Proteomic Insight into the Molecular Function of the Vitreous
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{"title"=>"Proteomic insight into the molecular function of the vitreous", "type"=>"journal", "authors"=>[{"first_name"=>"Jessica M.", "last_name"=>"Skeie", "scopus_author_id"=>"8863030100"}, {"first_name"=>"C. Nathaniel", "last_name"=>"Roybal", "scopus_author_id"=>"8066631200"}, {"first_name"=>"Vinit B.", "last_name"=>"Mahajan", "scopus_author_id"=>"7102215618"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84935014608", "sgr"=>"84935014608", "pui"=>"604923329", "pmid"=>"26020955", "doi"=>"10.1371/journal.pone.0127567"}, "id"=>"4e903686-4091-3b4c-a9dc-5273f50a08f2", "abstract"=>"The human vitreous contains primarily water, but also contains proteins which have yet to be fully characterized. To gain insight into the four vitreous substructures and their potential functions, we isolated and analyzed the vitreous protein profiles of three non-diseased human eyes. The four analyzed substructures were the anterior hyaloid, the vitreous cortex, the vitreous core, and the vitreous base. Proteins were separated by multidimensional liquid chromatography and identified by tandem mass spectrometry. Bioinformatics tools then extracted the expression profiles, signaling pathways, and interactomes unique to each tissue. From each substructure, a mean of 2,062 unique proteins were identified, with many being differentially expressed in a specific substructure: 278 proteins were unique to the anterior hyaloid, 322 to the vitreous cortex, 128 to the vitreous base, and 136 to the vitreous core. When the identified proteins were organized according to relevant functional pathways and networks, key patterns appeared. The blood coagulation pathway and extracellular matrix turnover networks were highly represented. Oxidative stress regulation and energy metabolism proteins were distributed throughout the vitreous. Immune functions were represented by high levels of immunoglobulin, the complement pathway, damage-associated molecular patterns (DAMPs), and evolutionarily conserved antimicrobial proteins. The majority of vitreous proteins detected were intracellular proteins, some of which originate from the retina, including rhodopsin (RHO), phosphodiesterase 6 (PDE6), and glial fibrillary acidic protein (GFAP). This comprehensive analysis uncovers a picture of the vitreous as a biologically active tissue, where proteins localize to distinct substructures to protect the intraocular tissues from infection, oxidative stress, and energy disequilibrium. It also reveals the retina as a potential source of inflammatory mediators. The vitreous proteome catalogues the dynamic interactions between the vitreous and surrounding tissues. It therefore could be an indirect and effective method for surveying vitreoretinal disease for specific biomarkers.", "link"=>"http://www.mendeley.com/research/proteomic-insight-molecular-function-vitreous-1", "reader_count"=>27, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Student > Doctoral Student"=>6, "Researcher"=>4, "Student > Ph. D. Student"=>6, "Student > Postgraduate"=>2, "Other"=>4, "Student > Master"=>1, "Student > Bachelor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Student > Doctoral Student"=>6, "Researcher"=>4, "Student > Ph. D. Student"=>6, "Student > Postgraduate"=>2, "Other"=>4, "Student > Master"=>1, "Student > Bachelor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>5, "Medicine and Dentistry"=>10, "Agricultural and Biological Sciences"=>6, "Arts and Humanities"=>1, "Physics and Astronomy"=>1, "Chemistry"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>10}, "Chemistry"=>{"Chemistry"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>6}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"United States"=>1, "Japan"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2086163"], "description"=>"<p>The images are shown in the order they are dissected. A. The vitreous core is aspirated using a 23-gauge needle following the removal of the anterior portion of the eye. B. After the vitreous core is aspirated, the anterior hyaloid becomes visible as a translucent ring. This tissue can be grasped with Colibri forceps, cut, and collected. C. The vitreous base is a thick, viscous tissue lying over the ora serrata. This image is for visualization purposes (still containing the anterior iris and lens) to show the pars plicatta, pars plana, ciliary body, and ora serrata. The vitreous base is grasped using Colibri forceps, pulled away from the ora serrata, and cut with Vannas scissors. D. The vitreous cortex is collected by cutting the posterior pole into quadrants and grasping between two sections. It is lifted and cut away from the posterior pole.</p>", "links"=>[], "tags"=>["vitreous protein profiles", "Tandem mass spectrometry", "blood coagulation pathway", "rho", "vitreous core", "damp", "vitreous proteome catalogues", "extracellular matrix turnover networks", "pde", "Oxidative stress regulation", "vitreous cortex", "vitreous base", "glial fibrillary acidic protein", "gfap", "substructure", "energy metabolism proteins"], "article_id"=>1429086, "categories"=>["Biological Sciences"], "users"=>["Jessica M. Skeie", "C. Nathaniel Roybal", "Vinit B. Mahajan"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0127567.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Human_vitreous_component_dissection_images_/1429086", "title"=>"Human vitreous component dissection images.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-28 03:17:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2086166"], "description"=>"<p>A. The human vitreous was dissected into core, anterior hyaloid, cortex, and base. B. Fractions of proteins were isolated and digested. C. The peptide fragments were analyzed using multi-dimensional LC-MS/MS. D. X!Hunter, X!!Tandem, and OMSSA were used for peptide fragment identification. E. Proteins were further analyzed using bioinformatics software. F. Interpretation of the protein datasets in reference to disease biology.</p>", "links"=>[], "tags"=>["vitreous protein profiles", "Tandem mass spectrometry", "blood coagulation pathway", "rho", "vitreous core", "damp", "vitreous proteome catalogues", "extracellular matrix turnover networks", "pde", "Oxidative stress regulation", "vitreous cortex", "vitreous base", "glial fibrillary acidic protein", "gfap", "substructure", "energy metabolism proteins"], "article_id"=>1429089, "categories"=>["Biological Sciences"], "users"=>["Jessica M. Skeie", "C. Nathaniel Roybal", "Vinit B. Mahajan"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0127567.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Vitreous_proteome_analysis_pipeline_/1429089", "title"=>"Vitreous proteome analysis pipeline.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-28 03:17:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2086168"], "description"=>"<p>A. Cross section of human eye depicts the four regions of vitreous tissue collected and includes the anterior hyaloid, vitreous base, vitreous cortex, and vitreous core. B. Gene ontology of the four distinct vitreous regions shows that within the cellular component category, most proteins are intracellular. C. Venn diagram shows the number of unique and overlapping proteins identified in each of human vitreous substructure.</p>", "links"=>[], "tags"=>["vitreous protein profiles", "Tandem mass spectrometry", "blood coagulation pathway", "rho", "vitreous core", "damp", "vitreous proteome catalogues", "extracellular matrix turnover networks", "pde", "Oxidative stress regulation", "vitreous cortex", "vitreous base", "glial fibrillary acidic protein", "gfap", "substructure", "energy metabolism proteins"], "article_id"=>1429091, "categories"=>["Biological Sciences"], "users"=>["Jessica M. Skeie", "C. Nathaniel Roybal", "Vinit B. Mahajan"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0127567.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Global_analysis_of_human_vitreous_substructures_/1429091", "title"=>"Global analysis of human vitreous substructures.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-28 03:17:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2086169"], "description"=>"<p>Expressed proteins of the anterior hyaloid, vitreous cortex, vitreous base, and vitreous core. Proteins were grouped into sub-categories of biological processes, molecular functions, and cellular component for each of the four regions.</p>", "links"=>[], "tags"=>["vitreous protein profiles", "Tandem mass spectrometry", "blood coagulation pathway", "rho", "vitreous core", "damp", "vitreous proteome catalogues", "extracellular matrix turnover networks", "pde", "Oxidative stress regulation", "vitreous cortex", "vitreous base", "glial fibrillary acidic protein", "gfap", "substructure", "energy metabolism proteins"], "article_id"=>1429092, "categories"=>["Biological Sciences"], "users"=>["Jessica M. Skeie", "C. Nathaniel Roybal", "Vinit B. Mahajan"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0127567.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_ontology_GO_distributions_and_pathway_analysis_of_human_vitreous_proteins_show_tissue_similarity_/1429092", "title"=>"Gene ontology (GO) distributions and pathway analysis of human vitreous proteins show tissue similarity.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-28 03:17:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2086171"], "description"=>"<p>Expressed proteins of the anterior hyaloid, vitreous cortex, vitreous base, and vitreous core. Proteins were grouped into sub-categories of biological processes, molecular functions, and cellular component. These proteins are unique to each region of the vitreous as determined using the Venn diagram in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127567#pone.0127567.g003\" target=\"_blank\">Fig 3C</a>.</p>", "links"=>[], "tags"=>["vitreous protein profiles", "Tandem mass spectrometry", "blood coagulation pathway", "rho", "vitreous core", "damp", "vitreous proteome catalogues", "extracellular matrix turnover networks", "pde", "Oxidative stress regulation", "vitreous cortex", "vitreous base", "glial fibrillary acidic protein", "gfap", "substructure", "energy metabolism proteins"], "article_id"=>1429094, "categories"=>["Biological Sciences"], "users"=>["Jessica M. Skeie", "C. Nathaniel Roybal", "Vinit B. Mahajan"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0127567.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_ontology_GO_distributions_and_pathway_analysis_of_human_vitreous_proteins_show_tissue_differences_/1429094", "title"=>"Gene ontology (GO) distributions and pathway analysis of human vitreous proteins show tissue differences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-28 03:17:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2086173"], "description"=>"<p>A. Top ten pathways represented in all four of the vitreous regions. The relative abundance of proteins in each pathway is shown for each tissue. Not all proteins represented in one substructure are the same as another. B, C, D, E. The top ten pathways based on uniquely expressed proteins are listed for each substructure: (B) anterior hyaloid, (C) vitreous cortex, (D) vitreous base, and (E) vitreous core.</p>", "links"=>[], "tags"=>["vitreous protein profiles", "Tandem mass spectrometry", "blood coagulation pathway", "rho", "vitreous core", "damp", "vitreous proteome catalogues", "extracellular matrix turnover networks", "pde", "Oxidative stress regulation", "vitreous cortex", "vitreous base", "glial fibrillary acidic protein", "gfap", "substructure", "energy metabolism proteins"], "article_id"=>1429096, "categories"=>["Biological Sciences"], "users"=>["Jessica M. Skeie", "C. Nathaniel Roybal", "Vinit B. Mahajan"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0127567.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proteome_pathway_analysis_of_human_vitreous_substructures_/1429096", "title"=>"Proteome pathway analysis of human vitreous substructures.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-28 03:17:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2086175"], "description"=>"<p>MMP2 is the largest network common to all four regions of the human vitreous humor. MMP-2 is involved in the proteolysis of extracellular matrix proteins, and 108 targets were found in the vitreous.</p>", "links"=>[], "tags"=>["vitreous protein profiles", "Tandem mass spectrometry", "blood coagulation pathway", "rho", "vitreous core", "damp", "vitreous proteome catalogues", "extracellular matrix turnover networks", "pde", "Oxidative stress regulation", "vitreous cortex", "vitreous base", "glial fibrillary acidic protein", "gfap", "substructure", "energy metabolism proteins"], "article_id"=>1429098, "categories"=>["Biological Sciences"], "users"=>["Jessica M. Skeie", "C. Nathaniel Roybal", "Vinit B. Mahajan"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0127567.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Matrix_metalloproteinase_2_MMP_2_network_/1429098", "title"=>"Matrix metalloproteinase 2 (MMP-2) network.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-28 03:17:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2086177"], "description"=>"<p>A. The largest hub in the vitreous base was the GSK3 beta hub. B. In the vitreous core, the largest unique network is the ATM network. C, D. The largest hub in the anterior hyaloid is the kallikrein 3 (PSA) network. E, F. The largest network in the vitreous cortex is casein kinase II.</p>", "links"=>[], "tags"=>["vitreous protein profiles", "Tandem mass spectrometry", "blood coagulation pathway", "rho", "vitreous core", "damp", "vitreous proteome catalogues", "extracellular matrix turnover networks", "pde", "Oxidative stress regulation", "vitreous cortex", "vitreous base", "glial fibrillary acidic protein", "gfap", "substructure", "energy metabolism proteins"], "article_id"=>1429100, "categories"=>["Biological Sciences"], "users"=>["Jessica M. Skeie", "C. Nathaniel Roybal", "Vinit B. Mahajan"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0127567.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Network_analysis_reveals_the_largest_unique_protein_networks_for_vitreous_substructures_/1429100", "title"=>"Network analysis reveals the largest unique protein networks for vitreous substructures.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-28 03:17:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2086180"], "description"=>"<p>Proteins represented in this cluster analysis were determined by ANOVA, p<0.05. The heatmap is divided into regions: A. proteins highest in the vitreous cortex, B. proteins highest in the anterior hyaloid and the vitreous base, C. proteins highest in the anterior hyaloid, D. proteins absent or low in the vitreous core but represented in the other three tissues, E. proteins highest in the vitreous base, F. proteins in all tissues except the anterior hyaloid, G. proteins unique to the vitreous core, and H. proteins highest in the vitreous core and vitreous cortex.</p>", "links"=>[], "tags"=>["vitreous protein profiles", "Tandem mass spectrometry", "blood coagulation pathway", "rho", "vitreous core", "damp", "vitreous proteome catalogues", "extracellular matrix turnover networks", "pde", "Oxidative stress regulation", "vitreous cortex", "vitreous base", "glial fibrillary acidic protein", "gfap", "substructure", "energy metabolism proteins"], "article_id"=>1429103, "categories"=>["Biological Sciences"], "users"=>["Jessica M. Skeie", "C. Nathaniel Roybal", "Vinit B. Mahajan"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0127567.g009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Unbiased_clustering_of_differentially_expressed_proteins_p_lt_0_05_in_the_four_human_vitreous_substructures_/1429103", "title"=>"Unbiased clustering of differentially expressed proteins (p<0.05) in the four human vitreous substructures.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-28 03:17:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2086181", "https://ndownloader.figshare.com/files/2086182", "https://ndownloader.figshare.com/files/2086183", "https://ndownloader.figshare.com/files/2086184", "https://ndownloader.figshare.com/files/2086185", "https://ndownloader.figshare.com/files/2086186", "https://ndownloader.figshare.com/files/2086187", "https://ndownloader.figshare.com/files/2086188", "https://ndownloader.figshare.com/files/2086189"], "description"=>"<div><p>The human vitreous contains primarily water, but also contains proteins which have yet to be fully characterized. To gain insight into the four vitreous substructures and their potential functions, we isolated and analyzed the vitreous protein profiles of three non-diseased human eyes. The four analyzed substructures were the anterior hyaloid, the vitreous cortex, the vitreous core, and the vitreous base. Proteins were separated by multidimensional liquid chromatography and identified by tandem mass spectrometry. Bioinformatics tools then extracted the expression profiles, signaling pathways, and interactomes unique to each tissue. From each substructure, a mean of 2,062 unique proteins were identified, with many being differentially expressed in a specific substructure: 278 proteins were unique to the anterior hyaloid, 322 to the vitreous cortex, 128 to the vitreous base, and 136 to the vitreous core. When the identified proteins were organized according to relevant functional pathways and networks, key patterns appeared. The blood coagulation pathway and extracellular matrix turnover networks were highly represented. Oxidative stress regulation and energy metabolism proteins were distributed throughout the vitreous. Immune functions were represented by high levels of immunoglobulin, the complement pathway, damage-associated molecular patterns (DAMPs), and evolutionarily conserved antimicrobial proteins. The majority of vitreous proteins detected were intracellular proteins, some of which originate from the retina, including rhodopsin (RHO), phosphodiesterase 6 (PDE6), and glial fibrillary acidic protein (GFAP). This comprehensive analysis uncovers a picture of the vitreous as a biologically active tissue, where proteins localize to distinct substructures to protect the intraocular tissues from infection, oxidative stress, and energy disequilibrium. It also reveals the retina as a potential source of inflammatory mediators. The vitreous proteome catalogues the dynamic interactions between the vitreous and surrounding tissues. It therefore could be an indirect and effective method for surveying vitreoretinal disease for specific biomarkers.</p></div>", "links"=>[], "tags"=>["vitreous protein profiles", "Tandem mass spectrometry", "blood coagulation pathway", "rho", "vitreous core", "damp", "vitreous proteome catalogues", "extracellular matrix turnover networks", "pde", "Oxidative stress regulation", "vitreous cortex", "vitreous base", "glial fibrillary acidic protein", "gfap", "substructure", "energy metabolism proteins"], "article_id"=>1429104, "categories"=>["Biological Sciences"], "users"=>["Jessica M. Skeie", "C. Nathaniel Roybal", "Vinit B. Mahajan"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0127567.s001", "https://dx.doi.org/10.1371/journal.pone.0127567.s002", "https://dx.doi.org/10.1371/journal.pone.0127567.s003", "https://dx.doi.org/10.1371/journal.pone.0127567.s004", "https://dx.doi.org/10.1371/journal.pone.0127567.s005", "https://dx.doi.org/10.1371/journal.pone.0127567.s006", "https://dx.doi.org/10.1371/journal.pone.0127567.s007", "https://dx.doi.org/10.1371/journal.pone.0127567.s008", "https://dx.doi.org/10.1371/journal.pone.0127567.s009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proteomic_Insight_into_the_Molecular_Function_of_the_Vitreous_/1429104", "title"=>"Proteomic Insight into the Molecular Function of the Vitreous", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-05-28 03:17:56"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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