform for quantitative omics data Empowering the detection of ChIP-seq "basic peaks" (bPeaks) in small eukaryotic genomes with a web user-interactive interface A hypothesis-driven approach identifies CDK4 and CDK6 inhibitors as candidate drugs for treatments of adrenocortical carcinomas Characterization of the replication timing program of 6 human model cell lines." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASL010.
Full textBiological research is changing. First, studies are often based on quantitative experimental approaches. The analysis and the interpretation of the obtained results thus need computer science and statistics. Also, together with studies focused on isolated biological objects, high throughput experimental technologies allow to capture the functioning of biological systems (identification of components as well as the interactions between them). Very large amounts of data are also available in public databases, freely reusable to solve new open questions. Finally, the data in biological research are heterogeneous (digital data, texts, images, biological sequences, etc.) and stored on multiple supports (paper or digital). Thus, "data analysis" has gradually emerged as a key research issue, and in only ten years, the field of "Bioinformatics" has been significantly changed. Having a large amount of data to answer a biological question is often not the main challenge. The real challenge is the ability of researchers to convert the data into information and then into knowledge. In this context, several biological research projects were addressed in this thesis. The first concerns the study of iron homeostasis in the pathogenic yeast Candida glabrata. The second concerns the systematic investigation of post-translational modifications of proteins in the pathogenic yeast Candida albicans. In these two projects, omics data were used: transcriptomics and proteomics. Appropriate bioinformatics and analysis tools were developed, leading to the emergence of new research hypotheses. Particular and constant attention has also been paid to the question of data reproducibility and sharing of results with the scientific community
Huang, Zhen-Wei, and 黃振維. "Label-free Quantitative MS-based Proteomic Analysis of Dopamine Modulation in Aged Drosophila Male." Thesis, 2016. http://ndltd.ncl.edu.tw/handle/16478334466312825492.
Full text國立暨南國際大學
應用化學系
104
Dopamine (DA) acts as a key neurotransmitter in the brain and plays a vital role is sexual motivation in old male drosophila melanogaster. In order to understand how dopamine (DA) affects sexual behavior, quantitative MS-based proteomic analysis and RNA microarray analysis were used to explore the mechanisms of dopaminergic controls at the molecular level. Our results shows that increasing DA levels in the PPL2ab neurons resulted in the significant alternation of 1870 transcript level (909 up-regulated and 961 down-regulated) and 100 protein levels (75 up-regulated and 58 down-regulated). The identified dys-regulated proteins and RNAs are mainly involved in the metabolic process and biosynthetic process. Gene overlap analysis identified six promising candidate genes that could play a role in DA-associated hyper-sexuality such as Fat body protein, Cuticular protein, Larval serum protein, Yolk protein, Heat-shock-protein, and Plasma membrane calcium ATPase. Further investigation will be pursued to investigate the correlation of these candidate genes with hyper-sexuality of old male drosophila melanogaster.
Chen, Yen-Fu, and 陳彥甫. "Hydrophilic Interaction Chromatography Fractionation in Combination with Label-Free Quantitative Shotgun Proteomic Analysis of Rice Mutants." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/qhuy3s.
Full text國立中興大學
分子生物學研究所
101
Proteins are the final pigment of central dogma, they can strongly describe the phenotype of organism as such. Nowadays, some of scientist focused on protein research, and the disciplines to study protein called proteomics. Traditionally, the two-dimensional gel electrophoresis couple with gel image quantification is widely used to adapt quantitative proteomics, though it can provide large-scale and visible information, however, it still have some challenge and drawback. Multidimensional protein identification technology is the alternative way in quantitative proteomics research; it uses multidimensional liquid chromatography and mass spectrometry to separate and identify analyte. In other hand, photosynthesis is the only way to convert and storage light to other energy formation and it widely exist in plant leaf and bacteria. Chlorophyll is the core compound of photosynthesis reaction, it reflect green light instead of absorbing, because of it, most of plant leaf are green. However, the abnormal leaf color yellow or white occurred in rice mutant SA0405, SA0407 and SA0408 different phenotype from others plant leaf. In this study, hydrophilic interaction liquid chromatography and ultra performance liquid chromatography mass spectrometry were used in peptides separation and protein identification, and MASCOT Distiller software were used in label-free quantification. Here, we demonstrated hydrophilic interaction liquid chromatography was able to separate peptides, and MASCOT Distiller was able to using label-free quantification. We also applied in rice mutants, total of 205, 250 and 279 proteins were quantified successfully in SA0405, SA0407 and SA0408. According to protein quantification result, we speculated the mutant of MGD, TRX and GGT genes may indirectly cause abnormal leaf color.
Luber, Christian A. [Verfasser]. "Pattern recognition receptors are subset specific in dendritic cells : In-vivo quantitative proteomic investigations using label-free analysis and the SILAC mouse / Christian A. Luber." 2009. http://d-nb.info/1006352929/34.
Full textWu, Chien-Peng, and 吳建朋. "Altered Membrane Proteomic Signature in Colorectal Cancer Revealed by Label-free Quantitation Strategy." Thesis, 2008. http://ndltd.ncl.edu.tw/handle/97520208761927235499.
Full text國立臺灣海洋大學
生物科技研究所
96
Human colorectal cancer is one of the common cancer-related death diseases due to absence of a fast and specified diagnostic biomarker. Abnormal expressions of membrane proteins, such as receptors, have been linked to diseases and drug targets. To decipher the key modulators of tumorigenesis and the potential candidate proteins as biomarkers or therapeutic targets for colorectal cancer, we have developed a label-free quantitative membrane proteomic strategy for analysis of paired normal and tumor colorectal cancer tissues from 27 patients in different colon cancer stages. By four-dimensional alignment algorithm, termed SEMI, on Sequence, Elution time, Mass to charge and Internal standard, the unidentified peptide can be computationally located and thus increase the numbers of quantifiable proteins. Without conventional isotopic labeling, we used the integrated chromatographic peak areas for peptide quantification. By addition of internal standard protein before gel-assisted digestion, the quantitation deviation during tryptic digestion and LC-MS/MS can be normalized. Using HeLa cell lysate containing different amount of BSA as a model system, reliable linear correlation can be obtained (R2=0.9972) with 40-fold dynamic concentrations of bovine serum albumin (BSA). High quantitation accuracy and reasonable standard deviation (15.5% ~17%) were demonstrated in cell and tissues models. Furthermore, we applied this strategy to quantitative membrane proteomic analysis of paired normal and colorectal cancer tissues. On contrast to most previous studies using pooled samples, the high throughput strategy offers advantage for providing individual proteomic pattern of patients. A total of 868, 2017, 2040 and 1127 proteins were identified from colorectal cancer patients of Duke’ A、B、C、D stage, respectively. We identified 120 up-regulated (> 2-fold) and 37 down-regulated proteins (< 0.5-fold) in stage A, 6 up-regulated and 30 down-regulated proteins in stage B, 4 up-regulated and 4 down-regulated proteins in stage C and 3 up-regulated and 4 down-regulated proteins in stage D. In this study, we also found that six proteins, CEACAM5、CEACAM6、C6、DEFA1、RPH3Al and SEC61B, show overexpression in 60% patients. In previous literatures, CEACAM has been found to be associated with human colorectal cancer. We expect that the these differentially express proteins may provide insight into the molecular mechanism underlying the development and progression of colon cancer as well as an opportunity to provide panel of membrane proteins as biomarker candidates, enabling early diagnosis of human colorectal cancer to decrease the mortality.
Lento, S., M. Brioschi, S. Barcella, Md Talat Nasim, S. Ghilardi, S. S. Barbieri, E. Tremoli, and C. Banfi. "Proteomics of tissue factor silencing in cardiomyocytic cells reveals a new role for this coagulation factor in splicing machinery control." 2015. http://hdl.handle.net/10454/8001.
Full textIt has long been known that Tissue Factor (TF) plays a role in blood coagulation and has a direct thrombotic action that is closely related to cardiovascular risk, but it is becoming increasingly clear that it has a much wider range of biological functions that range from inflammation to immunity. It is also involved in maintaining heart haemostasis and structure, and the observation that it is down-regulated in the myocardium of patients with dilated cardiomyopathy suggests that it influences cell-to-cell contact stability and contractility, and thus contributes to cardiac dysfunction. However, the molecular mechanisms underlying these coagulation-independent functions have not yet been fully elucidated. In order to analyse the influence of TF on the cardiomyocitic proteome, we used functional biochemical approaches incorporating label-free quantitative proteomics and gene silencing, and found that this provided a powerful means of identifying a new role for TF in regulating splicing machinery together with the expression of several proteins of the spliceosome, and mRNA metabolism with a considerable impact on cell viability.
Cordeiro, Joana Flores. "Pinpointing new urinary biomarkers for bladder cancer detection and stage differentiation by label-free quantitative mass spectrometry." Master's thesis, 2018. http://hdl.handle.net/10362/53146.
Full textSantos, Fátima Raquel Milhano dos. "Human vitreous proteome in vitreoretinal diseases." Doctoral thesis, 2020. http://hdl.handle.net/10400.6/11130.
Full textO vítreo, também denominado por corpo vítreo ou humor vítreo, é um fluido transparente que preenche a cavidade posterior do olho entre a retina neurossensorial e o cristalino. Durante muitos anos, o papel do vítreo na saúde e na doença foi negligenciado, pensando-se que a sua função era meramente estrutural. No entanto, tem-se registado um crescente interesse pela análise do proteoma vítreo nos últimos anos. Estes estudos comprovaram que o vítreo é altamente complexo e biologicamente mais ativo do que se pensava inicialmente. De facto, alterações a nível do proteoma do vítreo refletem o estado fisiológico e patológico do olho e, portanto, esta é a matriz ideal para o estudo das doenças vitreorretinianas. Embora a procura de biomarcadores no vítreo, mais sensíveis e específicos para cada patologia ocular, não tenha sido bem-sucedida até o momento, a análise do proteoma vítreo mostrou-se promissora na elucidação de alguns dos mecanismos patológicos subjacentes a estas patologias. Neste projeto, diversas técnicas proteómicas baseadas na separação de proteínas em gel de poliacrilamida (gel-based proteomics) ou no fracionamento de péptidos por cromatografia líquida (gel-free proteomics) foram desenvolvidas e aplicadas para a análise do proteoma do vítreo no descolamento da retina (RD), na retinopatia diabética (DR) e na degeneração macular relacionada com a idade (AMD). Desde os primeiros estudos em proteómica, a eletroforese bidimensional do gel (2DE) foi o método preferencial para a separação e a identificação de proteínas do vítreo. A 2DE é uma ferramenta valiosa para a separação com elevada resolução e análise de rotina de proteoformas, principalmente se for combinada com técnicas de deteção mais sensíveis, com um processamento de imagem mais refinado e com uma preparação adequada das amostras. Portanto, na primeira parte deste trabalho, aplicou-se uma rede neural artificial (ANN) para a otimização da extração de proteínas do vítreo e da sua análise por 2DE, através da combinação de vários agentes solubilizantes (CHAPS, Genapol, DTT, tampão IPG) e parâmetros físicos (temperatura e voltagem total). Pela aplicação de um modelo matemático criado por ANN, a extração de proteínas e o número de spots detetados após a sua análise por 2DE melhoram significativamente. A resposta otimizada (580 spots detetados) representa um incremento melhoria de 2,4 vezes comparando com as condições padrão utilizadas no desenho experimental inicial. Os resultados alcançados indicam claramente que é crucial combinar as concentrações adequadas de agentes solubilizantes para melhorar a extração, solubilização e a deteção das proteínas do vítreo, assim como para obter géis bem resolvidos. Para além disso, os nossos resultados também indicam que os parâmetros físicos têm uma influência significativa na focagem isoelétrica e, por esta razão, devem ser ajustados e monitorizados neste tipo de análise. Quando se trabalha com fluidos biológicos também é importante reduzir a sua complexidade antes da análise por 2DE, de modo a facilitar a deteção de proteínas pouco abundantes e a aumentar a cobertura do proteoma. Após a remoção da albumina e da imunoglobulina G, o número de proteínas detetadas no gel aumentou 1,3 vezes quando comparado com o ponto ótimo do modelo proposto por ANN, com uma média de 761 spots detetados no vítreo em doenças vitreorretinianas, como, por exemplo, o descolamento regmatogénico da retina (RRD) ou a retinopatia diabética proliferativa (PDR). Na segunda tarefa deste projeto de doutoramento, testou-se a performance das técnicas de marcação isobárica, na análise de amostras de vítreo de RRD. O RRD é uma das causas de cegueira e é caracterizado por uma separação física entre a retina neurossensorial e o epitélio pigmentar da retina (RPE). O vítreo tem um papel central no aparecimento do RRD, que pode ser provocado pela liquefação do vítreo. Esta reduz a adesão vitreorretiniana, conduzindo assim à acumulação de líquido do vítreo no espaço subretinal, e, consequentemente, à separação física entre a retina e o RPE. Assim, a proteómica quantitativa pode contribuir para a compreensão das alterações que ocorrem no olho, providenciando uma informação complementar sobre os mecanismos moleculares subjacentes à patogénese do RRD. No presente estudo, o proteoma do vítreo recolhido de doentes com RRD foi analisado e comparado com amostras de vítreo de membranas epimaculares (MEM) usando reagentes iTRAQ (Isobaric tags for relative and absolute quantitation) em combinação com análise por Cromatografia Líquida Bidimensional acoplada à Espectrometria de Massa em Tandem (2D-LC-MS/MS). A análise destas amostras por LC-MS/MS resultou na identificação de 6078 péptidos relativos a 1030 proteínas, 2613 dos quais correspondem a péptidos únicos. Das proteínas identificadas, um total de 150 estava diferencialmente expressa no vítreo de doentes com RRD, incluindo 96 proteínas sobreexpressas e 54 subexpressas. Entre as sobreexpressas encontraram-se várias enzimas glicolíticas (frutose-bifosfato aldolase A, gama-enolase e fosfoglicerato cinase 1), transportadores de glicose (GLUT-1), e inibidores de proteases (inibidor da metaloproteinase 1, inibidor do ativador de plasminogénio 1) que são regulados pelo fator induzido por hipóxia (HIF-1), o que sugere que a via de sinalização HIF-1 pode ser activada em resposta à RRD. Além disso, a acumulação no vítreo de proteínas intracelulares dos fotorreceptores, incluindo fosducina, rodopsina e S-arrestina, ou da vimentina revela que a RRD leva a uma degeneração significativa das células fotorreceptoras. No entanto, a sobreexpressão de proteínas envolvidas no metabolismo do carbono ou chaperones moleculares, entre outras, indica que diversos mecanismos são ativados em resposta ao RRD de forma a promover a sobrevivência das células retinianas através de respostas celulares complexas, como por exemplo, a ativação da via de sinalização HIF-1. Na terceira tarefa, aplicou-se um método quantitativo label-free (LFQ) para analisar o proteoma do vítreo na PDR e na forma seca da AMD (dry AMD). DR e AMD são as principais causas de deficiência visual e cegueira em indivíduos com idade igual ou superior a 50 anos, em países industrializados ou de rendimento médio. Embora as terapias direcionadas à inibição do fator de crescimento vascular (VEGF) tenham melhorado o tratamento da forma neovascular da AMD (nAMD) e da PDR, neste momento não existem opções terapêuticas para a AMD seca. Portanto, a proteómica quantitativa pode contribuir para o conhecimento dos mecanismos biológicos subjacentes a estas patologias e a encontrar novos potenciais biomarcadores e/ou alvos terapêuticos. Com esta finalidade, o proteoma do vítreo recolhido de doentes com PDR (n=4) foi comparado com o de doentes com AMD seca (n=4) e com membranas epiretinianas (ERM) (n=4) utilizando um método LFQ, que combina o fracionamento “curto” por eletroforese desnaturante em gel de poliacrilamida e análise por LC-MS/MS. Foram identificadas 680 proteínas, das quais 586 foram identificadas com recurso ao software MASCOT e 580 com o software MaxQuant. Posteriormente, foram realizados testes post hoc, métodos hierárquicos para análise de agrupamento de dados e testes t múltiplos para diferenciar os três grupos de doenças em termos de expressão proteica com base na sua intensidade. Os testes post hoc revelaram que 96 proteínas são capazes de diferenciar entre os diferentes grupos, enquanto 118 proteínas (17 para sobreexpressas e 101 subexpressas) foram identificados como diferencialmente expressas na PDR em comparação com doentes com ERM e 95 proteínas (10 sobreexpressas e 85 subexpressas) em comparação com os doentes com AMD seca. A análise de enriquecimento funcional indica que estas proteínas subexpressas estão correlacionadas com vias/processos biológicos, como reorganização da matriz extracelular (ECM), desgranulação das plaquetas, digestão intracelular nos lisossomas, adesão celular e desenvolvimento do sistema nervoso central. Por sua vez, os resultados indicam que o vítreo de doentes com PDR é enriquecido em mediadores dos sistemas de complemento e coagulação e da fase aguda da inflamação, reforçando o papel destas vias na sua patogénese. Por último, alguns potenciais biomarcadores foram selecionados de acordo com os resultados obtidos na quantificação do proteoma do vítreo por iTRAQ e LFQ e validados pela monitorização de múltiplas reações (MRM) num maior número de amostras de vítreo. Assim, desenvolveu-se um método de MRM scheduled para a análise de 35 proteínas, em amostras de vítreo recolhidas de doentes com ERM (n=21), DR/PDR (n=20), AMD (n=11) e RRD (com e sem vitreorretinopatia proliferativa) (n=13). Desta forma, 26 proteínas demostraram potencial para discriminar entre os diferentes grupos de doenças de acordo com os resultados obtidos no MRM e as respectivas curvas ROC (receiver operating characteristic curve). Componentes das cascatas do complemento e coagulação (C6, C8B, protrombina), proteínas de fase aguda (alfa-1-antiquimotripsina), moléculas de adesão (proteína galectina-3), componentes da ECM (opticina) e biomarcadores de neurodegeneração (beta-amilóide, proteína tipo-precursora amilóide 2) destacam-se como os biomarcadores mais eficientes para discriminar entre os diferentes grupos de doenças. Em conclusão, foram desenvolvidas e implementadas diversas estratégias para a preparação e análise do proteoma do vítreo em diferentes doenças vitreorretinianas, baseadas na separação por 2DE ou por LC. Em relação ao método baseado na separação em gel, um modelo matemático criado por ANN permitiu o desenvolvimento de um protocolo altamente eficiente para a análise de elevada resolução do proteoma do vítreo por 2DE, o que pode ser vantajoso para a detecção de proteoformas específicas, incluindo diferentes isoformas e proteínas com modificações pós-traducionais. Por outro lado, métodos de alta produtividade, como iTRAQ e LFQ, proporcionaram uma análise mais aprofundada do proteoma do vítreo. Nestas técnicas, foram identificadas 1030 proteínas pela técnica de iTRAQ e 680 por LFQ, sendo que algumas não tinham sido identificadas anteriormente. Ainda mais relevante é o fato de que a análise do proteoma do vítreo, com base nestas técnicas, forneceu novos perspetivas sobre a patogénese do RRD, PDR e AMD. Além disso, estes estudos forneceram informações fundamentais sobre potenciais biomarcadores, o que permitiu a validação de 26 proteínas por MRM. No entanto, deve ter-se em consideração que os biomarcadores encontrados no vítreo não podem ser utilizados para um diagnóstico médico regular, devido ao modo de recolha invasivo deste tipo de amostras. Porém, estes podem ser candidatos a novos alvos farmacêuticos e, quando as amostras são obtidas como parte da rotina clínica, podem ser usados para o prognóstico da evolução da doença e/ou para prever a resposta adequada ao tratamento.
(9520208), Lakshya Mittal. "EFFICIENT AND ECONOMICAL ELECTROCHEMOTHERAPY TREATMENTS FOR TRIPLE NEGATIVE BREAST CANCER: AN IN VITRO MODEL STUDY." Thesis, 2020.
Find full textWith 2.1 million new cases, breast cancer is the most common cancer in women. Triple negative breast cancer (TNBC), which is 15-20% of these breast cancer cases is clinically negative for expression of estrogen and progesterone receptors (ER/PR) and human epidermal growth factor receptor 2 (HER2) receptors. It is characterized by its unique molecular profile, aggressive behavior, distinct patterns of metastasis, and lack of targeted therapies. TNBCs utilize glycolysis for growth, proliferation, invasiveness, chemotherapeutic resistance and hence has poor therapeutic response. There is an urgent need for novel/alternate therapeutic strategies beyond current standard of treatment for this subset of high-risk patients. Electrical pulse-based chemotherapy, known as electrochemotherapy (ECT) could be a viable option for TNBC therapy. ECT involves the local application of precisely controlled electrical pulses to reversibly permeabilize the cell membrane for enhanced uptake. ECT can increase the cytotoxicity of the chemotherapeutics up-to 1000 times, facilitating a potent local cytotoxic effect.
The high cost and severe side-effects of conventional chemotherapeutics motivate the application of effective natural compounds. Combining electrical pulses with natural compounds will enhance the treatment efficacy. This dissertation focuses on curcumin, the yellow pigment of natural herb turmeric, that has been used for over 5000 years for its excellent anticancer properties. Previous studies have demonstrated the effectiveness of curcumin for treating multiple cancers, including TNBC, with limited side effects. The potency of curcumin can be enhanced further by combining it with ECT to provide an attractive and cost-effective alternative for TNBC treatment.
Towards this we studied the effect of ECT with curcumin on MDA-MB-231 cell line, a human adenocarcinoma epithelial TNBC cell line. We performed various assays, including cell viability, colony forming, cell cycle, apoptosis, H2O2 reactive oxygen species (ROS), immunoblotting, real time quantitative PCR (qPCR), and cellular metabolites detection to study the impact of ECT with curcumin on MDA-MB-231 cells. In addition, to better understand the underlying mechanisms, we used high throughput, label-free quantitative proteomics. While several studies have attempted to define the mechanism of action of curcumin on cancer cells, little is known on the action mechanism of the curcumin delivered with electrical pulses. This work unravels the molecular mechanism behind the enhanced effects observed under the ECT-based curcumin therapy in TNBC cells, employing a high-throughput, quantitative, label-free mass spectroscopy-based proteomics approach. The proteomics approach provides information on the thousands of cellular proteins involved in the cellular process, allowing a comprehensive understanding of the electro-curcumin-therapy mechanism. Similar studies were also performed for ECT with cisplatin to compare the efficacy of the electro-curcumin-therapy to the standard stand-alone cisplatin-based therapy.
Our results revealed a switch in the metabolism from glycolysis to mitochondrial metabolic pathways. This metabolic switch caused an excessive production of H2O2 ROS to inflict apoptotic cell death in MDA-MB-231 cells, demonstrating the potency of this ECT based curcumin therapy. These results encourage further studies to extend the application of ECT for clinical practice.