How PCR has prevailed during the COVID-19 pandemic
Season 2, Ep. 5
In Part 3 of our COVID-19 diagnostics and detection miniseries, supported byRoche, we explore the contributionPCRhas made towards diagnosis during the pandemic. Providing me with an insight into the world of PCR diagnostics is Tyler Miller, Clinical Pathology Resident and Research Fellow atMassachusetts General Hospital(MA, USA), where he was instrumental in setting up the testing regimen for the Hospital.Ty details the attributes of PCR that lead to it becoming the gold standard for diagnostic tests, before explaining the variance in clinical detection rate during a patient’s disease course and how this variation correlates with the infectivity of the patient. Ty also delves into the variety of sample collection methods available, how each of these methods compares in terms of sensitivity and their ability to be integrated into exciting novel PCR techniques.We also look at the work of theBroad Institutein establishing a mass testing effort that involved automation, workflow optimization and hundreds of new staff, ultimately leading to the delivery of 100,000 tests a day, almost 5% of the USA’s total COVID-19 testing at the time. All of this rapid work has led to dramatic changes in the PCR technique and process. These changes are perhaps exemplified by PCR testing without RNA extraction and purification, which Ty explains was partly developed due to the limited supplies available to researchers at the beginning of the pandemic.ContentsIntroduction: 00:00-02:00Why PCR tests are so valuable: 02:00-03:10Changes in clinical detection rate and infectivity: 03:10-8:00Infectivity and exceptions to the rule: 08:00-09:00Sample collection methods, sensitivity and encouraging testing uptake 09:00-17:00The Broad Institute’s mass testing regimen: 17:00-21:00Developments during the pandemic and no RNA extraction PCR: 21:00-27:00Dreams for improving COVID-19 testing: 27:00- 30:00This episode was supported byRoche sequencing and life science. Follow these links to find out more about theLightCycler 480System andLightCycler 96 System.
Reproducibility in microbiomics
Season 2, Ep. 4
Returning to the contentious topic of the Reproducibility crisis –the inability of many study results to be replicated by different research groups or labs –this episode, supported by Zymo Research, zeros in on the topic within the field of microbiomics. Speaking to me about the topic is Raul Cano, Chief Scientific Officer at the BioCollective. Raul discusses the crisis and explains why it is prevalent in the emerging field of microbiomics before taking a look at the key role that microbiomics is beginning to play in the field of diagnostics, and how – if we make changes now – lasting improvements can be made in the field. Raul also lays out the three key areas that are holding back reproducibility in microbiomics and explains the actions that can be taken to improve the situation.Contents:Introduction: 00:00-02:00Explaining the reproducibility crisis: 02:00-02:55How microbiomics compare to other fields in terms of reproducibility: 02:55-04:05Challenges in reproducibility specific to microbiomics: 04:05-05:45The importance of reproducibility in microbiomics: 05:45-07:00Microbiomics in diagnostics: 07:00-10:00 Three key causes of poor reproducibility in microbiomics: 10:00-11:30Is detailed documentation improving in the life sciences? 11:30- 13:00Actions that can improve reproducibility: 13:00-14:15Fecal references: 14:15-16:05The realities of preparing fecal references: 16:05-18:1 5The reception to the new fecal references: 18:15-20:35References vs Standards: 20:35-22:15Standardizing microbiomics data: 22:15-23:20Assessing reproducibility in previous studies: 23:20-25:15Dreams for reproducibility in microbiomics: 25:15-26:55 This episode is supported by Zymo Research. If you would like more information about the fecal reference mentioned in the podcast, you can visit the product page here.
How can we achieve gender equality in STEM?
Season 2, Ep. 3
This International Women’s Day takeover episode, with special guest host BioTechniques’ Senior Digital Editor Abi Sawyer, takes a look at the results of Future Science Group’s (London, UK) survey for the scientific community on gender equality and parity in STEM.Abi’s guests on this episode are the Vice President of Epidemiology and Clinical Evidence at IQVIA (NC, USA), Dr Christina Mack; the Executive Director for the Pharmaceutical Research Computing Center at the University of Maryland School of Pharmacy (MD, USA), Dr Ebere Onukwugha; a Lecturer, Science Communicator and Author based in Cardiff (UK), Dr Emma Yhnell; and the Director of the Neuroscience Center Microscopy Core at the University of North Carolina–Chapel Hill (NC, USA), Dr Michelle Itano.They discuss the results of Future Science Group’s survey, share their own experiences of gender inequality as well as situations where they’ve felt supported, and outline how the STEM community can push further towards gender equality and parity. Contents:Introduction: 00:00 – 1:47Gender inequality, experiences and impact on STEM careers: 1:48 – 10:41Underlying reasons for gender disparity in STEM: 10:42 – 17:51Promoting gender equality in the STEM work environment: 17:52 – 30:34Looking forward: representation and mentoring: 30:35 – 39:32Conclusions: 39:33 – 40:10
COG-UK: sequencing SARS-CoV-2 and detecting the novel variant B.1.1.7
Season 2, Ep. 2
This episode, supported by Tecan, takes a look at the role the COVID-19 Genomics UK Consortium (COG-UK) has played sequencing SARS-CoV-2 and surveying for COVID-19. To do this I speak to two key members of the consortium; Steve Paterson, Professor of genetics at the University of Liverpool and lead for the wastewater working group of COG-UK; and Josh Quick, Future Leaders Fellow at the University of Birmingham and lead at the COG-UK Sequencing working group.Steve discusses some of the techniques required to detect SARS-CoV-2 in wastewater, the challenges that such a vibrant sample can present, and gives his account of the part that wastewater surveillance played in the management of the new variant B.1.1.7.Josh provides us with further insight into the technologies used to sequence SARS-CoV-2, explains how he designed the ARTIC protocol for sequencing the virus and why it came to be so widely used. We go on to discuss the issues of limited lab consumables such as pipette tips and how you can make the most out of your limited lab supplies. Josh also describes the bizarre act of serendipity that aided in the discovery of the B.1.1.7 variant.ContentsIntroduction: 00:00-01:30Steve Paterson introduction: 01:30-02:15Introducing COG-UK: 02:15-03:20Becoming the wastewater working group lead: 03:20-04:35Key techniques and essential work in wastewater surveillance: 04:35-08:00Improving the sensitivity of sequencing and technological developments: 08:00-10:00Detecting new variants in wastewater screening: 10:00-12:15Learnings from the pandemic: 12:15-13:40Josh Quick introduction: 14:35-15:32The ARTIC protocol: 15:32-18:35Sequencing working group key techniques and key focuses 18:35-22:00Challenges of limited consumable supply and how to make the most of what you have got 22:00-24:30Learnings from the pandemic: 24:30-26:28New technologies, RC-PCR: 26:28-29:38Fantasy technology to assist with SARS-CoV-2 sequencing: 29:38-31:00Discovering the new variant B.1.17:31:00-33:30Conclusions: 33:30-34:40
COVID-19 diagnostics: which test should you choose?
Season 2, Ep. 1
RT-PCR, antigen and antibody testing; each has its niche and each has a flaw. But what are the key differences between each of these tests and what are the key things to consider when selecting the appropriate COVID-19 diagnostic for you? In this podcast, supported by Zymo Research, I speak to Senior Scientist in assay development Paolo Piatti in order to answer this question. Whether you are a concerned citizen looking for the best test to take to inform your behavior, or a researcher aiming to understand which testing systems you need to set up in your lab – this episode should have the answers for you.In addition to these key points, Paolo addresses the importance of testing during the rollout of vaccine programs and issues of false negatives in diagnostics, examining what, if anything, can be done to improve the accuracy of testing programs.
Andy Tay: Forbes, awards and championing diversity in STEM
Season 1, Ep. 12
In this episode, I speak to a very special guest. Winner of this year's Future Science Future Star award, Andy Tay is a fantastic example of an early career researcher who has seized every opportunity with both hands and is not content to leave science as he found it. We discuss Andy's fascinating research into pain modulation using magnetic biomaterials, which got him included on the Forbes 30 under 30 list for 2019 and his work in science communication. Andy is a champion of diversity in STEM, something he embodies both in his science communication and in the organization of his lab.Here, he delves into the tactics he uses to promote diversity and gives us his tips on how to set up and run a diverse and inclusive lab.Andy pairs all this information with some key tips for early career researchers who may be looking to emulate his success, giving us an insight into the key moments in his childhood and early career that lead him to where he is today and teaching us some lessons about the importance of curiosity.
How has neuroimaging continued and flourished during the COVID-19 pandemic?
Season 1, Ep. 11
In this episode, I speak to Michelle Itano, Director of the Neuroscience Center Microscopy Core at UNC-Chapel Hill and recent addition to the BioTechniques Editorial Board, about her work at the core. Michelle outlines how she has modified the core to make it possible for imaging research to continue throughout the pandemic, using a combination of specialist users and remote working techniques. Michelle provides her key learnings, from this process and last 7months, in keeping the core and her labs COVID-secure.We discuss some of the projects that have been able to continue throughout the pandemic and the recent successes of an autism trial, which provides key information on the behavioral effects, diagnosis prediction of the condition. Michell also informs me of the work the core has been involved in that directly address COVID-19, using resonance scanning to examine epithelial organoids and cell models, elucidating the utility of resonance scanning in the study of 3D structures.Episode image created by Damaris Lorenzo of the Lorenzo Lab at the UNC Microscopy Core
The reproducibility crisis: where are we now and how can we progress?
Season 1, Ep. 11
In this episode I address the 'reproducibility crisis'. The concerning trend in the life sciences in which published papers and established principals are unable to be repeated by other researchers and, at times, even by the researchers who provided the initial results. To do this I speak to two researchers driving forward reproducibility in the life sciences, Marc Raphael from the United States Naval Research Laboratory, and Elizabeth Iorns, CEO of Science Exchange. Marc discusses his recent trial of independent verification and validation (IV&V) labs in a live science setting, highlighting the lessons learned from the experience and exploring the differences observed in attitudes and approaches to reproducibility between the life sciences and engineering, where mark began his career. Elizabeth discusses her work with Science Exchange and the reproducibility project: cancer biology. Elizabeth notes the key themes that have been exposed by the reproducibility project that are holding back the resolution of the crisis and explains what she thinks has worked so far in improving reproducibility. This leads to a fascinating discussion between Marc and Elizabeth, comparing and contrasting their experiences and noting the different challenges that they face in trying to improve the state of research in the life sciences. In fact, their camaraderie was so strong that interviewing these two was a real treat and for lots of it, it was much better for me to sit back and watch as they debated a topic that they are both clearly very passionate about!I hope you enjoy listening as much as I enjoyed recording this episode!*The Talking Techniques podcast is hosted and produced by Tristan Free for BioTechniques. We would love to here more from our listeners about your opinions on the podcast, what you would like to hear more of and what you think we could do better!Please get in contact on any of the platforms below.Twitter: @TristanFreefsgEmail: email@example.com
CRISPR: developing an equitable technology amidst a global pandemic
Season 1, Ep. 10
In this episode, I speak to Geoffrey Siwo about CRISPR and the challenges facing its development into a technique that can be applied equitably across the globe. Geoffrey talks about the importance of seizing the opportunity to influence the progress of the embryonic gene-editing technology for the better, before the data bias in genomic data and the disparity in researchers working on the technique leads to ingrained differences in the success of the application in different populations. The impact of the COVID-19 pandemic on this development is also exposed.We also discuss Geoffrey's work, using CISPR in antiviral research to as a way of identifying small molecules capable of inducing broad-spectrum antiviral responses, with the potential to combat SARS-CoV-2. Tune in to find out how Geoffrey believes we can develop CRISPR to be a truly equitable technology and to hear just how hopeful he is for the future of the technique. *The Talking Techniques podcast is hosted and produced by Tristan Free for BioTechniques. We would love to here more from our listeners about your opinions on the podcast, what you would like to hear more of and what you think we could do better!Please get in contact on any of the platforms below.Twitter: @TristanFreefsgEmail: firstname.lastname@example.org