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Model organism
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- 2. A modelorganism is a non-human species that is suitable for studying a specific trait, disease, or phenomenon, due to its short generation time, characterized genome, or similarity to humans. Model organisms are in vivo models and are widely used to research human disease when human experimentation would be unfeasible or unethical. Examples; Fly, fish, rodent or pig, whose biology is well known and accessible for laboratory studies. 2
- 3. Small size. They mustdevelop rapidly with short generation time. Must be amenable to observation and experimentation. Availability of genome sequence. Easy for transformation. A comprehensive online database. A growing array of tools and techniques for molecular genetic studies. E.g., Genetic manipulation, identification and selection of genes. 3 While selecting model organism the following features such as…
- 4. Escherichia coli Escherichiacoli or E. coli is a Gram-negative, rod- shaped bacteria that is a normal inhabitant of the lower gastrointestinal tract of warm blooded animals. E. coli is expelled into the environment within fecal matter. The bacterium grows massively in fresh fecal matter under aerobic conditions for 3 days, but its numbers decline slowly afterwards. The E. coli genome is relatively small, 4.5 to 5.5 Mbp and simple when compared to our own. 4
- 5. E. coli isa model organism because… • It is an unicellular organism. There are no ethical concerns about growing, manipulating, and killing bacterial cells, unlike multicellular model organisms like mice or chimps. • They are able to reproduce and grow very rapidly, doubling its population about every 20 minutes. This is helpful in research to get subsequent generations within a short time. • They can survive and adaptive to variable growth conditions. 5
- 6. • Culture mediacontaining simple and inexpensive ingredients and nutrients can successfully spur E. coli to grow and divide. • It is easy to culture in laboratory in liquid medium or solid medium within petriplates. • In liquid culture, E.coli cells will grow to a concentration of a billion cells per milliliter, and trillion of bacterial cells can be easily grown on a single test tube. • When E. coli cells are diluted and spread onto the solid medium of a petridish, individual bacteria reproduce asexually, giving rise to a concentrated clump of 10 million -100million genetically identical cells , called a colony. 6
- 7. • This colonyformation makes it easy to isolate genetically pure strains of the bacteria. • Most strains are harmless. • They can be manipulated and engineered easily. • Mutants are easily obtained using well established methods and screening techniques, which has enabled many biochemical processes to be linked to the molecular genetic level. • E Coli Genome is found to be a circular DNA molecule 4.6 million base pairs in length, containing 4288 annotated protein-coding genes (organized into 2584 operons), seven ribosomal RNA (rRNA) operons, and 86 transfer RNA (tRNA) genes. • Current research areas for E. coli include acting as a vector, a host for genetic elements and synthesis of proteins of interest 7
- 8. Arabidopsis thaliana • Arabidopsisis a popular model organism used in plant biology and genetics. • It is a member of Brassicaceae family. • It is a small flowering weed. • It grows luxuriantly in temperate regions of the world. • They are vary in size, shape, physiological characters and DNA sequence. • It has a small genome and It has only 5 chromosomes. 8
- 9. 9 • The immunesystem of plants are widely diversified and can recognize viruses, microbes, worms, insects, etc. • These are biotic stress caused to plants. • Now a days, A. thaliana mostly used in the study of genome structure, gene regulation, development and evolution of plants. • Also it provides the important basic information about plant genetics, that is applied to other economically important plants. • Efficient transformation by Agrobacterium tumefaciens. Forward genetics identified many mutants over 1500 freely available from stock centre; Reverse genetic resources excellent and over 100,000 insertions at precise sequenced locations.
- 10. • Plants constituteover 90% of the world‘s biomass; 250,000 species of flowering plant. • Each plant can produce the 10,000 to 40,000 seeds. • It has ability to grow in the laboratory. • Many variants are available. • Ability to self fertilization and out cross. • It found 125 million base pairs of DNA and 18 % genes were common with human genome. • Average gene size is about 200 bp. • It is the first plant has done Complete genome were sequenced in year of 2000. 10 Why do we need Arabidopsis as a model….?
- 11. 11 • Important biologicalprocesses are plant specific; photosynthesis that fixes carbon and produces oxygen. • Plants are economically important; in agriculture or in secondary metabolites as medicines and in nutrition. • Plants evolved multicellularity independently, and use different mechanisms of cell to cell communication. • Plants represent important genetic model systems; transposons and gene silencing were first identified in plants.
- 12. 12 Arabidopsis is auseful model plant, Simple genome. Easy maintenance and space-efficient. Applicable similarities with other plants. It has a potential to help increase food production quantity and quality to feed a growing world population. Due to these overall applications makes Arabidopsis as a model plant organism
- 13. yeast Yeasts areeukaryotic, single-celled microorganisms classified as members of the fungus kingdom. Most yeasts reproduce asexually by mitosis, and many do so by the asymmetric division process known as budding. With their single-celled growth habit, yeasts can be contrasted with molds, which grow hyphae. Yeast sizes vary greatly, depending on species and environment, typically measuring 3–4 µm in diameter, although some yeasts can grow to 40 µm in size. 13
- 14. Yeast is oneof the simplest eukaryotic organisms but many essential cellular processes are the same in yeast and humans. It is therefore an important organism to study to understand basic molecular processes in humans. Yeast was the first eukaryotic organism to have its genome sequenced. Yeast chromosomes share a number of important features with human chromosomes. Fission yeast (Schizosaccharomyces pombe) has become a popular system for studying cell growth and division. It is useful partly because it is easy and inexpensive to grow in the lab, but also because its cells have a regular size and grow only in length, making it very simple to record cell growth. 14
- 15. • 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 15 Yeast has many High-throughput genomics data
- 16. Yeast is apowerful model organism that has 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. The genome of S. cerevisiae yeast was published in 1996 and the S. pombe sequence in 2002. As a result, projects have been initiated to determine the functions of all the genes in these genomes. One such project, the Saccharomyces Genome Deletion Project, aimed to produce mutant strains of yeast in which each one of the 6,000 genes in yeast is mutated. 16
- 17. Caenorhabditis elegans • Caenorhabditiselegans is a free-living, transparent nematode (roundworm), about 1 mm in length, which lives in temperate soil environments. • C.elegans is unsegmented, vermiform, and bilaterally symmetrical, with a cuticle integument, four main epidermal cords and a fluid-filled pseudocoelomate cavity. • C. elegans has two sexes: hermaphrodites and males. • Individuals are almost all hermaphrodite, with males comprising just 0.05% of the total population on average. 17
- 18. • The organismis transparent and easy for manipulation and observation , feeds on bacteria ,cheaply housed and cultivated in large number (1000 worms / petridish) in the laboratory. • Most investigators grow C.elegans on agar-filled petridishes that are covered with a lawn of bacteria. • It is a multicellular eukaryotic organism that is simple enough to be studied in great detail. • Strains are cheap to breed and can be frozen. When subsequently thawed they remain viable, allowing long- term storage. • In addition, C. elegans is transparent, facilitating the study of cellular differentiation and other developmental processes in the intact organism. C.elegans is studied as a model organism for a variety of reasons… 18
- 19. • Researchers whostudy apoptosis (programmed cell death) use C. elegans as an experimental organism in the hope of finding treatments for certain types of human cancers, such as leukemia. • By studying apoptosis in C. elegans, researchers hope to identify genes that switch-on cell death in cancer cells. • Researchers have explored the neural mechanisms responsible for several interesting behaviors shown by C. elegans, including chemotaxis, thermotaxis, mechanotransduction, and male mating behavior. • It can be stored for a long term in the laboratory. • C. elegans was the first multicellular organism to have its genome completely sequenced. 19
- 20. • A usefulfeature of C. elegans is that the function of specific genes can be disrupted by by RNA interference. • Silencing the function of a gene in this way can sometimes allow a researcher to infer what the function of that gene may be. • The nematode can either be soaked in or injected with a solution of double stranded RNA , the sequence of which is complementary to the sequence of the gene that the researcher wishes to disable. • RNA interference in C. elegans can also be done by simply feeding the worms transgenic bacteria expressing RNA complementary to the gene of interest. • This strategy for gene loss of function experiments is the easiest of all animal models, and thus, scientists were able to knock down 86% of the ~20,000 genes in the worm, establishing a functional role for 9% of the genome 20
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