Friday, 25 September 2015

Here we go!!! Greenland Biodesign 2015

Well hello, communications director Liam here, welcome to my first ever post on the UTC Innovation Labs blog! I aim to give weekly updates on the dealings of Greenland, and any new aspects within the labs. I hope to be consistent, though I cannot promise this. If I do miss any weeks, I will sincerely apologize while I’m ahead. Now… On to the post!

It’s a new year and a new start to the UTC, and I hope by now that everyone is now settled in and ready for what the year will bring, we at Greenland sure have. Already, we have begun creating ideas for projects, and have undergone a management restructuring, with year 13 and year 12 alike. The new senior scientific supervisor for Greenland is Rachael Winrow, with Tom Garvey as the director of research and development, and Moira Morgan as the laboratory superintendent. A full summary of the current members of Greenland can be seen below:

The process of enrolling new members for Greenland was a long and challenging task for Professor Hornby and Dr Dyer, as there was a great abundance of enthusiastic young minds that were already itching to go. As you can most likely see, there are still places available at Greenland, and I do encourage you to join if you are interested, as it is an opportunity that can open many doors in the future of scientific careers. In other news, I have recently finished creating the prep room requisition forms. These forms are going to be used for requesting materials from the prep rooms, while also making it easier for the lab team to get you what is needed, as they will now have a record of what is needed, and who needs. The form is as follows:

The forms will be located near each prep room door. Note that your desired materials will not be ready at the correct time if you do not use one of these forms, as the lab team can only handle so much!

That’s all for this week Hope it has given you a good overview of the week, and I will be back next week.


Wednesday, 23 September 2015

Greenland Biodesign Projects 2015

The Greenland Biodesign team at the UTC have undergone a management restructuring over the summer (you can read all about this shortly in a forthcoming post from their communications director), and, following an initial meeting with team members, below, you will find a summary of the research projects for the coming year that will form a collaboration with my own research lab at the University of Sheffield. Before I outline the projects though, here is a little background to how the research project idea and Greenland Biodesign came about.

The Greenland group was initially set up during the opening year of the Liverpool Life Sciences UTC in order to provide an outlet for students who wanted to take their own interests in Science a little bit further. The team initially comprised Y12 students from both A Level and BTEC courses, and was aimed at combining all the features associated with a "Translational Biotechnology" research team. This provided an environment for bringing students whose aptitude was more experimental, with students who wanted to develop their communication and leadership skills, and of course with students who simply love Science and see themselves as Liverpool's next Nobel Laureates! 

With the help of George Rule, a physics graduate working in the Studio school at the time, and a number of other staff; students in the Greenland group proved instrumental in getting the Innovation Lab experience off the ground in that first year. I should perhaps say why Greenland! Briefly, the Life Sciences UTC in Liverpool occupies a refurbished Victorian sugar warehouse. The original site was however, part of Liverpool's highly successful, but relatively short-lived romance with Arctic whaling. The arrival of the son of a Yorkshire whaling pioneer, William Scoresby, (William Scoresby Jr.), triggered the development of Liverpool's whaling industry. The Merseyside built Baffin set sail for Greenland at the beginning of the 19th century and Scoresby's journey is described in his book "An Account of the Arctic Regions and Northern Whale Fishery", published in 1820). However, his motivation wasn't purely economical; he also mapped part of the Greenland Coast (sometimes referred to as the Liverpool Coast) and later in life became a prominent educationalist. I think the connection works well for this adventure too! Chris Routledge has a nice web site devoted to Scoresby and whaling (as well as some other nice local interest topics and images, if you are interested). And of course everyone should read Herman Melville's Moby Dick.

Moving on to the projects (at last I hear you say?), I wanted to build on my experiences with students over the last two years and provide a new model for research engagement, now that I am back in my old job at Sheffield. Naturally, my own research interests are limited and single handedly, I can't hope to provide projects that will interest every student. However here are the topics that emerged from the meeting a couple of weeks ago. Dr Dyer and I will manage the logistics and I will be putting you in touch with undergraduates, postgraduates and academic colleagues at Sheffield as the projects develop. This will help us move towards a publishable outcome, as we have done over the previous year, as well as build your research experience. All projects will be led by me from Sheffield, but may often include additional input from academic and/or commercial collaborators (as indicated). My involvement usually ranges from extreme enthusiasm and unreasonable expectation to helping to find someone who knows what they are talking about!

The Projects

1. Development of applications using the Polymerase Chain Reaction (Suitable for Chemists, Biochemists, Geneticists, Computer Scientists)

2. Rapid extraction of genomic DNA and its amplification from a wide range of organisms (in conjunction with Bioline, London). [Suitable for Chemists, Biochemists, Geneticists]

3. Optimising random mutagenesis using a novel error prone hyperthermophilic DNA Polymerase (in conjunction with ATY Biotech, California). [Suitable for Chemists, Biochemists, Geneticists, Computer Scientists]

4. Analysing raw genome sequence data from the meal worm, Tenebrio molitor (in collaboration with the Liverpool School of Tropical Medicine). [Suitable for Chemists, Biochemists, Geneticists, Computer Scientists]

4. Comparison of the meal worm and the wax worm as model organisms in teh development of new antibiotics (in collaboration with the John Innes Centre at Norwich) [Suitable for Biologists, Biochemists, Geneticists, Computer Scientists]

5. Proteomics of mealworm during development and metamorphosis (in collaboration with the Department of Chemical and Biological Engineering, University of Sheffield) [Suitable for Chemists, Biochemists, Physicists, Computer Scientists]

6. Development of innovative, low cost, laboratory classes for the REAL programme (Research Enhance Active Learning), for implementation Schools and Universities [Suitable for all students]

7. Applications of 3D printing in Molecular Biology: developing new instruments and solutions for experimental research [Suitable for all students]

8. Comparative annotation of the meal worm genome.

9. Using RasMol and PyMol for the interpretation of mutational data on DNA methyltransferases (epigenetics), Chloramphenicol resistance enzymes (antibiotics) and the Krebs Cycle enzymes Pyruvate Dehydrogenase and 2-oxoglutartae dehydrogense. [Suitable for Chemists, Physicists, Mathematicians, Computer Scientists and Biochemists]

 10. Open projects. Students are invited to submit their own ideas and Dr Dyer and I will attempt to accommodate the ideas, possibly through collaborative partnerships. [Suitable for all students].

Dr. Dyer will provide you all with further details on how to sign up for these projects and as soon as you have been allocated a project, there will be a meeting at which resources will be allocated. However in the meantime, I would like you to use the information (and key words) in the titles to find out more yourselves. Below here, there is a comment box, if you have any questions at all relating to the topics, please enter your questions/comments and either me or Dr. Dyer or I will do our best to respond.

Friday, 11 September 2015

Turn and face the strange, ch-ch-changes

This time of year is always associated with great change within schools and universities. Many of our students have left the UTC and are set to embark upon an exciting new era in their lives by starting in jobs, apprenticeships or higher education courses. Other students are moving up a year, in some cases making the challenging transition from GCSEs to A Levels. We also welcome a new cohort of Y10 and Y12 students, joining us in the innovation labs at Liverpool Life Sciences for the first time. I have enjoyed meeting you this week and look forward to an exciting year of research in the labs.

The inspiration for my first blog post came to me during my first innovation lab session with Y11 on Friday. During the session the students were making observations about the different stages in the life cycle of our very own model organism – the darkling beetle. It never fails to fascinate the students and indeed myself that an organism can go through such a transition or metamorphosis and emerge as what often looks like a completely different species. So what better topic to begin this time of great change than one of the greatest changes in the animal kingdom; complete metamorphosis. 

It was only after nearly finishing writing this post that I realised that Dave Hornby had already written a little on this topic before the summer, including a title based upon song lyrics. I guess that means I have spent too much time in the labs with him over the last year! Anyway, it is a useful topic to revisit as we continue to develop our use of the darkling beetle as a model organism for genomics and proteomics.

Let us start with the great Charles Darwin. The Voyage Of The Beagle covers Darwin’s part in the second survey expedition of the ship HMS Beagle, which set sail on 27 December 1831. In this book Darwin tells the story of a German Naturalist called Renous, who was arrested for heresy in Chile for claiming that he could turn a caterpillar into a butterfly. Today it is common knowledge that many insects, like the caterpillar go through a process of complete metamorphosis and emerge as a very different looking organism. In fact, people have known since at least as early as Egyptian times that grubs and worm-like 
(they are not really worms) larval stages develop into adult insects. However, there has been much confusion surrounded this incredible process. It is something which has always fascinated me since being a child, collecting caterpillars to look at in an insect viewer, through my final year university project studying the life stages of the swallowtail butterfly (below) and now working on the darkling beetle in the innovation labs at the UTC.

So what is metamorphosis?

According to Thain and Dixon’s - Dictionary of Biology (1992), metamorphosis is a 

“process during, and as a result of, which an animal undergoes a comparatively rapid change from larval to adult form. Under hormonal control, it is most noteable in the life histories of many marine invertebrates, the majority of insects and of Amphibia. Often requires destruction of much larval tissue and changes in gene expression.” 

Basically, what occurs is a reorganisation of the organism’s tissues. Inside the pupae the larvae essentially digests some of its own tissues into their constituent proteins. Some organs stay intact and others are broken down into groups of cells that can be reused. Some groups of highly specialised cells called imaginal discs start the formation of a specific body part of the adult stage, such as an antennae. The obvious physical changes that occur during metamorphosis are accompanied by changes in the biochemistry, physiology and behaviour of the organism.

So the questions which arise are what is the point in going through this complex, potentially costly transformation? How does the organism benefit? 

The most likely explanation comes from a reduction in intraspecific competition for food and space. By having distinct life stages which exploit different resources, these insects avoid direct competition with their young, increasing their survival chances.

The evolution of complete metamorphosis in insects is still considered a great mystery and many theories have been proposed to explain it. An early attempt is the rather entertaining but implausible idea proposed by Donald Williamson that the butterfly metamorphosis is the result of an accidental mating between a ground dwelling species and a flying species. More recent attempts have focused on the more likely idea that complete metamorphosis evolved from incomplete metamorphosis. This theory is supported by evidence from the fossil record as the earliest insects have life cycles which are similar to modern ametabolous insects, like grasshoppers where the young appear more like smaller versions of the adult and there is no pupal stage. It is only later in the fossil record that we find examples with life cycles similar to modern day holometabolous insects, those that undergo complete metamorphosis, like butterflies and our very own darkling beetle. 

To read more about this follow the link below to a good summary by Ferris Jebr in the Scientific American (

Since adopting the darkling beetle as a model organism, our students have had great success and with Professor Hornby’s help, published a paper in the current issue of the Young Scientists Journal ( I am hugely optimistic that our new students will embrace their change in environment and build upon the successes of those who have moved on to the next stage in their lives.

So in the words of the great David Bowie - "Turn and face the strange, ch-ch-changes"

Monday, 7 September 2015

The importance of being observant!

Image result for portrait alan bennett
I was listening to the marvellous writer Alan Bennett on the radio recently, talking about his work, and it inspired me to rethink how I should introduce the importance of observational skills in experimental science (and indeed in any form of data analysis). Bennett wrote a series of monologues called Talking Heads, which were famously broadcast on the BBC in the late '80s, involving several of Britain's finest actors. These short monologues were a vehicle for Bennett to express his observations on human behaviour mainly in the face of perceived adversity: dealing with death or loneliness for example. [You will probably be more familiar with his theatrical and film successes such as "The History Boys" or "The Madness of King George"].

So let me move onto "observation" now, before I return to my opening introduction to Alan Bennett. Experimental Science originally relied completely on observations made via the human senses. The fascination shown by the ancients for the moon, the stars and our solar system, is one example. The curiosity shown by the early scientists such as Aristotle to investigate the inside of a fruit, a seed, a rat, a snail etc, using dissection, accompanied by some form of annotated illustration, is another example. As mankind began to explore the world around him/her, by perturbing things; the ability to make observations, note them down and communicate them, formed the basis of scientific knowledge. [I am not proposing to discuss note taking and communication in this post, but they are equally important.]

The picture on the right, is a bacterial culture (in fact a strain of Escherichia coli), plated on nutrient agar. I remember asking a group of Y12 students to give me their observations. After a slow start, I suggested that they should try explaining it as if they were on the radio. Undoubtedly, my favourite description was "a pale brown jelly, covered by very small drops of candle wax". I like this description, because to me it uses very strong images, "set jelly" and "molten candle wax": things that most people will have seen. It is in my view a memorable description. This is also the skill of a great writer. When Bennett describes an experience, a feeling or somebody's expression, for me it is often memorable and thought provoking. This is what a good observation should be. Why is the agar like a jelly? and just what is the material that looks like molten wax? And.....why does it smell the way it does, unpleasant like a waste bin on a summer's day?

When pioneering chemists and physicists began conducting systematic experiments, they were measured largely by their ability to make and explain their observations. However, as the centuries rolled on, we became frustrated by the limitations of our senses. Newton's experiments with optics for example paved the way for modern spectroscopy, where we not only observe the colour (say) of a solution, but we can determine the concentration of the coloured molecules, and we can also measure chemical changes as a solution is heated, or following the addition of a catalyst such as an enzyme. In fact analytical sciences has grown out of our limited ability to observe events which lie beyond our aural, visual, olfactory and tactile senses. Our desire to find out how things work has driven the development of instruments like the telescope, the microscope, the radio telescope, the spectrophotometer, the mass spectrometer, the infra red spectrometer, the Nuclear Magnetic Resonance spectrometer.....I could go on. However, we still rely on our own senses a great deal.

When as a professional scientist, we receive the spectrum from an NMR experiment (in a drug discovery lab), or the sequence of bases in a gene from a DNA sequencer (in a genomics lab), or the reading from a spectrophotometric analysis of a patient's blood sample (in a diagnostics lab), we must make a judgement based on our observations of these different kinds of data. So observational skills are not limited to first hand witnessing of an event, they also relate to our ability to see patterns in data or to quickly spot something unexpected: a "shoulder" (see above, RHS) on a chromatography peak, a transient rate that precedes a steady rate of chemical change, or a transient orange colour that appears momentarily in a biological observation, or in a chemical reaction. It might even be a minute change in a read-out from an experiment at the Large Hadron Collider that suggests the presence of a new particle. Which of course should be treated with scepticism until it is observed again, and again, and by several others! But it is such observational skills that led to the discovery of the Higgs Boson.

Those writers, artists, actors, footballers and scientists who appreciate and work hard at developing their observational skills are likely to be the most successful. When you begin your experiments in the Innovation Labs, make sure you look closely at everything you handle and make copious notes. Getting into this habit early will really help you succeed in the future. Good luck with your experiments!