Wednesday, 23 July 2014

"It was the best of times, it was the worst of times, it was the age of wisdom, it was the age of foolishness..."

The opening lines of "A Tale of Two Cities" by Charles Dickens, seem to capture my thoughts as we enter the last week of the first year since the Liverpool Life Sciences UTC first opened. Not only are the opening lines apt, but this year has seen me negotiate between the two cities of Liverpool and Sheffield: as I have tried to combine my new role at the UTC, with my role as an academic at the University of Sheffield. I'll cover both the successes (the best of times?) and also the challenges that lie ahead, since next year will probably be more important than the year behind us. It is of course understandable that for our students, their parents, and those who will employ or educate them further, examination results will be the major focus, but I shall concentrate on the activities in the Innovation Labs, which have been my primary concern.

September saw the doors open, shortly after the paint had dried and about 20% of the equipment had been set up in the labs. The sun was shining and the sense of anticipation at the UTC was stronger even than it would be at the end of the month, when freshers would arrive at Sheffield. Why? A complete team of new teaching staff, new support staff and no time for a dry run! I decided to play safe and combine some elementary Bioinformatics with the basic principles of visible light spectroscopy. Easy enough? Well, actually, yes. Of course there were some blank expressions, anxious looks, nerves etc., but the students were OK, that was just me and the teachers! By the end of the month I was feeling confident that the Y10s and Y12s would be capable of considerably more than I imagined. So I decided to get more ambitious. I was also very conscious that the planning of classes had to be almost spontaneous in order that I could react to students on a weekly basis. However, this made it somewhat challenging for the teachers, but thanks to their patience (and I like to think a level of enjoyment!) we managed to muddle through, while the students grew in confidence on a daily basis.

By October, I was using my regular walk from Lime Street station to Greenland Street, to plan the day's activities, with further reminders of the Dickens theme in view (I don't think we get to know Uriah's father's name, but he had endowed within Uriah the positive (in his eyes) value of being a yes man, and this was of course something I wanted to make sure didn't happen with UTC students). I decided I could easily challenge the students a little more than I had originally intended and importantly, that rather than use the tried an tested model of structured class practicals, I would begin to empower the students and teach them the value of failure. The lab classes were now combining skills such as  spectroscopy, microbiology, chromatography, electrophoresis and Bioinformatics, with planning, teamwork and the need to organise and label samples. All of which prepared the Y10s for proteomics of milk and the Y12s for a Biotechnology project with the aim of purifying recombinant Green Fluorescent Protein. Before I leave October, I have to say that emotions ran high (in me) when the entire lab broke into a round of applause when the Nobel Prize for Physiology or Medicine was announced over the lab screen via a live stream from Stockholm!

The dark nights were upon us, it was now November, but I was brightened by the prospect of delivering a tube of Green Fluorescent Protein. GFP has not only proved to be a major help in elucidating a range of Biological phenomena from the early stages of cell division, to the protein mediated cues in animal development, but has also brought high visual impact to Molecular Life Sciences, in a way that I decided could capture the imagination of the students in Y12. In fact the project that was associated with our partners Eden Biodesign incorporated an understanding of the mathematical basis of cell growth, the principles of gene repression and induction, the fundamentals of affinity chromatography and the power of spectroscopy. By the end of term, we were well on the way to the "Green" Prize.

Through November and December, the students were alerted to the requirement to present their results in front of staff and representatives from our partner industries. Eden Biodesign kindly sent a a team of senior research staff to judge our Y12 presentations, while staff judged the Y10 presentations. In the latter case, we had developed the use of supermarket milk as a vehicle for exploring the analytical methods used to analyse the proteins present in milk (see left). We also investigated one of the earliest forms of Biotechnology: cheese production. When I mentioned "...the worst of times", the quality of the cheese produced may be the best candidate in this respect. It looked like a reasonable French soft cheese, but I am afraid that's were the similarity ended. Nevertheless, the students managed to pool together their results and background reading and I was incredibly proud of their presentations. Leaving me with Great Expectations for 2014! The presentations from Y12s to Eden, filled me and the teachers with enormous pride. This was the first real sign that we had shifted the aspirations and capabilities of students of this age into one that made the panel raise a few eyebrows in pleasant surprise. I must also say a special thanks to Geoff Dickinson in the Central Teaching Labs at the University of Liverpool for his unwavering help in providing last minute equipment to bail me out of what could have been a few embarrassing moments in the lab!

With the opportunity to reflect on the first term over Christmas and of course enjoy the festivities, it wasn't long before Christmas was behind us, and my main undergraduate teaching at Sheffield too. The New Year provided an opportunity to introduce the Y12 students to experimental logic of drug discovery and the Y10 students to meal worms and practical genomics. This involved the introduction of microbial plate based and broth assays for the detection of bacterial growth inhibition. 

Recalling the discovery of penicillin, we set out in Y10 to investigate the effects of bleach and detergents compared with some common antibiotics. This provided a vehicle for sneaking in the use of log graph paper plotting exponential relationships, which in turn fired my enthusiasm for making maths a focus of lab classes wherever possible. Around this time I also started using Twitter to try and engage a wider audience in the innovation lab activities. Possibly my most unlikely idea (a result of the sight of ten pomegranates in a box at Tesco) to teach the metrics of viral infection using fruit and veg, proved fun and took us into unexpected avenues of Greek maths and science. A bit of a eureka moment in teaching methods for me! I think I have developed a reputation for science on the cheap and I am sure the students will fondly recall the first tub of 99p dried mealworms and the 6 pack of Poweraid: my best source of a negatively charged brilliant blue dye in chromatography classes!

February saw the students dealing with extraction methods from plants and fruit through to meal worm larvae, either dried or fresh. These experiments took us into unknown territory for the first time, with students being expected to decide and evaluate the methodology that they would employ to obtain the most active extracts. In the case of the plants, we were looking at the use of different solvents and cell breakage methods, with activity against E.coli plate growth as our assay. In the case of the mealworm, we utilised a range of techniques and managed to settle on the use of a glass-teflon homogenizer (kindly donated by the University of Sheffield teaching labs) whilst keeping the larval extracts ice cold. This generated protein extracts and both DNA and RNA, which will form the basis of our meal worm "omics" project. Dr. Moore and I thought we would try our luck with the Royal Society in view of the students' success and bid for research funding. The grant was submitted and a decision would follow in April....

 In March we hosted as usual, a number of visitors  and amongst them we were fortunate to host  Professor Phil Ingham FRS, from Singapore who  chatted to students and staff. Phil, kindly provided  our first guest Blog (which you can find earlier in  the series). I was absolutely delighted by the  success of the Y12 group in taking on a challenge  from Dr. Doug Cossar at Croda. Lyndsay and I had  been impressed by the warm welcome at Croda, and in particular the suggestion for a project in synthetic biology, one of the most exciting, emerging research areas in Biotechnology. Doug asked if we could obtain a set of genes and their proteins from Blue Green algae, that related to the synthesis of tri-peptides. Recalling a colleague worked on Synechocystis and having my lap top on hand to carry out a quick BLAST search, I decided we should give it a go. What you can see top left is the result of the first UTC, mass PCR experiment. Importantly on Synechocystis genomic DNA isolated by a method developed by the class. We finally completed the amplification of the genes and several Y13 students will move onto the next stage as part of a small project team and produce recombinant proteins in order to establish whether we can synthesise tri-peptides in this way.

April saw the arrival of Easter and exams! This enabled us to a little time out fro lab classes to expand our interest in the use of 3D printing in the labs. George had given us a tantalising insight into the power of 3DP, but it was only when we began to design and print lab equipment, that we realised the significance of this new technology. The Greenland Biodesign team warmed to the opportunity of incorporating 3DP into the lab, and soon we were able to print our own lab equipment which now ranges from column chromatography racks, through to a fully operational, battery operated microcentrifuge: all for a fraction of the price! George is keen to establish the labs as part of the Fab (for fabrication) Lab network and, with the award of a number of further printers in the new academic year, I can see us becoming much more dependent on this technology in the future. Another important development on the Blog site was the contribution from Dr. Antal Kiss from the Hungarian Academy of Sciences; exposing students to the wider community of scientists and promoting the UTC as part of a new venture in Science, which s of course a major part of the UTC's mission. Recognising our place in the wider Scientific and Educational communities is something that will continue over the coming years. (All of the earlier Blog which contain more detail can be accessed on the RHS) 

 By May, the examinations were in the air for the  Y12s, but the most exciting news was the award  from the Royal Society of our first grant application!  The mealworm, or Tenebrio molitor, to give it its  full scientific name, was now our very own model  organism and we completed a set of ambitious  experiments aimed at developing a proteomics   approach to understanding a range of Biological phenomena using contemporary methods. As this was going on, discussions were afoot with the University of Liverpool Genome Centre to begin to sequence the mealworm genome (we are currently carrying out preliminary DNA extractions for this and hope to get started in the new academic year). 

Probably the most significant outcome of the month was my quest for the key skills (sorry but the artful dodger's craft was the best Dickens reference to skills training I could think of!) needed by an experimental Life Scientist. It is easy to assume that after over 35 years as a trainee Biochemist, I would know the answer to this, but it is important to remember that scientists depend on collaboration and communication; so I decided to ask as many people as I could, ranging from our partners to research scientists from all over the UK, the USA, Europe and indeed the East Asia. What do they think are the skills that a contemporary Life Scientist should possess? The answers came in two waves: immediate responses, Sir Rich Roberts being an early responder as always! Followed by a steady stream of response (still coming in!). This information, combined with a detailed survey of our regional partners, forms the basis of our Skills Passport. More than a piece of paper, the aim of this initiative is to empower UTC students by preparing them in a robust manner for experimental Science in the 21st century. However, this does not mean that we only focus on the methods of the day, we include in our initiative key transferable skills in Science (and indeed in Life in general), such as project planning, sample tracking, analysis of data, computational skills, numeracy, literacy all of which are essential not only for understanding Science, but also in communicating it.

With June came the sun, the Minster for Business  and Skills and the return of the students to the  Innovation Labs. It is also examination season for  me at University and this includes my job  examining final year undergraduates at the  Universities of Lancaster and Cambridge. So Miss  Hudson kindly stepped into the breech for the Y10  students and delivered a phenomenal class on the  anatomy, physiology and genomics of the locust. The locust has been used widely in Biological education, owing to its rapid breeding, its size (making it easy to observe and to dissect) and its reproductive organs contain easy-access and easy to see chromosomes. More recently the locust genome has been published and the opportunity to combine classical biology with contemporary bioinformatics represents a superb example of how Life Science has developed over the last 10 years and this lab class illustrates the power of the Liverpool Life Sciences UTC in being able to deliver such a confident experimental programme through our teachers. 

The Y12s, unfortunately had to contend with me and the dreaded exercise of "primer design". My old PhD supervisor (actually he looks younger and is certainly still more active than me!) wrote in his undergraduate text on Enzyme Kinetics, that Enzyme Kinetics (the study of the reaction rates and intermediates in enzyme catalysis) is a little like "Latin and cold showers". Whilst the curriculum has changed somewhat since he and I attended school, it is true to say that "primer design" has been the cause of many tears in the lab! The logic is simple: DNA is made of a sequence of 4 bases (GATC), knowing the sequence of one strand allows you to predict that of its "complement". So an A on one strand will have a T on the other, a G pairs with a C and so forth. The direction of the strands is polarised in the opposite direction, and this is where the confusion comes (hence the Twist top left!), since the enzyme we use to incorporate the synthetic primer into DNA for the "forensic" technique of PCR (the Polymerase Chain Reaction is a means of amplifying minute quantities of DNA for analysis in all areas of Science) can only run in one direction. I am pleased to say that everyone (in the end!) cracked the primer design problem. We then used this predictive logic to design primers to amplify genes from a Blue Green algae to round off our Synthetic Biology project. Presentations will follow after summer, since we have many students away on placements.

Student ideas are incredible

July marked the time for students to consolidate their skills passport and to design their own Y11 and Y13 projects. Once again, more surprises were in store for me! My year in the Innovation Lab has taught me many things about Science, but I think the most important lesson I have learnt is never (ever) underestimate the ability of young people. Science projects, in which individuals or small teams of students design plan and execute a piece of research based on some observations of others (or sometimes their own observation) is the cornerstone of Science: it is the way that we "stand on the shoulders of giants". However, at University, students usually carry out their first research projects in the lab after their second year of study. I decided (as you can read in an earlier Blog) to ask students to design their own projects (something that used to be the way PhDs were managed) and the ideas that came back were exceptional. Of course the use of gamma rays to explore fungal responses to DNA damage may not be easy to accommodate in the Innovation Labs and we may not be switching on the first mass spectrometer designed and built in a school, but we will work within our limitations to accommodate these ideas. I have most of the project ideas in hand and over the summer I shall be obtaining resources finding research mentors from Industry and Academia and I am confident that by this time next year I will not only be writing up research papers from class experiments, but from research groups within the UTC. This represents a major shift in Science education in schools and will be a defining moment for the Liverpool Life Sciences UTC

One of the lesser known works of Charles Dickens is the "Battle of Life", published as a metaphor (which reminds me of the discussion with Mr. Harries about the origin of electro-phor-esis!) for the struggles of domestic life and life and death on the battlefield. Life Science is all about our struggle to understand where we come from, how we "tick", why we sometimes get sick and how we can manage to maintain a good quality of life as we get older. The UTC aims to provide its students with an unprecedented opportunity to be a key player in this journey and I feel delighted that with our first steps, the next year will bring even more challenges, but I am looking forward to sharing them with you and the new teachers and students!

Have a great summer, thanks to all the students, teachers, support staff and partners for helping me over the last year, but most of all Mr. Ward for giving me the opportunity. It has really been the Best of Times!

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