Journal of ocular biology, diseases, and informatics最新文献_第7页

Journal of ocular biology, diseases, and informatics Pub Date : 2010-02-05 DOI: 10.1007/s12177-009-9048-0

Justine R Smith

引用次数: 2

Genetic analysis of typical wet-type age-related macular degeneration and polypoidal choroidal vasculopathy in Japanese population. 日本人群中典型湿型老年性黄斑变性和息肉样脉络膜血管病变的遗传分析。

Journal of ocular biology, diseases, and informatics Pub Date : 2009-12-22 DOI: 10.1007/s12177-009-9047-1

Asako Goto, Masakazu Akahori, Haru Okamoto, Masayoshi Minami, Naoki Terauchi, Yuji Haruhata, Minoru Obazawa, Toru Noda, Miki Honda, Atsushi Mizota, Minoru Tanaka, Takaaki Hayashi, Masaki Tanito, Naoko Ogata, Takeshi Iwata

{"title":"Genetic analysis of typical wet-type age-related macular degeneration and polypoidal choroidal vasculopathy in Japanese population.","authors":"Asako Goto, Masakazu Akahori, Haru Okamoto, Masayoshi Minami, Naoki Terauchi, Yuji Haruhata, Minoru Obazawa, Toru Noda, Miki Honda, Atsushi Mizota, Minoru Tanaka, Takaaki Hayashi, Masaki Tanito, Naoko Ogata, Takeshi Iwata","doi":"10.1007/s12177-009-9047-1","DOIUrl":"https://doi.org/10.1007/s12177-009-9047-1","url":null,"abstract":"Age-related macular degeneration (AMD) is a common cause of blindness in the elderly. Caucasian patients are predominantly affected by the dry form of AMD, whereas Japanese patients have predominantly the wet form of AMD and/or polypoidal choroidal vasculopathy (PCV). Although genetic association in the 10q26 (ARMS2/HTRA1) region has been established in many ethnic groups for dry-type AMD, typical wet-type AMD, and PCV, the contribution of the 1q32 (CFH) region seem to differ among these groups. Here we show a single nucleotide polymorphism (SNP) in the ARMS2/HTRA1 locus is associated in the whole genome for Japanese typical wet-type AMD (rs10490924: p = 4.1 x 10(-4), OR = 4.16) and PCV (rs10490924: p = 3.7 x 10(-8), OR = 2.72) followed by CFH (rs800292: p = 7.4 x 10(-5), OR = 2.08; p = 2.6 x 10(-4), OR = 2.00), which differs from previous studies in Caucasian populations. Moreover, a SNP (rs2241394) in complement component C3 gene showed significant association with PCV (p = 2.5 x 10(-3), OR = 3.47). We conclude that dry-type AMD, typical wet-type AMD, and PCV have both common and distinct genetic risks that become apparent when comparing Japanese versus Caucasian populations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12177-009-9047-1) contains supplementary material, which is available to authorized users.","PeriodicalId":73873,"journal":{"name":"Journal of ocular biology, diseases, and informatics","volume":" ","pages":"164-175"},"PeriodicalIF":0.0,"publicationDate":"2009-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12177-009-9047-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28714116","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 62

Transcriptomic comparison of the retina in two mouse models of diabetes. 两种糖尿病小鼠模型视网膜的转录组比较。

Journal of ocular biology, diseases, and informatics Pub Date : 2009-12-12 DOI: 10.1007/s12177-009-9045-3

Willard M Freeman, Georgina V Bixler, Robert M Brucklacher, Erin Walsh, Scot R Kimball, Leonard S Jefferson, Sarah K Bronson

{"title":"Transcriptomic comparison of the retina in two mouse models of diabetes.","authors":"Willard M Freeman, Georgina V Bixler, Robert M Brucklacher, Erin Walsh, Scot R Kimball, Leonard S Jefferson, Sarah K Bronson","doi":"10.1007/s12177-009-9045-3","DOIUrl":"10.1007/s12177-009-9045-3","url":null,"abstract":"Mouse models of type I diabetes offer the potential to combine genetic approaches with other pharmacological or physiological manipulations to investigate the pathophysiology and treatment of diabetic retinopathy. Type I diabetes is induced in mice through chemical toxins or can arise spontaneously from genetic mutations. Both models are associated with retinal vascular and neuronal changes. Retinal transcriptomic responses in C57BL/6J mice treated with streptozotocin and Ins2(Akita/+) were compared after 3 months of hyperglycemia. Specific gene expression changes suggest a neurovascular inflammatory response in diabetic retinopathy. Genes common to the two models may represent the response of the retina to hyperglycemia, while changes unique to each model may represent time-dependent disease progression differences in the various models. Further investigation of the commonalities and differences between mouse models of type I diabetes may define cause and effect events in early diabetic retinopathy disease progression. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12177-009-9045-3) contains supplementary material, which is available to authorized users.","PeriodicalId":73873,"journal":{"name":"Journal of ocular biology, diseases, and informatics","volume":" ","pages":"202-213"},"PeriodicalIF":0.0,"publicationDate":"2009-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/25/18/12177_2009_Article_9045.PMC2816812.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28715156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The role of DNA microarrays in Toxoplasma gondii research, the causative agent of ocular toxoplasmosis. DNA微阵列在眼部弓形虫病病原刚地弓形虫研究中的作用。

Journal of ocular biology, diseases, and informatics Pub Date : 2009-12-12 DOI: 10.1007/s12177-009-9040-8

Kevin M Brown, Ira J Blader

{"title":"The role of DNA microarrays in Toxoplasma gondii research, the causative agent of ocular toxoplasmosis.","authors":"Kevin M Brown, Ira J Blader","doi":"10.1007/s12177-009-9040-8","DOIUrl":"10.1007/s12177-009-9040-8","url":null,"abstract":"Ocular toxoplasmosis, which is caused by the protozoan parasite Toxoplasma gondii, is the leading cause of retinochoroiditis. Toxoplasma is an obligate intracellular pathogen that replicates within a parasitophorous vacuole. Infections are initiated by digestion of parasites deposited in cat feces or in undercooked meat. Parasites then disseminate to target tissues that include the retina where they then develop into long-lived asymptomatic tissue cysts. Occasionally, cysts reactivate and growth of newly emerged parasites must be controlled by the host's immune system or disease will occur. The mechanisms by which Toxoplasma grows within its host cell, encysts, and interacts with the host's immune system are important questions. Here, we will discuss how the use of DNA microarrays in transcriptional profiling, genotyping, and epigenetic experiments has impacted our understanding of these processes. Finally, we will discuss how these advances relate to ocular toxoplasmosis and how future research on ocular toxoplasmosis can benefit from DNA microarrays.","PeriodicalId":73873,"journal":{"name":"Journal of ocular biology, diseases, and informatics","volume":" ","pages":"214-222"},"PeriodicalIF":0.0,"publicationDate":"2009-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/8a/e6/12177_2009_Article_9040.PMC2816810.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28714118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Ocular disease in patients with ANCA-positive vasculitis. anca阳性血管炎患者的眼部疾病。

Journal of ocular biology, diseases, and informatics Pub Date : 2009-12-12 DOI: 10.1007/s12177-009-9044-4

Angela S Watkins, John H Kempen, Dongseok Choi, Teresa L Liesegang, S S Pujari, Craig Newcomb, Robert B Nussenblatt, James T Rosenbaum, Jennifer E Thorne, C Stephen Foster, Douglas A Jabs, Grace A Levy-Clarke, Eric B Suhler, Justine R Smith

{"title":"Ocular disease in patients with ANCA-positive vasculitis.","authors":"Angela S Watkins, John H Kempen, Dongseok Choi, Teresa L Liesegang, S S Pujari, Craig Newcomb, Robert B Nussenblatt, James T Rosenbaum, Jennifer E Thorne, C Stephen Foster, Douglas A Jabs, Grace A Levy-Clarke, Eric B Suhler, Justine R Smith","doi":"10.1007/s12177-009-9044-4","DOIUrl":"https://doi.org/10.1007/s12177-009-9044-4","url":null,"abstract":"Anti-neutrophil cytoplasmic antibody (ANCA)-positive vasculitis-the term recently applied to Wegener's granulomatosis-is a rare multi-system inflammation characterized by necrotizing granulomas and vasculitis. We investigated the ocular manifestations of this disease in a group of patients drawn from five inflammatory eye disease clinics across the United States. Of 8,562 persons with ocular inflammation, 59 individuals were diagnosed with ANCA-positive vasculitis; 35 males and 21 females, aged 16 to 96 years, were included in this study. Ocular diagnoses were scleritis (75.0%), uveitis (17.9%), and other ocular inflammatory conditions (33.9%) including peripheral ulcerative keratitis and orbital pseudotumor. Mean duration of ocular disease was 4.6 years. Oral corticosteroids and other systemic immunosuppressive agents were used by 85.7% and 78.5% of patients, respectively. Over time, patients with ANCA-positive vasculitis experienced 2.75-fold higher mortality than other patients with inflammatory eye disease.","PeriodicalId":73873,"journal":{"name":"Journal of ocular biology, diseases, and informatics","volume":"3 1","pages":"12-19"},"PeriodicalIF":0.0,"publicationDate":"2009-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12177-009-9044-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40063400","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 57

Techniques for accurate protein identification in shotgun proteomic studies of human, mouse, bovine, and chicken lenses. 在人类、小鼠、牛和鸡晶状体的鸟枪蛋白质组学研究中精确的蛋白质鉴定技术。

Journal of ocular biology, diseases, and informatics Pub Date : 2009-12-12 DOI: 10.1007/s12177-009-9042-6

Phillip A Wilmarth, Michael A Riviere, Larry L David

{"title":"Techniques for accurate protein identification in shotgun proteomic studies of human, mouse, bovine, and chicken lenses.","authors":"Phillip A Wilmarth, Michael A Riviere, Larry L David","doi":"10.1007/s12177-009-9042-6","DOIUrl":"10.1007/s12177-009-9042-6","url":null,"abstract":"Analysis of shotgun proteomics datasets requires techniques to distinguish correct peptide identifications from incorrect identifications, such as linear discriminant functions and target/decoy protein databases. We report an efficient, flexible proteomic analysis workflow pipeline that implements these techniques to control both peptide and protein false discovery rates. We demonstrate its performance by analyzing two-dimensional liquid chromatography separations of lens proteins from human, mouse, bovine, and chicken lenses. We compared the use of International Protein Index databases to UniProt databases and no-enzyme SEQUEST searches to tryptic searches. Sequences present in the International Protein Index databases allowed detection of several novel crystallins. An alternate start codon isoform of betaA4 was found in human lens. The minor crystallin gammaN was detected for the first time in bovine and chicken lenses. Chicken gammaS was identified and is the first member of the gamma-crystallin family observed in avian lenses. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12177-009-9042-6) contains supplementary material, which is available to authorized users.","PeriodicalId":73873,"journal":{"name":"Journal of ocular biology, diseases, and informatics","volume":" ","pages":"223-234"},"PeriodicalIF":0.0,"publicationDate":"2009-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/0d/b8/12177_2009_Article_9042.PMC2816815.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28715158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Gene expression microarray analysis of early oxygen-induced retinopathy in the rat. 大鼠早期氧致视网膜病变基因表达微阵列分析。

Journal of ocular biology, diseases, and informatics Pub Date : 2009-12-12 DOI: 10.1007/s12177-009-9041-7

Melinda Tea, Rhys Fogarty, Helen M Brereton, Michael Z Michael, Mark B Van der Hoek, Anna Tsykin, Douglas J Coster, Keryn A Williams

{"title":"Gene expression microarray analysis of early oxygen-induced retinopathy in the rat.","authors":"Melinda Tea, Rhys Fogarty, Helen M Brereton, Michael Z Michael, Mark B Van der Hoek, Anna Tsykin, Douglas J Coster, Keryn A Williams","doi":"10.1007/s12177-009-9041-7","DOIUrl":"https://doi.org/10.1007/s12177-009-9041-7","url":null,"abstract":"Different inbred strains of rat differ in their susceptibility to oxygen-induced retinopathy (OIR), an animal model of human retinopathy of prematurity. We examined gene expression in Sprague-Dawley (susceptible) and Fischer 344 (resistant) neonatal rats after 3 days exposure to cyclic hyperoxia or room air, using Affymetrix rat Genearrays. False discovery rate analysis was used to identify differentially regulated genes. Such genes were then ranked by fold change and submitted to the online database, DAVID. The Sprague-Dawley list returned the term \"response to hypoxia,\" absent from the Fischer 344 output. Manual analysis indicated that many genes known to be upregulated by hypoxia-inducible factor-1alpha were downregulated by cyclic hyperoxia. Quantitative real-time RT-PCR analysis of Egln3, Bnip3, Slc16a3, and Hk2 confirmed the microarray results. We conclude that combined methodologies are required for adequate dissection of the pathophysiology of strain susceptibility to OIR in the rat. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12177-009-9041-7) contains supplementary material, which is available to authorized users.","PeriodicalId":73873,"journal":{"name":"Journal of ocular biology, diseases, and informatics","volume":"2 4","pages":"190-201"},"PeriodicalIF":0.0,"publicationDate":"2009-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12177-009-9041-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10653490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 15

Use of bioanalyzer electropherograms for quality control and target evaluation in microarray expression profiling studies of ocular tissues. 眼组织微阵列表达谱研究中生物分析仪电泳质量控制和靶标评价的应用。

Journal of ocular biology, diseases, and informatics Pub Date : 2009-12-12 DOI: 10.1007/s12177-009-9046-2

Christina A Harrington, Michael Winther, Michelle M Garred

{"title":"Use of bioanalyzer electropherograms for quality control and target evaluation in microarray expression profiling studies of ocular tissues.","authors":"Christina A Harrington, Michael Winther, Michelle M Garred","doi":"10.1007/s12177-009-9046-2","DOIUrl":"https://doi.org/10.1007/s12177-009-9046-2","url":null,"abstract":"Expression profiling with DNA microarrays has been used to examine the transcriptome of a wide spectrum of vertebrate cells and tissues. The sensitivity and accuracy of the data generated is dependent on the quality and composition of the input RNA. In this report, we examine the quality and array performance of over 200 total RNA samples extracted from ocular tissues and cells that have been processed in a microarray core laboratory over a 7-year period. Total RNA integrity and cRNA target size distribution were assessed using the 2100 Bioanalyzer. We present Affymetrix GeneChip array performance metrics for different ocular samples processed according to a standard microarray assay workflow including several quality control checkpoints. Our review of ocular sample performance in the microarray assay demonstrates the value of considering tissue-specific characteristics in evaluating array data. Specifically, we show that Bioanalyzer electropherograms reveal highly abundant mRNAs in lacrimal gland targets that are correlated with variation in array assay performance. Our results provide useful benchmarks for other gene expression studies of ocular systems.","PeriodicalId":73873,"journal":{"name":"Journal of ocular biology, diseases, and informatics","volume":" ","pages":"243-249"},"PeriodicalIF":0.0,"publicationDate":"2009-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12177-009-9046-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28714117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 11

Differential gene expression in the developing human macula: microarray analysis using rare tissue samples. 发育中的人类黄斑的差异基因表达:使用罕见组织样本的微阵列分析。

Journal of ocular biology, diseases, and informatics Pub Date : 2009-11-22 DOI: 10.1007/s12177-009-9039-1

Peter Kozulin, Jan M Provis

引用次数: 12

Metabolomic analysis of human disease and its application to the eye. 人类疾病的代谢组学分析及其在眼部的应用。

Journal of ocular biology, diseases, and informatics Pub Date : 2009-11-13 DOI: 10.1007/s12177-009-9038-2

Stephen P Young, Graham R Wallace

引用次数: 44