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. 

http://phenomena.nationalgeographic.com/2013/05/14/3-d-scans-caterpillars-transforming-butterflies-metamorphosis/

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 (http://www.scientificamerican.com/article/insect-metamorphosis-evolution/)

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 (http://lifesciencesutc.co.uk/blog/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"

The importance of being observant!

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!

Ice Cream and Biotechnology

In my effort to whip up enthusiasm for the new academic year at the UTC, I thought I would draw your attention to the recent work by a group of scientists in Scotland. I was waking up to the Today programme on Radio 4 when I heard Professor Cait McPhee from the University of Edinburgh discussing how a protein could delay the melting of ice cream. Since I love the use of common concepts for teaching Biochemistry, I thought what a perfect combination: much better than milk and proteins that I have been using for a few years. I hope I have whetted your appetite; so what is the science behind this interesting news story?

The key to the Science is two fold. First, understanding the interfaces between air, water and oil (the three main ingredients of ice cream (well if you are a Biophysicist!). And second the way in which proteins can "bridge" different chemical environments through the inter-digitation of amino acid side chains. The reason that ice cream melts is owing to a break down in a structure, which is stabilised at low (freezing) temperatures. So how can we stabilise ice cream at higher temperatures; just for a little longer, to stop the above happening?

First what holds water molecules together? For this you can visit one of my old

Molecules of the Month: Water: Hydrogen Bonds of course! In order to keep the water molecules and oily fats "happy"  at the same time, Nature makes "amphipathic" proteins (from the Greek amphi (both sides) and pathos (experience: although this has a more specific meaning if you study literature and drama, perhaps "compassion" works for both?). The structure of BsIA (a bacterial hydrophobin) give us the answer. And work from the laboratories of Professor Cait McPhee in Edinburgh and Dr. Nicola Stanley-Wall in Dundee in Dundee, reveals the power of collaboration between disciplines (Biophysics and Microbiology). The two images above are taken from a paper describing the molecular basis for the amphipathic nature of this class of molecules called hydrophobins. The amino acid side chains shown in black at the top of this view of the molecule are the hydrophobic residues that interact with the oily components, while the underpinning parts have an affinity with the polar (water:compatible) elements of the ice cream. As Prof MacPhee said BsIA works by keeping oil and water mixed together, stops air from escaping and coats the ice crystals in ice cream which stops them from melting so quickly. She told BBC Radio 5 live: "This is a natural protein already in the food chain. It's already used to ferment some foods so its a natural product rather than being a 'Frankenstein' food. By using this protein we're replacing some of the fat molecules that are currently used to stabilise these oil and water mixtures so it can reduce the fat content, but it shouldn't taste any different. 

She went on to say, it also had the prospect of reducing the sugar content and could be used in other foods such as chocolate mousse and mayonnaise to help reduce the calories. So there you have the power of Biochemistry! By studying Molecular Sciences, you too can improve everyone's quality of life!