Preprints in Motion

This week we discuss the exocyst with Dr Hannes Maib @hannes_maib a Post-Doctoral Researcher at the University of Dundee @dundeeuni!! He explains the complexities of the exocyst as well as the exciting biochemistry and binding assays used to understand its formation. In addition Hannes speaks candidly about starting working in a new lab as a Post-Doc, his views of hierarchical journal systems and how preprinting can help ECR take back ownership of their work in a great discussion with our host Dr Jonny Coats.

Read the full preprint -> https://www.biorxiv.org/content/10.1101/2021.10.14.464363v1.full

Other links -> LINK

This episode was produced by Emma Wilson and edited by John D Howard .

If you enjoyed this show then hit that subscribe button and leave a review. If you love what we are trying to do then support us on Patreon https://www.patreon.com/preprintsinmotion where tiers start at as little as £1 a month!

For the latest podcast news and updates follow us on Twitter @MotionPod or visit our website; www.preprintsinmotion.com.

Produced by JEmJ Productions (find us on Twitter: Jonny @JACoates, Emma @ELWilson92, John @JohnDHoward8) and generously supported by ASAPbio (https://asapbio.org | @asapbio_).

This week we discuss prefigurative politics in academia with Stefano Davide Vianello, a PhD student at @EPFL_en in Switzerland. This is the idea that in order to change how a system works we should act in a way that reflects the change we want to see. In Stefano’s case: preprinting to be the end goal and he has therefore submitted a preprint without any intention of submitting it to a journal. We speak to him about his reasons for this, why he is against academics paying for open access as well as 4 key points on what has to change to make academia more open for everyone, not just the global north.

Read Stefano’s preprint: https://www.biorxiv.org/content/10.1101/2020.06.07.138883v3

Read Stefano’s opinion piece: https://commonplace.knowledgefutures.org/pub/vzn21ssv/release/2

This episode was produced by Jonny Coates and Emma Wilson, with editing by John D Howard.

If you enjoyed this show then hit that subscribe button and leave a review. If you love what we are trying to do then support us on Patreon https://www.patreon.com/preprintsinmotion where tiers start at as little as £1 a month!

For the latest podcast news and updates follow us on Twitter @MotionPod or visit our website; www.preprintsinmotion.com.

Produced by JEmJ Productions (find us on Twitter: Jonny @JACoates, Emma @ELWilson92, John @JohnDHoward8) and generously supported by ASAPbio (https://asapbio.org | @asapbio_).

This week we discuss mice in space and the impact of prolonged space flight and how this can relate to austraunoughts with Jessica L Braun @jess_l_braun a PhD Student at the Brock University @BrockUniversity. Jessica speaks about her work looking at soleus and tibialis anterior muscles of mice which have spent 35-37 days on the international space station comparing Ca2+ uptake and SERCA function. We discuss everything from a mice mission control to cardigan rhythms and the different effects on males and female mice. We also talk about preprints and the increased attention it can bring as well as how to improve public engagement.

Read the full preprint: https://www.biorxiv.org/content/10.1101/2021.09.27.462048v1.full

This episode was produced by Emma Wilson and edited by John D Howard.

If you enjoyed this show then hit that subscribe button and leave a review. If you love what we are trying to do then support us on Patreon https://www.patreon.com/preprintsinmotion where tiers start at as little as £1 a month!

For the latest podcast news and updates follow us on Twitter @MotionPod or visit our website; www.preprintsinmotion.com.

Produced by JEmJ Productions (find us on Twitter: Jonny @JACoates, Emma @ELWilson92, John @JohnDHoward8) and generously supported by ASAPbio (https://asapbio.org | @asapbio_).

This week we discuss Parkinson’s Disease and single molecule spectroscopy with Dr Derrick Lau, a PostDoc at the University of New South Wales (@UNSW). Single molecular spectroscopy can be used to track the formation and purification of α-synuclein aggregates, a hallmark of PD, and potentially lead to a tool for early diagnosis of Parkinson’s Disease. We discuss how single molecular spectroscopy is transferable to medium throughput and use bio fluids for early diagnosis of Parkinson Disease but also potentially other neurodegenerative diseases. Finally, we discuss preprints, what it it like to apply for PostDocs in a pandemic as well transitioning from immunology and neuroscience. 

Read the full preprint - https://www.biorxiv.org/content/10.1101/2021.08.09.455607v1.full

Other links

Microbiome in PD- https://www.nature.com/articles/s41531-021-00156-z

Immunotherapy in PD - https://pubmed.ncbi.nlm.nih.gov/31978602/

α-synuclein in PD patients biofluides - https://pubmed.ncbi.nlm.nih.gov/32444560/

AttoBright - https://www.nature.com/articles/s41467-019-13617-0

https://www.nature.com/immersive/d41586-021-02563-x/index.html

This episode was produced by Emma Wilson and edited by John D Howard .

If you enjoyed this show then hit that subscribe button and leave a review. If you love what we are trying to do then support us on Patreon https://www.patreon.com/preprintsinmotion where tiers start at as little as £1 a month!

For the latest podcast news and updates follow us on Twitter @MotionPod or visit our website; www.preprintsinmotion.com.

Produced by JEmJ Productions (find us on Twitter: Jonny @JACoates, Emma @ELWilson92, John @JohnDHoward8) and generously supported by ASAPbio (https://asapbio.org | @asapbio_).

This week we discussed the transfer of mitochondria from macrophages to cancer cells with Dr Chelsea Kidwill & Joseph Casalin, a Post-Doctoral Research Associate and PhD student at University of Utah (@UUtah) in the school of medicine. We delve into why this transfer occurs, the mechanism of transfer and how this impacts the recipient cells. We also speak to Joseph about his alternative schooling, in addition to our usual chat about the importance of preprints and our ideas for how to improve academia.

Read the full preprint https://www.biorxiv.org/content/10.1101/2021.08.10.455713v1

This episode was produced by Emma Wilson and edited by John D Howard.

If you enjoyed this show then hit that subscribe button and leave a review. If you love what we are trying to do then support us on Patreon https://www.patreon.com/preprintsinmotion where tiers start at as little as £1 a month!

For the latest podcast news and updates follow us on Twitter @MotionPod or visit our website; www.preprintsinmotion.com.

Produced by JEmJ Productions (find us on Twitter: Jonny @JACoates, Emma @ELWilson92, John @JohnDHoward8) and generously supported by ASAPbio (https://asapbio.org | @asapbio_).

This week we discuss The Paywall Movie with Professor Jason Schmitt, chair of communication and Media at Clarkson University. We talk about academic publishing, the problems of the current system and more. 

In 2018, UK universities spent over £210 million on publication costs (access etc). This could have paid for; 700 ECR fellowships or 6500 postdocs or >8500 technicians or 3,500 PhDs (4yr fees + stipend). Meanwhile, Elsevier had profit margins of 37%. This week we discuss the broken publishing system and Jason’s documentary - The Paywall Movie; the business of scholarship.

Watch The Paywall Movie for free -> https://paywallthemovie.com/ 

Learn more about Plan S - https://www.coalition-s.org/ 

DORA - https://sfdora.org/

Picture a scientist - Netflix.com

Retraction Watch - https://retractionwatch.com/

This episode was produced by Emma Wilson & Jonny Coates and edited by John D Howard.

If you enjoyed this show then hit that subscribe button and leave a review. If you love what we are trying to do then support us on Patreon https://www.patreon.com/preprintsinmotion where tiers start at as little as £1 a month!

For the latest podcast news and updates follow us on Twitter @MotionPod or visit our website; www.preprintsinmotion.com.

Produced by JEmJ Productions (find us on Twitter: Jonny @JACoates, Emma @ELWilson92, John @JohnDHoward8) and generously supported by ASAPbio (https://asapbio.org | @asapbio_).

This week we discuss how published nucleotide sequences are not always correct or to be trusted with Yasunori Park and Professor Jennifer A Byrne (@JAByrneSci), a research Assistant and PI at the University of Sydney (@Sydney_uni). We delve into the details of their nifty new text mining tool (Blast and Seek) which highlights papers with incorrect nucleotide sequences. We also discuss the most common mistakes found, the impact of these mistakes, and what we can do as researchers to prevent errors from occurring. We also talk about prepints and Australian Research Council’s recent decision to ban preprints in their grant applications as well as some insight into our very own PhD’s.

Read the full preprint https://www.biorxiv.org/content/10.1101/2021.07.29.453321v1?fbclid=IwAR2LibD1DD8q6b5df3vMzgFXpmmA6q1E_UarbyaB0dq55fOaY8mmFvzbe14

Other links

Open letter to ARC https://asapbio.org/arc

This episode was produced by Emma Wilson and edited by John D Howard.

If you enjoyed this show then hit that subscribe button and leave a review. If you love what we are trying to do then support us on Patreon https://www.patreon.com/preprintsinmotion where tiers start at as little as £1 a month!

For the latest podcast news and updates follow us on Twitter @MotionPod or visit our website; www.preprintsinmotion.com.

Produced by JEmJ Productions (find us on Twitter: Jonny @JACoates, Emma @ELWilson92, John @JohnDHoward8) and generously supported by ASAPbio (https://asapbio.org | @asapbio_).

This week we discuss high throughput CRISPR/Cas9 screening and how these have been adapted to investigate novel treatments for COVID-19 with Emily Sherman a former Post Doc and Brian Emmer (@brianemmer), a new PI at University of Michigan (@UMIntMed)

In this episode we cover details on how to conduct a high throughput CRISPR/Cas9 screen, the exciting advances in NextGen sequencing as well as what it's like to set up your own lab while working as a clinician during a pandemic. We also speak to Emily about her transition from academia to industry and our usual discussion about the benefits of preprints.

Read the full preprint - https://www.biorxiv.org/content/10.1101/2021.06.10.447768v1.full

Brian’s lab homepage (https://emmer.lab.medicine.umich.edu/)

https://www.nature.com/articles/nm1267

This episode was produced by Emma Wilson and edited by Jonny Coates and John D Howard.

If you enjoyed this show then hit that subscribe button and leave a review. If you love what we are trying to do then support us on Patreon https://www.patreon.com/preprintsinmotion where tiers start at as little as £1 a month!

For the latest podcast news and updates follow us on Twitter @MotionPod or visit our website; www.preprintsinmotion.com.

Produced by JEmJ Productions (find us on Twitter: Jonny @JACoates, Emma @ELWilson92, John @JohnDHoward8) and generously supported by ASAPbio (https://asapbio.org | @asapbio_).

This week we discuss BET inhibitors and fibroblast activation with Michael Alexanian @m_alexanian a Postdoctoral researcher at Gladstone Institutes @Gladstoneinst. Michael explains how BET inhibitors have emerged as a potent tool to reversibly interfere with enhancers to promoter signalling. This has been shown to ameliorate heart failure in mouse models and is a highly translatable method of preventing heart failure in humans. We discuss two powerful tools, scRNASeq and scATAC-seq, and how they were used to investigate transcription and epigenetic changes of activated fibroblasts. We then discuss the impact of downstream targets and the impact on drug discovery and the limitation of BET inhibitors. Like every week we also highlight the benefits of preprinting, and increasing the accessibility of data within them to scientists around the world.

Read the full preprint - https://www.biorxiv.org/content/10.1101/2020.07.21.214874v1.full

Other links

https://www.nature.com/articles/s41586-021-03674-1

This episode was produced by Emma Wilson and edited by John D Howard.

If you enjoyed this show then hit that subscribe button and leave a review. If you love what we are trying to do then support us on Patreon https://www.patreon.com/preprintsinmotion where tiers start at as little as £1 a month!

For the latest podcast news and updates follow us on Twitter @MotionPod or visit our website; www.preprintsinmotion.com.

Produced by JEmJ Productions (find us on Twitter: Jonny @JACoates, Emma @ELWilson92, John @JohnDHoward8) and generously supported by ASAPbio (https://asapbio.org | @asapbio_).

This week we discuss how to non-destructively extract and sequence DNA from historical mosquito and tsetse fly samples from the Natural History Museum’s collection. We discover a new method for doing just that with Dr Petra Korlevic (@petrathepostdoc), a Post-doctoral researcher at the EMBL-EBI (@emblebi)/Sanger Institute (@sangerinstitute), and Dr Erica McAlister (@flygirlNHM), Senior Curator of Diptera at the Natural History Museum (@NHM_London). Erica and Petra explain how this method can be used to open up museum collections to molecular researchers in order to answer questions around subjects such as the rise of insecticide resistance amongst these disease vector insects, and the diet, behaviour and ecology of key pollinator species during the rise of global warming or changes in farming practice. We talk about the benefits of preprinting, and how digitising museum collections and developing molecular methods such as this, is increasing the accessibility of data on the specimens within them to scientists around the world.

Read the full preprint https://www.biorxiv.org/content/10.1101/2021.06.28.450148v1.full

Other links

https://www.nhm.ac.uk/our-science/collections/entomology-collections.html

https://www.nhm.ac.uk/our-science/departments-and-staff/life-sciences/insects.html

https://www.nhm.ac.uk/our-science/our-work/digital-collections/digital-collections-programme.html

https://www.liverpoolmuseums.org.uk/insect-collections

This episode was produced by John D Howard & Emma Wilson and edited by John D Howard.

If you enjoyed this show then hit that subscribe button and leave a review. If you love what we are trying to do then support us on Patreon https://www.patreon.com/preprintsinmotion where tiers start at as little as £1 a month!

For the latest podcast news and updates follow us on Twitter @MotionPod or visit our website; www.preprintsinmotion.com.

Produced by JEmJ Productions (find us on Twitter: Jonny @JACoates, Emma @ELWilson92, John @JohnDHoward8) and generously supported by ASAPbio (https://asapbio.org | @asapbio_).