Graduate Research and Training

GRADUATE RESEARCH & TRAINING HANDBOOK 2018 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Welcome

IGMM Graduate Research and Training Contacts

Staff Student Liaison Committee/Officer 1 40,000 5.0 0 0

!"#$%&$%'& & 5.0 Number of promoters ()*+&,)-).%+/0-&1(2&,)-0+34) 546)-0+34)&7%44/-,8 & of promoters Proportion

& 1 9)-07)&:);")-&%-#&<$0:)&+0&%&7/$$/0-&4)04$)& 30,000 Matched expression Vagina

6%=)&6%#&+6)/.&,)-07)&:);")-<)#8&?0&/-+).4.)+&+6/:&7%::/=)&%70"-+&0@&Divergent expression Neurons

Diminished promoter activity Epididymis Ovary, adult Ovary, Testis, adult Testis, CD8+ T cells CD8+ T cells CD4+ T Uterus, adult Uterus, - cerebellum Thymus, fetal Thymus, CD19+ B cells CD19+ B

No promoter activity Housekeeping

/[email protected]%+/0->&0".&$%'&#)=)$04:&)@@/&%-#& adult oblongata, lla

Deleted promoter sequence adult Diencephalon, Hippocampus, adult Hippocampus, Ambiguous promoter alignment adult brain, Olfactory Naive r Astrocytes

#)=)$04&6/,65+6.0",64"+&%::%3:&+0&7)%:".)&+6)&)@@)<+:&0@&7"+%+/0-:&0-& Medu Naive c 70$)<"$%.&%-#&<)$$"$%.&46)-0+34):>&:"<6&%:&4.0+)/-&%-#&1(2&%'"-#%-<)>Astrocytes &4.0+)/- 5 1(2&/-+).%<+/0-:>&%-#&@/+-)::&CD"<6+%&)+&%$8>&E&FGHIJ8&A)&":)&%&=%./)+3&0@& )*4)./7)-+%$&+)<6-/;"):>&/-<$"#/-,&,)-)&:3-+6):/:>&-)*+ 5,)-).%+/0-&:);")-& 7/<.0%..%3:>&%-#&%"+07%+)#&7/<.0:<043>&%-#&)*4)./7)-+%$&:3:+)7:&/-<$"#/-,& '%<+)./%>&3)%:+>&%-#&7%77%$/%-&<)$$:8& &

& & & &

1 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Welcome In the first instance you will mainly deal with We are delighted to welcome you to your your supervisors, Graduate Convenor or Nick PhD programme at the Institute of Genetics Gilbert (Director of Graduate Research and and Molecular Medicine. On the following Training for the IGMM). You will also have a pages you will find information relating to thesis committee (normally setup abour 10 the different programmes, timetable for weeks into your PhD) which will be made up the first 6 months, and the assessment of your supervisors, an external advisor and a timetable for the next 3 or 4 years. committee Chair. Formal issues (interruption of studies and so on) are dealt with by the As you probably know, we have a mixture Director of Graduate Research and Training of students on campus, some of whom and the College PG Office. are following a four year programme with rotations and others who are starting a Head of School of MGPHS three year PhD in a specific lab. There Professor Sarah Cunningham-Burley are some teaching elements of the four Director of Graduate Research and Training, year taught course that might be of IGMM: Professor Nick Gilbert interest to other students, for example covering different technologies, computer Graduate Convenor, CRUK Edinburgh programming, aspects of clinical reserach Centre: Professor Val Brunton and research ethics - these are shown Graduate Convenor, MRC Human Genetics in a detailed timetable on page 5 - 8. Unit: Professor Nick Gilbert This teaching is only compulsory for the 4-year HGU students, but other students Graduate Convenor, Centre for Genomic & (and postdocs) are welcome to sign up Experimental Medicine: Dr Kathy Evans and attend any sessions that you find Director of PG Studies, College of MVM useful; you might want to discuss your choice with your supervisor(s). We hope Dr Paddy Hadoke that the IGMM Graduate Research and Staff Student Liaison Officer Training environment will provide a useful Dr Martin Reijns framework for your studies. Please feel free to air your views, and to approach us about Graduate Research and Training any issues you have, and help us to make Administrator the IGMM a huge success! Pauline McDonald Graduate Research and Training Assistant Graduate Research and Training Alana Johnson contacts The IGMM is made up of three centres, the MRC Human Genetics Unit (HGU), the Centre for Genomics and Experimental Medicine (CGEM) and the Cancer Research UK Edinburgh Centre (ECRC), each with their own Graduate Convenor. The IGMM falls within the School of Molecular, Genetic and Population Health Sciences (you will need to know this School affiliation when you apply for Transkills courses amongst other things), and the SMGPHS is within the College of Medicine and Veterinary Medicine or CMVM.

2 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Staff Student Liaison Committee/ Officer At the IGMM we are committed to ensuring a high-quality student experience. To ensure we are able to deliver this, and to “maximise our students’ potential”, we encourage students to communicate their views and suggestions to help influence any required changes to policies and procedures. The IGMM Staff Student Liaison Committee (SSLC) meets biannually to discuss matters of mutual concern of staff and students. The SSLC is composed of student and staff representatives, and we strongly encourage students at any stage of their graduate degree to consider joining the SSLC. In addition, we introduced a Staff Student Liaison Officer (SSLO) in August 2014. Martin Reijns is an senior research scientist in Professor Andrew Jackson’s laboratory in the Disease Mechanisms section of the Human Genetics Unit. Martin has been a Email: [email protected] member of the Jackson lab since 2007. Telephone: 651 8633 In 2014 we setup a mentoring system for Location: MRC Human Genetics Unit PhD students. This “buddying” programme pairs 1st-year students who wish to be involved with friendly and supportive final What to do if things go wrong year students; and aims to help with their integration into the institute, informally If you have a problem with your project answer any questions and queries and/or supervisor, you should first try regarding starting their PhD, and also to to resolve it between yourselves - it is offer support with beginning a new life in important to keep lines of communication Edinburgh. open where possible and not let things degenerate. If there is still a problem, then If you want to know more, or would like to be please seek advice - you should feel free paired up, please get in touch with Martin; to speak to your second supervisor, your also if you are interested in becoming a thesis committee Chair, the Directors of the representative to the SSLC. Graduate School or the PG Convenor for your building. If in the end problems can’t be solved locally, then official complaints can be made to a committee in the PG Office. These conversations will be in confidence and a strategy will be devised to try and address any problems. Additional meetings of thesis committees can be arranged (subject to members’ availability) if the student and/or supervisors feel that this would help.

3 1 40,000 5.0 0 0

!"#$%&$%'& & 5.0 Number of promoters ()*+&,)-).%+/0-&1(2&,)-0+34) 546)-0+34)&7%44/-,8 & of promoters Proportion

& 1 9)-07)&:);")-&%-#&<$0:)&+0&%&7/$$/0-&4)04$)& 30,000 Matched expression Vagina

6%=)&6%#&+6)/.&,)-07)&:);")-<)#8&?0&/-+).4.)+&+6/:&7%::/=)&%70"-+&0@&Divergent expression Neurons

Diminished promoter activity Epididymis Ovary, adult Ovary, Testis, adult Testis, CD8+ T cells CD8+ T cells CD4+ T Uterus, adult Uterus, - cerebellum Thymus, fetal Thymus, CD19+ B cells CD19+ B

No promoter activity Housekeeping

/[email protected]%+/0->&0".&$%'&#)=)$04:&)@@/&%-#& adult oblongata, lla

Deleted promoter sequence adult Diencephalon, Hippocampus, adult Hippocampus, Ambiguous promoter alignment adult brain, Olfactory Naive r Astrocytes

& & & & GRADUATE RESEARCH & TRAINING HANDBOOK 2018 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

MRC Human Genetics Unit 4 year programme • Introduction to programme • Projects available 1 40,000 5.0 0 0

!"#$%&$%'& & 5.0 Number of promoters ()*+&,)-).%+/0-&1(2&,)-0+34) 546)-0+34)&7%44/-,8 & of promoters Proportion

& 1 9)-07)&:);")-&%-#&<$0:)&+0&%&7/$$/0-&4)04$)& 30,000 Matched expression Vagina

6%=)&6%#&+6)/.&,)-07)&:);")-<)#8&?0&/-+).4.)+&+6/:&7%::/=)&%70"-+&0@&Divergent expression Neurons

Diminished promoter activity Epididymis Ovary, adult Ovary, Testis, adult Testis, CD8+ T cells CD8+ T cells CD4+ T Uterus, adult Uterus, - cerebellum Thymus, fetal Thymus, CD19+ B cells CD19+ B

No promoter activity Housekeeping

/[email protected]%+/0->&0".&$%'&#)=)$04:&)@@/&%-#& adult oblongata, lla

Deleted promoter sequence adult Diencephalon, Hippocampus, adult Hippocampus, Ambiguous promoter alignment adult brain, Olfactory Naive r Astrocytes

& & & &

5 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

The first six months The PhD The HGU PhD program is following an After three rotations you will choose a PhD exciting and innovative format. You will project. We will have individual meetings spend the first 6 months on an intensive with you to discuss your choices in the training period leading up to your final event of any clashes. No supervisor will choice of PhD project. This period be able to take on more than one student, comprises taught courses, talks from HGU students must choose projects within individual group leaders about their the HGU, but apart from this you can go work, teaching sessions on a variety to any lab within the available project of topics from technology to clinical section. It is up to you to discuss possible research, journal club sessions which will projects with PIs you are interested in; this give you a chance to hone your analytic is a dynamic process in which you should and presentation skills, and three short be fully engaged. Note that supervisors rotation projects. The detailed timetable are not obliged to take you on, you need can be found in the handbook. to ask whether they are willing, or whether they have other interested students and The choice of rotation projects is up so on. If your research project involves to you (available projects are listed at the use of animals or human participants, the end of this section) and you can work must not commence until the relevant approach any relevant group leader to Home Office project and personal licences discuss the projects. You will see that have been awarded, and appropriate Local there is some time between rotations, Ethical Approval Committee has been giving you a chance to look around granted. We will not be producing PhD and choose a new lab. The only formal project outlines from supervisors. Rather, at constraint is that you must spend time in the PhD 10 week stage (June) you will have 3 different labs. You may find, of course, to produce a short report that outlines the that another student has already been project that you will pursue. This will then accepted and that the PI is only willing be discussed and refined if necessary by to take on one student (as is normally your supervisors (more detailed guidelines expected of PIs). If this happens then are given under Assessment Procedures). try again in the next rotation period; if You will then spend 3 years in the lab, there is a real clash then Nick Gilbert winding up by April of your final year. You will help but do please try and resolve will then have a further 6 months to write up things between yourselves in the first your thesis but remember it is imperative instance. Bear in mind that there is no that you submit your thesis by the final formal requirement for you to choose a university deadline of September of year 4, PhD project in a lab in which you have otherwise you will incur significant financial done a rotation project, the rotations are penalties. just a chance for you to try different labs and projects out. We hope that this novel structure for PhD study will be as exciting for you as it has Many of the group leaders welcome been for us to develop it. We will be asking students coming to their lab meetings for your feedback at several stages of the which is a good way of seeing life in labs course - please feel free to air your views, other than the ones where you are doing and approach us about any issues you rotation projects, but please be sure to have, and help us to make the HGU PhD make contact with the appropriate PI in programme a huge success! advance. Nick Gilbert

6 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Lab Rotations This abstract should be submitted to the Each student will do three rotation projects IGMM PGSC by emailing: of around seven or eight weeks. Contact [email protected] details and summaries of research interests of eligible supervisors are all given in this Supervisors will be asked for feedback on booklet (note there are some people unable your performance in the lab and we will to take students for rotations, please ask to meet up with you if there are any check), and during the first week you will concerns. Towards the end of each rotation be hearing research talks by these PIs. most sections (Biomedical Genomics, Genome Research, Disease Mechanisms) The choice of rotation projects is up to invite the rotation students from their you - you are responsible for approaching section to do a short talk about your mini- potential supervisors to discuss their project. willingness to take you on and to jointly come up with a plan of work. Remember the project won’t be formally assessed as part of your PhD, so make the most of your time to experience different techniques, and just get a feel for life in different labs. The only formal constraint is that you must spend time in 3 different labs. You may find, of course, that another student has already been accepted and that the PI is only willing to take on one student (as is normally expected of PIs). If this happens then try again in the next rotation period; if there is a real clash then one of us will intervene but do please try and resolve things between yourselves in the first instance. Bear in mind that there is no formal requirement for you to choose a PhD project in a lab in which you have done a rotation project, the rotations are just a chance for you to try labs out. At the end of each rotation you are asked to write a one page abstract about your project, to be handed in by the end of the week after you finish in that lab. This should be in the format used by journals such as those on Biomedcentral, i.e. divided up into brief sections of background, results and conclusions and no longer than one side of A4.

7 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Chromosome Segregation in the Mouse Germline Primary Supervisor: Dr Ian Adams This PhD project will investigate how mouse germline cells ensure that chromosomes are faithfully segregated in meiosis. Chromosome mis-segregation in the germline can result in the transmission of aneuploidy to the next generation, which in humans causes genetic diseases such as Down syndrome and Klinefelter syndrome. This PhD project will use embryonic stem cells and mouse genetics to investigate Email: [email protected] mechanisms that contribute to faithful Telephone: 651 8562 chromosome segregation in the mouse Location: MRC Human Genetics Unit germline. Centre of Affiliation: MRC Human Genetics Unit

Decoding the precise spatial and temporal dynamics of PAX6 cis- regulatory landscape Primary Supervisor: Professor Wendy Bickmore Aberrations in the function of cis-regulatory elements (CREs) has been identified as a major cause of human diseases. CREs act as primary determinants of precise spatial and temporal regulation of their target genes by serving as docking sites for tissue-specific transcription factors. The PAX6 locus has been a paradigm for Email: [email protected] understanding CRE-mediated control of Telephone: 651 8583 target gene expression, with the regulatory Location: MRC Human Genetics Unit domain extending around 200kbp on both Centre of Affiliation: sides of the transcription start site and MRC Human Genetics Unit harbouring several CREs which together orchestrate the complex expression pattern of PAX6 in the developing eye, brain, neural tube and pancreas. The project will utilize high resolution live imaging in zebrafish transgenics and a serum free embryoid body (SEFB) differentiation system to uncover the precise dynamics of CRE action in this massive regulatory domain.

8 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

A dedicated Nonsense-mediated (NMD) pathway in the endoplasmic reticulum (ER-NMD) Primary Supervisor: Professor Javier F. Caceres NMD selectively degrades mRNAs harboring premature termination codons (PTCs) but also regulates the abundance of a large number of cellular RNAs. Most studies to date have focused on cytoplasmic NMD; however, we have recently uncovered evidence suggesting the existence of an NMD pathway dedicated to Endoplasmic Reticulum (ER)-localized mRNAs. We will define the subcellular localization of NMD for those transcripts that are translated at the ER, and will identify mRNA targets and novel Email: [email protected] components of the ER-NMD pathway. We Telephone: 651 8699 will focus on the physiological role of this novel pathway, as well as on the biological Location: MRC Human Genetics Unit consequences of manipulating its activity. Centre of Affiliation: MRC Human Genetics Unit

Functional genomic interrogation of trans-eQTL regulatory hubs and the role of functional epistasis in the development of large bowel cancer Primary Supervisor: Professor Malcolm Dunlop Colorectal cancer (CRC) is a common fatal cancer. Heritable common genetic variation influencing gene expression in normal large bowel epithelium contributes to CRC risk. We have generated a wealth of human functional and genomic data from blood, Email: [email protected] epithelium and tumour samples. This Telephone: 651 8631 exciting project melds functional genomic Location: MRC Human Genetics Unit analysis of trans-eQTL regulatory hubs with Centre of Affiliation: statistical genetic approaches to identify MRC Human Genetics Unit epistatic mechanisms influencing cancer risk. The candidate will gain computational and quantitative skills, alongside wet-lab expertise in genome editing to interrogate the functional genomic landscape of CRC risk. The ultimate aim is to prevent cancer by defining and exploiting cancer susceptibility pathways.

9 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Functional Analysis of Eye Field Transcription Factors Using In Vitro Differentiation of Embryonic Stem Cells Primary Supervisor: Professor David FitzPatrick My lab uses in vitro differentiation of mouse embryonic stem cells to create the optic vesicle-like organoids in MRC HGU. We are interested in the gene regulatory networks controlling early eye development. We are using CRISPR Cas9 Email: [email protected] to insert protein tags into the endogenous Telephone: 651 8569 loci of eye field transcription factors that are critical to these networks. These tags allow Location: MRC Human Genetics Unit us to use live cell imaging, FACS sorting Centre of Affiliation: and immunoprecipitation (chromatin MRC Human Genetics Unit and protein-protein) to understand cell behaviour during differentiation project. We can also use them for timed degradation of the protein to observe the effect on the differentiation cascade.

Understanding mitotic chromosome unpackaging Primary Supervisor: Professor Nick Gilbert In mammalian cells DNA is packaged with histone proteins to form chromatin. In every cell cycle chromatin is folded up to form mitotic chromosomes to facilitate chromosome segregation and to separate genetic information into daughter cells. Despite being a fundamental process we do not understand the molecular mechanisms responsible for unpackaging mitotic chromosomes into the interphase Email: [email protected] configuration. To investigate this we will Telephone: 651 8551 use CRISPRi genetic screens in mammalian Location: MRC Human Genetics Unit cells to identify key factors responsible and Centre of Affiliation: will characterise their properties by super- MRC Human Genetics Unit resolution STORM microscopy. We predict many of these factors will also be mutated in cancers, linking together fundamental cellular mechanisms with human disease.

10 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Chromatin Architecture, Enhancer Structure and Congenital Abnormalities Primary Supervisor: Professor Bob Hill Mutations which affect gene regulation are becoming increasingly recognised as important disease causing variations. A number of mechanisms perturb enhancer activity to generate abnormal phenotypes and we propose to investigate novel regulatory mechanisms that cause disease. Our model system for understanding Email: [email protected] abnormal gene regulation is the sonic Telephone: 651 8621 hedgehog (Shh) gene, a signalling molecule Location: MRC Human Genetics Unit that controls early development, and Centre of Affiliation: requires a genomic region of one million MRC Human Genetics Unit basepairs of DNA to regulate precise gene expression. To further elucidate mechanism, we will use CRISPR/Cas9 to engineer the chromosomal landscape for molecular analysis and to further develop imaging techniques to analyse chromatin structure.

DNA outside the nucleus in autoinflammation and carcinogenesis Primary Supervisor: Professor Andrew Jackson The cGAS-STING pathway senses cytoplasmic DNA to identify and combat microbial pathogens, while strict compartmentalisation of our own DNA in the nucleus prevents autoimmunity. We recently established that our own DNA can activate this pathway after DNA damage, Email: [email protected] when cGAS detects micronuclei. This Telephone: 6518560 has implications for how cells may detect early cancer-inducing events, and for how Location: MRC Human Genetics Unit DNA damage could lead to inflammation Centre of Affiliation: (Mackenzie et. al Nature 2017). This PhD MRC Human Genetics Unit aims to build on these findings, addressing whether this pathway oppose cancer formation in vivo, if there other processes that deliver DNA to the cytoplasm, and why is cGAS not activated during normal mitosis?

11 Kudla lab

Next generation RNA genotype-phenotype mapping.

Genome sequencing has become relatively cheap, and close to a million people have had their genome sequenced. To interpret this massive amount of information, our lab develops efficient methods for measuring and predicting the effects of genetic variation. We synthesize large collections of mutated genes, and develop high-throughput assays to measure the effects of mutations on molecular and cellular phenotypes, such as protein and RNA abundance, protein- GRADUATE RESEARCH & TRAINING HANDBOOKRNA interactions, and fitness (Puchta et al., Science, 2016). W 2018 e use a variety of experimental techniques, including gene synthesis, next-generation sequencing, microarrays, and automated microscopy, and experimental systems including bacteria, yeast, and mammalian cells. Next generation RNA genotype- phenotype mapping Primary Supervisor: Dr Grzegorz Kudla NMD selectively degrades mRNAs harboring premature termination codons (PTCs) but also regulates the abundance of a large number of cellular RNAs. Most studies to date have focused on cytoplasmic NMD; however, we have

recently uncovered evidence suggesting Email: [email protected] the existence of an NMD pathway Telephone: 651 8628 dedicated to Endoplasmic Reticulum (ER)-localized mRNAs. We will define the Location: MRC Human Genetics Unit subcellular localization of NMD for those Centre of Affiliation: transcripts that are translated at the ER, MRC Human Genetics Unit and will identify mRNA targets and novel components of the ER-NMD pathway. We will focus on the physiological role of this novel pathway, as well as on the biological consequences of manipulating its activity.

Protein assembly in human genetic disease and cancer Primary Supervisor: Dr Joe Marsh Despite the huge amount of genome sequence data now available, our ability to predict the consequences of damaging mutations is very limited. One reason for this has been a failure to take into consideration the fact that most proteins can assemble into complexes within the cell. This project will use a variety of computational approaches, including Email: [email protected] uk structural bioinformatics, molecular Telephone: 651 8538 modelling and machine learning, in order Location: MRC Human Genetics Unit to first understand and then predict how Centre of Affiliation: missense mutations can interfere with MRC Human Genetics Unit protein assembly and cause a variety of genetic disorders, and how non-coding variants can contribute to cancer by disrupting protein stoichiometry.

12 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

The Role of DNA methylation in cellular transitions Primary Supervisor: Professor Richard Meehan DNA methylation represents a primary epigenetic mechanism in vertebrate genomes that can repress the regulatory function of DNA sequences associated with promoter/enhancer activity and act as a general silencer of intergenic transposons. New evidence suggests that DNA methylation acquires these roles Email: [email protected] during differentiation of embryonic stem Telephone: 651 8548 cells. We have developed assay systems that allow us to capture when the repressive Location: MRC Human Genetics Unit function of DNA methylation becomes Centre of Affiliation: dominant. The project involves combining MRC Human Genetics Unit expertise in epigenetics in embryos and stem cells with advanced imaging, to reveal context-dependent epigenetic signalling mechanisms in differentiating cells – leading to improved stem cell applications for bioscience and biomedicine.

Decoding mammalian cilial diversity in the brain Primary Supervisor: Dr Pleasantine Mill Cilia are small, ubiquitous, microtubule- based organelles required during development and adult homeostasis. Ciliopathies are a growing spectrum of human syndromes caused by mutations in genes disrupting cilia structure or function. What is particularly puzzling is the pleiotropy of clinical features observed Email: [email protected] in ciliopathy patients, with varying degrees Telephone: 651 8616 of severity among different tissues. This Location: MRC Human Genetics Unit suggests all cilia are not created equal. In Centre of Affiliation: order to better understand the functional MRC Human Genetics Unit and structural diversity of mammalian cilia in different cell types, this project will use genome editing to engineer a mouse where components of a common intraciliary transport system required to build and maintain all cilia types have been genetically tagged. This tag allows exquisitely resolution, both temporally and spatially, providing molecular snapshots of ciliary composition for biochemical, structural and super-resolution imaging studies needed to fully capture the functional diversity of cilia types in vivo. 13 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Dynamics of transcription factor concentration, chromatin-binding kinetics and cell-to-cell variability during zebrafish Zygotic Genome Activation Primary Supervisor: Dr Dimitrios Papadopoulos During early zebrafish development, maternally deposited mRNAs in the embryo are degraded, while the zygotic genome Email: [email protected] becomes primed for taking genetic Telephone: 651 8648 control of development. The awakening of the zygotic genome is a temporally Location: MRC Human Genetics Unit precise process, controlled by pioneer Centre of Affiliation: transcription factors at the 1024 cell MRC Human Genetics Unit stage. We are interested in understanding how the absolute amount, chromatin- binding kinetics and cell-to-cell variability of transcription factor concentration contribute to the temporal precision of Zygotic Genome Activation (ZGA). For this, we will generate fluorescently- tagged transcription factors and address their dynamic behaviour quantitatively during ZGA by Fluorescence Microscopy Imaging and Fluorescence Correlation Spectroscopy.

ALDH enzymes in melanoma stem cell lineages Primary Supervisor: Dr Liz Patton ALDH enzymes are aldehyde detoxifying enzymes that are expressed in somatic and cancer stem cell lineages. We are using the zebrafish model system to study the role of ALDH enzymes in the melanocyte stem cell and in melanoma stem cell populations in cancer progression, regression and recurrence. The Aim of Email: [email protected] this PhD project is to identify the ALDH Telephone: 651 8536 enyzmes in melanoma stem cells, and use genetics and live-imaging to determine Location: MRC Human Genetics Unit their function and expression patterns in Centre of Affiliation: melanoma progression, and in response to MRC Human Genetics Unit drug treatment. Ultimately, we aim to target these subpopulations and determine the effect on disease outcome.

14 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Predicting disease risk from the genetic determinants of RNA velocity Primary Supervisor: Professor Chris Ponting This project applies cutting-edge experimental and computational approaches to discover causal links between DNA variants and disease risk. Using single cell RNA-seq, we will measure gene expression change in a time course following calcitriol-stimulation in cells derived from 100 individuals. In parallel, Email: [email protected] we will sequence pooled bulk samples Telephone: 651 8506 using both short (Illumina) and long Location: MRC Human Genetics Unit (Oxford Nanopore) read technologies. This Centre of Affiliation: should allow us to identify the genetic MRC Human Genetics Unit determinants of RNA velocity (the rate of change over time of RNA abundance or splicing). By imputing these velocities into large GWAS cohorts, we will identify genes whose rate of expression change causes altered disease risk.

Identifying rare large-effect variants in isolate populations Quantitative Trait Loci (QTL) This project will use computational approaches to identify rare variants affecting traits at the level of the phenotype and intermediate metabolism (e.g. proteome, metabolome, methylome) in isolate populations from Scotland and Croatia. Our long-term projects in these populations provide a wealth of health-related and other trait data. Using genome–wide SNP data with exome and Email: [email protected] whole-genome sequence data the project [email protected] will identify rare variants with large [email protected] effects that are at enhanced frequency in these populations. With the possibility of Location: MRC Human Genetics Unit/ functional studies of promising variants, Centre for Genomic & Experimental this project offers exceptional students the Medicine opportunity to develop both computational Centre of Affiliation: and laboratory skills at the cutting edge of MRC Human Genetics Unit genomics.

15 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Using synthetic biology to understand how the epigenome is programmed in cancer Primary Supervisor: Dr Duncan Sproul Epigenetic dysfunction has recently been recognised as a fundamental hallmark of cancer that results in altered DNA methylation levels. It is associated with the repression of tumour suppressor genes such as BRCA1 but we don’t understand how these potential epimutations occur. Email: [email protected] We have recently developed synthetic Telephone: 651 8628 epialleles, manufactured DNA with defined DNA methylation levels. This project will Location: CRUK Edinburgh Centre use these tools to understand how the Centre of Affiliation: cancer epigenome is programmed and CRUK Edinburgh Centre identify the factors responsible for DNA methylation alterations in cancers. The student will become an expert in cutting- edge laboratory techniques including CRISPR genome and epigenome editing and gain experience in bioinformatics.

Chromatin manipulation to enhance genome editing outcomes Primary Supervisor: Dr Andrew Wood Genome editing allows chromosomal DNA sequences to be modified within chromatin of living cells. This project will study how the local chromatin environment surrounding target sites for CRISPR/Cas9 nucleases and base editors contributes to genome editing mechanisms. The aim is to identify strategies to enhance the efficiency of genome editing by manipulating the Email: [email protected] chromatin environment. The candidate will Telephone: 651 8542 gain experience in DNA damage and repair, Location: MRC Human Genetics Unit working with state-of-the-art technologies Centre of Affiliation: for genome manipulation, chromatin MRC Human Genetics Unit biology and next generation sequencing.

16 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Training Timeline 2018 - 2019

COLLEGE/IGMM INDUCTIONS 2018 September Week Begining 10th September

ROTATION 1 17th September - 16th November

ROTATION 2 November 19th November - 25th January

ROTATION 3 January 2019 28th January - 22nd March

March CHOOSING / START PhD Start 25th March

GRADUATE RESEARCH & TRAINING HANDBOOK 2018 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Induction Week

Teaching Timetable 1 40,000 5.0 0 0

!"#$%&$%'& & 5.0 Number of promoters ()*+&,)-).%+/0-&1(2&,)-0+34) 546)-0+34)&7%44/-,8 & of promoters Proportion

& 1 9)-07)&:);")-&%-#&<$0:)&+0&%&7/$$/0-&4)04$)& 30,000 Matched expression Vagina

6%=)&6%#&+6)/.&,)-07)&:);")-<)#8&?0&/-+).4.)+&+6/:&7%::/=)&%70"-+&0@&Divergent expression Neurons

Diminished promoter activity Epididymis Ovary, adult Ovary, Testis, adult Testis, CD8+ T cells CD8+ T cells CD4+ T Uterus, adult Uterus, - cerebellum Thymus, fetal Thymus, CD19+ B cells CD19+ B

No promoter activity Housekeeping

/[email protected]%+/0->&0".&$%'&#)=)$04:&)@@/&%-#& adult oblongata, lla

Deleted promoter sequence adult Diencephalon, Hippocampus, adult Hippocampus, Ambiguous promoter alignment adult brain, Olfactory Naive r Astrocytes

& & & &

17 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Induction Week

Monday 10th September CMVM Graduate School Welcome Event - MSc students (including MSc by Research) - 10:00-11:00 Anatomy Lecture Theatre, Medical School, Teviot Place, EH8 9AG

CMVM Graduate School Welcome Event - Research students (PhD and pure research masters) - 11:00-12:00 Anatomy Lecture Theatre, Medical School, Teviot Place, EH8 9AG

General Welcome - 14:00-14:15 Nucleus Café, IGMM

Course specific inductions – PG Directors - 14:15-15:00 Nucleus Café, IGMM

Buddy session - 15:00-16:30 Nucleus Café, IGMM

Tuesday 11th September IT familiarisation - Dave Perry & team - 09:00-11:30 Medical Education Centre Computing Lab, Western General Hospital

Postgraduate Research students talk and service fair - 12:00-14:00 McEwan Hall, Edinburgh, EH8 9AG

Imaging Discussion - Harris Morrison - 15:00-15:30 East Seminar Room

Technical Services induction - Stewart Mckay - 16:00-16:30 East Seminar Room

FACS - Elizabeth Freyer - 16:30-17:00 East Seminar Room

18 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Wednesday 12th September Public Engagement Event - Dee Davison - 09:00-12:00 CRUK Edinburgh Centre - Seminar Room

Librarian - Ruth Jenkins - 14:00-14:30 CRUK Edinburgh Centre - Seminar Room

Good Practice in PhD Research - to be delivered by students - 14:30-16:30 CRUK Edinburgh Centre - Seminar Room

Thursday 13th September HGU Scientific Talks (for HGU 4 year programme students) - 09:15-09:30 - 4 Nick Gilbert - 09:30-09:45 - Malcolm Dunlop - 09:45-10:00 - Chris Ponting - 10:00-10:15 - Richard Meehan - 10:15-10:30 - David Fitzpatrick - 10:30-11:00 - break - 11:00-11:15 - Greg Kudla - 11:15-11:30 - Andrew Wood - 11:30-11:45 - Javier Caceres - 11:45-12:00 - Joe Marsh - 12:00-12:15 - Ian Adams - 12:30-13:30 - Lunch - 13:30-13:45 - Shipra Bhatia - 13:45-14:00 - Duncan Sproul - 14:00-14:15 - Laura Lettice - 14:15-14:30 - Pleasantine Mill - 14:30-14:45 - Dimitrios Papadopoulos - 15:00-15:30 - Break - 15:30-15:45 - Caroline Hayward CRUK Edinburgh Centre - Seminar Room, IGMM

19 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Friday 14th September Health & Safety induction - 09:30-10:30 East Seminar Room

IAD session - 11:00-11.30 East Seminar Room

Timetable

September 2018

Monday 17th Sequencing – Lee Murphy 10:00 – 11:00 East Seminar Room Prof. Luke Boulter 11:00 – 11:30 East Seminar Room Dimitrios Papadopoulos 11:30 – 12:00 East Seminar Room

Friday 21tst Q Pulse training – Rosie Russell 14:00 – 15:15 session 1 (incl. refreshments/cake) 15:30 – 16:45 session 2

Monday 24th Disease Mechanisms 1 – 09:00 – 12:00 East Seminar Room Toby Hurd Disease Mechanisms 2 – 14:00 – 17:00 East Seminar Room Alex Von Kreigsheim

October 2018

Thursday 4th Quantitative Skills 1 - ENSEMBL 09:00 – 17:00 MEC

Monday 8th Journal Club 1 04:00 – 17:00 East Seminar Room

Tuesday 9th or Quantitative Skills 2 – The Unix 09:30 – 17:00 MEC Wednesday 10th Shell –James Jarvis & IGMM IT - TBC

Thursday 11th Quantitative Skills 3 – 10:00 – 16:00 MEC Understanding Eddie – Steven Thorn / Dave Perry

Monday 15th Biomedical Genomics 1 – 14:00 – 17:00 MEC Colin Semple / Alison Meynert

20 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Tuesday 16th Biomedical Genomics 2 – 09:00 – 12:00 MEC Katie Nicoll Baines (Lead) & Neil Clark

Biomedical Genomics 3 – 14:00 – 17:00 MEC Martin Taylor

Monday 22nd Disease Mechanisms 3 – 10:00 – 12:00 East Seminar Room Andrew Jackson / David FitzPatrick Journal Club 2 14:00 – 17:00 East Seminar Room

November 2018

Monday 5th Quantitative Skills 4 – R for 09:00 – 17:00 MEC Biologists - Graeme Grimes - TBC

Tuesday 6th Quantitative Skills 5 – Plotting 09:00 – 17:00 MEC and programming with Python – Andy Turner

Thursday 15th Quantitative Skills 6 – UCSC 09:00 – 12:00 MEC Genome Browsers - Phillippe Gautier

Friday 16th Good Research practice and 09:00 – 12:00 East Seminar Room Data Management – Helen Nickerson / Kerry Millar Disease Mechanisms 4 – 14:00 – 17:00 East Seminar Room Genome Editing - Andrew Wood

Monday 19th Interacting with Industry – 09:00 – 12:00 East Seminar Room Andrea Taylor / Emma Mickley / Helen Nickerson Journal Club 3 14:00 – 17:00 East Seminar Room

Monday 26th Genome Regulation 1 – 14:00 – 17:00 East Seminar Room Richard Meehan

21 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

December 2018

Monday 3rd Biomedical Genomics 4 – 09:00 – 12:00 East Seminar Room Chris Haley Imaging – Laura Murphy 14:00 – 17:00 East Seminar Room

Thursday 6th Student Christmas Lectures 14:00 – 17:00 East Seminar Room

Monday 10th Biomedical Genomics 5 – 09:00 – 12:00 East Seminar Room QTL Team – Hayward / Vitart Biomedical Genomics 6 – 14:00 – 17:00 East Seminar Room Malcolm Dunlop / Maria Timfeeva

Monday 17th Translating your Research – 09:00 – 12:00 East Seminar Room Helen Nickerson / Andrea Taylor

Friday 21st Break for Christmas

January 2019

Monday 7th Interdisciplinary Interactions 09:00 – 12:00 East Seminar Room 1 – Davide Marenduzzo / Chris Brackley Journal Club 5 14:00 – 17:00 East Seminar Room

Monday 14th Interdisciplinary Interactions 2 09:00 – 12:00 East Seminar Room – Drug Discovery – Asier Unciti-Broceta Interdisciplinary Interactions 3 14:00 – 17:00 East Seminar Room – Drug Development – Neil Carragher

Monday 21st Genome Regulation 2 – 09:00 – 12:00 East Seminar Room Nick Gilbert Biomedical Genomics 7 – 14:00 – 17: 00 East Seminar Room Susan Farrington

Monday 28th Genome Regulation 3 – 09:00 – 12:00 East Seminar Room Javier Caceres Journal Club 6 14:00 – 17:00 East Seminar Room

22 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

February 2019

Monday 4th Genome Regulation 4 – 09:00 – 12:00 East Seminar Wendy Bickmore Room

Monday 11th The role of the Clinical Scientist 09:00 – 12:00 East Seminar in the NHS – Eddy Maher Room

Journal Club 7 14:00 – 17:00 East Seminar Room

Monday 18th Disease Mechanisms 5 – 09:00 – 12:00 East Seminar Ian Jackson Room Disease Mechanisms 6 – 14:00 – 17:00 East Seminar Pleasantine Mill Room

Monday 25th Case study – Toshiba 09:00 – 12:00 East Seminar visualisation – Ken Sutherland Room – TBC Journal Club 8 14:00 – 17:00 East Seminar Room

March 2019

Monday 4th Protein regulation in health and 09:00 – 12:00 East Seminar disease – Maria Christophorou Room Interdisciplinary Interactions 3 14:00 – 17:00 East Seminar – Molecular Probes – Room Marc Vendrell

Monday 18th Biomedical Data Science – 09:00 – 12:00 East Seminar Catalina Vallejos Room Journal Club 9 14:00 – 17:00 East Seminar Room

Monday 25th HGU 4 year students – Start PhD

23 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

MRC Institute of Genetics & Molecular Medicine

MRC Human Genetics Unit IG

B Pedestrian Access Western General Hospital Cancer Research UK Edinburgh MRC Centre Human Genetics Unit IG S IG C D IG S B B C S Centre for Genomic & Experimental MRC Institute of Genetics Medicine Bus Stop to & Molecular Medicine IG N City Centre IG E Pedestrian Disabled B Access Parking N

Bike Bus Stop from MAIN ENTRANCE Parking City Centre (Reception) Crewe Road South Porterfield Road

Pedestrian Access Western General Hospital Car Park Access

NHS Outpatients Building Computing Suite 1 Medical Education Centre, 3rd Floor S BUIDING

CREE ROAD SOUTH ORTERIED ROAD Centre for Genomics O & Molecular Medicine tr nnce I NORTH CORRIDOR Medical Education Centre MRC Institute OUTPATIENT (Top Floor, Outpatient Building) INK CORRIDOR of Genetics & G BUIDINGNG Molecular Medicine

Cancer Research UK C S Edinburgh Centre R WER G

24 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

MRC Institute of Genetics & Molecular Medicine Cancer Research UK Edinburgh Centre South Seminar Room S1.14 First Floor FirstIGMM Floor South IGMM South The IGMM South Building can be accessed via Link The IGMM South Building Bridge South from the 2nd S1.08 S1.06 S1.07 S1.01 can be accessed via Link Toilets and 3rd Floors of IGMM Bridge South from the 2nd S1.08 S1.06 S1.07 S1.01 Central. Toilets Fire and 3rd Floors of IGMM Lift exit Fire Central. exit Meeting S1.02 Fire S1.05 S1.04 Room Lift exit Fire Lift S1.03 exit Meeting S1.02 S1.05 S1.04 Room Lift S1.03 Meeting Room S1.16 Meeting Room S1.16 S1.10 S1.13

S1.10 S1.09 S1.13 Seminar Room Common Room S1.14 S1.15 S1.09 Seminar Room Common Room S1.11 S1.12 S1.14 S1.15 S1.11 S1.12

MRC Institute of Genetics & Molecular Medicine East Seminar Room E4.07

Link Bridge Link Fourth Floor North Bridge FourthIGMM FloorEast North IGMM East

Toilets Disabled Access Toilets Fire Lift exit Disabled Access E4.02 Fire Lift exit E4.02

E4.03

E4.03 Lift

Lift

E4.04

E4.01 E4.04

E4.01 E4.05

E4.05

Board Room E4.06 Board Room E4.06

Seminar Room SeminarE4.07 Room E4.07

Fire exit

Fire exit 25

GRADUATE RESEARCH & TRAINING HANDBOOK 2018 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Assessment Guidelines 1 40,000 5.0 0 0

!"#$%&$%'& & 5.0 Number of promoters ()*+&,)-).%+/0-&1(2&,)-0+34) 546)-0+34)&7%44/-,8 & of promoters Proportion

& 1 9)-07)&:);")-&%-#&<$0:)&+0&%&7/$$/0-&4)04$)& 30,000 Matched expression Vagina

6%=)&6%#&+6)/.&,)-07)&:);")-<)#8&?0&/-+).4.)+&+6/:&7%::/=)&%70"-+&0@&Divergent expression Neurons

Diminished promoter activity Epididymis Ovary, adult Ovary, Testis, adult Testis, CD8+ T cells CD8+ T cells CD4+ T Uterus, adult Uterus, - cerebellum Thymus, fetal Thymus, CD19+ B cells CD19+ B

No promoter activity Housekeeping

/[email protected]%+/0->&0".&$%'&#)=)$04:&)@@/&%-#& adult oblongata, lla

Deleted promoter sequence adult Diencephalon, Hippocampus, adult Hippocampus, Ambiguous promoter alignment adult brain, Olfactory Naive r Astrocytes

& & & &

27 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Assessment Guidelines

MSc by Research 3 year PhD 4 year PhD MD

10 week report � � � �

1st year report � � � �

2nd year report � �

3 year report �

10 week report: These reports should be fairly short, so Keep the report succinct and to the point. On the word limit is set to approximately completion, this report should be submitted 1000 words (this is just text so does not to the Graduate Research and Training team: include title, references, abstract or figure [email protected]. Following legends). Since this report is being written submission of your 10- week report, you at the beginning of your PhD, we are most will be given feedback in the form of an interested in what you plan to investigate email and/or meeting (depends on PhD over the next year. The report should programme). include: • Title, and the names of you and your First Year Review: supervisor. The next assessment stage is the first year • An abstract of less than 100 words. review. College guidelines are followed, as • Introduction that provides below. enoughbackground information for the This rigorous review will consist of three reader to understand the proposal and elements: that puts the scientific question(s) into context. • a written report from the student • A section that states the scientific • a meeting between the student and the question(s) that are being asked and the thesis committee aims of the project. • a written report by the interview panel • A short section on any progress made (incorporating supervisors’ reports) to date. • A section describing your proposal for Students’ written report: The written report the next year’s work. should adopt a logical format and be of a • Figures can be added in any section high standard. It should be typed and free to help describe the project or to show of typographical and grammatical errors. A any data that you have obtained in clear statement of the aims of the project the first few weeks of your project. should be included in addition to a brief Figure legends should provide succinct account of methods and their validation. description of the figure. Whilst it is recognised that at this stage • Reference List. students may not have substantial data, preliminary results should be documented

28 GRADUATE RESEARCH & TRAINING HANDBOOK 2018 and interpreted with a clear statement Feedback of intent as to immediate future studies The panel should make a formal (these might be expected to form the assessment of the student’s written basis of discussion at interview). The text report, performance at interview and should be referenced as for a scientific overall progress. The student should be paper and references listed at the end of informed of the panel’s view immediately the report. It is expected that the report thereafter. The panel will then write a report should be around 5000 words. It should normally within 1 week of the interview incorporate diagrams, figures and tables as summarising the assessment. Good and necessary. Preliminary drafts of the report very good progress should be credited; should be discussed with supervisors. It is any unsatisfactory aspects of performance often useful to ask your supervisor for an should be clearly defined with an attempt example report from a previous student. to identify underlying reasons for this. It The thesis committee meeting will consist should make clear recommendations as of the student, all the student’s supervisors to subsequent progress and action and be including a day to-day lab supervisor where signed by all members of the Panel. The appropriate, an external committee member student will have an opportunity to see the and a Chair. The external may be from the report, and be able to discuss strengths, same building if necessary, but should weaknesses and any issues of concern with be independent of the supervisors. The the Chairman of the panel in the absence of Chair should be someone with extensive his/her supervisor(s). The student should experience of PhD student supervision of also be able to add comments separately at least Senior Lecturer level. before signing the report. The student’s report should be available to Copies of the final signed report members of the thesis committee at least and the signed report of the thesis one week before the thesis committee committee must be sent to the meeting, allowing time for adequate Graduate Research and Training team: consideration of the reports. [email protected], who will then make copies available to the IGMM PGSC and will forward a copy to the Meeting Secretary of the College Postgraduate This is the student’s opportunity to Studies Committee. It should be stressed demonstrate his/her suitability to progress that an unsatisfactory report may be used as a PhD student. The meeting is normally as the basis for re-registering students for expected to include a short (10-15 minute) a different degree or even discontinuing presentation by the student introducing the studies (see outcomes). It is therefore project, describing methodology and any essential in the case of a student failing preliminary results and identifying future to achieve required standards at review, studies. Students are strongly encouraged that clear details of remedial action or to rehearse with supervisors before the the reasons for change in registration are interview. It should be expected that the documented. assessment panel will discuss specific points of content and organisation arising from the written report during the course of interview. The student should have an opportunity to initiate a dialogue and, if appropriate, raise matters of concern with the panel.

29 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Outcomes Postgraduate research annual review An initial recommendation is required as to Postgraduate students are required to whether student progress is satisfactory complete an annual review form regarding or is inadequate in one or more aspects. their studies, with their Postgraduate Satisfactory students will continue to be Supervisor or Lead Supervisor’s input. registered as PhD students. In the case of inadequate performances a further The form will be completed online via the recommendation from the review panel will MyEd Student Self Service channel, and be needed in terms of whether the student students should receive an automated is: email to let them know that their review is active. Students should upload all relevant • re-assessed at the end of a period of documents and reports in the review. study not exceeding 18 months of initial registration The online student portal (EUCLID) can also be used to record other important • re-registered for a different degree milestones in your training in Edinburgh or change in period of study or and your supervisor may log individual discontinued meetings with you on this system. It would be expected that students should be totally unsatisfactory or severely deficient in several areas of their study for Regulations and guidance options (b) and (c) to be recommended The Postgraduate Assessment Regulations without the opportunity for reassessment. for Research Degrees require that all Postgraduate Research students (with exception of MSc (R) students) Second / Third Year Review have an annual review – and give the There is a second year thesis committee recommendations that are available meeting for which the student is expected following each annual review. to produce a second year report. This need not be as long as the first year report Guidance and instructions can be found but should contain a clear indication of on the Student Systems website, which achievable plans for the final year and provides instructions on how students are an outline plan for the thesis. The signed notified of their requirement to complete report of the thesis committee and the the form online and how the annual review College official report form should be sent form is processed within the University: to the Graduate Convenor for signing as for https://edin.ac/2OVdkDJ first year reviews (above). For four year and continuing students there will be continuing For futher information also check the reviews every year until submission. CMVM postgraduate Wiki http://edin.ac/2crLMTx Final Year Students should prepare to give a seminar to IGMM staff. Students should plan to talk for approximately 20 minutes (5 min Q&A session) and should include a summary of their project to date.

30 GRADUATE RESEARCH & TRAINING HANDBOOK 2018 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

General information • Social media • Seminars • POGS 1 40,000 5.0 0 0

!"#$%&$%'& & 5.0 Number of promoters ()*+&,)-).%+/0-&1(2&,)-0+34) 546)-0+34)&7%44/-,8 & of promoters Proportion

& 1 9)-07)&:);")-&%-#&<$0:)&+0&%&7/$$/0-&4)04$)& 30,000 Matched expression Vagina

6%=)&6%#&+6)/.&,)-07)&:);")-<)#8&?0&/-+).4.)+&+6/:&7%::/=)&%70"-+&0@&Divergent expression Neurons

Diminished promoter activity Epididymis Ovary, adult Ovary, Testis, adult Testis, CD8+ T cells CD8+ T cells CD4+ T Uterus, adult Uterus, - cerebellum Thymus, fetal Thymus, CD19+ B cells CD19+ B

No promoter activity Housekeeping

/[email protected]%+/0->&0".&$%'&#)=)$04:&)@@/&%-#& adult oblongata, lla

Deleted promoter sequence adult Diencephalon, Hippocampus, adult Hippocampus, Ambiguous promoter alignment adult brain, Olfactory Naive r Astrocytes

& & & &

31 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Advice on using social media Be mindful of your responsibilities networks & confidentiality of • Data Protection legislation - do not information disclose other people’s personal information without prior permission. Facebook, Twitter and other social media networks have changed the way we interact • Be aware that any posts you make in with each other and like them or not, they a professional capacity (even private are a part of our society. posts) are subject to data protection and freedom of information and may need to As some of you will carry out research be disclosed. where animals are involved, please ensure • University policies apply: Students must that you follow procedures to ensure our not post materials about their work work continues to be ethical, credible and and locations if doing so would carry professional. Sharing images/discussions a risk to themselves and especially to of animal work outside of the context of others, including the University as an academic discourse is not appropriate. organisation (see section 5 University This not only applies to posts on social policies). network sites but to informal discussions in the pub or on the bus. www.ed.ac.uk/website-programme/ training-support/guidelines/social-media Please remember you must not post the following information: • Scientific research information, analysis, results or any other information and /or images relating to your work. • Location details of research buildings where animal work is carried out.

32 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Forthcoming seminars

September 2018

Thursday 6th September: A receptor-selective Jag1 mutation induces an Alagille syndrome phenotype in mice: New models and tools to study cholangiopathies

Dr Emma Andersson, Karolinska Institute Host: Dr Luke Boulter

Thursday 13th September: Mechanisms of membrane protein biogenesis

Dr Ramunajan Hegde, MRC Laboratory of Molecular Biology Host: Dr Andy Finch

Thursday 20th September: Title to be announced

Professor Nada Jabado, McGill University Host: Professor Wendy Bickmore

October 2018

Thursday 4th October: Title to be announced

Professor Caroline Dean, John Innes Centre, University of York Host: Professor Andrew Jackson

Tuesday 9th October: Capitalizing on Psychiatric Genetics: Pathways for Translating Genetic Findings into the Clinic

Professor David Glahn, Yale University Host: Professor Pippa Thomson

Thursday 11th October: Title to be announced

Dr Atlanta Cook, Wellcome Trust Centre for Cell Biology, University of Edinburgh Host: Professor Javier Caceres

33 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Tuesday 16th October: Title to be announced

Professor Jef Boeke, Institute for Systems Genetics, New York University Host: Professor Wendy Bickmore

Thursday 25th October: Professor Massimo Palmarini, MRC Centre for Virus Research, University of Glasgow

Host: Professor Nick Hastie

November 2018

Thursday 8th November: Title to be announced

Professor Robert Russell, University of Heidelberg Host: Dr Joe Marsh

Tuesday 15th November: Title to be announced

Dr John Marioni, EBI, Hinxton Host: Professor Chris Ponting

Thursday 22nd November: Title to be announced

Professor Moira Whyte, Centre for Inflammation Research, University of Edinburgh Host: Professor Andrew Jackson

Thursday 29th November: Title to be announced

Dr Adam Butterworth, University of Cambridge Host: Professor Jim Wilson

34 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

January 2019

Thursday 17th January: Title to be announced

Professor Jussi Taipale, University of Cambridge Host: Professor Colin Semple

Thursday 24th January: Mental health and circadian rhythms in the UK Biobank cohort

Professor Daniel Smith, University of Glasgow Host: Professor David Porteous

Thursday 31st January: Title to be announced

Professor Didier Trono, Ecole Polytechnique Federale de Lausanne Host: Professor Martin Taylor

February 2019

Thursday 7th February: Title to be announced

Professor Paul Mischel, Ludwig Cancer Research, UC San Diego Host: Juliet Luft

Thursday 21st February: Cell type specific translation profiling in mouse models of autism

Dr Emily Osterweil, Centre for Discovery Brain Sciences, University of Edinburgh Host: Dr Tamir Chandra

Thursday 28th February: Title to be announced

Professor Steve Jackson, University of Cambridge Host: Professor Neil Carragher

35 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

March 2019

Thursday 7th March: Title to be announced

Professor Paul Lehner, Cambridge Institute of Medical Research Host: Professor Yanick Crow

Thursday 14th March: Title to be announced

Dr Gaelle Legube, CBI Toulouse Host: Dr Martin Reijns

Thursday 21st March: Coping with a stressful start in life

Dr Alex Gould, Francis Crick Institute Host: Dr Andy Finch

Thursday 28th March: Organising the nucleus during tissue differentiation: silencing repeats and turning on genes

Professor Susan Gasser, Friedrich Miescher Institute Host: Professor Wendy Bickmore

April 2019

Thursday 25th April: Mechanistic insights into the mRNA poly(A) tail machinery

Dr Lori Passmore, MRC Laboratory of Molecular Biology Host: Professor Javier Caceres

May 2019

Thursday 2nd May: Title to be announced

Professor Lalita Ramakrishnan, University of Cambridge Host: Kathy Evans

Tuesday 28th May: Title to be announced

Professor Ibrahim Cisse, MIT Host: Professor Wendy Bickmore

36 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

June 2019

Thursday 27th June: Title to be announced

Professor Nicolas Manel, Institut Curie, Paris Host: Professor Yanick Crow

July 2019

Thursday 4th July: Title to be announced

Dr Gaia Pigino, Max Panck Institute of Molecular Cell Biology and Genetics Host: Dr Pleasantine Mill

37 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

POGS The post graduate society (POGS) is a student run initiative who organise events for students in order to enrich their postgraduate experience. The aim of the society is to encourage collaborations between postgraduate students from the three constituent buildings (CGEM, CRUK EC and MRC HGU) that make up the recently formed Institute of Genetics and Molecular Medicine (IGMM). Each year we organise a student-led symposium for students within the institute which usually consists of a day of student talks and a poster session, followed by a key note speech by a representative of the host university to give a flavour of the high quality research of that institution. Furthermore, we organise monthly events that consist of invited speakers with successful careers after having completed their own PhDs in order to give the students ideas of career pathways, either in academia, industry or elsewhere after their PhD. Finally, PhD life is not just about working hard and doing research but it is also about being sociable and interactive. That is why POGS also organise annual social events, such as the very popular Pub Quiz at the beginning of the academic year and a Ceilidh evening on Burn’s night. Overall, these events help to unify the students across the institute and provide a great opportunity to discover more about the research of their peers, to prepare them for a future successful and fulfilling career, while at the same time enjoying their PhD life. We look forward to meeting you!

Best wishes, POGS

38 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Postgraduate transferable skills Communication and Impact programme - Institute of Academic • Designing Effective Slides Development (IAD) • Public Speaking, Networking and www.ed.ac.uk/institute-academic- Engaging development • Poster Production The acquisition and development of • Presenting made Easy – Presentation generic research and transferable skills Techniques is an important part of postgraduate • Presenting Made Easy – Delivering training. Courses covering a wide Presentations range if these skills are available to postgraduate research students in the • Presenting your Poster Pitch Graduate School of Medicine & Veterinary • Research, Researchers and the Media, Medicine through the transferable skills a hands on approach to communicating programme. This programme concentrates your research on the professional development of postgraduates, providing courses directly Writing and Publishing linked to postgraduate study (e.g. Thesis • Academic writing peer review Workshop, Good Practice and Academic Paper Writing) and future careers (e.g. • Beating Writers Block Successful Career Strategies for PhD • Developing a Writing and Publishing Students, Local GRADschools). The Strategy in the Internet Age programme also provides information • Effective Writing: Grammar on other training opportunities for postgraduates. • How to be your own best editor • Is my writing ‘Academic’ Enough? Courses are free of charge to postgraduate students in the College of Medicine and • Just Write Veterinary Medicine. The programme has • Proof Reading been designed to be as flexible as possible • Text, Coherence, Structure and so that each student can tailor the content Argumentation and timing of the programme to their own requirements. Most courses are run several • The Writing Process: Getting Started times each year and last for between half a • Writing a Literature Review day and a day. • Writing Abstracts • Writing Clinic Workshops for postgraduate • Writing for Publication researchers by theme • Writing Retreat The following workshops make up the • Writing Well: Language and Style core programme open to all postgraduate researchers, and are displayed by theme. • Academic Writer – Creative Writer • An Introduction to Copyright and Publishing Research Planning and Management • This is what I do… and this is why it • Managing your Research Project matters • Practical Project Management for Research Students Digital and Library Skills • Viva Survivor • Beginners Guide to Imaging • Innovation School • Searching Literature and Managing • Managing your Research Data Bibliographies

39 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

• Managing a Bibliography in Endnote Online learning • Finding Academic Literature PhD student online training courses (topics • Social media for impact: strategy, include statistics; imaging; academic connecting & metrics writing; and data management). Some you can do any time, and others run at specific times of the year. Statistics • Statistical Consultancy 1:1 Session • Statistics courses • Introductory Statistics for Life Scientists • Imaging for scientists • Academic writing Personal Effectiveness • Research Ethics and Integrity - • Conference and Events Organising an introduction • Creating Effective Collaboration • Data management training • Ready to research

• Creative Problem Solving for 1

Researchers 40,000

• Imposter Syndrome: Why Successful The Edinburgh Local GRADschool is 5.0 people often feel like frauds open to all PhD students in their final or 0 • Ease the Load – Feel good about your penultimate year of study: 0 busy life !"#$%&$%'& www.ed.ac.uk/institute-academic- & 5.0 Number of promoters • How to be an Effective Researcher development/postgraduate/doctoral/ ()*+&,)-).%+/0-&1(2&,)-0+34) 546)-0+34)&7%44/-,8 & of promoters Proportion

& 1 • Mapping your Mind courses/gradschool 30,000 9)-07)&:);")-&%-#&<$0:)&+0&%&7/$$/0-&4)04$)& Matched expression Vagina

6%=)&6%#&+6)/.&,)-07)&:);")-<)#8&?0&/-+).4.)+&+6/:&7%::/=)&%70"-+&0@&Divergent expression Neurons

• Seven Secrets of a Highly Successful Diminished promoter activity Epididymis Ovary, adult Ovary, Testis, adult Testis, CD8+ T cells CD8+ T cells CD4+ T Uterus, adult Uterus, - cerebellum Thymus, fetal Thymus, CD19+ B cells CD19+ B

No promoter activity Housekeeping

/[email protected]%+/0->&0".&$%'&#)=)$04:&)@@/

Research Student adult Cerebellum, adult cord, Spinal Bro onventional T cells onventional )@@)<+:&0@&,)-)+/<&=%./%+/0-8&A)&:3-+6):/B)&$%.,)&<0$$)<+/0-:&0@&7"+%+)#&,)-):>&%-#& adult oblongata, lla

Deleted promoter sequence adult Diencephalon, Hippocampus, adult Hippocampus, Ambiguous promoter alignment adult brain, Olfactory Naive r Astrocytes • Simply Assertive #)=)$04&6/,65+6.0",64"+&%::%3:&+0&7)%:".)&+6)&)@@)<+:&0@&7"+%+/0-:&0-& Medu Naive c 70$)<"$%.&%-#&<)$$"$%.&46)-0+34):>&:"<6&%:&4.0+)/-&%-#&1(2&%'"-#%-<)>Astrocytes &4.0+)/- 5 • Speed Reading 1(2&/-+).%<+/0-:>&%-#&@/+-)::&CD"<6+%&)+&%$8>&E&FGHIJ8&A)&":)&%&=%./)+3&0@& )*4)./7)-+%$&+)<6-/;"):>&/-<$"#/-,&,)-)&:3-+6):/:>&-)*+ 5,)-).%+/0-&:);")-& • Teambuilding and Leadership 7/<.0%..%3:>&%-#&%"+07%+)#&7/<.0:<043>&%-#&)*4)./7)-+%$&:3:+)7:&/-<$"#/-,& Fundamentals '%<+)./%>&3)%:+>&%-#&7%77%$/%-&<)$$:8& & • Think Strategically Respond Rapidly • Managing your Work, your Goals and Yourself

Public Engagement • Communications Toolkit for a Public Audience • Dialogue: Public Engagement Beyond Public Lectures! • Storytelling Techniques for Effective Communication • Voice and Presentation Skills Workshop & & • How to Design a Public Engagement & Process & • Facilitation skills for public engagement • An Introduction to Public Engagement

40 GRADUATE RESEARCH & TRAINING HANDBOOK 2018 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Useful Links

Advice Place 1 40,000 5.0 0 0

!"#$%&$%'& & 5.0 Number of promoters ()*+&,)-).%+/0-&1(2&,)-0+34) 546)-0+34)&7%44/-,8 & of promoters Proportion

& 1 9)-07)&:);")-&%-#&<$0:)&+0&%&7/$$/0-&4)04$)& 30,000 Matched expression Vagina

6%=)&6%#&+6)/.&,)-07)&:);")-<)#8&?0&/-+).4.)+&+6/:&7%::/=)&%70"-+&0@&Divergent expression Neurons

Diminished promoter activity Epididymis Ovary, adult Ovary, Testis, adult Testis, CD8+ T cells CD8+ T cells CD4+ T Uterus, adult Uterus, - cerebellum Thymus, fetal Thymus, CD19+ B cells CD19+ B

No promoter activity Housekeeping

/[email protected]%+/0->&0".&$%'&#)=)$04:&)@@/&%-#& adult oblongata, lla

Deleted promoter sequence adult Diencephalon, Hippocampus, adult Hippocampus, Ambiguous promoter alignment adult brain, Olfactory Naive r Astrocytes

& & & &

41 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Useful links A free online alternative to Endnote and Reference Manager www.zotero.org/ General College PG Office contacts (note also that many journals have free www.ed.ac.uk/schools-departments/ apps for browsing abstracts). medicine-vet-medicine/postgraduate/ contacts Research Ethics College PG research wiki (includes PG General handbook, software available to students www.pnas.org/content/86/23/9053.full.pdf etc.) http://edin.ac/2crLMTx http://www.niehs.nih.gov/research/ resources/bioethics/whatis.cfm Code of Practice www.docs.sasg.ed.ac.uk/ Image manipulation AcademicServices/Codes/ www.jci.org/articles/view/21717/pdf CoPSupervisorsResearchStudents.pdf www.cell.com/abstract/S0092- Assessment regulations 8674(06)00676-3 www.docs.sasg.ed.ac.uk/ www.nature.com/ncb/journal/v6/n4/full/ AcademicServices/Regulations/PGR_ ncb0404-275.html AssessmentRegulations.PDF http://jcb.rupress.org/content/166/1/11.full Transferable skills training and support www.ed.ac.uk/schools-departments/ institute-academic-development/ Writing papers, giving talks postgraduate/doctoral Advice on writing papers www.nature.com/nature/journal/v467/ Handbook of Biological Statistics n7317/full/nj7317-873a.html http://udel.edu/~mcdonald/statintro.html How to give a good talk Ten simple rules collection- lots of www.cell.com/molecular-cellfulltext/ extremely useful advice here in an easily S1097-2765(09)00742-4?large_figure=true digestible form, covering everything from being a graduate student to getting grants How to give a bad talk www.ploscollections.org/article/browse/ www.sciencedirect.com/science/article/ issue/info%3Adoi%2F10.1371%2Fissue. pii/S0960982299802929 pcol.v03.i01 Useful advice ranging from lab techniques to giving talks and posters Searching the literature/ http://bitesizebio.com bibliographic management The Advice Place, Potterrow Reception, A tool for running daily searches EUSA5/2, Bristo Square, Edinburgh EH8 http://pubcrawler.gen.tcd.ie/ 9AJ Information about literature searching and Tel: 0131 650 2656 www.eusa.ed.ac.uk/ using Endnote adviceplace/adviceguides www.mmc.med.ed.ac.uk/useful-info/ literature Advice Guides and Resources www.mmc.med.ed.ac.uk/useful-info/ endnote/ Here you can read all of our advice guides. If you would like them in an alternative format, please contact us and we will do our utmost to accommodate this.

42 GRADUATE RESEARCH & TRAINING HANDBOOK 2018

Advice guides and resources

Health and C Card Drugs and Alcohol General Health Welbeing

Mental Health Mental Health Sexual Health of a Friend Academic

Other Sources Special Plagiarism and Appeals of Support Circumstances Misconduct

Personal Tutors Peer Proofreading FAQs Read.Write.Cite

Looking for During your Tenacy Moving Out Accomodation Accomodation

Community Money and Student Funding Running Out Funding of Money

Council Tax Money Management Consumer Issues Employment and Benefits

Harassment and Harrassment Complaints Contact and Complaints About Us

Students with International Disabled Students LGBT+ Students Children or Caring Students Responsibilities

Part-time Students EU Students Graduating Students Safety and Crime

Reporting a Crime Safety Advice

43 GRADUATE RESEARCH & TRAINING HANDBOOK 2018