ECR Journal Club
Our fantastic ECR team have established a monthly journal club, taking turns to discuss a paper of interest. This month, Karl Norris led the discussion on this paper by Sophia Häfner and colleagues:
The team then discussed the blurred lines between specialised ribosomes empowered by ribosome-associated factors and RNA-binding proteins recruiting specific mRNAs to the ribosome.
If you have any tips for our budding journal club or any paper suggestions, get in touch!
RiboCode kick-off meeting: Leeds, December 2023
The RiboCode sLoLa has officially launched! On 5th December 2023, the RiboCode team hosted a day of scientific discussion, poster presentations and breakout sessions at the University of Leeds. In attendance was our Scientific Advisory Board (Professors Anne Willis OBE and Alan Warren, both University of Cambridge; Dr Olivia Rissland, University of Colorado, and Dr Mark Bruce, Oxford Nanopore Technologies) and BBSRC Senior Portfolio Manager, Dr Tamsin Shepherd-Waring. We are fortunate to be supported by this inspiring board of advisors and thank them for giving their time and energy to this project.
We were also joined by a number of guests from the University of Leeds, including Simon Wilkins (R&I Development Manager in the Faculty of Engineering and Physical Sciences, who supported the development of the project) and a group of scientists from across the Faculty of Biological Sciences with an interest in the field of specialised ribosomes.
The meeting showcased the work started by our RiboCode scientists, with a real emphasis on the exceptional collaborative nature of the project.
Read more about the RiboCode kick-off meeting here.
Public engagement activity: BioFest 2023
On Wednesday 15th November, our Sheffield scientists – primarily involved in Theme 2 (mRNA translation) – took part in the University of Sheffield’s BioFest Discovery Nights 2023. BioFest is the University of Sheffield’s new bioscience festival, showcasing cutting-edge bioscience research taking part across the university.
Dr Emma Thomson, Dr Jo Cunningham, Vincent Chan and Veronica Thuburn led a fun and engaging activity called ‘Enter the RiboZone’. Here, they used Lego models to how ribosomes decode mRNA and produce protein. Participants took on the role of the ribosome and matched tRNA molecules to an mRNA sequence to spell a word, thus discovering a new appreciation for the complex and essential job of the ribosome in all of our cells!
A whopping 200 visitors visited the stall, with ‘Enter the RiboZone’ proving popular with children of all ages.
Read more about BioFest 2023 here.
Public engagement activity: Be Curious 2023
On Saturday 13th May 2023, members of Theme 3 (structure of specialised ribosomes) took part in Be Curious 2023: the University of Leeds’ annual family open day, which showcases research taking place all over the university. Dr Juan Fontana and colleagues, together with other cryo-electron microscopy experts, led an activity called “Up Close and Really Cold”. Here, they introduced over 200 visitors to cryo-EM sample preparation, freezing samples and studying them under microscopes. The researchers explained how these techniques allow us to understand how diseases can occur in cells and what we can do to intervene.
Read more about Be Curious 2023 here.
BBSRC FTMA-funded visit to Oxford Nanopore Technologies
Three researchers (Elton Vasconcelos, Tayah Hopes and Karl Norris) from the RiboCode team visited Oxford Nanopore Technologies (ONT) for a fortnight in March 2023 to gain a better understanding of an exciting nanopore-based long-read direct RNA sequencing method (ONT dRNA-Seq). They were also keen to discover how research and development was conducted in an industrial setting.
The first week was dedicated to wet lab skills and the second week to bioinformatic analysis. The team learned how to prepare samples for direct RNA sequencing, load MinION flow cells, basecall with Guppy and align to the genome with Minimap2. They also spent time quantifying transcript expression with NanoCount, differential splicing with IsoformSwitchAnalyzeR, and assessing both poly-A tail length and m6A modification with tailFindR and m6anet respectively.
The team wanted to test this technology and perform analyses that would not be possible using next generation sequencing (NGS) technologies. First, they aimed to find out which spliceoforms were being transcribed in their samples. Due to the requirement for RNA to be fragmented to 100bp reads, spliceoform information is often lost during an NGS run. With ONTs long-read sequencing, it is possible to find out exactly which transcript is being sequenced. NGS technologies also require an RNA template to be converted to DNA, losing RNA modification information. With ONTs direct-RNA sequencing methods, it is possible to identify certain RNA modifications. Since the nanopore recognises and initiates sequencing from the PolyA, they were also able to analyse poly-A tail length in different samples.
Samples were run on a MinION chip and achieved read lengths up to 4kb, with a median read length of 1kb. Both the reads’ and bases’ quality fitted above expected (Q score > 7) and, at the end of the full pipeline execution, they were able to identify differentially regulated spliceoforms, different polyA tail lengths and m64A-modified transcripts.
The team were inspired by their industry visit: the technology developed by ONT is hugely exciting and Elton, Tayah and Karl can’t wait to apply what they’ve learned back in Leeds. Thank you to BBSRC for this opportunity and to the ONT team for their warm welcome and hospitality!