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Pristionchus Pacificus and Its Relevance for Evolution

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Pristionchus Pacificus and Its Relevance for Evolution Molecular aspects of t he g enetic switch regulating phenotypic plasticity of feeding structures in Pristionchus pacificus and its relevance for evolution Dissertation der Mathemathisch - Naturwissenschaftlichen Fakultät der E BERHARD K ARLS U NIVERSITÄT T ÜBINGEN zur Er langung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) vorgelegt von Manuela Rebecka Kieninger aus Waiblingen Tübingen 2015 Gedruckt mit Genehmigung der Mathematisch - Naturwissenschaftlichen Fakultät der E BERHARD K ARLS U NIVERSITÄT T ÜBINGEN . Tag der mündlichen Qualifikation: 09.06.2016 Dekan: Prof. Dr. Wolfgang Rosenstiel 1. Berichterstatter: Prof. Dr. Ralf J. Sommer 2. Berichterstatter: Prof. Dr. Rolf Reuter 3. Berichterstatter: Prof. Dr. Siegfried Roth A cknowledgements First of all I want to thank Prof. Dr. Ralf J. Sommer for giving me the possibility to do my PhD studies in his department and his great support during my studies. I like to thank Prof. Dr. Rolf Reuter for being my supervisor at university and for examining this thesis. Additionally, I thank my PhD defense c ommittee members Prof. Dr. Ul r ike Zentgra f and Dr. Patrick Müller for their willingness of being an examiner of my work. Very special thanks go to Prof. Dr. Erik Ragsdale for his invaluable support and help. I enjoyed working with him and spending ti me dis cussing about the great my stery of plasticity . I wish you all the best Prof. Erik! I thank my dear friend Vahan Serobyan for his support and great discussions, which have not always been related to the mouth - form. Thanks for all the coffees and the chats we had. Great thanks go to Dr. Gilberto Bento for introducing me to the mouth - form. When I started working he gave me great support and confidence in myself. Many thanks to the new mouth - form group Bogdan Sieriebriennikov, Suryesh Namdeo and Masa Lenuzzi. I thank Dr. Christian Rödelsperger for all the bioinformatic analys e s and his patience in explaining them to me. I like to thank all m embers of Lab 1. Gabi, Cameron, Vahan, Suryesh and Tobias; you are simply great! I thank Hanh Witt e for all her help and advice. Many thanks to Heike Haus s mann for her help with freezing and thawing worms . I am grateful to Metta Riebesell for her help and assistance concerning microscopy techniques. I am grateful to Lorena, Kostadinka, and Karin for the ir administrative assi stance . I thank James, Martin, Jan, and Melanie for helping me with new techniques and protocols. Thank you, that you always had time for my questions. Thanks to all members of Department 4 for your help, support and discussions. Also , I like to thank all the past members of the Sommer lab, especially Simone, Akira, Isabella , Dan , and Ruxandra for their tremendous support and encouragement. All of you m ake and made the lab a great atmosphere to work in. I consider myself lucky that I could wor k with all of you and I will also never forget all the fun we had outside the lab. I am thankful to the Max Planck Society for granting my work. Special thanks goes to my friends outside and off the bench , Elisabeth and Thomas Bürkle, Claudia and Dominique Kiefner, and David Schäfer. During the sometimes turbulent times in my PhD studies your friendship was like a solid rock in the waves and created my own essential retreat whenever I got the feeling that things are going on the top of me. Vielen lieben Dank an meine Schwiegereltern für ihre Unterstützung und Hilfe. Ein großer Dank geht an meine Eltern für ihre Fürsorge und unentweg t e Unterstützung. Zuletzt , möchte ich mich bei meinem Mann, Martin und bei meinen zwei Töchtern, Lea und Tanea bedanken. Eure Liebe, Geduld sowie de r Rüc khalt, den ihr mir gegeben habt, waren für mich von größter Wichtigkeit. Danke dafür! C ontents 1 Summary ................................ ................................ ................................ .............. 8 2 Zusammenfassung ................................ ................................ .............................. 9 3 List of Public ations ................................ ................................ ........................... 10 4 Introduction ................................ ................................ ................................ ....... 11 4.1 Phenotypic plasticity ................................ ................................ ................................ ........ 11 4.1.1 Genetic accommodation and genetic assimilation ................................ ................ 14 4.1.2 Role of plasticity in speciation ................................ ................................ ................ 16 4.2 Evo - devo ................................ ................................ ................................ .......................... 18 4.3 Pristionchus pac ificus ................................ ................................ ................................ ...... 20 4.3.1 Ecology of Pristionchus pacificus ................................ ................................ ............ 20 4.3.2 Population genetics in Pristionchus pacificus ................................ ........................ 22 4.3.3 Mouth - form development ................................ ................................ ....................... 2 3 4.3.4 Mouth dimorphism in Pristionchus pacificus ................................ ........................ 26 4.4 Sulfatases and development ................................ ................................ ............................ 28 4.5 Nuclear hormone receptors ................................ ................................ ............................. 31 4. 6 Aims of research ................................ ................................ ................................ .............. 35 5 Results and Discussion ................................ ................................ ..................... 36 5.1 Feeding plasticity in the nematode Pristionchus pacificus is influenced by sex and social context and is linked to developmental speed ................................ ................................ 36 5.1.1 Synopsis ................................ ................................ ................................ .................... 36 5.1.2 Own Contribution ................................ ................................ ................................ ... 37 5.2 A Developmental Switch Coupled to the Evolution of Plasticity Acts through a Sulfatase ................................ ................................ ................................ ................................ ...... 38 5.2.1 Synopsis ................................ ................................ ................................ .................... 38 5.2.2 Own Contribution ................................ ................................ ................................ ... 39 5.3 The nuclear hormone receptor Ppa - nhr - 40 is a downstream target of eud - 1 and part of a developmental switch mechanism ................................ ................................ ......................... 40 5.3.1 Introduction ................................ ................................ ................................ ............ 40 5.3.2 eud - 1 suppressor screen ................................ ................................ .......................... 40 5.3.3 Mapping of the suppressor mutants ................................ ................................ ....... 41 5.3.4 The nuclear hormone receptor Ppa - nhr - 40 and its influence on the mouth dimorphism ................................ ................................ ................................ ............................ 44 5.3.5 The long isoform of Ppa - nhr - 40 acts downstream of eud - 1 ................................ .... 45 5.3.6 tu505 is a dominant mutation ................................ ................................ ................ 46 5.3.7 Ppa - nhr - 40 expression ................................ ................................ ............................. 47 5.3.8 Ppa - nhr - 40 is epistatic to Ppa - daf - 12 ................................ ................................ ...... 48 5.3.9 Predicted acetylation sites are necessary for Ppa - nhr - 40 function ....................... 49 5.3.10 Materials and methods ................................ ................................ ............................ 51 5.4 Phenotypic and molecular characterization of euc mutants isolated from a clade C strain of Pristionchus pacificus ................................ ................................ ................................ ... 57 5.4.1 Introduction ................................ ................................ ................................ ............. 57 5.4.2 Mutant screen for euc mutants in RSB020 ................................ ............................. 57 5.4.3 Mapping by RAD sequencing ................................ ................................ .................. 59 5.4.4 Candidate mutations responsible for the Euc phenotype ................................ ...... 62 5.4.5 Mapping of tu469 ................................ ................................ ................................ .... 65 5.4.6 Materials and methods ................................ ................................ ............................ 67 6 References ................................ ................................ ................................ ......... 71 7 Appendix ................................ ................................ ...............................
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