Spooky Science Take 2!

Nearly 300 primary school pupils from across Merseyside visited campus on Wednesday 23rd October 2019 to take part in some ‘spooky science’ activities led by Institute of Integrative Biology and School of Life Sciences in collaboration with World Museum Liverpool, the event used the Halloween theme to capture the imagination of the pupils and introduce them to some different areas of life sciences research.

During the workshops, pupils learnt about how animals adapt to their environment, communicate with each other and protect themselves from prey. Activities included exploring the anatomy of creepy-crawlies under microscopes, examining animal skulls from different species, discovering how bats see in the dark and understanding how the human body reacts to fear.

Zoology staff from the World Museum also brought along some taxidermy specimens, including a raven, for the pupils to interact with.

It was amazing to hear the enthusiasm from the pupils from the minute they entered the lab exclaiming wow this is what a real science lab is like! Followed by comments like science is great, I now want to be a scientist when I grow up.

The primary schools that took part were Banks Road, Litherland Moss, Pleasant Street, St Cuthbert’s, St Sebastian’s, Croxteth, St Nicholas and St Anne’s. Academic staff, PDRAs, PhD, masters and undergraduate students helped with running activities throughout the day.

Biochemists inspiring School of Medicine A-level Students at West Lancashire College

A-level students at the School of Medicine at West Lancashire College were inspired by talks from three biochemists Dr Jill Madine, Dr Nigel Jones and Professor Sonia Rocha during November and December 2019. Students learnt about the research carried out within our research groups relating to diseases and their underpinning mechanisms and the career paths each of us followed to reach our current positions. The students were some of the most attentive audience members we have ever spoken to asking questions that wouldn’t be out of place at large International Scientific Conferences. We hope to welcome some of the students for summer work experience placements in IIB.

Shrewsbury School Visit

46 year 12 pupils and 4 teachers from Shrewsbury School visited IIB on Wednesday 8th January to discover the amazing technology and facilities we have within the institute. The day organised by Dr Jill Madine began with an unmissable opportunity to promote UG courses at Liverpool from Dr Andy Bates, School of Life Sciences. The pupils then learnt about a wide range of applications using the available technologies from Dr Marie Phelan, Dr Linda D’Amore, Dr Gareth Wright and Professor Pat Eyers. In the afternoon the students got to see the facilities up close and ask questions during tours of Barkla X-Ray laboratory of Biophysics, NMR Centre for Structural Biology and Centre for Genomic Research from PhD students Liam McCormick and Kangsa Amporndanai.

Empowering girls from Holly Lodge Girls’ College and inspiring them to pursue scientific careers – 19th June 2019

As part of the volunteering undertaken by Dr Eva Caamano-Gutierrez with the charity The Girls’ Network we hosted a group of girls from Holly Lodge College and showed them how the real life of scientists looks like.

Our aim was to showcase the multidisciplinary and collaborative research that is undertaken in the institute while trying to encourage all the girls to pursue further education, especially in scientific fields.

Arriving just after 16:00 the groups of 19 girls and a few curious mentors arrived to the IIB and were greeted by Dr Jill Madine, Dr Marie Phelan and Dr Eva Caamano. They took all the girls to visit the Biochemistry labs, the NMR Centre for Metabolomics and the Bioinformatics office where both the CBF and the CGR are hosted. Our message was clear: we work on very cool projects, we only succeed working together as a team, our jobs are hard but flexible and overall science is really exciting!

The cherry on the cake was put on by our software developer Dr Tony McCabe who showcased a number of software solutions applied to life sciences that really brought the ‘wow’ factor into the conversation.

The girls were interested in multiple aspects discussed during the visit ranging from specifics of an academic career, including what is a PhD? Or do you get paid while doing one? To being surprised about the fact that Charities such as the British Heart Foundation fund many different research projects.

Following this visit we had our last mentoring session for the academic year. When the girls were asked what they think they can they achieve in their lives they all answer unison “Anything”.

We are doing something good here. Let’s keep them coming in future years!

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Inspiring the next generation of NMR scientists during British Science Week

On Friday 15th March 10 chemistry A-Level students from Range High School visited the Institute for the annual Analytics Day held in the NMR Centre for Structural Biology organised by Dr Jill Madine and Dr Marie Phelan. This visit has been an annual event for the past several years which the students look forward to in order to gain enhanced understanding of NMR to help with their A-level courses and also provide an opportunity to chat with PhD students about what is involved in University life and academic research.  The students were given lectures on the basic applications of mass spectrometry and NMR from Stephen Moss (School of Physical Sciences) and Dr Marie Phelan. This was the followed by practical workshops where the students carried out chromatography and learnt to prepare and run NMR samples along with how to interpret the data.  Prior to their visit, as part of a school practical, they have made salicylic acid – a precursor for aspirin. We obtained these samples and collected NMR spectra of their products ready for analysis on the day.  This enabled them to establish how successful their synthesis had been and compare their results across the class, with previous years’ students (and to the teacher!). The pupils response at the end of the day was that they had learnt a lot and they can now ‘do’ NMR. Watch out for future budding NMR Nobel Prize Winners inspired during British Science Week in IIB!

Pupils were assisted on the day by Michelle Tan, Adika Sen (visiting interns in the NMR Centre), Zain Ghanameh (IACD), Jeremy Chazot (IACD) and James Torpey (IIB).

Halloween Science at the Institute of Integrative Biology

spooky science

Post by Dr Jill Madine

On Wednesday 31st October 2018 IIB and SoLS held the first Institute-wide School Engagement event within the Life Sciences Building. 82 children from Banks Road, Litherland Moss Primary Schools and home-schooled pupils from the local area attended the morning session with 128 Secondary school children from Notre Dame Catholic College, Prescot School, Kings Leadership Academy Hawthornes, Academy of St Nicholas, Archbishop Blanch and St Michaels High attending the afternoon session.

Pupils took part in a range of fun spooky science activities:

  • exploring relationships between skulls and other features of animals (e.g. diet and faeces!) with Michael Berenbrink and PhD student Kelly Ross
  • finding out about blood flow and gravity, how holding your breath slows your heart and which animals that make your heart race with SoLS Terry Gleave and Rachel Floyd
  • making zombie proteins out of magnetic beads with Luning Liu and Fang Huang, assisted by many students
  • looking at model organisms under the microscope with the Centre for Cell Imaging (CCI – Violaine See, Dave Mason, Jen Adcott, Daimark Bennett, Anne Herrmann, Marco Marcello and PhD students Kit Sampat, Hammed Badmos, Rebecca Kelly)
  • finding out how much protein is in the foods we eat including fishing in cauldrons for the answers from the Centre for Proteome Research (CPR – Kimberley Burrow, Jos Harris, Victoria Harman and PhD students Max Harris, Rosie Maher, Iris Wagner, Natalie Koch)
  • pupils could also get up close and find out more about a range of animals kindly provided by staff from World Museum and from within SoLS with Carl Larsen

Additional student and staff helpers including Alice Clubbs Coldron, Lauren Tomlinson, members of Jill Madine group (Hannah Davies, James Torpey and Alana Maerivoet), Louise Colley and Laura Winters were invaluable in organising the day and logistic arrangements on the day.

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.