Jade joined Warwick in October 2018 as the fourth Singapore Trust scholar. Follow her blog below to find out how she's getting on.
As of January 2022 I've been based in Oxford University working as a research laboratory technician at the Centre for Neural Circuits and Behaviour (CNCB). Currently, I use molecular, genetic, behavioural and anatomical approaches in the model organism Drosophila (fruit fly) to support the research projects of the Goodwin Group, aiming to elucidate the neural circuits and mechanisms of sex-specific behaviours.
Despite the limitations of the COVID-19 pandemic, my course and professors at Warwick still effectively taught me the scientific thinking and methods that form the foundation of my work now. I've also had many opportunities to pursue my academic and extracurricular passions, from lab work to outreach volunteering to the arts. It is without a doubt that these wonderful experiences at Warwick were made possible for me thanks to the support of the Singapore Scholarship and its Trustees!
May and June of this year was exam season, which I spent researching and writing my final exams of my undergraduate degree! Due to COVID the exams were not done in person, and were instead a series of take-home essays for each module. Though I’ve written plenty of scientific essays throughout my schooling years, completing 12 fully-referenced essays within the 28 day exam period was still a challenging endeavour! Despite the hard work it was still an enjoyable experience consolidating my learning over the year and delving into the recent literature to build up my writing. I'm elated to report having scored High 1st (88%) marks in several essays, such as "Experimental strategies for obtaining rare antimicrobial compounds" and discussing in-vitro experiments used to identify essential components for protein import and translocation to the endoplasmic reticulum.
One of the many diagrams I'd created for use in my exam essays - this one describes the general workflow of using synbio approaches to biosynthesise useful compounds.
Following exam submissions, I then got started on my final year research/dissertation project! As I have mentioned before on this blog, my assigned project was mainly based in deep-learning, a field I had minimal exposure to at the time. The project period was just about a month, so it was a whirlwind of attempting to learn enough about the field, generating sufficient data and eventually writing a (hopefully) engaging and well-researched report. Under the wonderful supervision of Dr. Munehiro Asally, I trained a StarDist 2D network on progressively increasing amounts of self-generated cell segmentation data, before testing and analysing its performance versus that of a human (me) or on pre-trained StarDist models.
Some screenshots from my report, which hopefully give some visual explanation to what I was up to for that month!
Figure explaining the benefit of using the StarDist object detection model rather than the typical bounding boxes used in most object detection programmes.
A simple example illustrating how model performance is evaluated - basically, the more overlap between the model's prediction and the human-annotated "answer," the better.
Examples of cell segmentation predictions produced by the models I had trained.
Having worked with microscopes in previous internships, it was exciting to learn first-hand its applications for bacterial cell imaging, compared to the fruit fly brains I was more used to! The most satisfying part of the process for me was the successful creation of multiple pre-trained models, which could then be downloaded and utilised by members of the Asally lab to hopefully speed up and semi-automate their own microscopy cell segmentation tasks in their own projects. The overall experience was an excellent way to learn “on the job,” as the Asally lab members kindly provided real data from their projects for me to train and test my deep-learning models with. Despite the relatively short project period of just under a month, I felt it was a great way to end off my last-ever piece of undergraduate work, as it allowed me to gain great insight and initial experience with computing-based approaches to bioimage analysis - an extremely important aspect of basically any biological field that involves visual data. Even though I aim to pursue further research based more in Neuroscience rather than Microbiology, the knowledge and skills I'd gained during this project have definite transferable applications to other experiments I may undertake.
Plans for the rest of the year:
As I write this, I am in the middle of my final exam season of my undergraduate degree!
(Although it’s technically the Easter holidays at the moment, some rescheduling had to be done by the Department in order to give us time to complete our dissertations before the end of the year.)
As almost all my exams are essay based, it’s also been a great way for me to consolidate all the learning I’ve done this year in some very interesting modules, ranging from Biological Clocks to System Dynamics.
After exams, I will undertake my dissertation in “Deep-Learning Microscopy Data Analysis” and then embark on a very interesting Summer research project!
As the wet-lab research component of my internship last year was sadly cancelled, I was set on seeking a lab-based internship for this Summer in order to gain further hands-on experience for my intended career in research. Thankfully, I was able to find a Professor at Life Sciences willing to supervise my application for a £1000 research grant from the University, which I am glad to announce was successful!
As such, later this year I will be exploring whether human mutations of Connexin32 (a protein that forms plasma membrane channels between cells) affect its sensitivity to CO2. This in the context of understanding the biological cause of Charcot-Marie-Tooth disease, a hereditable motor-sensory neurological disorder that progressively reduces quality of life, with symptoms such as numbness of limbs and muscle weakness. Although this disease is not directly life-threatening, it can severely reduce mobility and independence of patients and does not yet have a cure. A major challenge in the development of therapies/cures for this disease is that it comes in many different forms, all with different genetic causes. As such, I hope to add to its current genetic understanding with my project, in order to support the approach towards current and future treatment.
Additionally, I am currently mentoring the new Warwick iGEM team and will continue to do so over the Summer, until the Competition near the end of this year. As my cohort was the first batch having to work through COVID, I would like to help them make a smoother transition to virtual teamworking and biological research!
Due to schools in the UK being closed for lockdown, we were unfortunately unable to do as much volunteering in BioSoc as originally planned. Societies were made to cancel all in-person activites, and it would have been unsafe for us to travel into schools or carry out hands-on experiments during this time. Doing virtual volunteering was also a difficult task to coordinate as our teacher liaisons reported difficulties finishing the assigned teaching syllabi, let alone putting aside time for us to teach external material to students.
However, in February I was contacted by a member of staff asking for help with the then-upcoming Women in Science Day programme at Warwick as another team of volunteers had pulled out of the project at late notice. As such, we had less than a week’s time to come up with a topic and teaching resources for Year 11 students to explore biology at home.
After deciding to take on the challenge, I recruited a friend on the BioSoc exec to brainstorm and churn out the material over the weekend. We decided to base the activity off fermentation, as we wanted to engage the students through something we all do (eat food) as well as only require materials that are easily found in the home. I created an instruction and tracking sheet teaching students how to make their own sourdough bread starter, which only requires water, flour and time to make. In case they had a teacher running through the programme with them, I also created a short slideshow presentation explaining the science behind fermentation and the creation of sourdough bread.
Afterwards, we were left scratching our heads trying to figure out how to keep a group of 14/15 year olds interested in our activity through online learning. My friend Jerry came up with the amazing idea to create an Among Us-themed quiz, as Among Us was a incredibly popular game at the time. I once again fell back on my Visual Arts training to design and draw Among Us characters with different foods, much like how the characters have customisable hats in the actual game.
Jerry the editing whiz did some video-making magic, creating an interactive “choose your adventure” style set of videos for the students to click through. Clicking on the wrong answers would bring them to the game’s end screen, while successful completion of the short quiz would show the game’s Victory screen. After recording further videos explaining how to use the resource pack, we sent it off to the University, hopefully for the young students to enjoy.
Staying at Home:
The heavy snow back in January gave us a welcome excuse to have some fun outside, as my housemates and I spent hours in the garden building my first ever snowman!
For Christmas and Chinese New Year, we also had cozy celebration dinners in our shared kitchen.
Overall, despite it being an incredibly busy time, I’ve greatly enjoyed my last year at Warwick so far and will be reluctant to officially leave when graduation comes! Thanks to all the fulfilling endeavours I've been able to carry out this year, I’ve had a good time in the past two terms despite the limitations of lockdown 😁
(This term's entry separated into 2 parts due to character limits)
Term 2 was a true test of my time management skills, as on top of gearing up for the final exams of my degree I was also applying to internships and postgraduate courses, planning Society events for the BioSoc, and also launching my self-founded Society – the brand new Warwick Knitting and Crochet Society!
Knitting has always been one of my favourite hobbies for years. In the past two years of my time at Warwick, I frequently saw online talk about starting a KnitSoc and signed their interest forms, however perhaps due to not having enough student numbers they were not launched. Now in my third year, I decided to take the plunge and try my luck with collecting sufficient signatures of interest, writing up a proposal, and pitching it to the Societies’ Committee of the Students’ Union.
I was overjoyed when I heard back from the SU that KnitSoc was approved, and set off asking around for other students to join the pioneering executive committee of the Society.
The main goals I wished to achieve with founding this Society were to:
1) Provide a community for total beginners to advanced members to hone their craft, virtually socialise during lockdown and pursue a hobby that is calming, fulfilling and a great way to de-stress.
2) Teach knitting/crochet as a fun and creative skill through educational sessions and mentoring.
3) Support vulnerable persons through volunteering projects such as donations of useful items to homeless shelters or “preemies,” and charity auctions of handmade items.
To give us the best chance of success of fulfilling these goals, I created specialised roles such as Education Officers and a Charities Officer, on top of the usual roles such as Social Secretaries and a Treasurer.
While advertising the Society virtually through social media, I was initially worried that there again wouldn’t be sufficient interest for what I assumed was a niche hobby, especially for the average university age group. However I was pleasantly surprised as I received an overwhelming response of people asking to join the Committee and the Society in general! As such, our Society was able to start off with a strong Exec of 13, and over 80+ members joined our chat group within a matter of weeks.
In order to give members a way to socialise over lockdown, we planned casual weekly sessions every Friday evening for people to just get together on a video call and talk about our projects, troubleshoot difficult pieces or just chat about how the week had gone. I am very proud to announce that our first ever session was a great success with almost 30 attendees! I continued to host these sessions throughout the 10 weeks of term, and even received heartwarming feedback that people looked forward to our sessions to end off their week of school work. Our Society group chat was also incredibly active with members sharing their work or recommendations for tools and patterns. So far, my only regret is not applying to start this Society earlier, as I won’t be able to dedicate as much time to it after graduating!
A couple of pieces I completed over the course of the term:
On the academic side, I was wrapping up one of my favourite modules, Navigating Psychopathology which is taught by Warwick’s Institute of Advanced Teaching and Learning (IATL). I am incredibly grateful for the opportunity this year to take modules outside of my home Department, as this class allowed me to experience the learning of other subjects (ranging from psychology and neuroscience to film and literature) with classmates from many other Departments.
We were also given great flexibility in our final assessment – a reflective essay compiling the 10 weeks of learning/discussion as well as a final essay on a topic of our choice. I chose to explore the DSM-based system of diagnosing mental disorders, writing about the increasing evidence against using it for the diagnosis of psychiatric conditions.
This included an overview of its rather chequered past, to the harmful consequences to Medicine of dependence on a rigidly categorised form of diagnosis. I then analysed the sociocultural changes towards mental health and psychiatry, especially as a consequence of changes to the manual over its editions – for example, the decision made by its editorial committee to change the maximum age of ADHD diagnosis criteria.
Despite this, I made sure to weigh the benefits of having such a manual, such as for the purposes of administration, legislation and medical record-keeping for patients.
The research and thinking that I carried out for this essay was a period of great learning and introspection, as it allowed me to consider how my degree/field of Biology is applied in the “real world.”
Overall, undertaking this module gave me an increased appreciation of interdisciplinarity across seemingly unconnected subjects, and also opened my eyes to my great interest in this field as a potential pathway for integrating scientific and humanistic research.
Preparing for exams was a unique challenge this year for both students and staff as they had to be open book this year! Despite the stressful experience I was glad to be back home in Singapore with family, with plenty of outlets to de-stress ranging from brushing up on my knitting, showing off the cooking skills I picked up while feeding myself in the UK, or tending to the plants I can't grow in British weather. Due to COVID restrictions I also spent some time video calling with friends, including Chandra, Iffah and Hayati to lament about final examinations or catch up on postgraduate life.
Ironically, my cooking skills in Asian food in particular were honed primarily during my time in the UK.
Portulaca flowers - one of my favourite plants to grow which unfortunately requires the bright sun and warmth of Singapore.
I also took advantage of many summer school programmes becoming free and virtual this year, allowing me to attend a wide range of programmes to diversify my skills.
One of my favourites was the Centre for the Physics of Biological Function's Biophysics Summer School, hosted by Princeton University. Through the weekly lectures and insightful discussions, I was able to study Biology from the perspective of Physicists, giving me a whole new appreciation for my subject and reinforcing my goals of pursuing interdisciplinary Biological learning and work in the future.
Example lecture from the CPBF Summer School on wrinkling - such as on our fingertips when submerged in water or of our brains. Previously I had learned of the biological basis behind such phenomena, but exploring the physical triggers and processes occuring "behind the scenes" gave me a deeper appreciation.
It was also an interesting experience celebrating my 21st birthday during COVID restrictions - I was happy to take a day off exam preparations and relaxing at home with my family, however my wonderful friends coordinated a birthday surprise for me from across the UK and Singapore! It was times like this that really made me grateful for the technology we have to connect with others even while unable to meet in person.
Video calls will never be the same as meeting friends in-person, however the surprise cake delivery and gifts were more than I could have asked for! It was also great being able to celebrate with my friends from both Singapore and the UK at the same time via video call.
Aside from all this, most of my Summer holidays were spent working on the Warwick iGEM project, which I spoke about in my last blog post. Though it was disappointing not being able to carry out our project in the lab like initially planned, I still learned valuable skills in the "dry" aspects of scientific research which I'm sure will be very useful in my future.
One great aspect of doing iGEM was learning how to do science in a more hands-on manner - such as studying and rewriting genetic coding sequences rather than simply learning the theory of it in lectures.
In the BioSoc realm, myself and the rest of the exec focused greatly on engagement and welcoming of the new freshers who would join us in October, as the amazing experience of beginning university life was unfortunately derailed. Finding myself with more free time while staying in at home, I decided to give website creation a try and initiated the brand-new BioSoc website, hoping to create an integrated resource for new students to navigate University virtually.
Wishing to give an idea of "normal" first year for incoming freshers, I collated blog posts from current students about their experiences on each of the Life Science courses, before getting a bit carried away and creating a 43-page pdf document as a Guide to Life (Sciences) with information ranging from structing lab reports to choosing where to rent off-campus housing after first year. As always, I was grateful for a supportive BioSoc exec who were willing to help out and feedback on my ideas, despite my piling on of more work for them!
We also focused stronger than in previous years on fostering connections between current and incoming BioSoc members, hoping to at least slightly overcome the barrier of virtual interaction. I was able to dust off my training from SOTA to create some promotional/publicity material for the Society, such as these visuals for introduction posts of exec members:
Engagement with students also included various virtual social events, such as a start of year Quiz hosted in collaboration with the Department of Life Sciences who kindly sponsored prizes for quiz winners.
Singapore Society also got in touch to ask me to design their new Society hoodie, which I gladly took up and worked on over the holidays:
I also "engaged" with other prospective Warwick students via some work I did for the British Council's Study UK!
This was once again an interesting challenge as I'm not great in front of cameras... something which I've definitely had to get over in the past year doing online learning, meetings and seminars! Still, I enjoyed the opportunity to promote the benefits for other Singaporeans to consider studying in the UK - I especially wanted to acknowledge the work of Warwick Life Sciences Department in particular, as they've been incredibly supportive and understanding towards students throughout the pandemic, despite the uncertainty and unpredictabiliity of the global pandemic.
As I looked towards the beginning of my final year in October, it was definitely a bittersweet feeling knowing that I'd be soon moving on to the next stage of my life. My time living and learning in Warwick has given me many memories I'll treasure for life.
Hope that all are doing well despite the pandemic, and I will report back on how Term 1 went in the next update!
After a gruelling 9 months of work, I am happy to announce that the 2020 Warwick iGEM team has been awarded a Gold medal at the recent, virtually held, iGEM Jamboree! Despite a lack of lab access throughout March to November and having to work across various timezones, we developed a colibactin derivative biosensor that would ideally aid in the speedy and non-invasive detection of colorectal cancer.
Unfortunately due to COVID, most of the iGEM process was done entirely at my bedroom desk... so there are not as many interesting pictures in this blog post as I would have liked.
Though without lab access we were unable to create a physical prototype of our biosensor, we were able to utilise in silico protein modelling software to create a theoretically functional receptor. In a wet lab, this could be converted into sequences to grow in bacterial cultures to produce our biosensor. Afterwards, we would have tested our biosensor's accuracy and activity e.g. false positives, using different ligand concentrations in cell-free systems. Following a few more refinement and design cycles, we may create an even more sensitive biosensor.
The proposed implementation of our biosensor would be as a complementary test kit, initially in conjunction with current tests carried out in the UK and many other countries - such as the FIT or Fecal Immunochemical Test. After further testing of its accuracy and usefulness to benefit healthcare, our big-picture goal would be for our test kit to be used on its own to pre-emptively measure risk of developing colorectal cancer, therefore allowing earlier treatment and improved patient outcomes.
I am incredibly grateful to have had the chance to represent Warwick at this international competition, which I had known about since my IB years at SOTA. Back then, I read about the amazing projects the teams were getting up to with awe, never imagining that I would be able to do the same!
At the iGEM Jamboree, the first-ever virtual one (where in normal years the team would fly over to Boston, Massachusetts to present and defend our project in front of a live audience and judging panel, as well as take part in a multitude of workshops and poster presentations) we created a 20-minute video, presented for 20-minutes for a judging panel, and created a wiki from scratch outlining all aspects of our project. As the Jamboree occurred in November 2020, I was still working on the iGEM project during the first half of Term 1 of my final year at University. I had to juggle lectures, assignment deadlines and Society responsibilities along with plenty of iGEM work, in the hopes of earning us a Gold medal. Additionally, as we were a relatively small team of 9 this year I was tackling entire branches of the project on my own. Thankfully my effort (and lack of sleep) paid off, as the two areas of the project that I did, Human Practices and Education, were the two criteria that qualified us for the Gold medal! In fact, several members of the Judging panel specifically commended Human Practices in their judging feedback, which was incredibly rewarding to read after all the stress and hard work.
It was also a great experience to be able to work in a multi-disciplinary team in an academic setting, as our team had members from Life Sciences as well as the departments of Mathematics, Computer Science and Economics. This required us to work extremely collaboratively and make sure that we never got too lost in the technical jargon of our respective fields in order to function as a group, which I felt was very useful in preparing me for work after graduation - even though I aim to pursue a career in biological sciences, "Biology" is becoming increasingly interdisciplinary both in the directions of hard sciences like Math and Physics as well as the social sciences like Economics and Psychology.
Having to work on the project virtually was another challenge - admittedly our team had some initial issues making sure that everyone was on the same page early in our project, problems exacerbated by us living in a range of different time-zones. Due to other responsibilities some team members had taken up during lockdown it was also incredibly difficult to get everyone to meet with video calls to keep up with progress on our project. I eventually figured out a shared spreadsheet for all members, writing down a list of actionable steps for every member of the team along with suggested deadlines, which appeared to work for the most part. Though it was quite technologically complicated and awkward leading the team in this way, it was still a useful idea for virtual working which I was able to gradually refine over the months of the project, and will likely be utilising for future group projects as we are still working from home in the UK.
As I am interested in pursuing further study/research in Neuroscience, I actually applied to join the iGEM team hoping to be able to create a neuroscience-related project, though of course I knew it wouldn't be guaranteed and would have to be a subject agreed on by the whole team. During the interview, we were actually asked to come up with and briefly research a potential synthetic biology project on the spot, and complete a short presentation on our idea within 20 minutes! In the mad rush that ensued we created an idea for a colour-changing sticker that could detect levels of lactic acid (a waste product of the bacteria that cause milk to spoil) and tell the consumer whether the milk had actually gone bad and could no longer be used. The goal of it was to reduce food waste and reassure consumers, as currently all we have to go by is the "best before" dates printed on the carton.
This project then evolved into another food project - we broke into subteams and created presentations for a range of potential projects: from microplastic pollution, to a vegan and ethical synthetic egg substitute for baking, to a probiotic food supplement that could "re-balance" the gut microbiome and improve overall health. Funnily enough, it was the smallest idea that didn't have a presentation that eventually became out final project - which was to engineer a colorectal cancer detection system.
As part of the Education and Science Communication efforts of the project, I was able to interact with iGEM teams from all over the world via virtual meetups. It was a great experience to see how other teams worked on their chosen projects, and it gave us the chance to share science casually in a way that we would have if COVID did not put a stop to the usual in-person iGEM Jamboree! Though virtual meetings simply cannot replace the immersion of the normal iGEM Jamboree it did allow us to take part in and host even more international events throughout the Summer, without needing to spend money.
Presenting our project to the other UK iGEM teams at a meetup hosted by the University of St. Andrew's team
Warwick-hosted meetup with other iGEM teams in the Diagnostics track.
I was also able to present our project to incoming students at the Department of Life Sciences as part of the Fresher's orientation week events on student research. Hopefully it got the new students excited about the amazing opportunities they can try out for in their time at Warwick!
My favourite work done for the project was definitely the Human Practices. I enjoyed it immensely as it gave me a taste of what "real" science would actually be. Although I enjoy my laboratory modules in my degree and they definitely contribute very much to my learning, the experiments done are largely planned for us in the syllabus and have been repeated across the years as they are effective for teaching us students foundational techniques and knowledge. However, if I were to successfully go into higher education and research in Biology, I will no longer have the privilege to have my projects nicely planned out and curated for me!
Tackling the iGEM project's human practices gave me insight to more of the full process of science, including seeking and applying for funding with a self-proposed idea, considering the social, ethical, safety and legal implications, developing the idea (including deciding which softwares to use, which stakeholders and organisations to interview) and doing market research in order to find out how our final test kit could be best implemented. I delved into legal documents and policies, economic and business analyses, and sociological and psychological papers that were all relevant to the issue of cancer testing kits despite their seemingly disconnected fields of study. One aspect I found particularly interesting was researching why large numbers of at-risk individuals refuse to or avoid taking the current FIT kit, which is already non-invasive and relatively speedy. As I usually read scientific papers for my modules but enjoyed doing the Humanities back in IB, making sense of social science research papers was an exciting challenge.
Another challenge I faced was the building of our wiki - as I was not well-versed (i.e. a complete beginner) at HTML code and website building, it was tricky attempting to put my pages together! Luckily I had friends who were coding experts who were able to help me out, and I eventually started getting the hang of the basics.
To wrap up all the information I had gleaned from the entire Human Practices branch of the project, I created various reports and comparisons, as well as an overview timeline of our process, all of which can be seen on my wiki page here: https://2020.igem.org/Team:Warwick/Human_Practices . As we weren't able to test our product in a lab due to COVID, I hope that by making all this information available (and hopefully clearly written) on our wiki, future teams that are pursuing projects in similar areas can speed up their own research process and benefit from my work!