The Genomics Lab

We're back after the Easter Break with an extremely interesting episode with Dr Peter Ellis from the School of Biosciences at the University of Kent! Dr.Ellis is a Lecturer in Molecular Genetics and Reproduction at the University of Kent. His research thus far has involved the identification of novel genes on the mouse Y chromosome that affect sperm head shape and fertility; the discovery of a genomic conflict between the mice sex chromosomes as they compete to influence offspring sex ratio. Also the identification of mechanisms regulating meiotic and post-meiotic transcriptional silencing of the sex chromosomes. His lab investigates the molecular biology of reproduction, the conflicting roles played by sex-linked genes in regulating this process, and the relationship between DNA damage repair mechanisms and the checkpoints governing meiotic progression. 

Find Peters profile here where you can access his publications

Connect with Peter on twitter here

Join us today as we speak to Dr Maxim Greenberg, located at the Institut Jacques Monod in the heart of Paris. IJM is one of the premier institutes for fundamental research in the life sciences in France. Maxim's lab aims to better understand the epigenetic consequences of DNA methylation during a specific window of development which occurs in the first week of embryogenesis but ripples throughout life. Another aim of the Greenberg lab is to better understand what DNAme is doing when it is not at promoters? And its corollary: how do promoters stay DNA methylation free?

Today we discuss several of Maxims publications (linked below), the function of DNA methylation and the process of DNA methylation deposition and removal. Maxim also gives us an interesting insight into the details of how his lab aim to better understand epigenetic reprogramming in development. 

Connect with Maxim on twitter

Maxims Lab website

Publications discussed in todays episode are linked below:

Greenberg M.V.C. (2021) Get Out and Stay Out: New Insights Into DNA Methylation Reprogramming in Mammals. Frontiers in Cell and Developmental Biology

The diverse roles of DNA methylation in mammalian development and disease.

Join us today as we speak to Dr David Tumbarello, from the University of Southampton, as he talks to us about his dynamic and varied academic career that has taken him from New York, to Southampton, stopping off at a number of places in between!! David's lab currently focuses on understanding the cellular mechanisms and molecular machinery required for subcellular trafficking of membrane associated and cytosolic cargo via endocytosis and autophagy. Knowledge of these mechanisms is critical for understanding the molecular mechanisms of cancer and neurodegenerative diseases , which stem from defects in various membrane trafficking and cell signalling pathways.

Today we discuss one of David's lab's recent papers, published June 2020, which looks at multiple mitochondrial quality control pathways that exist to maintain the health of mitochondria, the mitochondrial stress response and identify the interaction of molecules associated with this response with E3 ubiquitin ligase Parkin - involved in Parkinson's disease.

Read the paper here: https://eprints.soton.ac.uk/438725/

Find David on Twitter here: @DavidTumbarello

Check out Biobox Analytics here, the ideal platform for working with NGS data, running and designing bioinformatic pipelines and generating the perfect plots: https://biobox.io/

In today's episode, we speak to Dr Jordi Paps-Montserrat, lecturer in the School of Biological Sciences at the University of Bristol. Jordi did his PhD at the University of Barcelona, before completing his post-doc at the University of Oxford. We talk with Jordi today about his work on evolutionary genomics, and how we can elucidate biological adaptations and the origins on animals and plants throughout evolution by looking at the genomic and molecular pathways underlying these evolutionary shifts.

Contact Jordi here: [email protected]

Jordi's Twitter: @JordiPaps

View Alex's paper, which Jordi discusses, here: https://linkinghub.elsevier.com/retrieve/pii/S0960982219315957

Check out Biobox Analytics here, the ideal platform for working with NGS data, running and designing bioinformatic pipelines and generating the perfect plots: https://biobox.io/

Join us today as we speak to an inspirational Woman in STEM, Sethlina Naa Dodua Aryee, raised in Ghana, who moved to the University of Cambridge to complete her PhD in sustainable food production through the use of genomic and bioinformatic tools - a global issue that she has been passionate about for her whole life. Sethlina speaks to us today about her research into the genomics of the indigenous Ashanti Dwarf pig, following cross-breeding of the indigenous species with some overseas species, as well as the differences between studying in Ghana and the UK. The indigenous Ashanti dwarf pig is hugely disease-resistant, so it is of great importance to harness this trait for sustainable food security.

Email Sethlina here: [email protected]

Check out Biobox Analytics here, the ideal platform for working with NGS data, running and designing bioinformatic pipelines and generating the perfect plots: https://biobox.io/

In order to celebrate International Women's Day 2021, we have picked two inspirational role models at our University and invited them to speak to us about their experiences of being a woman in science. We learn about their varied and exciting careers, and then we discuss all of our personal experiences of being a woman in science - from how we were inspired into the field, what we feel are the biggest barriers and how to overcome them, as well as some really great advice from both Dr Louise Beard and Dr Michelle Taylor on all stages of the academic journey. We are very lucky at the University of Essex to be working within a hugely inclusive and supportive environment, but it is important to recognise not all women are this lucky. We discuss the Athena Swan charter, an initiative in academia and the workplace to increase equality for all people, in all roles, and how some of the specific action plans within the charter have directly impacted the University of Essex in order to make it a more inclusive workplace.

Check out Biobox Analytics here, the ideal platform for working with NGS data, running and designing bioinformatic pipelines and generating the perfect plots: https://biobox.io/

In today's episode, we are excited to be talking to Dr Christopher Clarkson, currently based at UCL, where he has just started a post-doctoral research position.

In 2020, Dr. Clarkson completed his PhD at the University of Essex where he investigated changes of nucleosome positioning and 3D chromatin organization! In today's episode, we discuss how CTCF binding strength correlates with nucleosome repeat length and what the implications are of this on gene regulation. We further discuss how regions in the genome where CTCF is able to bind are extremely important for cellular differentiation and boundary formation within the genome.

Email: [email protected]

Chris' Nucleic Acid Research article: CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length

Twitter: find Chris on twitter here.

Check out Biobox Analytics here, the ideal platform for working with NGS data, running and designing bioinformatic pipelines and generating the perfect plots: https://biobox.io/

In today's episode, we are privileged to be speaking to Professor Darren Griffin, who is currently based at the University of Kent, where he is the director of the Centre for Interdisciplinary Studies of Reproduction, and Professor of Genetics.

In addition to talking to us about his hugely exciting research, we also hear from Darren about his experience in science communications. Darren is passionate about making scientific research publicly accessible, and has authored a book (available: https://www.amazon.co.uk/Preimplantation-Genetic-Testing-Advances-Reproductive/dp/1138333301), as well as taking part in 2 documentaries. Darren also has some very exciting other endeavours on the horizon, and we speak to him about his upcoming 6-part documentary series for young adults, as well as a course he is involved with that is taking some of this pioneering IVF research over to Dubai, to teach students there.

Email: [email protected]

Website: http://www.kent.ac.uk/bio/griffin/

Twitter: @darrenkgriffin

Instagram: @profdazzy

Don't miss today's episode, as we are joined by Nicky Hales, who runs a Genomics Core Facility in Texas! This episode is a little different to usual, as we are focusing more on a genomics based career path, and excitingly, it's a career path we did not know much about - so it was a real learning curve to talk to Nicky. Nicky explains to us how she found herself in this position, what a Core Facility is (we had no idea before chatting to Nicky!), the significance of core facilities, and what a typical day looks like for Nicky. We discuss some of the techniques that Nicky runs at her facility, how she learnt all about how to perform each technique, and her favourite techniques (as well as the ones she doesn't enjoy quite so much..!).

If you have any further questions, don't hesitate to contact Nicky:

Google Scholar: Nicole Hales

Twitter: @nicky_rosemarie

IG: @nicky.rosemarie

Email: nicole.hales@unths

Something a little different - our first BONUS episode. Today we talk to Brad and Joe about our experience of using social media as a networking an science communications tool. Brad and Joe briefly introduce their research (for once, not genomics......) and we then discuss the pros and cons of a number of social media platforms, as well as the power of social media as a networking and opportunities tool. We had so much fun filming this episode, so we hope you enjoy listening to something a little more relaxed than the usual hardcore science!

Contact Joe: Twitter @festafitness or Instagram @festa.science or listen to his podcast The Research Lounge!

Contact Brad: @Twitter B_D_Richardson or Instagram @the.neuro.scientist