MODEL ORGANISM

TOP MODELS- IN BIOLOGY RAVIKUMAR09M51A2304

In any field of study, it is prudent to learn processes in a simple setting, understand the basis for these processes and then progress onto more complex settings to see if the same apply there as well.WHAT IS MODEL ORGANISM?Over the last century, research on a small number of organisms has played a pivotal role in advancing our understanding of numerous biological processes. This is because many aspects of biology are similar in most or all organisms, but it is frequently much easier to study a particular aspect in one organism than in others. These much-studied organisms are commonly referred to as model organisms, because each has one or more characteristics that make it suitable for laboratory study.

HOW to choose a model organism? It depends on what question is being asked. When studying fundamental issues of molecular biology, simpler unicellular organisms or viruses are convenient. For developmental questions, more complicated organisms should be used.

MAMMALIAN MODELSMOUSERATRABBITPIG

NON-MAMMALIAN MODELSS. cerevisiae (budding yeast)S. pombe (fission yeast)Neurospora (filamentous fungus)D. discoideum (social amoeabae)C. elegans (round worm)Daphnia (water flea)D. melanogaster (fruit fly)D. rerio (zebrafish)Xenopus (frog)Gallus (chicken)Other MODEL ORGANISMSARABIDOPSISZEA MAYSPISUM SATIVUMSchizosaccharomyces pombe

This image shows vegetatively growing fission yeast cells stained with DAPI to visualize the nucleus.micro-mammalSchizosaccharomyces pombe, or fission yeast, is an African brewing yeast originally isolated from millet beer. This species has a distinguished research history in studies of the cell cycle and mitosis, chromosome dynamics, and epigenetics.With a doubling time of 2-4 hours and simple culture conditions,S. pombeis easily adapted to any molecular biology laboratory. Investigators from non-genetic systems are frequent recruits to the fission yeast community, usingS. pombeas a genetic adjunct in their laboratories, which has led toS. pombebeing nicknamed the micro-mammal.Schizosaccharomyces pombeNeurospora crassa

This image shows a rosette of maturing asci (meiotic cells) of Neurospora crassa, from Wild type x histone H1-GFP. Histone H1 being a chromosomal protein, the GFP-tagged nuclei (two per spore at this stage) glow in four of the eight ascospores of each ascus; the remaining four ascospores carry the untagged nuclei from the wild-type parent.Neurospora crassaNeurospora crassais a eukaryotic multicellular fungus with a sequenced 43 mb genome that contains 10,620 predicted genes a complexity comparable to that of animal model systems such as Drosophila. Neurospora offers numerous advantages for basic research in genetics, molecular, cell, and evolutionary biology.Genetic analysis is readily accomplished. Haploid progeny are easily obtained as random isolates by manual isolation of ascospores or by ascospore plating. Tetrad analysis employs ordered or unordered asci to obtain the four products of individual meiotic events.Among other pioneering contributions, Neurospora was used to demonstrate the one-gene-one-enzyme hypothesis and has provided novel examples of genetic and epigenetic gene silencing. Study of rhythmic vegetative sporulation in Neurospora has resulted in major advances toward understanding the mechanism of circadian rhythms.Neurospora crassaDaphniaThe microcrustaceanDaphnia, commonly referred to as the water flea, has been subject to intense biological investigations for over a century. The development of genomic infrastructure coupled with a wide range of phenotypic diversity make Daphniaa versatile model system to investigate fundamental mechanisms of inheritance and development, cellular function, physiological systems, immunity response, disease, macromolecular structure/function relationships, and the genetic basis of complex phenotypic traits.

Daphniaare an exceptional model for studying developmental and disease processes. Daphnia are transparent throughout lifeallowing for studies of tissue-specific gene expression at any life stage and direct observation of parasites and pathogens.. Dictyostelium discoideum (Slime Mold)

Dictyostelium discoideum: Model System in MotionThe ameboid protozoanDictyostelium discoideumis a powerful system for genetic and functional analysis of gene function. The 34 Mb genome contains many genes that are homologous to those in higher eukaryotes and are missing inSaccharomyces cerevisiae. The organism is uniquely suited for studing cytokinesis, cell motility, phagocytosis, chemotaxis, signal transduction, and cell differentiation during development. Many of these processes, which play important roles in health and disease, are either absent or are less accessible in other model organisms.

Though we may not appear to have much in common with a slime mold, scientists have discovered that many of its genes are close copies of our own. Because of its unusual properties and ability to live alone or in a group, the slime mold intrigues researchers who study cell division, movement and various aspects of organ and tissue development. Drosophila melanogasterIn 1908, Thomas Hunt Morgan and his research associates at Columbia University placed rotting fruit on the window ledge of their laboratory. Among the menagerie of creatures that were captured, the fruit fly emerged as the animal of choice.

There is disks for appendages, eyes, antennae, the mouthparts, and genitalia.Disks are composed of fewer than 100 cells in the embryo but thousands of cells in mature larvae.The wing imaginal disk has become an important model system for the control of complex patterning processes by gradients of secreted signaling molecules.Arabidopsis thaliana (the cress in stress)A small flowering plant related to cabbage and mustard, Arabidopsis the most popular model for studying plant genetics is appealing to biologists because ithas almost all of the same genes as other flowering plants and has relatively little DNA that doesn't encode for proteins. It also grows quickly, going from seed to mature plant in only 6 weeks.

ZEAMAYS

Maize (Zea mays)

Zea mays ssp. mays is one of the worlds most important crop plants, boasting a multibillion dollar annual revenue. In addition to its agronomic importance, maize has been a keystone model organism for basic research for nearly a century. Within the cereals, which include other plant model species such as rice (Oryza sativa), sorghum (Sorghum bicolor), wheat (Triticum spp.),Advantageslarge flowers and inflorescencesimportant crop plant

Pisum sativum

This model was built with a rule-based computer modelling system using the information from the crystal structures of the photosynthetic reaction centres of Rhodopseudomonas viridis and Rhodobacter sphaeroides. An alignment of the primary sequences of twenty three D1, nine D2, eight bacterial L and eight bacterial M subunits predicts strong similarity between bacterial and higher plant reaction centres, especially in the transmembrane region where the cofactors responsible for electron transport are located. The ancestral relationship between the bacteria and higher plant sequences allowed both the L and M subunits to be used as structural templates as they were equally related to the higher plant polypeptides. The regions with the highest predicted structural homology were used as a framework for the construction of the structurally conserved regions. E. COLI

E.COLIGram-negative rodFacultative anaerobe

Named for Theodor EscherichGerman physician (ca. 1885)Demonstrated that particular strains were responsible for infant diarrhea and gastroenteritis

Normal flora of the mouth and intestine Protects the intestinal tract from bacterial infectionAssists in digestionProduces small amounts of vitamins B12 and K

Colonizes newborns GI tract within hours after birth

There are more than 700 different serotypes of E. coliDistinguished by different surface proteins and polysaccharides

Escherichia colicoli- large intestine, colonMammalian large intestineEscherichia blattaeblattae. L. n. blatta cockroach Hindgut of cockroach Blatta orientalis

Mus musculus (the mouse from your warehouse)

The predominance of the mouse model

The mouse is an excellent model for human development and disease, although, the life cycle of the mouse is slow by the standard of the nematode worm and fruit fly. The mouse provides the link between the basic principles, discovered in simpler creatures like worms and flies, and human disease.The chromosome complement is similar between the mouse and human (autosomomes and X,Y sex chromosomes) Extended regions of a given mouse chromosome contain homologous regions of the corresponding human chromosomes. (more than 85% of the mouse genes are correspond to human genes.)

Mice are the premier model organism for human disease

Saccharomyces cerevisiae (aka, Baker's yeast)

BAKERS YEASTSaccharomyces cerevisiae

Features of S. cerevisiaeHave small genomesCan be grown rapidly in the labCentral characteristics: they contain a discrete nucleus with multiple linear chromosomes packaged into chromatin; their cytoplasm includes a full spectrum of intracellular organelles and cytoskeletal structures.

The Existence of Haploid and Diploid Cells Facilitate Genetic Analysis of S. cerevisiae

S. Cerevisiae can grow in either a haploid state (one copy of each chromosome) or diploid state (two copies of each chromosome).Conversion between the two states is mediated by mating (haploid to diploid) and sporulation (diploid to haploid).

Figure 21-10 S. Cerevisiae exist in three forms: two haploid cell types, a and , and the diploid product of mating between these two.S. Cerevisiae Has a Small, Well-Characterized Genome

S. Cerevisiae was the first eukaryotic organism to have its genome entirely sequenced. (1996)1.3X106 bp, approximately 6,000 genes.The availability of the complete genome sequence has allowed genome-wide approaches to studies of this organism. THE NEMATODE WORM, Caenorhabditis elegans

The nematode worm,C. elegansis used extensively in the fields of genetics and developmental biology. The suitability of this organism for research in these fields was first identified by Sydney Brenner and through his and other scientists work, the complete wiring diagram ofC. elegansshowing the developmental fate of each cell of the adult organism is now known. This incredible knowledge makesC. elegansa real favourite among geneticists and developmental biologists worldwide.

Suitable characteristics:Rapid generation timeHermaphrodite reproduction producing large numbers of self-progenySexual reproduction so that genetic stocks could be constructedA small number of transparent cells so that development could be followed directly

Figure 21-14 b The body plan of the wromMutations that disrupt the formation of the vulva form a bag of worms (the hatched worms devour their mother The genes are components of a highly conserved receptor tyrosine kinase signaling pathway that controls cell proliferation. and become trapped inside her skin).Mutations that inactivate this pathway eliminate vulva development.Mutations that activate this pathway cause overproliferation of the vulva precursor cells. The cell Death Pathway Was Discovered in C. elegansCell death is under genetic control (a mutated ced gene).Analysis of the ced mutants showed that the cell commits suicide. In males, a cell known as the linker cell is killed by its neighbor.Caenorhabditis elegansZebrafish in genome researchWhat is zebrafish?Danio rerioSmall freshwater fish from South Asia.4 cm long when fully grown.Common aquarium fish.Very easy to look after.

Why use zebrafish? Small size.All major organs present within 5 days post fertilisation.Short generation time (3-4 months).Produces 300-400 eggs every 2 weeks.Translucent embryos.Lots of genome resources available.

The zebrafish embryo~3.5 mm

eyeheart

swim bladder

muscle block segments

ear

brain

notochordZebrafish and human diseaseZebrafish mutants have been produced to model human diseases such as:Alzheimer's diseasecongenital heart diseasepolycystic kidney diseaseDuchenne muscular dystrophymalignant melanomaleukaemia

Chicken (Gallus gallus)

The domesticated chicken is a modern descendant of dinosaurs. It is the premier non-mammalian model organism with a large international research community dedicated to developing and sharing information. The chicken provides a new perspective on vertebrate genome evolution. Its genome is composed of approximately one billion base pairs and approximately 20,000-23,000 genes organized in 39 chromosome pairs. Although it shares a similar number of genes, the chickens genome is only about a third the size of mammalian genomes. This reflects a reduction in interspersed repeat content, pseudogenes and duplications. There are hundreds of mutant chicken stocks and inbred lines available for study. Research using the chicken as a model organism has resulted in important discoveries in virology, immunology, oncology, vertebrate development, genetics and evolution.

XENOPUS

Xenopus

Model organisms are often assumed to be representative of some more inclusive taxon of which the species is a part. This assumption leads to mistaken generalizations about the evolutionary and comparative significance of the data gathered. This paper reviews comparative and evolutionary studies of Xenopus laevis and its relatives. Phylogenetic analysis of data from DNA sequences and morphology indicate that Xenopus is monophyletic and that Silurana is its sister group. The most basal lineages of Pipidae diverged prior to the breakup of Gondwana. The bizarre morphology of Xenopus is in part due to changes in the mode of metamorphosis. Speciation in Xenopus is unique among Anura in being associated with various levels of polyploidy owing to allopolyploidy. THANK YOU