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Issue 4: September 2015

Biology’s most important journey:

a voyage that opened up a new world

but almost didn’t happen

Plus: Anthrax: bioterrorist’s friend, our foe Facebook for mice: a murine network Microalgae: a small solution to a big problem – and more!


Editorial

Welcome to Issue 4 of Diffusion, a science magazine run by and for Cardiff University students. Diffusion is free to join and relies upon submissions from the student body. Get involved by joining us on Facebook – search for ‘Diffusion science student magazine’ – or send an email to diffusionmagazine@outlook.com. Thank you to all our contributors for Issue 4 and best of luck to everyone for the next academic year or, to our recent graduates, whatever comes next! Lindsay

Contributors Authors

Harry Bligh

Kelly Evans

Cormac Kinsella Kirsty Marsh Ashley Otter

Lindsay Pike Laura Pratt

Nikki Vivian

Matthew Wilcox Robin Williams Editors

Lindsay Pike

Cormac Kinsella

Jennifer Saunders Matthew Turner

Diffusion logo design Tom Hostick

Production and graphic design Lindsay Pike

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Cormac Kinsella


I want to learn more about... Features:

Spectrum: Data capture p13 Pulse p19 Figure/Legend: Beatrix Potter – beyond Peter Rabbit p20

Articles:

Facebook for mice: a murine network p5 Microalgae: a small solution to a big problem p6 Biology’s most important journey: a voyage that opened up a new world but almost didn’t happen p8 Beyond academic study p10 Making the most of your degree p12 Anthrax: a bioterrorist’s friend, our foe p14 MRI cartography – maps for mental illness prediction p17 Black Smokers: a paradigm for nature’s mysteries p18

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Facebook for mice: a murine network by Kirsty Marsh Biosciences MRes student (2014–) Cardiff University Almost everyone in the developed world is familiar with the popular social network website ‘Facebook’, even if not everyone has an account. It allows people to stay connected with friends and family across the globe and is arguably a vital component of a student’s everyday life. But what exactly is a social network? People are linked to one another through social ties and this can be represented graphically in the form of a network of ‘nodes’ (individuals) connected by ‘edges’ (social ties). Representing relationships in this way has a wide range of applications across disciplines such as economics, sociology and, more recently, biology. For instance, the sociologist Stanley Milgram’s classic 1960s ‘small world’ experiment demonstrated that people in Nebraska were, on average, only five or six social ‘steps’ away from people in Boston. Studies such as this have led to the concept of ‘six degrees of separation’ and the creation of websites such as ‘oracleofbacon.org’. This site is based around the joke that the actor Kevin Bacon is the “centre of the universe” due to his appearance in so many films and creates a ‘Bacon number’. This calculates the number of steps fellow actors are separated from Bacon; it is notoriously hard to find a Bacon number >3.

In biology, networks have been applied to studies of how individuals in a population can behave differently to each other and, more recently, to epidemiological studies linking behavioural differences to the transmission of diseases. If certain individuals in a network are highly connected (i.e. many social ties) they may play an important role in spreading a disease throughout a population. An example of one such ‘superspreader’ is the infamous ‘typhoid Mary’ of the early 1900s who, over the course of her career as a (very unhygienic) cook, managed to infect an estimated 53 unsuspecting people with typhoid fever. The identification of these superspreaders has significant implications for a targeted approach to disease control. Wildlife systems provide excellent models for such epidemiological studies as individuals can be effectively monitored to produce a network of social contacts for a population. My own Masters of Research project focusses on one such wildlife system – the yellow-necked mouse (Apodemus flavicollis) – for which over ten years of data has been collected from a population in northern Italy. This long-term dataset will allow me to create a ‘network movie’ to see how the structure of the network changes over time, in terms of the presence of individual mice and contacts between them. I aim to link these changes in the social network to patterns in the occurrence of diseases in the population. By building a network of contacts I should also be able to identify individuals who move between groups within the population, and whether these individuals are superspreaders who help diseases to spread between social groups. So there you have it; my Masters project is to create a ‘Facebook for mice’!

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Microalgae: a small solution to a big problem by Kelly Evans Graduate, BSc Genetics (2015), Cardiff University Global energy reserves are rapidly depleting. As fuel availability begins to decrease, the struggle for resources will become more evident, leading to increased fuel costs, fuel shortages, and possible altercations between fuel producing and non-producing nations. It has been estimated that current fossil fuel stocks will be completely exhausted within the next 40 years, indicating the necessity of developing sustainable fuel sources in order to avoid a global energy crisis.

from maize possesses some major risks. Firstly, the diversion of arable land from food production to fuel manufacture places a strain on global food availability, and with the world population now reaching over 7 billion, this is not a viable solution. Furthermore, maize growth for biofuel production requires a high energy input, making the process unsustainable on a large-scale. Therefore, another alternative fuel source needed to be discovered. When people think about renewable energy resources, massive wind turbines, shining solar panels, and tidal energy are usually the first examples that spring to mind. But would you ever think of powering your car with microalgal oil? Well, that is exactly what scientists are currently trying to achieve.

Current efforts have focussed mainly on producing fuel sources from lignocellulosic biomass, derived from crops such as maize and sugar cane. For example, America have become large producers of bioethanol derived from maize, which has been found to have a lower environmental impact than renewable fuels derived from additional sources. In particular, this includes biodiesel from palm oil; a fuel source for which widespread deforestation, destruction of natural habitats, and exploitation of native populations have been serious concerns. However, despite its apparent low environmental impact, bioethanol production

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Microalgae are photosynthetic microorganisms that are naturally found in marine and freshwater systems, and convert sunlight, water, and carbon dioxide into algal biomass. Many are rich in oil, providing an excellent basis for the production of biodiesel, and despite their small size (some can be as miniscule as 5Âľm) they can produce a vast quantity of biomass. Unlike agricultural oil crops such as oil palm, biomass doubling time for microalgae can be as short as three and a half hours during exponential growth, identifying this unlikely microorganism as a major contender for the production of alternative biofuels. Unlike maize and oil palm, one key advantage of using microalgae in biofuel production is that it provides no


adverse impact on food supplies and other Of course, as with many scientific discoveries, a number of hurdles need to be overcome agriculture products. before any of us will be purchasing However, some argue that growing microalgal ‘microalgal biodiesel’. It is possible that biomass on a large-scale, using such methods metabolic engineering techniques, that is, as water farms, is not efficient in terms of editing the metabolic processes involved in water-usage and space utilised. Therefore, a the production of microalgal oil using genetic theoretical concept for producing microalgal engineering, may have to be investigated to oils has been proposed. This technique further increase productivity. Nevertheless, involves the use of a photobioreactor, a closed microalgae possess huge potential in system that can obtain high algal productivity. producing biodiesel that may meet increasing Not only can water and residual nutrients world energy demand, while being both costbe recovered and recycled back to the algal and energy-efficient. cultivation stage after biomass extraction, but any remaining biomass residue left behind can So it looks like size doesn’t always matter be used to produce biogas, which can then be after all. utilised as the primary source of energy for the entire reaction, reducing overall energy input. Furthermore, the photobioreactor can be coupled with industrial processes, such as using waste water for algal growth, providing an obvious advantage in comparison with crop-based fuel production.

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Biology’s most important journey: a voyage that opened up a New World but almost didn’t happen by Cormac Kinsella Graduate, BSc Zoology (2014), Cardiff University Almost 180 years ago, in October of 1836, a young man of twenty-seven stepped off a returned ship onto Falmouth harbour. He must have felt a good deal of excitement to be home – he had left England in 1831 at the age of twenty-two, and had not been back since. He may have felt daunted by the mountain of work that lay before him. During his voyage he had forwarded over five thousand biological specimens home, to await him on his return. As a private man, he might also have been quite nervous. Partly due to his notes made during the voyage and the forwarded specimens, on his arrival home he was somewhat of a celebrity among naturalists, and remains an even greater one today.

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His name was, of course, Charles Darwin. Small events can change the course of history. This is true for evolution, a phenomenon that Darwin eventually explained through the theory of natural selection, but was also true for Darwin himself. His place on the voyage was barely secured. The trip was intended as a hydrographic survey (studying all sorts of physical features of coastal areas), but a place opened up for a ‘gentleman of science’ to undertake collections and provide the captain companionship. Two others had already turned down the berth, and Darwin also wrote a letter refusing the offer as his father was not keen on the idea originally. Once his father was convinced, the captain of the ship was not, due to perceived political differences and even the shape of Darwin’s nose – which apparently suggested he lacked the capacity for hard graft. Darwin at one stage virtually gave up on the idea, aiming to continue with his plan of becoming a country parson (a priest). But eventually, and thankfully, he got the position, and the Beagle set sail. Darwin’s analytical eye, glaringly evident from insightful observations in his writings, was put to good use during the voyage. He drew from his strong training in zoology and geology, andworked extremely hard, collecting, travelling on excursions, and writing during the trip.


The venture included the East and West of South America, the Falklands, the Galapagos, New Zealand, Australia, and South Africa. Darwin noticed great similarities between species from disparate places, such as a fungus in South America with a foul smell, attractive to insects. He commented that a similar species existed in England, with the same kind of partnership. On the back of this observation, he went on to comment that species introduced by man outside of their range lose these established relationships. His example was the cabbage, plagued by slugs in England, but uneaten in South American gardens – as there was nothing adapted to eat it (as an aside, it would be interesting to see if something native has expanded to fill this role in the last 180 years – or indeed whether European slugs have also been introduced by now). It is a testament to his thinking that his writing remains so relevant today; we are still introducing species and dealing with their negative consequences. However the true value of the voyage of the beagle was not to emerge until 1859, when Darwin published ‘On the Origin of Species’, a book that no doubt can attribute its own origins to a spark somewhere at the back of Darwin’s mind during his travels. The difference between evolution and natural selection is a vital one. Evolution is simply changes in a species through time, and it is not a theory but a fact – look at dogs, cows, bacteria, or broccoli for examples of changes made in species through artificial selection. The theory that everyone mentions in discussions on evolution, is evolution via natural selection (Darwin and Alfred Russel Wallace’s theory1), with natural selection being the explanatory process for evolution in wild systems. If over the course of a thousand years the average

temperature decreases by 5°C on a particular island, the resident mammal fauna will be ‘naturally selected’ to have thicker fur in order to keep warm. Natural variations in the thickness of the fur occur among offspring; just as human offspring all have variations. As the temperature drops, the variants with slightly thicker fur cope better on average, and pass on their genes more often, and so the fauna will evolve. Evolution as a concept was around during Darwin’s younger days, but was often called transmutation. During his voyage, Darwin had not formed his ideas on natural selection, but he noticed and noted evidence that he would later ascribe to it. It took him many years to formulate and finalise his theory, partly through reservation caused by the implications, i.e. man also evolved, and that if natural selection caused divergence and diversity, could we trace it so far back in time that we only find one organism, the last common ancestor? However, he did eventually publish his work, twenty-three years after his return on the Beagle. Quite simply, biology has never looked back.

1. Darwin and Alfred Russel Wallace co-published on natural selection in 1858, using one of Darwin’s essays from 1844 (talk about sitting on a theory), and Wallace’s recent essay on the matter. They didn’t see the process in exactly the same way (Darwin ended up coming to the more accurate conclusion on a few points), but that’s for another day.

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Beyond academic study This section includes advice and anecdotes about how to make the most of an undergraduate degree. As a recent graduate who completed a professional training year, I can personally recommend one; the transferable skills learnt can set you up well for your future. If a PTY is not an option, or academic research is not your thing, a summer internship is equally worthwhile and there are many options available. Each university and school will have its own advisors you can seek help from; in this issue we also hear from Nikki Vivian, the Employability Adviser for Cardiff University's School of Biosciences. My placement involved spending 12 months in the Conservation Genetics laboratory at the Royal Botanic Gardens, Kew, London. There, I learnt a great deal of important skills - from molecular techniques that are widespread in modern research to lab maintenance, negotiation, self-motivation and so on that helped enormously with my final year and will continue to do so. Although I decided not to continue in the research area I’d been working in at Kew, it helped me realise how enjoyable and rewarding research can be. I’ll be starting a PhD in October and it’s unlikely I’d have got the position without my placement experience, but it would have been just as beneficial had I been applying for training schemes or permanent jobs. (Lindsay Pike, Graduate, BSc Genetics (2015), Cardiff University)

“I would say my main bit of advise would be to definitely do a PTY if you can! It’s the best time to get loads of voluntary experience while you can still receive some student loan to support yourself. I worked at the Gloucestershire Wildlife Trust for my PTY because I’m interested in a career in conservation. I got loads of valuable experience in public engagement and land management practice that looks great on a C.V., but whilst they weren’t so big on research at the Trust, this actually helped me to realize that research was what I really wanted to be doing! It’s also great for making those all-important contacts in your field of interest and the research project – Rhian Patterson, BSc Chemistry, Cardiff you do is really good practice for your final year dissertation” University (2012–). “Diamond Light Source is the U.K.’s synchrotron. A synchrotron accelerates electrons close to the speed of light where they give off a beam of electromagnetic radiation. This “synchrotron light” can then be used for various experiments. I was one of twenty placement students working there over the summer. I worked out a protocol for the use of a transmission electron microscope in the imaging of biominerals. I met a lot of new people and students from different disciplines and the opportunity to work at such a large research centre with ties all over the world was enlightening.”

– Kirsty Marsh, Biosciences MRes, Cardiff University (2014–)

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“This summer I decided to take part in a CUROP internship at the Sustainable Places Institute. Returning from my second year field course in Tobago, I didn’t really know what to expect when going into the project and was given my title ‘Fisheries productivity: evidencing the role of seagrass meadows in the Philippines. The aim of my project was to provide the background knowledge of how fisheries are using seagrass meadows in the Philippines by looking at their status, importance and threats that are causing them to decline. Seagrass meadows are extremely important in the sustainability of fisheries as they provide both a temporary and permanent habitat for juvenile reef fish. They are also important for other ecological processes such as carbon fixation; yet are declining rapidly at about 7% a year due influences such as poor water quality, coastal developments, sedimentation and overfishing. The Philippines were chosen as it was a new case study for the Project Seagrass Team and the information I provided would be helpful to them before they were to visit the field.

The structure of the project was based on one they had previously used for other case studies such as Indonesia; I had to write a literature review and produce a database containing all known species that I could find as being reported inhabitants of seagrass meadows. Little research has been done in the Philippines, which made it even more challenging, but enabled me to improve my research and organisational skills that will prove extremely useful when writing my dissertation in the coming months. I thoroughly enjoyed my CUROP placement and would definitely recommend it to any first or second year students that are looking for a summer internship to further your studies. As a result I have chosen to do my PTY with Project Seagrass next year as it has recently become an official charity and I hope to research more into the seagrass meadows around Wales.” – Laura Pratt, BSc Biology (2013–), Cardiff University

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Making the most of your degree By Nikki Vivian

I’m the Employability Advisor for Biosciences at Cardiff University. My job is to help you find meaningful work experience and activities throughout your time at university that will help you gain the skills you need to compliment your degree. This may be a summer placement, advice on PTYs, term time activities or simply working with you to put your CV together. I’m here to help you see the full range of work experience options within and beyond biosciences and to work with you to identify your employability skills. I offer drop-ins, e-support and one-2-one work experience consultations. Your degree is really important but these days it’s essential that you stand out from your peers who will all have done a similar degree to you. A PTY year is an excellent way to gain work place experience and to give you a foot in the door, so is a summer placement. Every year Bioscience students source their own work experience over the summer or apply for vacancies that I have helped to create. We work closely with Welsh Water who take students from Cardiff University every year. “The overall purpose of the Work Experience Programme is to facilitate young people in their development to becoming “work-ready” and to raise awareness of the diverse employment opportunities offered within Welsh Water. Work Experience students are provided with an opportunity to learn and develop in order to inspire aspirations and increase employability. Our work experience placements are tailored specifically to meet student’s individual requirements. At Welsh Water we believe that students have unique skills and ideas to contribute to our business and seek to provide them with an opportunity to demonstrate their abilities in a working environment. In addition to this, providing a best in class Work Experience Programme contributes to securing a strong workforce which will in turn support us to meet the challenges of the future.” – Jodie King, Head of Talent Development- Welsh Water. However, it’s also important to remember that all work experience is valuable, whether it is directly related to a career in science or not. Transferable skills such as communication, team work and problem solving are very important in securing a job these days and these types of skills are recognised and essential in all forms of employment. Making sure you develop these skills whilst at university will put you ahead. Such skills can be developed through a part-time job, volunteering, taking on a lead role in a society or participating in activities run by Cardiff University Enterprise Team among other things. The more inventive and active you are, the better.

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Spectrum: data capture by Cormac Kinsella

Graduate, BSc Zoology (2014), Cardiff University Certain types of data degrade over time – as some of you will know far too well after experiencing the horror of finding the flash drive with your essay stored on it refusing to be read. But it can also be a challenge collecting data in the first place as many targets of data collection are themselves transient, rare, or incomplete. Certain elementary particles blink in and then out of existence virtually at the same time, necessitating finely tuned, high resolution detectors like ATLAS and CMS at the Large Hadron Collider. Unlike the particle physicists at CERN who have many of these – albeit brief – windows in which to gather data, other scientists are not so lucky. For forensic scientists, time is of the essence and they have a diminishing window of opportunity to work effectively. In the case of a murder, the faster they can act, the more accurate key evidence lines such as time of death will be. Even having forwarning of where and when data will be available won’t necessarily help.

Guillaume Le Gentil set off from France to India in March 1760 to observe the June 1761 transit of Venus, in order to gather important data which would help calculate the distance from the Earth to the Sun. Despite the early start, he found himself at sea during the transit thanks to war between France and England that prevented his ship from docking on arrival. Not in the least put off, he waited, away from home, a further eight years for the next transit only to miss it again due to cloud cover. For those scientists interested in ancient life, the loss of data during intervening time periods is a sobering thought. Of all the organisms that have ever lived, only a tiny fraction were fossilised. Of that fraction, the majority have been destroyed by natural processes, and of the survivors only a selection will ever be discovered by human with no guarantee that those found will be preserved for study or of a high enough quality. Despite the loss of data, vast amounts remain, and some fossils from many millions of years ago tell us very detailed and intimate stories about the world of the past and the creatures that inhabited it.

It’s still worth backing up your hard drive though!

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Anthrax: bioterrorist’s friend, our foe

by Ashley Otter Graduate, BSc Microbiology (2015), Cardiff University Anthrax is a zoonotic disease caused by the Gram-positive, spore-forming bacterium Bacillus anthracis and has been of considerable interest since the 1800s with its identification as the cause of anthrax in cattle and humans by both Casimir Davaine and Aloys Pollender. The most famous experiment involving anthrax is undoubtedly that performed by Robert Koch, where he was able to completely confirm anthrax is caused by the bacterium B. anthracis, rejecting the then idea of spontaneous generation and aiding in forming Koch’s Postulates, four of the core fundamentals of bacteriology.

that loosely surrounds cells to enable immune system evasion. What makes anthrax an even more formidable pathogen is the ability to form spores; hardy structures capable of surviving heat, desiccation and UV radiation. Spores form when the bacterium is in unfavourable conditions such as nutrient deprivation and are able to survive prolonged periods of time, up to several years, without nutrients. Spores of B. anthracis can usually be found in the soil around where an animal has previously died of anthrax. Spores can then be carried by other animals to other locations where they could infect humans through contaminated meat or soil, germinating in response to favourable conditions.

As well as being extremely hardy, anthrax spores can become aerosolised, i.e. airborne, aiding in dispersal. All of these attributes make B. anthracis the ideal weapon for bioterrorists. Due to the high pathogenicity and the ability for B. anthracis to be aerosolised, it can be regarded as one of the most dangerous microorganisms to be used as a biological weapon. Anthrax is regarded as a ‘Category A’ organism where Anthrax is a highly virulent bacterium due research is regulated and limited to highto the production of toxins (Lethal Toxin and containment and security laboratories such Edema Toxin) that cause tissue destruction, as the Defence Science and Technology as well as a poly-γ-D-glutamic acid capsule Laboratory (UK), national Public Health England (PHE) laboratories (UK) or United States Army Medical Research Institute of Infectious Diseases (USA).

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There was vast research conducted in countries such as the USA, UK, Canada, Japan and Russia on anthrax as a bioweapon during both world wars until the 1950s. However, it was soon dropped upon the formation of the Biological Weapons Convention in 1972, signed and ratified by 173 out of 196 world states. This convention was designed to ensure states do not develop, produce or stockpile biological weapons such as virulent bacteria or bacterial toxins, as well as destruction of biological weapon stockpiles.

comprised of all B. anthracis, B. cereus and B. thuringiensis strains and isolates. Difficulty in identifying anthrax is yet another factor in the favour of bioterrorists, as an anthrax bioterrorist attack could go undetected. The time required to confirm of a suspected case can delay plans of action, potentially leading to undiagnosed infections and additional deaths.

Unfortunately this has not stopped individuals and groups exploiting the high pathogenicity of anthrax as a bioweapon. Signing and ratifying the convention also did not directly prevent a nation from producing biological weapons, as is the case with such countries as Iraq. Here, biological weapons such a anthrax, ricin and botulinum toxin continued to be stockpiled up to as late as 2003, upon the collapse of the Thankfully, the number of bioterrorism acts government led by Saddam Hussein. involving anthrax has been low. The most wellknown is the ‘Amerithrax’ incidents in 2001 in In addition to increased pathogenicity and the USA, occurring shortly after 9/11. Anthrax ease of spore dispersal, infection with anthrax spores were dried as a fine powder and sent is often difficult to identify: traditional culturing in envelopes to news media offices and on blood agar is indistinguishable from US congress politicians; the drying process other Bacillus species such as B. cereus or causes spore aersolisation upon opening B. thuringiensis unless by an experienced the letters, spreading anthrax further. This microbiologist and even then 24 hours of resulted in a total of 17 anthrax infections incubation is still required, potentially delaying and five deaths, including some attributed diagnosis. to postal workers handling the anthrax-laden letters (see image above for an example). The difficulty in identifying anthrax is also shared with new genetic methods such as multi-locus Though the number of deaths was low, the sequence typing (MLST) and whole genome 2001 incident has been estimated to cost sequencing, both of which are poor at rapidly $445 million (adjusted to 2015 value based on identifying B. anthracis. This is due largely to 2.16% annual inflation rate), with the majority the low genetic diversity between members of the Bacillus cereus sensu lato group, a group

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spent on decontaminating buildings exposed to spore-containing envelopes. The culprit behind the Amerithrax attack was never conclusively proved, although Dr. Bruce Ivins, a researcher of anthrax at USAMRIID who had helped with the investigation itself, was suspected. He committed suicide upon being investigated by the FBI and many questions still surround the case. Another example includes the “doomsday� cult Aum Shinrikyo, the same group behind the 1995 Tokyo subway bioterrorist attacks using the nerve agent sarin, a highly toxic compound that inhibits acetylcholinesterase, an enzyme fundamental for synaptic transmission between neurons. In June 1993, they created a fake air vent as a cover for pumping anthrax spores into the air around Tokyo. Their plot was to isolate virulent anthrax from soil and release spores into the air but ultimately failed, as upon investigation it was found that they isolated an avirulent strain called B. anthracis Sterne that had been used to vaccinate animals in Japan and throughout the world. Before the 2001Amerithrax attacks, B. anthracis was considered a bioterrorism agent, but assumed to be a relatively low threat due to the difficulty in producing large quantities of pure and virulent B. anthracis spores. Yet

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with the ever-increasing availability of science articles and experimental procedures online, the potential threat from a bioterrorism attack has increased. As described, anthrax is still difficult to turn into a bioweapon. This is partly due to the requirement of high containment to prevent exposure to anthrax, such as Containment Level 3 laboratories. More over, purchasing of strains is regulated and limited to culture collections (such as ATCC) and there is difficulty in producing large quantities of sterile and pure anthrax spores outside of a laboratory setting. Thus, the threat is limited although still possible.

Vast research has been conducted on anthrax, primarily for methods to detect the organism, to quickly determine if an anthrax attack has happened and determine those infected through methods such as microwavebased autofluorescence, rapid phage typing and faster DNA sequencing. Methods of anthrax disease prevention have also been studied, such as new protein fusion vaccines (combined toxin subunits) and monoclonal antibody therapies such as Raxibacumab. These can be used in addition to traditional, effective antimicrobial therapies such as Penicillin and Doxycycline. The threat of a bioterrorism attack using anthrax may be heightened, but with advances in detection and prevention, the arsenal of treatments and identification methods ensure that if future anthrax attacks occur, we will have the upper hand.


MRI cartography – maps for mental illness by Harry Bligh, BSc Chemistry (2014–), Cardiff University A recent study into new methods of Magnetic Resonance Imaging (MRI) may have found a way to predict which people may be at risk of developing schizophrenia.

produce an image. During an MRI scan, the patient lies down inside the machine for 15 to 90 minutes, depending on the area of the body.

The team used a specific type of MRI scan to Schizophrenia is a serious, long-term, map the wiring of the brain to scan 123 people psychological disorder that affects 26 million at risk of psychosis plus 125 people who are people globally – one of the most common not at risk and compared the differences. The mental health conditions. It is most commonly MRI technique implements the mathematical diagnosed between 15 and 35 years of age, graph theory to examine the brain’s complex with approximately 1 in 100 people experiencing network architecture, such as the efficiency of symptoms of schizophrenia in their lifetime. information transfers. These symptoms can include hallucinations, delusions, changes in behaviour and disordered This method provided new insights into how thoughts. schizophrenia affects brain networks. In a paper published in Human Brain Mapping, July Schizophrenia is considered a ‘dysconnectivity’ 20151, it was described how subtle differences disorder that arises when anatomical links were detected in brain topology. For example, or connections (e.g. synapses and neurons some information pathways were redirected between distinct nervous system units) go awry. using alternative connections and were less MRI has been used to study this connectivity efficient in subjects vulnerable to schizophrenia, by a team of scientists including those from particularly in central processing regions. This Cardiff University’s Brain Research Imaging could lead to more widespread problems. Centre (CUBRIC), the Institute of Psychiatry, Psychology and Neuroscience at Kings College The researchers hope to develop this type London and the University of Bristol. In a novel of MRI as a new tool for predicting future application of MRI, the group collaborated to mental illness that uses topology changes compare the connection topology in brains of as a biomarker of schizophrenia. It is expected those who suffer, or at risk, of schizophrenia that within 20 years, this novel technique will with the brains of those who are not. mean that schizophrenia can be diagnosed and treated more effectively. In addition, it is MRI scanning is a medical imaging technique hoped that scientists will be able to adapt the used in radiology to produced detailed images tool to understand more about causes of other that see inside the body. It is widely used in conditions such as dementia and multiple hospitals and is preferable to X-ray imaging, as sclerosis and eventually improve the quality of it does not involve ionising radiation. It works thousands of lives. on nuclear magnetic resonance, which involves strong magnetic fields and radio waves. The 1. Drakesmith M, Caeyenberghs K, Dutt A, et al. Schizophrenia-like topological changes in the structural magnetic field excites hydrogen atoms in the connectome of individuals with sub-clinical psychotic body, which then emit a radio frequency signal experiences. Human Brain Mapping. 2015;36(7):2629-2643. that can be measured by a receiving coil to doi:10.1002/hbm.22796.

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Black Smokers: a paradigm for nature’s mysteries

by Matthew Wilcox

BSc Exploration and Resource Geology (2013–), Cardiff University In 1977 scientists were studying ridges along the seafloor off the coast of the Galapagos Islands when they found a heat anomaly in their data. They tracked it to a point and boarded the Alvin submersible craft to begin their long descent into the darkness of the deep sea. Here, they found a large vent releasing towering plumes of jet black smoke and so, using all of their ingenuity, decided to name these structures ‘Black Smokers’. Black Smokers are hydrothermal vents that circulate cold sea water through the Earth’s crust, enriching the water with minerals and heating it to around 350 °C. They can grow rapidly, approximately 30 centimetres a day, reaching peaks of around 20 metres – although the largest known Black Smoker is the Trans-Atlantic Geotraverse (TAG) vent site in the Atlantic Ocean, which stands 40m high and reaches 200m in diameter. Usually after reaching such a peak, the smokers crumble under their own weight, leading to a significant collapse. The process immediately restarts and the build, collapse and rebuild cycle gives rise to two of the most unique features found at Black Smoker sites; world class mineral deposits and hydrothermophiles. Firstly, the mineral deposits are of a very high quality and are reasonably easy to access, though as they are at great depths the actual extraction is not always economical. Although they form on the seafloor this does not mean that they always stay there: Cyprus and Oman both have mineral deposits formed from Black Smoker processes which have been dragged above sea level by complex plate tectonics. These deposits

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can include gold, silver, copper and zinc but are dominated by iron and manganese. Secondly, hydrothermophiles are animals that can survive in levels of extreme temperature, such as those found at Black Smokers. Not only this but the animals found at these vent sites are the only known species that live in a major ecosystem without sunlight; they rely on chemosynthesis rather than photosynthesis and take advantage of the mineral rich fluids. There is a diverse range of fauna found around vent sites including primitive varieties of tube worms, clams and shrimps. Although these creatures may be related to species we are more familiar with they are in fact very different, as a certain researcher found out. The story goes that when these sites were first discovered, Professor Joe Cann, now Emeritus Professor Oceanography at Leeds University, was on a quest to be the first man to eat one of these newfound creatures. He decided the only way to cook the shrimp was on a barbeque (obviously), so he grilled it and achieved his goal of becoming the first man to try one of these other-worldly creatures. It is said that he was dreadfully ill after his meal, which as later research showed was probably due to the high levels of mercury and other toxic metals found in these animals – a result of their unique habitat. Although it is now nearing 40 years since humans first laid eyes on Black Smokers, they still stand as an example of how much we have yet to learn about our complex planet.


300 million years ago mushrooms developed the ability to break down lignin, a compound present in plant cell walls and the second most abundant organic compound on Earth, after cellulose. This adaption allowed mushrooms to feast easier upon decayi ng pl ant mat t er and sl owed down t he formation of coal, ending the Carboniferous period and causing the release of carbon back into the atmosphere,warming the planet. The Dyson Sphere is a conceptual megastructure conceived by Freeman Dyson, a physicist and mathematician, in 1960. It describes a colossal shell of solar panels surrounding the sun or star, to harness all available energy emitted. A shell with a radius of 1AU, the distance of Earth from the Sun, would collect 384.6 yottawatts (3.846×10^26 watts).

The Hyperloop is a conceptual transportation system designed by Elon Musk, founder of Tesla, SpaceX and PayPal, described as “cross between a Concorde and a railgun and an air hockey table”. 2.23 metre diameter pods are shot through a steel tube under a partial vacuum, and are predicted to reach speeds of up to 760mph, beating the average speed of a Boeing 747-400 at 570mph. Earthstar fungi are a group of mushrooms whose outer leathery layers split open and resemble the rays of a star. Genera include Geastrum, from geo meaning earth and aster meaning star, or Astraeus, after the Titan of Greek mythology meaning ‘the starry one’. One particular earthstar fungus, Geastrum fornicatum, was originally named Fungus anthropomorphus in 1688 from its uncanny resemblance to a human figure. It was renamed in 1821 to more accurately describe the structural features: despite certain connotations, ‘fornicatum’ comes from the latin for ‘arches’.

The first microbial age was before the evolution of more complex life. It is thought that as the sun gradually becomes hotter over time the planet will become inhospitable to large bodied animals and plant species. Eventually 600 million years in the future, one final, all will go extinct except for microbes, and the total solar eclipse will shadow Earth. The Earth will enter the second microbial age. moon is drifting away from our planet at the rate of 2 centimetres per year (about as fast as our fingernails grow), and it will eventually be too far away to completely cover the solar disc.

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Figure/Legend Beatrix Potter – beyond Peter Rabbit

and fungi. The latter she was particularly drawn to, as she loved ‘their colours and shapes and the fact that they appeared and disappeared in the ground’, according to Potter’s biographer Linda Lear.

Graduate, BSc Genetics (2015) Cardiff University

After a meeting with the revered naturalist and mycologist, Charles McIntosh, in the 1890s she learnt about fungi and lichen taxonomy and how to produce more accurate illustrations. Becoming ever more curious of their lifestyle, Potter began creating microscopic drawings of spores and experimenting with fungal spore germination. She observed how fungal spores and algal cells could establish a symbiotic relationship to form lichen. This was not a novel theory, having been hypothesised in 1867 by the German mycologist Simon Schwendener. It was, however, very unpopular and was vehemently denied by other mycologists. This was despite the lack of any competing hypotheses – lichens had been

by Lindsay Pike

I’m sure you’ve all heard of Beatrix Potter. Who didn’t enjoy reading about Peter Rabbit, Flopsy, Mopsy and Cottontail as a child, told through beautiful illustrations? If you were a child of the 80s/90s (or parent of), you may even have watched the animated TV series based on Potter’s original artwork – The Tailor of Gloucester with the little waistcoat-sewing mice was a personal childhood favourite. At least some of you will be wondering why Potter is being included in a “STEM” magazine – what does Tom Kitten have to do with technology or science? Well in addition to her literary career, Potter was a keen natural scientist. This is something I only discovered quite recently – when I was researching potential botanists to do a feature on for this magazine, in fact. I was quite surprised to see ‘Beatrix Potter’ pop up but a quick read of websites dedicated to Potter’s life and works made it clear that natural science ought to be as synonymous with Beatrix Potter as Peter Rabbit is. Helen Beatrix Potter (28 July 1866 – 22 December 1943) was born and raised in Kensington, London, where the family possessed a menagerie of animals, including rabbits and mice – animals that later became particular features of the Peter Rabbit stories. Throughout her childhood she holidayed in Scotland and the Lake District, where her love of the natural world developed and flourished, forming the subject of her early artwork. Potter was interested in many scientific aspects and other subjects of her illustrations included insects, fossils, archaeological artefacts


particularly puzzling to the botany and mycology communities of the 1800s. Potter’s lichen work was attracting attention and through her uncle, the Vice-Chancellor of the University of London Sir Henry Roscoe FRS, she was introduced to scientists at the Royal Botanic Gardens, Kew. Although the Director of Kew, William Thiselton-Dyer, refused to even look at her drawings due to her gender and amateur status, fortunately the Kew mycologist George Massee was impressed by her work, despite initial reservations. Potter was encouraged to write her conclusions up as a paper, On the Germination of the Spores of the Agaricineae, to the Linnean Society in 1897. As a woman, she was not allowed to present her own paper and so Massee introduced it for her, and it was reportedly well received. However, Potter soon withdrew the paper having realised some samples had been contaminated and it remains lost to this day, although its general meaning can be assumed from other sources. The symbiotic nature of lichens was shown to be relatively accurate, although is now considered more of a mutualistic relationship between a fungi and either an algae or cyanobacteria. At the same time though, Potter was attracting attention for her children’s illustrations and it was this she turned her focus to. She sought to publish her first book, The Tale of Peter Rabbit, in 1901 at the age of 35 and in 1905 moved to a farm in the Lake District. There, she devoted herself not only to her literary career but adopted farming life with enthusiasm. Potter became known for breeding prize-winning sheep and was key in saving the

traditional Cumbrian Herdwick sheep from extinction. Perhaps not as news-worthy as if she had saved a flagship species, but an admirable feat nonetheless. Potter died in 1943 from pneumonia and heart disease, and the majority of her properties, literary and artistic works were bequeathed to the National Trust; they can be found on display in numerous museums of the Lake District and further afield. After her death, many of her mycology illustrations were used to illustrate Dr. W P K Findlay’s 1967 Wayside and Woodland Fungi, a field guide to British fungi and lichens – completing Potter’s dream of having her scientific illustrations featured in a book. In 1997, the Linnean Society issued a posthumous apology for the sexist attitudes displayed towards Potter, and in 2012 a synopsis of her work was presented at a celebratory event marking the centenary of the Armitt Library and Museum in Cumbria, which boasts an extensive collection of Potters illustrations. Potter’s success continues to be celebrated; at present, she is being considered for the face of the new £20 notes that will enter circulation in around four years time. To be nominated, the person must be non-fictional, dead and from the visual arts field – the full list is available at the Bank of England website and the final decision will be based upon the contribution to British culture. It would be quite fitting for this great artist to be honoured by having her portrait illustrated on British currency. Further reading: http://www.telegraph.co.uk/women/womens-life/11750877
/New20-bank-note-Beatrix-Potter-must-be-Britains-next
-woman-ofnote.html Beatrix Potter: A Life in Nature, Linda Lear, 2007.

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