Relevant bibliographies by topics / 2D-DIGE ( Two Dimensional Differential In Gel Electrophoresis)

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Academic literature on the topic '2D-DIGE ( Two Dimensional Differential In Gel Electrophoresis)'

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Published: 10 March 2023

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Journal articles on the topic "2D-DIGE ( Two Dimensional Differential In Gel Electrophoresis)"

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Ercan, Huriye, Ulrike Resch, Felicia Hsu, Goran Mitulovic, Andrea Bileck, Christopher Gerner, Jae-Won Yang, Margarethe Geiger, Ingrid Miller, and Maria Zellner. "A Practical and Analytical Comparative Study of Gel-Based Top-Down and Gel-Free Bottom-Up Proteomics Including Unbiased Proteoform Detection." Cells 12, no. 5 (February 26, 2023): 747. http://dx.doi.org/10.3390/cells12050747.

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Proteomics is an indispensable analytical technique to study the dynamic functioning of biological systems via different proteins and their proteoforms. In recent years, bottom-up shotgun has become more popular than gel-based top-down proteomics. The current study examined the qualitative and quantitative performance of these two fundamentally different methodologies by the parallel measurement of six technical and three biological replicates of the human prostate carcinoma cell line DU145 using its two most common standard techniques, label-free shotgun and two-dimensional differential gel electrophoresis (2D-DIGE). The analytical strengths and limitations were explored, finally focusing on the unbiased detection of proteoforms, exemplified by discovering a prostate cancer-related cleavage product of pyruvate kinase M2. Label-free shotgun proteomics quickly yields an annotated proteome but with reduced robustness, as determined by three times higher technical variation compared to 2D-DIGE. At a glance, only 2D-DIGE top-down analysis provided valuable, direct stoichiometric qualitative and quantitative information from proteins to their proteoforms, even with unexpected post-translational modifications, such as proteolytic cleavage and phosphorylation. However, the 2D-DIGE technology required almost 20 times as much time per protein/proteoform characterization with more manual work. Ultimately, this work should expose both techniques’ orthogonality with their different contents of data output to elucidate biological questions.
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Oliva, Karen, Gillian Barker, Clyde Riley, Mark J. Bailey, Michael Permezel, Gregory E. Rice, and Martha Lappas. "The effect of pre-existing maternal obesity on the placental proteome: two-dimensional difference gel electrophoresis coupled with mass spectrometry." Journal of Molecular Endocrinology 48, no. 2 (February 1, 2012): 139–49. http://dx.doi.org/10.1530/jme-11-0123.

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Our aim was to study the protein expression profiles of placenta obtained from lean and obese pregnant women with normal glucose tolerance at the time of term Caesarean section. We used two-dimensional difference gel electrophoresis (2D-DIGE), utilising narrow-range immobilised pH gradient strips that encompassed the broad pH range of 4–5 and 5–6, followed by MALDI-TOF mass spectrometry of selected protein spots. Western blot and quantitative RT-PCR (qRT-PCR) analyses were performed to validate representative findings from the 2D-DIGE analysis. Eight proteins were altered (six down-regulated and two up-regulated on obese placentas). Annexin A5 (ANXA5), ATP synthase subunit beta, mitochondria (ATPB), brain acid soluble protein 1 (BASP1), ferritin light chain (FTL), heterogeneous nuclear ribonucleoprotein C (HNRPC) and vimentin (VIME) were all lower in obese patients. Alpha-1-antitrypsin (A1AT) and stress-70 protein, mitochondrial (GRP75) were higher in obese patients. Western blot analysis of ANXA5, ATPB, FTL, VIME, A1AT and GRP75 confirmed the findings from the 2D-DIGE analysis. For brain acid soluble protein 1 and HNRPC, qRT-PCR analysis also confirmed the findings from the 2D-DIGE analysis. Immunohistochemical analysis was also used to determine the localisation of the proteins in human placenta. In conclusion, proteomic analysis of placenta reveals differential expression of several proteins in patients with pre-existing obesity. These proteins are implicated in a variety of cellular functions such as regulation of growth, cytoskeletal structure, oxidative stress, inflammation, coagulation and apoptosis. These disturbances may have significant implications for fetal growth and development.
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Tajima, Takashi, Fusako Kito, Akihiko Yoshida, Akira Kawai, and Tadashi Kondo. "Calreticulin as A Novel Potential Metastasis-Associated Protein in Myxoid Liposarcoma, as Revealed by Two-Dimensional Difference Gel Electrophoresis." Proteomes 7, no. 2 (April 10, 2019): 13. http://dx.doi.org/10.3390/proteomes7020013.

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Myxoid liposarcoma (MLS) is a mesenchymal malignancy. To identify innovate seeds for clinical applications, we examined the proteomes of primary tumor tissues from 10 patients with MLS with different statuses of postoperative metastasis. The protein expression profiles of tumor tissues were created, and proteins with differential expression associated with postoperative metastasis were identified by two-dimensional difference gel electrophoresis (2D-DIGE) and mass spectrometry. The validation was performed using specific antibodies and in vitro analyses. Using 2D-DIGE, we observed 1726 protein species and identified proteins with unique expression levels in metastatic MLS. We focused on the overexpression of calreticulin in metastatic MLS. The higher expression of calreticulin was confirmed by Western blotting, and gene silencing assays demonstrated that reduced expression of calreticulin inhibited cell growth and invasion. Our findings suggested the important roles of calreticulin in MLS metastasis and supported its potential utility as a prognostic biomarker in MLS. Further investigations of the functional properties of calreticulin and other proteins identified in this study will improve our understanding of the biology of MLS and facilitate novel clinical applications.
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Di Carli, Mariasole, Anita Zamboni, Mario Enrico Pè, Mario Pezzotti, Kathryn S. Lilley, Eugenio Benvenuto, and Angiola Desiderio. "Two-Dimensional Differential in Gel Electrophoresis (2D-DIGE) Analysis of Grape Berry Proteome during Postharvest Withering." Journal of Proteome Research 10, no. 2 (February 4, 2011): 429–46. http://dx.doi.org/10.1021/pr1005313.

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Dhingra, V., Q. Li, A. B. Allison, D. E. Stallknecht, and Z. F. Fu. "Proteomic Profiling and Neurodegeneration in West-Nile-Virus-Infected Neurons." Journal of Biomedicine and Biotechnology 2005, no. 3 (2005): 271–79. http://dx.doi.org/10.1155/jbb.2005.271.

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West Nile virus, a mosquito-borne flavivirus, is a human, equine, and avian pathogen. High-resolution two-dimensional differential-gel electrophoresis (2D-DIGE) was used to characterize protein expression in primary rat neurons and to examine the proteomic profiling to understand the pathogenesis of West-Nile-associated meningoencephalitis. Three pH ranges, 3–10, 4–7, and 5–6, were used to analyze the protein spots. The proteins are labeled with fluorescent dyes Cy3 and Cy5 before being separated on the basis of charge and size respectively on a two-dimensional platform. About 55 proteins showed altered expression levels. These were then subsequently digested and identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis using peptide mass fingerprinting and database searching. These cellular proteins could represent distinct roles during infection related to apoptosis. Our findings show that two-dimensional differential gel electrophoresis combined with mass spectrometry is a powerful approach that permits the identification of proteins whose expression was altered due to West Nile virus infection.
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Orenes-Piñero, Esteban, Marta Cortón, Pilar González-Peramato, Ferrán Algaba, Ignacio Casal, Alvaro Serrano, and Marta Sánchez-Carbayo. "Searching Urinary Tumor Markers for Bladder Cancer Using a Two-Dimensional Differential Gel Electrophoresis (2D-DIGE) Approach." Journal of Proteome Research 6, no. 11 (November 2007): 4440–48. http://dx.doi.org/10.1021/pr070368w.

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Wang, X., A. Kaya, and E. Memili. "195 SPERMATOZOAL PROTEIN MARKERS FOR ANGUS BULL FERTILITY." Reproduction, Fertility and Development 23, no. 1 (2011): 198. http://dx.doi.org/10.1071/rdv23n1ab195.

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Fertility is one of the most economically important traits controlling animal reproduction. Despite its significant economic impact, there are no reliable markers to predict semen quality. The objective of this study was to identify spermatozoal proteins associated with bull fertility, the ability of the sperm to fertilize the oocyte and support embryonic development. To accomplish our objectives, we isolated total spermatozoal proteins from 4 Angus bulls with different fertility phenotypes. Next, differentially expressed proteins were determined using two-dimensional differential in-gel electrophoresis (2D-DIGE), followed by sequencing of the most differentially expressed proteins. Immunoblotting experiments were conducted to confirm expression of key proteins detected by 2D-DIGE. Our results from 2D-DIGE experiments showed approximately 2000 detectable spermatozoal proteins. Of these comprehensive lists of proteins, we identified 80 of the proteins with the highest differential expression in spermatozoa from high- and low-fertility bulls. Diverse sets of differentially expressed proteins known to play roles in sperm motility, metabolism, and cell morphology were identified. These proteins included outer dense fibre of sperm tails 2 and manganous superoxide, heat shock protein, tubulins, α-enolase, and acrosomal vesicle protein-1. Expression profiles of outer dense fibre of sperm tails 2 and manganous superoxide dismutase were confirmed using immunoblotting. The findings are significant because they help us understand the fundamental biology of the male gamete and early development. In addition, the identified proteins can be used as molecular markers to predict bull fertility, an economically important trait. Funded in part by the Mississippi Agricultural and Forestry Experiment Station, American Angus Association, and Alta Genetics, Inc.
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Martínez-Gomariz, M., M. L. HernÁez, D. GutiÉrrez, P. XimÉnez-EmbÚn, and G. PrÉstamo. "Proteomic Analysis by Two-Dimensional Differential Gel Electrophoresis (2D DIGE) of a High-Pressure Effect in Bacillus cereus." Journal of Agricultural and Food Chemistry 57, no. 9 (May 13, 2009): 3543–49. http://dx.doi.org/10.1021/jf803272a.

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Subong, Bryan John J., Arturo O. Lluisma, Rhodora V. Azanza, and Lilibeth A. Salvador-Reyes. "Differentiating Two Closely Related Alexandrium Species Using Comparative Quantitative Proteomics." Toxins 13, no. 1 (December 23, 2020): 7. http://dx.doi.org/10.3390/toxins13010007.

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Alexandrium minutum and Alexandrium tamutum are two closely related harmful algal bloom (HAB)-causing species with different toxicity. Using isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics and two-dimensional differential gel electrophoresis (2D-DIGE), a comprehensive characterization of the proteomes of A. minutum and A. tamutum was performed to identify the cellular and molecular underpinnings for the dissimilarity between these two species. A total of 1436 proteins and 420 protein spots were identified using iTRAQ-based proteomics and 2D-DIGE, respectively. Both methods revealed little difference (10–12%) between the proteomes of A. minutum and A. tamutum, highlighting that these organisms follow similar cellular and biological processes at the exponential stage. Toxin biosynthetic enzymes were present in both organisms. However, the gonyautoxin-producing A. minutum showed higher levels of osmotic growth proteins, Zn-dependent alcohol dehydrogenase and type-I polyketide synthase compared to the non-toxic A. tamutum. Further, A. tamutum had increased S-adenosylmethionine transferase that may potentially have a negative feedback mechanism to toxin biosynthesis. The complementary proteomics approach provided insights into the biochemistry of these two closely related HAB-causing organisms. The identified proteins are potential biomarkers for organismal toxicity and could be explored for environmental monitoring.
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Gemoll, Timo, Svitlana Rozanova, Christian Röder, Sonja Hartwig, Holger Kalthoff, Stefan Lehr, Abdou ElSharawy, and Jens Habermann. "Protein Profiling of Serum Extracellular Vesicles Reveals Qualitative and Quantitative Differences after Differential Ultracentrifugation and ExoQuick™ Isolation." Journal of Clinical Medicine 9, no. 5 (May 12, 2020): 1429. http://dx.doi.org/10.3390/jcm9051429.

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Solid tumor biopsies are the current standard for precision medicine. However, the procedure is invasive and not always feasible. In contrast, liquid biopsies, such as serum enriched for extracellular vesicles (EVs) represent a non-invasive source of cancer biomarkers. In this study, we compared two EV isolation methods in the context of the protein biomarker detection in inflammatory bowel disease (IBD) and colorectal cancer (CRC). Using serum samples of a healthy cohort as well as CRC and IBD patients, EVs were isolated by ultracentrifugation and ExoQuick™ in parallel. EV associated protein profiles were compared by multiplex-fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) and subsequent identification by mass spectrometry. Validation of gelsolin (GSN) was performed using fluorescence-quantitative western blot. 2D-DIGE resolved 936 protein spots in all serum-enriched EVs isolated by ultracentrifugation or ExoQuick™. Hereof, 93 spots were differently expressed between isolation approaches. Higher levels of GSN in EVs obtained with ExoQuick™ compared to ultracentrifugation were confirmed by western blot (p = 0.0006). Although patient groups were distinguishable after both EV isolation approaches, sample preparation strongly influences EVs’ protein profile and thus impacts on inter-study reproducibility, biomarker identification and validation. The results stress the need for strict SOPs in EV research before clinical implementation can be reached.
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Dissertations / Theses on the topic "2D-DIGE ( Two Dimensional Differential In Gel Electrophoresis)"

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Guterres, Sheila Barreto. "Busca de biomarcadores para esquizofrenia em plaquetas utilizando eletroforese diferencial em gel bidimensional (2D-DIGE) e espectrometria de massas." Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/75/75132/tde-16112011-150931/.

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A esquizofrenia é uma doença crônica, grave e incapacitante que afeta cerca 24 milhões de pessoas em âmbito mundial. É caracterizada por uma desorganização no pensamento que prejudica a funcionalidade do indivíduo. Existem intervenções que são efetivas e contribuem para a diminuição da prevalência do transtorno, pois ajudam o portador a levar uma vida produtiva e integrada à sociedade, porém devem ser ministradas nos estágios iniciais da doença. No entanto, existe uma grande dificuldade em se diagnosticar a esquizofrenia precocemente devido a sua complexidade e às sutilezas dos seus sintomas apresentados antes do surgimento da psicose. O cérebro não é acessível a exames invasivos in vivo e por esse motivo a exploração de fluidos periféricos é de grande importância. As plaquetas e neurônios serotonérgicos possuem características bioquímicas e morfológicas em comum que possibilitam a comparação entre a estrutura e a função de ambos e, por causa dessa similaridade, muitos trabalhos utilizam plaquetas como modelo para o estudo de doenças neuropsiquiátricas, inclusive a esquizofrenia. A detecção precoce da esquizofrenia é um objeto de investigação atual e relevante não somente para revolucionar os meios atuais de diagnóstico, mas também para desenvolver novos tratamentos aplicados aos estágios iniciais da doença, diferenciar os subgrupos de doentes e monitorar as intervenções preventivas. A proposta do presente trabalho é fazer o estudo da expressão de proteínas em plaquetas de pacientes esquizofrênicos e controles com o objetivo de identificar proteínas candidatas a biomarcadores utilizando técnicas proteômicas quantitativas e confiáveis, como 2D-DIGE e a espectrometria de massas.
Schizophrenia is a disabling, serious, and chronic illness, which affects about 24 million people worldwide. It is characterized by a severe disorganization of the thoughts that harms the social life of patients becoming them dependent of the family and/or government. There are effective treatments that contribute to decrease the prevalence of the disorder because they improve the life and social conditions of the patients, but they are only advantageous if the intervention is made in the early stages of the disease. It is difficult to obtain early diagnosis due to the complexity of the disease and its insidious symptoms before the beginning of the psychosis. The brain is not easily accessed in vivo and, because of this, it is very important to study the peripheral tissues like blood, which makes the use of the platelets very interesting. Furthermore, platelets and serotonergic neurons share biochemical and morphological characteristics that allows the comparison between structure and function of both. From these similarities many authors has used platelets as a neuron model to study many neurodegenerative diseases including schizophrenia. The early detection of schizophrenia is a current and suitable goal, not only to improve the early diagnosis but also to develop new treatments, differentiate the subtypes, and monitor the preventive interventions. The purpose of this project is to do a comparative screening of expressed proteins in platelets from schizophrenics and controls with the objective of finding differently expressed proteins that could be candidates to biomarkers using 2D-DIGE and mass spectrometry.
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Kultima, Kim. "Transcriptomics and Proteomics Applied to Developmental Toxicology." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7921.

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Marroncini, Giada. "Ambiente e Genetica: due attori nello sviluppo e progressione del danno epatico." Doctoral thesis, 2018. http://hdl.handle.net/2158/1125023.

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Lo scopo di questo studio è stato quello di indagare i meccanismi dello sviluppo della malattia epatica analizzandone i vari steps che culminano nella cirrosi e nell` epatocarcinoma. Avendo a disposizioni alcuni dati preliminari che individuavano la sirtuina 1 come possibile regolatore della fibrogenesi epatica il mio lavoro ha cercato di approfondire tale argomento. Ho modulato l’attività di questo enzima attraverso l’uso di farmaci inibitori selettivi (EX527) e attivatori (Resveratrolo) per valutare il suo ruolo nella regolazione delle cellule stellate epatiche mediante l’uso di linee cellulari primarie di HSC e su modelli murini di danno indotto da “Bile Duct Ligation” (BDL) e da NASH. Allo stesso tempo ho cercato di analizzare più da vicino le fasi finali della progressione della steatosi, studiando l’inquinamento ambientale come possibile fattore in grado di portare ad un peggioramento del quadro clinico della NASH a cirrosi e ad HCC. Attraverso analisi effettuate su un modello murino di NASH su cui abbiamo anche eseguito un impianto ortotopico singenico di cellule di epatocarcinoma, abbiamo valutato la tossicità epatica del particolato atmosferico (PM10) e la sua capacità in vivo di favorire la progressione della steatoepatite e creare un ambiente protumorale. Aim of the study was to evaluate the mechanisms involved in liver disease, by the pre-clinical analysis of different pathogenetic steps. In particular the study analyze the role of the protein sirtuin 1, as a possible modulator of liver fibrosis and the toxic role played by the atmospheric particles PM 10. If about the relationship between sirtuin 1 and liver disease, literature present many evidences, on the role of PM10 as a toxic agent for the liver, this is an original topic for hepatology research.
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Book chapters on the topic "2D-DIGE ( Two Dimensional Differential In Gel Electrophoresis)"

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Meleady, Paula. "Two-Dimensional Gel Electrophoresis and 2D-DIGE." In Methods in Molecular Biology, 3–15. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2831-7_1.

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Meleady, Paula. "Two-Dimensional Gel Electrophoresis and 2D-DIGE." In Methods in Molecular Biology, 3–14. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7268-5_1.

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Aquino, Adriano, Paul C. Guest, and Daniel Martins-de-Souza. "Simultaneous Two-Dimensional Difference Gel Electrophoresis (2D-DIGE) Analysis of Two Distinct Proteomes." In Multiplex Biomarker Techniques, 205–12. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6730-8_17.

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Hariharan, Deepak, Mark E. Weeks, and Tatjana Crnogorac-Jurcevic. "Application of Proteomics in Cancer Gene Profiling: Two-Dimensional Difference in Gel Electrophoresis (2D-DIGE)." In Methods in Molecular Biology, 197–211. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-59745-545-9_11.

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Guest, Paul C. "A Two-Dimensional Difference Gel Electrophoresis (2D-DIGE) Protocol for Studies of Neural Precursor Cells." In Advances in Experimental Medicine and Biology, 183–91. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-52479-5_14.

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Minden, Jonathan S. "Two-Dimensional Difference Gel Electrophoresis (2D DIGE)." In Methods in Cell Biology, 111–41. Elsevier, 2012. http://dx.doi.org/10.1016/b978-0-12-405914-6.00006-8.

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"2D-DIGE A Powerful Tool for Proteome Analysis." In Protocols used in Molecular Biology, edited by Sudhir K. Shekhar, Jai Godheja, and Dinesh Raj Modi, 67–73. BENTHAM SCIENCE PUBLISHERS, 2020. http://dx.doi.org/10.2174/9789811439315120010010.

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In the recent past, two dimensional gel electrophoresis has emerged as a powerful molecular biology tool for the comparative expression profiling of complex protein sample. It involves the separation as well as the resolution of diverse proteins sample on the basis of isoelectric points and molecular mass of protein in two dimension ways. In this way, it reflects the view of overall proteome status including differentiation in protein expression levels, post-translational modifications etc. Moreover, this allows the identification of novel biological signatures, which may give a particular identity of pathological background to cells or tissues associated with various types of cancers and neurological disorders. Therefore, by utilizing such tools, one can clearly investigate and compare the effects of particular drugs on cells of tissues and also one can analyze the effects of disease on the basis of variations in protein expression profile at broad spectrum. Recently, to get more error-less and accurate proteome profile, conventional 2-D gel electrophoresis has been enhanced with the inclusion of different types of protein labeling dyes which enables a more comparative analysis of diverse protein sample in a single 2-D gel. In this advanced technique (2-D-DIGE), protein samples are labeled with three different types of CyDyes (Cy2, Cy3, and Cy5) separately and combined and further resolved on the same gel. This will facilitate the more accurate spot matching on a single gel platform and will also minimize the experimental variations as commonly reported in the conventional 2D-gel electrophoresis. Therefore, in the present proteomic research era, 2D-DIGE has proved to be an extremely powerful tool with great sensitivity for up to 125 ng of proteins in clinical research volubility especially, neurological and cancer related disorders.
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Conference papers on the topic "2D-DIGE ( Two Dimensional Differential In Gel Electrophoresis)"

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Kikuchi, Ryoko, Kei-ichi Iwaya, and Osamu Matsubara. "Abstract 3948: Proteome analysis of ovarian cancer cell lines under hypoxic conditon by two-dimensional difference gel electrophoresis (2D-DIGE)." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-3948.

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