Training Course

Isolation, Preservation and Control of Yeast Strains

date: 2017 TBC

Imparted by members of the NCYC team, this course will be of interest to anyone involved in the handling, distribution and storage of Yeasts

The course will cover aspects of isolation, cultivation, identification & preservation of yeast cultures. The course will be held at the National Collection of Yeast Cultures (NCYC) and both the theoretical and practical sessions will be imparted by the NCYC team

Course programme

The training course runs for 3 days and it will cover different theoretical and practical demonstrations. Participants will have the opportunity to discuss aspects of their work with NCYC staff and will update their skills and knowledge of:

  • Isolation methods. Aseptic technique
  • Microscopy basics
  • Preservation methods. (Long and short-term preservation)
  • Recovering freeze-dried cultures.
  • Culturing yeast preserved by other methods.
  • Quality control checks: viability, purity checks (conventional and PCR based).
  • Identifying potential spoilage yeasts.

Venue

The Institute of Food Research houses the National Collection of Yeast Cultures.

Norwich Research Park, Colney Lane, Norwich, NR4 7UA, UK.

If you need any further information please contact:

Carmen Nueno Palop,
T.+44 (0) 1603255093,
E: carmen.nueno-palop@ncyc.co.uk

PhD Opportunity within NCYC

Applications are now open for 4 year PhD studentships at the Institute of Food Research, to start in October 2016.

One of these PhD studentships entitled “Computing a yeast Tree of Life” is within the NCYC research programme. We have recently sequenced the genomes of approximately 600 yeast strains. The resulting dataset, potentially the largest of its kind worldwide, will enable us to compare current computational approaches to developing such a yeast Tree of Life and to further develop new Next Generation Sequencing (NGS)-based approaches for evolutionary tree reconstruction.

You will gain an opportunity to develop key skills in the analysis of NGS data, phylogenetic analysis and software development. Membership of an interdisciplinary and inter-institutional collaboration, including leaders in the fields of yeast genomics, phylogenetics, bioinformatics and software development, will also introduce you to best research practices within three Norwich-based research centres.

If you are interested in knowing more about this excellent opportunity, please contact Jo Dicksjo.dicks@ifr.ac.uk

Closing date is 30th November 2015.

Yeast treasure-trove goes live

A new project is sequencing the genomes of a collection of yeast strains, to help unlock the great biodiversity within yeasts to produce biofuels and other chemicals more sustainably.

NCYC is a world-leading biological resource, maintaining and supplying an extraordinarily diverse array of yeast strains for academia and industry in the UK and overseas.

In partnership with The Genome Analysis Centre (TGAC), the NCYC has begun an exciting new project to sequence the genomes of all of its ~4,000 strains, thereby revealing their genetic blueprints.

Dr Ian Roberts, NCYC Curator, marked a key milestone in this new project by announcing, “Today, we publicly release genome sequences for the first 48 yeast strains to be analysed within our ambitious new project. As more data become available, genome sequences of additional NCYC strains will be released from our website, adding greatly to this rich treasure-trove of information.”

The special capabilities of each yeast strain, whether in baking, brewing, biorefining or surviving in extreme conditions, can now – for the first time – be compared to its genome, thereby enabling the genetic basis of its talents to be uncovered. This rich new data cache will enable academic and industrial researchers to maximise the potential of currently available yeast strains and develop hyper-efficient strains with even better properties.

Dr Jo Dicks, yeast genomes project leader said “Today marks the beginning of an exciting journey to realise the full potential of yeast. We look forward to working with NCYC’s partners and customers to mine the entire diversity in the collection and gain maximum economic benefit from this unique resource”.

Dr David Swarbreck, Regulatory Genomics group leader at TGAC, who led TGACs efforts to generate the genome assemblies for the 48 yeast strains, said: “The release of the first genome sequences from this ambitious project showcases the advances that have been made in next generation sequencing technology that now enable us to cost-effectively sequence large microbial collections, which will facilitate further comparative analysis into the genetic differences between strains.” TGAC’s Platform & Pipelines group will be carrying out the sequencing for the second stage of the yeast genomes’ 4,000 plus strains, led by Platforms & Pipelines Team Leader Darren Heavens.

The NCYC is a Biotechnology and Biological Sciences Research Council (BBSRC)-funded National Capability within the Institute of Food Research (IFR), on the Norwich Research Park. It is one of the world’s largest, most biodiverse and well-characterised yeast collections. The yeasts have been collected from pole to pole and have great potential in producing renewable fuel and chemicals from non-food biomass. The NCYC supports businesses from established multinationals to local microbrewery start-ups. Rapid robotic screening methods are under development enabling further added value for NCYC and its user community. The NCYC endeavours to meet all obligations under the terms of the Convention on Biological Diversity and the Nagoya Protocol.

Download the yeast datasets

The NCYC yeast datasets are available for download from http://opendata.ifr.ac.uk/NCYC/.

Training Course: Isolation, Preservation and Control of Yeast Strains

NOTE: Registration for this training course has closed. If you need any further information please contact us:     Carmen Nueno Palop,  T.+44 (0) 1603255093, E: carmen.nueno-palop@ncyc.co.uk

Imparted by members of the NCYC team, this course, runs from: 22-24 September 2015, will be of interest to anyone involved in the handling, distribution and storage of Yeasts.

The course will cover aspects of isolation, cultivation, identification & preservation of yeast cultures and runs for 3 days.

Participants will have the opportunity to discuss aspects of their work with NCYC staff and will update their skills and knowledge of:

  • Isolation methods. Aseptic technique
  • Microscopy basics
  • Preservation methods. (Long and short-term preservation)
  • Recovering freeze-dried cultures.
  • Culturing yeast preserved by other methods.
  • Quality control checks: viability, purity checks (conventional and PCR based).
  • Identifying potential spoilage yeasts.

 

 

NCYC image shortlisted in the BBSRC’s “Images with Impact” competition

Saccharomyces cerevisiae NCYC1026

Saccharomyces cerevisiae – NCYC1026

An image of a traditional British ale yeast strain from NCYC has been shortlisted as a finalist in the in the BBSRC’s Images with Impact competition.

Saccharomyces cerevisiae NCYC1026 is a strain used in brewing, and is one of 4,000 strains collected and maintained in the NCYC collection. Voting for the competition is now open at http://bbsrc2014.picturk.com

The yeast  image was taken by IFR’s Kathryn Cross, using a scanning electron microscope, from a sample prepared by NCYC. The image was false coloured by Carmen Nueno-Palop, to highlight the features of the yeast. The yeast cells are dividing by budding, and the scars visible on the cell surface are from previous cell divisions.

The public vote is now open for the BBSRC Images with Impact competition. Anyone can vote for the winning pictures online at http://bbsrc2014.picturk.com

The competition sought images that represented how life sciences are changing the world, in areas like: food, farming, bioenergy, biotech, industry and health.

The shortlist has been selected by an esteemed panel of judges. Now the public get their say and can vote for the category winners and runners up.

This competition captures the exciting developments and challenges happening in bioscience today, with images from the Great British public, its students and its researchers.

The three category winners will go on to be shown at the Great British Bioscience Festival in London on 14-16 November where visitors will vote to decide the overall winner.

Voting will close on 31 October 2014 so get sharing and voting.

Visit by Minister for Life Sciences

It was a great pleasure to have the opportunity to discuss yeast’s growing role in the bioeconomy with George Freeman MP, Minister for Life Sciences and Jackie Hunter, CEO of BBSRC, on their recent visit to the IFR Biorefinery.

Geaorge-Freeman-visit 2014

As they observed, the tiny single-celled fungi we call yeasts are nature’s re-cyclers and have been an important part of environmental food chains ever since emerging from the primeval swamp. With the advent of new biotechnological processes driving a new industrial revolution, the huge gene pool that yeasts have assembled over the past 100 million years or so (give or take a few decades!) will find many applications in improving production of bio-based fuels and chemicals.

Efficient conversion of agrifood waste in the biorefinery is an important aspect of this revolution and higher yields and increased tolerance to industrial stresses are just two areas where yeast biodiversity can contribute.

In addition to providing natural solutions to effective waste utilisation, biological collections such as the NCYC will have a vital role to play in maintaining and distributing the new industrial work horses arising from synthetic biology, becoming in effect app stores for the new industrial biotechnology.

freeman-ncyc2

New online catalogue and website

websitesThe NCYC Team are pleased to announce the launch of a major upgrade to both our website and online catalogue. After many months of development, we have now launched the new NCYC Catalogue at catalogue.ncyc.co.uk. The new system should enable better searching and easier ordering. If you have any comments on the new Catalogue, please email them to ncyc@ncyc.co.uk.

Our new website now has a blog section to keep customers and other interested parties updated with our latest developments. We also have an e-mailing list to which we regularly post updates. If you would like to be added to the mailing list please complete the ‘Sign up’ form on the right of this page.

Visit from eco-hero

Chris Bond, SImran Sethi and Janette Newman

Chris Bond, SImran Sethi and Janette Newman

Simran-Sethi0157webNCYC were pleased to welcome Simran Sethi to Norwich. Named “the environmental messenger” by Vanity Fair & a top ten eco-hero of the planet by the UK’s Independent, Simran Sethi is a journalist and educator focused on environmentalism, sustainability & social change.

Simran is currently writing a book on the loss of biodiversity in our food system and wanted to find out more about yeast diversity and the role of NCYC. We explained to her the great diversity in the collection, including not only brewing and baking yeast but also medical research, biotechnological applications and many others. We also demonstrated the great geographical diversity as NCYC contains yeast from many different parts of the world.

Simran find out about us via our links with Truman’s brewery, as she was visiting them last week to learn more about the return of the heritage beer they are brewing with the historical yeast stored by NCYC.

If you want to find out a bit more about Simran, visit her website at simransethi.com

Mysteries of the Yeast

Ascus (sexual spore-bearing cell) plus ascospores of the yeast Saccharomyces paradoxus

Ascus (sexual spore-bearing cell) plus ascospores of the yeast Saccharomyces paradoxus

NCYC Researchers have turned a decades old problem in genome sequence analysis on its head to uncover hidden information on how yeasts evolved, giving insights into evolutionary processes common to all of life.

The National Collection of Yeast Cultures (NCYC) at the Institute of Food Research houses over 4,000 different strains of yeast. This represents a great source of biodiversity that could be exploited further for brewing and baking, as well as for new applications in biorefining, if the evolutionary relationships linking these strains were better understood.

To help understand how different yeast strains are related to one another, the researchers examined the part of their genomes that contains the instruction for making the ribosome – the molecular machinery responsible for converting genetic information into proteins. Ribosomal DNA (rDNA) is common to all cellular life, making it very useful for studying biodiversity at a number of different taxonomic levels. For example, in fungi it’s used as a DNA ‘barcode’ for species identification as well as to construct phylogenetic family trees.

Clock of Life

This sort of analysis relies on changes in the rDNA sequences that accumulate over time during evolution.  As ribosomes and their functions are so crucial, these changes were previously thought to be few in number.

“rDNA is like a molecular clock, ticking away in our cells” said Dr Ian Roberts, curator of NCYC, which is supported by the Biotechnology and Biological Sciences Research Council (BBSRC).

Identifying and contrasting changes to the rDNA that have occurred over time allows for very broad comparisons between diverse species, and even wider – ribosomal sequence was at the heart of classifying the Archaea as a separate domain of life.

However, one major problem associated with using rDNA for phylogenetic studies is the frequent presence of differences between the multiple adjacent copies of the rDNA within a single strain. These “micro-heterogeneities” , which have been observed in many species in the tree of life over the past few decades, can confuse phylogenetic analyses, which do not account for them.

However, Dr Jo Dicks and colleagues at the NCYC had a hunch that the rDNA micro-heterogeneities could be more than an inconvenience. And the Saccharomyces Genome Resequencing Project (SGRP) presented an opportunity to test this theory. Saccharomyces cerevisiae, or brewer’s/baker’s yeast, was the first eukaryote to have its genome sequenced. For some years now, the Wellcome Trust Sanger Institute has been leading a project to sequence, in greater detail than ever before, the genomes of 37 S. cerevisiae strains, as well as 26 strains of Saccharomyces paradoxus, a close wild relative.

The Norwich researchers’ strategy was to use the information from the resequencing project to characterise as much rDNA variation as they could find, also looking at parts of the rDNA usually ignored to find much greater quantities than anyone had thought existed.

“We turned the problem on its head,” said Dr Jo Dicks. “We used the very variation that had caused so many researchers headaches in creating phylogenetic trees to actually estimate those same trees.”

Over a period of four years, PhD student Claire West and NCYC researcher Dr Steve James went through the resequencing information coming out of the Sanger Institute, first by a specially created computer application and subsequently by hand, and the harder they looked the more variation they found. The problems previous researchers had had with the rDNA stemmed from the fact that they were only looking at a tiny proportion of it. By finding all, or close to all, of the variation, the NCYC team showed these problems simply went away.

Yeast culture crosses continents

“We found a signal in the noise” explains Dr Jo Dicks. “There is a huge amount of information in the rDNA, at multiple levels. For example, we were able to identify intercontinental hybridisation events among yeast strains.”

Saccharomyces cerevisiae – bakers’ yeast

Saccharomyces cerevisiae – bakers’ yeast

The information contained in the rDNA gives more clues as to the origins of modern yeasts. Comparing the evolutionary information of S. cerevisiae and S. paradoxus shows how domestication and human activity have moulded the genome of the yeast we use in baking and brewing. The S. cerevisiae genome is like a mosaic, with its chromosomal make-up derived from ancestral strains found in different regions of the world (e.g. Africa, Europe, Malaysia and North America), reflecting human movement across the globe and how yeast has travelled with us.

The study is also providing new insights into how rDNA itself evolves, and in general the process of concerted evolution. Concerted evolution occurs when a gene is duplicated in the genome, but instead of the two copies evolving separately they influence each other and evolve together in a concerted manner. Across the whole of life, rDNA shows concerted evolution, so the new information derived from this study will be invaluable in getting a better understanding of this mechanism.

The analysis was made possible through the development of software, called TURNIP, which was designed to handle large repetitive sequences, such as the rDNA tandem repeats in Saccharomyces yeasts. The NCYC researchers are now planning further work with Dr Rob Davey, who developed the TURNIP software, and is now based at The Genome Analysis Centre (TGAC). IFR and TGAC are two institutes on the Norwich Research Park that receive strategic support from BBSRC.

Together they will analyse some of the 4,000+ yeast strains held in the collection, to look for strains with potential for use in biorefining. They will be looking for yeast strains that can ferment different carbon sources (e.g. xylose), or produce novel, valuable products, and then linking these back to the information contained within the genome. And the insights provided by this new study will help to unlock this genomic potential held in yeast’s vast biodiversity.

Reference: Ribosomal DNA Sequence Heterogeneity Reflects Intra-Species Phylogenies and Predicts Genome Structure in Two Contrasting Yeast Species, West et al, Systematic Biology doi: 10.1093/sysbio/syu019 (In press)

Site maintained by the Institute of Food Research