Talking Techniques

We are talking all things DNA methylation in this episode, providing a brief explanation of epigenetics and the technologies involved in the study of DNA methylation, before exploring the application of these techniques in the study of infectious diseases and cancer.

Revealing all of this information is my guest Chloé Goldsmith, Postdoctoral Research Fellow at Canberra University, whose research focuses on DNA methylation, Hepatitis B Virus and the link between lifestyle and the epigenome. Chloé explains the strengths and weaknesses of the different techniques used to explore DNA methylation and highlights the advances in long-read sequencing that are dramatically improving this aspect of epigenomic research.

Chloé also discusses some of the most interesting insights that she has gained by taking a single-cell and single-molecule approach to her research and highlights some of the recent findings in the field that have caught her attention and broadened our understanding of epigenetics in disease.

Listen today to find out what functions remain to be improved for more insightful epigenetic studies and for some key insights into the future of the field.

Introduction: 00:00-01:45

Introducing the epigenetics and the different types of epigenetic regulation: 00:45-02:55

Techniques involved in the exploration of DNA methylation: 03:55-05:50

Challenges of bisulfite conversion techniques: 05:50-07:15

Recent developments in DNA methylation technologies: 07:15-09:40

Long reads vs short reads for epigenetic studies: 09:40-10:45

Epigenetics in infectious disease research: 10:45-13:15

Lifestyle, the epigenome and HBV: 13:15-16:00

Epigenetics in cancer research: 16:00-18:05

Recent developments in our epigenetic understanding of disease: 18:05-19:40

One area of technology that needs to be improved: 19:40-21:50

Aspirations for the field: 21:50-23:25

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In this episode, supported by Roche, we explore a vital aspect of many next-generation sequencing studies: target enrichment. Here, regions of interest are selectively amplified before sequencing takes place. More specifically we examine some of the new technologies improving this key step and their impact on oncology research.

My guest for this episode is Brian Godwin, Director of Reagent and Assay Development at Roche sequencing. Brian reveals the myriad of ways that poor target enrichment can impact a study while highlighting its importance at the foundations of many research efforts. Discover the key limitations of some target enrichment techniques and the new technologies that are improving this step, leading to a new suite of applications in oncology research, where damaged or degraded DNA samples are common.

Listen today for an overview of the target enrichment process, the most exciting applications of this technique future potential of this step.

• Intro: 00:00-01:30
• Why conduct target enrichment? 00:40-02:45
• Established technologies for target enrichment: 02:45-04:10
• Challenges of working with these technologies: 04:20-06:40
• The impact of these challenges on sequencing results: 06:40-07:35
• New technologies to address these challenges: 07:35-09:25
• Primer extension in PCR and target enrichment: 09:25-11:40
• Exciting applications of primer extension target enrichment: 11:40-13:25
• Improving target enrichment in oncology and its impact on the field: 13:25-16:15
• If you could ask for one thing to enable primer extension target enrichment to make the greatest possible impact on the NGS and oncology communities, what would it be? 16:15-18:00

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In this episode, we roam the world of recombinant proteins and their production, discussing the challenges of their production, and recent evolutions in protein engineering that have brought the field into a golden era of innovation.

I'm joined by recombinant protein engineering expert Yuning Chen, R&D Manager at Sino Biological, who discusses the key applications of recombinant proteins, the aspects of certain products that make them difficult to produce and how these difficulties can be overcome. Yuning also reveals how the manipulation of antibodies has been essential to multiple aspects of our response to the COVID-19 pandemic.

After a review of the recent evolutions in protein engineering, from cell-free systems to automation, Yuning describes his vision for the future of the field and reveals his support for the Terminator-style uprising that he believes could revolutionize it.

• The production of recombinant proteins: 00:48-02:11
• The key applications of recombinant proteins: 02:11-03:27
• What makes some proteins difficult to produce? 03:27-04:41
• Overcoming these challenges: 04:40-5:40
• Manipulating antibodies to take part in multiple aspects of pandemic response: 05:40-08:00
• The most exciting applications of recombinant proteins: 08:00-09:50
• Developments in high throughput and automated protein engineering: 09:50-11:00
• Cell-free protein engineering: 11:00-12:40
• The benefits of cell-free systems: 12:40-13:40
• What is next for recombinant protein production? 13:40-16:15
• The dream of automation for the recombinant protein production: 16:15-18:50 

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PCR has evolved rapidly over the last few years, an evolution that has been dramatically accelerated by the COVID-19 pandemic. New technologies and approaches have been brought to the fore and the full range of applications for which this technique can be applied have been highlighted, from diagnostics to basic disease research and immunology.

This episode explores this evolution, looking at how challenges presented by the pandemic forced the hand of researchers to think outside the box and build on lesser-known PCR technologies. Here, Eddy van Collenburg, Market Development Specialist at Bio-Rad (CA, USA), provides his insight into how ddPCR rose to prevalence during this time and explains how the technology is being used to enable trade, detect new variants and is being used outside of the pandemic.

Discover the key role that ddPCR can play in gene therapy research, liquid biopsies, cancer research, single-cell studies and more, in this fascinating overview of the development of PCR and where the technique can go in the future.

Contents:

• Introduction: 00:00-01:30
• Why was qPCR established as the gold standard for detection?  01:30-03:40
• Limitations of qPCR during the pandemic: 03:40-05:05
• New varieties of PCR for faster results: 05:05-05:40
• New varieties for more accurate results: 05:40-06:45
• ddPCR working principle and advantages: 06:45-09:00
• Nonclinical ddPCR applications for COVID-19: 09:00-10:45
• ddPCR in variant detection: 10:45-12:05
• ddPCR in gene therapy research: 11:05-12:30
• Liquid biopsy and cancer research: 12:30-15:20
• Combining ddPCR with NGS in research: 15:20-16:15
• What are some of the applications of ddPCR that you find most exciting? 16:15-17:10
• Applications of ddPCR in single-cell studies: 17:10-21:00
• Improvements in ddPCR: 21:00-21:45
• Tips for best practice when using ddPCR: 21:45-22:50
• What would you ask for to improve ddPCR? 21:50-24:20

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Uncover the history of molecular therapeutics, the staggering current applications and developments of these therapeutics and what their future could hold, in this episode of Talking Techniques.

To explore the field of molecular therapeutics and provide an insight into their production, is Aaron Clauson, Product Manager at Zymo research. First, we cover the ins and outs of targeting the therapies and how to select the correct type of molecular therapeutic to begin developing a drug for a specific disease, before looking at some of the setbacks and safety errors that have occurred during the development of molecular therapeutics and how researchers have learned from these tragic events.

Aaron also highlights the vital role of plasmids in almost all molecular therapeutic development, detailing the importance of keeping plasmid solutions and transfections free of endotoxins, revealing key solutions for avoiding these contaminants.

Listen today to get all you need to know about molecular therapeutics, from their inception to their most exciting examples and how we can better communicate their benefits to the public in order to avoid mistrust and confusion - as has occurred during the COVID-19 pandemic.

• What counts as a molecular therapeutic? 01:45-02:40
• Well known molecular therapeutics: 02:40-05:00
• What can molecular therapeutics achieve that synthetic chemicals can’t? 05:00-05:55
• Targeting molecular therapeutics and picking the right type of therapeutic: 05:55-08:25
• Selecting the appropriate molecular therapeutic: 08:35-11:00
• Setbacks and safety concerns in gene therapies: 11:00-15:45
• Preventing off-target effects in gene therapies: 15:45-17:35
• Challenges in the development of molecular therapeutics: 17:35-19:05
• Plasmids in molecular therapeutic development: 19:05-23:55
• Avoiding endotoxins: 23:55-27:45
• What fields do you find most exciting? 27:45-28:50
• Better communication of gene therapies to the public: 28:50-32:00
• Improving molecular therapeutic development: 32:00-37:10

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This episode centers on the critical role that high-performance liquid chromatography (HPLC) plays in the production of adeno-associated viral (AAV) therapies, the latest advances in AAV design and the next steps in their development.

Filling me in on all things HPLC and AAVs is Bella Neufeld, Director of R&D at Teknova. Bella reveals the essential validation and quality control steps required for the production of successful and safe AAV therapies and the role that both HPLC and liquid chromatography–mass spectrometry (LCMS) play in these steps. We also explore the latest development targets for these therapies, looking at how AAVs can be targeted to specific sites and tissues before descending into the treacherous topic of reproducibility in the field.

Listen today to find out the latest tips for best practice when working with HPLC, LCMS the advantages of LCMS over other analytical techniques to assess empty and full capsids and the key principles of AAV production!

• Intro: 00:00-01:25
• Explaining HPLC and its benefits: 01:25-03:30
• Developing adeno-associated viruses: 03:30-05:25 
• Chromatography in validation vs production of AAVs: 05:25-06:15
• Quality control vs hands on time: 06:15-07:35  
• Challenges in AAV production: 07:35-08:55
• Examining the level of empty and full capsids: 08:55-10:00
• The role of LCMS in determining and validating AAV contents: 10:00-11:30      
• Tips for best practice when using HPLC: 12:30-13:10
• The future of HPLC: 13:10-14:20
• Latest advances in AAV development: 14:20-15:50
• Targeting AAVs: 15:50-17:20
• Reproducibility issues in AAV development: 17:20-19:35
• Outro: 19:35-21:10

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As the transition from 2D to 3D cell cultures, or organoids, as the gold standard for modeling basic biology and disease continues, these models are being utilized in ever more intricate and impactful ways.

This episode covers the rise of organoids and their advantages over 2D cell cultures, before exploring just how representative these models are becoming and their new applications in drug discovery. To find out all this and more, I speak to Oksana Sirenko, Senior Scientist at Molecular Devices, who works extensively with the company's organoid model development programs. 

Oksana reveals the potential of these models in cancer therapeutics, driven forward by new patient-derived organoids, and notes the challenges presented by imaging these thicker, 3D models. We also explore the potential discoveries that can be unlocked by combining organoids with organ-on-a-chip models.

• What are organoids? 02:10-03:20
• Functions replicated by organoids? 3:20-04:00
• What are the advantages of 3D over 2D cell cultures? 04:00-05:40
• Just how representative are these models? 04:40-07:10
• Intestinal organoid formation 07:10-08:50
• The most exciting application of organoids 08:50-10:10
• Organoids in drug development 10:10-11:20
• Methodology of organoids in drug screening studies 11:20-13:30
• Examples of organoids in cancer drug discovery: 13:30-16:00
• Limitations of patient-derived and regular organoid models: 16:00-17:50
• Body-on-a-chip concepts and examples: 17:50-22:00
• Challenges posed by organoids for drug discovery: 22:00-24:20
• Techniques improving organoid models and analysis: 24:20-25:50
• Imaging organoid models: 25:50-26:55
• Tips for best practice when working with organoids: 26:55-28:20
• Organoid method development: 28:20-31:10
• One thing to improve organoid models or analysis for drug screening: 31:10-33:07

To find out more about the research and solutions discussed in this episode visit: www.moleculardevices.com/TechTalk8.

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Welcome to part two of this two-part episode on whole-genome sequencing (WGS) in rare disease research and treatment. In part one we discussed the impacts the technology has had on both improving the clinical diagnosis and management of rare diseases and on drug development and basic research studies.

This episode goes beyond the technology’s capabilities and into the debates surrounding how, when and why they should be used. What needs to change for the technique to be applied equitably? And how does reality stack up against science fiction in terms of people’s perceptions of ubiquitous WGS?

To do this I speak with David Dimmock, Senior Medical Director of the Rady Children’s Institute for Genomic Medicine (CA, USA); Christine Stanley, Chief Director of Clinical Genomics, Variantyx (MA, USA); and Take Ogawa, Vice President of Sales & Marketing at Psomagen (MD, USA). Each of these speakers provides their opinions on the impacts of race, religion and way of life on the application of WGS and how much is too much data.

Contents:

• Introductions: 00:00-02:20
• Gauging public perceptions of routine WGS 02:20-05:40
• The role of industry in improving WGS accessibility and capabilities: 05:40-07:35
• The appropriate use of pre-symptomatic and predictive risk findings: 08:00-11:15
• Debating the discovery of untreatable diseases: 11:15-12:45
• The impact of data biases in gene sequencing and the lack of gene references for different populations: 12:45-14:45
• The impact of religion and lifestyle on ethical considerations in the use of WGS data: 14:45-16:00
• Dealing with unintended findings or results that impact relatives: 16:00-16:45
• The value of WGS in pharmacogenomic variant findings and challenging the ACMG59 list: 16:45-19:20
• Striking the balance between fully utilizing WGS for all potential findings and ensuring maximum participation for all groups: 19:20-22:45
• Filtering data to avoid exclusion: 22:45-24:10
• Who owns WGS data? 24:10-25:15
• Consent conversations: 25:15-26:30
• Final comments: 26:30-27:15

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Love it or hate it, western blotting forms the bedrock of countless studies across numerous disciplines. Explore its history, development and applications in this episode all about the marmite of life science techniques.

Guiding me through the hand wringing, hair follicle destroying history and process of western blotting, and hopefully explaining the beauty and potential of the technique - is Kenneth Oh, Senior Project Manager at Bio-Rad Laboratories.

Kenneth reveals some of the latest developments in western blotting. Revealing how researchers are now able to validate the success of each stage of a western blot and work with smaller samples, Kenneth provides key tips for ensuring each of your western blots is a triumph.

Contents:

Intro: 00:00-01:15

History of western blotting: 01:15-3:50

What makes western blotting so tricky? 03:50-05:30

Stepwise optimization: 05:30-06:50

Stain-free western blotting: 06:50-08:50

The different variants of western blotting: 08:50-10:20

The right blot for the right application: 10:20-11:30

The most exciting developments in western bloting:11:30-13:35

New horizons for western blotting: 13:35-15:25

The impact of multiplex-western blotting: 15:25-16:30

Tips for best practice: 16:30-18:10

The future of western blotting: 18:10-20:30

Yearning for automation: 20:30-21:30

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In this episode, we take a look at one of the key steps of infectious disease research, sample collection; exploring the challenges associated with the step and the solutions available to improve infectious disease research around the globe.

Exploring the trials and tribulations of infectious disease sample collection with me is Stanislav Forman, Product Developer at Zymo Research (CA, USA). Stan explains the extreme environments in which sample collection often occurs; revealing the difficult transit and storage requirements – often involving cold chain logistics – that can derail infectious disease studies early on.

Find out how key solutions to these problems have been successfully workshopped with the US military and have even been used in work with NASA to conduct safe sample collection in space. And discover just how successful these solutions can be when faced with the blazing wreckage of a transit vehicle…

Contents

• Introductions: 00:00-01:20
• Key challenges of sample collection for infectious disease research: 01:20-02:30
• Additional challenges presented by COVID-19: 02:30-05:00
• The emergence of at-home testing: 05:00-07:00
• Established practices for sample collection and introducing DNA/RNA shield: 07:00-09:00
• Protecting DNA/RNA samples: 09:00-11:00
• Working with NASA on sample collection and protection in space: 11:00-14:20
• Protecting samples in a blazing transit van: 14:20-15:25
• The impact of inactivating and preserving sample collection products on infectious disease research: 15:30-16:30
• Areas for improvement in sample collection: 16:30-17:30
• Closing statements: 17:30-19:20

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