Richard J. Acton
POB: Scotland – UK
1 Research Experience
1.1 Current - The Epigenomics of Human Aging (PhD)
Supervisor Dr. Chris Bell C.G.Bell@soton.ac.uk
1.2 MSc Research Project – circRNAs in daf-2 and daf-2/16 mutant C. elegans Neurons.
This project sought to identify circRNA product with differential expression between the neurons of C. elegans with normal and extended lifespan mutants. I analysed RNA-seq data, performing QC with FASTQC and read trimming with Trimmomatic. I performed alignments with bowtie2 and bwa. Followed by circRNA discovery with two dedicated circRNA detection tools. I made an index of circRNA discovery tools. The tools I used in this analysis were find_circ and CIRI. I used the DESeq2 tool for differential expression analysis. We found very low levels of agreement in circRNA detection, even between biological replicates. I was not able to find differential expression in any of the circRNAs detected between the long-lived and normal lifespan worms.
Supervisor: Irilenia Nobeli email@example.com
1.3 4th year project – Working on the B methylase in the N6-methyladensine RNA modification system in Arabidopsis.
Gene knock out in Arabidopsis using CRISPR, involving designing guide RNAs and producing transfection vectors using PCR and Golden Gate cloning. Using agrobacterial floral dip transfection to produce Arabidopsis transformants. Screening Arabidopsis plants for antibiotic resistance markers. Extracting RNA, using reverse transcription PCR to assess expression levels of cas9 in putative transformant plants and using capillary electrophoresis to screen for small mutations.
Supervisor: Dr. Rupert Fray firstname.lastname@example.org
1.4 Summer Studentship 2014 (BBSRC REP [Research experience placement]) – Working on Bd1483 a Bdellovibrio bacteriovorus protein.
Restriction cloning to attempt to create bacterial two hybrid vectors. Attempted to create vectors to produce genomic deletion and GFP tagged Bd1483 mutants by recombination using Gibson assembly cloning. Bd1483 expression analysis using reverse transcription PCR on existing RNA samples. Basic bioinformatic and phylogenetic analysis of Bd1483 [Sockett Lab]. Produced and purified by nickel affinity chromatography quantities of His Tagged Bd1483 protein from an existing construct. Bd1483 was identified by molecular weight using Denaturing SDS-PAGE. Screened for metal cation binding using native PAGE. Prepared crystal trays for Bd1483, successfully producing X-ray diffracting crystals. Produced and attempted to purify DivIVA protein in solution containing surfactants [Lovering Lab].
Supervisors: Professor Liz Sockett email@example.com, Dr. Andy Lovering firstname.lastname@example.org
1.5 3rd year project – Interactions of PilZ proteins of the Cyclic-dimeric-3’→5’-Guanosine Mono Phosphate (c-di-GMP) signalling system in Bdellovibrio bacteriovorus.
Restriction cloning to produce Bacterial two hybrid vectors and Screening for interactions with other Bdellovibrio Proteins. Involving preparative and analytic DNA agarose gel electrophoresis and the Miller Assay to assess β-galactosidase activity as semi-quantitative indicator of the extent of interaction.
Supervisor: Professor Liz Sockett email@example.com
1.6 Summer research placement – Identifying and expressing possible chlamydial effector protein genes in Human cell lines.
Examining a set of previously identified chlamydial effector proteins I noted that one contained a nuclear localisation sequence, and considered that searching for chlamydial genes with an NLS might be an effective method of identifying a sub-set of chlamydial effector proteins. Produced mammalian expression vectors containing fluorescently tagged possible chlamydial effector proteins using SLICE cloning; a recombination based cloning technique, this process involved custom primer design. Used high speed lithium borate DNA agarose gel electrophoresis. Transfected HeLa and U20s derived cell lines with the resulting vectors using lipotransfection. examined the subcellular localisation of proteins using wide-field fluorescence microscopy.
Supervisor: Dr. Alan Huett Alan.Huett@nottingham.ac.uk
2 Programming Skills
3.1 Birkbeck University of London (2015-16)
MSc in Bioinformatics and Systems biology (Distinction). I undertook this degree to learn to program (a long-standing intention) and to extend my knowledge of statistics. Biology is increasingly a field to which data science is integral and in my experience the best wet work has a well-informed background in dry work and the best experimental design comes out a solid understanding of statistics.
3.2 Undergraduate (University of Nottingham 2011-15)
1st Class MSci with Honours in Biochemistry and Genetics from the University of Nottingham. (See 5.1 for detailed breakdown by module)
3.3 A-levels (The Sixth Form College Farnborough 2009-11)
|Biology (A2)||Chemistry (A2)||Physics (A2)||Maths (A2)||Economics (AS)||General Studies (A2)|
(See 5.2 for results by module)
3.4 GCSEs (Frensham Heights School 2005-2009)
|Double Science||Maths||ICT||French||Photography||Design Tech(RM)||Art and Design 3D||Geography||English||English Literature|
(Photography taken as an extra-curricular in 2007, French taken 1 year early in 2008)
3.5 Early life education
- École Internationale de Genève (La Grande Boissière campus), from 2003-2005 (Switzerland, Geneva)
- Cheddington Combined School 2000-2003 (UK)
- Osgood Elementary 1999 – 2000 (USA, Massachusetts)
- Cohasset Montessori 1997-1999 (USA, Massachusetts)
- Bagshot Montessori 1996-1997 (UK)
4 Activities outside of core studies
4.1 During time at Birkbeck
Elected President of the National Federation of Atheist, Humanist and Secular Student Societies (AHS) in July 2015 and served a 1 year term. This role involved among other things working as a part of a 3 person executive team and managing a team of volunteers. The planning and execution of national events with several 10s to several hundred attendees and reporting our activities to our board.
4.2 During time at Nottingham
- Website officer of the then Secular society for 1 year, President of the University of Nottingham Agnostics, Secularists and Humanists Society (UNASH) for 2 years. During my tenure the society or its members won 4 national awards including one for raising the highest total in the country (£1200) during our charity week, and one for organising the best regional convention.
- Course representative providing feedback on the experience of students to staff for 3 years, during which time I won a silver award from the education network for my contribution.
4.3 During A-levels
- Elected president of the Student Association (an NUS affiliated Student’s union) at the Sixth Form College Farnborough an institution with >3000 students. During which time I lead a 12 person team who, among other things; started a network of Subject Reps to feed back to staff on student experience, broke the record for the most money raised for charity in our Raising and Giving Week, organised events with budgets of up to £30,000 and dramatically reduced the college paper use by having all printers set to duplex by default. During this time I also sat on the college’s board of governors, sharing responsibility for the oversight of the college’s major strategic decisions and ~£17M budget.
- Winner of an award for outstanding contribution to college life.
- Recipient of the Farnborough advanced level extend project award (analogous to the Extended Project Qualification: EPQ) for a project entitled: As advances in genomics and recombinant DNA technology become available what aspects of the human genome will be changed and when will we begin to effect these changes?
- Participant in Computer Games Creation classes; creating simple games in basic.
- Member of the Farnborough Debating Union, during which time I represented the college in a competition.
- Royal Society of Chemistry - 43rd International Chemistry Olympiad 2011, 1st round, Bronze
- Emergency First Aider at work.
4.4 Academic Society memberships
- Member of the Biochemical Society
- Member of the British society for research on ageing
5.1 Birkbeck MSc Bioinformatics with Systems Biology - Results by Module
|CRYS008H7||Sequence Analysis and Genomics||15||70|
|CRYS015D7||Project MSc Bioinformatics with Systems Biology||60||71|
5.2 Nottingham MSci Biochemistry and Genetics - Results by Module
|4th Year (2014-15), 40% weighting|
|C14702||Cutting Edge Research Technologies and Ideas in Molecular Biology||10||Autumn||79|
|C14703||Advanced Experimental Design and Analysis||10||Autumn||73|
|C14705||Research Presentation Skills||20||Full Year||64|
|4th year credit weighted average||76|
|3rd Year (2013-14), 40% weighting|
|C73510||Research Project BG||20||Autumn||74|
|C13698||Molecular Evolution: Constructing the Tree of Life||10||Spring||62|
|C43629||Ageing, Sex and DNA Repair||10||Spring||60|
|C73611||Research Project BG||20||Spring||74|
|C73ADB||Advanced Biochemistry||20||Full Year||59|
|C73B47||Biochemistry of Disease||10||Full Year||57|
|C73Y03||Data Analysis||10||Full Year||73|
|3rd year credit weighted average||67|
|2nd Year (2012-13), 20% weighting|
|C12341||Molecular and Developmental Neurobiology||10||Autumn||73|
|C12364||Genetics Dissertation II||10||Autumn||69|
|C12365||Medical Molecular Genetics||10||Autumn||76|
|C42324||Genes, Genomes and Chromosomes||10||Autumn||68|
|C72304||Laboratory Analysis of Proteins & Enzymes||10||Autumn||77|
|C72340||Proteins: Structure and Function||10||Autumn||70|
|C42418||Bacterial Genes and Development||10||Spring||66|
|C72445||Lipid Metabolism and Oxidative Phosphorylation||10||Spring||60|
|C72ISM||Introductory Signals and Metabolic Regulation||10||Spring||71|
|C72PAG||Principles and Analysis of Gene Function||20||Full Year||70|
|2nd year credit weighted average||70|
|1st Year (2011-12), 0% weighting|
|C11111||Experimental Design and Analysis 1||10||Autumn||76|
|C11120||Genetics, Ecology and Evolution||10||Autumn||78|
|C71101||Cell Structure and Metabolism (L)||10||Autumn||79|
|C71102||Cell Structure and Metabolism (P)||10||Autumn||94|
|F11MSB||Molecular Structure and Bonding||10||Autumn||75|
|C11212||Introductory Human Physiology and Pharmacology 2||10||Spring||75|
|C41202||Genes and Cellular Control I (L)||10||Spring||96|
|C41204||Genes and Cellular Control I (P)||10||Spring||76|
|C71205||Fundamentals of Biochemistry||10||Spring||69|
|F11OMC||Reactivity of Organic Molecules and Coordination Chemistry||10||Spring||92|
|C11118||Biochemistry and Genetics Tutorial and Study Skills Module||10||Full Year||69|
|1st year credit weighted average||80|
|Weighted degree average||71|
5.3 A-level Results By module
|Exam Session||Module Code||Module Description||Exam Board||UMS||Max||Grade|
|Jan-10||107101||BY1: BASIC BIOCHEMISTRY AND ORGANISATION||WJEC||110||120||A|
|Jun-10||107201||BY2: BIODIVERSITY AND PHYSIOLOGY OF BODY SYSTEMS||WJEC||120||120||A|
|Jun-10||107301||BY3: PRACTICAL ASSESSMENT||WJEC||36||60||C|
|Jan-11||107401||BY4: METABOLISM, MICROBIOLOGY AND HOMEOSTASIS||WJEC||110||120||A|
|Jun-11||107501||BY5: ENVIRONMENT, GENETICS AND EVOLUTION||WJEC||96||120||A|
|Jun-11||107601||BY6: PRACTICAL ASSESSMENT||WJEC||39||60||C|
|Subject Score and Grade||511||600||A|
|Jan-10||F321||ATOMS, BONDS AND GROUPS||OCR||78||90||A|
|Jun-10||F322||CHAINS, ENERGY AND RESOURCES||OCR||122||150||A|
|Jun-10||F323||PRACTICAL SKILLS IN CHEMISTRY 1||OCR||54||60||A|
|Jan-11||F325||EQUILIBRIA, ENERGETICS AND ELEMENTS||OCR||114||150||B|
|Jun-11||F324||RINGS, POLYMERS AND ANALYSIS||OCR||61||90||C|
|Jun-11||F326||PRACTICAL SKILLS IN CHEMISTRY 2||OCR||51||60||A|
|Subject Score and Grade||480||600||A|
|Jan-10||F581||MARKETS IN ACTION||OCR||92||100||A|
|Jun-10||F582||THE NATIONAL AND INTERNATIONAL ECONOMY||OCR||76||100||B|
|Subject Score and Grade||168||200||A|
|Jan-10||GENA1||CULTURE AND SOCIETY||AQA||78||100||B|
|Jun-10||GENA2||SCIENCE AND SOCIETY||AQA||73||100||B|
|Jan-11||GENA4||SCIENCE AND SOCIETY||AQA||72||100||B|
|Jun-11||GENA3||CULTURE AND SOCIETY||AQA||74||100||B|
|Subject Score and Grade||297||400||B|
|Jan-10||MPC1||PURE CORE 1||AQA||86||100||A|
|Jun-10||MPC2||PURE CORE 2||AQA||81||100||A|
|Jan-11||MPC3||PURE CORE 3||AQA||86||100||A|
|Jun-11||MPC4||PURE CORE 4||AQA||72||100||B|
|Subject Score and Grade||477||600||B|
|Jan-10||G491||PHYSICS IN ACTION||OCR||70||90||B|
|Jun-10||G492||UNDERSTANDING PROCESSES, EXPERIMENTATION AND DATA HANDLING||OCR||139||150||A|
|Jun-10||G493||PHYSICS IN PRACTICE||OCR||58||60||A|
|Jan-11||G494||RISE AND FALL OF THE CLOCKWORK UNIVERSE||OCR||54||90||C|
|Jun-11||G495||FIELD PARTICLE PICTURES||OCR||137||150||A|
|Jun-11||G496||ADVANCES IN PHYSICS||OCR||58||60||A|
|Subject Score and Grade||516||600||A|