Model organism* Model organism: « Anon-human species * are extensively studied to understand a specific phenomenon expecting that the knowledge gained can be applied to other species as well * are studied as an example for other species and/or biological phenomena that are more difficult to study directly * are in vivo model for research purpose * consists of different non-human species * because human experimentation is unfeasible and unethical for experimentwidely used to research human disease strategy + common decendent of all living organisms + conservation of metabolic and developmental pathways * genetic material over the course of evolution Research using animal models + central to many of the achievements of modern medicine. * gontributed most of the basic knowledge in. fields such as human physiology, biochemistry and cell biology, diseases and many m + Polio eradication + Organ transplantation Some of the common model organisms are; + E. coli- used as model for bacterial genetics and metabolism * Saccharomyces cerevisiae (Yeast): used as model for cell and molecular biology + Dorsophila: used as model for developmental biology + Zebra fish: used as model for embryonic development + Arabidopsis thanilanaHistory * use of animals in research dates back to ancient Greece Aristotle (384-322 BCE) and Erasistratus (304-258 BCE) first to perform experiments on living animals 18th and 19th centuries + Antoine Lavoisier > use of a guinea pig in a calorimeter to prove that respiration was a form of combustion : to Pasteur> demonstration of the germ theory of disease in the 1880s using anthrax in sheep From 1910 to 1927 + Thomas Hunt Morgan> Drosophila melanogaster identified chromosomes as the vector of inheritanée for genes * Drosophila + one of the first, and or some time the most widely used, eukaryotic model organisms + Mouse genetic animals + William Ernest Castle & Abbie Lathrop + generation of the DBA ("dilute, brown and non-agouti’) inbred mouse strain + systematic generation of other inbred strains + mouse + extensively as a model organism + associated with many important biological discoveries of the 20th and 2st conturies.* In the late 19th century + Emil von Behring + isolated the diphtheria toxin + Demonstration its effects in guinea pigs + Frederick Banting's research in dogs + isolates of pancreatic secretion could be used to treat dogs with diabetes + In the 1940s + Jonas Salk + hesus monkey studies to isolate the most virulent forms of the polio virus + polio vaccine + Albert Sabin * improved the vaccine by passing the polio virus through animal hosts, including monkeys; * Other 20th-century * medical advances and treatments that relied on research performed in animals + Invivo models« Requirements for model organisms + Smallsize. + Must develop rapidly withs hort generation time + Must be amenable to observation and experimentation. + Availability of genome sequence + Easy for transformation + Acomprehensive online database + Agrowing array of tools and techniques for molecular genetic studies + E.g.,Genetic manipulation, identification and selection of genes + Phylogeny and genetic relatednessMicroorganisms as model organisms * advantages Bacteria as a Model Organism * E. coli + dicovered by doctor Theodor Escherich in 1885 + Escherichia coli or E. coli is a Gram-negative, rod- shaped bacteria t + anormal inhabitant of the lower gastrointestinal tract of warm blooded animals + is expelled into the environment within fecal matter + grows massively in fresh fecal matter under aerobic conditions for 3 days, + but its numbers decline slowly afterwards. * genome is relatively small, 4.5 to 5.5 Mbp. + no ethical concerns about growing, manipulating, and killing bacterial cells,reproduce and grow very rapidly doubling its population about every 20 minutes helpful in research to get subsequent generations within a short time. + can survive and adaptive to variable growth conditions Culture media + simple and inexpensive ingredients nutrients easy to culture in laboratory in liquid medium or solid medium within petriplates * billion cells per milliliter, and trillion of bacterial cells can be easily grown on a single test tube.This colony formation makes it easy to isolate genetically pure strains of the bacteria. Most strains are harmless. ‘They can be manipulated and engineered easily. well established methods and screening techniques + which hos enabled many biochemical processes tobe Inked tothe molecular genetic level Genome Circular DNA molecule 46 milion base pais in length + 4288 annotated protein-coding genes (orgeized into 2584 operons). + seven ribosomal RNA RNA) operons, +86 transfer RNA (HINA) genes. Current research areas for E. coli + acavector + ahost for genetic elements + synthesis of proteins of intorestViruses Bacteria Proteins involved in DNA, RNA, Proteins involved in DNA, RNA, protein synthesis protein synthesis, Gene regulation metabolism Cancer and control of cell SI Gene regulation proliferation Targets for new antibiotics ‘Transport of proteins and Call cycle organelles inside cells Signaling Infection and immunity Possible gene therapy approachesMoaet Organis Virus Prokaryote Bukaryote, unicellular Informal ce classification Phi X174 @xi74 Escherichia coli B. coli Dictsostelium Brewer's Baker's yeast Saccharomyces Schizosaccharnwwees. Seaiza Fission yeast ‘Chlamydomonas reinhardesi Tetrahganena Gexppanbile. T: periformis Exailianin, boaslen. Usage (examples) Virus Bacte Yeast Algae Citiate Plankton usr bacterial genetics, metabolism immunology. host-pathogen cell division cell cycle, cytokinesis, chromosome biology, telomeres, DNA metabolism, cytoskeleton ‘organization, industrial applications hydrogen production ‘education, biomedical research* Yeast (S. cerevisiae) + Yeasts are eukaryotic, single-celled microorganisms * members of the fungus kingdom. * reproduce asexually by mitosis * many by the asymmetric division process known as budding * With their single-celled growth habit + Different from molds, which grow hyphae * sizes vary greatly, depending on species and environment + typically measuring 3-4 um in diameter, + although some yeasts can grow to 40 um in size+ Yeast + first eukaryotic organism to have its genome sequenced + chromosomes share a number of important features with human chromosomes. + Fission yeast (Schizosaccharomyces pombe) * a popular system for studying cell growth and division « useful partly because + itis easy and inexpensive to grow in the lab + cells have a regular size and grow only in length, + making it very simple to record cell growth.Yeast + powerful model organism tha + enabled a better understanding of human biology and disease Between 2001 and 2013, four Nobel Prizes were awarded for discoveries involving yeast research, an impressive number for a single organism. genome of S. cerevisiae yeast + published in 1996 + 23% homologous gones to humans S. pombe sequence + 2002 Result: * initiated to determine the functions of all the genes in these genomes + Saccharomyces Genome Deletion Project * produce mutant strains of yeast * 6,000 genes in yeast were mutated+ Yeast + One of the simplest eukaryotic organisms with many essential processes similar to humans + Thus is an important model organism to understand basic molecular processes in humans.* Yeast has many High-throughput genomics data * Gene expression (by microarray or RNA-seq) — Cell cycle, deletion strain, chemical perturbations + Transcription regulation (binding by transcription factors) — ChIP-chip, ChIP-seq * Protein-protein interactions and complex data — Yeast Two-Hybrid (Y2H), TAP-tagging, literature curation * Genetic interactions and pathways — Synthetic Genetic Array (SGA) * Chemical genomics + — Small molecule — gene interactions * High content morphological screeningYeast (Saccharomyces cerevisiae) Control of cell cycle and cell division Protein secretion and membrane biogenesis Function of the cytoskeleton Cell differentiation Aging Gene regulation and chromosome structureAnimals in research + Why Use Animals in Research? + most medical breakthroughs in the past century * prevented much human suffering + examples: ® polio vaccine = dialysis ™ cataract surgery techniques + Animal research has also directly benefited animal health: = 111 USDA-approved veterinary biologics heartworm, arthritis, parasites, allergies, and heart disease = vaccines to prevent rabies and feline HIV« Why testing on animal is required ? « Why not animal cell culture enough? « finasteride (Propecia). - hair growth + hair growth + Warning: Pregnant women should not handle broken or crushed pills+ Types of Animals Used in Research ee srt * Genetic and physiological similarities § + Mice & rats as model organism Granulocytes + Pure-bred “ + Known and controlled genetics 2 j Lymphocytes + Other species ™ + Vertebrates (Zebrafish } Myeloid cals + Invertebrates ( fruit flies & worms) <& Transfer stem calls from human cord blood FIGURE 1 Mice Tell Us about Ourselves Here, after the immune system of a developing mause is destroyed, it can be replaced by injecting human stem cells, In this way it is possi- ble to study therapies for humans using mice as models.+ Types of Animals Used in Research + + Zebrafish (Brachydanio rerio) i Le * extremely valuable , popular and hardy aquarium fish + Small (about 3 cm in length) and rapidly growing + Continuous spawning (only about 3 months between generations) average number of progeny per female per week can exceed 200» ideal for studies of development and for genetic research + complete embryogenesis in about 120 hours + gut, liver, and kidneys development in first 48 to 72 hours = . or adverse effects testing in about 5 days Easy gene transfer to eggs + no need to of a donor mother for gestation Transparent embryos + cell division study under the microscope in its first hr SR 2. Reatih Ae Common ade Aa@ Zebrafish Development of ve tissues Formation and function of brain and Birth defects Cancer Mico, including cultured cells, Development of body tissues Function of mammalian immune system Formation and function of brain ‘and nervous system Models of eancars and othe human disesses Gene regulation and inheritance Infectious disease+ Rats: + relatively large size of rats * superior to mice for many early drug toxicity tests’ + More close to human physiologically * more humanlike responses to drugs « surgical and physiologic experimentation « dissection or isolation of specific cell types and organ structures + pharmacokinetics (drugs interaction with tissues and metabolism) « preferred model organism + determining drug metabolism + early toxicology profiles Rat models are preferential for the ‘ae following studies: + Neurobiology « Cardiology «Immunology « Toxicology « Physiology ¢ Pharmacology «= Nutrition « Behavior * And more!+ Dogs + the lung and cardiovascular systems + More close to human + Better choice for heart and lung disease « monkeys and chimpanzees + For HIV/AIDS * cats, dogs, and primates like monkeys and chimps . are used only in specific instances +» make up less than 1% of the total number of research animals + majority are mice + Decrease in number of those animals used in experiments + increased use and availability of alternative methods of testing« Regulations in Animal Research + FDA regulations to pass safety test before marketing + new drugs + medical procedures + cosmetic products « Safety testing involves a rigorous scientific methodology known as phase testing + FDA requirements + Before availability of drug to the general public conduct a statistically significant number of trials on + cell cultures + trials in live animals and + human research participants‘TABLE 1 FOOD AND DRUG ADMINISTRATION REQUIRED TESTING PHASES FOR DRUG APPROVAL FDA Phase testing involves the use of animals for pre-clinical testing before allowed in humans. If the new drug candidate has proven to be non-toxic and has benefit, then it can be awarded and Investigational New Drug (IND)status. IF it is successful in the three phases of human testing it can receive a New Drug Application (NDA) and likely approval for marketing, The FDA continues evaluating the NDA for another 2.5 years, resulting a total of about 12 years for a successful drug approval. Preclinical Testing Years 35 Tested on Animats in the lab Purpose Assess safety and file IND biological activity Epa. Success rate 5,000 compounds evaluated ase 1 20-80 healthy volunteers Determine safety and dosage Phase It Phase IIT 2 3 100-300 1,000-3,000 patient patient volun- volunteers teers Evaluate Verify effectiveness effectiveness, and look for monitor adverse side effects reactions from long-term use S enter trials File NDA. at FDA FDA 25 Review process/ approval 1 approved 12 total Phase IV Additional testing after approval required by FDA Source: www.fa.aov/cder/handbook/develoo.htmResults of initial tests on in cell cultures + Toxicity detection + Choice of animal to test + To mimic the conditions in human + Genetic similarity + Number species for trial + To test different effects in different animals + Toxicity and unexpected nontarget effects + Drug Testing + Animal models can provide information about: + Toxicity + rate of absorption + specific chemical metabolism + time required to excrete (eliminate from the body) ete « Failure in animal tests + No clinical phase trials * Rare and unintended results can occur + Requirement of informed consent from participants + Disclose all the information participant+ Alternatives to the Use of Animals + Whenever possible in initial testing + cell cultures and computer-generated models + significantly less expensive than research animals + Time saving Animal thotechnotogy — —— je acai SS —_ ating — Transfection ‘Cutture Nuclear transfer Cunure expansion+ cell culture studies + Frequently used for pralminary sen of toxey of estan Toansmer furdarental questions about biology + Fomectecingerdenceat te cer kvl + Drawback poteniimpactson an etre living eganem + Computers/ computer based models/systems + Are becoming more sophisticated + Excellent for processing data and observe emerging patterns + are frequently used for 1+ simulation o specie molecule a hares stuetras an ther iteractins + Drawbacks + United by prowaring Imgoet ona ivinsstem + Forerample ‘semputermodalte asthe efleny of marae goed Neinlormationebout unageted prblrfbith eles + Anorgan-on-a-chip (OOC) + isa multi-channel 3-D microfluidic cell culture, integrated circuit (chip] that simulates the activities, mechanics and Physiological response of an entire organ or an organ system, a type of artifical organ.Caenorhabditis elegans + a free-living, transparent nematode (roundworm) + about 1 mm in length + temperate soil environments + unsegmented, vermiform, and bilaterally symmetrical + lacks respiratory or circulatory systems + with a cuticle integument + four main epidermal cords + a fluid-filled pseudococlomate cavity + has two sexes + hermaphrodites and males. + mostly hermaphrodite + males comprising just 0.05% of the total population « first multicellular organism to have its genome completely sequenced in 2019Caenorhabditis elegans + a free-living, transparent nematode (roundworm) + about 1 mm in length + temperate soil environments + unsegmented, vermiform, and bilaterally symmetrical + lacks respiratory or circulatory systems + with a cuticle integument + four main epidermal cords + a fluid-filled pseudococlomate cavity + has two sexes + hermaphrodites and males. + mostly hermaphrodite + males comprising just 0.05% of the total population « first multicellular organism to have its genome completely sequenced in 2019* multicellular eukaryotic organism * Transparent and simple to study ° Facilitate + study of cellular differentiation * other developmental processes in the intact organism + Easy to miniplate & observe * feeds on bacteria * cheaply housed and cultivated in large numbers (1000 worms / Petri dish) in the laboratory * Growth on agar-filled Petri dishes covered with a lawn of bacteria * Strains are cheap to breed + long- term storage * can be frozen-> — subsequent thaw, > remain viable+ Sydney Brenner * In 1963. proposed C. elegans for research in neuronal development + and started research into molecular and developmental biology of C. elegans + since then C. elegans _ extensively used as a model organism* experimental organism for * study apoptosis (programmed cell death) + For finding treatments for certain types of human cancers, such as leukemia. * to identify genes that switch-on cell death in cancer cells. ¢ Exploration of neural mechanisms responsible for several interesting behaviors * chemotaxis, thermotaxis, mechanotransduction, and male mating behavior * Metabolic disease* Gene silencing by RNAi + Disruption of specific genes functions ¢ To find out the gene function * establishing a functional role for 9% of the genome Roundworm (Caenorhabditis elegans) ‘ent of the body plan e ‘and function of the nervous system Control of programmed cell death Cell proliferation and cancer genes Aging Behavior Gene regulation and chromosome structureMidgut/ intestine Distal tip cell Anterior arm of gonad Distal gonad —s Pharynx Germ cells Corpus uren6/ Embiyos uC Rectum & anus Vulva Spermatheca Terminal bulb i Lumen of intestine 00 Pharyngeal-intestinal valve Posterior arm of gonad [- ~lmmDrosophila melanogaster as a Model Organism Fruit fly Thomas Hunt Morgan developed Drosophila as a model system in 1909. extensively studied for over a century as a model organism for genetic investigations ‘any characteristics which make it an ideal organism for imal development and behavior + searbiology + Iman genetic diseases + conditions ‘A good model organism needs to share, on the molecular level, many similar features and pathways with humans. Approximately 60% of a group of readily identified genes that are mutated, amplified, or deleted in a diverse set of human diseases have a counterpart in DrosophilaBenefits of Fruit fly The fruit fly has many practical features that allow scientists to carry out research with ease: A short life eycle, Ease of culture and maintenance, and Less number of chromosomes Small genome size (in terms of base pairs), but Giant salivary gland chromosomes, known as polytene chromosomes.Life cycle Life Cycle of Drosophila melanogaster * female fruit fly> about 3 mm in length + lay between 750 -1,500 eggs in her lifetime + only takes about 12 days to complete at room temperature (25°C) * after egg fertilization > embryo emerges in ~24 hours Drosophila | Life Cycle* Genome of Drosophila * D. melanogaster four chromosomes pairs + | pair of sex chromosomes (two X chromosomes for females, one X and one Y for males) + 3 of autosomes (non-sex chromosomes) labeled 2 through 4 + Chromosome 4 + smallest * known as dot chromosome. * represents the just ~2% of the fly genomea = 2R & PP coves omar oF et ee; = a (one . 2 cones gus “ie , < = a ® baad <“ 5 F : ee ag? ae 09 wr = ” oF » re ©, aL = 3R oS € 7 Sy Chromocenter Sav er ae ie giant polytene chromosomes found in the fly's salivary glands ( ith the chromosomes from the fly's ovary) are another character ie fruit fly an important organism for laboratory studies. These romosomes provided a road map for early geneticists. age source: Modified from T. S. Painter, J. Hered. 25, 465-47¢Genome of Drosophila + 132 million base pairs compared with 3.2 billion base pairs for the human + around 5% of the size of the human genome * 15,500 genes on its four chromosomes * 22,000 genes among their 23 chromosomes in human * density of genes per chromosome in Drosophila is higher than for the human genome « humans and flies have retained the same genes from their common ancestor + (Known as homologs) over about 60% of their genome. * approximately 60% of genes associated with human cancers and other genetic diseases are found in the fly genome. * Just like C. elegans Connectome ( neural circuits ) are available in fruit fly« Is being used for large number of studies + From genetic analysis, mutation, and bevioural studies + Examples Fruit fly (Drosophila melanogaster) Development of the body plan Generation of differentiated cel! Control of cell polarization, Effects of drugs, alcohol, pesticidesname USE Caenorhabditis Won differentiation, elegans Round development developmental biology, Drosophila | eit hy i. human brain degenerative disease Callosobruchus oyna Weevil | Insect developmental biologyCommon name Danio rerio Eundulus. heterochitus. Nethobranchius. furzeri. Oryzias latipes Anolis carolinensis Mus musculus Gallus gallus. amiaeae castanotis Xenopus laevis, Informal Usage classification (examples) | Zebrafish _ Fish Mummichog Fish | Turquoise | killifish, mee Japanese rice | a Fish Carolina anole Reptile House mouse Mammal Red junglefowl Bird Australian zebra yy, finch Bit African clawed USE embryonic development _ effect of hormones on behavior aging, disease, evolution fish biology, sex determination reptile biology, evolution disease model for humans embryological development and organogenesis vocal learning, neurobiology embryonic development+ Regulation of Animal Research * Animal research - heavily regulated + federal Animal Welfare Act specific standards + housing, feeding, cleanliness, and medical care of research animals + Need to prove + Why to use animal models + Appropriate number + institutional and federal standards + Government agencies regularly monitor the conditions in the laboratories + funding for research from FDA, NIH, CDC + “Three Rs” of animal research: = Reduce the number of higher species (cats, dogs, primates) that are used = Replace animals with alternative models whenever possible = Refine tests and experiments to ensure the most humane conditions possibleArabidopsis thaliana * also known as rockcress or thale cress * a small plant with white flowers * often considered to be a weed * found across Europe, Asia and Africa * very popular model organism for plant studies + plant genetic research, cell biology etc Order Family: Genus: Species: Plantae Tracheophytes Angiosperms Eudicots Rosids Brassicales Brassicaceae Arabidopsis A. thaliana+ A. thaliana as a model system becat * small genome (114.5 Mb) * genetically well characterised + rapid life cycle * high transformation efficiency * completely sequenced genome * powerful reverse and forward genetics Genetic Mapeing Inggrtional mutageresta ecto mera =i = s—° GENOME It having five pairs of chromosomes (2n=10) i es, Z Sig found 125 million base pairs of DNA 18 % genes were common with human genome Average gene size is about 201 15t plant has done Complete genome were sequenced in year of 2000Atti ‘Model system -Smallsize- requiring less growth space -Shorter generation time -increasing the pace of research -Large progeny for genetic analysis -Small genome size (125Mb)- completely sequenced -Smalll number of chromosomes (n=5) -Amenabie to transformation + Spectrum of genetic and molecular + Rapid life cycle * genetically well characterized + high transformation efficiency * completely sequenced genome * powerful reverse and forward genetics* first mutant in A. thaliana * documented in 1873 by Alexander Braun + describing a double flower phenotype \ + Friedrich Laibach + had published the chromosome number in 1907 + Erna Reinholz + thesis > describing the first collection of A. thaliana mutants * generated using X-ray mutagenesis. + John Langridge and George Rédei * In 1950s and 1960s, played an important role in establishing A. thaliana as a useful organism for biological laboratory experiments * first International Arabidopsis Conference + held in 1965, in Gottingen, Germany + In the 1980s, . a thaliana started to become widely used in plant research laboratories around e world.Established as 2 mode for plant Physial map of aS ‘gets. chromosome completed. cise Punetional genomics project launched. | | | ener ‘Agrobacteriam mediated ‘Microarray/Tiling/ aperimental baa. corr ees Epigenticmap Report fist Xayindued Reeth geome sequence ‘801 Gnome projet__| MBL Reamesegened Arabidopsis mutants. Fig 1.2. Milestones in Arabidopsis researchModel Genetic Organism = Arabidopsis thaliana Genome Sequenced Genetic Resources Rapid cyclers Self Pollinated Genetically ‘Thousands Transformed of Seeds Bioinformatic Functional Genomic Resources Tools Extensive Natural Varlation in Accessions Exists Dissection of natural variation major challenge* Contribution in genetic « Plant genome organization + Gene regulation + Genetics of plant development + Genetic of flowering + Pathogenicity studies + Traits associated with virulence to Pseudomonas « Making knockouts + Easy susceptible to agrobacterium + Tiplasmid, TDNA insertion + Easy to establish many knockout lines within short itme + Basic life processes are similar to those of more complex crops plants + Com, soybean & wheat + Same basic sets of genes for controlling different process Possible to find applications in other spoARABIDOPSIS TRANSFORMATION BY FLORAL DIPPINGEXPRESSION IN DIPPED PLANTS OF MARKERS FOR PLANT GENE EXPRESSION PRESENT ON THE T-DNA Agrobacterium enters the developing flower and the T-DNA is introduced into the developing female gametophyte, and transmitted Through the ovule to the next generation.Plant (Arabidopsis thaliana) Development and patterning of tissues Genetics of cell biology Agricultural applications Physiology Gene regulation Immunity Infectious diseaseThe Arabidopsis Genome: “Catalyst” for Plant Research + Arelatively smalier genome size (approx. 125 Mb) — + tho simple reason Arabidopets was chosen as a subject for tho fst plant gonome sequencing project. + first plant genome to be completely sequenced in the year 2000 under an international Arabidopsis Genome Initiative (AGI). + Analysis of the genome using various gene-finding algorithms« Genetic resources‘Table 1.1. Listof resources available for the Anabidopris research community “Transceipiome Rerource name ‘Arabidopsis Biological Resource Comicr (ABRC) Nottingham Arabidopsis Stock Center (NASC) SENDAI Ambidopsts Sced Stock Center (SASSC) Versailles Arabidopsis Stock Center (VNAT) ‘SeedGenes Project Database CSHL Trapper DB. SALK Lines GABLKAT Lincs AGRIKOLA RNAI ‘Activation tagging and FOX hunting system RARGE ML 1001 Genomes project ‘The SIOBAL Arabidopsis SNP, Deletion and SFP Database POLYMORPH too! QTL mapping tools for MAGIC population Mattipte SNP Query Too! (MSQT) Arrayix press ‘Arabidopsis Transcriplome Genomic Express Database pss (CressExpres - Co-expression analysis AUTAX (Tiling Array Express) MAPMAN tool ATTED-It Web address apiece ae upe/Jarabisopsis infor npe/eassc.epa.bre-riken,jp/ ‘bup//publiclnes. versalles.nra.fr/ up: //seedgenes org/index hurl Inup://geneteap eshl.ors tp //sigmal.salk.edu/tabout hte Iup//wreweabichat ded Inn ors agrikola one? Iups:/database riken jp/sw/en/Home/eria3O1ut tp /rarge-v2 psc riken jp? Inu arabidopsis orgnoolsnndex jsp ‘nup//plants-ensembl.orp/ Arabidopsis_thaliana/lnfo/Index ‘hup:/100 genomes. ore! ‘tp /Isigmal sallcdu/ogi-bin/ ‘SEP up: /polymorph weigchworld ong! ‘ap-/mus well ox ac uk/magic! up/msqtwoigehwort. oes inups:rwerw ebl.ac ub/arrayen press? hitp//signal.salledu/ogi-bin/ata bup://planex plantbicintormatics.ors/ Ihup//empassidel ed up: www swcigelwerld orghresourcevimicroaray! MGenExpress! bapi/foreasexpress.ore/ inup://ww. seigel world orpiresourceshmicroarray/a-tax Ihup.mapman.sabipd.ors/ Inup atted pd Inup:/astp danforthcenter ores ‘hep ta rutoronto.ca/etp/egt- bin/efpWeb.cgiProteome Metabolome Epigenome Systems biology ‘SubCellular lacalization Database for Arabidopsis proteins (SUBAS) MASCP, lant Proteome DataBase (PPDB) ‘AiProteome Database PMN. Plant Metabolite Nework Arabidopsis Metabolomics Consortium KEGG MetaCrop ‘UniPathway EPIC (Epigenomics of Plants Intemational Consortium) ‘The EPIC-CoGe Epigenomies Webbrowser Epigenetic Natural Variation browser Arabidopsis thaliana Protein Interactome Database (ALPID) ‘Arabidopsis thaliana protein imeraction network (AWPIN) Arabidopsis protein interaction network analysis (ANAP) AP AGRIS (Arabidopsis Gene Regulatory Information Server) ‘Systems biology toolkit Viewal Plant ‘Plant Collaborative ~a eyberinfrastructure for plant sciences Intpoubs plantenergy awa eda aul Ip: wow mase-proteomics.orp/mascp/index php/Databases Itp:/fppate.cornelLec! hntpfger-atproteome wnizh.ch! hap: planteye.org” ‘nup:/plantmetabolomics. rac iastate.edu/ver2/ nap: worw.genomejprkego/ ‘ntp:/imetacrop.ipk-gatersleben.de vwivw.grenoble.prabifrobiwarehouse/unipahway Iitps:/Aeww:plant-epigenome.orp/ hatps// _genomevolution org/wikifindex php/EPIC-CoGe_Totorial Ingp:chromatincshl edu/egi-bin/gbrowsefepivariaton/ Inup:/worw.megabionet.ory/apidwebsiles Ip: /bioinfoesalg.usp.befatpin hiep/fgmad.shgrno.org/Computational-Biology/ANAP. Ips:/Avww.arapor. org! Imtp:/arabidopsis.med ohio-state.edu/ hep! wwvw.garnetcommunity.org.ukiresources systems-biology-tool-kit gp: /virtualplantbio.nyy edulegi-bin/ypwelv nap: www iplantcollaboratve.ong/Informal Usage Common nam) classification (examples) USE Arabidopsis Flowering i , thaliana Thale cress plant population genetics Physcomitrella Spreading . patens Moss molecular farming drought tolerance, lignin Populus Balsam biosynthesis, wood formation, trichocarpa poplar Plant biology, morphology, genetics, and ecology