1
|
Li FG, Shi XY, Yang L, Lu X, Qi Y, Li P, Yang H, Gao W. Quantitative proteomics based bioactive proteins discovery and quality control of medicinal leeches. JOURNAL OF ETHNOPHARMACOLOGY 2024; 319:117117. [PMID: 37659761 DOI: 10.1016/j.jep.2023.117117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/04/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Leech, a classical traditional Chinese medicine for promoting blood circulation and removing blood stasis, is mainly used in the clinical treatment of cardiovascular and cerebrovascular diseases. The discovery of activity proteins or peptides in the dead and dried medicinal leech is an important task with great challenges. AIM OF THE STUDY The aim of this study was to provide a basic proteome profile and help further discover active proteins and quality control for medicinal leeches, which would also provide insight into the research of animal medicines. MATERIALS AND METHODS Seventeen batches of dried medicinal leeches covering three species were collected from medicinal markets, which were authenticated by DNA barcoding. Then the proteome of different species leeches was profiled to reveal the significantly different proteins using label-free proteomics. The characteristic peptides were screened out based on biological pathways analysis, which were further absolutely quantified using the developed stable isotope-labeled based parallel reaction monitoring method. RESULTS Seventeen batches of leech materials were Whitmania pigra Whitman (WP), Whitmania laevis Whitman (WL) and Poecilobdella manillensis Lesson (PM), respectively. A total of 1,035 proteins (452 in WP, 425 in WL and 158 in PM) were identified. Among them, 90 overlapping proteins were mainly concentrated in diverse metabolic pathways and primarily localized in the cytoplasm and mitochondrial inner membrane, which mainly related to ATP binding, catalytic activity and structural molecular activity. In total of 51 uniquely expressed proteins (21 in WP, 23 in WL and 7 in PM), associated with multiple key signaling pathways, including Rap1, cGMP-PKG, PI3K-Akt, Wnt and HIF-1, etc., relevant to treating cardiovascular diseases, diabetes, cancer and even a variety of neurodegenerative diseases. Three proteins with potential bioactivities, including Neurohemerythrin, Hirudin and Eglin C, were selected as the quality makers and then quantified based on the characteristic peptides. CONCLUSIONS This work profiled the proteome of three species of leeches, and addressed potential active proteins of the medicinal leech, which would help to provide the potential molecular mechanisms involved in disease treatment. The proteomics-based approach developed in this work is not only useful for the discovery of proteins with potential bioactivities but also helpful for the bioactivity relevant quality control of animal medicines.
Collapse
Affiliation(s)
- Fu-Gui Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Xin-Yue Shi
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Liu Yang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Xu Lu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Yan Qi
- Yangshengtang Pharmaceutical Co., Ltd, Hangzhou, 310000, China
| | - Ping Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Hua Yang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Wen Gao
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| |
Collapse
|
2
|
Huang CF, Su P, Fisher TD, Levitsky J, Kelleher NL, Forte E. Mass spectrometry-based proteomics for advancing solid organ transplantation research. FRONTIERS IN TRANSPLANTATION 2023; 2:1286881. [PMID: 38993855 PMCID: PMC11235370 DOI: 10.3389/frtra.2023.1286881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/13/2023] [Indexed: 07/13/2024]
Abstract
Scarcity of high-quality organs, suboptimal organ quality assessment, unsatisfactory pre-implantation procedures, and poor long-term organ and patient survival are the main challenges currently faced by the solid organ transplant (SOT) field. New biomarkers for assessing graft quality pre-implantation, detecting, and predicting graft injury, rejection, dysfunction, and survival are critical to provide clinicians with invaluable prediction tools and guidance for personalized patients' treatment. Additionally, new therapeutic targets are also needed to reduce injury and rejection and improve transplant outcomes. Proteins, which underlie phenotypes, are ideal candidate biomarkers of health and disease statuses and therapeutic targets. A protein can exist in different molecular forms, called proteoforms. As the function of a protein depends on its exact composition, proteoforms can offer a more accurate basis for connection to complex phenotypes than protein from which they derive. Mass spectrometry-based proteomics has been largely used in SOT research for identification of candidate biomarkers and therapeutic intervention targets by so-called "bottom-up" proteomics (BUP). However, such BUP approaches analyze small peptides in lieu of intact proteins and provide incomplete information on the exact molecular composition of the proteins of interest. In contrast, "Top-down" proteomics (TDP), which analyze intact proteins retaining proteoform-level information, have been only recently adopted in transplantation studies and already led to the identification of promising proteoforms as biomarkers for organ rejection and dysfunction. We anticipate that the use of top-down strategies in combination with new technological advancements in single-cell and spatial proteomics could drive future breakthroughs in biomarker and therapeutic target discovery in SOT.
Collapse
Affiliation(s)
- Che-Fan Huang
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
| | - Pei Su
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
- Department of Chemistry, Northwestern University, Evanston, IL, United States
| | - Troy D. Fisher
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
| | - Josh Levitsky
- Division of Gastroenterology and Hepatology, Comprehensive Transplant Center Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Neil L. Kelleher
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
- Department of Chemistry, Northwestern University, Evanston, IL, United States
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Surgery, Feinberg School of Medicine, Comprehensive Transplant Center, Northwestern University, Chicago, IL, United States
| | - Eleonora Forte
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
- Department of Surgery, Feinberg School of Medicine, Comprehensive Transplant Center, Northwestern University, Chicago, IL, United States
| |
Collapse
|
3
|
SjHSP90 recombinant protein and its possible application in the diagnosis of schistosomiasis and treatment efficacy monitoring. Acta Trop 2023; 238:106793. [PMID: 36509131 DOI: 10.1016/j.actatropica.2022.106793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/14/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
PURPOSE The fraction antigen of Schistosoma japonicum (107-121 kDa) eggs can be used for treatment efficacy monitoring, but the methods are laborious. This study analyzed the antigen and its feasibility for infection screening and treatment efficacy monitoring, which is the key to schistosomiasis control. METHODS The fraction antigens have been analyzed by shotgun mass spectrometry. The recombinant proteins of candidates from the fraction antigens have been prokaryotic expression and purification in large amounts with high purity. The sera have been collected from rabbits and mice models of schistosomiasis infection and treatment. ELISA evaluated the diagnostic value of the candidate proteins. RESULTS SJCHGC00820 and SJCHGC06900, with higher credibility, were identified through Shotgun mass spectrometry. ELISA results showed that rSj00820 has a diagnostic value for schistosomiasis (positive OD/negative OD P/N=3.6), while rSj06900 showed negative (P/N)<2. In rabbits, the specific serum antibodies for SjHSP90(rSj00820) in the infected animals peaked 6 weeks after infection and gradually decreased after treatment, reaching negative levels at 11 weeks. SjHSP90-ELISA was used to test serum samples from infected mice. The sensitivity and specificity reached >90%, similar to the diagnostic value obtained with soluble egg antigen (SEA) (SEA-ELISA). After treatment, the negative conversion rate reached >80%, significantly superior to SEA-ELISA. CONCLUSIONS The SjHSP90-ELISA can be used for the immunological diagnosis and treatment efficacy monitoring of schistosomiasis. The study lays a foundation for further developing screening and diagnostic kits.
Collapse
|
4
|
Su P, McGee JP, Durbin KR, Hollas MAR, Yang M, Neumann EK, Allen JL, Drown BS, Butun FA, Greer JB, Early BP, Fellers RT, Spraggins JM, Laskin J, Camarillo JM, Kafader JO, Kelleher NL. Highly multiplexed, label-free proteoform imaging of tissues by individual ion mass spectrometry. SCIENCE ADVANCES 2022; 8:eabp9929. [PMID: 35947651 PMCID: PMC9365283 DOI: 10.1126/sciadv.abp9929] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/24/2022] [Indexed: 05/25/2023]
Abstract
Imaging of proteoforms in human tissues is hindered by low molecular specificity and limited proteome coverage. Here, we introduce proteoform imaging mass spectrometry (PiMS), which increases the size limit for proteoform detection and identification by fourfold compared to reported methods and reveals tissue localization of proteoforms at <80-μm spatial resolution. PiMS advances proteoform imaging by combining ambient nanospray desorption electrospray ionization with ion detection using individual ion mass spectrometry. We demonstrate highly multiplexed proteoform imaging of human kidney, annotating 169 of 400 proteoforms of <70 kDa using top-down MS and a database lookup of ~1000 kidney candidate proteoforms, including dozens of key enzymes in primary metabolism. PiMS images reveal distinct spatial localizations of proteoforms to both anatomical structures and cellular neighborhoods in the vasculature, medulla, and cortex regions of the human kidney. The benefits of PiMS are poised to increase proteome coverage for label-free protein imaging of tissues.
Collapse
Affiliation(s)
- Pei Su
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - John P. McGee
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Kenneth R. Durbin
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Michael A. R. Hollas
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Manxi Yang
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Elizabeth K. Neumann
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
| | - Jamie L. Allen
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
| | - Bryon S. Drown
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | | | - Joseph B. Greer
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Bryan P. Early
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Ryan T. Fellers
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Jeffrey M. Spraggins
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Departments of Chemistry and Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Julia Laskin
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Jeannie M. Camarillo
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Jared O. Kafader
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Neil L. Kelleher
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| |
Collapse
|
5
|
Li J, Yang R, Jiang Y, Sun S, Li J, Gu H, Lin Y, Luo X, He C, Chen Y. Comparative Proteomic Analysis by Isobaric Tags for the Relative and Absolute Quantification Reveals the Responses of Tobacco ( Nicotiana tabacum L.) Roots to Different Soil Types. FRONTIERS IN PLANT SCIENCE 2022; 13:847388. [PMID: 35548306 PMCID: PMC9082669 DOI: 10.3389/fpls.2022.847388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 02/14/2022] [Indexed: 06/15/2023]
Abstract
Tobacco (Nicotiana tabacum) root affects the yield and quality of tobacco leaves. To gain insight into the responses of the tobacco root system to different soil types, we integrated morphological characteristics, the physiological index, the metabolic pathways of the root system, and the aboveground biomass of tobacco cultivated in limestone soil (LS), paddy soil (PS), and red soil (RS). Compared with plants growing in LS and PS, the chemical composition of tobacco leaves in RS tended to be coordinated. Red soil facilitated the accumulation of aboveground and belowground biomass of flue-cured tobacco and had the most significant effect on the dry matter quality of the roots. In addition, it promoted an increased root length, root surface area (RSA), root volume, and a higher number of root forks and improved root vigor and nitrate reductase (NR) activity; however, the activities of superoxide dismutase (SOD) and peroxidase (POD) were decreased. We studied differentially the abundant proteins (DAPs) of the flue-cured tobacco roots cultivated in different soil types by isobaric tags for the relative and absolute quantification (iTRAQ) of the proteomic profiles of cultivar. In total, 699, 650, and 569 differentially abundant proteins (DAPs) were identified from limestone soil (LS) vs. PS, LS vs. RS, and PS vs. RS, respectively, including 412/287, 291/359, and 323/246 up-/downregulated proteins, respectively. These DAPs were mainly involved in starch and sucrose metabolism, phenylalanine metabolism, the biosynthesis of secondary metabolites, microbial metabolism in different environments, and ribosomes. The parallel reaction monitoring (PRM) and quantitative reverse transcription PCR (qRT-PCR) analysis showed that the results of the iTRAQ proteomics were reliable. Overall, our study facilitates a new understanding of the responses of tobacco roots to different soil types at the protein level.
Collapse
Affiliation(s)
- Jialiang Li
- Yunnan Academy of Tobacco Agricultural Sciences, Yuxi, China
- College of Tobacco Science, Yunnan Agricultural University, Kunming, China
| | - Rui Yang
- College of Tobacco Science, Yunnan Agricultural University, Kunming, China
- Shiyan Branch of Hubei Tobacco Company, Shiyan, China
| | - Yonglei Jiang
- Yunnan Academy of Tobacco Agricultural Sciences, Yuxi, China
| | - Shubin Sun
- Research Center of Hubei Tobacco Industrial Co., Ltd., Xiangyang, China
| | - Junying Li
- Yunnan Academy of Tobacco Agricultural Sciences, Yuxi, China
| | - Hao Gu
- College of Tobacco Science, Yunnan Agricultural University, Kunming, China
| | - Ying Lin
- Research Center of Hubei Tobacco Industrial Co., Ltd., Xiangyang, China
| | - Xianxue Luo
- Hunan Zhangjiajie Municipal Tobacco Co., Zhangjiajie, China
| | - Chenggang He
- College of Tobacco Science, Yunnan Agricultural University, Kunming, China
| | - Yi Chen
- Yunnan Academy of Tobacco Agricultural Sciences, Yuxi, China
| |
Collapse
|
6
|
Bahmani M, O’Lone CE, Juhász A, Nye-Wood M, Dunn H, Edwards IB, Colgrave ML. Application of Mass Spectrometry-Based Proteomics to Barley Research. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8591-8609. [PMID: 34319719 PMCID: PMC8389776 DOI: 10.1021/acs.jafc.1c01871] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Barley (Hordeum vulgare) is the fourth most cultivated crop in the world in terms of production volume, and it is also the most important raw material of the malting and brewing industries. Barley belongs to the grass (Poaceae) family and plays an important role in food security and food safety for both humans and livestock. With the global population set to reach 9.7 billion by 2050, but with less available and/or suitable land for agriculture, the use of biotechnology tools in breeding programs are of considerable importance in the quest to meet the growing food gap. Proteomics as a member of the "omics" technologies has become popular for the investigation of proteins in cereal crops and particularly barley and its related products such as malt and beer. This technology has been applied to study how proteins in barley respond to adverse environmental conditions including abiotic and/or biotic stresses, how they are impacted during food processing including malting and brewing, and the presence of proteins implicated in celiac disease. Moreover, proteomics can be used in the future to inform breeding programs that aim to enhance the nutritional value and broaden the application of this crop in new food and beverage products. Mass spectrometry analysis is a valuable tool that, along with genomics and transcriptomics, can inform plant breeding strategies that aim to produce superior barley varieties. In this review, recent studies employing both qualitative and quantitative mass spectrometry approaches are explored with a focus on their application in cultivation, manufacturing, processing, quality, and the safety of barley and its related products.
Collapse
Affiliation(s)
- Mahya Bahmani
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
| | - Clare E. O’Lone
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
| | - Angéla Juhász
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
| | - Mitchell Nye-Wood
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
| | - Hugh Dunn
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
| | - Ian B. Edwards
- Edstar
Genetics Pty Ltd, SABC - Loneragan Building, Murdoch University, 90 South Street, Murdoch, Western Australia 6150, Australia
| | - Michelle L. Colgrave
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
- CSIRO
Agriculture and Food, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
- Phone: +61-7-3214-2697. . Fax: +61-7-3214-2900
| |
Collapse
|
7
|
Boeira CZ, Silvello MADC, Remedi RD, Feltrin ACP, Santos LO, Garda-Buffon J. Mitigation of nivalenol using alcoholic fermentation and magnetic field application. Food Chem 2020; 340:127935. [PMID: 32891895 DOI: 10.1016/j.foodchem.2020.127935] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/01/2020] [Accepted: 08/23/2020] [Indexed: 12/20/2022]
Abstract
This study aimed at evaluating mitigation of nivalenol (NIV) in alcoholic fermentation with magnetic field application (MF). Mitigation was related to both the glutathione (GSH) redox molecule and the enzyme peroxidase (PO), which were synthesized by Saccharomyces cerevisiae US-05. Conditions under evaluation were NIV (0.2 µg mL-1), MF application (35 mT) and simultaneous use of mycotoxin and MF. The GSH content and the PO activity were increased when the culture contained NIV and the alcohol profile was altered after 48 h of fermentation. At the end of the alcoholic fermentation, NIV was mitigated by 56.5%. Therefore, this process is a promising method to reduce contamination by NIV, although the mycotoxin affects the chemical characteristics of the final product.
Collapse
Affiliation(s)
- Carolina Zulian Boeira
- Mycotoxin and Food Science Laboratory, Chemistry and Food School, Federal University of Rio Grande - FURG, Brazil
| | | | - Rafael Diaz Remedi
- Mycotoxin and Food Science Laboratory, Chemistry and Food School, Federal University of Rio Grande - FURG, Brazil
| | - Ana Carla Penteado Feltrin
- Mycotoxin and Food Science Laboratory, Chemistry and Food School, Federal University of Rio Grande - FURG, Brazil
| | - Lucielen Oliveira Santos
- Laboratory of Biotechnology, Chemistry and Food School, Federal University of Rio Grande - FURG, Brazil.
| | - Jaqueline Garda-Buffon
- Mycotoxin and Food Science Laboratory, Chemistry and Food School, Federal University of Rio Grande - FURG, Brazil.
| |
Collapse
|
8
|
Lebkuchen A, Freitas LS, Cardozo KHM, Drager LF. Advances and challenges in pursuing biomarkers for obstructive sleep apnea: Implications for the cardiovascular risk. Trends Cardiovasc Med 2020; 31:242-249. [PMID: 32413393 DOI: 10.1016/j.tcm.2020.04.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/31/2020] [Accepted: 04/06/2020] [Indexed: 12/14/2022]
Abstract
Obstructive sleep apnea (OSA) is a common clinical condition associated with increased cardiovascular morbidity and mortality. Recent evidence from clinical studies and animal models suggest that OSA can promote cardiovascular disease by inducing autonomic, hemodynamic, inflammatory and metabolic dysregulation. However, most of the evidence addressing hard endpoints in humans is derived from observational studies. Several challenges have been noted in the pursuit of a comprehensive knowledge base about the impact of OSA including: 1) the precise mechanisms by which OSA causes metabolic and cardiovascular consequences are not clear, which limits our current ability to address potential targets in OSA; 2) several patients with OSA, even with severe forms, present with no or mild daytime symptoms. Beyond the obvious challenges for obtaining good adherence for conventional OSA treatments, there is evidence that symptomatic vs. asymptomatic patients with OSA do not necessarily have the same metabolic and cardiovascular outcomes; and 3) the cardiovascular response to OSA treatment may vary even in those patients with good adherence. In this scenario, there is an obvious need to develop biomarkers in the OSA research area. This review focuses on describing the advances that have occurred so far in exploring potential OSA biomarkers with clear emphasis for the cardiovascular risk. Particular attention will be devoted to discuss molecular biomarkers including the potential role of microRNAs, proteomics and metabolomics. We also discuss the major challenges and perspectives in this growing research field.
Collapse
Affiliation(s)
| | - Lunara S Freitas
- Hypertension Unit, Heart Institute (InCor), University of Sao Paulo Medical School
| | | | - Luciano F Drager
- Hypertension Unit, Heart Institute (InCor), University of Sao Paulo Medical School; Hypertension Unit, Renal Division, University of Sao Paulo Medical School.
| |
Collapse
|
9
|
Lim J, Cho J, Paik Y, Chang Y, Kim H. Diagnostic Application of Serum Proteomic Patterns in Gastric Cancer Patients by ProteinChip Surface-Enhanced Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. Int J Biol Markers 2018; 22:281-6. [DOI: 10.1177/172460080702200407] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) is one of the currently used techniques to identify biomarkers for cancers. This study was planned to establish a system to accurately distinguish gastric cancer patients by using SELDI-TOF-MS. A total of 100 serum samples obtained from 60 individuals with gastric cancer and 40 healthy individuals were screened. Protein expression profiles were expressed on CM10 ProteinChip arrays and analyzed. Peak intensities were analyzed with the Biomarker Wizard software to identify peaks showing significantly different intensities between normal and cancer groups. Classification analysis and construction of decision trees were done with the Biomarker Pattern software 5.0. Seventeen protein peaks showed significant differences between the two groups. The decision tree which gave the highest discrimination included four peaks at mass 5,919, 8,583, 10,286, and 13,758 as splitters. The sensitivity and specificity for classification of the decision tree were 96.7% (58/60) and 97.5% (39/40), respectively. When the protein biomarker pattern was tested on a blinded test set, it yielded a sensitivity of 93.3% (28/30) and a specificity of 90% (18/20). These results suggest that serum protein profiling by the SELDI system may distinguish gastric cancer patients from healthy controls with relatively high sensitivity and specificity.
Collapse
Affiliation(s)
- J.Y. Lim
- Department of Internal Medicine, Yonsei Yongdong Cancer Center, Yonsei University College of Medicine, Seoul
| | - J.Y. Cho
- Department of Internal Medicine, Yonsei Yongdong Cancer Center, Yonsei University College of Medicine, Seoul
| | - Y.H. Paik
- Department of Internal Medicine, Yonsei Yongdong Cancer Center, Yonsei University College of Medicine, Seoul
| | - Y.S. Chang
- Department of Internal Medicine, Yonsei Yongdong Cancer Center, Yonsei University College of Medicine, Seoul
| | - H.G. Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul - South Korea
| |
Collapse
|
10
|
E Y, Yuan J, Yang F, Wang L, Ma J, Li J, Pu X, Raza W, Huang Q, Shen Q. PGPR strain Paenibacillus polymyxa SQR-21 potentially benefits watermelon growth by re-shaping root protein expression. AMB Express 2017; 7:104. [PMID: 28549372 PMCID: PMC5445060 DOI: 10.1186/s13568-017-0403-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 05/11/2017] [Indexed: 12/02/2022] Open
Abstract
Paenibacillus polymyxa (SQR-21) is not only a plant growth-promoting rhizobacteria, but also an effective biocontrol agent against Fusarium wilt disease of watermelon. For the better understanding and clarifying the potential mechanisms of SQR-21 to improve watermelon growth and disease resistance, a split-root methodology in hydroponic and LC-MS technology with the label free method was used to analyze the key root proteins involved in watermelon metabolism and disease resistance after the inoculation of SQR-21. Out of 623 identified proteins, 119 proteins were differentially expressed when treatment (SQR-21 inoculation) and control (no bacterial inoculation) were compared. Among those, 57 and 62 proteins were up-regulated and down-regulated, respectively. These differentially expressed proteins were identified to be involved in signal transduction (ADP-ribosylation factor, phospholipase D), transport (aspartate amino-transferase), carbohydratemetabolic (glucose-6-phosphate dehydrogenase, UDP-glucose pyrophosphorylase), defense and response to stress (glutathione S-transferase, Ubiquitin-activating enzyme E1), and oxidation-reduction process (thioredoxin peroxidase, ascorbate peroxidase). The results of this study indicated that SQR-21 inoculation on the watermelon roots benefits plant by inducing the expression of several proteins involved in growth, photosynthesis, and other metabolic and physiological activities.
Collapse
Affiliation(s)
- Yaoyao E
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization and Jiangsu Collaborative Innovation Center for Organic Solid Waste Utilization, and National Engineering Research Center for Organic-based Fertilizer, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jun Yuan
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization and Jiangsu Collaborative Innovation Center for Organic Solid Waste Utilization, and National Engineering Research Center for Organic-based Fertilizer, Nanjing Agricultural University, Nanjing, 210095 China
| | - Fang Yang
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization and Jiangsu Collaborative Innovation Center for Organic Solid Waste Utilization, and National Engineering Research Center for Organic-based Fertilizer, Nanjing Agricultural University, Nanjing, 210095 China
| | - Lei Wang
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization and Jiangsu Collaborative Innovation Center for Organic Solid Waste Utilization, and National Engineering Research Center for Organic-based Fertilizer, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jinghua Ma
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization and Jiangsu Collaborative Innovation Center for Organic Solid Waste Utilization, and National Engineering Research Center for Organic-based Fertilizer, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jing Li
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization and Jiangsu Collaborative Innovation Center for Organic Solid Waste Utilization, and National Engineering Research Center for Organic-based Fertilizer, Nanjing Agricultural University, Nanjing, 210095 China
| | - Xiaowei Pu
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization and Jiangsu Collaborative Innovation Center for Organic Solid Waste Utilization, and National Engineering Research Center for Organic-based Fertilizer, Nanjing Agricultural University, Nanjing, 210095 China
| | - Waseem Raza
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization and Jiangsu Collaborative Innovation Center for Organic Solid Waste Utilization, and National Engineering Research Center for Organic-based Fertilizer, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qiwei Huang
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization and Jiangsu Collaborative Innovation Center for Organic Solid Waste Utilization, and National Engineering Research Center for Organic-based Fertilizer, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization and Jiangsu Collaborative Innovation Center for Organic Solid Waste Utilization, and National Engineering Research Center for Organic-based Fertilizer, Nanjing Agricultural University, Nanjing, 210095 China
| |
Collapse
|
11
|
Sun L, Min L, Zhou H, Li M, Shao F, Wang W. Adolescent social isolation affects schizophrenia-like behavior and astrocyte biomarkers in the PFC of adult rats. Behav Brain Res 2017; 333:258-266. [DOI: 10.1016/j.bbr.2017.07.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 07/05/2017] [Accepted: 07/09/2017] [Indexed: 10/19/2022]
|
12
|
Procopio N, Chamberlain AT, Buckley M. Intra- and Interskeletal Proteome Variations in Fresh and Buried Bones. J Proteome Res 2017; 16:2016-2029. [PMID: 28436665 DOI: 10.1021/acs.jproteome.6b01070] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteomic methods are acquiring greater importance in archaeology and palaeontology due to the longevity of proteins in skeletal remains. There are also developing interests in forensic applications, offering the potential to shed light on post-mortem intervals and age at death estimation. However, our understanding of intra- and interskeletal proteome variations is currently severely limited. Here, we evaluated the proteomes obtained from five distinct subsamples of different skeletal elements from buried pig carcasses to ascertain the extent of variation within and between individuals. We found that reproducibility of data depends on the skeletal element used for sampling and that intrabone differences exceed those observed between the same skeletal element sampled from different individuals. Interestingly, the abundance of several serum proteins appeared to correlate with biological age with relative concentrations of alpha-1 antitrypsin and chromogranin-A increasing and those of fetuin-A decreasing. We also observed a surprising level of divergence in data from different LC-MS/MS runs on aliquots of similar samples analyzed months apart, adding constraints to the comparison of results of such methods across different studies.
Collapse
Affiliation(s)
- Noemi Procopio
- School of Earth and Environmental Sciences, The University of Manchester, Manchester Institute of Biotechnology , 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Andrew T Chamberlain
- School of Earth and Environmental Sciences, The University of Manchester , Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Michael Buckley
- School of Earth and Environmental Sciences, The University of Manchester, Manchester Institute of Biotechnology , 131 Princess Street, Manchester, M1 7DN, United Kingdom
| |
Collapse
|
13
|
Liu W, He J, Lin R, Liang J, Luo Q. Differential proteomics of the synovial membrane between bilateral and unilateral knee osteoarthritis in surgery‑induced rabbit models. Mol Med Rep 2016; 14:2243-9. [PMID: 27430254 DOI: 10.3892/mmr.2016.5511] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 06/21/2016] [Indexed: 11/06/2022] Open
Abstract
The present study investigated the differential proteomics of synovial membranes between bilateral and unilateral anterior cruciate ligament transection (ACLT) in rabbits with knee osteoarthritis (KOA), in order to elucidate the pathological biomarkers of different degrees of KOA. A total of 6 New Zealand rabbits were randomly divided into groups A and B (three rabbits per group). The two groups were subjected to bilateral and unilateral ACLT, respectively. A total of 6 weeks following surgery, proteins were extracted from the knee joint synovial membranes of KOA rabbits and were separated by two‑dimensional polyacrylamide gel electrophoresis. The differentially expressed proteins in the OA synovial membranes were selected for further analysis by linear ion trap‑Fourier transform ion cyclotron resonance mass spectrometry. Ten protein spots were identified to be different between the synovial membranes of the bilateral and unilateral KOA rabbits. Protein disulfide‑isomerase and creatine kinase M‑type were identified in the unilateral KOA rabbit synovial membranes. Serum albumin (three spots), lumican, α‑2‑HS‑glycoprotein and three uncharacterized proteins were identified in the synovial membranes of the bilateral KOA rabbits. The differential proteomic expression demonstrated the different biomarkers associated with bilateral and unilateral KOA, and indicated that spontaneous and secondary KOA require diverse methods of treatment; thus the underlying mechanism of KOA requires further investigation.
Collapse
Affiliation(s)
- Weilin Liu
- Department of Physiotherapy, College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Jian He
- Department of Physiotherapy, College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Ruhui Lin
- Medical Experimental Center, Fujian Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Jie Liang
- Department of Physiotherapy, College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Qinglu Luo
- Department of Physiotherapy, College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| |
Collapse
|
14
|
Mass Spectrometry-Based Metabolomic and Proteomic Strategies in Organic Acidemias. BIOMED RESEARCH INTERNATIONAL 2016; 2016:9210408. [PMID: 27403441 PMCID: PMC4923558 DOI: 10.1155/2016/9210408] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 05/15/2016] [Indexed: 12/17/2022]
Abstract
Organic acidemias (OAs) are inherited metabolic disorders caused by deficiency of enzymatic activities in the catabolism of amino acids, carbohydrates, or lipids. These disorders result in the accumulation of mono-, di-, or tricarboxylic acids, generally referred to as organic acids. The OA outcomes can involve different organs and/or systems. Some OA disorders are easily managed if promptly diagnosed and treated, whereas, in others cases, such as propionate metabolism-related OAs (propionic acidemia, PA; methylmalonic acidemia, MMA), neither diet, vitamin therapy, nor liver transplantation appears to prevent multiorgan impairment. Here, we review the recent developments in dissecting molecular bases of OAs by using integration of mass spectrometry- (MS-) based metabolomic and proteomic strategies. MS-based techniques have facilitated the rapid and economical evaluation of a broad spectrum of metabolites in various body fluids, also collected in small samples, like dried blood spots. This approach has enabled the timely diagnosis of OAs, thereby facilitating early therapeutic intervention. Besides providing an overview of MS-based approaches most frequently used to study the molecular mechanisms underlying OA pathophysiology, we discuss the principal challenges of metabolomic and proteomic applications to OAs.
Collapse
|
15
|
HONG XY, LI SM, WANG Y. Analysis of Urine Peptidome and Post-translation Modifications by Nano Liquid Chromatography-High Resolution Tandem Mass Spectrometry. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60931-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
16
|
Overview of proteomics studies in obstructive sleep apnea. Sleep Med 2015; 16:437-45. [PMID: 25770042 DOI: 10.1016/j.sleep.2014.11.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 11/25/2014] [Accepted: 11/27/2014] [Indexed: 02/06/2023]
Abstract
Obstructive sleep apnea (OSA) is an underdiagnosed common public health concern causing deleterious effects on metabolic and cardiovascular health. Although much has been learned regarding the pathophysiology and consequences of OSA in the past decades, the molecular mechanisms associated with such processes remain poorly defined. The advanced high-throughput proteomics-based technologies have become a fundamental approach for identifying novel disease mediators as potential diagnostic and therapeutic targets for many diseases, including OSA. Here, we briefly review OSA pathophysiology and the technological advances in proteomics and the first results of its application to address critical issues in the OSA field.
Collapse
|
17
|
MIĘKUS NATALIA, OLĘDZKA ILONA, PLENIS ALINA, WOŹNIAK ZOFIA, LEWCZUK ANNA, KOSZAŁKA PATRYCJA, SEROCZYŃSKA BARBARA, BĄCZEK TOMASZ. Gel electrophoretic separation of proteins from cultured neuroendocrine tumor cell lines. Mol Med Rep 2014; 11:1407-15. [DOI: 10.3892/mmr.2014.2864] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 06/05/2014] [Indexed: 11/05/2022] Open
|
18
|
Haga SW, Wu HF. Overview of software options for processing, analysis and interpretation of mass spectrometric proteomic data. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:959-969. [PMID: 25303385 DOI: 10.1002/jms.3414] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 05/23/2014] [Accepted: 06/13/2014] [Indexed: 06/04/2023]
Abstract
Recently, the interests in proteomics have been intensively increased, and the proteomic methods have been widely applied to many problems in cell biology. If the age of 1990s is considered to be a decade of genomics, we can claim that the following years of the new century is a decade of proteomics. The rapid evolution of proteomics has continued through these years, with a series of innovations in separation techniques and the core technologies of two-dimensional gel electrophoresis and MS. Both technologies are fueled by automation and high throughput computation for profiling of proteins from biological systems. As Patterson ever mentioned, 'data analysis is the Achilles heel of proteomics and our ability to generate data now outstrips our ability to analyze it'. The development of automatic and high throughput technologies for rapid identification of proteins is essential for large-scale proteome projects and automatic protein identification and characterization is essential for high throughput proteomics. This review provides a snap shot of the tools and applications that are available for mass spectrometric high throughput biocomputation. The review starts with a brief introduction of proteomics and MS. Computational tools that can be employed at various stages of analysis are presented, including that for data processing, identification, quantification, and the understanding of the biological functions of individual proteins and their dynamic interactions. The challenges of computation software development and its future trends in MS-based proteomics have also been speculated.
Collapse
Affiliation(s)
- Steve W Haga
- Department of Computer Science and Engineering, National Sun Yat Sen University, Kaohsiung, 804, Taiwan
| | | |
Collapse
|
19
|
Altuntaş EG, Ayhan K, Peker S, Ayhan B, Demiralp DÖ. Purification and mass spectrometry based characterization of a pediocin produced by Pediococcus acidilactici 13. Mol Biol Rep 2014; 41:6879-85. [DOI: 10.1007/s11033-014-3573-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 06/27/2014] [Indexed: 11/30/2022]
|
20
|
Vijayendran C, Flaschel E. Impact of profiling technologies in the understanding of recombinant protein production. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 121:45-70. [PMID: 20186528 DOI: 10.1007/10_2009_56] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2023]
Abstract
Since expression profiling methods have been available in a high throughput fashion, the implication of these technologies in the field of biotechnology has increased dramatically. Microarray technology is one such unique and efficient methodology for simultaneous exploration of expression levels of numerous genes. Likewise, two-dimensional gel electrophoresis or multidimensional liquid chromatography coupled with mass spectrometry are extensively utilised for studying expression levels of numerous proteins. In the field of biotechnology these highly parallel analytical methods have paved the way to study and understand various biological phenomena depending on expression patterns. The next phenomenological level is represented by the metabolome and the (metabolic) fluxome. However, this chapter reviews gene and protein profiling and their impact on understanding recombinant protein production. We focus on the computational methods utilised for the analyses of data obtained from these profiling technologies as well as prominent results focusing on recombinant protein expression with Escherichia coli. Owing to the knowledge accumulated with respect to cellular signals triggered during recombinant protein production, this field is on the way to design strategies for developing improved processes. Both gene and protein profiling have exhibited a handful of functional categories to concentrate on in order to identify target genes and proteins, respectively, involved in the signalling network with major impact on recombinant protein production.
Collapse
Affiliation(s)
- Chandran Vijayendran
- International NRW Graduate School in Bioinformatics and Genome Research, CeBiTec, Bielefeld University, 33594, Bielefeld, Germany,
| | | |
Collapse
|
21
|
Schulte I, Tammen H, Selle H, Schulz-Knappe P. Peptides in body fluids and tissues as markers of disease. Expert Rev Mol Diagn 2014; 5:145-57. [PMID: 15833045 DOI: 10.1586/14737159.5.2.145] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The general awareness of the importance of peptides in physiology and pathophysiology has increased strongly over the last few years. With worldwide progress in the analysis of whole genomes, the knowledge base in gene sequence and expression data useful for protein and peptide analysis has drastically increased. The medical need for relevant biomarkers is enormous. This is particularly true for the many types of cancer, but other diseases such as Type 2 diabetes also lack useful and adequate diagnostic markers with high specificity and sensitivity. Despite advances in imaging technologies for early detection of diseases, proteomic and peptidomic multiplex techniques have evolved in recent years. This review focuses on the application of peptidomics technologies to peptides in health and disease. Peptidomics technologies provide new opportunities for the detection of low-molecular-weight proteome biomarkers (peptides) by mass spectrometry. Improvements in peptidomics research are based on separation of peptides and/or proteins by their physicochemical properties in combination with mass spectrometric detection, identification and sophisticated bioinformatics tools for data analysis. Therefore, peptidomics technologies offer an opportunity to discover novel biomarkers for diagnosis and management of disease (e.g., prognosis, treatment decision and monitoring response to therapy).
Collapse
Affiliation(s)
- Imke Schulte
- BioVisioN AG, Feodor-Lynen-Str. 5, 30625 Hannover, Germany.
| | | | | | | |
Collapse
|
22
|
Comba González N, Vallejo AF, Sánchez-Gómez M, Montoya D. Protein identification in two phases of 1,3-propanediol production by proteomic analysis. J Proteomics 2013; 89:255-64. [PMID: 23811541 DOI: 10.1016/j.jprot.2013.06.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 05/04/2013] [Accepted: 06/13/2013] [Indexed: 10/26/2022]
Abstract
UNLABELLED Proteomic analysis by two-dimensional electrophoresis (2D)-mass spectrometry was used to identify differentially expressed proteins in the Clostridium sp. native strain (IBUN 158B) in two phases of the 1,3-propanediol (1,3-PD) production (lag phase and exponential growth phase). Intracellular protein fraction extraction conditions were standardised, as well as the 2D electrophoresis. Differences were found between both of the growth phases evaluated here. Thirty-two of the differentially expressed proteins were chosen to be identified by tandem mass spectrometry (MALDI TOF/TOF). The presence of four enzymes implicated in the 1,3-PD metabolic pathway was recorded: one from the reductive route (1,3-propanediol dehydrogenase) and three from the oxidative route (3-hydroxybutyryl-CoA dehydrogenase, NADPH-dependent butanol dehydrogenase and phosphate butyryl transferase). The following enzymes which have not been previously reported for Clostridium sp., were also identified: phosphoglycerate kinase, glucose 6-phosphate isomerase, deoxyribose phosphate aldolase, transketolase, cysteine synthetase, O-acetylhomoserine sulphhydrylase, glycyl-tRNA ligase, aspartate-β-semialdehyde dehydrogenase, inosine-5-monophosphate dehydrogenase, aconitate hydratase and the PrsA protein. The foregoing provides a novel contribution towards knowledge of the native strain for the purpose of designing genetic manipulation strategies to obtain strains with high production of 1,3-PD. BIOLOGICAL SIGNIFICANCE The article "Protein identification in two phases of 1,3-propanediol production by proteomic analysis" provides a novel contribution towards knowledge regarding the Colombian Clostridium sp. native strain (IBUN 158B) because this is a new approximation in comparative proteomics in two phases of the bacterial growth and 1,3-propanediol (1,3-PD) production conditions. The proteomic studies are very important to identify the enzymes that are expressed at different stages of production and therefore genes of interest in the genetic manipulation strategies; the results can be taken into account in future studies in metabolic engineering when optimising 1,3-PD production, in a cost-effective process having direct industrial applications.
Collapse
Affiliation(s)
- Natalia Comba González
- Bioprocesses and Bioprospecting Group, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | | | | | | |
Collapse
|
23
|
Toxicogenomic approaches for understanding molecular mechanisms of heavy metal mutagenicity and carcinogenicity. Int J Hyg Environ Health 2013; 216:587-98. [PMID: 23540489 DOI: 10.1016/j.ijheh.2013.02.010] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 02/26/2013] [Accepted: 02/26/2013] [Indexed: 12/24/2022]
Abstract
Heavy metals that are harmful to humans include arsenic, cadmium, chromium, lead, mercury, and nickel. Some metals or their related compounds may even cause cancer. However, the mechanism underlying heavy metal-induced cancer remains unclear. Increasing data show a link between heavy metal exposure and aberrant changes in both genetic and epigenetic factors via non-targeted multiple toxicogenomic technologies of the transcriptome, proteome, metabolome, and epigenome. These modifications due to heavy metal exposure might provide a better understanding of environmental disorders. Such informative changes following heavy metal exposure might also be useful for screening of biomarker-monitored exposure to environmental pollutants and/or predicting the risk of disease. We summarize advances in high-throughput toxicogenomic-based technologies and studies related to exposure to individual heavy metal and/or mixtures and propose the underlying mechanism of action and toxicant signatures. Integrative multi-level expression analysis of the toxicity of heavy metals via system toxicology-based methodologies combined with statistical and computational tools might clarify the biological pathways involved in carcinogenic processes. Although standard in vitro and in vivo endpoint testing of mutagenicity and carcinogenicity are considered a complementary approach linked to disease, we also suggest that further evaluation of prominent biomarkers reflecting effects, responses, and disease susceptibility might be diagnostic. Furthermore, we discuss challenges in toxicogenomic applications for toxicological studies of metal mixtures and epidemiological research. Taken together, this review presents toxicogenomic data that will be useful for improvement of the knowledge of carcinogenesis and the development of better strategies for health risk assessment.
Collapse
|
24
|
Salmenkova EA. Molecular genetic bases of adaptation processes and approaches to their analysis. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413010110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
25
|
Chao TC, Hansmeier N. Microfluidic devices for high-throughput proteome analyses. Proteomics 2012; 13:467-79. [PMID: 23135952 DOI: 10.1002/pmic.201200411] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 09/06/2012] [Accepted: 10/05/2012] [Indexed: 12/14/2022]
Abstract
Over the last decades, microfabricated bioanalytical platforms have gained enormous interest due to their potential to revolutionize biological analytics. Their popularity is based on several key properties, such as high flexibility of design, low sample consumption, rapid analysis time, and minimization of manual handling steps, which are of interest for proteomics analyses. An ideal totally integrated chip-based microfluidic device could allow rapid automated workflows starting from cell cultivation and ending with MS-based proteome analysis. By reducing or eliminating sample handling and transfer steps and increasing the throughput of analyses these workflows would dramatically improve the reliability, reproducibility, and throughput of proteomic investigations. While these complete devices do not exist for routine use yet, many improvements have been made in the translation of proteomic sample handling and separation steps into microfluidic formats. In this review, we will focus on recent developments and strategies to enable and integrate proteomic workflows into microfluidic devices.
Collapse
Affiliation(s)
- Tzu-Chiao Chao
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, USA
| | | |
Collapse
|
26
|
Luk VN, Fiddes LK, Luk VM, Kumacheva E, Wheeler AR. Digital microfluidic hydrogel microreactors for proteomics. Proteomics 2012; 12:1310-8. [PMID: 22589180 DOI: 10.1002/pmic.201100608] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Proteolytic digestion is an essential step in proteomic sample processing. While this step has traditionally been implemented in homogeneous (solution) format, there is a growing trend to use heterogeneous systems in which the enzyme is immobilized on hydrogels or other solid supports. Here, we introduce the use of immobilized enzymes in hydrogels for proteomic sample processing in digital microfluidic (DMF) systems. In this technique, preformed cylindrical agarose discs bearing immobilized trypsin or pepsin were integrated into DMF devices. A fluorogenic assay was used to optimize the covalent modification procedure for enzymatic digestion efficiency, with maximum efficiency observed at 31 μg trypsin in 2-mm diameter agarose gel discs. Gel discs prepared in this manner were used in an integrated method in which proteomic samples were sequentially reduced, alkylated, and digested, with all sample and reagent handling controlled by DMF droplet operation. Mass spectrometry analysis of the products revealed that digestion using the trypsin gel discs resulted in higher sequence coverage in model analytes relative to conventional homogenous processing. Proof-of-principle was demonstrated for a parallel digestion system in which a single sample was simultaneously digested on multiple gel discs bearing different enzymes. We propose that these methods represent a useful new tool for the growing trend toward miniaturization and automation in proteomic sample processing.
Collapse
Affiliation(s)
- Vivienne N Luk
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | | | | | | | | |
Collapse
|
27
|
High throughput profiling of serum phosphoproteins/peptides using the SELDI-TOF-MS platform. Methods Mol Biol 2012; 818:199-216. [PMID: 22083825 DOI: 10.1007/978-1-61779-418-6_14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Protein phosphorylation is a dynamic post-translational modification that plays a critical role in the regulation of a wide spectrum of biological events and cellular functions including signal transduction, gene expression, cell proliferation, and apoptosis. Determination of the sites and magnitudes of protein phosphorylation has been an essential step in the analysis of the control of many biological systems. A high throughput analysis of phosphorylation of proteins would provide a simple, logical, and useful tool for a functional dissection and prediction of biological functions and signaling pathways in association with these important molecular events. We have developed a functional proteomics technique using the ProteinChip array-based SELDI-TOF-MS analysis for high throughput profiling of phosphoproteins/phosphopeptides in human serum for the early detection and diagnosis as well as for the molecular staging of human cancer. The methodology and experimental approach consists of five steps: (1) generation of a total peptide pool of serum proteins by a global trypsin digestion; (2) rapid isolation of phosphopeptides from the total serum peptide pool by an affinity selection, purification, and enrichment using a novel automated micro-bioprocessing system with phospho-antibody-conjugated paramagnetic beads and a hybrid magnet plate; (3) high throughput phosphopeptide analysis on ProteinChip arrays by automated SELDI-TOF-MS; and (4) bioinformatics and statistical methods for data analysis. This method with appropriate modifications may be equally applicable to serine-, threonine- and tyrosine-phosphorylated proteins and for selectively isolating, profiling, and identifying phosphopeptides present in a highly complex phosphor-peptide mixture prepared from various human specimens such as cells, tissue samples, and serum and other body fluids.
Collapse
|
28
|
Kaur P, Asea A. Quantitation of heat-shock proteins in clinical samples using mass spectrometry. Methods Mol Biol 2012; 787:165-88. [PMID: 21898236 DOI: 10.1007/978-1-61779-295-3_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Mass spectrometry (MS) is a powerful analytical tool for proteomics research and drug and biomarker discovery. MS enables identification and quantification of known and unknown compounds by revealing their structural and chemical properties. Proper sample preparation for MS-based analysis is a critical step in the proteomics workflow because the quality and reproducibility of sample extraction and preparation for downstream analysis significantly impact the separation and identification capabilities of mass spectrometers. The highly expressed proteins represent potential biomarkers that could aid in diagnosis, therapy, or drug development. Because the proteome is so complex, there is no one standard method for preparing protein samples for MS analysis. Protocols differ depending on the type of sample, source, experiment, and method of analysis. Molecular chaperones play significant roles in almost all biological functions due to their capacity for detecting intracellular denatured/unfolded proteins, initiating refolding or denaturation of such malfolded protein sequences and more recently for their role in the extracellular milieu as chaperokines. In this chapter, we describe the latest techniques for quantitating the expression of molecular chaperones in human clinical samples.
Collapse
Affiliation(s)
- Punit Kaur
- Division of Investigative Pathology, College of Medicine, Scott & White Memorial Hospital and Clinic, Temple, TX, USA
| | | |
Collapse
|
29
|
Diz AP, Martínez-Fernández M, Rolán-Alvarez E. Proteomics in evolutionary ecology: linking the genotype with the phenotype. Mol Ecol 2012; 21:1060-80. [PMID: 22268916 DOI: 10.1111/j.1365-294x.2011.05426.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The study of the proteome (proteomics), which includes the dynamics of protein expression, regulation, interactions and its function, has played a less prominent role in evolutionary and ecological investigations in comparison with the study of the genome and transcriptome. There are, however, a number of arguments suggesting that this situation should change. First, the proteome is closer to the phenotype than the genome or the transcriptome, and as such may be more directly responsive to natural selection, and thus closely linked to adaptation. Second, there is evidence of a low correlation between protein and transcript expression levels across genes in many different organisms. Finally, there have been some recent important technological improvements in proteomics methods that make them feasible, practical and useful to address a wide range of evolutionary questions even in nonmodel organisms. The different proteomic methods, their limitations and problems when interpreting empirical data are described and discussed. In addition, the proteomic literature pertaining to evolutionary ecology is reviewed with examples, and potential applications of proteomics in a variety of evolutionary contexts are outlined. New proteomic research trends such as the study of posttranslational modifications and protein-protein interactions, as well as the combined use of the different -omics approaches, are discussed in relation to the development of a more functional and integrated perspective, needed for achieving a more comprehensive knowledge of evolutionary change.
Collapse
Affiliation(s)
- Angel P Diz
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidade de Vigo, Vigo, Spain
| | | | | |
Collapse
|
30
|
Paramanik V, Thakur MK. Overexpression of mouse estrogen receptor-β decreases but its transactivation and ligand binding domains increase the growth characteristics of E. coli. Mol Biotechnol 2011; 47:26-33. [PMID: 20589455 DOI: 10.1007/s12033-010-9308-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Escherichia coli is one of the most common and widely used prokaryotic hosts for the expression of recombinant proteins. The overexpression of recombinant proteins occasionally increases bacterial growth but sometimes reduces it and becomes lethal to the host cells. Here, we report the overexpression of mouse ER-β and its domains in the prokaryotic expression system and its opposite effect on the growth characteristics of E. coli. ER-β protein was immunologically detected as a 53 kDa his-tag protein in the pellet of the bacterial lysate. Its overexpression, as reflected by the total protein content and expression pattern, resulted in the decrease of bacterial growth. However, the overexpression of ER-β transactivation domain (TAD) using pIVEX and ligand binding domain (LBD) using pRSETA in E. coli BL21 (DE3) show opposite pattern. TAD was immunologically detected as 20 kDa and LBD as 22 kDa protein in the supernatant of the bacterial lysate and their overexpression increased the bacterial growth.
Collapse
Affiliation(s)
- Vijay Paramanik
- Biochemistry and Molecular Biology Laboratory Centre of Advanced Study, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India
| | | |
Collapse
|
31
|
Sultana R, Butterfield DA. Identification of the oxidative stress proteome in the brain. Free Radic Biol Med 2011; 50:487-94. [PMID: 21111808 PMCID: PMC3052741 DOI: 10.1016/j.freeradbiomed.2010.11.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 11/14/2010] [Accepted: 11/16/2010] [Indexed: 12/15/2022]
Abstract
The redox proteomics technique normally combines two-dimensional gel electrophoresis, mass spectrometry, and protein databases to analyze the cell proteome from various samples, thereby leading to the identification of specific targets of oxidative modification. Oxidative stress that occurs because of increased levels of reactive oxygen species and reactive nitrogen species can target most biomolecules, consequently leading to altered physiological function of the cells. Redox proteomics has identified oxidatively modified protein targets in various pathological conditions, consequently providing insight into the pathways involved in the pathogenesis of these conditions. This approach also can be used to identify possible protective mechanisms to prevent or delay these disorders.
Collapse
Affiliation(s)
- Rukhsana Sultana
- Department of Chemistry, University of Kentucky, Lexington, KY 40506
- Center of Membrane Sciences, University of Kentucky, Lexington, KY 40506, USA
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40506, USA
| | - D. Allan Butterfield
- Department of Chemistry, University of Kentucky, Lexington, KY 40506
- Center of Membrane Sciences, University of Kentucky, Lexington, KY 40506, USA
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40506, USA
| |
Collapse
|
32
|
Lee J, Soper SA, Murray KK. Development of an efficient on-chip digestion system for protein analysis using MALDI-TOF MS. Analyst 2009; 134:2426-33. [PMID: 19918612 DOI: 10.1039/b916556h] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A solid-phase trypsin microreactor was constructed and operated with electrokinetically-driven flow for the digestion of proteins and coupled off-line with MALDI-TOF MS. The bioreactor was fabricated from poly(methyl methacrylate), PMMA, by hot embossing using a mold master prepared by micro-milling. The solid-phase bioreactor consisted of a 4 cm long, 200 microm wide, and 50 microm deep microfluidic channel that was populated with an array of 50 microm diameter micropost structures with a 50 microm inter-post spacing. The bioreactor was prepared by covalently attaching the proteolytic enzyme, trypsin, to the UV-modified surface of the PMMA microstructures using the appropriate coupling reagents. The performance of the system was evaluated using a set of proteins. The bioreactor provided efficient digestion of cytochrome c at a field strength of 375 V/cm, producing a reaction time of approximately 20 s to produce 97% sequence coverage for protein identification. Bovine serum albumin (BSA), phosphorylase b, and beta-casein were also assessed and the sequence coverages were 46, 63, and 79%, respectively, using the same reactor residence time. Furthermore, Escherichia coli was used as a model to demonstrate the feasibility of fingerprint analysis for intact cells using this solid-phase bioreactor.
Collapse
Affiliation(s)
- Jeonghoon Lee
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | | | | |
Collapse
|
33
|
Barderas MG, Tuñón J, Dardé VM, De la Cuesta F, Jiménez-Nácher JJ, Tarín N, López-Bescós L, Egido J, Vivanco F. Atorvastatin modifies the protein profile of circulating human monocytes after an acute coronary syndrome. Proteomics 2009; 9:1982-93. [PMID: 19294693 DOI: 10.1002/pmic.200700583] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Aggressive treatment with high-dose atorvastatin reduces more effectively the incidence of cardiovascular events than moderate statin therapy. The mechanism of this benefit has not been fully elucidated. In order to know the potential effects of statin treatment on the protein expression of circulating monocytes in acute coronary syndrome (ACS) patients, a proteomic analysis of these cells was carried out by 2-DE and MS. Twenty-five patients with non-ST-elevation acute coronary syndrome (NSTEACS) were randomized, the fourth day after admission, to receive ATV 80 mg/dL (n = 14) or conventional treatment (CT) (n = 11), for two months. Blood was withdrawn at the end of the treatment, and monocytes were extracted for proteomic analysis and their protein expression patterns determined. Age, sex, total cholesterol, LDL, HDL, triglycerides, body mass index, presence of hypertension, diabetes, and smoking status were not significantly different between the two groups of patients. The expression of 20 proteins was modified by intensive ATV. Among the most relevant results stand out the normalization by intensive ATV treatment of the expression of proteins that modulate inflammation and thrombosis such as protein disulfide isomerase ER60 (PDI), Annexin I, and prohibitin, or that have other protective effects as HSP-70. Thus, this approach shed light at the molecular level of the beneficial mechanisms of anti-atherothrombotic drugs.
Collapse
|
34
|
Lee J, Soper SA, Murray KK. Microfluidics with MALDI analysis for proteomics--a review. Anal Chim Acta 2009; 649:180-90. [PMID: 19699392 DOI: 10.1016/j.aca.2009.07.037] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 07/13/2009] [Accepted: 07/15/2009] [Indexed: 01/01/2023]
Abstract
Various microfluidic devices have been developed for proteomic analyses and many of these have been designed specifically for mass spectrometry detection. In this review, we present an overview of chip fabrication, microfluidic components, and the interfacing of these devices to matrix-assisted laser desorption ionization (MALDI) mass spectrometry. These devices can be directly coupled to the mass spectrometer for on-line analysis in real-time, or samples can be analyzed on-chip or deposited onto targets for off-line readout. Several approaches for combining microfluidic devices with analytical functions such as sample cleanup, digestion, and separations with MALDI mass spectrometry are discussed.
Collapse
Affiliation(s)
- Jeonghoon Lee
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | | | | |
Collapse
|
35
|
Sultana R, Butterfield DA. Proteomics identification of carbonylated and HNE-bound brain proteins in Alzheimer's disease. Methods Mol Biol 2009; 566:123-135. [PMID: 20058169 DOI: 10.1007/978-1-59745-562-6_9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Free radicals and oxidative stress play a crucial role in the pathophysiology of a wide variety of diseases including cancer and neurodegenerative disorders. Reactive oxygen and reactive nitrogen species can react with biomolecules such as proteins, lipids, nucleic acid, etc. resulting in the formation of protein carbonyls, 3-nitrotyroine, HNE-bound proteins, etc. Such modifications in proteins often lead to functional impairment, and the identification of such oxidatively modified proteins may help in delineating the mechanism of disease 1pathogenesis or progression.In this chapter, we described the protocol for the identification of oxidatively modified proteins, i.e., protein carbonyls and HNE-bound proteins in a given biological sample using three important techniques, i.e., proteomics coupled with mass spectrometry and immunochemical detection. These methods are placed in the context of our studies on Alzheimer's disease.
Collapse
Affiliation(s)
- Rukhsana Sultana
- Department of Chemistry, Sanders-Brown Center on Aging, University of Kentuck, Lexington, KY, USA
| | | |
Collapse
|
36
|
|
37
|
Warda M, Han J. Retracted: Mitochondria, the missing link between body and soul: Proteomic prospective evidence. Proteomics 2008. [DOI: 10.1002/pmic.200700695] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
38
|
Oh YJ, Gamble TC, Leonhardt D, Chung CH, Brueck SRJ, Ivory CF, Lopez GP, Petsev DN, Han SM. Monitoring FET flow control and wall adsorption of charged fluorescent dye molecules in nanochannels integrated into a multiple internal reflection infrared waveguide. LAB ON A CHIP 2008; 8:251-8. [PMID: 18231663 DOI: 10.1039/b711682a] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Using Si as the substrate, we have fabricated multiple internal reflection infrared waveguides embedded with a parallel array of nanofluidic channels. The channel width is maintained substantially below the mid-infrared wavelength to minimize infrared scattering from the channel structure and to ensure total internal reflection at the channel bottom. A Pyrex slide is anodically bonded to the top of the waveguide to seal the nanochannels, while simultaneously enabling optical access in the visible range from the top. The Si channel bottom and sidewalls are thermally oxidized to provide an electrically insulating barrier, and the Si substrate surrounding the insulating SiO(2) layer is selectively doped to function as a gate. For fluidic field effect transistor (FET) control, a DC potential is applied to the gate to manipulate the surface charge on SiO(2) channel bottom and sidewalls and therefore their zeta-potential. Depending on the polarity and magnitude, the gate potential can accelerate, decelerate, or reverse the flow. Here, we demonstrate that this nanofluidic infrared waveguide can be used to monitor the FET flow control of charged, fluorescent dye molecules during electroosmosis by multiple internal reflection Fourier transform infrared spectroscopy. Laser scanning confocal fluorescence microscopy is simultaneously used to provide a comparison and verification of the IR analysis. Using the infrared technique, we probe the vibrational modes of dye molecules, as well as those of the solvent. The observed infrared absorbance accounts for the amount of dye molecules advancing or retracting in the nanochannels, as well as adsorbing to and desorbing from the channel bottom and sidewalls.
Collapse
Affiliation(s)
- Youn-Jin Oh
- Department of Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Otero JM, Panagiotou G, Olsson L. Fueling industrial biotechnology growth with bioethanol. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2007; 108:1-40. [PMID: 17684710 DOI: 10.1007/10_2007_071] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Industrial biotechnology is the conversion of biomass via biocatalysis, microbial fermentation, or cell culture to produce chemicals, materials, and/or energy. Industrial biotechnology processes aim to be cost-competitive, environmentally favorable, and self-sustaining compared to their petrochemical equivalents. Common to all processes for the production of energy, commodity, added value, or fine chemicals is that raw materials comprise the most significant cost fraction, particularly as operating efficiencies increase through practice and improving technologies. Today, crude petroleum represents the dominant raw material for the energy and chemical sectors worldwide. Within the last 5 years petroleum prices, stability, and supply have increased, decreased, and been threatened, respectively, driving a renewed interest across academic, government, and corporate centers to utilize biomass as an alternative raw material. Specifically, bio-based ethanol as an alternative biofuel has emerged as the single largest biotechnology commodity, with close to 46 billion L produced worldwide in 2005. Bioethanol is a leading example of how systems biology tools have significantly enhanced metabolic engineering, inverse metabolic engineering, and protein and enzyme engineering strategies. This enhancement stems from method development for measurement, analysis, and data integration of functional genomics, including the transcriptome, proteome, metabolome, and fluxome. This review will show that future industrial biotechnology process development will benefit tremendously from the precedent set by bioethanol - that enabling technologies (e.g., systems biology tools) coupled with favorable economic and socio-political driving forces do yield profitable, sustainable, and environmentally responsible processes. Biofuel will continue to be the keystone of any industrial biotechnology-based economy whereby biorefineries leverage common raw materials and unit operations to integrate diverse processes to produce demand-driven product portfolios.
Collapse
Affiliation(s)
- José Manuel Otero
- Center for Microbial Biotechnology, BioCentrum, Technical University of Denmark, BioCentrum-DTU, 2800, Kgs. Lyngby, Denmark
| | | | | |
Collapse
|
40
|
Domenici E, Muglia P. The search for peripheral disease markers in psychiatry by genomic and proteomic approaches. ACTA ACUST UNITED AC 2007; 1:235-51. [DOI: 10.1517/17530059.1.2.235] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
41
|
Ghosh S, Thakur MK. Overproduction of mouse estrogen receptor alpha-ligand binding domain decreases bacterial growth. Mol Biol Rep 2007; 35:589-94. [PMID: 17786586 DOI: 10.1007/s11033-007-9128-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Accepted: 08/14/2007] [Indexed: 11/27/2022]
Abstract
Escherichia coli (E. coli) is the most widely used prokaryotic host system for the synthesis of recombinant proteins. The overproduction of recombinant proteins is sometimes lethal to the host cells. In the present study, we expressed the ligand binding domain (LBD) of mouse estrogen receptor alpha (mouse ERalpha) using an expression vector (pIVEX) in E. coli BL21(DE3) and examined the effect of production of this protein on bacterial growth. The expressed protein was immunologically detected as a 30 kD histidine-tagged protein in the soluble part of the bacterial lysate. The overproduction of mouse ERalpha-LBD, as reflected by total protein content and expression pattern, resulted in the decrease of bacterial growth.
Collapse
Affiliation(s)
- Swati Ghosh
- Biochemistry and Molecular Biology Laboratory, Center of Advanced Study in Zoology, Banaras Hindu University, Varanasi, 221005, India
| | | |
Collapse
|
42
|
Doull J, Borzelleca JF, Becker R, Daston G, DeSesso J, Fan A, Fenner-Crisp P, Holsapple M, Holson J, Craig Llewellyn G, MacGregor J, Seed J, Walls I, Woo YT, Olin S. Framework for use of toxicity screening tools in context-based decision-making. Food Chem Toxicol 2007; 45:759-96. [PMID: 17215066 DOI: 10.1016/j.fct.2006.10.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2006] [Accepted: 10/27/2006] [Indexed: 11/25/2022]
Abstract
One of the principal applications of toxicology data is to inform risk assessments and support risk management decisions that are protective of human health. Ideally, a risk assessor would have available all of the relevant information on (a) the toxicity profile of the agent of interest; (b) its interactions with living systems; and (c) the known or projected exposure scenarios: to whom, how much, by which route(s), and how often. In practice, however, complete information is seldom available. Nonetheless, decisions still must be made. Screening-level assays and tools can provide support for many aspects of the risk assessment process, as long as the limitations of the tools are understood and to the extent that the added uncertainty the tools introduce into the process can be characterized and managed. Use of these tools for decision-making may be an end in itself for risk assessment and decision-making or a preliminary step to more extensive data collection and evaluation before assessments are undertaken or completed and risk management decisions made. This paper describes a framework for the application of screening tools for human health decision-making, although with some modest modification, it could be made applicable to environmental settings as well. The framework consists of problem formulation, development of a screening strategy based on an assessment of critical data needs, and a data analysis phase that employs weight-of-evidence criteria and uncertainty analyses, and leads to context-based decisions. Criteria for determining the appropriate screening tool(s) have been identified. The choice and use of the tool(s) will depend on the question and the level of uncertainty that may be appropriate for the context in which the decision is being made. The framework is iterative, in that users may refine the question(s) as they proceed. Several case studies illustrate how the framework may be used effectively to address specific questions for any endpoint of toxicity.
Collapse
|
43
|
Schmidt MW, Houseman A, Ivanov AR, Wolf DA. Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe. Mol Syst Biol 2007; 3:79. [PMID: 17299416 PMCID: PMC1828747 DOI: 10.1038/msb4100117] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2006] [Accepted: 12/13/2006] [Indexed: 02/04/2023] Open
Abstract
The fission yeast Schizosaccharomyces pombe is a widely used model organism to study basic mechanisms of eukaryotic biology, but unlike other model organisms, its proteome remains largely uncharacterized. Using a shotgun proteomics approach based on multidimensional prefractionation and tandem mass spectrometry, we have detected ∼30% of the theoretical fission yeast proteome. Applying statistical modelling to normalize spectral counts to the number of predicted tryptic peptides, we have performed label-free quantification of 1465 proteins. The fission yeast protein data showed considerable correlations with mRNA levels and with the abundance of orthologous proteins in budding yeast. Functional pathway analysis indicated that the mRNA–protein correlation is strong for proteins involved in signalling and metabolic processes, but increasingly discordant for components of protein complexes, which clustered in groups with similar mRNA–protein ratios. Self-organizing map clustering of large-scale protein and mRNA data from fission and budding yeast revealed coordinate but not always concordant expression of components of functional pathways and protein complexes. This finding reaffirms at the protein level the considerable divergence in gene expression patterns of the two model organisms that was noticed in previous transcriptomic studies.
Collapse
Affiliation(s)
- Michael W Schmidt
- NIEHS Center for Environmental Health Proteomics Facility, Harvard School of Public Health, Boston, MA, USA
- Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA, USA
- Institute for Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Andres Houseman
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Alexander R Ivanov
- NIEHS Center for Environmental Health Proteomics Facility, Harvard School of Public Health, Boston, MA, USA
- Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA, USA
- Department of Genetics and Complex Diseases, Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA. Tel.: +1 617 432 2093; Fax: +1 617 432 2059;
| | - Dieter A Wolf
- NIEHS Center for Environmental Health Proteomics Facility, Harvard School of Public Health, Boston, MA, USA
- Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA, USA
- Department of Genetics and Complex Diseases, Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA. Tel.: +1 617 432 2093; Fax: +1 617 432 2059;
| |
Collapse
|
44
|
Choi CJ, Cunningham BT. Single-step fabrication and characterization of photonic crystal biosensors with polymer microfluidic channels. LAB ON A CHIP 2006; 6:1373-80. [PMID: 17102852 DOI: 10.1039/b603514k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
A method for simultaneously integrating label-free photonic crystal biosensor technology into microfluidic channels by a single-step replica molding process is presented. By fabricating both the sub-micron features of the photonic crystal sensor structure and the >10 microm features of a flow channel network in one step at room temperature on a plastic substrate, the sensors are automatically self-aligned with the flow channels, and patterns of arbitrary shape may be produced. By measuring changes in the resonant peak reflected wavelength from the photonic crystal structure induced by changes in dielectric permittivity within an evanescent field region near its surface, detection of bulk refractive index changes in the fluid channel or adsorption of biological material to the sensor surface is demonstrated. An imaging detection instrument is used to characterize the spatial distribution of the photonic crystal resonant wavelength, gathering thousands of independent sensor readings within a single fluid channel.
Collapse
Affiliation(s)
- Charles J Choi
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Nano Sensors Group, Micro and Nanotechnology Laboratory, 208 N. Wright St., Urbana, IL 61801, USA
| | | |
Collapse
|
45
|
Butterfield DA, Perluigi M, Sultana R. Oxidative stress in Alzheimer's disease brain: New insights from redox proteomics. Eur J Pharmacol 2006; 545:39-50. [PMID: 16860790 DOI: 10.1016/j.ejphar.2006.06.026] [Citation(s) in RCA: 253] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2005] [Revised: 11/28/2005] [Accepted: 06/13/2006] [Indexed: 12/20/2022]
Abstract
Alzheimer's disease, an age-related neurodegenerative disorder, is characterized clinically by a progressive loss of memory and cognitive functions. Neuropathologically, Alzheimer's disease is defined by the accumulation of extracellular amyloid protein deposited senile plaques and intracellular neurofibrillary tangles made of abnormal and hyperphosphorylated tau protein, regionalized neuronal death, and loss of synaptic connections within selective brain regions. Evidence has suggested a critical role for amyloid-beta peptide metabolism and oxidative stress in Alzheimer's disease pathogenesis and progression. Among the other indices of oxidative stress in Alzheimer's disease brain are protein carbonyls and 3-nitrotyrosine, which are the markers of protein oxidation. Thus, in this review, we discuss the application of redox proteomics for the identification of oxidatively modified proteins in Alzheimer's disease brain and also discuss the functions associated with the identified oxidized proteins in relation to Alzheimer's disease pathology. The information obtained from proteomics may be helpful in understanding the molecular mechanisms involved in the development and progression of Alzheimer's disease as well as of other neurodegenerative disorders. Further, redox proteomics may provide potential targets for drug therapy in Alzheimer's disease.
Collapse
|
46
|
Ivanova EP, Wright JP, Pham DK, Brack N, Pigram P, Alekseeva YV, Demyashev GM, Nicolau DV. A comparative study between the adsorption and covalent binding of human immunoglobulin and lysozyme on surface-modified poly(
tert
-butyl methacrylate). Biomed Mater 2006; 1:24-32. [DOI: 10.1088/1748-6041/1/1/004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
47
|
Abstract
We report on an observed regularity in the overall response of cell proteome under influence of different doses of a peroxisome proliferator. Our analysis for the first time demonstrates presence of hormesis at the cellular level. It is shown that despite the fact that the response of individual proteins remains unpredictable, the perturbation of proteome as a whole (measured as the average departure of protein abundances from the corresponding values of the control group) shows regularity: It initially decreases, reaches a minimum, and then increases as the concentration of the used proliferator continue to increase. The work is based on the available data of Anderson at al. on the effects of peroxisome proliferator LY171883 on protein abundances in mouse liver when administrated at different concentrations.
Collapse
Affiliation(s)
- Milan Randić
- Complex Systems Research Group, X-rays Unit, RIAIDT, Edificio CACTUS, University of Santiago de Compostela, Spain
| | | |
Collapse
|
48
|
Abstract
Fish cell lines are relatively easy to culture and most have simple growth requirements that make cross contamination a potential problem. Cell line contamination is not an uncommon incident in laboratories handling more than one cell line and many reports have been made on cross contamination of mammalian cell lines. Although problems of misidentification and cross-contamination of fish cell lines have rarely been reported, these are issues of concern for cell culturists that can make scientific results and their reproducibility unreliable. Proper identification of cell lines is thus crucial and protocols for routine and rapid screening are preferred. Cytogenetic evaluation, DNA fingerprinting, microsatellite analysis and PCR methods have been published for inter-species identification of many cell lines, but discerning intra-species contamination has been challenging. More complex DNA fingerprinting and hybridization techniques coupled with isoenzyme analysis have been developed to discriminate intra-species contamination, however, these require complex and time consuming procedures to enable cell identification thus are difficult to apply for routine use. A simple proteomic approach has been made to identify several fish cell lines derived from tissues of the same or differing species. Protein expression signatures (PES) of the evaluated fish cell lines have been developed using 2-DE and image analysis. A higher degree of concordance was seen among cell lines derived from rainbow trout, than from other fish species. Similar concordance was seen in cells derived from the same tissues than from other tissues within the same species. These profiles have been saved in an electronic databank and could be made available to be used for discerning the origins of the various cell lines evaluated. This proteomic approach could thus serve as an additional, valuable and reliable technique for the identification of fish cell lines.
Collapse
Affiliation(s)
- Sarah K Wagg
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, Canada
| | | |
Collapse
|
49
|
Ruyani A, Sudarwati S, Sutasurya LA, Sumarsono SH, Kim DJ, Chung JH. A teratoproteomics analysis: heat shock protein 70 is upregulated in mouse forelimb bud by methoxyacetic acid treatment. ACTA ACUST UNITED AC 2005; 73:517-21. [PMID: 15959878 DOI: 10.1002/bdra.20146] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Methoxyacetic acid (MAA) causes fetal limb abnormalities when the substance is administrated on gestation day (GD) 11 in mice. Limb abnormalities are caused mainly by extensive cell death in the mesoderm of the limb plate. This investigation focused on identifying a protein that is linked with mouse limb teratogenicity. METHODS A single dose of MAA at 10 mmol/kg body weight was administered by gavage on GD 11; controls were administered vehicle only. Dams were killed by cervical dislocation 4 hr after treatment and forelimb buds were isolated from both the control and treated embryos. Proteins in forelimb buds GD 11 + 4 hr were precipitated out using 40-60% ammonium sulfate and were then analyzed by 2D SDS-PAGE. Excised protein spots were identified by mass spectrometry and amino acid internal sequence analysis. Identified protein was further confirmed by Western blotting. RESULTS Two-dimensional gel analysis indicated that 1 protein spot of 81.7 kDa/pI 7.3 was overexpressed, and the protein matched heat shock protein 70 (HSP70; accession no. P08109, SwissProt). CONCLUSIONS The results suggest that MAA, when administered to pregnant mice, upregulates HSP70 in the forelimb buds.
Collapse
Affiliation(s)
- Aceng Ruyani
- Program Studi Pendidikan Biologi, Universitas Bengkulu, Jalan Raya Kandang Limun, Bengkulu, Indonesia
| | | | | | | | | | | |
Collapse
|
50
|
Srivastava S, Srivastava RG. Proteomics in the forefront of cancer biomarker discovery. J Proteome Res 2005; 4:1098-103. [PMID: 16083258 DOI: 10.1021/pr050016u] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sudhir Srivastava
- Cancer Biomarkers Research Group of National Cancer Institute, EPN 3142, 6130 Executive Boulevard, Rockville, MD 20852, USA.
| | | |
Collapse
|