Local schools take on Future Food Challenge

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An innovative schools outreach programme that encourages students to think about sustainable food production is set to return after a successful first run earlier this year.

Future Food Challenge, a 12 week programme delivered by social enterprise Farm Urban and the University’s Institute of Integrative Biology, challenges Year 9 students to think up new ideas for growing food in urban environments using aquaponics – a sustainable method of raising both fish and vegetables.

The programme, funded by Shaping Futures, the Merseyside partner for the National Collaborative Outreach Programme (NCOP), gives school teams the chance to immerse themselves in the science of aquaponics with their very own Farm Urban Produce Pod system, before forming their own start-up, developing a business idea and designing and building their own aquaponic food system.

The programme provides students with the opportunity to gain an insight into start-up businesses, social enterprise and how they link into Higher Education activity, whilst developing skills in project management, leadership, finance, teamwork, communication and scientific research.

This year’s finale event, held at Farm Urban’s agri-lab space at the Liverpool Life Sciences UTC in July, gave teams the opportunity to exhibit their work, display their systems and pitch their business idea to a panel of judges, comprised of local business leaders and university academics.

Business ideas ranged from systems for use in primary schools to hospitals and local cafes. The overall winners from Woodchurch High School in Wirral carried out research and spoke to local charities and churches to create a system that would provide fresh food for those accessing food banks. The winning team said: “We have loved our aquaponics journey from fish to free fresh food for everyone. It has made us more aware of food problems people face and how to help them using science.”

Dr Iain Young, University lead for the programme commented: “Teaming up with organisations outside the University can be a really powerful way of delivering public engagement, showcasing our science and involving the public in research. This project gave us the opportunity to partner with Farm Urban to reach hundreds of school children from less advantaged backgrounds. Farm Urban are an inspiration in themselves, promoting local, healthy food production, and they also deliver exceptional events and programmes. I have found the whole experience of working with them on this project very rewarding.”

Farm Urban is now encouraging the Future Food Challenge teams to act as Future Food Ambassadors, sharing what they’ve learnt and inspiring their fellow students to think about what they can do collectively to continue to tackle global food challenges in their own communities.

Registrations for the 2018/19 Future Food programme are now open for schools. Please visit http://www.farmurban.co.uk/future-food-challenge for more information.

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Woodchurch High School students were the overall winners for 2018.

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VG&M ‘Marvellous Molecules’ Summer Science Club

VG&M ‘Marvellous Molecules’ Summer Science Club

Guest post by Victoria Harman, Centre for Proteome Research at the Institute of Integrative Biology

On Tuesday 28th August, six members from the Centre for Proteome Research held a Victoria Gallery and Museum Summer Science Club session for local primary school children. The session, entitled ‘Marvellous Molecules’, began with a messy activity where the children were able to explore the components of ‘blood’. We used water beads, ping pong balls and square pieces of sponge to represent the red blood cells, white blood cells and platelets, respectively. The three components were bathed in water to represent blood plasma. All four components were correctly identified by the children and they even knew all the functions!

We then went on to explain that blood cells contain DNA sequences and that these sequences can be used to make proteins in our body. The children each selected a blood cell from the ‘blood’ mixture and opened them to reveal a laminated DNA sequence that coded for a different protein from different organisms. For example we had the DNA code for a protein in the venom of a cobra and the protein that causes oranges to ripen. Using this code the children could create DNA code bracelets where each nucleobase corresponded with a particular colour of bead. After creating the parent strand, using base coding pairs, the children were able to create the daughter strand.  The children enjoyed this so much some made up to three bracelets!

Next we moved onto ‘DNA whispers’. This was a Chinese whispers activity using sentences about DNA to explain how it can sometimes be copied incorrectly causing errors. Some changes often don’t cause a problem, however, other errors (or mutations) can cause genetic diseases such as sickle cell anaemia. One of the sentences used in the game was “Even identical twins don’t have identical DNA” which got changed to “Even identical twins don’t have DNA”, proving a point about how small changes can have a big effect on the meaning of the sentence, or in terms of proteins, their function. We explained about sickle cell anaemia and the children were able to mix some blue water beads into the ‘blood’ mixture, representing the less oxygenated sickle cells. We explained that people with sickle cell anaemia can experience pain, but using some ‘marvellous molecules’ we can treat these symptoms. We looked at the structure of three of these molecules; paracetamol, ibuprofen and aspirin and got the children to make the structures out of paper and pipe cleaners.

We finished the session by asking the children questions about what they had learnt during the session. They were able to answer every question and were awarded with stickers for the correct answers.

We were all very impressed by the knowledge and enthusiasm of the children that attended the session and we look forward to helping out again next year!

 

 

 

Learning synthetic biology techniques in Denmark – Johnston Post Doc Fund report

Learning synthetic biology techniques in Denmark – Johnston Post Doc Fund report

Guest post by Dr Hannah McCue, postdoctoral researcher at the Institute of Integrative Biology

With the help of IIB’s Johnston Postdoctoral Development Fund, I was able to visit a world-leading lab in Denmark in order to enhance my knowledge of advanced synthetic biology techniques. Prof Mortensen’s lab is situated at the technical University of Denmark (DTU) located in Lyngby, just outside central Copenhagen. The Johnston Fund kindly covered costs for my travel and AirBnB accommodation close to the DTU, giving me almost two weeks to experience life working at the DTU and learning novel molecular biology techniques.

The key aim of my trip was to learn the ‘tricks of the trade’ of Uracil-Specific Excision Regent (USER) cloning, a technique which multiple scientists at the university have struggled to utilise. In principle, USER cloning should be a straight forward one-pot cloning reaction which holds several advantages over other traditional and more modern cloning methods. Specifically, USER cloning utilises a ligation-free protocol, generates highly specific sticky ends and does not rely on the presence of restriction enzyme recognition sequences. The premise of USER cloning is that by incorporating a single deoxyuracil around 8-12 bases from the 5’ end of each primer, highly specific and long sticky ends can be created on the resulting PCR product with the USER enzyme mix. USER enzyme contains uracil DNA glycosidase (UNG) which excises uracil nucleotides from PCR products and DNA glycosylase-lyase endo VIII which releases the sequence upstream of the uracil nucleotide. The overhangs created are sufficiently long that DNA assembled into a circular plasmid is suitably stable to be transformed into bacteria without prior ligation.

My visit to Prof Mortensen’s lab gave me hands on experience of USER cloning alongside established experts in the field of cell factory construction and engineering. Whereas my expertise lies mainly with the use of bacteria for the production of heterologous proteins and secondary metabolite pathways, Prof Mortensen’s lab focuses on yeast and fungi such as Aspergillus. The main focus of the lab is the discovery of valuable products from fungi and the development of optimal cell factories for their production. To this end, they use CRISPR technology both to insert gene pathways into the organism of interest and to regulate the pathway to give optimal output of the desired molecule.

I was lucky enough to work alongside Dr Katherina Vanegas Garcia who developed “SWITCH” and “TAPE” techniques to help speed up strain construction when developing yeast cell factories. Using these techniques strains can be generated that can iteratively switch between a genetic engineering and a pathway control state. For instance a multi-gene pathway can be inserted into an innocuous location in the genome of the desired strain using Cas9 nuclease in genetic engineering mode. Subsequently the cell factory can be switched into the pathway control state using a dCas9 mutant to up or down regulate different genes in the pathway and monitor the effects to optimise final product yield. She also helped developed a Technique to Assess Protospacer Efficiency (TAPE) whereby the efficiency of particular sgRNA protospacer sequences are assessed for their efficiency to target Cas9 to genomic DNA and cause double strand breaks. The principle is that double strand breaks are lethal in yeast and therefore the efficiency of a protospacer sequence should be reflected in the survival rate of transformants in the absence of a repair template. This technique is also applicable in Aspergillus nidulans NID1 strain which is deficient for non-homologous end joining and hence double strand breaks will also be lethal in this strain.

I designed two experiments to test the application of USER cloning for future use in GeneMill. The first was to assemble 5 stretches of DNA encoding an operon of 13 genes and spanning almost 14 kilobases. USER overhangs were designed to assemble these genes into a USER backbone developed by Dr Vanegas Garcia. Unfortunately, a plasmid encoding all 13 genes was not obtained from these experiments, however, staff and students at the DTU have succeeded in cloning large gene constructs in this manner. Presumably there is an issue with the specific DNA sequence used in this construct which has also proved problematic when using other cloning techniques in the past.

The second experiment was to clone three sgRNA protospacer sequences into a USER backbone designed for CRISPR in Aspergillus nidulans. This cloning was successful on the first attempt and subsequently I was able to carry out CRISPR TAPE experiments to assess the efficiency of targeting of the protospacer sequences to my gene of interest in A. nidulans. All three sgRNA constructs were lethal in NID1 strain when compared to the control transformation showing that all three protospacer sequences were highly efficient. In parallel, I also transformed each sgRNA along with a repair oligo to insert single amino acid changes in my gene of interest. Unfortunately, all three transformants were extremely sick with only one colony from one sgRNA proving viable. This could indicate either that the mutations encoded by the rescue oligos were also lethal or repair using the rescue oligo was not achieved. Without viable transformants to PCR from this is difficult to check. Instead I plan to design oligos encoding silent mutations in the hope that I will then obtain viable transformants.

In summary, my visit to the DTU gave me the opportunity to test USER cloning in both challenging and simple applications. I was also able to conduct a series of CRISPR experiments in A. nidulans, an organism with which I had no prior experience. In addition to receiving hands-on training in the lab, I was given the opportunity to speak to members of different research groups and attend a number of research seminars during my stay. Research areas ranged from discovery of novel antibiotics in fungi to pleasant smelling moss that can be used as an alternative to air freshener! Of particular interest was the Diversify project which is a huge collaboration between many different researchers at the DTU and industrial partners Novozymes and Novo Nordisk. This project aims to take hundreds of yeast and fungal strains and adapt them for the aforementioned SWITCH technique by identifying innocuous sites for heterologous pathway integration. These strains can then be rapidly screened for optimal production of desired metabolites. Ambitious, high throughput, multi-partner, synthetic biology challenges such as this have the ability to change the wider approach to industrial biotechnology enabling sufficient production of useful or valuable compounds that would otherwise be ignored due to underperforming host strains.

I have been extremely privileged to have been selected for receipt of the Johnston Fund and as a consequence I have obtained invaluable experience of how another synthetic biology-focused research lab works. I have renewed enthusiasm that synthetic biology can revolutionise biological research and has the potential to have a significant impact on how we think about the future of industrial biotechnology. Not only am I now equipped to teach and supervise students and colleagues about how to utilise USER cloning, the visit to Denmark has given me a wider perspective on how to approach various industrial projects with which I am involved. I therefore believe that the experience has greatly enhanced my professional development and will aid my productivity across all aspects of my work.

Future research priorities for conservation management in the Masai Mara

GroupPicture_MasaiMaraWorkshopThe Masai Mara in southern Kenya offers some of the most spectacular wildlife sightings on the planet. Exceptionally high densities of large predators and the annual wildebeest migration attract a large number of visitors each year. However, in recent years scientist witnessed a drastic decline in many wildlife populations. Human population growth seems to be the key driver of these changes and the major challenge in upcoming years will be the coordination of land use to ensure development as well as conservation goals.

In September 2017, the Mara Herbivore Project organized a workshop to identify research priorities to support the conservation management of the Masai Mara National Reserve and the adjoining conservancies. The invited participants included protected area managers and research programme directors from the Masai Mara National Reserve, Kenya Wildlife Service, Enonkishu Conservancy, Maasai Mara Wildlife Conservancies Association, Kenya Wildlife Trust, Mara Predator Project, Peregrine Fund, Hyena Project, and of course the Mara Herbivore Project. After a day of brainstorming and intense discussion, we voted on the importance and urgency of 35 research questions raised within three main categories: (i) habitat & species management, (ii) management of tourism & exploitation and (iii) livestock management & human wildlife conflict. Ranked highest by all participants was the question how habitat fragmentation due to increased fencing of private land effects wildlife populations in the Masai Mara. Many species in the area conduct seasonal movements in response to differences in monthly rainfall and currently there is no knowledge on how these spatial dynamics are affected by fencing. Other important questions were related to the strategic location of new wildlife areas, the impact of tourism infrastructure on wild populations and the effect of livestock management on resource availability within the reserve.

To raise awareness for the urgent threats the team led by Jakob Bro-Jorgensen published an article in SWARA, a magazine published by the East African Wildlife Society. It is aimed at non-specialists with a general interest in the problems experienced in today’s wildlife and habitat management.  The team hope that the article encourages a debate on the sustainability of current land-use practices, and that it leads to a closer cooperation between managers, researchers, and local communities in preserving the wider Masai Mara ecosystem.

 

Dementia Public Engagement Day

On Wednesday 23rd May, scientists from Team Madine and Team Turnbull went on a mission to educate the public about dementia research as part of dementia awareness week, at the Alzheimer’s Research UK North West public engagement event hosted at the Institute for Dementia (University of Salford). The event was a hive of activity and a cornucopia of fun! Through the media of Lego®, giant KerPlunk!, cells and real brains members of the public were introduced to all things dementia, including how diet can affect your dementia risk, the development of novel inhibitors of dementia-associated proteins and the links between dementia and other diseases.

Kiani Jeacock, James Torpey (Madine group) and Scott Guimond (Turnbull group) showcased the fantastic research happening at the University of Liverpool through informative posters and a ‘Draw for Dementia’ activity. People were invited to draw the first thing that came to mind when they heard the word “dementia”, which resulted in some really interesting and thought-provoking work!

On the day, they also met people who had dementia themselves or who had friends or family with dementia. This was an educational experience for the scientists too, as it highlighted the translational aspect of their work and emphasised the importance of research into these poorly-understood conditions.

Overall it was a well-organised and enlightening day, and events like these are fantastic for both researchers and the general public alike.

Thanks to ARUK and the Institute for Dementia for hosting!

 

Warrington Collegiate Student Work Placement

Louis O’Brien, a student from Warrington Collegiate, sitting their BTEC Level 3 National Diploma in Applied Science, applied to do a work placement in the lab of Natasha Savage.

Louis worked with Natasha for a full week during February 2018. They did a variety of experiments and simulations together:

  • Plasmid Preparation. Bulking up plasmids using bacteria, performing a midi plasmid prep.
  • Cell culture. Growing up 3T3 cells from frozen, ready for plasmid transfection.
  • Time Course Imaging. Bacterial colonies, grown from swabs of Louis’s phone, were put in suspension and filmed under a light microscope to observe their proliferation.Polarity Simulations. Louis ran simulations of cells breaking symmetry. By changing reaction strengths Louis worked out the key molecular components.

    Louis doing bacterial work for time course imaging. Growing 3T3 cells from frozen stocks. DNA extracted using midi plasmid prep.

Farm Urban’s Future Food Challenge – launch Event – Speed Date a Scientist

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150 year 9 pupils from local schools visited the University of Liverpool for one day in
February to take part in the Farm Urban Future Food Challenge Launch Event. During
the launch event students engaged in a number of activities, including speed dating
scientists.
The speed date scientist event was great fun. The scientist sat at a dating table and awaited the students. Students arrived in groups of around 6. During a 5 minute period the scientist introduced themselves and their work, after which the students were free to ask any questions they wished. Questions ranged from, ‘Is being a scientist hard?’ to ‘Do you think there is a god?’ Once a conversation started it could go anywhere from eprogramming humans to the origin of names. The event was great fun for all.

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