BioPOD

In this episode, Rose Doyle talks to BioPOD alumnus and PhD student Eddie Martin. They discuss different ways of visualising protein structures and how sound can help us get more information from protein sequences. In his research, he turns a protein sequence into a short melody. From this melody, it is then possible to “hear out” some distinct features of the protein. Eddie also explains the intricacies of sound design and how to best convey the variations between different amino acids.  

Artwork by Chris Donohoe and editing by Ruby White.

Link to the paper: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04362-7 

In the second episode of our PhD advice series, Liz talks to Dr Lizzie Wadsworth, who recently finished her PhD at the University of Edinburgh. Looking back on her experience she gives very valuable advice to new and current PhD students about how to address common struggles with a graduate degree. She shares with us how she got started with her PhD, tips on how to have a good relationship with your supervisor, and strategies to deal with mental health issues. We also get to hear about her current work as a teaching fellow and discuss some less well-known career paths in academia.  

In the second episode of our COP26, Chris chats to Dr Annis Richardson about her research on food security. With climate change causing extreme weather, crop growth is getting increasingly difficult, so of course food security is a major topic of research. Annis Richardson works closely with the agricultural department on understanding how plants grow and how much food the plant then produces, so that we can more effectively feed the world. 

In this episode of our COP26 series, Chris talks to Prof. Louise Horsfall, Chair of Sustainable Biotechnology at the University of Edinburgh, about her participation in the COP26 conference in Glasgow. We get to hear about her experience as a scientist hearing the sometimes conflicting ideas of politicians and companies. Prof. Horsfall also talks about how her lab uses engineered microbes to recycle metals from battery waste. 

Resources mentioned: 

Faraday Institution: the UK’s battery research programme https://www.faraday.ac.uk 

In the first episode of our PhD Advice series, Liz (@lizgaberdiel) talks to Rev. Dr. Harriet Harris, the University of Edinburgh Chaplain, about how PhD students can look after themselves through practicing mindfulness with everyday tasks, and overall building healthy habits. We get to learn about services being offered by the Chaplaincy to help support PhD students who may be struggling with mental health, as well as those who wish to find a community. 

Resources mentioned:  

Taming your inner critic and Imposter Syndrome: https://www.ed.ac.uk/chaplaincy/abundant-academy/compassion-for-our-times/taming-your-inner-critic-and-imposter-syndrome-at
This blog has embedded in it a recording plus links to two other blogs on Imposter Syndrome. 

This podcast series, episode 3, ‘The Joy and Vitality of Not Knowing’, provides a tonic for perfectionism and a corrective to white privilege. 

https://www.ed.ac.uk/chaplaincy/blogs-podcasts-and-reflections/the-chaplaincy-of-joyful-abandon-podcast-series 

In this extra special episode, 5 different PhD students at different stages discuss their own unique PhD journey. We hear from the recent graduate Miguel (@mcueva89) about how his career plans changed during the highs and lows of his experience. Rist discusses how he dealt with getting scooped – and how he experienced fatherhood at the same time. Joan (@JoanCortadaGar) moved with his supervisor from Glasgow to Edinburgh in the midst of his second year and talks about the impact this had on his research. We hear from Lindsay what it was like to have children during her PhD and how working part-time has helped her with that. Finally, Liz (@LizGaberdiel) discusses the benefits and difficulties of moving to a new discipline when starting her PhD. 

 Interviewing and editing by Sam Haynes @youvegotmyname. 

What does algae photosynthesis have to do with solving food insecurity? 

In this episode on crop improvement, @_applechew interviews Liat Adler (@noodlyscientist) to hear how algae can help us improve the photosynthesis efficiency of “land plants”! 

Crop photosynthesis is not exactly perfect. One key enzyme in the mechanism called RuBisCo is slow and gets confused between carbon and oxygen: not what you want from your energy storage mechanism! 

Algae, however, have developed a system to improve both the speed and the accuracy of this process. The @McCormick_Lab is trying to integrate this system into land plants. That way, crops could use sunlight more efficiently, grow faster, and thus produce more food!

Art by @donohoho, intro and editing by @_applechew

Have you ever wondered what neglected regions of the genome do? In this episode we hear about the search for AT rich region binding proteins.

Jack Suitor (@JackTSuitor) talks to Raphael Pantier (@R_Pantier) and Kashyap Chhatbar (@kashyapchhatbar) from the Bird lab at the University of Edinburgh about their work on the DNA binding protein Sall4. They discover that Sall4 binds to AT rich regions which affects large scale gene expressions and enables differentiation.
 Sall4 could help time cellular differentiation as part of embryonic development and is therefore implicated in developmental disease. By getting more insight into proteins that bind AT rich regions we could learn more about the cause of some diseases.

Art by @donohoho, intro and editing by @_applechew

This is the second episode of the BioPOD series: Scotland's Biotech Stories.

In this instalment, BioPodder Liz Gaberdiel interviews Professor Lynne Regan on how to design biologically useful proteins. Proteins with unusual properties can enable super-resolution imaging, spontaneously self-assemble into structures, or coat a surface with a particular protein layer!


Introduction and editing by Apple Chew

Media by Liz Gaberdiel and Chris Donohoe

Welcome to a new BioPOD series: Scotland's Biotech Stories.

In this installment, BioPodder Liz Gaberdiel interviews Dr. Marcus Wilson on Cryogenic electron microscopy (CryoEM), a  technique that has undergone some serious upgrades since its initial development in the 1960s.

Introduction by Neelakshi Varma & Editing by Sam Haynes

Media by Hanna Peach and Chris Donohoe 

Dear listeners,

Welcome back to another episode of BioPod!

Today we walk you through to potential of cyanobacteria: turning tasty sunlight into a high-product value delight!

Apple Chew interviews Anton Puzorjov  from The McCormick Lab at The University of Edinburgh on his project supported by ScotBio

Art by Christian Donohoe , Editing by Apple, Media by  Hanna Peach

In the fourth and final installment of BioPOD's #Vaccine15 miniseries, we have Liz Gaberdiel interviewing Professor Neil Babbott on how vaccines can block viral transmission.

Edited by Ruby White, Media by Hanna Peach. 

Ever wondered how vaccines are made in smaller batch scales, then upscaled to a world market? Hint: it's not the same as cooking a larger lasagne when family comes to visit. Tune into our third installment of #Vaccine15 to learn about the large scale production of vaccines.

In this episode, BioPodder Liz Gaberdiel interviews Dr Prerna Vohra. Editing by Hanna Peach.

Enjoy, and #GetVaccinated! 

In this episode of our four-part vaccine 15-minute miniseries, biopodder Chris Donohoe  interviews Dr. Thomas Williams on how to track and tackle the different COVID variants.

edited by Apple Chew (Yen Peng) media and art by Hanna Peach

Our #Vaccine15 four-part 15-minute miniseries begins today! This week is all about how COVID vaccines were developed and designed with @CTaitBurkard from @EdinburghUni @roslininstitute

Interviewer and Art @donohoho
Editing by @_applechew
Media and Art @hanna_peach_

In this episode, we talk about the Darwin Tree of Life: Sequencing the Biome of the Great Britain with Professor Mark Blaxter & Dr Alex Twyford

The Darwin Tree of Life project aims to sequence the genomes of all 70,000 species of eukaryotic organisms in Britain and Ireland. It is a collaboration between biodiversity, genomics and analysis partners that hopes to transform the way we do biology, conservation and biotechnology.  The Darwin Tree of Life Project is one of several initiatives across the globe working towards the ultimate goal of sequencing all complex life on Earth, in a venture known as the Earth BioGenome Project.

Prof. Mark Blaxter and his group use modern sequencing and bioinformatics technologies to investigate the genomes of many different species of animals. Professor Mark Blaxter is the Founder and Director of Genome Science of Edinburgh Genomics (http://genomics.ed.ac.uk) the University's advanced genomics facility.  Dr Alex Twyford is an evolutionary geneticist interested in the ecology and evolution of plants.

Interviewed by Hazel (Wu) Huang, Introduced by Ruby White, Edited by Sam Haynes. Media by Hanna Peach, Artwork by Chris Donohoe 

This episode is about the use of synthetic organisms to produce pharmaceuticals and other high-value products. 

 Preceding the development of synthetic drugs in the 18th and 19th centuries, medicine relied on the use of products found in nature. It is not surprising even nowadays that a lot of drug discovery undertaken by the pharmaceutical industry incorporates compounds found in nature. Biotechnology offers the opportunity to create these same natural products in large quantities, in a sustainable manner. 

In order to do that, bioscientists can take genes for metabolic pathways that create a specific compound with human health benefits from plant genomes and replicate them in microorganisms such as bacteria and yeast. These modified microbes can now be used as factories to sustainably and efficiently produce the drug of interest in the lab or in a controlled industrial environment. 

To help us understand this topic a bit better and the potential advantages and challenges of this technology, Joan Cortada-Carcia interviewed Dr. Tessa Moses, a former postdoc in the Rosser lab group at the University of Edinburgh and current head of metabolomics at the university’s mass spectrometry facility called Edinomics. Media by Hanna Peach.

#BioPod #BiologyPodcast #SciencePodcast #SyntheticBiology #SynBio #SynthSys 

The parasite Trypanosoma brucei is transmitted via tsetse flies. It causes a disease known as trypanosomiasis or sleeping sickness in humans, but in cows, it's known as nagana or animal African trypanosomiasis. In this episode, Joan Cortada García interviews Maria Contreras-Garcia from The Roslin Institute on her work to validate and characterize the use of a small RNA as a diagnostic test for trypanosomiasis. Media by Hanna Peach. 

Here is a link to the event mentioned by Ruby White in our episode coda.  The event is a joint University of Edinburgh and University of Sydney Workshop Series on sustainable food production, antimicrobial resistance and One Health https://www.eventbrite.com.au/e/university-of-sydney-and-university-of-edinburgh-joint-workshop-series-2021-tickets-142438833385?utm_campaign=2889898_UoE-UoSyd%20OH%20workshops%20EID&utm_medium=email&utm_source=College%20of%20Science%20%26%20Engineering%2C%20The%20University%20of%20Edinburgh&dm_i=2MP0,1PXUY,9QQ8JI,5VOLI,1

How can we produce useful materials from Bacteria? Today we have PhD Student Jack Suitor to tell us how we can modify bacteria against their own nature to act as mini-factories to convert guaiacol, a paper industry byproduct, to adipic acid, a key component of Nylon production that is otherwise produced from oil!

Our CODA is a special dive into microbiology with our resident microbiologist Hanna Peach. 

Join us for this interesting installment of BioPod featuring Associate Professor Kyle Dexter, interviewed by Hazel Huang. from the department of Geosciences here at the University of Edinburgh. The episode is about monitoring the carbon dynamics of the dry tropics and climate change. 

A lot of people know about vegetation, biodiversity, and the abundance of wet tropics such as the Amazonian Rainforest, but let us take you on a journey through the dry tropics and the way climate change will affect habitats for vegetation, animals, and humans over time. This research is important, to understand the dynamics between carbon cycling, vegetation, and the interplay of factors that are both driving and affected by climate change.