Category: BBI Seminars

A spotlight on Plant Synthetic Biology – BBI Webinar

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This webinar is a spotlight on plant synthetic biology, featuring three rising stars in one dynamic interactive session. Three early career researchers, hosted by Dr. Thomas Gorochowski and Dr. Emily Larson, discuss plant biology topics including reprogramming plant root growth, genome engineering, and the biodesign potential of marchantia polymorpha. The speakers include:

  • Dr. Jennifer Brophy (keynote) – ‘Reprogramming plant root growth using synthetic developmental regulation.’
  • Dr Quentin Dudley – ‘Genome engineering of Nicotiana benthamiana as an improved plant-based bioproduction system for medicinal alkaloids.’
  • Dr Eftychis Frangedakis – ‘Marchantia polymorpha: an emerging system for plant synthetic biology.’

You can watch the full recording, including Q&A here:

BBI International Webinar Series – Professor Elisa Franco, UCLA

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The Bristol BioDesign Institute‘s newly imagined webinar series for 2021 has been designed as a platform to invite the best international speakers that are aligned to our core areas of interest. These include; biomolecular design and assembly in the cell, development and delivery of bioactive molecules, minimal biology towards cell-like systems, advanced computing and digital biology. You can find our upcoming speakers for the year on the International Webinar Series section of our website.

The first speaker of 2021 is Professor Elisa Franco from UCLA, with BBI Directors, Thomas Gorochowski and Dek Woolfson, panelling. The seminar is followed by an audience Q&A session, and then a one-to-one interview where Dr. Gorochowski asks Professor Franco questions about how she got into synthetic biology and her predictions for its future. 

You can watch Professor Franco’s seminar, on ‘Programming dynamic behaviors in molecular systems and materials‘ below, or on the BBI YouTube Channel.

Abstract – Biological cells adapt, replicate, and self-repair in ways that are unmatched by man-made devices. These processes are enabled by the interplay of receptors, gene networks, and self-assembling cytoskeletal scaffolds. Taking inspiration from this architecture, we follow a reductionist approach to build synthetic materials by interconnecting nucleic acid components with the capacity to sense, compute, and self-assemble. Nucleic acids are versatile molecules whose interactions and kinetic behaviors can be rationally designed from their sequence content; further, they are relevant in a number of native and engineered cellular pathways, as well as in biomedical and nanotechnology applications. I will illustrate our approach with two examples. The first is the construction of self-assembling DNA scaffolds that can be programmed to respond to environmental inputs and to canonical molecular signal generators such as pulse generators and oscillators. The second is the encapsulation of these dynamic scaffolds in droplets serving as a mimic of cellular compartments. I will stress how mathematical modeling and quantitative characterization can help identify design principles, guide experiments, and explain observed phenomena.

A glimpse into the nanoscale world.

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By Dr Thomas Gorochowski and insights from PhD student Janine McCaughey and Research Associate Ulrike Obst.

On the 2nd October 2019, Professor Nico Sommerdijk visited Bristol for the monthly BBI seminar and provided a picture of the hidden nanoscale world underpinning biology. Nico, who describes himself as a synthetic organic chemist who got carried away when introduced to the expanding capabilities of electron microscopy (EM), has since then never looked back. His work spans the development and application of new EM imaging and microscopy methods to not only image molecular assemblies in a single static pose, but also to record movies that help unravel the steps involved in their self-assembly.

The seminar focused on the mineralisation of collagen fibril that act as the basic building block of our bones. The nanoscopic dimensions and complex, hybrid composition of mineralised collagen makes it difficult to examine. Trickier still is monitoring the multi-step process that collagen goes through to mineralise, as it forms not only at a billionth of a meter in scale, but also in an intricate, aqueous environment.

Why is understanding this process important?

Understanding the process of collagen mineralization could enable the development of new treatments for bone defects and disorders of bone mineralization, such as rickets and hypophosphatasia.

Nico highlighted that “it will also offer new opportunities for the design of new bio-inspired materials”. This can be in the form of an in vitro unit that can be biologically engineered to form mineralized collagen to precise specifications. Unravelling the minute process of mineralization could therefore benefit many branches of science, from medicine and pharmaceuticals to bioengineering.

What did the audience think?

Janine McCaughey from the School of Biochemistry explained that “Nico presented an interesting approach to enabling live cell TEM in form of a liquid chamber. This allows for imaging of dynamic processes in high resolution compared to cryoTEM that requires one sample per timepoint and therefore only delivers very limited insight into such processes”.

Ulrike Obst, a Research Associate from Cellular and Molecular Medicine, was amazed by the sheer scope of the work. “It was fascinating to find out about so many different electron microscopy techniques, and especially how they can be combined to observe dynamic biological processes at a nanoscale!”

Ulrike was also amused by this idea of “having a mini-aquarium in a microscope”, where a tiny pocket of water allows for molecular self-assembly to be watched in real-time. “It is crazy that such things are possible. It’s like a window into another world.”

Interested to find out more?

As part of his recent ERC Advanced Grant award titled “A Google Earth Approach to Understanding Collagen Mineralization”, Nico recently moved to the Radboud Institute for Molecular Life Sciences in Nijmegen, Netherlands (https://www.radboudumc.nl/en). As part of this project, his group will try to figure out how collagen is assembled by developing and combining methods able to image from the nano- to cellular-scales, providing an unprecedented understanding of this crucial biological process.

Can we build a minimal form of life? A bottom-up perspective.

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Hosted by Dr Thomas Gorochowski and PhD students Veronica Greco and Matthew Tarnowski from the Biocompute Lab. 

Dr Bert Poolman, a biochemist from the University of Groningen, visited Bristol on the 4th September to pose the question of whether it is possible to artificially create and control the physicochemistry of a cell. The ability to manipulate, control, or even create a new cell from scratch are fundamental directions for synthetic biology research.

What if we could build a cell in the lab?

Bert Poolman is part of an EU-wide project – aptly named BaSyC, or, ‘Building a Synthetic Cell’, which emerged in September 2017 combining leaders in physics, chemistry and biology from across the Netherlands to test out this theory.

“In the next decade they aim to achieve a physicochemical homeostatis in a cell where metabolic pathways and energy consumption/production systems can be better understood, optimised and synthetically built.” Veronica Greco explains. She was in the audience during his seminar.

Matthew Tarnowski, who also attended the seminar, said that Bert “highlighted some fascinating properties of cells: they are incredibly crowded, yet molecules move surprisingly fast within them.” Matthew was struck by Bert’s results demonstrating the sheer complexity of cells. “He [Bert] showed that engineering systems that mimic fundamental cellular processes is challenging”.

What was the audience reaction?

Intrigued audience members questioned the sustainability of such an ambitious project, such as how to overcome the challenge of building a synthetic ribosome and the new methods required to carefully assemble the numerous parts of a synthetic cell in a controllable way.

“The talk left me curious about how minimal life research could be completed responsibly: have the economic, social and environmental impacts been anticipated?” Matthew pointed out that the purpose behind building minimal forms of life went unanswered.

Veronica ended by noting that, “Overall, it is a very well thought out project that will require lots of different expertise and time, and surely it has all the credentials to give a big contribution to science and to change once again how the growing scientific field of synthetic biology is perceived.”

Are you a PhD or Postdoc?

BaSyC are offering various work packages to PhDs and Postdocs within one of their partner institutions. Due to the interdisciplinary nature of the work (combining physicists, chemists and biologists), “working at different locations and labs is more the rule than the exception”. There are opportunities to be involved in BaSyC activities: progress meetings and trainings, summer schools and the biennial international symposium on Building a Synthetic Cell.

Interested in joining the project?

Visit the BaSyC website for more information.

No jobs available for the specific part of the programme you are interested in? Feel free to send an open application to the corresponding PI directly – the PI’s contact details can be found at their people page.

For general questions and queries: info@basyc.nl