Project description:Rabbits have been widely used for studying ocular physiology and pathology due to their relatively large eye size and similar structures with human eyes. Various rabbit ocular disease models, such as dry eye, age-related macular degeneration, and glaucoma, have been established. Despite the growing application of proteomics in vision research using rabbit ocular models, there is no spectral assay library for rabbit eye proteome publicly available. Here, we generated spectral assay libraries for rabbit eye compartments, including conjunctiva, cornea, iris, retina, sclera, vitreous humor, and tears using fractionated samples and ion mobility separation enabling deep proteome coverage. The rabbit eye spectral assay library includes 9,830 protein groups and 113,593 peptides. We present the data as a freely available community resource for proteomic studies in the vision field.
Project description:Innate immunity is expected to play a primary role in conferring resistance to novel infectious diseases, but few studies have attempted to examine its role in the evolution of resistance to emerging pathogens in wild vertebrate populations. Here we used experimental infections and cDNA microarrays to examine whether changes in the innate and/or acquired immune responses likely accompanied the emergence of resistance in house finches (Carpodacus mexicanus) in the eastern United States subject to a recent outbreak of conjunctivitis-causing bacterium (Mycoplasma gallisepticum- MG). Three days following experimental infection with MG, we observed differences in the splenic transcriptional responses between House Finches from eastern U.S. populations, with a 12-year history of MG exposure, versus western U.S. populations, with no history of exposure to MG. In particular, western birds down-regulated gene expression, while eastern finches showed no expression change relative to controls. Studies involving poultry have shown that MG can manipulate host immunity, and our observations suggest that pathogen manipulation occurred only in finches from the western populations, outside the range of MG. Fourteen days after infection, eastern finches, but not western finches, up-regulated genes associated with acquired immunity (cell-mediated immunity) relative to controls. These observations suggest population differences in the temporal course of the response to infection with MG, and imply that innate immune processes were targets of selection in response to MG in the eastern U.S. population.
Project description:Genome-scale DNA methylation profiling using the Infinium DNA methylation BeadChip platform and samples from normal human eye and five ocular- related diseases DNA methylation analysis of eye samples from patient suffering ocular diseases (retinal detachment, diabetic retinopathy, glaucoma, uveal melanoma and retinoblastoma) using the Infinium DNA methylation BeadChip platform .
Project description:MicroRNA expression in the mouse eye.MicroRNAs (miRNAs) are key regulators of biological processes. To define miRNA function in the eye, it is essential to determine a high-resolution profile of their spatial and temporal distribution. In this report, we present the first comprehensive survey of miRNA expression in ocular tissues, using both microarray and RNA in situ hybridization (ISH) procedures. We initially determined the expression profiles of miRNAs in the retina, lens, cornea and retinal pigment epithelium of the adult mouse eye by microarray. Each tissue exhibited notably distinct miRNA enrichment patterns and cluster analysis identified groups of miRNAs that showed predominant expression in specific ocular tissues or combinations of them. Next, we performed RNA ISH for over 220 miRNAs, including those showing the highest expression levels by microarray, and generated a high-resolution expression atlas of miRNAs in the developing and adult wild-type mouse eye, which is accessible in the form of a publicly available web database. We found that 122 miRNAs displayed restricted expression domains in the eye at different developmental stages, with the majority of them expressed in one or more cell layers of the neural retina . This analysis revealed miRNAs with differential expression in ocular tissues and provided a detailed atlas of their tissue-specific distribution during development of the murine eye. The combination of the two approaches offers a valuable resource to decipher the contributions of specific miRNAs and miRNA clusters to the development of distinct ocular structures. microRNA profiling of ocular tissues from mouse. In particular we analysed the cornea, lens, Retina Pigment Epithelium (RPE) and retina and compared them against RNA extracted from the entire eye. The purpose of this experiment was to understand which microRNAs are present nd/or show differential expression in the various structures of the eye (cornea, lens, RPE, retina). The samples numbered 1 & 2 (i.e. CORNEA1, CORNEA2 etc ) are biological replicates, prepared from tissues dissecyed from different groups of wild-type animals. RNA extracted from the entire eye (EYE) served as the unique reference sample. For each tissue to be analysed we performed the following hybridizations: - 2 slides for lens (LENS1, LENS2) vs entire eye (EYE) - 2 slides for RPE (RPE1, RPE2) vs entire eye (EYE) - 2 slides for retina (RETINA1, RETINA2) vs entire eye (EYE) - 2 slides for cornea (CORNEA1, CORNEA2) vs entire eye (EYE) - 1 slide for entire eye (EYE) vs entire eye (EYE)
Project description:We report the proteome composition of the Drosophila eye – a compound organ that is highly enriched in membrane proteins. The fly eye is a popular model to study the physiology of vision by means of genetic, pharmacological, and dietary interference.While the eye transcriptome and development-related changes of gene expression profiles have been extensively studied, little is known about the eye proteome.we employed GeLC-MS/MS to identify and rank the abundances of 3516 eye proteins. Moreover, we applied our MS Western method to determine the absolute (molar) abundances of a related set of proteins that are important for photoreceptor structure (including maintenance) and function (phototransduction). Altogether, we provide a comprehensive and expandable proteomics resource that will be valuable for a variety of studies of ocular biochemistry, physiology, and development.
Project description:Innate immunity is expected to play a primary role in conferring resistance to novel infectious diseases, but few studies have attempted to examine its role in the evolution of resistance to emerging pathogens in wild vertebrate populations. Here we used experimental infections and cDNA microarrays to examine whether changes in the innate and/or acquired immune responses likely accompanied the emergence of resistance in house finches (Carpodacus mexicanus) in the eastern United States subject to a recent outbreak of conjunctivitis-causing bacterium (Mycoplasma gallisepticum- MG). Three days following experimental infection with MG, we observed differences in the splenic transcriptional responses between House Finches from eastern U.S. populations, with a 12-year history of MG exposure, versus western U.S. populations, with no history of exposure to MG. In particular, western birds down-regulated gene expression, while eastern finches showed no expression change relative to controls. Studies involving poultry have shown that MG can manipulate host immunity, and our observations suggest that pathogen manipulation occurred only in finches from the western populations, outside the range of MG. Fourteen days after infection, eastern finches, but not western finches, up-regulated genes associated with acquired immunity (cell-mediated immunity) relative to controls. These observations suggest population differences in the temporal course of the response to infection with MG, and imply that innate immune processes were targets of selection in response to MG in the eastern U.S. population. Birds were randomly selected to be kept either as controls or infected via ocular inoculation with 20 μl of culture containing 1 x 104 to 1 x 106 color changing units/ml of an early 2007 Auburn MG isolate. All infected birds were inoculated with precisely the same volume of the same culture. Control birds were sham infected using sterile SP4 medium (Whitcomb 1983). Infected birds were euthanized three days (N=6 from Arizona and N=11 from Alabama) and 14 days (N=11 from Arizona and N=12 from Alabama) after treatment. Control birds were euthanized 14 days after sham-inoculation; Control (N=11 birds from Arizona and 9 from Alabama) and infected birds were maintained under identical conditions, but in separate rooms of an aviary. Infected birds were euthanized three days (N=6 from Arizona and N=11 from Alabama) and 14 days (N=11 from Arizona and N=12 from Alabama) after treatment. Control birds were euthanized 14 days after sham-inoculation. We used a common reference design (Yang & Speed 2002), in which we pooled 2 to 6 spleens from birds from the same population in the same treatment to generate enough mRNA for microarray hybridizations and hybridized two pools for each treatment from each population.
Project description:Genome-scale DNA methylation profiling using the Infinium DNA methylation BeadChip platform and samples from normal human eye and five ocular- related diseases
Project description:MicroRNA expression in the mouse eye.MicroRNAs (miRNAs) are key regulators of biological processes. To define miRNA function in the eye, it is essential to determine a high-resolution profile of their spatial and temporal distribution. In this report, we present the first comprehensive survey of miRNA expression in ocular tissues, using both microarray and RNA in situ hybridization (ISH) procedures. We initially determined the expression profiles of miRNAs in the retina, lens, cornea and retinal pigment epithelium of the adult mouse eye by microarray. Each tissue exhibited notably distinct miRNA enrichment patterns and cluster analysis identified groups of miRNAs that showed predominant expression in specific ocular tissues or combinations of them. Next, we performed RNA ISH for over 220 miRNAs, including those showing the highest expression levels by microarray, and generated a high-resolution expression atlas of miRNAs in the developing and adult wild-type mouse eye, which is accessible in the form of a publicly available web database. We found that 122 miRNAs displayed restricted expression domains in the eye at different developmental stages, with the majority of them expressed in one or more cell layers of the neural retina . This analysis revealed miRNAs with differential expression in ocular tissues and provided a detailed atlas of their tissue-specific distribution during development of the murine eye. The combination of the two approaches offers a valuable resource to decipher the contributions of specific miRNAs and miRNA clusters to the development of distinct ocular structures.
Project description:Within a mutatgenesis screen, we identified the new recessive mouse mutant KTA48 with a kinky tail, white spots on coat and with small eyes. Aim of the actual study was the molecular characterization of the mutant and the functional consequences of the mutation. We mapped the mutation to mouse chromosome 12 within a critical interval of 2.4 Mb between the markers D12Mit171 and D12Mit270; sequence analysis of Pxdn revealed a T->A mutation at position 3816 (T3816A) resulting in a premature stop codon (Cys1272X) in teh perosidasin domain. Histological analysis revealed variable, but severe defects in teh eye including all major ocular tissues (cornea, lens and retina). These findings demonstrate severe clinical findings of a recessive mutation affecting peroxidasin. Total RNA obtained from homozygote embryos E12.5 and wildtype embryos E12.5, each sample include 4 eyes of two embryos