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Institute Development Scheme successes highlight range of fascinating science research at Earlham Institute

Our funding scheme promotes major research in health, nutrition and food security through multidisciplinary expertise in academia and industry.

March 07, 2017

The Institute Development Scheme (IDS), set up in late 2015, aimed to support research at EI in several ways: through promoting creative, innovative and novel research, fostering the development of interdisciplinary teams and increasing collaboration both among academics and with industry.

We report here on several important projects, which highlight the range of applications of our next-generation sequencing and bioinformatics capabilities.

From helping to identify and unravel the genomics of plant pathogens; through to better understanding of the genetic factors underlying nutrition and investigating how fish can adapt to extreme conditions - the IDS helped stimulate some fascinating outcomes.

I have a gut feeling about this.

At EI, we are not only interested in sequencing and decoding organisms and living systems but also in finding better ways to do this. After all, it’s great that we can produce reams and reams of genomic data - but if this data isn’t stored,shared and analysed efficiently, then it’s not of much use to anyone.

Thankfully, many of our research groups focus precisely on this. The Jurkowski Group, who is the beneficiary of one of the IDS awards are also heavily interested in developing better tools to analyse and integrate omics data, a good example being the recently-released Brassica Information Portal.

In particular, the Group is interested in better understanding nutrition, both from the plant-nutrient side and from the perspective of the animals digesting them. As such, the group is part of a wider collaborative effort on Norwich Research Park that contributes toward the ‘MindTheGut’ (MTG) project - a platform aiming to better understand gut health through better sharing and analysis of data.

The objective of the MTG IDS is two-fold. Firstly, to provide a user-friendly and customised environment to help researchers access and share gut-related projects in one place. MTG seamlessly brings together relevant CyVerse and Galaxy workflows, including those developed by others e.g. NavigOmix developed in the Korcsmaros Group.

Secondly, to assist the interpretation of biological data, the Group have also produced a prototype for ‘MulEA’ - an enrichment analysis tool developed in collaboration with the Eötvös Loránd University in Budapest. This combines a multitude of biological information types: from chromatin structure, gene and protein-based to user defined knowledge, currently supporting over ten species and access to set, ranking and network-based statistics to chose what is most appropriate for given biological questions and data.

So, was the project a success?

A year on, most certainly. For both objectives, the group have already developed working prototypes, with a web-based application allowing researchers to explore a whole range of biological tools, making it much easier and quicker to start analysing data with their collaborators.1

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This project will not only help us better understand how evolutionary processes can shape adaptation to extremes, but also how we can preserve native biodiversity and provide better nutrition and livelihoods for people through sustainable aquaculture programmes.

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Something fishy going on here.

We’re passionate about researching a wide range of organisms at EI, and one particularly interesting group is the cichlid fish, which Tarang Mehta of the Di Palma Group has been focusing on.

Cichlids are fascinating for a multitude of reasons, particularly because they exist in such a rich number of different species that are unique to the lakes in which they reside. More fascinating still is that many of these species, from just a few common ancestors, have been evolving in separate lakes yet developing very similar strategies to coping with life in parallel environments.

Thus, Tarang received an IDS in order to better understand the genomics underlying these incredibly adaptable fish - focusing on one in particular, the soda cichlid (Alcoapia grahami).

Soda cichlids live in a place that most life would try and avoid if at all possible. That place is Lake Magadi, which is ultra-salty, has a pH of 10 and a temperature of around 40°C - all while receiving higher-than-usual UV radiation and fluctuating oxygen levels in the water. Overall, rather inhospitable.

The project, which is continually expanding, therefore aims to compare three species (A. grahami, O. mossambicus and the Nile tilapia) with different tolerances to salt and other conditions of importance for fish farming (aquaculture), in order to find out the genetic secrets that allow the soda cichlids to survive at extreme environments.

From each of the species, various body parts have been collected, including the gill, gut, operculum, liver, whole brain, eye, kidney, heart and gonads.

If you are wondering why, it’s because each of these body parts is regulated differently - and adaptation mechanisms come in all shapes and forms. By analysing and comparing the transcriptome of species, i.e. the specific genes turned on at certain times, we can better understand what is happening (genetically) - and where.

It turns out that one such adaptation that helps the soda cichlids survive in such tricky conditions is how they excrete waste. They have a different urea cycle to most other fish, which normally excrete ammonia. This isn’t possible in alkaline lakes, therefore soda cichlids actually excrete urea - from their gills. They have also adapted to tolerate the low oxygen conditions so well that they can respire using atmospheric oxygen - and can be seen gulping air from the surface of the lake.

The genetic mechanisms behind these adaptations are therefore very interesting to study.

Furthermore, this project has wider significance due to the importance of cichlid fish for food security and socio-economic stability in Africa - a continent with a very high rate of poverty and food insecurity.

The ongoing project into better understanding the genetics of cichlid fish, along with the development of a Tanzania Aquaculture Resolution, is allowing EI to be at the heart of an international collaboration helping to promote and foster better aquaculture practises in Tanzania - a country home to a vast array of cichlid biodiversity.

This project will not only help us better understand how evolutionary processes can shape adaptation to extremes, but also how we can preserve native biodiversity and provide better nutrition and livelihoods for people through sustainable aquaculture programmes.

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Through this IDS funding we are expanding our remit to use our Field Pathogenomics technology to investigate stem rust and get to “know our enemy”.

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Doctor, doctor! My wheat is rusty …

Cereal rusts are a devastating plant disease also known as the ‘polio of agriculture’. Rusts are parasitic fungi associated with many crop failures and famine throughout history. In particular, ‘stem rust’ - a cereal rust usually found in warmer climates - did not affect the large number of people dependent on wheat for sustenance for many decades.

In 1999, an epidemic caused by a very aggressive form of stem rust on wheat emerged and is currently spreading across Africa, Asia and the Middle East. Its spread poses a significant threat to global food security. Most of the wheat grown around the world is vulnerable to this epidemic. In areas susceptible to disease development, losses are often severe (average 50% to highest 90%) over a large area and individual fields can be totally destroyed.

In temperate climates, the environmental conditions and farming practices have not supported large-scale stem rust epidemics so far. However, climate and epidemiology models predict that stem rust will become widespread as far north as Scotland by 2050. This is supported by recent events where in 2013, Germany experienced its first major outbreak of stem rust in 50 years and Nature published an article in response to an unusually devastating strain being found in Sicily.

Scientists at the Norwich Research Park have developed a cutting edge technology to track cereal rusts: ‘Field Pathogenomics’ – a genomics-driven surveillance method to obtain a genetic fingerprint from samples collected in the field and determine their relation. This information is vital for detecting changes in the rust disease, ensuring breeders, farmers and agronomists have access to the best possible information.

This helps them to be prepared for new outbreaks and effectively manage rusts by breeding new generations of plants which can withstand the disease. Through this IDS funding we are expanding our remit to use our Field Pathogenomics technology to investigate stem rust and get to “know our enemy”. This will help establish the likely global migration routes of stem rust and characterise its future threat.

Although emergent diseases are spreading, we certainly have a better toolkit than ever before when it comes to understanding and responding to them. Further updates will be presented on this research once the grant’s publication is released later in the year.

All in a year’s work.

These EI-led projects all go to show the tremendous applicability of next-generation genome sequencing and big data analysis - and the importance of having such a hub for interdisciplinary genomics research that provides not only technical and analytical capability, but also fosters open data sharing and international collaborations to the benefit of the scientific and wider international community.

“It’s wonderful to see that our funding scheme has driven forward creative and innovative in-house research,” said our Director of Science Prof Federica Di Palma. “Where such funding opportunities were previously non-existent this scheme has enabled early-career scientists to lead collaborative pilot projects, working with industry and other stakeholders, through to proof of concept. This has supported their ongoing career development and encouraged networking with their peers, promoting research that appeals to a wider commercial life science community.”

1The MindTheGut project team are currently working on the prototype together with Norwich Research Park, due for release in Spring 2017. We’ll keep you updated!

Article author

Peter Bickerton

Scientific Communications Officer (Part time)