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Year in Industry: wheat genomics boosting crop yield to single-cell cancer discoveries

Earlham Institute offers two students each year a place on our Year in Industry programme. We hear from two recent students who have completed their placements and find out about their research, as well as what they plan to do next.

October 08, 2021

Here at the Earlham Institute, we offer a Year in Industry programme which has gone from strength to strength over the last ten years.

The placement gives life science students the unique opportunity to work alongside leading academics in varied fields of data intensive bioscience. With access to advanced biotechnology platforms, genomics and bioinformatics data methods, the experience helps students broaden their skill sets, knowledge, and career opportunities.

We hear from two recent students who have completed their placements and find out about their research, as well as what they plan to do next.

Akemi Ramos, Year in Industry 2020-2021

I was attracted to the Earlham Institute’s core emphasis on genetics and using computational approaches to analyse results, while working on a wide variety of organisms. This was a perfect blend as someone who studies genetics but has always had a curiosity with computing - giving the freedom to choose a project that suited. I also found the Institute to be a friendly, professional environment with a sense of community.

As I went on to study genetics at the University of Manchester, the Earlham Institute was invaluable in gaining experience in interdisciplinary research - to see first-hand how genetics is used to answer a wide range of biological questions.

Implementing my individual project, the placement required me to do my own research, a project proposal and learn new computing skills. Development of these new skills will help with my third-year research project, especially as it will also be computationally based.

Akemi at her desk at home preparing to present her final seminar at EI

Akemi at her desk at home preparing to present her final seminar at EI

Wheat MITEs

My Year in Industry at the Earlham Institute was a side project of PhD student Benedict Coombes, whose research focuses on analysing Transposable Elements (TEs) in wheat. TEs are a DNA sequence that, when active, can move to another region of the genome. Over 80% of the wheat genome is composed of TEs, which contribute to the variation and evolution of this plant.

The project focuses on the analysis of Miniature-Inverted Repeat Transposable Elements (MITEs), which are a type of TE, in the wheat genome. MITEs are smaller than most TEs and tend to be found in genic regions. By understanding more about MITEs’ contribution to variation in the wheat genome, we can better understand how MITEs can alter genes to increase wheat yield - this is particularly important with the global target to raise wheat production 60% by 2050.

As exploratory research, I utilised computational skills - such as writing scripts in coding programmes such as python, R and Linux - to find where in the genome MITEs were inserted. I investigated their location preference for insertion in and around the genes to see if they had any generic effect on gene expression.

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The Earlham Institute was invaluable in gaining experience in interdisciplinary research - to see first-hand how genetics is used to answer a wide range of biological questions.

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Akemi Ramos, Year in Industry student

‘Junk’ DNA

Due to the ‘jumping’ nature of these transposable elements, I wanted to know more about their effect on the wheat genome - learning new computational skills along the way. Only a short time ago these gene elements were considered to be part of ‘junk DNA’. We now know that the TEs can cause mutation, variation, and are drivers of evolution.

The wheat genome has only recently been genetically sequenced and has not been as fully analysed compared to other species, which also means their MITEs have not been explored fully. My research showed that the wheat genome has a higher distribution of MITE insertions in and around the genes compared to the intergenic regions, while other genic locations show an avoidance of MITEs.

Generally, areas that are less important to gene expression or function, such as introns, will show a higher distribution of MITEs. Areas that are imperative for gene expression or function, such as exons, will have an avoidance of MITEs.

Akemi's Year in Industry project focused on the analysis of Miniature-Inverted Repeat Transposable Elements (MITEs), which are a type of Transposable Element in the wheat genome.

Deeper Investigation

I was excited to help expand the scientific knowledge of the effects and characteristics of these MITEs in wheat, while directing possible future questions to improve the study of its genome. Further analysis could be done as to why the MITE’s insert in the wheat genome - where there could be a preferred target sequence which could affect gene function and regulation.

My research showed no generic relationship between MITE and gene expression. This may be because they have a varying effect, which could be analysed further by comparing MITE insertions in different wheat cultivars. I also found a subfamily with the highest distribution of MITEs in the genes called ‘DTT’, which are more likely to affect expression, so this would be interesting to explore further.

With wheat being a staple food that needs to increase yield in the future and feed a growing population, it’s fundamental that we learn more about its genetic composition and wheat variation. More research into MITEs will help us understand how wheat can adapt to have a higher crop yield and more resilience to climate change.

What's next?

Despite working from home for most the year during the pandemic, I had daily interactions with the Anthony Hall Group that made me feel part of the team. They were very supportive, making me feel comfortable to ask for help. I am also thankful to my supervisors: Anthony Hall, Benedict Coombes, Roanne Ephithite and Emily Angiolini, as they guided my project from start to finish.

In terms of what I would like to do next, I have one more year in order to complete my Bachelors and then would like to go on to do a Masters in computational biology, hopefully followed by a PhD.

I plan to work in bioinformatics as I’ve really enjoyed all the skills I have learnt at the Earlham Institute and would like to continue challenging myself to learn more complex computational biology methods.

10 Years of Year in Industry.

Jessica Peers, PhD student (2019/20 alumni)

“My YiI was an incredible opportunity to gain hands-on research experience and develop skills which I had not been able to do at University, such as computational biology, laboratory techniques and science communication.

“I was able to ask questions and learn from welcoming and supportive colleagues in an environment where I was surrounded by fascinating research. I especially enjoyed the opportunity to learn to code and become familiar with bioinformatics tools, which shaped my career goals.

“Completing my YiI at the Earlham Institute provided the experience and confidence I needed to pursue a PhD, and I’m thrilled to be returning this October. As part of the Haerty Group. I’ll be investigating the effects of inbreeding on non-coding regions of the genome in domesticated and wild endangered mammal populations, using computational biology, machine learning and synthetic biology.

10 Years of Year in Industry.

Dominic Smith, Scientist at CS Genetics (2013/14 alumni)

“I thoroughly enjoyed my placement year and would recommend it to any student considering it.”

“My Year in Industry at the Earlham Institute was an invaluable first experience into the world of next-generation-sequencing. I was able to experience the breadth of the field, from sample preparation to sequencing and bioinformatic analysis.

“I would recommend a placement at the Earlham institute to those that are interested in the applications of DNA analysis and sequencing as it serves as a first foot into the industry. Following my year-in-industry, I joined the product development team at Illumina, working on some of the leading platforms in the next-generation-sequencing space such as the NovaSeq 6000 and NextSeq 2000. After around five years at Illumina, I moved on to join an exciting new start-up in the single-cell sequencing field, CS Genetics.”

10 Years of Year in Industry.

Sam Horsfield, PhD student (2016/17 alumni)

“My time on placement at the Earlham Institute was invaluable to my development as a professional scientist. With my experiences in the lab and in bioinformatics, I went on to work for one of the biggest sequencing companies in the world, and I am now pursuing a PhD in bacterial genomics (epidemiology and evolution) at Imperial College, London.

As well as practical skills, the placement also taught me how to be a good scientist - how to network, research and write scientifically. I am incredibly grateful to everyone at the Earlham Institute who made my time there so special.”

10 Years of Year in Industry.

Nicole Forrester, PhD Student

"Looking back on my Year in Industry at the Earlham Institute five years later, it was jam-packed with learning, growing and a lot of new experiences.

“From cultivating a keen interest in genomics (thus deciding my career focus) to gaining an insight into independent research; expanding my laboratory techniques repertoire; networking with people from all over the world; being introduced to bioinformatics and coding and exercising my presentation skills - I still consider the time I spent at the Earlham Institute to be the one of the most significant and valuable chapters of my career and life so far.

“The real practical experience in a professional scientific environment allowed me to stand out in job applications straight out of university and quickly secure my first graduate role as a research assistant in an NGS Facility. I loved my time at the Earlham Institute so much that when the opportunity arose to return for a PhD this coming autumn, I eagerly accepted! I’ll be studying “alternative splicing and its functional consequences in blood cell development in mice at the single-cell level, in the Haerty Group."

Eleanor Calcutt, Year in Industry 2020-2021

I was attracted to the Earlham Institute because of the high calibre of genomics research in a field I am particularly interested in. It wasn’t just the innovative approaches that were being used in this research but how it was helping to tackle global issues with new technological advances.

The established Year in Industry programme also appealed to me and the way it was structured with the exciting prospect of spending a year on my own research project, giving independence in a way I’ve never had before.

During the first few weeks of my programme, I was introduced to the different Faculty research groups within the Institute, which gave us an insight into the wide range of research that was taking place. We were then able to choose a research project placement to pursue for the year.

I knew I wanted the opportunity to learn as many new skills as possible and really push myself out of my comfort zone. When I was first introduced to single-cell sequencing technology, I found it fascinating.

Our Year in Industry programme is also a great way to meet new people at the all important PhD student socials

All in a single cell

My project, titled ‘Developing a smart-seq3 pipeline for single-cell RNA-seq’ is a collaboration between Faculty groups: Macaulay, Haerty, Swarbreck and Genomic Pipelines.

The fact that you can sequence a single cell and distinguish it’s distinct genome or transcriptome from other cells in a population is very impressive.

I was therefore very excited to start the project, which would involve performing a comparison between Smart-seq3 and Smart-seq2 (the current protocol used), for their use in single-cell analysis of human cancer cell lines to assess gene expression heterogeneity.

During my time at the Earlham Institute, I have gained skills in cell sorting, method development, laboratory automation, next generation sequencing and the associated bioinformatic skills, in what is a very exciting and rapidly developing field.

Rare experience

As an undergraduate biological sciences student about to go into the final year of my degree, the placement has given me the unique opportunity to experience what it’s like to work in a research institute and academia before finishing my studies – something a lot of people at my stage in their careers will never get.

I’m very grateful that this year has allowed me to immerse myself among scientists at the top of their fields and have access to world-class equipment and technology, such as the liquid-handling robots and next-generation genomics sequencing platforms.

This, together with the support from colleagues I’ve received during my project, has really helped me to develop personally and professionally.

I’ve become more confident in my own abilities and been able to think more independently to plan my experiments or analyses. I’ve also been able to develop skills - whether that be trouble-shooting in the lab or problem solving in my sequencing analysis - which I wouldn’t have had the opportunity to do during a normal university year.

Eleanor worked in our specialist single-cell labs at Earlham Institute as part of her placement.

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The established Year in Industry programme also appealed to me and the way it was structured with the exciting prospect of spending a year on my own research project, giving independence in a way I’ve never had before.

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Eleanor Calcutt, 2020-21 Year in Industry student

New tech discoveries

I’m really proud that I have established Smart-seq3, a single-cell RNA sequencing protocol within the Macaulay Group, which will be used for their own research in technical development for understanding cells at a higher resolution.

As Smart-seq3 detects more genes and transcripts than the currently used Smart-seq2 protocol, I’m hoping that bringing this increased depth to their projects will allow them to make new discoveries in their research.

One of the things I’ve loved about working on method development is the many applications that it could be used for. From determining the lineage of hematopoietic stem cells to assessing the transcriptional differences within tumour cells or characterisation of different cell types and states at different phases of development – there really is no limit to what you could do with the technology.

Throughout my placement, I was surrounded by a wide team who helped me at different stages of my placement. Emily Angiolini and Roanne Ephithite, who coordinated the whole year, were also there for scientific and wellbeing support, not to mention my four project supervisors; Iain Macaulay, Wilfried Haerty, Karim Gharbi and David Swarbreck. Having a supportive network with expertise in different areas was key in helping develop the skills I needed to carry out a multidisciplinary research project.

My time at the Earlham Institute has really given me an insight into what it would be like to work in academia. I think the next step for me is to find a Masters in molecular biology or genomics, but this year has definitely made me more open to the prospect of completing a PhD in the future.

10 Years of Year in Industry.

“Over the decade that the Earlham Institute’s Year in Industry programme has been running, we have expanded our university reach from which students are enrolled and offered a diverse set of unique projects year-on-year - highlighting the novel and cutting edge research that our students are able to contribute to.

“The ability to explore the Institute’s research with a number of projects at their disposal at the start of the placement year is unique to EI, helping the students to become embedded as a member of staff - something that they highly regard. The support the students receive goes beyond the placement, with support for future career aspirations, references, and mentorship.

“Students categorically report that the skills developed at EI have helped them to secure positions in academia, industry and places on higher educational programmes. Many credit the breadth of skills - in particular, a combination of programming and sequencing technologies – as making them highly desirable. We have seen a high proportion of our students go on to higher education, with many choosing to return to EI; recognising and valuing the support on offer to students.

“As we build our Year in Industry Alumni, I hope to see the programme has an impact on opening up new career options for students and a continued sense of belonging to the EI community through collaborations and partnerships.”

Dr Emily Angiolini, Head of Advanced Training

Applications for our Year in Industry Programme for the academic year 2022/23 are now open, and close on 31 October 2021. Please visit our Year In Industry page for more information.

Year in Industry Programme

Hayley London

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Hayley London

Marketing and Communications Officer