Complement increases release of proinflammatory and proangiogenic mediators by retinal pigment epithelial cells

Objectives. A mutation in complement factor H (CFH) gene, leading to augmented complement activation, is correlated with development of age-related macular degeneration (AMD). Therefore, the influence of complement on retinal pigment epithelial (RPE) cells was examined concerning their production of proinflammatory and proangiogenic mediators relevant in AMD. Methods. ARPE-19 cells were cultured with human or fetal calf serum (FCS). Therefore, complement containing native serum as well as the heat-inactivated form with inoperable complement was used. Further, RPE cells were treated with zymosan, a complement activating yeast particle. Serum and zymosan in combination was also tested. Levels of interleukin (IL)-6, -8 and vascular endothelial growth factor (VEGF) in supernatants were examined by ELISA. Results. Untreated RPE cells produced IL-6, -8 and VEGF constitutively. FCS or human serum led to a concentration dependent release of all mediators. Thereby, FCS increased the cytokine production stronger than human serum, native serum stronger than heat-inactivated. Zymosan only intensified IL-6 and -8 secretion. Combined treatment with serum and zymosan resulted in an additive release of IL-8 and VEGF. In contrast, secretion of IL-6 was synergistic. Conclusion. The enhanced expression of IL-6, -8 and VEGF by RPE after exposure to complement might explain the correlation between augmented complement production and inflammatory processes accompanying AMD. IL-6 production was strongly increased due to activation of complement within the serum by zymosan. Thus, complement activation could stimulate inflammatory processes by activated RPE cells leading to AMD

Complement stimulates Retinal Pigment Epithelial Cells to undergo Pro-inflammatory Changes as in Early Age-Related Macular Degeneration

Purpose. A polymorphism in the complement factor H gene, leading to increased complement activation, is associated with the development of age-related macular degeneration (AMD). We therefore examined the effect of human complement sera (HCS) on retinal pigment epithelial (RPE) cells with respect to pro-inflammatory mediators relevant in early AMD. Methods. RPE cells were treated with HCS or heat-inactivated (HI)-HCS as a complement-deficient control. Cells were stained for C5b-9 using immunocytochemistry and immunofluorescence, and cell viability was determined. Interleukin (IL) -6, -8 and monocyte chemoattractant protein-1 (MCP-1) were quantified by ELISA and their expression was determined by RT-PCR. Intercellular adhesion molecule-1 (ICAM-1), vascular cell adhesion molecule-1 (VCAM-1) and tumour necrosis factor-α (TNF-α) were analysed by western blotting. The intracellular distribution of nuclear factor (NF)-ƙB was investigated by immunofluorescence. Results. Concentration-dependent increased staining for C5b-9 was observed after HCS treatment, whereas cell viability decreased. ELISA and RT-PCR analysis revealed increased secretion and expression of IL-6, -8 and MCP-1. Western blot analysis showed a concentration-dependent enhancement in ICAM-1, VCAM-1 and TNF-α in response to HCS, and immunofluorescence staining revealed cytosolic to nuclear translocation of NF-ƙB. Conclusions. This study suggests that complement may stimulate RPE cells to create a pro-inflammatory environment via NF-ƙB activation which may support early AMD development

Human Complement Sera stimulates Basolateral Secretion of VEGF by Retinal Pigment Epithelial Cells

Purpose. A mutation in the complement factor H (CFH) gene, leading to increased complement activation, is correlated with the development of age-related macular degeneration (AMD). Therefore, the influence of complement on human retinal pigment epithelial (RPE) cells was examined in respect to their polarized secretion of vascular endothelial growth factor (VEGF). Methods. RPE cells were cultured on transwell filters with DMEM and 1 % foetal calf serum. At six weeks post confluence, when the RPE have pigmented, the density of the cell monolayer was measured by a permeability assay using sodium fluorescein. The cells were treated with human complement sera for 24 hours. The amount of VEGF secreted into the media was quantified by enzyme-linked immunosorbent assay. Furthermore, the cellular distribution of VEGF in complement treated cells grown in chamber slides was detected by immunocytochemistry, and PCR analysis was used to determine the expression of the growth factor in RPE cells. Results. Untreated RPE cells produced VEGF constitutively. Basal stimulation of polarized cells with human complement sera led to a concentration dependent increased release of the growth factor towards the basal compartment. Immunocytochemical staining and PCR analysis for VEGF also demonstrated a concentration dependent enhancement in response to complement. Conclusions. VEGF production towards the basal side was strongly increased when RPE cells were exposed to human complement sera applied to the basal side. Therefore, complement might play a significant role in AMD, as VEGF is known to stimulate vessel growth in the choroid and support pro-angiogenic processes

FrameDP: sensitive peptide detection on noisy matured sequences

Summary: Transcriptome sequencing represents a fundamental source of information for genome-wide studies and transcriptome analysis and will become increasingly important for expression analysis as new sequencing technologies takes over array technology. The identification of the protein-coding region in transcript sequences is a prerequisite for systematic amino acid-level analysis and more specifically for domain identification. In this article, we present FrameDP, a self-training integrative pipeline for predicting CDS in transcripts which can adapt itself to different levels of sequence qualities

EST-PAC a web package for EST annotation and protein sequence prediction

With the decreasing cost of DNA sequencing technology and the vast diversity of biological resources, researchers increasingly face the basic challenge of annotating a larger number of expressed sequences tags (EST) from a variety of species. This typically consists of a series of repetitive tasks, which should be automated and easy to use. The results of these annotation tasks need to be stored and organized in a consistent way. All these operations should be self-installing, platform independent, easy to customize and amenable to using distributed bioinformatics resources available on the Internet. In order to address these issues, we present EST-PAC a web oriented multi-platform software package for expressed sequences tag (EST) annotation. EST-PAC provides a solution for the administration of EST and protein sequence annotations accessible through a web interface. Three aspects of EST annotation are automated: 1) searching local or remote biological databases for sequence similarities using Blast services, 2) predicting protein coding sequence from EST data and, 3) annotating predicted protein sequences with functional domain predictions. In practice, EST-PAC integrates the BLASTALL suite, EST-Scan2 and HMMER in a relational database system accessible through a simple web interface. EST-PAC also takes advantage of the relational database to allow consistent storage, powerful queries of results and, management of the annotation process. The system allows users to customize annotation strategies and provides an open-source data-management environment for research and education in bioinformatics

Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics

Nematode.net (http://nematode.net) is a publicly available resource dedicated to the study of parasitic nematodes. In 2000, the Genome Center at Washington University (GC) joined a consortium including the Nematode Genomics group in Edinburgh, and the Pathogen Sequencing Unit of the Sanger Institute to generate expressed sequence tags (ESTs) as an inexpensive and efficient solution for gene discovery in parasitic nematodes. As of 2008 the GC, sampling key parasites of humans, animals and plants, has generated over 500 000 ESTs and 1.2 million genome survey sequences from more than 30 non-Caenorhabditis elegans nematodes. Nematode.net was implemented to offer user-friendly access to data produced by this project. In addition to sequence data, the site hosts: assembled NemaGene clusters in GBrowse views characterizing composition and protein homology, functional Gene Ontology annotations presented via the AmiGO browser, KEGG-based graphical display of NemaGene clusters mapped to metabolic pathways, codon usage tables, NemFam protein families which represent conserved nematode-restricted coding sequences not found in public protein databases, a web-based WU-BLAST search tool that allows complex querying and other assorted resources. The primary aim of Nematode.net is the dissemination of this diverse collection of information to the broader scientific community in a way that is useful, consistent, centralized and enduring

ButterflyBase: a platform for lepidopteran genomics

With over 100 000 species and a large community of evolutionary biologists, population ecologists, pest biologists and genome researchers, the Lepidoptera are an important insect group. Genomic resources [expressed sequence tags (ESTs), genome sequence, genetic and physical maps, proteomic and microarray datasets] are growing, but there has up to now been no single access and analysis portal for this group. Here we present ButterflyBase (http://www.butterflybase.org), a unified resource for lepidopteran genomics. A total of 273 077 ESTs from more than 30 different species have been clustered to generate stable unigene sets, and robust protein translations derived from each unigene cluster. Clusters and their protein translations are annotated with BLAST-based similarity, gene ontology (GO), enzyme classification (EC) and Kyoto encyclopaedia of genes and genomes (KEGG) terms, and are also searchable using similarity tools such as BLAST and MS-BLAST. The database supports many needs of the lepidopteran research community, including molecular marker development, orthologue prediction for deep phylogenetics, and detection of rapidly evolving proteins likely involved in host–pathogen or other evolutionary processes. ButterflyBase is expanding to include additional genomic sequence, ecological and mapping data for key species