The molpigs Podcast molpigs

Join the molpigs team for a discussion with Prof. Katherine Dunn from the University of Edinburgh about her work on using DNA nanotechnology for medical applications and her exciting new ideas regarding "electrosynbionics," using biological engineering to tackle hard problems in energy production and storage. She also discusses her experiences transitioning from terahertz spectroscopy to biophysics and the challenges in teaching and mentoring students to prepare them for a variety of career paths in today's interdisciplinary world.

Katherine completed her undergraduate degree in physics at the University of Oxford. She started a PhD there in Terahertz Spectroscopy before seeing the light and changing to DNA Origami. She has continued to study molecular programming within an engineering context, working on DNA nanomachines for bioelectronic computing at the University of York. She is now a Senior Lecturer at the University of Edinburgh, and has been named as one of the Top 50 Women in Engineering 2021 by the Women’s Engineering Society.

---Find more information at the episode page here:https://podcast.molpi.gs/media/dunn-k-68bc3b6fe46f8f0d/

This week’s podcast is with Erika DeBenedictis, a new principal investigator who is founding her lab at the Crick Institute in London. Her lab will focus around the broad field of bioautomation, but before talking about any of that, we delve into her past. Erika is just another one in a long string of podcast guests who has had an unconventional entry into the field of molecular programming! She started her scientific career interested in space science, telling us that her interest was kindled as a child because of the accessibility of this field to anyone. This led her to work at NASA’s Jet Propulsion Laboratory. Afterwards she talks about her time as a PhD student in Kevin Esvelt’s lab working on massively parallelised directed evolution, harnessing the power of robotics in order to develop her technique known as PRANCE. She talks about the use of these techniques in expanding the genetic code, and the main hurdles in doing so.

We then move on to her post-doc at David Baker’s lab in Washington, where she worked on using machine learning for de novo protein engineering. At the same time we talk about the place of robots in modern laboratories, whether they will replace all hand pipettes (and wet lab scientists!), and the feasibility of cloud laboratories in making science more accessible.

Finally we move on to the start of Erika’s new lab at the Crick Institute, her vision for what she wants to do, and ultimately the bioautomation challenge, which is a programme spearheaded by her to get bioautomation equipment into more laboratories to accelerate research.

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Erika began her science career as a computational physicist and astronomer and worked on space mission design at NASA’s Jet Propulsion Laboratory. She received a BS in Computer science from Caltech in 2014. She then worked at Dropbox as a software engineer and at D. E. Shaw Research on computational biophysics.

She received a PhD in Biological Engineering from MIT in 2020, working with Kevin Esvelt. Erika’s research focused on developing techniques for robotics-accelerated evolution (PRANCE) and applying these techniques to quadruplet codon genetic code expansion and origin of life research in E. coli. Her postdoc in David Baker’s lab at the Institute for Protein Design at the University of Washington focused on using machine learning techniques to systematically engineer de novo proteins.

In 2022, she launched the Bioautomation Challenge, a program designed to make experimental life science more reproducible, scalable and sharable by giving researchers access to programmable experiments.

She now leads the Biodesign Laboratory at the Francis Crick Institute in London, UK.

---Find more information at the episode page here:https://podcast.molpi.gs/media/debenedictis-e-59f6feebc1495d48/

In this episode the molpigs team talks with Greg Tikhomirov about his experience starting a new molecular programming lab and his visions for “a new nanotechnology”. We learn about his journey from wanting to build large, beautiful molecules to his work at the interface between molecular design and material science.

Greg Tikhomirov is an assistant professor in Electrical Engineering and Computer Sciences, with a background in chemistry, bioengineering, medicine, and nanotechnology. He has a longstanding dream to engineer life-like artificial systems, motivated by the realization that incomprehensible natural complexity arises from comprehensible fundamental laws. Ti Lab at Berkeley is pursuing the design and fabrication of devices with atomic precision by combining the strengths of rational top-down engineering and bottom-up biomolecular assembly. A key goal is to adopt the powerful but still proof-of-concept self-assembly approaches of DNA nanotechnology to engineer new, useful devices.

---Find more information at the episode page here:https://podcast.molpi.gs/media/tikhomirov-g-cb5ef2637de05b5b/

Join the molpigs team for a conversation with Eva Bertosin about her work on building nanoscale rotors during her PhD with Hendrik Dietz. This is a "poster podcast," so we will occasionally be referencing figures in the associated poster which can be found at the link below. The DNA origami rotor was inspired by the rotational mechanism of ATP synthase, which Eva and her colleagues had to simplify and abstract to create a functional DNA structure which could demonstrate rotational diffusion. She explains how they used cryoEM to optimize design, and how new tools for analyzing cryo data made the ambitious data analysis involved in this process possible. And the promises of using molecular simulation to help inform design. We round out the conversation with discussion of how she got into DNA design, visions for the future, and advice to future students about tackling huge projects.

Eva is a postdoc in the Cees Dekker's research group at the Technical University of Delft. Her work is focussed on building artificial systems that are inspired by natural components of the cell. In particular, she is working on biomimetic systems to study transport of molecules through the nuclear pore complex. She obtained her PhD in 2021 working in Hendrik Dietz' group at the Technical University of Munich. During this time, she built a novel rotating nanostructure made of DNA origami components with interlocked and coupled motion. This work was chosen as one of the finalists of the CeNS Nano Innovation Award 2021. She got her MSc degree at the Technical University of Munich and her BSc in physics studying at Padua University and at the Georg-August-University Göttingen.

Poster: https://podcast.molpi.gs/media/bertosin-e-db84e966a4c6b894/poster.pdfVideo: https://podcast.molpi.gs/media/bertosin-e-db84e966a4c6b894/brownian.mp4

---Find more information at the episode page here:https://podcast.molpi.gs/media/bertosin-e-db84e966a4c6b894/

Join the molpigs team as they have a discussion with one of the theoretical giants of molecular programming: Anne Condon. Over the wide-ranging conversation, she shares her insights on NP-complete problems, solving RNA folding with good data, and how best to teach and mentor students in a manner that creates great researchers and facilitates diversity in the field.

Anne Condon is a professor of Computer Science at the University of British Columbia, of which she was formerly head of department, and also a fellow of the Royal Society of Canada. She is known for her extensive work in computational complexity theory and design of algorithms, in the context of bioinformatics, hardware verification, combinatorial auctions, and of course, DNA computing. As well as numerous awards for her work in Computer Science from bodies including the ACM, she has also received many awards for her leadership in advancing women in computing, and has previously held the NSERC/General Motors Canada Chair for Women in Science. She completed her bachelor’s degree at University College Cork, and her doctorate at the University of Washington.

For listeners who would like to skip to the less technical parts of the interview, and hear Anne’s insights on diversity, mentorship and creating a positive experience for students, that section begins 28:33 into the episode.

---Find more information at the episode page here:https://podcast.molpi.gs/media/condon-a-331aad943a3b7c48/

On this episode Hannah, Boya, Erik and new co-host Dhaval sit down with Jurek Kozyra, founder of the molecular programming startup, Nanovery. Over the course of this wide-ranging interview, he tells us about how learning biology can help your dating life, his PhD work at the intersection of biotech and computer science and his early ventures in cherry picking and private investigation before diving into his story of building a successful startup with funders, employees, and lab space.

Jurek Kozyra is the founder and CEO of Nanovery. He obtained his BSc in Computer Science with Artificial Intelligence from the University of Nottingham, where he studied bio-inspired and unconventional computing. Afterwards, Jurek earned his PhD in DNA nanotechnology and DNA computing from Newcastle University working at ICOS (one of the leading computational synthetic biology research groups in the UK). He was also an entrepreneurial lead for a university biotech spin-out based on the DNA barcoding technology he developed. In 2018 Jurek started Nanovery—a molecular diagnostic company developing DNA nanorobots for early detection of diseases from blood samples. The mission of the company is to enable accurate and simple testing closer to the patient bedside.

Nanovery: https://www.nanovery.co.uk

---Find more information at the episode page here:https://podcast.molpi.gs/media/kozyra-j-7f09821bb076e517/