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Alpha-Synuclein Aggregation: Visualization by X-Ray Alpha-synuclein aggregation: visualization by X-ray techniques and its modulation by iron Dissertation for the award of the degree “Doctor of Philosophy” Division of Mathematics and Natural Sciences of the Georg-August-Universität Göttingen within the doctoral program “Molecular physiology of the brain” of the Georg-August University School of Science (GAUSS) submitted by Eleonora Carboni From Urbino (Italy) Göttingen, September 2016 Thesis Committee Prof. Dr. Paul Lingor (Department of Neurology, University Medical Center Göttingen) Prof. Dr. Tim Salditt (Institute for X-ray physics, Faculty of Physics University of Göttingen) Prof. Dr. Tiago Fleming Outeiro (NeuroDegeneration and Restaurative Research, University Medical Center Göttingen) Members of the Examination Board 1st Referee: Prof. Dr. Paul Lingor (Department of Neurology, University Medical Center Göttingen) 2nd Referee: Prof. Dr. Tim Salditt (Institute for X-ray physics, Faculty of Physics University of Göttingen) Prof. Dr. Tiago Fleming Outeiro (NeuroDegeneration and Restaurative Research, University Medical Center Göttingen) Prof. Dr. Matthias Bähr (Department of Neurology, University Medical Center Göttingen) Dr. Kamin Dean (Trans-synaptic Signaling, European Neuroscience Institute Göttingen) Dr. Sebastian Kügler (Department of Neurology, University Medical Center Göttingen) Date of oral examination: 19.10.2016 Declaration I hereby declare that the thesis: “Alpha-synuclein aggregation: visualization by x-ray techniques and its modulation by iron” has been written independently and with no other sources and aids than quoted. Eleonora Carboni Göttingen, September 2016 Considerate la vostra semenza: fatti non foste a viver come bruti, ma per seguir virtute e conoscenza. Denkt euren Ursprungs und aus welchem Grunde Ihr seid geboren, nicht wie Vieh zu leben, Nein! zu der Tugend und der Weisheit Funde. Consider well the seed that gave you birth: you were not made to live as brutes, but to follow virtue and knowledge. Dante (1265-1321) Divina Commedia (Inferno, XXVI vv118-120) Table of Contents Table of Contents i List of the figures .......................................................................................................................................... iv Abbreviation List ............................................................................................................................................ v 1. Introduction ............................................................................................................................. 2 1.1. Neurodegenerative diseases ................................................................................................... 2 1.2. Parkinson’s disease.................................................................................................................. 3 1.2.1. Pathophysiology of Parkinson’s disease ............................................................................. 4 1.3. Alpha – synuclein in PD ........................................................................................................... 5 1.3.1. Alpha-synuclein aggregation ............................................................................................... 6 1.3.2. Alpha-synuclein and metals ................................................................................................ 8 1.3.3. Animal models of Parkinson’s disease ................................................................................ 9 1.3.4. Use of chelators in neurodegeneration and Parkinson’s disease ..................................... 12 1.4. X – ray imaging techniques and their principles ................................................................... 13 1.4.1. X-ray fluorescence and particle induced X-ray emission: principles and uses ................. 15 1.4.2. X ray scattering- based imaging techniques: SAXS, WAXS and STXM............................... 17 1.5. Aim of the thesis .................................................................................................................... 19 2. Materials and methods ......................................................................................................... 22 2.1. Materials ................................................................................................................................ 22 2.1.1. Chemicals and companies ................................................................................................. 22 2.1.2. Antibodies ......................................................................................................................... 23 2.1.3. Equipment ......................................................................................................................... 24 2.1.4. Buffers and solutions ........................................................................................................ 24 2.1.5. Animals .............................................................................................................................. 26 2.1.6. Human tissue .................................................................................................................... 27 2.1.7. Facilities ............................................................................................................................. 27 2.1.8. Vectors .............................................................................................................................. 28 2.1.9. qPCR primer list ................................................................................................................. 28 2.1.10. Software ............................................................................................................................ 29 2.2. Methods ................................................................................................................................ 30 2.2.1. H4 cell culture experiments .............................................................................................. 30 2.2.2. Tissue preparation for X-ray diffraction and X-ray fluorescence and analysis ................. 31 2.2.3. Tissue preparation for particle induced X-ray emission ................................................... 34 i 2.2.4. Primary midbrain neurons culture preparation for particle induced x-ray experiments and metal trafficking proteins ................................................................................................ 34 2.2.5. RNA isolation ..................................................................................................................... 35 2.2.6. Reverse transcriptase reaction ......................................................................................... 36 2.2.7. Real time PCR after reverse transcriptase ........................................................................ 37 2.2.8. Protein purification after RNA extraction ......................................................................... 38 2.2.9. SDS gel electrophoresis ..................................................................................................... 39 2.2.10. Western blots .................................................................................................................... 39 2.2.11. Iron intoxication protocol and chelator treatment ........................................................... 41 2.2.12. Genotyping of A53T TG mice ............................................................................................ 42 2.2.13. Behavioral and functional tests: Rotarod ......................................................................... 45 2.2.14. Behavioral and functional tests: Novel object recognition (NOR) test ............................. 47 2.2.15. Behavioral and functional tests: Catwalk .......................................................................... 48 2.2.16. Animal sacrifice and tissue processing .............................................................................. 48 2.2.17. Proteinase K digestions and dot blots ............................................................................... 49 2.2.18. Statistical analysis ............................................................................................................. 51 3. Results ................................................................................................................................... 52 3.1. Alpha-synuclein aggregation and X-ray imaging ................................................................... 52 3.1.1. Alpha-synuclein aggregation in H4 cells ........................................................................... 52 3.1.2. X- ray diffraction on PD patients tissue............................................................................. 54 3.1.3. X-ray fluorescence on PD patients tissue .......................................................................... 58 3.1.4. Particle induced X-ray emission on PD patient tissue ....................................................... 62 3.2. Alpha-synuclein and metal handling ..................................................................................... 64 3.2.1. Alpha synuclein overexpression and Fe supplementation in primary neuronal cultures 65 3.2.2. Alpha-synuclein overexpression and metal transporting proteins ................................... 68 3.3. In-vivo aggregation study: A53T mice and Fe supply ............................................................ 71 3.3.1. Behavioral analysis: rotarod.............................................................................................
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