Talking Techniques

Explore the realm of epigenetics and gene expression, discovering the different omic ‘lenses’ used to examine these processes and the power of single-cell studies to reveal a comprehensive multiomic view of cells and their biology.  

This episode features the ever-buoyant Will Greenleaf, Associate Professor of Genetics at Stanford University School of Medicine (CA, USA) and head of the Greenleaf Lab. Will takes us through his lab’s work, detailing his attempts to understand the compacting of DNA into cell nuclei and how this impacts gene expression and epigenetic regulation.

Discover the emerging new research focus that Will has coined the “Regulome” – the collection of physical molecular components that control gene expression through factors such as chromatin accessibility.

To explore these new frontiers Will often encounters questions with no technologies available to ask them. So what does he do? Invent the technologies he needs! Find out how his lab came to develop the, now widely used, ATAC-Seq and learn of the new tools that he is looking to develop to solve even more perceptive questions.

This episode has it all, and also reveals the potential of Will’s single-cell multiomic approaches in cancer research, virology and HIV.

Contents:

·      Introductions: 00:00-02:00

·      The exploring the physical genome: 02:00-03:15

·      Chromatin accessibility: 03:15-05:15

·      Introducing the ‘Regulome’: 05:15-07:15

·      The importance of multiomics for the study of gene expression: 07:15-07:55

·      DNA methylation and histone organization: 07:55-10:30

·      Real-world impact of this research:  10:30-12:30

·      Will’s varied career path: 12:30-16:15

·      Combining multiomic datasets with computational biology and physics experience: 16:15-18:40

·      Single-cell techniques: 18:40-21:50

·      Developing ATAC-Seq: 21:50-23:50

·      New tools in development: 23:50-27:30

·      Insights into the epigenetics of cancer: 27:30-29:35

·      Insights into virology and HIV latency: 29:35-32:10

·      One wish to help explore the regulome. 32:10-33:00

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This episode, supported by Bethyl, delves into the realm of the tumor microenvironment (TME), exploring the cells that reside there and how they interact to promote tumor growth and metastasis. Discover how immune cells are attracted and manipulated by tumor cells enabling the cancer to invade neurons where they can then travel throughout the body.

Providing an expert's insight into this topic is Moran Amit, Assistant Professor at the MD Anderson Cancer Center (TX, USA). Moran exposes the nebulous interactions in the TME and describes the techniques that he uses to interrogate it, in the hope that by further understanding these interactions we will be able to design more successful, targeted therapies for neurotropic cancers.

Contents:

·      Introductions: 00:00-01:20

·      The key cells of the TME:  01:20-02:50

·      How cells of the TME  support the tumor: 02:50-05:45

·      How cancer cells influence and impact immune cells: 05:45-07:25

·      The invasion of cancers into the neurons: 07:27-9:45

·      Recruitment of neurons to the TME: 09:45-10:55

·      The evolution of neuron recruitment to the TME: 10:55-15:00

·      Techniques involved in the study of the TME: 15:00-17:00

·      Tips for best practice: 17:00-18:00

·      Tumors with neural networks: 18:00-20:05

·      Clinical impact of research: 20:05-21:50

·      The cancers impacted the most by this research: 21:50-23:25

·      The impact of neural invasion on patients and neurons: 23:25-25:30

·      One thing to improve our understanding of the TME: 25:30-28:00

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Rare diseases present a series of challenges on numerous fronts. From simply deciphering what a patient is affected by to considering how best to manage a rare condition with limited pre-existing medications available for a rare disease, each new development or breakthrough brings clinicians to a new question. While these conditions are, in isolation, rare; in total rare diseases impact 25-30million people in the USA alone.

Supported by Psomagen and featuring four fascinating guests from across the spectrum of topics and focuses in the rare disease space, this episode explores the updates to whole-genome sequencing technology that have improved the "Diagnostic Oddysey" experienced by some patients, enabled more accurate drug development and provides insight into the diagnosis and characterization of undefined rare diseases, before exploring the clinical impact whole-genome sequencing can have on clinical outcomes.

This episode features insight from four field-leading experts in rare disease research, whole-genome sequencing technologies and clinical practice for patients with rare diseases, including:

• Alan Beggs: Director of The Manton Center for Orphan Disease Research, Sir Edwin and Lady Manton Professor of Pediatrics at Harvard medical school
• Christine Stanley: Chief Director of Clinical Genomics at Variantyx
• David Dimmock: Senior Medical Director of Rady Children's Institute for Genomic Medicine
• Take Ogawa: Vice President, Sales & Marketing at Psomagen 

Contents

1. Introduction: 00:00-02:30
2. Defining the Diagnostic Oddysey: 02:30-06:20
3. Rare disease discovery: 06:20-09:20
4. Techniques involved in Rare disease discovery: 09:20-12:05
5. Whole-genome sequencing updates impacting clinical diagnosis: 12:05-18:30
6. Currently required improvements in techniques for rare disease research and management: 18:30-24:10
7. Explaining long-read and short-read sequencing: 24:10-26:00
8. Developing therapeutics for rare diseases: 26:00-30:00
9. Whole-genome sequencing in animal model validation: 30:00-31:20
10. Improving access to whole-genome available to researchers and clinicians: 31:20-33:40
11. Whole-genome sequencing improving management and outcomes for rare diseases: 33:40-38:27

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In this episode, we explore the often overlooked technique of environmental sequencing for infectious diseases and how it is being applied to the response to COVID-19. Taking the state of California as a case study of this application, I speak to Micheal Lisek, Project Manager Environmental Microbiomics at Zymo Research Corp.

Micheal outlines the basis of environmental sequencing, predominantly the screening of wastewater for signs of viral RNA, the key techniques involved in the process and challenges associated with it. Micheal also explains the key pieces of information that can be obtained by environmental sequencing and the benefits of the approach vs exclusively using clinical testing.

Micheal highlights the value of environmental sequencing for monitoring variants, understanding transmission patterns and identifying outbreaks, providing examples of the information provided to the public health officials in California that were used to successfully manage rising infections and limit the impact of a surge in cases.

Contents

• Introduction: 00:00-01:58
• Introducing environmental surveillance for infectious diseases: 01:58-03:30
• COVID-19 response vs previous environmental sequencing work and how it has prepared people for COVID-19: 03:30-06:18
• The benefits of wastewater screening over clinical testing: 06:18-07:10
• Challenges of wastewater testing: 07:10-09:10
• Monitoring for SARS-CoV-2 variants: 09:10-10:55
• Understanding transmission patterns: 10:55-12:00
• Identifying signs of viral vaccine escape and tracing transmission: 12:00-14:50
• PCR vs NGS techniques for environmental sequencing: 14:50-16:05
• Tips for best practice when conducting environmental sequencing: 16:05-17:50
• Practical results of environmental sequencing data on outbreak suppression: 17:50-20:40
• Investigating mutation rates in the environmental samples: 20:40-23:20
• Emerging techniques in wastewater surveillance: 23:20-25:10
• Developing standard protocols and structure for wastewater surveillance: 25:10-28:20

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In Part 3 of our COVID-19 diagnostics and detection miniseries, supported by Roche, we explore the contribution PCR has 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 at Massachusetts 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 the Broad Institute in 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.

• Introduction: 00:00-02:00
• Why PCR tests are so valuable: 02:00-03:10
• Changes in clinical detection rate and infectivity: 03:10-8:00
• Infectivity and exceptions to the rule: 08:00-09:00
• Sample collection methods, sensitivity and encouraging testing uptake 09:00-17:00
• The Broad Institute’s mass testing regimen: 17:00-21:00
• Developments during the pandemic and no RNA extraction PCR: 21:00-27:00
• Dreams for improving COVID-19 testing: 27:00- 30:00

This episode was supported by Roche sequencing and life science. Follow these links to find out more about the LightCycler 480 System and LightCycler 96 System.

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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: 00:00-02:00
• Explaining the reproducibility crisis: 02:00-02:55
• How microbiomics compare to other fields in terms of reproducibility: 02:55-04:05
• Challenges in reproducibility specific to microbiomics: 04:05-05:45
• The importance of reproducibility in microbiomics: 05:45-07:00
• Microbiomics in diagnostics: 07:00-10:00
• Three key causes of poor reproducibility in microbiomics: 10:00-11:30
• Is detailed documentation improving in the life sciences? 11:30- 13:00
• Actions that can improve reproducibility: 13:00-14:15
• Fecal references: 14:15-16:05
• The realities of preparing fecal references: 16:05-18:1 5
• The reception to the new fecal references: 18:15-20:35
• References vs Standards: 20:35-22:15
• Standardizing microbiomics data: 22:15-23:20
• Assessing reproducibility in previous studies: 23:20-25:15
• Dreams 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.

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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 – 1:47

Gender inequality, experiences and impact on STEM careers: 1:48 – 10:41

Underlying reasons for gender disparity in STEM: 10:42 – 17:51

Promoting gender equality in the STEM work environment: 17:52 – 30:34

Looking forward: representation and mentoring: 30:35 – 39:32

Conclusions: 39:33 – 40:10

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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.

• Introduction: 00:00-01:30
• Steve Paterson introduction: 01:30-02:15
• Introducing COG-UK: 02:15-03:20
• Becoming the wastewater working group lead: 03:20-04:35
• Key techniques and essential work in wastewater surveillance: 04:35-08:00
• Improving the sensitivity of sequencing and technological developments: 08:00-10:00
• Detecting new variants in wastewater screening: 10:00-12:15
• Learnings from the pandemic: 12:15-13:40
• Josh Quick introduction: 14:35-15:32
• The ARTIC protocol: 15:32-18:35
• Sequencing working group key techniques and key focuses 18:35-22:00
• Challenges of limited consumable supply and how to make the most of what you have got 22:00-24:30
• Learnings from the pandemic: 24:30-26:28
• New technologies, RC-PCR: 26:28-29:38
• Fantasy technology to assist with SARS-CoV-2 sequencing: 29:38-31:00
• Discovering the new variant B.1.17:31:00-33:30
• Conclusions: 33:30-34:40

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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.

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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.

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