What we’re about
This is a group for people interested in Synthetic and Engineering Biology and open technologies: the DNA-based reprogramming and computational modelling of living systems and low-cost hardware for biological instrumentation. It is based in the University of Cambridge, supported by the Engineering Biology Interdisciplinary Research Centre (EngBio IRC, formerly SynBio IRC). The meetings provide a venue to explore new joint projects and there will be opportunities for funding. Register with the site to stay in touch and up to date.
For more information on the Engineering Biology IRC go to http://www.engbio.cam.ac.uk
Upcoming events (4)See all
- MRC Toxicology Unit Seminar “Engineering the assembly of microbial communities”MRC Toxicology Unit, Cambridge
Date and time: 12.50-14 pm 26th September. Note: External participants should be 12.50 pm at reception to get access to the room by 13pm.
Please RSVP to ensure your place. Any problems signing up please contact Indra Roux email email@example.com
Location: Main Seminar Room, MRC Toxicology Unit. Gleeson Building, Tennis Court Road.
Title: “Engineering the assembly of microbial communities”
Speaker: Prof. Kerwyn Casey Huang from Standford University
KC Huang was an undergraduate Physics and Mathematics major in Page House at Caltech, and spent a year as a Churchill Scholar at Cambridge University working with Dr. Guna Rajagopal on Quantum Monte Carlo simulations of water cluster formation. He received his PhD from MIT working with Prof. John Joannopoulos on electromagnetic flux localization in polaritonic photonic crystals and the control of melting at semiconductor surfaces using nanoscale coatings. During a short summer internship at NEC Research Labs, he became interested in self-organization in biological systems, and moved on to a postdoc with Prof. Ned Wingreen in the Department of Molecular Biology at Princeton working on the relationships among cell shape detection, determination, and maintenance in bacteria. His lab is currently situated in the departments of Bioengineering and Microbiology & Immunology at Stanford, and his current interests include cell division, membrane organization, cell wall biogenesis, and the organizational principles of bacterial communities. He has been director of the Biophysics Graduate Program since 2015, and the chair of the DEI committee for the Aspen Center for Physics board.
Microbiota dynamics arise from a plethora of interspecies interactions, including resource competition, cross-feeding and pH modulation. The individual contributions of these mechanisms are challenging to untangle, especially in natural or complex laboratory environments where the landscape of resource competition is unclear. Here, we developed a framework to estimate the extent of multi-species niche overlaps by combining metabolomics data of individual species, growth measurements in pairwise spent media, and mathematical models. When applied to an in vitro model system of human gut commensals in complex media, our framework revealed that a simple model of resource competition described most pairwise interactions. By grouping metabolomic features depleted by the same set of species, we constructed a coarse-grained consumer-resource model that predicted assembly compositions to reasonable accuracy. Moreover, deviations from model predictions enabled us to identify and incorporate into the model additional interactions, including pH-mediated effects and cross-feeding, which improved model performance. In sum, our work provides an experimental and theoretical framework to dissect microbial interactions in complex in vitro environments.
- Cafe SynthetiquePanton Arms, Cambridge
Any Problems Signing Up - please email firstname.lastname@example.org to sign up
Café Synthetique is the monthly meetup for the Cambridge synthetic and engineering biology community with informal talks, discussion and pub snacks. Kindly sponsored by Cambridge Consultants.
We meet monthly at the Panton Arms to share the latest developments in engineering biology and related approaches and techniques. Speakers range from students and group leaders to industry professionals and entrepreneurs. We are always open to speaker suggestions so if you would like to nominate yourself or another person, please get in touch via email@example.com.
### Monday 2 October- Dr Diana Fusco, Assitant Professor, Dept of Physics
### Crispr-trapping bacteriophages to shine the light on phage-bacteria interactions at single-cell resolution.
Despite the long history and wide-spread use of bacteriophage-derived molecular biology tools in molecular biology and microbiology, the level and importance of stochasticityin the infection timeline is poorly understood, as most standard methods rely on bulk, population average measurements. By combining the Crispr approach to genetically edit T7 phages and introduce fluorescent markers and mother-machine microfluidic devises, we are finally visualizing the different events in the phage infection timeline and uncovering new mysteries in phage biology.
During the talk, I'll explain the details of how we use Crispr to edit the phage genome, the current challenges with the technique, and also some unexpected new findings that we would have never guessed before.
Diana's interest in biology started as a physics undergrad studying topological properties of the transcriptional network in budding yeast. After that, she was hooked and moved to soft matter and protein self-assembly for her PhD, under the supervision of Dr. Charbonneau at Duke. Unsatisfied with addressing questions exclusively on the computational side, she embarked onto a hybrid postdoc in Dr. Hallatschek lab at UC Berkeley, where she studied the evolutionary consequences of spatial range expansion combining microbiology and mathematical modeling. She is currently an assistant professor in biological physics at the Cavendish lab, where she pursues fundamental questions in microbial life and evolution using a combination of physical modelling, synthetic biology and fluorescence microscopy.
It would be great to see the community coming together again with free aromi food available! Drinks available to purchase at the bar. We look forward to seeing you at the Panton Arms, Cambridge.
Places are limited to 30. Please rsvp sign up here. Any Problems Signing Up - please email firstname.lastname@example.org to sign up
- Cambridge Opentrons Meet n GreetHopkins Building, Cambridge
The Opentrons Team will be visiting Cambridge on Wed 11 Oct 2023 and is looking for an opportunity to get to know the OT and automation users within the University of Cambridge!
The Engineering Biology IRC has kindly agreed to organise a Cambridge Opentrons User Group Meet-and-Greet event, which will be held at Stephenson Seminar Room, Dept. of Biochemistry, Tennis Court Road, Cambridge CB2 1QW (find us https://www.bioc.cam.ac.uk/about-us/how-to-find-us) on Wed 11 Oct at 10:00-11:30 BST.
We welcome you to come along and showcase what/how you currently use your OT-2s and automation workflows, learn more about the Opentrons Flex (including demos of some new Flex components: 96-channel pipette, gripper, and onboard tablet display), and get a chance to network with other OT users within the university.
Schedule of events:
09:45 Registration and Welcome Teas/Coffees
10:00 Opentrons Team Introduction and Opentrons Flex Demo
10:30 Cambridge OT Users Flash Talks/Showcase (5min per speaker, any format of choice)
Please rsvp at MeetUp to attend this event. Any problems signing up please email email@example.com
If you have any questions, please don't hesitate to get in touch with Vicky or Yan-Kay firstname.lastname@example.org
- EngBio ECRs Meet, Greet and TalkPostdoc Centre, Cambridge
NOTE Time Change to 4pm-5pm, Postdoc Centre, 16 Mill Lane Basement
Monthly meeting of the University of Cambridge EngBio Postdoc & Postgrad Groups. Open to postdocs, students and research staff from across the University and affiliated institutes (MRC-LMB, Babraham Institute, Wellcome Sanger Institute).
Join our monthly meets to meet fellow Early Career Researchers from across the University interested in biology, engineering, design, computer science, bioethics and more. This is a great opportunity to meet postdocs from other schools and departments, share knowledge and ideas, establish connections and collaborations, and find out more about EngBio Postdocs activities such as funding calls and support.
Each session will host 1-2 lightening talks from ECRs covering research, tools & technologies, and fields & applications of synthetic and engineering biology. This will be followed by informal discussion (and free food and drink!).
Please RSVP as below.. Any problems with RSVP, please email email@example.com
Monday 16 October, 4pm -5pm at Postdoc Centre, Basement, 16 Mill Lane
### Short Talk by Guillermo Serrano Najera, Dept. of Genetics
### Title: Inferring individual cell behaviours from the tissue movements.
Abstract: During my PhD I worked with very large image time-lapse dataset of living embryos. We developed techniques to analyse these data to study cell behaviours including individual cell segmentation and tracking. However, we also developed computational techniques far easier and faster to use that give information on cell behaviours analysing the tissue flows even when individual cells cannot be detected either because they are not labelled, or because the quality of the image is poor.
Bio: Dr Guillermo Serrano Nájera is interested in how cells coordinate their behaviours to generate tissues and organs during animal embryonic development. He completed his PhD at the University of Dundee, where he combined computational analysis, microscopy, and developmental biology to study early chick embryos. He described how to manipulate chick embryos to reproduce tissue movement typical of other species (frogs, fish, and chameleons). These results show the plasticity of embryonic development and illuminate how different animal morphologies can evolve. He continues exploring embryonic development and evolution using novel stem cells based in vitro systems that mimic essential aspects of early development such as germ-layer differentiation and morphogenesis.
There is an attendee limit of 20 people. Please register/rsvp here, and we will send a confirmation. A waitlist will be made available once spaces are filled.
For more information about EngBio Postdocs and to register see: https://www.engbio.cam.ac.uk/postdocs or contact firstname.lastname@example.org