School of Life SciencesAnnual Research Symposium

Crieff Hydro Hotel 14–16 March 2019

Thursday 14th March – Scientific Posters – ODD Numbers1 ‘Development of Ub/ Ubl~E2 activity-based probes for the identification of novel E3s’

Lucy Barnsby and Satpal Virdee3 ‘An X-linked intellectual disability missense mutation that affects protein

O-GlcNAcylation’ Veronica M. Pravata, Mehmet Gundogdu, Andrew T. Ferenbach, Marios Stavridis, Katrin Õunap, Sander Pajusalu, Riina Žordania, Monica H. Wojcik and Daan M. F. van Aalten

5 ‘Get a grip - mechanisms underlying variation in barley grain hull adhesion’ Trisha McAllister7 ‘ERK5 induces embryonic 2-cell stage genes through a KLF2-ZSCAN4 auto-

regulatory module’ Helen A. Brown, Charles A.C. Williams, Rosalia Fernandez-Alonso, Julien Pelltier, Diana Rios-Szwed, Nora Dieguez, Dorothee Kern, Jose M. Lizcano, Matthias Trost and Greg M. Findlay

9 ‘FAM83D directs protein kinase CK1α to the mitotic spindle for proper spindle positioning’ Luke J. Fulcher1, Zhengcheng He2, Lin Mei2, Thomas J. Macartney1, Nicola T. Wood1, Alan R. Prescott3, Arlene J. Whigham4, Joby Varghese1,

Robert Gourlay1, Graeme Ball3, Rosemary Clarke4, David G. Campbell1, Christopher A. Maxwell2, and Gopal P. Sapkota1

11 ‘IRAK-3 can rescue IL-1R/TLR signalling in the absence of IRAK-1’ C.B. Aitken, J. Zhang, Y. Mao and P. Cohen13 ‘Chagas Disease: A new approach for identifying the localisation of Trypanosoma

cruzi persisters in organs of chronically infected mice directly after drug treatment’ Julia Wcislo, Erika Pinto, Michael Conneely, Liam Ferguson, Frederick Simeons,

Laste Stojanovski and Kevin Read15 ‘What’s new from the Proteomics Core Facility’ Abdel Atrih, Kenny Beattie, Jodie Donachy, Sam Kosto, Dougie Lamont, Cara Rogers, Alan Score17 ‘Discovery of Potential New Drug Targets against Gram-Negative ESKAPE Pathogens’

Eleanor Adams, Ian Gilbert, Sarah Coulthurst, Anthony Hope, Colin Robinson, Katherine Mathers, James Martin

19 ‘Raspberry Root Rot: Investigation of the story behind the infection’ Aurelia Bezanger21 ‘Identification of novel protein kinase regulators of TGF-beta’ Luke D. Hutchinson, Dr. Nicola Darling. Prof. Philip Cohen and Dr. Gopal P. Sapkota23 ‘Studying the structure and binding mode of the glycine receptor, a pentameric

ligand gated ion channel’ Mathew J. Jones, Alice Dawson and William N. Hunter25 ‘Constructing the JAK/STAT pathway in Drosophila S2 Cells’ Alison McFarlane and Dr Ignacio Moraga Gonzalez27 ‘SIK3 kinase activity is required for the IL-33-dependent production of IL-13, a

mediator of allergic asthma’ Nicola J. Darling, J. Simon C. Arthur, Philip Cohen29 ‘Visualisation of organ vascularisation by endoscopic Laser Speckle Flow Imaging’

Lukas Markwalder, Prof Faisel Khan, Dr. Nikola Krstajic, Dr. Colin Murdoch31 ‘Splicing factor kinases control RNF12 substrate targeting to pattern developmental

gene expression’ Bustos F, Segarra-Fas A, Cassidy A, Gourlay R, Vargesse J, Toth R, Macartney T, Zhang T, Brandenburg L, Nardocci G, Montecino M, Gray N, Findlay GM

33 ‘BAZ2A PROTACs: Is ternary complex formation sufficient for degradation?’ Scott J. Hughes, Mattia Cocco, Vittoria Zoppi, Chiara Maniaci, Alessio Bortoluzzi,

Alessio Ciulli35 ‘3D RNA-seq App for RNA-seq analysis’ Wenbin Guo1, Nikoleta A. Tzioutziou1,

Cristiane P.G. Calixto1, Robbie Waugh1,2, John W.S. Brown1,2, Runxuan Zhang3

37 ‘Kinetochore-Independent spindle assembly checkpoint functions during oocyte meiosis’ Laura Bel Borja, Federico Pelisch’

39 ‘aDAPt or perish: A starvation secret revealed by C. elegans’ Yasir Malik, Dalila Bensadek, Mark Larance and Anton Gartner41 ‘Contractile acto-myosin network on nuclear envelope remnants positions

chromosomes for mitosis’ Alexander JR Booth, Zuojun Yue, John K Eykelenboom, Tom Stiff2, GW Gant Luxton, Helfrid Hochegger, Tomoyuki U Tanaka1

43 ‘Structure-based PROTAC design: from bivalent molecules to macrocycles’ A. Testa, S. J. Hughes, X. Lucas, J. E. Wright, K. Riching, D. Daniels, A. Ciulli45 ‘Identification of novel cell cycle PHD-dependent targets’ Jimena Druker, Hao Jiang,

Dalila Bensaddek, Angus Lamond, Sonia Rocha and Jason Swedlow47 ‘Development of a new technology to analyse chromatin environment at origins

of replication’ Vanesa Álvarez, Eva Griesser, Jens Hukelmann, Angus Lamond and Constance Alabert

49 ‘Maintenance of chromatin state in cycling cells’ Susanne Bandau, Diana Rios Szwed, Jens Hukelmann, Eva Griesser, Angus Lamond and Constance Alabert

51 ‘Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome’ Ramasubramanian Sundaramoorthy, Amanda L. Hughes, Hassane El-Mkami, David G. Norman, Helder Ferreira, Tom Owen-Hughes Image ‘Bustos & Findlay (MRC-PPU) ‘Nucleolar function of RNF12 E3 ubiquitin ligase in ES cells

Friday 15th March – Scientific Posters – EVEN Numbers2 ‘Investigating non-canonical deubiquitylation by MALDI-TOF mass spectrometry’

Virginia De Cesare, Daniel Carbajo-Lopez, Axel Knebel, Satpal Virdee4 ‘An intellectual disability syndrome with mutations in O-GlcNAc transferase’ Michaela Omelkova, Veronica Pravata and Daan van Aalten6 ‘MINK1 is regulated by APC in epithelial cells’ Melanie S Volka, Olesja Popowbc, Ian P Newtona, Carol MacKintosha, Inke Näthkea8 ‘Targeting phosphohexomutases and pyrophosphorylases in Candida albicans and

Aspergillus’ Kaizhou Yan, Mathew Stanley, Olawale Raimi, Daan van Aalten10 ‘Advanced TiO2-PTFE nanocomposite coatings on stainless steel surfaces exhibit

significant antibacterial and anti-corrosion properties’ Shuai Zhang1, Xinjin Liang2, Geoffrey Michael Gadd2 and Qi Zhao1

12 ‘Tayside Centre for Genomic Analysis’ Kathy Walls and Amanda Baizan Edge14 ‘Genetic Approaches to Explore the Oocyst Wall Proteins of the Parasite

Cryptosporidium parvum’ Ross Bacchetti, Mattie Pawlowic16 ‘Direct RNA sequencing reveals the Arabidopsis epitranscriptome’ Matthew Parker,

Anya Sherwood, Kasia Knop, Nick Schurch, Geoff Barton and Gordon Simpson18 ‘Nanopore Direct RNA sequencing unveils full repertoire of RNA isoforms and a

new level of gene regulation guided by m6A mRNA methylation’ Anna Sherwood, Katarzyna Knop, Nick Schurch, Matthew Parker, Celine Duc, Geoff Barton and Gordon Simpson

20 ‘Launching Jalview into the Future’ Suzanne Duce, Ben Soares, Jim Procter, Mungo Carstairs and Geoff Barton22 ‘New approaches to studying the GPI biosynthesis pathway in T. brucei: uncovering

the missing links’ Zhe Ji, Michele Tinti, Samuel Duncan, M. Lucia S. Güther and Michael A. J. Ferguson

24 ‘Identification and validation of lanosterol synthase as the target of a phenotypically-active anti-leishmanial compound’ Luciana Paradela, Richard Wall,

Sandra Carvalho, Julio Martin, Ian Gilbert & Susan Wyllie26 ‘What can human variation tell us about proteins?’ Stuart A. MacGowan, Fábio Madeira, Thiago Britto-Borges, Melanie S. Schmittner, Christian Cole and Geoffrey J. Barton28 ‘Automated computational workflows for NGS analysis’ James Abbott30 ‘Generating triple-reporter strains for the advancement of drug discovery against the

Cryptosporidium parasite’ Beatrice Colon and Mattie Pawlowic32 ‘Impact of chromatin replication upon pluripotency maintenance’ Jane Wright,

Lindsay Davidson and Constance Alabert34 ‘Reconstituting the human Exocyst complex’ Hannes Maib and David Murray36 ‘Characterization of an E3 SUMO ligase targeted by pests and pathogens’ Shan Liu, Edgar Huitema & Jorunn Bos38 ‘Phosphorylating LRRK2 substrate Rab GTPases in vitro using MST3 kinase - a tool

for effector assays’ Elena Purlyte, Dieter Waschbusch, Amir Khan, Dario Alessi40 ‘Homeostatic regulation of O-GlcNAcylation is required for Drosophila habituation

learning and synapse development’ Villo Muha, Michaela Fenckova, Andrew T. Ferenbach, Daniel Mariappa, Mehmet Gundogdu, Vasudha Vandadi, Marica Catinozzi, Erik Storkebaum, Annette Schenck and Daan M. F. van Aalten42 ‘14-3-3 regulation of the autophagy-initiating kinase ULK1’ Longo M., Toth R.,

Macartney TJ., MacKintosh C., Ganley IG44 ‘Characterization of potential pathogenic mutation of UDP-N-acetylhexosamine

pyrophosphorylase’ Xiping Chen, Andrew Ferenbach and Daan van Aalten46 ‘Characterization of WD40 containing CRL4 E3 ubiquitin ligase’ Kwok-Ho Chan and

Alessio Ciulli48 ‘Dissecting spinal cord ependymal cell heterogeneity using single-cell

transcriptomics’ Aida Rodrigo Albors, Gail Singer, Andy May, Chris Ponting, Kate Storey50 ‘Structural insights into substrate recognition by the SOCS2 E3 ubiquitin ligase’

Sarath Ramachandran, Wei-Wei Kung, Nikolai Makukhin and Alessio Ciulli

Programme – Thursday 14th March0840–0950 Hotel Check-in (Ballroom)

Coffee (The Hub)

Session 1 – Chaired by Dario Alessi (Melville Hall)

0950–1000 Introduction and welcome by Julian Blow

1000–1025 Ron Hay (GRE)‘Arsenic unleashes thePML-SUMO-RNF4 axis to cure cancer’

1025–1050 Kim Dale (CDB)‘Turning it up a Notch –to build the embryonic body plan’

1050–1115 Helge Dorfmueller (MMB)‘New approaches to target lethal ‘Strep throat’ bacteria’

1115–1140 Gordon Simpson (GRE/PS)‘The Long Read’

1140–1150 SLS Resource: DougieLamont: FingerPrints Proteomics

1150–1220 SLS-Showcase: The 2018 SLS Award winnersChristina Rollings (DC/CSI; Howard Elder): IL-2 regulation of the CTL proteome

Wenbin Guo (JB/PS; Cell Signalling):3D RNA-seq App for RNA-seq analysis

Suzanne Duce (Engagement):Kirsty’s Project: Searching for a New Medicine

Lesley-Anne Pearson/Lauren Webster (Engagement):It's legal now: 2 girls get engaged

1220–1330 Buffet Lunch (The Hub)

Session 2 – Chaired by Jens Januschke (Melville Hall)1330–1410 SLS showcase: Talks selected from submitted

abstractsNicola Darling (PC/PPU): SIK3 activity is required for IL-33-dependent production of IL-13

Luke Fulcher (GS/MRC-PPU): FAM83D directs CK1α to the mitotic spindle

Helen Brown (GF/MRC-PPU): Embryonic 2-cell stage transcriptional control by ERK5

Laura Bel Borja (FP/GRE): Kinetochore-independent spindle-checkpoint function during meiosis

Yasir Malik (AG/GRE): aDAPt or perish: A starvation secret revealed by C. elegans

Zuojun Yue (TT/GRE): Contractile acto-myosin networkpositions chromosomes in mitosis

1410–1435 Sara Brown (Medicine)‘Molecular mechanisms in atopic eczema’

1435–1500 Piers Hemsley (PS)‘Protein S-acylation –more than just a fatty anchor?’

1500–1525 Alessio Ciulli (BCDD) ‘How PROTACs work’

1525–1555 Tea and Coffee

1555–1600 Introduction of the Keynote Lecturer by Claire Halpin

1600–1700 Keynote Lecture delivered by:Professor Dame Janet ThorntonEuropean Bioinformatics Institute(EMBL-EBI), Cambridge, UK. ‘Drug repurposing for ageing research’

1700–1830 Posters (odd numbers) and drinks (Melville Hall)Sponsored by MRC PPU Reagents and Services

1930-2100 Dinner (Meikle Restaurant)

2100-2330 Ceilidh (Ballroom)

Programme – Friday 15th March0730–0900 Breakfast (Meikle Restaurant)

Session 3 – Chaired by Constance Alabert (Melville Hall)

0900–0925 Geoffrey Barton (CB)‘Bringing population genetics to protein structure’

0925–0950 Greg Findlay (MRC-PPU)‘From Stem to Stern: Exploring Kinase Functions in Pluripotent Cells’

0950–1025 SLS showcase: Talks selected from submitted abstracts Virginia De Cesare (SV/PPU): Investigating non-canonical deubiquitylation by MALDI-TOF

Shan Liu (JB/PS): An E3 SUMO ligase targeted by pests and pathogens

Anna Sherwood (GS/GRE): Gene regulation guided by m6A mRNA methylation

Michaela Omelkova (DVA/GRE): OGT mutations in an intellectual disability syndrome

Ross Bacchetti (MCP/BCDD): Exploring oocyst wall proteins of Cryptosporidium parvum

Matthew Parker (GS/GRE): Direct RNA sequencing reveals Arabidopsis epitranscriptome

1025–1055 Tea and Coffee

1055–1120 Colin Murdoch (Medicine)‘In vivo phenotyping of redox signalling in cardiovascular disease’

1120–1145 Ignacio Moraga-Gonzalez (CSI)‘Manipulating cytokine signalling and activities with protein engineering’

1145–1210 Sarah McKim (PS)‘Putting on the brakes – reproductive architecture in barley’

1210–1400 Buffet Lunch (The Hub)

Session 4 – Chaired by Alan Fairlamb (Melville Hall)

1400–1425 Angus Lamond (GRE)‘Deep proteomes: iPS cells and navigating the data mountain’

1425–1450 David Murray (CDB)‘Polarity, membranes, and the machinery that tethers’

1450–1515 Gabriele Schweikert (CB)‘Machine Learning Methods to Elucidate Epigenomic Control of Gene Expression’

1515-1545 Tea and Coffee

1545-1555 Inke Nathke SLS Athena Swan

1555-1620 David Horn (BCDD)‘E pluribus unum – out of many, one’

1620-1645 Philip Cohen (MRC-PPU)‘Identification of an atypical E3 ubiquitin ligase forming ester and not isopeptide bonds’

1700-1830 Posters (even numbers) and drinks (Melville Hall)Sponsored by FingerPrints Proteomics

1930-2100 Dinner (Meikle Restaurant)

2100-2230 Pub quiz (Melville Hall)

Programme – Saturday 16th March0730–0900 Breakfast (Meikle Restaurant)

0900– Free time