2023 BBSRC Bursaries for Birmingham Metabolomics Training Centre

Dates: 15th – 18th of May 2023
Location: School of Biosciences, the University of Birmingham

Do you want to attend this course for FREE?

There are a limited number of bursaries available for LC-MS Based Metabolomics and Metabolite Identification with the Q Exactive Plus and Orbitrap ID-X Tribrid. These bursaries cover the registration cost of BBSRC-funded researchers, making it completely free for them to attend. Further guidance, eligibility criteria, terms and conditions can be found on the application form below. Please apply promptly to avoid disappointment.

Apply online: Bursary Application Form

Deadline: Friday 3rd of March, 5pm GMT

If you have any questions or queries, please contact: bmtc@contacts.bham.ac.uk

Course Overview

This 4-day course introduces LC-MS based metabolomics and metabolite identification using both the Q-Exactive Plus (QE+) and Orbitrap ID-X Tribrid mass spectrometers, guiding delegates through experimental design, sample preparation, using the QE+ and ID-X, data processing, univariate and multivariate data analysis, and metabolite annotation/identification. It is an intensive course designed to provide foundational knowledge for delegates to develop further skills and undertake their own metabolomics experiments.

This course is led and delivered by five experts in the field of metabolomics and includes lectures, hands-on laboratory sessions, and computer workshops to provide a detailed overview of the metabolomics pipeline.

Topics Covered

·       Introduction to QE+ and the ID-X mass spectrometers and the metabolomic workflow

·       Experimental design and the importance of quality control (QC) samples

·       Sample preparation including extraction of polar metabolites and lipids from biofluids (urine and plasma) and tissue samples

·       Hands-on data acquisition for untargeted metabolomics and hybrid metabolomics, the latter combining targeted and untargeted measurements

·       Setting up the Vanquish UHPLC coupled to the QE+

·       Types of data which can be collected on the QE+ and the ID-X (m/z, retention time, MS/MS, MSn)

·       MS/MS and MSn experiments

·       Data processing workshop

·       Data analysis workshop (univariate and multivariate analysis)

·       Introduction to metabolite identification applying Data Dependant Analysis

·       Conversion of raw data to molecular formula and putative metabolite annotations

·       Mass spectral libraries (using mzCloud), and how to search them

·       Tools for mass spectral interpretation

·       Reporting standards for metabolite identification

·       Question and answer session with a panel of experts

See here for further information.

Normal registration costs:

Early-bird Registration£1,349
Standard Registration£1,810

Newsletter – Spring 2023

BBSRC WRDTP Newsletter Autumn 2022

Happy New Year! Welcome to the first 2023 edition of the WRDTP Newsletter, a regular email which will go out at the start of each semester! The aim of this newsletter is to keep you informed on upcoming events and opportunities, as well as to share with you the achievements of our students.

If you have any news items you wish to be included in future newsletters, please email them to a member of the Comms Team!

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News

DTP Symposium, Dec 12th 2022

A huge thank you to everyone who took part in our December symposium! Whether you helped to organise the event, gave a talk about your research or PIPS placement, brought along a poster or even just attended, you helped to make the event a roaring success.

Congratulations to those who won prizes on the day! Jess Davis won first place for her research talk, followed by Theo Issitt and Laura Cowell. Our first place poster prize went to Victoria Hill, second to Lydia Barber and third to Aidan Johnson. Joanna Greenman won first place for her flash talk, followed by Jessica Edge and Liam Barratt, and Roz Latham won best PIPS talk.

We also heard from some excellent Keynote speakers: Dr Richard Malham (Head of Research Policy, Integrity and Governance, University of St Andrews) and Dr Rupert Lewis (Chief Science Policy Officer at the Royal Society), and our Q&A panel allowed for interesting discussions about life after finishing a PhD. Thank you to Dr Sarah Harvey (Mewburn Ellis LLP), Dr Claire Stoker (Spirit Medical Communications Group Limited) and Dr Elspeth Ransom (Defra) for forming our panel this year!

Spring Training Day, 29th March 2023, York

The first event of our new training programme is the Spring Training Day, which will be held in York on the 29th of March. The Spring Training Day aims to bring together the whole cohort: with years 1-2 having analytics training and years 3-4 training hopefully focusing on essential skills such as public speaking, publishing, job hunting and interviews/viva. There will also be time for social activities and cohort building! Make sure you have completed this form by the 20th of January. This is a compulsory part of the DTP training schedule so please make every effort to attend!

A note from your comms team  

Are you interested in science communication and/or are wanting to fill that CV? We’re looking for new members to join the WRDTP Comms Team! No experience required and time commitment can be flexible. Whether it is writing one-off blog posts or becoming a permanent member of the team, it would be great to welcome some new faces and perspectives onto the team! If you are interested or would like more information, please contact a member of the Comms Team.

Student Achievements 

Prizes and awards

Congratulations to: Patrick Hunter, who won 3rd place for research and career showcase poster prize; Theo Issit for winning a £9000 Elsie may Sykes award for a pilot study in cancer patients at York hospital, being a 3-minute thesis national finalist and Falling walls Delft winner; and Gemma Banister for a successful grant application for a 3-month placement under the UK-Canada Globalink Doctoral Exchange Scheme with UKRI.

Publications

Below is a list of recent publications from some of our students: 

We understand that there are many more achievements worth celebrating that are not mentioned above, and we apologise to anybody not included! To avoid this in the future, it would be great if you could let us know what you have been up to, either via email or by tagging the WRDTP account (@BBSRCWhiteRose) on twitter.

Newsletter – Autumn 2022

BBSRC WRDTP Newsletter Autumn 2022

Welcome to the first edition of the WRDTP Newsletter, a regular news update which will be released at the start of each semester! The aim of this newsletter is to keep you informed on upcoming events and opportunities, as well as to share with you the achievements of our students.

If you have any news items you wish to be included in future newsletters, please email them to a member of the Comms team!

~~~~~~~~~~~~~

News

Welcome to our new cohort of 2022 starters! We are so excited for you to be a part of the White Rose DTP, and look forward to seeing all that you accomplish.

Masterclasses 2022

DTP masterclasses were a brand new, exciting concept launched in 2021. Our 2022 masterclasses hosted at Leeds, York and Sheffield were a great way for students to delve into the latest developments in an area of research with top academics from each university. 

This year, talks were focussed in the areas of: Navigating the academic environment, genome engineering, super-resolution imaging, analysis of microbial omics data, single-cell RNAseq, and cryo electron microscopy. We hope that most students were able to attend at least one of the masterclasses that was relevant to their research, and that you were also able to get to know your DTP colleagues from across all years and universities!

We are looking forward to running our masterclasses again in 2023, and would love some suggestions as to which topic areas you wish to be covered! It would be great to cover the areas that you will find the most interesting and useful in order for everyone to get the most out of these sessions.

“Learning about how to work with raw RNAseq data in our Masterclass on microbial omics” – @GavinHThomas on Twitter

DTP Symposium, Dec 12th 2022 

Registration for our annual symposium is now open! Attendance is compulsory for all students, except for those on placements. Unlike the past two years, this year’s event will be held entirely in person! This means that no posters or talks will be accessible virtually and we encourage everyone to attend.

This year, the symposium will take place at The University of York on Monday 12th December, 09:00 – 18:00. 

  • 4th Year students must submit an abstract (deadline Monday 31st October)
  • 3rd year students will need to make a poster based on their research. Poster criteria and submission deadlines will be communicated nearer the time.

A note from your comms team

Are you interested in science communication and/or are wanting to fill that CV? We’re looking for new members to join the WRDTP comms team! No experience required and time commitment can be flexible. Whether it is writing one-off blog posts or becoming a permanent member of the team, it would be great to welcome some new faces and perspectives onto the team! If you are interested or would like more information, please contact a member of the comms team!

Student Achievements (Easter-Summer 2022)

Prizes 

Congratulations to Ezra Herman, a student in the Friman lab from York who has been awarded the Enrichment Placement Award from the The Alan Turing Institute! 

A huge well done also to Alex Holmes who won the Leeds Partnership Awards 2022

Publications

Below is a list of recent publications from some of our students: 

Other achievements

See what else our students have been up to!

  • University of York students Harry Pink and Ethan Redmond both presented their research at the ICAR conference in Belfast. Read about their experience here!
  • Leeds student Alex Holmes hosted a gameshow at Be Curious 2022. See here to read more! 

We understand that there are many more achievements worth celebrating that are not mentioned above, and we apologise to anybody not included! To avoid this in the future, it would be great if you could let us know what you have been up to, either via email or by tagging the WRDTP account (@BBSRCWhiteRose) on twitter.

Jess Davis – Roundabout

For her PIPS, Jess chose to do something slightly different. She volunteered for Roundabout: South Yorkshire’s biggest youth homelessness charity which supports over 300 16-25 year olds every day. Roundabout provide a range of support from emergency accommodation, to bespoke career advice and tenancy support.

The featured image is of the roundabout logo

What did you do?

I worked for a charity called Roundabout, which is South Yorkshire’s biggest youth homelessness charity, supporting over 300 16-25 year olds, every day. They provide a range of support from emergency accommodation, to bespoke career advice and tenancy support. Because Roundabout is a relatively small, local, charity I got the opportunity to work across multiple different departments, and therefore got a great feeling of the charity overall, and how charities are managed and operate.

Two days a week I worked in ‘Central services’. This is the administrative and financial side of the charity. Here I helped with housing benefit applications, balancing books and working out why some client accounts were in arrears. I also helped in the maintenance of the client database, and learnt about the legislation surrounding trustees.  

Once a week I worked at ‘Homeless prevention services’. This is a drop in service in Sheffield city centre, where young people who are homeless, or need housing advice can come, and get free, unbiased support. The best part about this service is that no young person is ever turned away, the Roundabout staff always find a safe place for them to stay. Here, I shadowed and learnt how to interview young people who presented at the service and learnt about the different streams of support available to homeless young people, either from the council or local charities. I also helped in writing their 2021 National Lottery Annual Report, and the final Children in Need report for Roundabout’s five-year funding cycle. I interpreted data collected by the drop in service and made graphs to best display the charities output and contribution towards preventing youth homelessness in South Yorkshire.  

Twice a week I worked at the Roundabout hostel. Here I improved some of their documentation for recording client information, making it more stream lined and user friendly. I also spent a lot of time getting to know the young people, and supported them in day-to-day tasks. I also independently ran ‘life skill’ sessions where I baked and cooked with the residents, and organised their Christmas party.

Cooking for the Roundabout hostel Christmas party

In addition to this, I also did some work with the fundraising team. I assisted in the organisation and running of multiple events including the ‘South Yorkshire chocolate festival’, which was attended by 2000 people, a ‘Sleep out’ event, and I also ran a stall at the Sheffield Christmas market educating the public about youth homelessness and the work of Roundabout. Finally, I also got the opportunity to work with the Grants team. I successfully wrote an application to a community grant sponsored by Vodaphone, which was awarded. I also researched and wrote a letter to City Fibre enquiring about obtaining free Wi-Fi for all residents, and applied to a community grant with the South Yorkshire Community Foundation (SYCF), both of which we are yet to hear the outcome of. 

Jess running the Roundbout ‘Sleep Out’ stall at the Sheffield Christmas market

 What made you want to do that particular placement?

I wanted to take this PIPS opportunity to experience something outside of science, and to hopefully make a positive impact on my local community. I also wanted to gain experience and skills that are more easily recognised by companies outside of science and academia, for example in finance, management and teamwork.  

How did you go about finding and planning your PIPS?  

I had already heard of the amazing work being done by Roundabout in South Yorkshire, so I sent them a message on the ‘Contact us’ portion of their website, describing who I am, the skills I have, and explaining what a PIPS placement entails.

I wasn’t expecting to hear back from them, but they emailed me back almost straight away! I then arranged to meet with them in person and discuss what I could potentially do during my internship. Before this meeting I had made a fresh CV and made a list of things I would like to do during the placement, which really helped steer the meeting and plan what I could be involved in. I then started 2 months later and had the best time!

What have you gained from doing your PIPS?

The biggest thing that I gained from my PIPS was confidence in my abilities. Working in an environment where there were no expectations put on me meant that I really thrived. I have learnt that it’s always best to just give something a go even if you’re not 100 % sure on what you’re doing, it’s better to just try than to not do anything at all!

I gained more confidence in my ability to back myself and confidently put forward ideas. Working with a wide range of people at Roundabout has made me realise that as PhD students we have strong problem-solving skills and often come up with good ideas. It was really nice to be surrounded by other positive, enthusiastic members of staff. I also learnt so much about business and people management. Being an intern and working in so many different teams meant that I saw a lot of different working and management styles. I learnt so much about the general organisation of the charity, the hiring process, and how everyone’s roles fit into the overall running of Roundabout. Very interesting! 

How would you sum up your PIPS experience?

My PIPS has been an amazing time and has made me realise that as PhD students we have a lot more skills than we think we do! I think I have grown a lot as a person. I am so grateful to my PIPS supervisor Geoff for taking me on, and to everyone at Roundabout for making it such a lovely time. Every day was so varied and I genuinely looked forward to going in every day!

What advice would you give to other PGRs about PIPS?

PIPS seem like a really daunting and stressful thing to organise, but in truth they are not, I promise! If you are interested in working in the charity sector I would definitely recommend reaching out to a smaller, local charity rather than a ‘big name’ charity (i.e. CRUK, the NSPCC, Age UK etc). Smaller charities have less infrastructure and are therefore more flexible and more likely to be able to take on a PIPS. Additionally, because they generally don’t take on PhD interns you can really shape what you spend your time doing and you are special because you are the first/only one!

Robert Brench – ADAS

Robert is a 3rd-year PhD student at the University of Sheffield who completed his PIPS placement at ADAS, the UK’s largest independent provider of agricultural and environmental consultancy, policy advice and research and development. He was able to connect to ADAS with the help of LinkedIn, which has proven to be a vital networking tool. The WRDTP has its own LinkedIn group and page for our students to join and follow which we hope will enable more connections such as Robert’s in the future.

The featured image is of the logo for ADAS.

What did you do?

I worked with crop physiology and agronomy consultants at ADAS.

My first task was to review existing methods of analysing data gathered on farms and similar data sets and examine different methods to analyse the data collected over the last 7 years. I delivered the results of this as a presentation to the crop physiology group within ADAS.

The next part of my placement involved working with various consultants with trial carried out with various industrial partners using new products and techniques. This largely involved data preparation and analysis.

What made you want to do that particular placement?

I have long had an interest in the agricultural sector understanding how it works, the improvements that can be made and the changes necessary to move towards a more sustainable future. As a group who work closely with UK growers and the larger companies that support these growers, ADAS was centrally placed to provide insight into these interests.

How did you go about finding and planning your PIPS?

I reached out to a previous researcher at the university of Sheffield via LinkedIn and they helped me to arrange a placement.

What have you gained from doing your PIPS?

I have gained a larger appreciation of agricultural consulting. The skills that are required and the expertise and knowledge necessary. I have a greater appreciation for a range of statistical tools required in this field, some of which are transferable to my PhD work.

Secondly, the requirement to work to strict deadlines with multiple projects running in tandem has allowed the development of my organisation and time keeping skills. As well as a greater appreciation of my own abilities keeping to deadlines and the importance of reasonable expectations, particularly workload.

Finally, I have developed a network of contacts within an industry I am interested in working in after my PhD.

How would you sum up your PIPS experience?

Overall, my PIPS placement was a very positive experience, allowing me to work in an engaging environment and providing me with first-hand experience in an industry that greatly interests me. Not only will the skills I have been able to develop, but the contacts I have made, will undoubtedly provide new potential opportunities after finishing my PhD.

What advice would you give to other PGRs about PIPS?

I would strongly suggest investing time in researching potential roles and industries that might interest you. Linked in is a very powerful tool for reaching out to companies, with will mostly be more than happy to receive enthusiastic and skilled individuals such as those completing a PhD. Even if a role is not advertised, just contacting potential companies is a great way to potentially craft a more bespoke placement that suits what you are trying to get out of the experience.

Jake Leese – Oxitec

Jake is a PhD student at the University of Leeds who completed his PIPS placement at at Oxitec’s UK facility in Milton Park, Oxfordshire. Oxitec are a company that have been leading the way in the use of genetically modified insects as a tool for targeted pest control in areas of global health and agriculture. The most advanced of their projects is with the mosquito Aedes aegypti that transmits several viral diseases including Dengue, Zika and yellow fever. Oxitec’s FriendlyTM Aedes aegypti have been through field trials in Brazil, Panama, Cayman Islands and Florida, and are even now commercially available direct to consumers in Brazil.

The featured image is of the Molecular Building at Oxitec.

What did you do?

My placement was split into three rotations that gave me a broad overview of the work that is required to develop and maintain Oxitec’s transgenic insects. The first of these rotations was within the molecular lab, where transgene constructs are designed and transgenic individuals are genotyped to assess the viability and safety of candidate strains. The molecular team also support field trials by genotyping trap samples to monitor the spread of the transgene in wild populations. My work primarily involved DNA extractions and a variety of PCR reactions to support these tasks across several projects.

My second month was spent with the mass rearing team whose job it is to scale up insect production for future field release. I was brought into the team during a proof of concept experiment to produce 20,000 soy bean looper adults a week. This is a species of moth whose larval stage represents a serious agricultural pest in the Americas. Much of the day to day work revolved around preparing the diet and plastic housing for the larvae, and harvesting the pupae for adult cages before their eclosion. We also had to contend with consistent drawbacks from mould and viral outbreaks. We ran experiments alongside to try and establish the most efficient conditions for producing the best insect yield.

Mosquito Larva Screening

My final month was with the mosquito strain development team. Here I was performing micro-injections on Anopholes mosquito eggs, attempting to generate transgenic lines. I supported the team in maintaining and penetrance testing new lines, as well as screening the offspring larvae of injected mosquitos for first generation transgenics. The transgene includes a DsRed fluorescent marker so that the transgenic insects can easily be distinguished from their wild type counterparts.

Transgenic Larva

What made you want to do that particular placement?

I wanted to get a taste for R&D work within an industry setting and Oxitec is one of the few companies I came across that could offer this whilst combining two areas of biology that I am particularly interested in, insect biology and genetics.

How did you go about finding and planning your PIPS?

For a while I was scanning through the directory of biotech companies listed in biopharmguy.com. I had reached out to several companies with no luck and then I happened upon a BBC article about Oxitec’s Aedes aegypti field trial in Florida and was immediately drawn to the company’s science and objectives.

After I saw this, I found out that an old post-doc from a partner lab at Leeds was now working there. I reached out to her and she helped bring it all together and became my key host contact throughout. This was very fortunate and reinforced the importance of having good connections.

What have you gained from doing your PIPS?

My time at Oxitec gave me a great insight into an industry R&D setting. Having worked in three different areas of the company and across several different projects at differing stages of development, I gained a clear overview of how the company operates. I was also lucky enough to attend two presentations by the CEO of the company whilst I was there which gave me a great perspective of how the technology was being field tested and rolled out abroad.

As well as an appreciation for the inner workings of the company, I developed a wide range of new research skills. My experience moving between labs also gave me a deeper appreciation for the subtle differences that team dynamics and communication can make in research.

Mosquito Blood Plates

How would you sum up your PIPS experience?

My time working at Oxitec showed me first-hand how my skills can be applied directly to tackling real world problems. The rotations gave me a good variety of experience across several different scientific disciplines and meant I was consistently being challenged over the course of the internship. The PIPS has provided me with a refreshing break from the PhD and I’m now going back to my own project with a new perspective and enthusiasm.

What advice would you give other PGRs about PIPS?

When you are looking, think about where you may have contacts already as this will help you get your foot in the door. That being said, there’s no harm in contacting places regardless of whether you know anyone there. Perhaps most importantly, don’t be afraid to keep asking questions throughout your internship… The better understanding you have of what you are doing, the more you will get out of the experience.

Defra: Environment & Public Health Secondment Opportunities

Are you interested in opportunities in the area of Environment and Public Health? If so, Defra are offering three different internship roles that you should consider applying for!

Please note that these each have different experience requirements (some postgrad qualifications, some postdoc, some postdoc preferred but PGRs considered).

The closing date for applications is the 1st of July.

To apply for any of these opportunities please fill in the form that can be found here.

Please direct any queries to: external.advice@defra.gov.uk

Role 1:  Environment- Health Partnerships

Defra’s involvement in the Environmental Monitoring for Health Protection (EMHP) programme has demonstrated benefits from close collaboration with health colleagues across government for the purpose of delivering innovative and large-scale environmental monitoring. We are keen to realise some of the wider benefits to the department from this environment-health partnership. An important step is to ensure there is a central view of existing connections and engagements between Defra Group and DHSC and its agencies. With this in mind, the Environment & Public Health team in the Chief Scientific Advisor’s Office wish to map Defra’s engagement with health to understanding existing activity and relationships and identify opportunities for better coordination and join up across the environment and health interface in government.

This is an exciting opportunity to gain a broad understanding of Defra’s health-related scientific and policy work and to establish a strong network across Defra Group, DHSC, UKHSA and other government organisations.

Specialism: A post doctorate qualification (or equivalent experience) or experienced current PhD student. Understanding of the environment-public health interface would be beneficial, experience with systems thinking and analysis methods would be useful.

Location: Any- some UK travel may be required, especially to Weymouth, Exeter and London.

Time commitment: 3-6 months

Contact for more information: Josh Bunce josh.bunce@defra.gov.uk

Role 2: Future Wastewater Monitoring Capability Development

The CSAO’s Environment & Public Health team lead on the realisation of benefits to Defra from the partnered delivery of wastewater monitoring as part of the national Covid-19 response. A component of this work involves ensuring policy and central teams remain informed of post-Covid-19 developments and that our activity in CSAO aligns with policy and strategic priorities, particularly as the Public Inquiry commences. Practically, this may involve providing rapid briefings and query responses but also supporting on cross-government coordination and communications related to knowledge sharing and future wastewater monitoring capability development.

This is a unique opportunity to contribute to realising a lasting legacy from investment made during the last two years which has yielded substantial scientific development and collaboration across government.  You will gain a firm understanding of central policy work in Defra and a government perspective on the use of science in decision-making, as well as having the opportunity to establish a large network across government.

Specialism: A post doctorate qualification (or equivalent experience). An experienced current PhD student would be considered. Understanding of environmental or public health policy would be useful. 

Location: London (other locations can be considered)

Time commitment: minimum three months, preferred six months

Contact for more information: Josh Bunce josh.bunce@defra.gov.uk

Role 3 New Environmental Monitoring Capability Within Defra

Environment and Public Health is a new area of interest for Defra’s Chief Scientific Advisor’s Office (CSAO). Through the experience of delivering wastewater monitoring as part of the national Covid-19 response through the Environmental Monitoring for Health protection (EMHP) programme, we have developed new capabilities across Defra in environmental molecular monitoring, (including large scale qPCR analysis, genomic sequencing, bioinformatics and statistics) and have strengthened our relationship with health colleagues in government. We are now seeking to realise wider benefits from these developments ensuring there is lasting legacy from the investment made during Covid-19.


This placement will be to support the design and, potentially, build phase of a new environmental monitoring capability within Defra Group that builds on the expertise developed through the delivery of the EMHP programme.


The main activities for the placement will be to:
Provide expert advice to ensure that the design of the capability is scientifically robust
Take a lead on elements of the design process
Provide advice and progress updates to Defra’s Chief Scientific Advisor and other senior stakeholders
Engage with stakeholders from across Defra group and other Government departments and agencies, including UKHSA.

This is an exciting role in a newly emerging and fast-paced area that will provide opportunities to engage directly with senior stakeholders, to work on a high-profile government science project and to directly influence the direction of Defra’s work in environmental monitoring for public health purposes.

Specialism: A postgraduate qualification (or equivalent experience) in one of the follows areas: public health, epidemiology, environmental molecular-microbiology, environmental science.

Location: Any – although occasional travel may be required to London, Weymouth and Exeter

Time Commitment: Minimum of 3-4 months, but could extend to March 23

Contact for more information: Robin Cutler robin.cutler@defra.gov.uk

Egle Beigaite – CasZyme

Egle Beigaite is a 4th year PhD student at the University of York who completed her PIPS placement at CasZyme, a biotech company based in Vilnius, Lithuania. CasZyme are an organisation whose research focuses on revolutionising the field of CRISPR-based Molecular Tools.

The featured image is of Egle with her PIPS colleagues.

What did you do?

My project focused on the characterisation of Cas proteins which could be used in genome editing. The techniques that I was exposed to included: colony PCR, protein purification using AKTA system (Ni and Heparin columns for affinity purification), bacterial cell transformation, cloning, RNA, DNA and plasmid purification using minipreps and midi preps. One of the main aims of my project was to determine the optimal growth and expression conditions for bacterial cells, which were then used to purify Cas proteins. I was also introduced to RNA synthesis (in vitro transcription), Cas protein and gRNA complex assembly as well as Cas activity assays.

What made you want to do that particular placement?

While relatively recent, CRISPR genome editing technology is becoming the main workhorse for genome editing in both academia and industry. Dr Gasiunas, who established the company, has previously worked in Prof. Siksnys’s lab and published several key papers in CRISPR research (Gasiunas et al 2012; Karvelis et al 2015; Gasiunas et al 2020). Prof. Siksnys, together with Prof Charpentier and Prof Doudna have received a prestigious Kavli prize for his independent development of CRISPR. I believed that it was the best accessible location for me to deepen my understanding in CRISPR technology and learn new protein characterisation techniques. In addition, this is a start-up company with only 10 employees. I thought that, by starting in such a small company, it would be easier for me to adapt and would also allow me to learn more things.

Egle working at CasZyme

How did you go about finding and planning your PIPS?

Initially, I picked two countries I believed I could easily find an internship: the Netherlands and Lithuania (I am originally Lithuanian and started search way before COVID began), and researched biotech companies in both countries. After the interviews, I received two offers from Centre for Human Drug Research (CHDR, Netherlands) and CasZyme (Lithuania). Eventually, I chose to go to work for CasZyme as I really wanted to broaden my understanding of CRISPR technology.

Regarding CHDR, my project there would have focused on neurological conditions, which is what my PhD project is about, so I found it less interesting (although it seemed like an amazing place to learn new things).

What have you gained from doing your PIPS?

I have become more confident with working with large number of samples and have also learnt how to prioritise the experiments and to perform them as efficiently as possible. In addition, I have learnt how to use AKTA protein purification system and performing CRISPR complex assembly and Cas protein activity assays (which are performed in RNAase-free box).

I also gained invaluable experience in working as part of a small biotech company and learnt first-hand the importance of collaboration and teamwork. To ensure that projects were finished according to the deadlines, experiments were efficiently redesigned and redistributed to several staff members. I learned that great communication and flexibility with your team members is extremely important, as these people also teach you new techniques and can also help you to troubleshoot.

How would you sum up your PIPS experience?

Of course, pandemic has made it a bit more difficult to travel, but I am glad I did my PIPS in CasZyme as it was great experience. I have learnt a lot of new techniques and developed friendly relationship with my colleagues. My primary laboratory manager planned the project in such a way that allowed me to learn as much as possible during my placement and made the internship comfortable during these difficult post-pandemic times. I really enjoyed being part of research team and part of CasZyme community.  Most of the staff were of my age, some also doing industrial PhDs. It was great to share the experience and support each other.

What advice would you give to other PGRs about PIPS?

Don’t be afraid to explore options outside your project (and comfort zone)! PIPS are aimed to help you learn new things, and add extra skills on your CV. I would personally recommend testing yourself in industry to see if you could work in a team with other people. The experience is also beneficial to see how industrial projects are managed and how things are generally organised (it might be quite different from your lab). I would recommend starting in a relatively small industrial company, as usually these biotechs are highly collaborative with academia and thus the working environment is slightly closer to the PhD in academia. Also, it means that you will be able to meet most of the staff during the placement and learn from them as much as possible.

Amy Stonadge (nee Brown) – LAMP Labs

Amy Stonadge (nee Brown) is a PhD student at the University of York who took part in a 3-month placement in the new COVID-19 LAMP Labs at the University of York. The LAMP Labs are a new collaboration between the University, Capita and the NHS and are working to establish a COVID-19 testing laboratory for frontline NHS staff. Read on to find out more about Amy’s PIPS experience!

Read moreAmy Stonadge (nee Brown) – LAMP Labs