Mixing biology with mathematics, engineering and computing
As with any biological engineering group, we take the Richard Feynman quote "What I cannot create, I do not understand" as scripture. While developing a greater understanding of existing biological systems, we also aim to develop new systems that can help to solve some of the key challenges facing the world. To do this we combine wet and dry lab work to explore three inter-related areas: microbial communities, self-organisation, and quantitative methods.
"A scientific drawing of a synthetic microbial community in the style of Santiago Ramón y Cajal" generated by DALL·E
I had the pleasure of being the external examiner for Harman Mehta's PhD viva. Harman (a student in Rodrigo Ledesma-Amaro's group) has undertaken some fantiastic work on bioproduction with synthetic microbial communities.
The culmination of our Research Culture award was a day of discussions and fun to support the new group leaders at UCL. We had a website hacktathon, candid talks from inspirational acadmemics, plenty of food and drink, and a fantastic arts session hosted by Mary Yacoob.
We're very sad for Pedro Fontanarrosa, from the Barnes group, to be leaving us. He's done some really great computational work on microbial communities and will be missed. He managed to get one great paper out before he left and there's another one in the works.
Our annual departmental PhD symposium was a great success. First and final year PhD students give oral presentations and second years present posters. There's always an amazing variety of research and it's a great opportunity to catch up with everyone.
Alice Cook attended the EMBO practical course in computational modelling of multicellular systems. We look forward to her returning with new insights and ideas.
Paula Mugica, from Angel Goni-Moreno's group in Madrid, is joiing us for a few months over the Summer to work on spatial biocomputation.
We had our BBSRC New Investigator grant funded! This will support our work on synthetic microbial communities over the next five years. We're going to be hiring 2 postdocs and a Research Assistant, so if you are interested in working with us, please reach out.
We were lucky enough to welcome Sonja to UCL. She's recently moved to Imperial College London from the Netherlands and presented her research on toxins targeting fungi.
Kim Owen from the Barnes group successfully defended her PhD thesis. She did some really cool work with bacteriocins targeting cancer associated pathogens and some RRI work to understand public acceptance of engineered bacterial therapies.
Louie returned to Goldsmiths University to give his microbiology workshop to art students.
Alice Cook attended the Alan Turing Institute's annual Living Systems Symposium organised by the Learning the Organisational Principles of Living Systems Interest Group.
I travelled to Belgium to exam a PhD viva for Lucas Henrion from Frank Delvigne's group. Lucas gave an excellent public presentation on his work assessing heterogeneity in microbial phenotypes.
Chania's paper on bacterial microcompartments has been published!
Chengtai Yin will be joining us for his MRes Synthetic Biology research project. He will be working on using the dCas13 system to control the growth of populations within microbial communities.
The whole group headed off to Hinxton for this year's SBUK. Alice, Casey and Louie all presented posters on their work. It was a great opportunity to catch up with friends and colleagues in the field.
Miranda Xiyao Shou will be joining us for a project as part of her Masters in Biointegrated Design. She is interested in cultuing microbial communities with funcitons such as electron production, at architectural scales.
We were lucky enough to be visited by several members of Chao Zhong's group while they were in the UK. We had a great time discussing our work and sharing ideas over coffee.
Donny Chang will be joining us for his final year dissertation project. He will be working on analysing the dynamics of a toggle switch within a microbial community.
We say goodbye to Paul. Having finished his Master's thesis with us, he is going on to do a PhD at Cambridge University.
Louie travelled to Heidelberg to attend the EMBO workshop on Synthetic Biology in Action. I (Alex) attended the first of these workshops when I started my PhD and found it to be a fantastic experience.
Congratualtions to Mod on her graduation. She is going off to York to do a Masters in Bioinformatics. We will be excited to see her progress.
Once again, we got together to have some food and play games. Despite Alice perpetually avoiding being photographed, she somehow always ends up on the winning team.
Casey is bringing the lab into the kitchen. She has been fermenting the first batch of (non-alcoholic) rice wine. We are all excited to see how it turns out.
Jack and Linda, from the Barnes group, have published a paper on targeting pathogenic bacteria with bacteriocins.
Along with the Barnes group, we had a fantastic day white water rafting and then walking through the Lee Valley, ending with a lovely meal with some old lab members.
All three PhD students in the group contributed to a review titled Synthetic microbial ecology: engineering habitats for modular consortia , published in the Journal of Applied Microbiology.
Casey and I were invited to attend a workshop at the Nuffield Council on Bioethics. It was a fantastic opportunity to discuss the ethical implications of our work with a diverse group of experts, most of whom were not scientists.
Today Mod gave her final project presentation and we bid her farewell.
It was excellent to be invited to join a British delegation of synthetic biologists to the US. We had a fantastic dinner at the British consular residence in Atlanta, and a fascinating day with the faculty at Georgia Tech. Most of our time was spent attending the Engineering Biology Research Consortium (EBRC) annual meeting, where I was lucky enough to present some of our work on engineering microbial communities.
Chania from Chris Barnes' group has a new pre-print on bioRxiv, looking at a micro-compartment in E. coli Nissle, that may be useful for future microbiome engineering applications.
Louie was invited to introduce some students at Goldsmiths University to the fun of microbiology. They learned about our work in synthetic biology, and spent the day learning how to culture environmental microbes. It will be really exciting to see where their creativity will take these concepts.
Griffin has finished his thesis on using ABC SMC to design microbial communities, and we bid him farewell.
It was a great pleasure to give a talk at the Gogec meeting. It's one of my favourite synbio endeavours, the organisers are fantastic and I'm always excited to see what the students come up with.
We had a great time with a pot-luck and playing games. My proudest moment was obviously winning at Mahjong.
I was invited to give a talk to one of our sister departments, Structurla and Molecular Biology. It was wonderful to properly meet some of the people working across the road from us and share our research.
We welcomed Prof. Lucia Marucci from Unviersity of Bristol to give a talk to the IPLS about her work on whole cell models.
We welcome Paul Goodman to the group to work on his MRes Synthetic Biology dissertation. He will be working on minimising the innate interactions between our E. coli chassis and their environment.
Sara from Sandrine Geranton's group has a new pre-print on bioRxiv, looking at effects of joint pain on behaviour in mice.
We had a joint Christmas lunch the Barnes group this year. It was great to unwind a bit with everyone and to celebrate the end of an exciting year.
I gave a talk at the MathBio series organised by Philip Pierce. It was the first time in a long time that I could go into detail about our modelling approaches and get feedback from a group of mathematicians.
I was fortunate to be invited to give a talk at the UCL Institute for the Physics of Living Systems meetup. I'm incrementaly getting better a presenting the spatial computing work.
We all went to Bristol for this year's SBUK conference. It has always been one of my favourite conferences, and is a lovely opportunity to catch up with friends and colleagues in the field. I had the opportunity to present the work that we recently finished up in Chris Barnes' group on spatial computing.
Chris Barnes' group has a new pre-print on bioRxiv, that I helped with, detailing our work targeting pathegenic bacteria. We created a new platform for the delivery of antimicrobial peptides using engineered bacteria.
We are very lucky to have three new students join the group for their final year dissertation projects.
Welcome Casey Chen and Louie Destouches! It's really starting to feel like a research group now. I'm very excited to see what we can all achieve together.
I helped to organise the department away day. We held it in a lovely space in the art nouveau Mary Ward House. As a relative newbie in the department, it was great to have the opportunity to meet everyone, put some names to faces, and have some fun.
I was in Leuven to give a talk to students on a summer school for Design and Control of Microbial Communities. It was a fantastic few days, arranged by Didier Gonze, Karoline Faust and Leo Lahti.
Welcome Alice Cook as the first PhD student in the group. She will be working on self-organising cellular communities in collaboration with Katie Bentley at the Francis Crick Institute.
I was honored to be invited to present at the Synbio Africa conference in Kampala, Uganda. It was a wonderful opportunity to meet many new researchers and hear about challenges that are unique to biological engineering in Africa.
We have a new pre-print on bioRxiv detailing our work with Chris Barnes' group on spatial computing. We developed a new digital computation platform using gradients of diffusible molecules that are interpreted by simply engineered E. coli.
I had a great time at the Microbiome Modelling Workshop orgainsed by Eriko Takano at Manchester University. Two days learning alot about soil and human microbiomes, genome scale and dynamic modelling, and a whole host of other things. The conference dinner was at the newly refurbished Manchester Museum - with a whale skeleton suspended above the dining tables.
I was very priveleged to be invited to give a talk to Rodrigo's group at Imperial College London. Their work in the area of microbial communities is excellent, and it was wonderful to have some time to talk science at seek his advice.
I had a fantastic day visiting Tom Gorochowski and the Biocompute Lab at Bristol University. It was great to find out what everyone was working on and to share some of our latest work.
I was asked to contribute a piece to a Cell Systems collection of opinions on the key challenges in engineering microbiomes. There are some fascinating ideas in there and it is a real privelage to be included alongside some incredible scientists.
I had a great time chatting to Otim about all of his work with SynBio Africa. It certainly seems like there's a lot to be excited about. But I don't know where he finds all of his energy!
I attended a fantastic workshop organised by Miao Guo to discuss future innovations in food production with researchers from King's College London and the food industry.
I have two EPSRC funded PhD positions available to start in Autumn 2023. The first project is working with Chris Barnes to produce a new platform for the assembly of microbial communities. The second project is working with Mike Sulu to understand the limits of using microbial communities in future bio-industrial applications.
Today is the day I start my own research group!