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Other-Model-Systems.Pdf 1 Yeast, Flies, Worms, Zebrafish, Mice, Arabidopsis As simple as possible to study the trait of interest: phage, bacteria, etc. BALANCE between these criteria An important part of the GMOD project is ensuring that the software components are interoperable. To this end, many of the tools use a common input/output file format https://en.wikipedia.org/wiki/File:Caenorhabditis_elegans.jpg https://en.wikipedia.org/wiki/File:Lightmatter_lab_mice.jpg 2 When challenged by starvation, the amoeba collect into aggregates and develop into multicellular fruiting bodies. Signal transduction, chemotaxis (cAMP signals during starvation ‐> aggregation), disease, phagocytosis and cellular differentiation. completed the genome sequence in 2005 D. Discoideum also has one of the most AT‐‐‐biases genomes known (78% AT, 22% CG) VIDEO: https://www.youtube.com/watch?v=bkVhLJLG7ug https://strassmannandquellerlab.wordpress.com/ http://www.nih.gov/science/models/d_discoideum/ http://genomics.nimr.mrc.ac.uk/online/dicty‐fl‐db.html http://dictybase.org/ https://strassmannandquellerlab.wordpress.com/home/photos/ 3 The micronucleus, which harbors the germ‐line genome, maintains its DNA in a silent, unabridged form to pass on to the next generation. The macronucleus, which contains the somatic genome, carries an active “Reader’s Digest” version the genome that has been highly edited. removal of nearly 20 Mbp = internal eliminated sequences 104 Mb in length macronuclear genome ‐‐ Sequenced by the Broad institute UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. Also used to study cytoskeleton; dynein was first isolated Telomeres ‐ The Nobel Prize in Physiology or Medicine 2009 jointly to Elizabeth H. Blackburn, Carol W. Greider and Jack W. Szostak for the discovery of "how chromosomes are protected by telomeres and the enzyme telomerase" Ribozymes 1989 Nobel Prize in chemistry jointly to Professor Sidney Altman, Yale University, New Haven, Connecticut, USA Professor Thomas Cech, University of Colorado, Boulder, USA 4 for their discovery of catalytic properties of RNA. The Genetics and Epigenetics of Developmentally‐Programmed DNA Rearrangements; chromosomal rearrangement that occurs during development of the ciliated protozoan Tetrahymena thermophila in which as many as 6,000 DNA segments are coordinately excised from the newly forming somatic nucleus. how eukaryotic cells can differentially regulate genes within the genome and thereby uncover mechanisms of epigenetic regulation. Small RNAs that are generated during meiosis guide the cell as to what DNA should be removed http://www.biology.wustl.edu/faculty/chalker/current.html http://www.biology.wustl.edu/faculty/chalker/research.html http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0040286 4 Ursula Goodenough; molecular basis and evolution of life‐cycle transitions lipid‐body biogenesis inChlamydomonas, the goal being to contribute to the international effort to produce algal biodieselsexual adhesion mechanism, A fascinating feature of the Chlamydomonas sexual cycle is its mode of uniparental inheritance of organelle DNA: chloroplast chromosomes deriving from the minus parent are selectively destroyed in the zygote, as are mitochondrial chromosomes deriving from the plus parent. The Dutcher Lab studies the assembly and function of basal bodies/centrioles and cilia (motor and sensory) During interphase, basal bodies are found at the anterior end of the cell at the proximal ends of the two flagella. During mitosis, the flagella are resorbed and the basal bodies are located near the poles of the mitotic spindle. How do cells move? How do cells respond to light? (an "eyespot" that senses light) How do cells recognize one another? How do cells generate regular, repeatable flagellar waveforms? How do cells regulate their proteome to control flagellar length? How do cells respond to changes in mineral nutrition? (nitrogen, sulfur, etc.) 5 Also Jim Umen’s lab studies them @ Danforth Plant Sciences https://en.wikipedia.org/wiki/File:UrsaMajor.jpg https://en.wikipedia.org/wiki/File:Cross_section_of_a_Chlamydomonas_reinhardtii_algae_c ell,_a_3D_representation.jpg https://en.wikipedia.org/wiki/File:Chlamydomonas6‐1.jpg http://news.wustl.edu/news/PublishingImages/11112_RJB_Susan%20Dutcher_006_standalo ne.jpg http://www.genetics.wustl.edu/sdlab/ 5 spherical colonies of up to 50,000 cells first reported by Antonie van Leeuwenhoek in 1700 The cells haveeyespots Cell Size Homeostasis and the RB Tumor Suppressor Pathway multiple fission cell cycle of Chlamydomonas uncouples cell growth and division and allows us unique access to a size checkpoint mechanism. A key regulator of this checkpoint is the Chlamydomonas retinoblastoma (RB) tumor suppressor pathway, Evolution of Developmental Complexity and Multicellularity Volvox carteri, a species that embodies many of the hallmarks of multicellular metazoans or plants. These include terminally differentiated somatic cells, reproductive stem cells, complex embryonic patterning, and formation of sexually dimorphic germ cells (eggs and sperm), none of which are present in its unicellular relative Chlamydomonas. Jim Umen is the corresponding author on the genome paper https://en.wikipedia.org/wiki/File:Mikrofoto.de‐volvox‐4.jpg http://www.algaeindustrymagazine.com/algae‐discovery‐reveals‐origin‐sexes/ http://www.phytozome.net/volvox.php 6 red bread mold phylum Ascomycota. "nerve spore" refers to the characteristic striations on the spores Often found on dead plants after fires Knockout project ongoing to generate one for all 10,000 genes. What is the benefit of a haploid life cycle? – Able to see recessive traits X‐ray mutagenesis ‐> "one gene, one enzyme" hypothesis Edward Tatum and George Wells Beadle Nobel Prize in Physiology or Medicine in 1958. mating in N. crassa can only occur between strains of different mating type suggests that some degree of outcrossing is favored by natural selection. The Neurospora genome was sequenced at the Broad Institute. Jonathan Arnold at UGA 7 http://www.fgsc.net/ https://en.wikipedia.org/wiki/Neurospora_crassa https://en.wikipedia.org/wiki/File:Neurospora_crassahyphae.jpg 7 Maize is the domesticated variant of teosinte The genome, 85% of which is composed of transposons, The Nobel Prize in Physiology or Medicine 1983 Barbara McClintock Prize share: 1/1 The Nobel Prize in Physiology or Medicine 1983 was awarded to Barbara McClintock "for her discovery of mobile genetic elements". https://permablitzhawaii.files.wordpress.com/2014/04/teosinte.jpg http://www.sciencemag.org/content/326/5956/1112 http://www.maizegdb.org/popcorn/main/index.php http://www.dnalc.org/view/16673‐Gallery‐32‐Barbara‐McClintock‐1953.html http://waynesword.palomar.edu/transpos.htm http://www.nobelprize.org/nobel_prizes/medicine/laureates/1983/ 8 Have CNS, Photoreceptors (eyespots) 1/279th of an animal is capable of producing a complete organism in <1week RNAi; identified functions of PIWI in stem cells Radiation can eliminate stem cells Sequencing the 4.8x108 bp genome of the sexual, diploid planarian S. mediterranea will provide a vital resource for the development of a unique model to study metazoan evolution, regeneration, and the regulation of the ability to differentiate into several types of cells. Insights into these basic biological problems will have deep and obvious implications for the improvement of human health. This genome has proven to be A/T rich, and very repetitious, heterozygous (even though the animals used for DNA preparation were clonally derived) having portions that recombine, making automated assembly of the genome very difficult. http://genome.wustl.edu/genomes/detail/schmidtea‐mediterranea/ http://www.hhmi.org/biointeractive/planarian‐regeneration‐and‐stem‐cells https://en.wikipedia.org/wiki/Schmidtea_mediterranea#/media/File:Smed.jpg http://morgana249.blogspot.com/2014/08/7‐biologically‐immortal‐organisms‐faces.html 9 easy to find in nature and easy to keep in aquaria. Cooperative Behavior (Tit‐For‐Tat Strategy, Partner‐Dependence) when doing predator inspection. an individual cooperates on the first move and then does whatever its opponent does on the previous move. This allows for a combination of collaborative (it starts by cooperating), retaliatory (punishes defection), and forgiving (respond to cooperation of others, even if they had defected previously) behavioral responses.[22] When three‐spined sticklebacks approaching a live predator were provided with either a stimulated cooperating companion or a stimulated defecting one, the fish behaved according to tit‐for‐tat strategy, supporting the hypothesis that cooperation can evolve among egoists. [23] sticklebacks operate in pairs. Prisoner's Dilemma in which selfish defection is always more rewarding than cooperation1. If the two protagonists have a certain minimum probability of meeting again a strategy called TIT FOR TAT is very successful. ` Manfred Milinski is a German Biologist who is Director of the Max Planck Institute for Evolutionary Biology a major research organism for evolutionary biologists trying to understand the genetic changes involved in adapting to new environments. The entire genome of a female fish from Bear Paw Lake in Alaska was recently sequenced by the Broad 10 Institute and many other genetic resources are available http://www.genome.gov/pages/research/sequencing/seqproposals/sticklebackseq.p
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