A New Method of Examining Coral Reef Ecosystems: A First Use of Genomic and Bioinformatics Techniques

A New Method of Examining Coral Reef Ecosystems: A First Use of Genomic and Bioinformatics Techniques Christopher Rosenthal Claudia Johnson (Geobiology) MehmetDalkilic (Bioinformatics) Indiana University School of Informatics Capstone Project Paper in Submission to Geoinformatics Conference

Outline • Motivation • Introduction • What is an ecosystem • Biotic components • Flow of energy in one direction • Recycling of energy • Toxic components • Flow of energy between ecosystems • Data • Architecture (Microsoft) • Programming • Algorithm • Results • Screen Shots • Results • Discussion Paper in Submission to Geoinformatics Conference

Motivation • Coral Reef Ecosystem Research Background • Claudia Johnson (Geology) • MehmetDalkilic (Bioinformatics) • Susan Morse Coleman (HCI/d) • Studied coral reef ecosystems first hand in the Dominican Republic • Interface and Design Paper in Submission to Geoinformatics Conference

Motivation • Overview of Geobiology • Research generally focused on a single ecosystem - Coral Reefs • Data is usually reported in raw form Paper in Submission to Geoinformatics Conference

Example • Study by Halpern et al 2008 • 20 different ecosystems around the world • 17 data sets of anthropogenic drivers Paper in Submission to Geoinformatics Conference

Motivation • Applying Bioinformatics • Even though Bioinformatics is in its infancy a lot of information and a lot of methodologies have been acquired by studying genomes • Biogeology is generally done on a much larger scale because the Earth itself can be thought of as the “DNA” of “Biogeoinformatics” (University of Kansas Geological Survey) • Name coined in a project of analyzing geospatial, taxonomic, and environmental data for a group of marine invertebrates • Metagenomics is an example of a bioinformatics methodologies based on environmental genomes Paper in Submission to Geoinformatics Conference

Introduction • Geologists have recently begun looking for complex relationships in their data to discover trends • A word on temporal extent • There exists millions of years of uncollected and unevaluated amounts of data • Can Bioinformatics approaches be applied to geological analysis of ecosystems? • What can ontologies tell us about coral reef ecosystems? • What can coral genomes tell us about the coral reef diseases? Paper in Submission to Geoinformatics Conference

Introduction • What is an Ontology? • Forming Relationships of Data Paper in Submission to Geoinformatics Conference

Introduction • DDont – Data Driven Ontologies (Costello et al) • Bloom – Data Driven Ontologies for Coral Reef Disease and Genomic Ontologies An example of a Data-Driven Ontology (DDOnt). The network of yeast genes (A) selected as a subnetwork of the bioPIXIE integrated gene network is used along with the Gene Ontology biological process annotations to synthesize the DDOnt (B) using the BuildOntology algorithm. The edge colors in B are discussed in Section 3.2. The root node in the ontology is designated by the teal arrow. The orange nodes in A are the genes that have been annotated with the rosette of terms in B designated by the red arrow. This rosette of terms are potentially novel relationships between biological processes where the parent node is response to DNA damage stimulus (GO:0006974). Paper in Submission to Geoinformatics Conference

Introduction • What genes correspond to which diseases? • What does the functionality of these genes tell us about the environmental stressors present in the ecosystem? Northwestern University Functional Disease Ontology Server Paper in Submission to Geoinformatics Conference

Introduction In particular, humans contain many of the same immune system genes as corals (Kortschak et al) Paper in Submission to Geoinformatics Conference

Introduction (Kortschak et al) Paper in Submission to Geoinformatics Conference

What is an Ecosystem? • Biotic Components • Primary producers (herbivores) • Plants and algae • Secondary consumers (mid-level carnivores) • Tertiary consumers (top predator in food chain) • Decomposers (bacteria and fungus) Paper in Submission to Geoinformatics Conference

What is an Ecosystem? • Flow of energy in one direction • Sun -> producers -> consumers • Marine Sulfur vents -> producers -> consumers • Subterranean heat -> ? -> ? Paper in Submission to Geoinformatics Conference

What is an Ecosystem? • Recycling of energy • Decomposers and primary consumers break down “waste” into nutrients • Dead biomass or returns to soil to be used by primary consumers Paper in Submission to Geoinformatics Conference

What is an Ecosystem? • Toxic components • Non-organic (Human made poisons) • Poisons • Factory waste • Organic • Fertilizer runoff into water streams causing algae blankets • Natural disasters • Volcanoes • Wild fires • Earthquakes • etc Paper in Submission to Geoinformatics Conference

What is an Ecosystem? • Flow of energy between ecosystems • Overlapping of biotic components between adjacent ecosystems • Migrating consumers on land or by water • Nutrient flow down rivers or along ocean currents Paper in Submission to Geoinformatics Conference

Application Paper in Submission to Geoinformatics Conference

Data • Data • Global Coral Disease Database • Philippines • Caribbean • Australia • Red Sea Paper in Submission to Geoinformatics Conference

Data • Data • National Oceanic Data Center – World Ocean Database (WODselect) • Caribbean • Australia Paper in Submission to Geoinformatics Conference

Data • Epizootic Cyanobacteria, Scytonema sp. • Yellow Band Disease • Brown Band Disease • Dark band • No disease observed at time of survey • Dark band syndrome • White spot • Bleaching disease • Red plague syndrome • Neoplasia • White disease • Fungal disease • Plague • Blistering necrosis • Red band disease • Fast tissue necrosis • White line disease • Aspergillosis • Pink line syndrome • Yellow Band Disease - Atlantic • Purple band • Hyperplasia • Red band disease II • Vibriocoralyticus disease • Black Band Disease • Disease unspecified • White plague • Coral Diseases • White band disease • Patchy necrosis • Ring syndrome • Necrotic patch syndrome • Abnormal development • Tissue necrosis • Cancer growth • Hyperplasmictumours • White syndrome • Pink spots • Pink blotch syndrome • Thin dark line • Orange patch Disease • White pox lesions • Yellowing disease • Porites ulcerative white spot disease • Tumours • Dark spots disease • Other disease • White pox • White Band Disease type I • Corallliphilaabbreviata, gastrapod predator • Atramentous necrosis • White band disease type II • Black Patch Disease • Skeleton eroding band Paper in Submission to Geoinformatics Conference

Data • Acroporadivaricata • Acroporagemmifera • Astreopora spp. • Acroporapolystoma • Poritesattenuata • Madreporaannularis • Eusmiliafastigiata • Turbinariareniformis • Poritesporites • Faviafragum • Pocilloporadamicornis • Acroporacytherea • Acroporahyacinthus • Acroporamicrophthalma • Platygyrasinensis • Faviafavus • Montiporainformis • Platygyra spp. • Faviastelligera • Acroporamonticulosa • Montiporapatula • Acroporapalifera • Lobophytumbatarum • Acroporahumilis • Helioseriscucullata • Acroporaformosa • Gonioporacolumna • Agaricialamarcki • Acroporacervicornis • Madracisdecactis • Pavona spp. • Astreoporamyriophthalma • Meandrinameandrites • Colpophylliabreviserialis • Faviavalenciennesii • Echinoporagemmacea • Poritesharrisoni • Montiporaverrucosa • Favitespentagona • Stephanocoeniamichelinii • Faviapallida • Podabaciacrustacea • Diploriaspp • Diploastrea spp. • (null) • Favia spp. • Cyphastreamicrophthalma • Acroporanobilis • Gorgonia flabellum • Platygyradaedalea • Acroporasquarrosa • Echinopora spp. • Acroporaclathrata • Mycetophyllialamarckiana • Acroporacapillaris • Montiporaflorida • Acroporamicroclados • Acroporapharaonis • Montastraeafaveolata • Lobophylliacorymbosa • Madracis mirabilis • Milleporaalcicornis • Leptoriaphrygia • Acanthastrea spp. • Montastraeaannularis • Acroporavariabilis • Turbinariamesenterina • Acroporadowningi • Agariciahumilis • Acroporasolitaryensis • Millepora spp. • Seriatopora spp. • Acroporarobusta • Leptoserismycetoseroides • Goniastreapectinata • Acroporasarmentosa • Acropora spp. • Porites spp. • Alveoporagigas • Cyphastreachalcidicum • Agariciaagaricites • Manicinaareolata • Acroporavalencennesii • Mycediumelephantotus • Pseudopterogorgiaamericana • Diploriaclivosa • Acroporamillepora • Symphyllia radians • Platygyralamellina • Mycedium spp. • Diploriastrigosa • Colpophyllianatans • Pavonagigantea • Fungia spp. • Madreporakauaiensis • Hydnophoramicroconos • Pocilloporaeydouxi • Siderastreasiderea • Acroporaprolifera • Acroporavirgata • Acroporaaustera • Poritesfurcata • Turbinariafrondens • Acroporaintermedia • Pachyserisgemmae • Dendrogyracylindrus • Montastraeacavernosa • Montiporatuberculosa • Milleporacomplanata • Oculinapatagonica • Poritescompressa • Isophyllastrearigida • Gonioporastokesi • Montastraea spp. • Solenastreabournonii • Madreporacavernosa • Montastraeafranksi • Diplorialabyrinthiformis • Acroporahemprichii • Acroporatenuis • Acroporaaspera • Psammocora spp. • Poritesnodifera • Leptoserisglabra • Stylophora spp. • Echinophylliaaspera • Montipora spp. • Acroporaflorida • Porites lichen • Montiporaaequituberculata • Leptoseriscucullata • Oulophyllia spp. • Pocillopora spp. • Goniastrearetiformis • Gorgoniaventalina • Pocilloporaverrucosa • Lobophyllia spp. • Pocilloporameandrina • Turbinariaradicalis • Mussaangulosa • Stylophorapistillata • Siderastrea radians • Acroporavalida • Stephanocoeniaintersepta • Poritesastreoides • Dichocoeniastokesii • Mycetophylliaferox • Faviamatthaii • Gonioporasomaliensis • Poriteslutea • Plexaurahomomalla • Platygyrapini • Agariciatenuifolia • Acroporapalmata • Poritesdivaricata Paper in Submission to Geoinformatics Conference

Data • Coral Genomes • The Marine Genomics Project • Montastraeaannularis • Poritesporites • Montastraeafaveolata • Poritesastreoides • Oculinavaricosa • Acroporapalmata • Ensembl • Acroporamillepora • Poriteslobata Paper in Submission to Geoinformatics Conference

Architecture • Programming (Microsoft) Web browser ASP.NET C# Server MS SQL Database Paper in Submission to Geoinformatics Conference

Results Data Entry: 7808 – lines of disease 57848 – line of environmental ~ 4,000 – corresponding geographical matches • Almost all data from the Caribbean Paper in Submission to Geoinformatics Conference

Results • Data Entry Paper in Submission to Geoinformatics Conference

Results • Specification of parameters Paper in Submission to Geoinformatics Conference

Results • Coral Reef Disease Ontology Paper in Submission to Geoinformatics Conference

Discussion and Notes • The lack of genomic data presents limited interpretation of on going analyses by our group • We will eliminate the data entry portion and just read straight from the database • Gene Ontology is speculative until further distinguishing data is available – • More genomic and environmental data • Better normalization techniques • The structure will evolve as the data collected evolves • Different ontological “engines” – Cosine comparisons and “Semantic Weight” • Temporal extent will add dimension to the interpretation • HCI contribution will improve usability and interpretation of results Paper in Submission to Geoinformatics Conference

Thank You • Claudia Johnson (Geology) • MehmetDalkilic (Bioinformatics) • Susan Morse Coleman (HCI/d) • School of Informatics Paper in Submission to Geoinformatics Conference

Questions? Paper in Submission to Geoinformatics Conference

A New Method of Examining Coral Reef Ecosystems: A First Use of Genomic and Bioinformatics Techniques