Speakers

As the Vice President of R&D - Biologics, Dr. Lakmal Jayasinghe oversees all biological research and development projects at Oxford Nanopore. Lakmal joined ONT in 2006 after finishing his PhD in chemical biology in the University of Oxford. During his PhD in the Hagan Bayley group, Lakmal has studied different nanopores and has gained a wealth of knowledge in engineering nanopores using genetic and chemical approaches. His responsibilities at ONT include improving the readout signal of ONT platforms by upgrading its current nanopore reader and motor, as well as discovering new versions of nanopores, motors and chemistries to suit various ONT applications including protein sequencing. Lakmal also works with many academic collaborators across the world to ensure that Oxford Nanopore uses the best possible biological components and chemistries in its platforms.

Democratising Sequencing

Oxford Nanopore Technologies (ONT) aims to disrupt the paradigm of biological analysis by enabling the analysis of any living thing, by any person, in any environment. Flexibility of nanopore technology has enabled researchers to use DNA and RNA sequencing in many different fields including basic genome research, human genetics, environmental research, plant research, transcriptome analysis, animal research or in clinical research.

Nanopore sequencing delivers short to ultra-long reads of DNA or RNA with rapid or automated library preparations. Coupled with flexible workflows, multiplexing, and real-time data analysis, ONT provides scalable sequencing solutions, from portable devices like MinION that has been designed to bring easy biological analyses to anyone, to large high throughput devices like PromethION suitable for large scale genomic projects. All these devices are based on nanopore sequencing technology in which a biological nanopore is being used as the sensor to read a characteristic ‘current signal’ when a DNA or RNA strand is moved by an enzyme motor through the nanopore under an applied potential.

I will discuss details of the underlying technology of ONT, current and upcoming platforms, and new chemistries that enable ONT to achieve over 99% 1D raw read accuracy. I will further explain why nanopore sequencing is being embraced by many countries over the world during the pandemic to combat Covid.

Sir Shankar Balasubramanian is the Herchel Smith Professor of Medicinal Chemistry at the University of Cambridge and senior group leader at the Cambridge Institute. He works on the chemistry, structure and function of nucleic acids. He is a co-inventor of the leading next generation DNA sequencing methodology, Solexa sequencing (now Illumina) that has made routine, accurate, low-cost sequencing of human genomes a reality and has revolutionised biology. He has invented chemistry to decode several modified (epigenetic) DNA bases and DNA secondary structures (G-quadruplexes) in the genome and has made seminal contributions towards the understanding of their dynamics and function. His work on small molecule recognition of nucleic acids has revealed molecular mechanisms that can be exploited to modulate the biology of cancer. His collective contributions span fundamental chemistry and its application to the biological and medical sciences. Sir Shankar was knighted in the Queen’s New Year’s Honours in 2017 for his services to science and medicine and awarded the Royal Society’s Royal Medal in 2018. In 2021, he was awarded the 2020 Millennium Technology Prize and the 2022 Breakthrough Prize with Professor Sir David Klenerman for their work on sequencing technologies.

Decoding DNA

DNA has a truly extraordinary capacity to store and transmit information via multiple molecular mechanisms that involve its sequence and also its dynamic characteristics that include its chemistry and structure. Decoding the layers of information in DNA can provide insights into biology and disease states. I will discuss methods for reading information from DNA that will include basic research in our lab and also technologies that were developed in the biotech companies Solexa and Cambridge Epigenetix that came out of our lab. I will also discuss some of the implications of such technologies for healthcare and society.

Dr. Ying Lia Li (Lia) was awarded the 2021 Institute of Physics Clifford Paterson Medal and Prize. She completed her combined undergraduate and master’s degree in physics at Imperial College before working at BAE Systems. Between 2012-2016 she pursued a Ph.D. at University College London developing optical sensors and exploring macroscopic quantum state preparation. Her work involves coupling optical resonances in microresonators to mechanical motion to sense displacement over 1000x smaller than a single atom. In 2016 she was selected for the Nature/Entrepreneur First Innovation Forum in Quantum Technologies. After completing her PhD, she was awarded an EPSRC Postdoctoral Fellowship, the prestigious Royal Academy of Engineering Intelligence Community Postdoctoral Fellowship and an executive fellowship in entrepreneurship from Bristol University’s Quantum Technology Enterprise Centre. Since 2016 she’s been focused on commercializing optomechanical inertial sensors after completing successful field-trials of a hand-fabricated accelerometer funded by Dstl. Lia founded Zero Point Motion in 2020 and will transition to full-time CEO in 2022 after raising investment.

Adding photonics to semiconductor chips will revolutionize our lives

Light has transformed the way we transmit data, perform medical procedures and image the smallest objects. In 2016 LIGO used light in a new way, through a technique called cavity optomechanics, to detect gravitational waves generated from black holes a billion light years away, finally confirming a century-old theory. LIGO is now the most sensitive human-made displacement sensor in the universe, demonstrating the power of cavity optomechanics to redefine sensing limits. In this talk I’ll introduce this research field and explain why semiconductor fabrication and photonic integrated circuit engineering is creating a revolution in chipscale cavity optomechanics. As the Founder and CEO of Zero Point Motion, a Bristol based start-up creating chipscale optomechanical inertial sensors, I’ll discuss how we’re creating accelerometers and gyroscopes to track motion with greater precision. I’ll also explain why I believe you’ll soon find chipscale photonics embedded in smartphones, AR/VR and autonomous cars.

Engineering human tissues for medical impact

The classical paradigm of tissue engineering involves the integrated use of human stem cells, biomaterial scaffolds (providing a structural and logistic template for tissue formation) and bioreactors (providing environmental control, dynamic sequences of molecular and physical signaling, and insights into the structure and function of the forming tissues). This biomimetic approach results in an increasingly successful representation of the environmental milieu of tissue development, regeneration and disease. Living human tissues are now being tailored to the patient and the condition being treated. A reverse paradigm is emerging in recent years, with the development of the “organs on a chip” platforms for modeling of integrated human physiology, using micro-tissues derived from human iPS cells and functionally connected by vascular perfusion. In all cases, the critical questions relate to our ability to recapitulate the cell niches, using bioengineering tools. To illustrate the state of the art in the field and reflect on the current challenges and opportunities, this talk will discuss: (i) anatomically correct bone regeneration, (ii) bioengineering of the lung, and (iii) the use of “organs on a chip” for patient-specific studies of human physiology, injury, healing and disease.

Chasing the Smart Toilet: from tears to the UrineBot

The era of personalised medicine is not yet properly open to us, because we are not able to track trace human biomarkers in real time. In this talk, I will discuss using my own examples how translational projects can repeatedly circle an opportunity over time, requiring persistence and an agile mindset to find the right ways forward. Over the last decade we have been exploring how using optical probing of nanostructures assembled in real-time when needed, can identify signatures of small molecules in biofluids.

Going viral: harnessing data science and advanced materials for early disease detection

COVID-19 highlights the enormous human and economic consequences of an emerging infectious disease. In this invited talk, I will discuss some of the recent breakthroughs by the i-sense EPSRC IRC programme in Agile Early Warning Sensing Systems for Infectious Diseases and Antimicrobial Resistance (www.i-sense.org.uk). We are a large UK-led interdisciplinary research consortium and aim to harness the power of advanced nanosensors, deep learning, genomics and data science to track, test and treat infections much earlier than ever before. Recent research highlights span from the first machine learning algorithms of online search queries (e.g. fever, cough) adopted by Public Health England for national COVID-19 and Influenza surveillance [1], advanced quantum materials to detect viruses [2] and antimicrobial resistance [3] and deep learning approaches to support quality assured field-based testing in resource limited settings. [4] Finally, I will discuss the findings of our landscape review of digital technologies in the global public health response to COVID-19 and future pandemic preparedness strategies. [5]

References
1. 'Tracking COVID-19 using online search' Lampos, Majumdar, Yom-Tov, Edelstein, Moura, Hamada, Rangaka, McKendry and Cox npg Digital Medicine 4, 17 (2021).
2. 'Spin-enhanced nanodiamond biosensing for ultra-sensitive diagnostics' Miller, Bezinge, Gliddon, Huang, Dold, Gray, Heaney, Dobson, Nastouli, Morton & McKendry Nature 587, 588 (2020).
3. 'Cantilever sensors for rapid optical antimicrobial sensitivity testing' Bennett, Pyne, McKendry ACS Sensors 5, 3133 (2020).
4. 'Deep learning of HIV field-based rapid tests' Turbe, Herbst, Mngomezulu, Meshkinfamfard, Dlamini, Mhlongo, Smit, Cherepanova, Shimada, Budd, Arsenov, Gray, Pillay, Herbst, Shahmanesh & McKendry Nature Medicine 27, 1165 (2021).
5. 'Digital technologies in the public health response to COVID-19' Budd, Miller, Manning, Lampos, Zhuang, Edelstein, Rees, Emery, Stevens, Keegan, Short, Pillay, Manley, Cox, Heymann, Johnson Nature Medicine 26, 1183 (2020).

Websites
- i-sense EPSRC IRC in Agile Early Warning Sensing Systems for Infectious Diseases and AMR www.i-sense.org.uk
- McKendry group website: https://themckendrylab.com/
- UCL website: https://www.london-nano.com/our-people/our-people-bios/rachel-mckendry

Fluidic Analytics – Understand the Machinery of Life

Proteins are the building blocks of life. They form the structure of cells, regulate cellular activity and carry out the biochemical processes that underpin function in every living organism. Fluidic Analytics envisions a world where information about proteins and their behaviour transforms our understanding of how the biological world operates, and helps all of us make better decisions about how we diagnose diseases, develop treatments and maintain our personal well-being.

Our products are based on a fundamentally new technology platform developed at the University of Cambridge. This platform quantifies and characterizes any protein interaction rapidly and entirely in solution to deliver unique quantitative insights into proteins, their conformation, and their interactions – even in complex backgrounds, even with challenging targets. Our Microfluidic Diffusional Sizing (MDS) Technology delivers unbiased, simultaneous evaluation of molecular interactions in physiologically relevant conditions. Moreover, our technology platform helps scientists in the lab understand protein interactions in a rapid, convenient workflow that consumes just microlitres of sample. Our platform can be accessed via the Fluidity One-M work system, our Protein Interactions Lab services and assay-development offering or our Fluidity Intelligence data science tools, we are committed to helping researchers discover more about their biological systems through the power of MDS.