Richard J. Acton

Email: RichardJActon@gmail.com

DOB: 30/10/1992

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 i.nobeli@mail.cryst.bbk.ac.uk

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 rupert.fray@nottingham.ac.uk

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 liz.sockett@nottingham.ac.uk, Dr. Andy Lovering a.lovering@bham.ac.uk

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 liz.sockett@nottingham.ac.uk

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

I mostly use linux operating systems and am familiar with the Bourne shell, basic bash scripting and the composing of command line tools. I learned to code in perl 5 a language in which I am proficient, I also know some perl 6 a relatively new language with excellent support for parallelism, asynchrony and concurrency. I have experience using high performance computing clusters. I now spend most of my time using R for data analysis. I make extensive use of the ‘tidyverse’ libraries and am proficient at data manipulation with dplyr and static plotting with ggplot2, I have some familiarity with making dynamic plots using shiny. I do a lot of my work using Rnotebooks in R markdown with some use of LaTeX. I also have a passing familiarity with python along with its Matplotlib library as well as tools such as jupyter notebooks. In the area of web based tools I have basic javascript, PHP, HTML and CSS skills and well as knowledge of creating a querying databases with MySQL. I have experience of the ‘full stack’ of web services from front end to setting up Linux servers in very small scale contexts but have limited security and user management knowledge. I also have a passing familiarity with docker for the creation of fully reproducible data analyses. I have made some small contributions to R libraries on github and habitually use git for version management.

3 Education

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)
A A A B A B

(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
(A*)A* A* A* A* A* A* A* A* A B

(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 Appendices

5.1 Birkbeck MSc Bioinformatics with Systems Biology - Results by Module

Code Title Credit (180/yr) Mark/%
CRYS001H7 BioComputing I 15 88
CRYS002H7 Molecular Structure 15 80
CRYS003H7 Statistics 15 85
CRYS004H7 Data Management 15 83
CRYS005H7 Structural Bioinformatics 15 71
CRYS006H7 BioComputing II 15 80
CRYS007H7 Systems Biology 15 93
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

Code Title Credit (120/yr) Semester Mark/%
  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
C14707 Project 80 Full Year 79
  4th year credit weighted average 76    
  3rd Year (2013-14), 40% weighting      
C13594 Gene Regulation 10 Autumn 69
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
C43630 Cancer Biology 10 Spring 68
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
C42443 Developmental Biology 10 Spring 74
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
C41105 Microbiology 10 Autumn 86
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    

L=Lecture, P=Practical  

5.3 A-level Results By module

Exam Session Module Code Module Description Exam Board UMS Max Grade
Biology            
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
Chemistry            
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
Economics            
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
General Studies            
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
Mathematics            
Jan-10 MPC1 PURE CORE 1 AQA 86 100 A
Jun-10 MM1B MECHANICS 1B AQA 91 100 A
Jun-10 MPC2 PURE CORE 2 AQA 81 100 A
Jan-11 MPC3 PURE CORE 3 AQA 86 100 A
Jun-11 MM2B MECHANICS 2B AQA 61 100 C
Jun-11 MPC4 PURE CORE 4 AQA 72 100 B
    Subject Score and Grade   477 600 B
Physics            
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