Genetic Model Organisms

SEMINAR ACCESS (password: 057601)

The seminar series "Genetic Model Organisms" aims for several goals. On the science side, we would like to introduce some of the most important eukaryotic model organisms for genetic research together with their respective features and advantages. At the same time, on each day we will discuss a recent paper that is a good example for the specific topics investigated in this model organism. This will also provide a good overview over methods used in molecular genetics. In addition to this, the seminar offers the opportunity to improve your presentation as well as your discussion skills, both of which are crucial abilities in research.

Each seminar consists of two parts:
1. Presentation of model organism and introduction into the topic of the paper
In the beginning of each seminar day the speaker introduces the respective model organsim and the topic of the day. For this, the speaker familiarizes her/himself with the model organism and the topic and asks her/himself the important questions: "What is interesting about this?" "What could I present that will help and interest my fellow participants?" From the (very individual) answers to these questions the speaker compiles a list of "Take-Home-Messages" (ca. 2-4) which she/he hands in at least 2 weeks before the seminar day for review. At least 1 week before the seminar date the speaker hands in the final presentation (max. 12 min) for feedback on content and design. Remember: the presentation should benefit all members of the group!
After this presentation there is time for questions and also evaluation and feedback on the performance, using the Genetics seminar talk evaluation sheet (provided online).
2. The original publication
Every participant has read the publication of the day and marked in the paper what she or he did not understand. These questions are compiled and clarified within the group before going through the paper. Then the speaker has prepared a PowerPoint presentation containing all the figures and tables (including supplementary data) in logical order and in sufficient quality. Using this presentation, a participant who has not read the publication moderates the figure-by-figure discussion within the group. The goal is that this student at the end understands the main messages of the publication.

IMPORTANT: In order to enable a fruitful discussion, thorough reading of the original publications is mandatory for all participants. Articles under the heading 'additional literature' are for further reading and as a starting point for the speaker. It is essential to contact the lecturer during preparation of your presentation for help and support. At least 2 weeks before the seminar date every speaker has to hand in the list of "Take-Home-Messages" (ca. 2-4) that will be covered in the talk. At least 1 week before the seminar date every speaker has to hand in the presentation for feedback on content and design.

Introductory articles on (genetic) model organisms

Müller B, Grossniklaus U (2010) Model organisms - A historical perspective. J Proteomics 73: 2054-2063
Davis RH (2004) The age of model organisms. Nat Rev Genet 5: 69-76
Tang B, Wang Y, Zhu J, Zhao W (2015) Web resources for model organism studies. Gen Proteom Bioinf 13: 64-68
Dietrich MR, Ankeny RA, Chen PM (2014) Publication trends in model organism research. Genetics 198: 787-794
Peng Y, Clark KJ, Campbell JM, Panetta MR, Guo Y, Ekker SC (2014) Making desinger mutants in model organisms. Development 141: 4042-4054
Hedges SB (2002) The origin and evolution of model organisms. Nat Rev Genet 3: 838-849

How to read a scientific article & How to make a good presentation

In the first two seminar sessions we will concentrate on how to get access to the contents of a scientific article and on how to prepare a good presentation on the respective topic. For this, we focus on a publication on mitochondrial integrity in Saccharomyces cerevisiae:
Original publication:
Osman C, Noriega TR, Okreglak V, Fung JC, Walter P (2015) Integrity of the yeast mitochondrial genome, but not its distribution and inheritance, relies on mitochondrial fission and fusion. PNAS 112: E947-E956
Review article:
Friedman JR, Nunnari J (2014) Mitochondrial form and function. Nature 505: 335-343
Additional literature:
Duina AA, Miller ME, Keeney JB (2014) Budding yeast for budding geneticists: a primer on the Saccharomyces cerevisiae model system. Genetics 197: 33-48
Forsburg SL (2001) The art and design of genetic screens: yeasts. Nat Rev Genet 2: 659-668

Schizosaccharomyces pombe - meiosis

Original publication:
Blyth J, Makrantoni V, Barton RE, Spanos C, Rappsilber J, Marston AL (2018) Genes important for Schizosaccharomyces pombe meiosis identified through a functional genomics screen. Genetics 208: 589-603
Review article:
Loidl J (2016) Conservation and variability of meiosis across the eukaryotes. Annu Rev Genet 50: 293-316
Additional literature:
Hoffman CS, Wood V, Fantes PA (2015) An ancient yeast for young geneticists: a primer on the Schizosaccharomyces pombe model system. Genetics 201: 403-423
Forsburg SL (1999) The best yeast? Trends Genet 15: 340-344
Forsburg SL (2001) The art and design of genetic screens: yeasts. Nat Rev Genet 2: 659-668
Rhind N, et al. (2011) Comparative functional genomics in the fission yeasts. Science 332: 930-936
Sunnerhagen P (2002) Prospects for functional genomics in Schizosaccharomyces pombe. Curr Genet 42: 73-84

Dictyostelium discoideum - cell-cell signaling

Original publication:
Hirose S, Benabentos R, Ho H-I, Kuspa A, Shaulsky G (2011) Self-recognition in social amoebae is mediated by allelic pairs of Tiger genes. Science 222: 467-470
Review article:
Medina JM, Shreenidhi PM, Larsen TJ, Queller DC, Strassmann JE (2019) Cooperation and conflict in the social amoeba Dictyostelium discoideum. Int J Dev Biol 63: 371-382
Additional literature:
Ostrowski EA (2019) Enforcing cooperation in the social amoebae. Curr Biol 29: R474-R484
Fets L, Kay R, Valezquez F (2010) Dictyostelium. Curr Biol 20: R1008-1010
Li SI, Purugganan MD (2011) The cooperative amoeba: Dicytostelium as a model for social evolution. Trends Genet 27: 48-54
Strassmann JE, Queller DC (2011) Evolution of cooperation and control of cheating in a social microbe. PNAS 108: 10855-10862
King JS, Insall RH (2009) Chemotaxis: finding the way forward with Dictyostelium. Trends Cell Biol 19: 523-530
Annesley SJ, Fisher PR (2009) Dictyostelium discoideum - a model for many reasons. Mol Cell Biochem 329: 73-91
Dictybase, a website with a lot of information on D. discoideum.
Hirose S, Santhanam B, Katoh-Kurosawa M, Shaulsky G, Kuspa A (2015) Allorecognition, via TgrB1 and TgrC1, mediates the transition from unicellularity to multicellularity in the social amoeba Dictyostelium discoideum. Development 142: 3561-3570
Hirisa S, Chen G, Kuspa A, Shaulsky G (2017) The polymorphic proteins TgrB1 and TgrC1 function as a ligand–receptor pair in Dictyostelium allorecognition. J Cell Sci 130: 4001-4012

Plasmodium falsiparum - antigen variation

Original publication:
Amit-Avraham I, Pozner G, Eshar S, Fastman Y, Kolevzon N, Yavin E, Dzikowski R (2015) Antisense long noncoding RNAs regulate var gene activation in the malaria parasite Plasmodium falciparum. PNAS 112: E982-E991
Review article:
Miller LH, Baruch DI, Marsh K, Doumbo OK (2002) The pathogenic basis of malaria. Nature 415: 673-679
Aditional literature:
Deitsch KW, Dzikowski R (2017) Variant gene expression and antigenic variation by malaria parasites. Annu Rev Microbiol 71: 625-641
Wahlgren M, Goel S, Akhouri RR (2017) Variant surface antigens of Plasmodium falciparum and their roles in severe malaria. Nat Rev Microbiol 15: 479-491

Chlamydomonas reinhardtii - photosynthesis

Original publication:
Dent RM, Sharifi MN, Malnoe A, Haglund C, Calderon RH, Wakao S, Niyogi KK (2015) Large-scale insertional mutagenesis of Chlamydomonas supports phylogenomic functional prediction of photosynthetic genes and analysis of classical acetate-requiring mutants. Plant J 82: 337-351
Review article:
Heinnickel ML, Grosman AR (2013) The GreenCut: re-evaluation of physiological role of previously studied proteins and potential novel protein functions. Photosynth Res 116: 427-436
Additional literature:
Blaby IK, Blaby-Haas CE, Tourasse N, Hom EFY, Lopez D, Aksoy M, Grossman A, Umen J, Dutcher S, Porter M, King S, Witman GB, Stanke M, Harris EH, Goodstein D, Grimwood J, Schmutz J, Vallon O, Merchant SS, Prochnik S (2014) The Chlamydomonas genome project: a decade on. Trends Plant Sci 19: 672-680
Karpowicz SJ, Prochnik SE, Grossman AR, Merchant SS (2011) The GreenCut2 resource, a phylogenomically derived inventory of proteins specific to the plant lineage. J Biol Chem 286: 21427-21439
Goodenough U (2015) Historical perspective on Chlamydomonas as a model for basic research: 1950–1970. Plant J 82: 365-369
Jinkerson RE, Jonikas MC (2015) Molecular techniques to interrogate and edit the Chlamydomonas nuclear genome. Plant J 82: 393-412
Minagawa J, Tokutsu R (2015) Dynamic regulation of photosynthesis in Chlamydomonas reinhardtii. Plant J 82: 413-428
Merchant SS et al. (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318: 245-251
Gutman BL, Niyogi KK (2004) Chlamydomonas and Arabidopsis. A dynamic duo. Plant Physiol 135: 607-610 

Arabidopsis thaliana - spontaneous mutations

Original publication:
Ossowski S, Schneeberger K, Lucas-Lledó Ji, Warthmann N, Clark RM, Shaw RG, Weigel D, Lynch M (2010) The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327: 92-94
Review article:
Weigel D, Mott R (2009) The 1001 genomes project for Arabidopsis thaliana. Genome Biol 10: 107
Additional information:
Woodward AW, Bartel B (2018) Biology in bloom: a primer on the Arabidopsis thaliana model system. Genetics 208: 1337-1349

Lotus japonicus - plant-microbe interactions

Original publication:
Soyano T, Shimoda Y, Kawaguchi M, Hayashi M (2020) A shared gene drives lateral root development and root nodule symbiosis pathways in Lotus. Science 366: 1021-1023
Commentary:
Bishopp A, Bennett MJ (2020) Turning lateral roots into nodules. Science 366: 953-954
Additional information:
Parniske M (2018) Uptake of bacteria into living plant cells, the unifying and distinct feature of the nitrogen-fixing root nodule symbiosis. Curr Opin Plant Biol 44: 164-174
Lagunas B, Schäfer P, Gifford ML (2015) Housing helpful invaders: the evolutionary and molecular architecture underlying plant root-mutualist microbe interaction. J Exp Bot 66: 2177-2186
Oldroyd GED (2013) Speak, friend, and enter: signalling systems that promote beneficial symbiotic associations in plants. Nat Rev Microbiol 11: 252-263
Antolín-Llovera M, Ried MK, Binder A, Parniske M (2012) Receptor kinase signaling pathways in plant-microbe interaction. Annu Rev Phytopathol 50: 451-473

Caenorhabditis elegans - gene silencing

Original publication:
Posner R, Toker IA, Antonova O, Star E, Anava S, Azmon E, Hendricks M, Bracha S, Gingold H, Rechavi O (2019) Neuronal small RNAs control behavior transgenerationally. Cell 177: 1814-1826
Review article:
Xu F, Guang S, Feng X (2018) Distinct nuclear and cytoplasmic machineries cooperatively promote the inheritance of RNAi in Caenorhabditis elegans. Biol Cell 110: 217-224
Additional literature:
Corsi AK, Wightman B, Chalfie M (2015) A transparent window into biology: a primer on Caenorhabditis elegans. Genetics 200: 387-407
Extensive information on C. elegans can be found on the WormBook-Homepage.
Sterken MG, Snoek LB, Kammenga JE, Andersen EC (2015) The laboratory domestication of Caenorhabditis elegans. Trends Genet 31: 224-231

Drosophila melanogaster - aging

Original publication:
Libert S, Zwiener J, Chu X, VanVoorhies W, Roman G, Pletcher SD (2007) Regulation of Drosophila life span by olfaction and food-derived odors. Science 315: 1133-1137
Review article:
Libert S, Pletcher SD (2007) Modulation of longevity by environmental sensing. Cell 131: 1231-1234
Additional literature:
Taormina G, Mirisola MG (2014) Calorie restriction in mammals and simple model organisms. BioMed Res Internat 2014: ID308690
He Y, Jasper H (2014) Studying aging in Drosophila. Methods 68: 129-133
Mair W, Dillin A (2008) Aging and survival: the genetics of life span extension by dietary restriction. Annu Rev Biochem 77: 727-754
Extensive information on Drosophila can be found on the FlyBase Homepage.
The Interactive Fly: a cyberspace guide to Drosophila development and metazoan evolution.

Danio rerio - embryonic development

Original publication:
Alemany A, Florescu M, Baron CS, Peterson-Maduro J, van Oudenaarden A (2018) Whole-organism clone tracing using single-cell sequencing. Nature 556: 108-114
Additional literature:
Holtzman NG, Iovine MK, Liang JO, Morris J (2016) Learning to fish with genetics: a primer on the vertebrate model Danio rerio. Genetics 203: 1069-1089
Lawson ND, Wolfe SA (2011) Forward and reverse genetic appoaches for the analysis of vertebrate development in the zebrafish. Dev Cell 21: 48-64
Schilling TF, Webb J (2007) Considering the zebrafish in a comparative context. J Exp Zool 308B: 515-522

Mus musculus - organ development

Original publication:
Behjati S, Huch M, van Boxtel R, Karthaus W, Wedge DC, Tamuri AU, Martincorena I, Petljak M, Alexandrov LB, Gundem G, Tarpey PS, Roerink S, Blokker J, Maddison M, Mudie L, Robinson B, Nik-Zainal S, Campbell P, Goldman N, van de Wetering M, Cuppen E, Clevers H, Stratton MR (2014) Genome sequencing of normal cells reveals developmental lineages and mutational processes. Nature 513: 422-425
Additional literature:
Beckers J, Wurst W, de Angelis MH (2009) Towards better mouse models: enhanced genotypes, systemic phenotyping and envirotype modelling. Nat Rev Genet 10: 371-380
Blake JA, Bult CJ, Eppig JT, Kadin JA, Richardson JE (2014) The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse. Nucl Acids Res 42: D810-D817

How does scientific publishing work?

In this optional seminar session we will answer a lot of relevant questions on scientific journals and scientific publishing.