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Carbonic Anhydrase VI Functional Characterization in PRXVHDQG]HEUD¿VKPRGHORUJDQLVPV

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Carbonic Anhydrase VI Functional Characterization in PRXVHDQG]HEUD¿VKPRGHORUJDQLVPV MAARIT PATRIKAINEN Carbonic Anhydrase VI Functional characterization in PRXVHDQG]HEUD¿VKPRGHORUJDQLVPV Tampere University Dissertations 134 7DPSHUH8QLYHUVLW\'LVVHUWDWLRQV 0$$5,73$75,.$,1(1 &DUERQLF$QK\GUDVH9, Functional characterization in mouse and zebrafish model organisms $&$'(0,&',66(57$7,21 7REHSUHVHQWHGZLWKWKHSHUPLVVLRQRI WKH)DFXOW\&RXQFLORIWKH)DFXOW\RI0HGLFLQHDQG+HDOWK7HFKQRORJ\ RIWKH7DPSHUH8QLYHUVLW\ IRUSXEOLFGLVFXVVLRQLQWKHDXGLWRULXP) RIWKH$UYREXLOGLQJ$UYR<OS|QNDWX7DPSHUH RQWK2FWREHUDWR¶FORFN $&$'(0,&',66(57$7,21 7DPSHUH8QLYHUVLW\)DFXOW\RI+HDOWK7HFKQRORJ\ )LQODQG Responsible 3URIHVVRU6HSSR3DUNNLOD supervisor 7DPSHUH8QLYHUVLW\ or/and Custos )LQODQG Pre-examiner(s) $VVLVWDQW3URIHVVRU $VVRFLDWH3URIHVVRU 0LNNR0HWVl.HWHOl 0RKDPPHG$O+DURQL 8QLYHUVLW\RI7XUNX 8L7WKH$UFWLF8QLYHUVLW\RI1RUZD\ )LQODQG 1RUZD\ Opponent(s) 3URIHVVRU-XKD7XXNNDQHQ 8QLYHUVLW\RI2XOX )LQODQG 7KHRULJLQDOLW\RIWKLVWKHVLVKDVEHHQFKHFNHGXVLQJWKH7XUQLWLQ2ULJLQDOLW\&KHFN VHUYLFH &RS\ULJKWDXWKRU &RYHUGHVLJQ5RLKX,QF ,6%1 SULQW ,6%1 SGI ,661 SULQW ,661 SGI KWWSXUQIL 851,6%1 3XQD0XVWD2\±<OLRSLVWRSDLQR 7DPSHUH TO MY FAMILY “Everybody is genius. But if you judge a fish by its ability to climb a tree, It will live its whole life believing that it is stupid.” -Albert Einstein iii iv ACKNOWLEDGEMENTS This PhD thesis was carried out at the Faculty of Medicine and Health Technology, Tampere University (Tampere, Finland) during 2013-2019 under the supervision of Professor Seppo Parkkila. I wish to express my gratitude to my supervisor Professor Seppo Parkkila (MD, PhD) for providing me the opportunity to do scientific research in the field of anatomy and tissue biology and for giving me a place in your CA group. I would like to thank my external reviewers of my thesis, Associate Professor Mikko Metsä-Ketelä (PhD) and Associate Professor Mohammed Al-Haroni (DDS, PhD), for their valuable comments and kind words. I would also thank Professor Juha Tuukkanen (DDS, PhD) for giving me the honor to be my opponent. I am extremely grateful for my awesome teacher Martti Tolvanen (PhD) who has been there for me since I started my bioinformatics studies and have introduced me to the world of CAs, and been my mentor during my PhD journey. I want to thank you for introducing me Turku and all those scientific and non-scientific discussions we have had over these years. Next, I like to thank former and present CA group members who have been working with me during these years: Peiwen Pan (PhD), Ashok Aspatwar (PhD), Harlan Barker (MSc), Linda Urbanski (MSc(Tech)), Sami Purmonen (PhD), Heimo Syvälä (PhD), Susanna Haapanen (BM), Reza Zolfaghari Emameh (PhD), Alma Yrjänäinen (MSc), Leo Syrjänen (MD, PhD), and Heini Kallio (PhD). I am grateful for being able to work with two excellent laboratory technicians Aulikki Lehmus and Marianne Kuuslahti. Your expertise, insight and help have been crucial for carrying out the laboratory work for this thesis. I want to thank all the other collaborators and co-authors for their valuable contribution: Chaba Ortutay (PhD), Vootele Voikar (PhD), Natalia Kulesskaya (PhD), Janne Jänis (PhD), Mikko Laitaoja (PhD), Vesa Hytönen (PhD), Latifeh Azizi (MSc), Prajwol Manandhar (MSc), Edit Jáger (PhD), Daniela Vullo (PhD), Sampo Kukkurainen (MSc), Mika Hilvo (PhD), Claudiu Supuran (PhD), people in the Zebrafish Facility (Tampere University), and people in Laboratory animal Centre in Oulu. I want to give special thanks to all of you I spend my coffee breaks with, bringing lots of joy, you bright up my days, and those that I have forgotten to mention here. v I want to give special thanks to my family and friends: “Vanhemmilleni, Antille ja Railille suuret kiitokset kaikesta avusta ja tuesta, jota ilman en olisi tässä nyt. Olette antaneet minulle eväät elämään ja vanhemmuuteen, sekä tukeneet minua hyvinä ja haastavina aikoina. Siskoani Minnaa haluan kiittää kaikista unohtumattomista seikkailuista ja tuestasi johon voin aina luottaa. Olet minulle rakas ja erittäin tärkeä esikuva. Rakkaalle tyttärelleni Miralle erityiskiitos kaikista halauksista ja hymyistä, sekä tuesta jota olet minulle antanut vuosien varrella. Sanat eivät riitä kertomaan kuinka tärkeä olet minulle. Lopuksi haluan kiittää ystäviäni joista on tullut minun toinen perheeni: Hanna, Heidi, Elina, Päivi ja Tuija, tuhannet kiitokset antamastanne tuesta. On ollut ilo ja kunnia jakaa nämä vuodet teidän kanssanne.” This thesis work was financially supported by the Marjatta Melkas-Rusanen and Anneli Melkas Memorial Foundation of the Finnish Cultural Foundation Pirkanmaa Regional Fund, Tampere Tuberculosis Foundation, Sigrid Juselius Foundation, Jane & Aatos Erkko Foundation, Academy of Finland, VTR-Funding of Tampere University Hospital, and Doctoral Programme on the Faculty of Medicine and Health Technology, Tampere University. All of the financial supporters are greatly acknowledged. Tampere, September 2019 Maarit Patrikainen vi Contents 1 INTRODUCTION......................................................................................................................... 19 2 REVIEW OF THE LITERATURE ........................................................................................... 21 2.1 General aspects of carbonic anhydrases ............................................................................... 21 2.1.1ơ-Carbonic anhydrase isozymes ....................................................................................... 24 2.2 General aspects of secretory carbonic anhydrase VI .......................................................... 28 2.2.1 Expression of CA VI ........................................................................................................ 28 2.2.2 Structure of CA VI ............................................................................................................ 30 2.2.3 Function of CA VI ............................................................................................................ 32 2.2.3.5 Nuclear carbonic anhydrase 6B (CA VI-b) ........................................................... 36 2.3 Taste perception ........................................................................................................................ 37 2.4 Pentraxin ..................................................................................................................................... 38 2.5 Functional genomics ................................................................................................................. 39 2.5.1Knockdown or knockout animal models for CAs ....................................................... 40 3 AIMS OF THE PRESENT STUDY .......................................................................................... 42 4 MATERIALS AND METHODS ................................................................................................ 43 4.1 Animal models ........................................................................................................................... 43 4.2 ca6 knockdown zebrafish (III) ................................................................................................ 43 4.3 DNA and total RNA extraction and synthesis of cDNA (I, II, III) ................................ 44 4.4 Polymerase chain reaction, PCR (I, II, III)........................................................................... 45 4.5 Quantitative reverse-transcription PCR (qRT-PCR) (II, III) ............................................ 46 4.6 Recombinant zebrafish (Danio rerio) CA VI-PTX protein production (III)................. 49 4.7 Enzyme activity measurement (III) ....................................................................................... 51 4.8 Light scattering analysis (III) ................................................................................................... 51 4.9 Mass spectrometry analysis (III) ............................................................................................. 52 4.10 Behavioral monitoring (I, III) ............................................................................................... 52 4.11 Histochemical staining and immunohistochemistry (I, II, III) ....................................... 52 4.12 Bioinformatics (III)................................................................................................................. 55 4.13 Data analysis (I, II, III) .......................................................................................................... 57 4.13.1 qRT-PCR (II, III) ............................................................................................................ 57 4.13.2 Statistical analyses (II, III) ............................................................................................. 57 4.13.3 Histochemical staining and immunohistochemistry (I, II, III) ............................... 58 vii 4.13.4 RNA-Seq and GO enrichment analysis ...................................................................... 59 5 RESULTS ......................................................................................................................................... 62 5.1 Gene expression studies .......................................................................................................... 62 5.1.1 Microarray analysis............................................................................................................ 62 5.1.2 qRT-PCR analysis ............................................................................................................. 62 5.1.3 Computational
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