Podcast by Future Science Group
In the Zone: phosphorylated biomarkers
In the Zone: phosphorylated biomarkers by Future Science Group
Environmental sequencing for COVID-19
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 and 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.
Introduction: 00:00-01:58Introducing environmental surveillance for infectious diseases: 01:58-03:30COVID-19 response vs previous environmental sequencing work and how it has prepared people for COVID-19: 03:30-06:18The benefits of wastewater screening over clinical testing: 06:18-07:10Challenges of wastewater testing: 07:10-09:10Monitoring for SARS-CoV-2 variants: 09:10-10:55Understanding transmission patterns: 10:55-12:00Identifying signs of viral vaccine escape and tracing transmission: 12:00-14:50PCR vs NGS techniques for environmental sequencing: 14:50-16:05Tips for best practice when conducting environmental sequencing: 16:05-17:50Practical results of environmental sequencing data on outbreak suppression: 17:50-20:40Investigating mutation rates in the environmental samples: 20:40-23:20Emerging techniques in wastewater surveillance: 23:20-25:10Developing standard protocols and structure for wastewater surveillance: 25:10-28:20
Implementing sensors into cell culture systems: an interview with Abbie Underhill
In this podcast, Tristan Free – Digital Editor at RegMedNet – speaks to Abbie Underhill (Scientific Bioprocessing) about the role that sensors have in regenerative medicine, including the biggest challenges behind implementing sensors in cell culture systems.
How PCR has prevailed during the COVID-19 pandemic
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, 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, which lead to the delivery of 100,000 tests a day, 5% of the USA's 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: 00:00-02:00Why 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- 30:00
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.
Reproducibility in microbiomics
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.
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.
Spotlight: precision medicine and companion diagnostics
Spotlight: precision medicine and companion diagnostics by Future Science Group