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Barrett A, Gnehm D, Jones J, Trask BC. α1‐antitrypsin and C‐reactive protein levels in tear fluid after continuous contact lens wear. Clin Exp Optom 2021; 97:66-71. [DOI: 10.1111/cxo.12093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 01/28/2013] [Accepted: 02/05/2013] [Indexed: 01/04/2023] Open
Affiliation(s)
- Aaron Barrett
- Medical Laboratory Sciences Department, Weber State University, Ogden, Utah, USA,
| | - Derek Gnehm
- Medical Laboratory Sciences Department, Weber State University, Ogden, Utah, USA,
| | - Jordan Jones
- Medical Laboratory Sciences Department, Weber State University, Ogden, Utah, USA,
| | - Barbara C Trask
- Zoology Department, Weber State University, Ogden, Utah, USA,
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2
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Singh S, Sharma S, Basu S. Rabbit models of dry eye disease: Current understanding and unmet needs for translational research. Exp Eye Res 2021; 206:108538. [PMID: 33771517 DOI: 10.1016/j.exer.2021.108538] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 11/17/2022]
Abstract
Dry eye disease (DED) is emerging as an eye health pandemic, affecting millions worldwide. The development of novel drugs, drug delivery systems, and targeted therapies for addressing the inflammation in DED necessitates progress in experimental models of DED. Animal models of DED have been created for simulating the two clinically described forms of DED: lacrimal insufficiency and the evaporative DED models. Although most DED models have relied upon rodents, the larger eye size and longer life span of rabbits and the closer resemblance to human lacrimal glands, render rabbits a promising near-ideal model for studying DED. Since the first rabbit DED model was described, numerous modifications including the use of topical epitheliotoxic drugs, neural abolition, activated lymphocytes injection, and surgical dacryoadenectomy have been introduced. The stability of these models, whether short-term or long-term, accordingly guides their experimental or therapeutic utility. A rabbit autoimmune dacryoadenitis model has successfully simulated DED signs and features of lacrimal gland inflammation, as observed in Sjogren's syndrome, that improved with mesenchymal stem cell therapy. This review summarizes the comparative microscopic anatomy of rabbit and human lacrimal glands, various existing rabbit DED models and their respective suitability for understanding pathogenetic mechanism of DED or for experimental drug testing. Also, the insights gained from animal models in dry eye management is described along with the future perspectives. There is still a pressing need of developing rabbit models for studying the pathogenesis of complex ocular surface changes in evaporative and aqueous deficiency DED other than autoimmune dacryoadenitis.
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Affiliation(s)
- Swati Singh
- Center for Ocular Regeneration (CORE), L V Prasad Eye Institute, Hyderabad, Telangana, India; Brien Holden Center for Eye Research (BHERC), L V Prasad Eye Institute, Hyderabad, Telangana, India
| | - Savitri Sharma
- Jhaveri Microbiology Centre, L V Prasad Eye Institute, Hyderabad, Telangana, India
| | - Sayan Basu
- Center for Ocular Regeneration (CORE), L V Prasad Eye Institute, Hyderabad, Telangana, India; Brien Holden Center for Eye Research (BHERC), L V Prasad Eye Institute, Hyderabad, Telangana, India; The Cornea Institute, L V Prasad Eye Institute, Hyderabad, Telangana, India.
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3
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Zhang T, Hu L, Ma H, Ni F, Liu F, Chen H. Detection of Tear Components Using Matrix-Assisted Laser Desorption Ionization/Time-of-Flight Mass Spectrometry for Rapid Dry Eye Diagnosis. J Proteome Res 2020; 19:3644-3651. [PMID: 32786892 DOI: 10.1021/acs.jproteome.0c00138] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The tear is a biological fluid that has the diagnostic potential for ocular diseases. Extracellular vesicles (EVs), widly detected in various biofluids including tears, are nanoparticles released by living cells and considered as promising detection sources for noninvasive liquid biopsy. Understanding the roles of tears and tear-EVs in ocular diseases such as dry eye can facilitate the studies of clinical diagnosis, which usually entails detecting such liquid objects with a rapid and effective method. In this study, we used a mass spectrometry-based strategy to analyze peptidome/proteome profiles of tears and EVs for rapid dry eye diagnosis. Nanosized EVs were isolated from tears of both healthy control (HC) individuals and dry eye syndrome (DES) patients, and the tear compositions were further analyzed by tracking their fingerprints with matrix-assisted laser desorption ionization/time-of-flight mass spectrometry. The fingerprints of tear-EVs could be observed in a dose-dependent manner and tears, allowing for comparison of the discriminant peaks between tears and EVs. By analyzing these peaks, the fingerprints of both tear and tear-EVs were showed to have the capability of distinguishing patients with DES from HC donors and providing an efficient way for screening potential DES biomarkers. The proposed tear and EV fingerprinting approach is expected to be a potential tool in the rapid diagnosis of ocular diseases and in-depth research on pathogenesis. Data are available via ProteomeXchange with identifier PXD020217.
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Affiliation(s)
- Ting Zhang
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Liang Hu
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Huixiang Ma
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Fangfang Ni
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Fei Liu
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.,Wenzhou Institute, University of Chinese Academy of Science, Wenzhou, Zhejiang 325001, China
| | - Hao Chen
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
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4
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Honkanen R, Huang W, Huang L, Kaplowitz K, Weissbart S, Rigas B. A New Rabbit Model of Chronic Dry Eye Disease Induced by Complete Surgical Dacryoadenectomy. Curr Eye Res 2019; 44:863-872. [PMID: 30983427 DOI: 10.1080/02713683.2019.1594933] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Purpose/Aim: Dry eye disease (DED), common and suboptimally treated, is in need of novel animal models to understand its pathophysiology and assess the efficacy and other parameters of new pharmacological agents for its treatment. The more than 10 rabbit models of DED described to date have significant limitations including induction of mild disease, lack of consistency, and off-target effects when chemical agents are used for disease induction. Our aim was to develop a new model of chronic DED in rabbits that overcomes the limitations of existing models. MATERIALS AND METHODS We performed a complete surgical resection of all orbital lacrimal glands (LGs; dacryoadenectomy) in normal adult New Zealand White rabbits. One week after removal of the nictitating membrane, we surgically removed the orbital superior LG, followed by removal of the palpebral superior LG, and finally removal of the inferior LG. Surgery was performed under anesthesia, required about 1 h/eye, and was well-tolerated. RESULTS Dacryoadenectomy induced severe DED, evidenced by >90% reduction in the tear break up time test, 50% reduction in the Schirmer tear test, 10% increase in tear osmolarity, and a marked increase in the rose bengal staining score. DED was sustained and essentially unchanged for the eight weeks of observation. Sham-operated rabbits showed no such changes, with the exception of a non-significant and transient reduction in the tear break up time test, a response to ocular surgery. CONCLUSIONS This model of stable, chronic, predominantly aqueous-deficient DED recapitulates key clinical and histological features of human DED and is suitable for the study of ocular surface homeostasis, of the pathophysiology of DED, and of the efficacy of candidate drugs for DED treatment.
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Affiliation(s)
- Robert Honkanen
- a Department of Ophthalmology, Health Sciences Center L2 , NY , USA
| | - Wei Huang
- a Department of Ophthalmology, Health Sciences Center L2 , NY , USA.,b Second Xiangya Hospital, Central South University , Hunan , China
| | - Liqun Huang
- c Department of Medicine, Health Sciences Center L17 , NY , USA.,d Medicon Pharmaceuticals, Inc, Long Island High Technology Incubator , Stony Brook , NY , USA
| | - Kevin Kaplowitz
- a Department of Ophthalmology, Health Sciences Center L2 , NY , USA
| | - Sarah Weissbart
- a Department of Ophthalmology, Health Sciences Center L2 , NY , USA
| | - Basil Rigas
- e Department of Preventive Medicine, Stony Brook University , Stony Brook , NY , USA
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5
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Nättinen J, Jylhä A, Aapola U, Parkkari M, Mikhailova A, Beuerman RW, Uusitalo H. Patient stratification in clinical glaucoma trials using the individual tear proteome. Sci Rep 2018; 8:12038. [PMID: 30104599 PMCID: PMC6089987 DOI: 10.1038/s41598-018-30369-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/24/2018] [Indexed: 12/20/2022] Open
Abstract
Glaucoma patients are prone to concomitant ocular surface diseases; however, switching from preserved to preservative-free medication can often alleviate these symptoms. The objective of this study was to examine how the adverse effects and tear proteome change for glaucoma patients (n = 28) during a 12-month drug switch from preserved latanoprost (Xalatan) to preservative-free tafluprost (Taflotan). We hypothesized that patient stratification could help identify novel recovery patterns in both tear proteomics and clinical data. In order to accomplish patient stratification, we implemented sequential window acquisition of all theoretical mass spectrometry (SWATH-MS) as a tool for quantitative analysis of individual tear protein profiles. During each visit (baseline and four follow-up visits), the patients' tears were sampled and the state of their ocular surface was evaluated clinically. Altogether 785 proteins were quantified from each tear sample using SWATH strategy and as these protein expression levels were compared between baseline and 12-month follow-up, three distinct patient groups were identified. We evaluated how these patient groups differed in their protein expression levels at baseline and discovered that the patients with increased levels of pro-inflammatory proteins and decreased levels of protective proteins benefitted most from the medication switch.
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Affiliation(s)
- Janika Nättinen
- SILK, Department of Ophthalmology, Faculty of Medicine and Life Sciences and BioMediTech, University of Tampere, Tampere, Finland.
| | - Antti Jylhä
- SILK, Department of Ophthalmology, Faculty of Medicine and Life Sciences and BioMediTech, University of Tampere, Tampere, Finland
| | - Ulla Aapola
- SILK, Department of Ophthalmology, Faculty of Medicine and Life Sciences and BioMediTech, University of Tampere, Tampere, Finland
| | - Minna Parkkari
- SILK, Department of Ophthalmology, Faculty of Medicine and Life Sciences and BioMediTech, University of Tampere, Tampere, Finland
| | - Alexandra Mikhailova
- SILK, Department of Ophthalmology, Faculty of Medicine and Life Sciences and BioMediTech, University of Tampere, Tampere, Finland
| | - Roger W Beuerman
- SILK, Department of Ophthalmology, Faculty of Medicine and Life Sciences and BioMediTech, University of Tampere, Tampere, Finland.,Singapore Eye Research Institute, Singapore, Singapore.,Duke-NUS Medical School Ophthalmology and Visual Sciences Academic Clinical Program, Singapore, Singapore
| | - Hannu Uusitalo
- SILK, Department of Ophthalmology, Faculty of Medicine and Life Sciences and BioMediTech, University of Tampere, Tampere, Finland.,Tays Eye Centre, Tampere University Hospital, Tampere, Finland
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6
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Shi Y, Jian L, Han D, Ren Y. Isolation of an Antifungal Pathogenesis-Related Protein from Naked Oat ( Avena nuda) Seeds. Cereal Chem 2015. [DOI: 10.1094/cchem-12-13-0251-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yawei Shi
- Corresponding author. Phone: +86-0351-7018268
| | - Liu Jian
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China
| | - Deping Han
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China
| | - Yemei Ren
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China
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7
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Saraygord-Afshari N, Naderi-Manesh H, Naderi M. Increasing proteome coverage for gel-based human tear proteome maps: towards a more comprehensive profiling. Biomed Chromatogr 2014; 29:1056-67. [DOI: 10.1002/bmc.3392] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Revised: 09/29/2014] [Accepted: 10/20/2014] [Indexed: 01/25/2023]
Affiliation(s)
- Neda Saraygord-Afshari
- Department of Biophysics, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| | - Hossein Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| | - Mostafa Naderi
- Department of Ophthalmology; Bina eye hospital; Tehran Iran
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8
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Farias E, Yasunaga KL, Peixoto RV, Fonseca MP, Fontes W, Galera PD. Comparison of two methods of tear sampling for protein quantification by Bradford method. PESQUISA VETERINARIA BRASILEIRA 2013. [DOI: 10.1590/s0100-736x2013000200021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The aim of this study was to compare two methods of tear sampling for protein quantification. Tear samples were collected from 29 healthy dogs (58 eyes) using Schirmer tear test (STT) strip and microcapillary tubes. The samples were frozen at -80ºC and analyzed by the Bradford method. Results were analyzed by Student's t test. The average protein concentration and standard deviation from tears collected with microcapillary tube were 4.45mg/mL ±0.35 and 4,52mg/mL ±0.29 for right and left eyes respectively. The average protein concentration and standard deviation from tears collected with Schirmer Tear Test (STT) strip were and 54.5mg/mL ±0.63 and 54.15mg/mL ±0.65 to right and left eyes respectively. Statistically significant differences (p<0.001) were found between the methods. In the conditions in which this study was conducted, the average protein concentration obtained with the Bradford test from tear samples obtained by Schirmer Tear Test (STT) strip showed values higher than those obtained with microcapillary tube. It is important that concentration of tear protein pattern values should be analyzed according the method used to collect tear samples.
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9
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Aluru SV, Agarwal S, Srinivasan B, Iyer GK, Rajappa SM, Tatu U, Padmanabhan P, Subramanian N, Narayanasamy A. Lacrimal proline rich 4 (LPRR4) protein in the tear fluid is a potential biomarker of dry eye syndrome. PLoS One 2012; 7:e51979. [PMID: 23272196 PMCID: PMC3525644 DOI: 10.1371/journal.pone.0051979] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 11/07/2012] [Indexed: 12/02/2022] Open
Abstract
Dry eye syndrome (DES) is a complex, multifactorial, immune-associated disorder of the tear and ocular surface. DES with a high prevalence world over needs identification of potential biomarkers so as to understand not only the disease mechanism but also to identify drug targets. In this study we looked for differentially expressed proteins in tear samples of DES to arrive at characteristic biomarkers. As part of a prospective case-control study, tear specimen were collected using Schirmer strips from 129 dry eye cases and 73 age matched controls. 2D electrophoresis (2DE) and Differential gel electrophoresis (DIGE) was done to identify differentially expressed proteins. One of the differentially expressed protein in DES is lacrimal proline rich 4 protein (LPRR4). LPRR4 protein expression was quantified by enzyme immune sorbent assay (ELISA). LPRR4 was down regulated significantly in all types of dry eye cases, correlating with the disease severity as measured by clinical investigations. Further characterization of the protein is required to assess its therapeutic potential in DES.
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Affiliation(s)
- Saijyothi Venkata Aluru
- Biochemistry and Cell Biology Department, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamilnadu, India
| | - Shweta Agarwal
- Ocular Surface Clinic, Medical Research Foundation, Sankara Nethralaya, Chennai, Tamilnadu, India
| | - Bhaskar Srinivasan
- Ocular Surface Clinic, Medical Research Foundation, Sankara Nethralaya, Chennai, Tamilnadu, India
| | - Geetha Krishnan Iyer
- Ocular Surface Clinic, Medical Research Foundation, Sankara Nethralaya, Chennai, Tamilnadu, India
| | | | - Utpal Tatu
- Biochemistry Department, Indian Institute of Science (IISc.), Bangalore, Karnataka, India
| | - Prema Padmanabhan
- Ocular Surface Clinic, Medical Research Foundation, Sankara Nethralaya, Chennai, Tamilnadu, India
| | - Nirmala Subramanian
- Oculoplasty Department, Medical Research Foundation, Sankara Nethralaya, Chennai, Tamilnadu, India
| | - Angayarkanni Narayanasamy
- Biochemistry and Cell Biology Department, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamilnadu, India
- * E-mail:
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10
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Zhou L, Beuerman RW, Chew AP, Koh SK, Cafaro TA, Urrets-Zavalia EA, Urrets-Zavalia JA, Li SFY, Serra HM. Quantitative Analysis of N-Linked Glycoproteins in Tear Fluid of Climatic Droplet Keratopathy by Glycopeptide Capture and iTRAQ. J Proteome Res 2009; 8:1992-2003. [DOI: 10.1021/pr800962q] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Lei Zhou
- Singapore Eye Research Institute, Singapore, Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Department of Chemistry, National University of Singapore, Singapore, CIBICI, Faculty of Chemistry, National University of Córdoba, Argentina, Department of Ophthalmology, Clínica Universitaria Reina Fabiola, Argentina, Ophthalmology, Catholic University of Cordoba, Argentina
| | - Roger W. Beuerman
- Singapore Eye Research Institute, Singapore, Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Department of Chemistry, National University of Singapore, Singapore, CIBICI, Faculty of Chemistry, National University of Córdoba, Argentina, Department of Ophthalmology, Clínica Universitaria Reina Fabiola, Argentina, Ophthalmology, Catholic University of Cordoba, Argentina
| | - Ai Ping Chew
- Singapore Eye Research Institute, Singapore, Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Department of Chemistry, National University of Singapore, Singapore, CIBICI, Faculty of Chemistry, National University of Córdoba, Argentina, Department of Ophthalmology, Clínica Universitaria Reina Fabiola, Argentina, Ophthalmology, Catholic University of Cordoba, Argentina
| | - Siew Kwan Koh
- Singapore Eye Research Institute, Singapore, Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Department of Chemistry, National University of Singapore, Singapore, CIBICI, Faculty of Chemistry, National University of Córdoba, Argentina, Department of Ophthalmology, Clínica Universitaria Reina Fabiola, Argentina, Ophthalmology, Catholic University of Cordoba, Argentina
| | - Thamara A. Cafaro
- Singapore Eye Research Institute, Singapore, Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Department of Chemistry, National University of Singapore, Singapore, CIBICI, Faculty of Chemistry, National University of Córdoba, Argentina, Department of Ophthalmology, Clínica Universitaria Reina Fabiola, Argentina, Ophthalmology, Catholic University of Cordoba, Argentina
| | - Enrique A. Urrets-Zavalia
- Singapore Eye Research Institute, Singapore, Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Department of Chemistry, National University of Singapore, Singapore, CIBICI, Faculty of Chemistry, National University of Córdoba, Argentina, Department of Ophthalmology, Clínica Universitaria Reina Fabiola, Argentina, Ophthalmology, Catholic University of Cordoba, Argentina
| | - Julio A. Urrets-Zavalia
- Singapore Eye Research Institute, Singapore, Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Department of Chemistry, National University of Singapore, Singapore, CIBICI, Faculty of Chemistry, National University of Córdoba, Argentina, Department of Ophthalmology, Clínica Universitaria Reina Fabiola, Argentina, Ophthalmology, Catholic University of Cordoba, Argentina
| | - Sam F. Y. Li
- Singapore Eye Research Institute, Singapore, Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Department of Chemistry, National University of Singapore, Singapore, CIBICI, Faculty of Chemistry, National University of Córdoba, Argentina, Department of Ophthalmology, Clínica Universitaria Reina Fabiola, Argentina, Ophthalmology, Catholic University of Cordoba, Argentina
| | - Horacio M. Serra
- Singapore Eye Research Institute, Singapore, Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Department of Chemistry, National University of Singapore, Singapore, CIBICI, Faculty of Chemistry, National University of Córdoba, Argentina, Department of Ophthalmology, Clínica Universitaria Reina Fabiola, Argentina, Ophthalmology, Catholic University of Cordoba, Argentina
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11
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WEI Y, MEI Y, XU Z, WANG C, GUO Y, DU Y, ZHANG W. A Novel MALDI Matrix for Analyzing Peptides and Proteins: Paraffin Wax Immobilized Matrix. CHINESE J CHEM 2009. [DOI: 10.1002/cjoc.200990000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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12
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13
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Proteomics as a research tool in clinical and experimental ophthalmology. Proteomics Clin Appl 2008; 2:762-75. [DOI: 10.1002/prca.200780094] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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14
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Ham BM, Yang F, Jayachandran H, Jaitly N, Monroe ME, Gritsenko MA, Livesay EA, Zhao R, Purvine SO, Orton D, Adkins JN, Camp DG, Rossie S, Smith RD. The influence of sample preparation and replicate analyses on HeLa Cell phosphoproteome coverage. J Proteome Res 2008; 7:2215-21. [PMID: 18412383 DOI: 10.1021/pr700575m] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ongoing optimization of proteomic methodologies seeks to improve both the coverage and confidence of protein identifications. The optimization of sample preparation, inclusion of technical replicates (repeated instrumental analysis of the same sample), and biological replicates (multiple individual samples) are crucial in proteomic studies to avoid the pitfalls associated with single point analysis and under-sampling. Phosphopeptides were isolated from HeLa cells and analyzed by nano-reversed phase liquid chromatography electrospray ionization tandem mass spectrometry (nano-RP-LC-MS/MS). We observed that a detergent-based protein extraction approach, followed with additional steps for nucleic acid removal, provided a simple alternative to the broadly used Trizol extraction. The evaluation of four technical replicates demonstrated measurement reproducibility with low percent variance in peptide responses at approximately 3%, where additional peptide identifications were made with each added technical replicate. The inclusion of six technical replicates for moderately complex protein extracts (approximately 4000 uniquely identified peptides per data set) affords the optimal collection of peptide information.
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Affiliation(s)
- Bryan M Ham
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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15
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Investigation of the human tear film proteome using multiple proteomic approaches. Mol Vis 2008; 14:456-70. [PMID: 18334958 PMCID: PMC2268847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Accepted: 02/27/2008] [Indexed: 11/18/2022] Open
Abstract
PURPOSE The purpose of this work was to examine the tear film proteome using a combination of one-dimensional (1D) and two dimensional (2D) gel electrophoresis and mass spectrometry-based techniques and to explore the effect of the tear collection methods on the tear proteome. METHODS Tear samples from eight normal non-contact lens wearing human subjects collected by Drummond glass microcapillary and Schirmer strips were subjected to 1D-sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), 2D-SDS-PAGE, and 2D LC-MS/MS (Multidimensional protein identification technology - MudPIT). Bands or cores from the 1D- and 2D-SDS-PAGE were cut, digested with trypsin, and analyzed by tandem mass spectrometry for identification by the generation of sequence tags. RESULTS In total (across sampling and proteomic methods), 97 unique proteins were observed, and a significant number of the spots/bands in the PAGE were from posttranslational modifications. Fifty-four unique proteins were identified from proteins extracted from the Schirmer strips in comparison to 13 unique proteins identified from capillary tubes, and 30 unique proteins were identified by both collection methods. Secreted (serum) proteins were predominantly observed from tears collected by capillary whereas a combination of cellular and serum proteins were identified from tear film collected by Schirmer strips. CONCLUSIONS Overall, these results suggest that the tear film collection and the proteomic method impacts the proteins present in the tear film and that care should be exercised in choosing a tear collection method to best correlate to the experiment being conducted or the hypothesis that is being tested.
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16
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Lam TC, Chun RKM, Li KK, To CH. Application of proteomic technology in eye research: a mini review. Clin Exp Optom 2008; 91:23-33. [PMID: 18045249 DOI: 10.1111/j.1444-0938.2007.00194.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Proteomics is a rapidly growing research area for the study of the protein cognate of genomic data. This review gives a brief overview of the modern proteomic technology. In addition to general applications of proteomics, we highlight its contribution to studying the physiology of different ocular tissues. We also summarise the published proteomic literature in the broad context of ophthalmic diseases, such as cataract, age-related maculopathy, diabetic retinopathy, glaucoma and myopia. The proteomic technology is a useful research tool and it will continue to advance our understanding of a variety of molecular processes in ocular tissues and diseases.
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Affiliation(s)
- Thomas C Lam
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
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17
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Zhou L, Beuerman RW, Huang L, Barathi A, Foo YH, Li SFY, Chew FT, Tan D. Proteomic analysis of rabbit tear fluid: Defensin levels after an experimental corneal wound are correlated to wound closure. Proteomics 2007; 7:3194-206. [PMID: 17676663 DOI: 10.1002/pmic.200700137] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The cornea is the major refracting optical element of the eye and therefore critical for forming a retinal image. The exposed surface of the eye is protected from pathogens by the innate immune system whose components include defensins, naturally occurring peptides with antimicrobial properties, and the physical barrier formed by the outer epithelial layer of the cornea. The proteomic approach has revealed that tear levels of defensins are correlated with the course of healing of an experimental corneal wound. Tears were collected from New Zealand White rabbits prior to (day 0) and daily for 5 days (days 1-5) following a standard unilateral 6 mm diameter corneal epithelial abrasion. Tear protein profiles obtained from wounded and contra-lateral control eyes were compared using SELDI ProteinChip technology. Peptides and proteins of interest were purified by RP-HPLC and characterized by nanoESI-MS/MS. Mass spectra of tears on post-wound day 1, revealed 13 peaks whose level decreased and five that increased. During wound healing the tear protein profile correlated with wound closure. An important finding was that the levels of rabbit defensins (NP-1 and NP-2), which were elevated after wounding returned to normal levels by the time the corneal abrasion healed. Relative quantification of NP-2 in tear fluid prior to (day 0) and after corneal wounding (days 1- 3) was determined using iTRAQ technology. A corneal wound eliminates the barrier function of innate immunity and puts the cornea at risk from microbial attack until the epithelial cells restore the surface barrier. The increased availability of defensins in the tears during healing suggests that these peptides could protect the cornea from microbial attack during a period of increased vulnerability.
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Affiliation(s)
- Lei Zhou
- Singapore Eye Research Institute, Singapore
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