The evolution of two-dimensional gel electrophoresis - from proteomics to emerging alternative applications

Lee, Pey Yee; Saraygord‐Afshari, Neda; Low, Teck Yew

doi:10.1016/j.chroma.2019.460763

Cited by 74 publications

(32 citation statements)

References 89 publications

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“…Those two proteomic methods represent different methodological approaches and deliver complementary results due to different physicochemical properties of proteins [21,22]. The 2DE allows for separation and detection of mostly soluble proteins with a molecular weight between 150 and 10 kDa.…”

Section: Resultsmentioning

confidence: 99%

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Urinary Proteome of Newborn Calves—New Potential in Non-Invasive Neonatal Diagnostic

Dratwa-Chałupnik

Wojdyła

Ożgo

et al. 2020

Animals

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Urine is a biological diagnostic material suitable not only for the analysis of kidney and urinary tract functions but also the function of other tissues and organs. The urine proteome of adult mammals differs from the urine proteome of neonatal ones. The establishment of urinary protein maps of healthy newborn calves is important for diagnosing and monitoring the progression of various diseases. The experiment was carried out on a Polish-Friesian var. of Black-and-White male calves in the sixth day of postnatal life. The two proteomics approaches used for separation and identification of urinary proteins were: 2-DE with MALDI-TOF-TOF-MS/MS and 1-DE with LC-MS/MS. This resulted in the identification of 692 urinary proteins. The majority of them were classified as extracellular proteins (40.32%), as well as proteins involved in regulation of major cellular processes (31.07%). We have observed the presence of unique proteins associated with embryonic (ameloblastin, alpha-fetoprotein, Delta-like protein, embryo-specific fibronectin 1 transcript variant, Indian hedgehog homolog) and kidney development (angiotensin-converting enzyme, angiotensinogen, aquaporin-1, calbindin, glypican 3, nidogen 1, pro-cathepsin H). Additionally, proteins involved in the renal regulation of water and electrolyte balance (angiotensinogen, angiotensin-converting enzyme, aquaporin-1, ezrin, uromodulin) were detected. Presented in the current study 1-D and 2-D urinary proteomic maps are the basis for the identification and detection of prognostic biomarkers important for defining a calf’s health status.

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Section: Resultsmentioning

confidence: 99%

“…A small amount of common proteins for three different types of urine samples may result from various preparation of samples for proteomic analyses and the proteomic techniques used [ 21 , 22 ]. In addition, differences in the protein composition between animal breeds and species are observed.…”

Section: Discussionmentioning

confidence: 99%

Urinary Proteome of Newborn Calves—New Potential in Non-Invasive Neonatal Diagnostic

Dratwa-Chałupnik

Wojdyła

Ożgo

et al. 2020

Animals

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“…Although gel-based proteomes are laboring and time-consuming, images of 2D-GE gels can be compared so as to quantify each protein spot from different samples, and these protein spots can subsequently be excised, sequenced, and identified with MS, especially LC-MS/MS ( Lee et al, 2019 ). Each protein has multiple forms as a result of genetic variations, splicing, truncation, degradation, and posttranslational modifications; therefore, innovated proteomic technologies such as MS-based shotgun proteomics ( Lee et al, 2018 ) should be employed to explore more virulence and resistance-associated factors in V. parahaemolyticus .…”

Section: Discussionmentioning

confidence: 99%

Comparative Proteomics and Secretomics Revealed Virulence and Antibiotic Resistance-Associated Factors in Vibrio parahaemolyticus Recovered From Commonly Consumed Aquatic Products

et al. 2020

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Vibrio parahaemolyticus is a seafoodborne pathogen that can cause severe gastroenteritis and septicemia diseases in humans and even death. The emergence of multidrug-resistant V. parahaemolyticus leads to difficulties and rising costs of medical treatment. The bacterium of environmental origins containing no major virulence genes (tdh and trh) has been reported to be associated with infectious diarrhea disease as well. Identification of risk factors in V. parahaemolyticus is imperative for assuming food safety. In this study, we obtained secretomic and proteomic profiles of V. parahaemolyticus isolated from 12 species of commonly consumed aquatic products and identified candidate protein spots by using two-dimensional gel electrophoresis and liquid chromatography tandem mass spectrometry techniques. A total of 11 common and 28 differential extracellular proteins were found from distinct secretomic profiles, including eight virulence-associated proteins: outer membrane channel TolC, maltoporin, elongation factor Tu, enolase, transaldolase, flagellin C, polar flagellin B/D, and superoxide dismutase, as well as five antimicrobial and/or heavy metal resistanceassociated ABC transporter proteins. Comparison of proteomic profiles derived from the 12 V. parahaemolyticus isolates also revealed five intracellular virulence-related proteins, including aldehyde-alcohol dehydrogenase, outer membrane protein A, alkyl hydroperoxide reductase C, phosphoenolpyruvate-protein phosphotransferase, and phosphoglycerate kinase. Additionally, our data indicated that aquatic product matrices significantly altered proteomic profiles of the V. parahaemolyticus isolates with a number of differentially expressed proteins identified. The results in this study meet the increasing need for novel diagnosis candidates of the leading seafoodborne pathogen worldwide.

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“…Technical developments in proteomics have progressed for the purpose of identifying all proteins expressed in a cell line, tissue, or body. Two-dimensional gel electrophoresis can reveal many proteins present in cells and tissues at any given time [ 62 , 63 , 64 ].…”

Section: Clinical Applications Of Mass Spectrometry Using Maldi-tomentioning

confidence: 99%

“…As one of the key concepts in the post-genome era, the proteome has been investigated, and disease-marker searches with gel-based and gel-free proteome analysis techniques are being performed widely. The results of proteome research have attracted attention because they are connected directly with diagnostic application and development of therapeutic targets [ 62 , 63 , 64 ].…”

Section: Clinical Applications Of Mass Spectrometry Using Maldi-tomentioning

confidence: 99%

Proteome Analysis of Molecular Events in Oral Pathogenesis and Virus: A Review with a Particular Focus on Periodontitis

Tsuchida

2020

IJMS

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Some systemic diseases are unquestionably related to periodontal health, as periodontal disease can be an extension or manifestation of the primary disease process. One example is spontaneous gingival bleeding, resulting from anticoagulant treatment for cardiac diseases. One important aspect of periodontal therapy is the care of patients with poorly controlled disease who require surgery, such as patients with uncontrolled diabetes. We reviewed research on biomarkers and molecular events for various diseases, as well as candidate markers of periodontal disease. Content of this review: (1) Introduction, (2) Periodontal disease, (3) Bacterial and viral pathogens associated with periodontal disease, (4) Stem cells in periodontal tissue, (5) Clinical applications of mass spectrometry using MALDI-TOF-MS and LC-MS/MS-based proteomic analyses, (6) Proteome analysis of molecular events in oral pathogenesis of virus in GCF, saliva, and other oral Components in periodontal disease, (7) Outlook for the future and (8) Conclusions. This review discusses proteome analysis of molecular events in the pathogenesis of oral diseases and viruses, and has a particular focus on periodontitis.

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The evolution of two-dimensional gel electrophoresis - from proteomics to emerging alternative applications

Cited by 74 publications

References 89 publications

Urinary Proteome of Newborn Calves—New Potential in Non-Invasive Neonatal Diagnostic

Urinary Proteome of Newborn Calves—New Potential in Non-Invasive Neonatal Diagnostic

Comparative Proteomics and Secretomics Revealed Virulence and Antibiotic Resistance-Associated Factors in Vibrio parahaemolyticus Recovered From Commonly Consumed Aquatic Products

Proteome Analysis of Molecular Events in Oral Pathogenesis and Virus: A Review with a Particular Focus on Periodontitis

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