Talking Techniques

In this episode, supported by Fortis Life Sciences, we delve into the relationship between mitochondria, inflammation and cancer, discussing the new techniques that are bearing fruit in this field, such as spatial analysis.

Our expert insight for this episode comes from Phillip West, Principle Investigator of the West lab at Texas A&M Medicine (TX, USA). Philip explains the role mitochondria can play in cancer and heart disease, reveals some of his most exciting discoveries of late and provides technical tips for investigating this field.

Listen on to discover how his use of spatial techniques has helped uncover mechanisms linking mitochondrial damage to the stifling of the immune system in the tumor microenvironment and the latest breakthroughs at the intersection of mitochondria and cancer.

Contents:

• Introduction: 00:00-01:30
• The innate immune system, in inflammation and disease: 01:30-04:20
• The role of mitochondria in innate immunity: 04:20-07:00
• Categorizing DAMPS and their role in cardiovascular disease: 07:00-08:40
• Mitochondria and cancer: 08:40-11:55
• Techniques for the investigation of mitochondria: 11:55-15:20
• Best practice techniques for spatial studies: 15:20-17:35
• Discoveries made using spatial approaches to mitochondrial investigations: 17:35-19:55
• The latest developments in the intersection of mitochondria, cancer and inflammation: 19:55-22:20
• What is one thing you would ask for to improve your understanding of this field? 22:20-24:20

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In this episode, sponsored by Zymo Research, we explore the microbiome and how long-read sequencing techniques are changing our approach to the field and the exciting discoveries that they have led to. To do this we speak to Kris Locken, Molecular Biologist in the Research & Development department of Zymo Research (CA, USA), and Jeremy Wilkinson, Global Marketing Specialist for Microbial Genomics at PacBio (CA, USA).

Find out how microbes compare to nuts and what this means for the challenges of metagenomic sample preparation, how long reads can stack up vs short reads for metagenome assembly and much more, all in this latest episode of Talking Techniques

Intro: 00:00-01:55

What is metagenomics and why is it important for microbial studies? 01:55-03:55

How has long-read sequencing impacted metagenomics? 03:55-06:05

Long-read vs short-read sequencing workflows: 06:05-07:15

Addressing barriers to long-read sequencing: 07:15-08:45

Sample preparation for long-read sequencing: 08:45-12:20

Development of long-read sequencing to improve accuracy and capabilities: 12:20-14:40

Best practice for assembly and analysis: 14:40-17:40

Exciting examples of the benefits of long-read sequencing: 17:40-20:00

What would you wish for to improve the ability long-read sequencing in microbiomics: 20:00-21:40

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This episode, our second recorded at Neuroscience 2022 (13-19th April 2022; San Diego, CA, USA), delves into the importance of open data in neuroscience and the FAIR guidelines, which encourage researchers to make their data Findable, Accessible, Interoperable and Reusable.

Sharing her considerable expertise in this area is one of the authors of the FAIR guidelines, Maryann Martone, who provides some key examples of the successes that open data practices have delivered so far and cautionary tales for how current practices are damaging the field.

Listen on to find out how to implement open data practices, how they can help your lab and why Maryann sees it as our responsibility to resolve!

Contents:

• Introduction: 00:00-02:00
• Introducing open neuroscience and the meaning of FAIR 02:00-03:00
• Exposing outdated paradigms in science: academic targets, publications, reproducibility and data accessibility: 03:00-06.30
• Incentivizing open data and reassigning value restructuring academia: 06:30-08.40
• The impact of FAIR within labs: 08:40-09:50
• Challenges of establishing and barriers to Open and FAIR neuroscience 09:50-12:00
• The reception of these guidelines in the field: 12:00-16:50
• Examples of the impact of open data in the spinal cord injury community: 16:50-18:10
• Marryann’s experience of enacting changes early in her career: 18:10-21:20
• Judging value in scientific research and understanding your purpose: 21:20-24:20
• The importance of investment: 24:20-26:30
• The impact of industry on lab data: 26:30-27:50
• Practical tips for addressing your lab data: 27:50-31:10
• Key tips for preparing data for an open-source repository 31:10-33.15
• The FAIR data principles explained: 33.15-37:50

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In this episode of Talking Techniques, we head to the Ecuadorian rainforest to chat about the use of sequencing in conservation with Zane Libke, a field researcher based at Sumak Kawsay In Situ (Pastaza, Ecuador). Zane discusses how he turned his fascination with nature into a career, his current work using nanopore sequencing technologies to find undescribed species and helping train future field researchers.

We also explore the benefits of fighting biodiversity in a more local-centric way and using research to protect the area from exploitative companies.

• Intro: 00:00–01:35
• Zane’s work at Sumak Kawsay In Situ: 01:35–05:05
• Turning a fascination with nature into a career: 05:05–08:20
• The importance of sequencing for conservation: 08:20–12:25
• Technologies being used to sequence in the field: 12:25–14:15
• Portable nanopore sequencing with the MinION: 13:15–15:35
• Exporting samples means exporting opportunity: 15:35–18:40
• The sequencing workflow: 17:40–24:50
• Data processing: 24:50–27:45
• Using these technologies to find undescribed species: 27:45–32:20
• Fighting biodiversity loss in a more local-centric way: 32:20–34:55
• Using research to protect the area from exploitation: 34:55–38:50

What the future holds: 38:50–43:22

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In this special episode of Talking techniques, one of two recorded at Neuroscience 2022, we speak to Tim Harris (Howard Hughes Medical Institute, VA, USA). Tim is the creator of Neuropixels, neural recording probes inserted into the brains of animal models, which allow researchers to collect signals from hundreds of individual neurons in different brain regions simultaneously over extended periods of time.

Here, he shares the story behind his creation and details how they have changed the data collection landscape in Neuroscience. Tim also considers every inventor’s greatest concern: has his invention led to purely positive outcomes for the field? By enabling the collection of huge datasets have Neuropixels led to studies that bury findings in vast swathes of data or have they enabled researchers to collect enough information to discover the emphatic truth?

Listen now to find out Tim’s opinions on these contentious debates in neuroscience and get key tips for utilizing neuropixels! 

• Introduction: 00:00-03:00
• Tim's symposium on the capabilities of Neuropixels: 03:00-04.00
• Key takeaways from the symposium: 04:00-07:45
• The story of the development of neuropixels: 07:45-13:50
• Best practice tips for utilizing neuropixels: 13:50-15:15
• Challenges of utilizing neuropixels: 15:15-15:50
• Addressing the challenge of big data and sharing uncertainty: 15:50-17:30
• How neuropixels have accelerated neuroscience data generation: 17:30-19:30 

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In this episode of Talking Techniques, we head to the Ecuadorian rainforest to chat about the use of sequencing in conservation with Zane Libke, a field researcher based at Sumak Kawsay In Situ (Pastaza, Ecuador). Zane discusses how he turned his fascination with nature into a career, his current work using nanopore sequencing technologies to find undescribed species and helping train future field researchers.

We also explore the benefits of fighting biodiversity in a more local-centric way and using research to protect the area from exploitative companies.

• Intro: 00:00–01:35
• Zane’s work at Sumak Kawsay In Situ: 01:35–05:05
• Turning a fascination with nature into a career: 05:05–08:20
• The importance of sequencing for conservation: 08:20–12:25
• Technologies being used to sequence in the field: 12:25–14:15
• Portable nanopore sequencing with the MinION: 13:15–15:35
• Exporting samples means exporting opportunity: 15:35–18:40
• The sequencing workflow: 17:40–24:50
• Data processing: 24:50–27:45
• Using these technologies to find undescribed species: 27:45–32:20
• Fighting biodiversity loss in a more local-centric way: 32:20–34:55
• Using research to protect the area from exploitation: 34:55–38:50
• What the future holds: 38:50–43:22

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In this episode of the Talking Techniques podcast, we explore microbiomes and the techniques used to profile them. Get an overview of the different techniques’ working principles, their pros and cons and the different applications that they are best suited to.

Providing an expert insight into this field is Annabelle Damerum, Microbiome R&D Scientist at Zymo Research. Annabelle reveals some key tips best practice when profiling the microbiome and details the importance of an emerging aspect of the field: the vaginal microbiome.

• Into: 00:00-01:50
• Why it is important to profile microbiomes. 01:50-04:15
• Key applications of microbiome profiling: 04:15-06:10
• Techniques used to profile the microbiome and their working principles: 06:10-09:20
• Targeted sequencing: 06:10-08:00
• Shotgun metagenomics: 08:00-09:00
• Metatranscriptomics: 09:00-9:15
• The strengths and limitations of these techniques: 09:12-             
• Targeted sequencing: 09:20-10.15
• Shotgun metagenomics: 10:15-11:25
• Metatranscriptomics: 11:25-11:50
• Matching techniques with applications: 11:50-13:30
• Tips for best practice for using these techniques: 13:30-16:25
• What is one thing you would ask for to improve the ability of microbiome profiling techniques: 16:55-18:10
• Investigating the vaginal microbiome: 18:10-20:55
• Conclusions and closing: 20:55-22:10

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In this special episode of Talking Techniques, brought to you from the Federation of European Neuroscience Societies Forum (FENS; 9th–13th July 2022), an expert panel discuss their research into the relationship between the gut–brain axis and addiction.

The panel features Benjamin Boutrel (Lausanne University Hospital; Switzerland), Lorenzo Leggio (NIH Intramural Research Program; MD, USA) and Nathalie Delzenne (University of Louvain; Louvain-la-Neuve, Belgium), who discuss their current research into the role of the microbiota in alcohol addiction, if this work could be translated into the clinic, and if similar processes are at play in other addictions, such as food and cocaine.

The discussion also features an audience Q&A, which explores the microbial relationship between mother and fetus, and social factors in addiction.

• Introduction: 00:00–01:35
• Introduction to panelists: 01:35–03:40
• Techniques being used to investigate the relationship between the gut and addiction: 03:40–06:55
• Translating this research to the clinic: 06:55–11:40
• Parallels between alcohol addiction and other addictions, such as food, cocaine and tobacco: 11:40–17:05
• Microorganisms as drivers of behavior: 17:05–18:30
• The hot topic of gut health: 18:30–20:30
• Future directions for the research, including microbiota transfers, precision medicine and avoiding alcohol dependence: 20:30–24:35
• Audience Q&A – microbial elements between mother and fetus, and social factors in addiction: 24:35–29:15

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In this episode, supported by BrandTech, returning guest Rob Vries, CEO of HUB organoids (Utrecht, The Netherlands), fills us in on the advancement of 3D cell cultures and organoids over the last 2 years, starting off by documenting how the pandemic impacted their development and uptake.

We also discuss how the recent FDA Modernization Act, removing the requirement for drug candidates to be tested on animals, has impacted the drive for improved models, the key techniques available to analyze them and what still needs to change for 3D cell cultures to fully replace animal models in the lab.

Listen today to find out which resources can help you begin to work with 3D cell cultures, their most exciting recent applications and how issues of reproducibility are currently being addressed in the field.

• Intro: 00:00-00:50
• How COVID-19 impacted the uptake and development of 3D cell cultures: 00:50-02:05
• Key developments in 3D cell culture technology in the last 2 years: 02:05-03:00
• Intestinal organoids and the investigation of irritable bowel syndrome: 03:00-5:50
• Evaluating assembloids: 05:50-08:35
• Complexity vs clinical relevance: 08:35-10:45
• The impact of 3D cell cultures in precision medicine in cancer: 10:45-12:40
• The impact of the FDA’s Modernization Act on 3D cell culture uptake: 12:40-14:45
• What needs to improve in organoid technologies to fully replace animal models? 14:45-16:10
• Changing inbuilt reliance on animal models: 16:10-18:30
• Key techniques to analyze organoids: 18:30-19:50
• Developments in imaging technology that have improved the analysis of organoids: 19:50-21:15
• Current challenges in 3D cell culture implementation and reproducibility: 21:15-24:15
• Improving access to 3D cell cultures: 24:15-25:55
• Resources to help people implement organoids into their work: 25:55-27:15
• Searching for the holy grail in 3D cell cultures: 27:15-28:00

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In this episode of Talking Techniques, supported by Bio-Rad, we discuss a key component of many gene therapies: recombinant adeno-associated viruses (rAAVs) and their production. These viruses act as efficient, accurate delivery vesicles for the gene therapy’s plasmid.

Speaking to Associate Director of Biopharma Product Marketing at Bio-Rad Laboratories, Mark White, we take a look at the different expression systems used for their production and compare their advantages, before looking at some of the challenges involved in the production rAAVs, such as host-cell contamination.

Discover the tools that can help minimize host-cell contamination and differentiate between nuclease resistant and nuclease reactive contaminant DNA and find out about some of the most exciting developments in rAAV technologies. 

• The role of rAAVs in gene therapies: 00:40-02:15
• The production of rAAVs and gene therapies: 02:15-03:30
• Why are HEK cells so popular for cell therapy production? 03:30-05:45
• HEK vs SF9 Insect cell expression systems: 05:45-06:45
• Challenges in cell therapy expression systems: 06:45-08:05
• Host DNA contamination: 08:05-10:30
• The risks of host DNA contamination: 10:30-12:45
• Key techniques to minimize host DNA contamination: 12:45-14:40
• The advantages of ddPCR in gene therapy production: 14:40-17:50
• Distinguishing between nuclease resistant and nuclease reactive host cell DNA: 17:50-19:10
• The most exciting developments in rAAV technology: 19:10-20:20
• What is one thing you would ask for to improve rAAV and gene therapy development 20:20-26:38

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