nonnon--classical model organisms:classical model organisms:What are they…. and should they be studied?What are they…. and should they be studied?

Crown groupradiation~ 965 million years ago

Classic eukaryote model organisms

invertebrates&

vertebrates

Arbacia punctulata, the purple-spined sea urchin, classical subject of embryological studies

Aplysia, a sea slug, whose ink release response serves as a model in neurobiology and whose growth cones serve as a model of cytoskeletal rearrangements.

Caenorhabditis elegans, a nematode, usually called C. elegans[2] - an excellent model for understanding the genetic control of development and physiology. C. elegans was the first multicellular organism whose genome was completely sequenced

Ciona intestinalis, a sea squirt

Drosophila, usually the species Drosophila melanogaster - a kind of fruit fly, famous as the subject of genetics experiments by Thomas Hunt Morgan and others. Easily raised in lab, rapid generations, mutations easily induced, many observable mutations. Recently, Drosophila has been used for neuropharmacological research[3]. (Molecular genetics, Population genetics, Developmental biology).

Euprymna scolopes, the Hawaiian bobtail squid, model for animal-bacterial symbiosis, bioluminescent vibrios

Hydra (genus), a Cnidarian, is the model organism to understand the evolution of bilaterian body plans

Loligo pealei, a squid, subject of studies of nerve function because of its giant axon (nearly 1 mm diameter, roughly a thousand times larger than typical mammalian axons)

Pristionchus pacificus, a roundworm used in evolutionary developmental biology in comparative analyses with C. elegans

Stomatogastric ganglion, arthropods digestive systems are a model for motor pattern generation seen in all repetitive motions

Symsagittifera roscoffensis, a flatworm, subject of studies of bilaterian body plan development

Tribolium castaneum, the flour beetle - a small, easily kept darkling beetle used especially in behavioural ecology experiments

invertebrates

vertebratesCavius porcellus, the guinea pig, used by Robert Koch and other early bacteriologists as a host for bacterial infections, hence a byword for "laboratory animal" even though rarely used today

Chick (Gallus gallus domesticus) - used for developmental studies, as it is an amniote and excellent for micromanipulation (e.g. tissue grafting) and over-expression of gene products

Dog (Canis lupus familiaris) - an important respiratory and cardiovascular model

Hamster - first used to study kala-azar (leishmaniasis)

Mouse (Mus musculus) - the classic model vertebrate. Many inbred strains exist, as well as lines selected for particular traits, often of medical interest, e.g. body size, obesity, muscularity. (Quantitative genetics, Molecular evolution, Genomics)

Human - used in various clinical studies

Oryzias latipes, Medaka (the Japanese ricefish) is an important model in developmental biology, and has the advantage of being much sturdier than the traditional Zebrafish

Rat (Rattus norvegicus) - particularly useful as a toxicology model; also particularly useful as a neurological model and source of primary cell cultures, owing to the larger size of organs and suborganellar structures relative to the mouse. (Molecular evolution, Genomics)

Rhesus macaque - used for studies on infectious disease and cognition

Sigmodon hispidus - Cotton rat formerly used in polio research

Taeniopygia guttata or zebra finch - used in the study of the song system of songbirds and the study of non-mammalian auditory systems

Takifugu rubipres, a pufferfish - has a small genome with little junk DNA

Xenopus laevis, the African clawed frog - used in developmental biology because of its large embryos and high tolerance for physical and pharmacological manipulation

Zebrafish (Danio rerio), a freshwater fish, has a nearly transparent body during early development, which provides unique visual access to the animal's internal anatomy. Zebrafish are used to study development, toxicology and toxicopathology[4], specific gene function and roles of signaling pathways.

Classic eukaryote model organisms

fungi

Aspergillus nidulans, subject of genetics studies

Neurospora crassa - orange bread mold (genetic studies of meiosis, metabolic regulation, and circadian rhythm)[1]

Ashbya gossypii, cotton pathogen, subject of genetics studies (polarity, cell cycle)

Saccharomyces cerevisiae, baker's yeast or budding yeast (used in brewing and baking)

Schizosaccharomyces pombe, fission yeast, subject of genetic studies

fungi

Classic eukaryote model organisms

plants

Arabidopsis thaliana, currently the most popular model plant. This herbaceous dicot is a crucifer, a member of the mustard family. Its small stature and short generation time facilitates genetic studies, and many phenotypic and biochemical mutants have been mapped. Arabidopsis was the first plant to have its genome sequenced. Its genome sequence, along with a wide range of information concerning Arabidopsis, is maintained by the TAIR database.

(Plant physiology, Developmental biology, Molecular genetics, Population genetics, Cytology, Molecular biology)

Brachypodium distachyon is an emerging experimental model grass that has many attributes that make it an excellent model for temperate cereals. (Agronomy, Molecular biology, Genetics)

Lotus japonicus a model legume used to study the symbiosis responsible for nitrogen fixation. (Agronomy, Molecular biology)

Lemna gibba is a rapidly-growing aquatic monocot, one of the smallest flowering plants. Lemna growth assays are used to evaluate the toxicity of chemicals to plants in ecotoxicology. Because it can be grown in pure culture, microbial action can be excluded. Lemna is being used as a recombinant expression system for economical production of complex biopharmaceuticals. It is also used in education to demonstrate population growth curves.

Maize (Zea mays L.) is a cereal grain. It is a diploid monocot with 10 large chromosome pairs, easily studied with the microscope. Its genetic features, including many known and mapped phenotypic mutants and a large number of progeny per cross (typically 100-200) facilitated the discovery of transposons ("jumping genes"). Many DNA markers have been mapped and the genome is being sequenced. (Genetics, Molecular biology, Agronomy)

Medicago truncatula is a model legume, closely related to the common alfalfa. Its rather small genome is currently being sequenced. It is used to study the symbiosis responsible for nitrogen fixation. (Agronomy, Molecular biology)

Tobacco BY-2 cells is suspension cell line from tobacco (Nicotiana tabaccum). Useful for general plant physiology studies on cell level. Genome of this particular cultivar will be not sequenced (at least in near future), but sequencing of its wild species Nicotiana tabaccum is presently in progress. (Cytology, Plant physiology, Biotechnology)

Rice (Oryza sativa) is used as a model for cereal biology. It has one of the smallest genomes of any cereal species, and sequencing of its genome is in progress. (Agronomy, Molecular biology)

Physcomitrella patens is a moss increasingly used for studies on development and molecular evolution of plants. It is so far the only non-vascular plant (and so the only "primitive" plant) with its genome completely sequenced .

Populus is a genus used as a model in forest genetics and woody plant studies. It has a small genome size, grows very rapidly, and is easily transformed.

plants

“Classic” eukaryote model organisms

the restChlamydomonas reinhardtii - a unicellular green alga used to study photosynthesis, flagella and motility, regulation of metabolism, cell-cell recognition and adhesion, response to nutrient deprivation and many other topics. Chlamy has a well-studied genetics, with many known and mapped mutants, and there are advanced methods for genetic transformation and selection of genes. A Chlamydomonas genetic stock center exists at Duke University, and an international Chlamydomonas research interest group meets on a regular basis to discuss research results. Chlamydomonas is easy to grow on an inexpensive defined medium.

Silvetia compressa – polarity establishment and asymmetric cell division

Dictyostelium discoideum is used in molecular biology and genetics (its genome has been sequenced), and is studied as an example of cell communication, differentiation, and programmed cell death.

Tetrahymena thermophila - a free living freshwater ciliate protozoan.

Publication levels (2006) ANIMALSChick development: 11,911C. elegans development: 2,502Mouse development: 98,204Xenopus development: 5,690Zebra fish development: 2,593

FUNGIAshbya development: 7,359

PLANTSArabidopsis development: 5,999

THE RESTChlamydomonas development: 312Dictyostelium development: 1,671Silvetia compressa: 2

120,900

7,359

5,999

1,985

What about the rest of the Eukaryotic tree of life?

What are these organisms and what do they do?

Diplomonadida

The diplomonads are a group of flagellates, most of which are parasitic. They include most notably Giardia lamblia, which causes giardiasis in humans. They are placed among the metamonads, and appear particularly close relatives of the retortamonads; these are very basal eukaryotes, classified as Protists (eukaryotes that are not animals or plants).

Most diplomonads are double cells: they have two nuclei, each with four associated flagella, arranged symmetrically about the body's main axis. Like the retortamonads, they lack both mitochondria and a Golgi apparatus. However they are now known to possess mitochondrial relics, called mitosomes. These are not used in ATP synthesis the way mitochondria are, but are involved in the maturation of iron-sulfur proteins. Instead they must obtain their energy from fermentative processes. Diplomonads are able to ferment sugars such as glucose to produce energy.

Hexamita inflata

Parabasala

The trichomonads are an order of anaerobic protists, included with the parabasalids. Most are either parasites or other endosymbionts of animals. They typically have four to six flagella at the cell's apical pole, one of which is recurrent - that is, it runs along a surface wave, giving the aspect of an undulating membrane. Like other parabasalids they typically have an axostyle, pelta, costa and parabasal bodies. In Histomonas there is only one flagellum and a reduced axostyle, and in Dientamoeba both are absent.

Trichomonads reproduce by a special form of longitudinal fission, leading to large numbers of trophozoites in a relatively short time. Cysts never form, so transmission from one host to another is always based on direct contact between the sites they occupy.

Euglenozoa

kinetoplastideuglenoid

The Euglenozoa are a large group of flagellate protozoa. They include a variety of common free-living species, as well as a few important parasites, some of which infect humans. There are two main subgroups, the euglenids and kinetoplastids. Euglenozoa are unicellular, mostly around 15-40 µm in size, although some euglenids get up to 500 µm long.

Most euglenozoa have two flagella, which are inserted parallel to one another in an apical or subapical pocket. In some these are associated with a cytostome or mouth, used to ingest bacteria or other small organisms. This is supported by one of three sets of microtubules that arise from the flagellar bases; the other two support the dorsal and ventral surfaces of the cell.[2]

Some other euglenozoa feed through absorption, and many euglenids possess chloroplasts and so obtain energy through photosynthesis. These chloroplasts are surrounded by three membranes and contain chlorophylls a and b, along with other pigments[1], so are probably derived from a captured green alga. Reproduction occurs exclusively through cell division. During mitosis, the nuclear membrane remains intact, and the spindle microtubules form inside of it.[2]

The kinetoplastid group is characterized by the ultrastructure of the flagella. In addition to the normal supporting microtubules or axoneme, each contains a rod (called paraxonemal), which has a tubular structure in one flagellum and a latticed structure in the other. Based on this, two smaller groups have been included here: the diplonemids and Postgaardi.[3]

The euglenozoa are generally accepted as monophyletic. They are related to Percolozoa; the two share mitochondria with disc-shaped cristae, which only occurs in a few other groups.[4] Both probably belong to a larger group of eukaryotes called the excavates.[5]

Kinetoplastid Trypanosoma bruceiAfrican sleeping sickness

Alveolata

ciliateapicomplexandinoflagellate

The dinoflagella are a large group of flagellate protists. Most are marine plankton, but they are common in fresh water habitats as well; their populations are distributed depending on temperature, salinity, or depth. About half of all dinoflagellates are photosynthetic, and these make up the largest group of eukaryotic algae aside from the diatoms. Being primary producers make them an important part of the aquatic food chain. Some species, called zooxanthellae, are endosymbionts of marine animals and protozoa, and play an important part in the biology of coral reefs. Other dinoflagellates are colorless predators on other protozoa, and a few forms are parasitic (see for example Oodinium, Pfiesteria).

The Apicomplexa are a large group of protists, characterized by the presence of a unique organelle called an apical complex. They are unicellular, spore-forming, and exclusively parasites of animals. Motile structures such as flagella or pseudopods are absent except in certain gamete stages. This is a diverse group including organisms such as coccidia, gregarines, piroplasms, haemogregarines, and malarias.

The ciliates are one of the most important groups of protists, common almost everywhere there is water —lakes, ponds, oceans, and soils, with many ecto- and endosymbiotic members, as well as some obligate and opportunistic parasites. Ciliates tend to be large protozoa, a few reaching 2 mm in length, and are some of the most complex in structure. The name ciliate comes from the presence of hair-like organelles called cilia, which are identical in structure to flagella but typically shorter and present in much larger numbers with a different undulateingpattern than flagellum. Cilia occur in all members of the group, although the peculiar suctoria only have them for part of the life-cycle,but usually only have them 4 hours of every day, and are variously used in swimming, crawling, attachment, feeding, and sensation.

Unlike other protists, ciliates have two different sorts of nuclei: a small, diploid micronucleus (reproduction), and a large, polyploid macronucleus (general cell regulation). The latter is generated from the micronucleus by amplification of the genome and heavy editing. Division of the macronucleus occurs by amitosis, the segregation of the chromosomes is by a process, whose mechanism is unknown. This process is by no means perfect, and after about 200 generations the cell shows signs of aging. Periodically the macronuclei must be regenerated from the micronuclei. In most, this occurs during sexual reproduction, which is not usually through syngamy but through conjugation. Here two cells line up, the micronuclei undergo meiosis, some of the haploid daughters are exchanged and then fuse to form new micro- and macronuclei.

dinoflagellate

apicomplexan

ciliate

stramenopila

Water moulds (or water molds) or Oomycetes are a group of filamentous, unicellular protists, physically resembling fungi. They are microscopic, absorptive organisms that reproduce both sexually and asexually and are composed of mycelia, or a tube-like vegetative body (all of an organism's mycelia are called its thallus). The name "water mould" refers to the fact that they thrive under conditions of high humidity and running surface water.

Water moulds were originally classified as fungi, but are now known to have developed separately and show a number of differences. Their cell walls are composed of cellulose rather than chitin and generally do not have septations. Also, in the vegetative state they have diploid nuclei, whereas fungi have haploid nuclei.

Instead, water moulds are related to organisms such as brown algae and diatoms, making up a group called the heterokonts. The name comes from the common arrangement and structure of motile cells, which typically have two unequal flagella. Among the water moulds, these are produced as asexual spores called zoospores, which capitalize on surface water (including precipitation on plant surfaces) for movement. They also produce sexual spores, called oospores, that are translucent double-walled spherical structures used to survive adverse environmental conditions. A few produce aerial asexual spores that are distributed by wind.

water molds or Oomycetes

Achyla is an aquatic fungus common in aquatic environments, particularly where there is an abundance of decaying organic matter. Achyla can cause fungal infections in fish, and often attack eggs, killing them before they hatch.

Diatoms (Greek: διά (dia) = "through" + τέμνειν (temnein) = "to cut", i.e., "cut in half") are a major group of eukaryotic algae, and are one of the most common types of phytoplankton. Most diatoms are unicellular, although some form chains or simple colonies. A characteristic feature of diatom cells is that they are encased within a unique cell wall made of silica (hydrated silicon dioxide). These walls show a wide diversity in form, some quite beautiful and ornate, but usually consist of two asymmetrical sides with a split between them, hence the group name. Fossil evidence suggests that they originated during, or before, the early Jurassic Period.

Diatoms

Valve size = division size difference

The golden algae or chrysophytes are a large group of heterokont algae, found mostly in freshwater. Originally they were taken to include all such forms except the diatoms and multicellular brown algae, but since then they have been divided into several different groups based on pigmentation and cell structure. They are now usually restricted to a core group of closely related forms, distinguished primarily by the structure of the flagella in motile cells, also treated as an order Chromulinales. It is possible membership will be revised further as more species are studied in detail. They come in a variety of morphological types, originally treated as separate orders or families.

golden algae

Brown algae~5,000 species

• ~ 75% of photosynthetic oxygen from algae (330 b tons)

• Alginates: mannuronic and guluronic acids

• (thickeners: ice cream, ketchup, beer, cosmetics)

• Agar: Lab medium for micropropogation

• food source: (6.7 kg/person per year in Japan)

• source of iodine

S. compressa

E. siliculosis

E. siliculosis naturally undergoes parthenogenesisGrowth or development w/o fertilization

Rhizoid

Thallus

eggegg 12 h AF12 h AF 24 h AF24 h AF

PolarityPolarityestablishmentestablishment

AsymmetricAsymmetricdivisiondivision

Brown algae: model organism for development (Hurd, 1916)….polarity and asymmetry established in the first cell cycle

fronds

holdfast

advantages of S. compressa- large numbers of gametes can beeasily harvested in the lab

- large eggs and zygotes (~100 um)diameter facilitate physiologic andmicroscopic investigation

- polarity can be manipulated easilyfor study

- synchronous development (1st cellcycle ~24h)

- invariant asymmetric 1st cell division

- Cytoskeleton well documentedduring 1st cell cycle

(vectorial inputs summed and establishment of growth axis)

Rhodophyta

The red algae (Rhodophyta, IPA: [�rəʊdə(ʊ)�fʌɪtə], from Greek: ῥόδον (rhodon) = rose + φυτόν (phyton) = plant, thus red plant) are a large group, about 5000 - 6000 species [1] of mostly multicellular, marine algae, including many notable seaweeds. Most of the coralline algae, which secrete calcium carbonate and play a major role in building coral reefs, belong here. Red algae such as dulse and nori are a traditional part of European and Asian cuisine and are used to make other products like agar, carrageenans and other food additives.

red algae

Chlorophyta

The Chlorophyta, or green algae, include about 8000 species[1] of mostly aquatic photosynthetic eukaryotic organisms. Like the land plants (Bryophyta and Tracheophyta), green algae contain chlorophylls a and b, and store food as starch in their plastids. They are related to the Charophyta and Embryophyta (land plants), together making up the Viridiplantae.

They contain both unicellular and multicellular species. While most species live in freshwater habitats and a large number in marine habitats, other species are adapted to a wide range of environments. Watermelon snow, or Chlamydomonas nivalis, of the class Chlorophyceae, lives on summer alpine snowfields. Others live attached to rocks or woody parts of trees. Some lichens are symbiotic relationships with fungi and a green alga. Members of the Chlorophyta also form symbiotic relationships with protozoa, sponges and coelenterates.

Chlorophytes

Mycetozoa

Slime moulds (or slime molds in American English) are peculiar protists that normally take the form of amoebae, but under certain conditions develop fruiting bodies that release spores, superficially similar to the sporangia of fungi. They should not be confused with true moulds, which are actually fungi. Although cosmopolitan in distribution, they are usually small and rarely noticed. There are several different groups.

Most notable are the plasmodial slime moulds or myxogastrids (also known as acellular or true slime moulds), where the feeding stage takes the form of a giant amoeba with thousands of nuclei, called a plasmodium. It is not divided by cell membranes, but rather is enclosed by a single outer one, and is thus like a single large cell. Most are smaller than a few centimetres, but the very largest reach areas of up to two square metres[citation needed], making them the largest undivided cells known. Many have bright colours such as yellow, brown, and white. Under dry conditions they may form resting structures called sclerotia. Once produced, spores release biflagellate or amoeboid gametes, which fuse pairwise to produce new plasmodia.

****Dictyostelium

Plasmodial and cellular slime moulds

Cytoplasmic streaming

Animalia

The choanoflagellates are a group of flagellate protozoa. They are considered to be the closest living relatives of the animals (hsp70 sequence), and the last unicellular ancestors of animals are thought to have resembled modern choanoflagellates.

Each choanoflagellate has a single flagellum, surrounded by a ring of actin-filled protrusions called microvilli, forming a cylindrical or conical collar (choanos in Greek). The flagellum pulls water through the collar, and small food particles are captured by the microvilli and ingested. The flagellum also pushes free-swimming cells along, as in animal sperm, whereas most other flagellates are pulled by their flagella. Many choanoflagellates build complex basket-shaped "houses" called lorica, from several silica strips cemented together.

Most choanoflagellates are sessile, with a stalk opposite the flagellum. A number of species are colonial, usually taking the form of a cluster of cells on a single stalk, but often forming planktonic clumps that resemble a miniature cluster of grapes in which each cell in the colony is flagellated. There exist historical accounts of an extracellular matrix and non-flagellated cells in some colonies, but these accounts are unsubstantiated.

The choanocytes (also known as "collared cells") of sponges have the same basic structure as choanoflagellates. Collared cells are occasionally found in a few other animal groups, such as flatworms. These relationships make colonial choanoflagellates a plausible candidate as representative of the ancestors of the animal kingdom.

-cadherins, tyrosine kinase-Where metazoan genes came from-Original function

choanoflagellates

• Cell death is one of the fundamental aspects of cell life. It isboth multi-faceted, as there are several types of cell death, and complex, involving many molecules and several pathways.

• Our representation of cell death is defined by the few model organisms studied so far. This representation includes caspase-dependent apoptosis and a variety of various, less well defined caspase-independent, non-apoptotic types of cell death. (autophagy)

• The use of alternative model organisms could modify this representation. In particular, it might help to reveal conservedmolecules and phenomena that are less prominent in the classicalmodel organisms.

• Alternative model organisms can be chosen as a function of theirability to answer some of the remaining questions in the cell-death field. The criteria for choice include, for example, their phylogeneticposition, as well as some biological properties and their genetic tractability.

• Examples of possible alternative model organisms to study cell death include Hydra, Podospora, Dictyostelium and Volvox, but investigating cell death in any new model organism is likely to provide new insights.

•Hydra can survive months without food, slowly decreasing in size,due to decrease in cell number not size

•Classic cell death hallmarks: condensation of chromatin, DNA laddering, caspaseactivation

•Economic efficiency of cell death

•Not a genetic model organism

•Filamentous fungi can undergo filament fusion forming a vegetative heterokaryon.

•Some strains though, upon fusion, form a barrier between the filaments by undergoing PCD

•Genetic model organism

•Already well studied organism

•Dictyostelium grows a one large cell with many nuclei until food limitation. Then the nuclei aggregate, differentiate, and develop into a multicellular fruiting body.

•Stalk cells undergo PCD

•Almost fully sequenced genome

•Haploid, easy to screen for mutants of function –associated genes

•Volvox exhibits synchronous developmental PCD

•Parental somatic cells die as juvenile spheriodsemerge

•Many characteristic morphological changes during PCD

•Genome being sequenced allows for genetic approaches