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Call for articles!

Call for ideas for Newcastle University's student-run science magazine

Want to make this your best year of university yet? Then get your creative science hats on and hang on tight, it's time to kick off the first issue of {react} for the 2013-2014 year!

 

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We are now accepting ideas for articles for {react} magazine Issue 4: In the Blink of an Eye

 

{react} articles are brief, thought-provoking and fun. We aren't looking for technical papers or 2000 word essays - we want you to tell us about the science, technology, engineering and maths topics that really interest you.

 

Your article can be a research piece, interview, review of a book or film, comic strip or anything else you can think of. Check out or past issues to see the topics other students have explored (http://reactmagazine.co.uk/the-latest-issue/). 

 

Our regular sections include:

 

• NCL:Research - showcase a fascinating research project taking place at Newcastle University. It doesn't have to be your own work, just something you find interesting.  
• Science Heroes - sing the praises of a favourite science personality
• Science:fiction - explore the science behind books and films. Is the rapid development of everyday technology outstripping writers' abilities to deal with it? When was the last time you saw a mobile phone work in a horror movie?
• Student stories - your inspiring science experiences from everyday life

We are also accepting articles linked to Issue 4's theme 'In the Blink of an Eye'.

 

Here are some of our ideas, but we're sure you can do better!

 

• How does body react so quickly to stimulus?
• On a geological timescale, humans are still just a blip. How do we know so much about the deep past?

• How fast are recycling and materials like biodegradable plastics helping our waste to vanish, if at all?

• Our perception of time is a strange thing. Degrees seem to stretch into forever at the start, but graduation comes all too soon...

To be considered for the next issue, please send a short proposal (~100 words) to e.ritchie@ncl.ac.uk and gesa.junge@ncl.ac.uk by September 23rd.

Elspeth and Gesa

Editors {react} magazine

Some new recruits!

Issue 3: Centre of the Earth, Bottom of the Sea

Issue 2: Running Out of Steam

Issue 1!

Here it is! Issue 1!

A day at the Maker Faire!

Verity Mitchell

The Maker Faire is an impressive gathering of inventors from all around the world. It was hard to know which stall to visit first! I started out my day at Genspace, a community biotechnology lab which aims to educate all age groups, from the young to the old. Here they were seeing what a bacterial imprint of your mouth would look like – which involved getting intimate with a petri dish! Everyone had the opportunity to return on the Sunday to see which bacteria had been living in their mouths. I had the chance to chat to some of the ‘makers’ at Genspace and learn more about what was going on in their main laboratories, including exciting ideas about the potential of hypoallergenic vegetables and biocrete (bacteria + cement = no more potholes because it grows back). Another biology stall was demonstrating how you can cheaply check the DNA of meat products to see which animal it is from, avoiding scandals like the horse meat lasagnes reported a few months ago. They showed how a small meat sample could be processed and its DNA compared against the DNA of other animals. You can then discover if your unknown sample matches what you think you are eating. The process involves a centrifuge, Polymerase Chain Reaction (PCR), fluorescent markers and gel electrophoresis which were all explained really well by the makers. This allowed the process to be much more accessible and help educate the general public so you didn’t need a science degree to get involved.

I then moved onto the electronics section, which is very new to me. Bare Conductive have combined art with electronics by creating conductive paint. They had a great selection of cards which demonstrated the cool effect paint circuits could have. It’s also a great way for everybody to learn about circuits through drawing them, even young children as the paint is very safe. I certainly learned a lot! When you have grasped the basic techniques you could move onto a Raspberry Pi, a tiny computer unit originally designed to introduce programming to children, which I learnt all about by attending one of the talks running throughout the weekend. The company behind the Raspberry Pi encourages people to develop technology themselves and make it fit around their lives. People shared some great projects they had already undertaken such as monitoring systems for plant moisture, devices which allow you to control your oven via twitter and hoovers which can be programmed to clean while you’re out, all starting with a computer not much bigger than a credit card.

Finally I went to see exhibits about the future of toys, and just about any other objects you can think of! Makies are dolls designed completely by you to look like someone you know, or even a mini-me. You can choose everything including the shape of their face, eye colour, hair colour and clothes so you have a completely unique doll. Sculpteo then caught my attention with their 3D printers. These printers also allow you to create self-designed items so that everything you own feels that little bit more special and individual. They work by ‘printing’ really thin layers of the selected material on top of one another, a wide range of materials can be used in the process, building them up to create a 3D object. Just like a regular printer they can be programmed to print just about anything, so are only limited by our imaginations. One of the many things they currently provide are built-to-order iPhone cases which have millions of possible designs.

These were just a few of the highlights from my day which left me feeling very inspired to get out there and create something myself. Not surprisingly there was a company present who could help me to do this. Make Things Do Stuff are looking for young people who can create new digital technology rather than just consume what is already being marketed. Once you have managed to create something, an iPhone app called HowDo allows you to share your ideas with the community so that you can potentially make life easier for others. There truly was something for everyone at the Maker Faire, so next time it’s around get down there and be inspired.

Emad’s Maker Faire Top 5

There was an incredible amount of engineering of all sorts on display at the Maker Faire – biohacking, 3D printing, dancing robots and even traditional computer hacking. I was amazed by it all. There was even a man who had programmed a 1987 plotter (printer) to produce colourful spirographs! (Yes, THOSE spirographs!)

Here are the top 5 picks which caught my eyes throughout the weekend event:

1. Sculpteo – 3D Printing

The 3D printing boom continues, with the technology becoming more advanced and cheaper, this could be something which revolutionises printing as we currently know it. Sculpteo, based in both France and the tech hub of San Francisco, California, offers cloud-printing services directly to consumers. Customers just have to upload a 3D image file, receive an instant quote, have their object printed and wait for it to be delivered straight to their door.

2. Genspace

Genspace is a non-profit organisation which has started a community lab in New York City, allowing wider public access to biotechnology labs. This will be covered in a longer article on the {react} website, so keep your eyes open.

3. Roslin Institute

The famous Roslin Institute, part of the University of Edinburgh, were showing off a new genome sequencing system. With advances similar in significance to those in the 3D printing industry, faster computer horsepower and wider availability is resulting in cheaper and more rapid DNA-based services being offered by private companies today. The demo included a small sensor pad which detects a sample, and is processed by proprietary software displaying significant proteins/parts of the DNA sequence. Their ambitions lie in creating an easy, fast “home sequencing kit” which everyone could use in the near future. Scary?

4. Knitic

Knitic’s stall was the one which surprised me the most. Using an Arduino microcontroller as the hub, Knitic have created open-source software which allows for particular models of old Brother knitting machines to be connected to a computer via USB, bringing knitting straight into the 21st century. This method allows for longer patterns to be designed with higher precision.

5. Paper Heart

Croat Gjino Sutic (aka Biotweaker) was able to produce a paper heart using bacteria. Weird! By using a paper-like product from bacterial growth, Gjino was able to then construct a model heart which can even carry out pumping functions. This was by far the most impressive biohack witnessed on the show floor.

Opening up Science

Emad Ahmed

How do scientists truly open their wacky worlds to others? Sure, we as students of science try our best to write about something that may be appealing to an everyday member of the public. But science is more than that.
There are subjects you can study with your head buried inside a big, old, dusty textbook at a desk. Or you can go out in the wild and explore, collect samples, gather data, get back to the lab and analyse whatever has started growing on that petri dish or construct visual and data models on a computer.

Genspace, founded by ‘Resident Journalist’ and Vice-President Daniel Grushkin and Director Oliver Medvedik have done exactly this in Brooklyn, New York. Touting itself as ‘New York City’s Community Biolab’, Genspace is a charity group determined to increase science learning and awareness by providing a small opening into the world of biotechnology. The organisation provides hands-on sessions for the public (including – most importantly – for those with no prior scientific knowledge) and hold outreach events to promote science. Daniel and Oliver gave an informative talk at the Maker Faire in Newcastle, explaining how Genspace came about and what they do.

Ellen Jorgensen, President and also a co-founder of Genspace, spoke of the positives outweighing any potential negatives of community labs in her passionate TED talk last year in Edinburgh. She spoke of the important responsibility scientists have in the public outreach and explanation of biotechnology, that public fear or hesitance can be removed once Joe Bloggs is in a safe lab and engaging with complete confidence.

Genspace isn’t by any means unique in providing lab classes for the public. These places are slowly opening up across the globe. On the other side of America in Sunnyvale, California, Eri Gentry and five other co-founders opened BioCurious, by raising $35,000 on Kickstarter. Its website lists a raft of resources available at its 2,400 square feet: PCR machines, micro-centrifuges, electrophoresis gels, CO2 incubators – the list goes on. Even larger (by a whole 210 square feet) is London Hackspace (LHS) right here in Britain. Although it’s not a biotech lab, LHS is a non-profit workshop-style hackerspace, boasting drilling equipment, soldering stations and even a 3D printer. (Don’t worry biology fans – LHS hold biohacking sessions too!)

There are many things to be happy about. The UK government having a clear STEM (science, technology, engineering and maths) strategy via a policy to grab the public’s attention is great news. Biohacking spaces are cropping up around the world in community labs, and starting in September 2013, Northumbria University will be delivering an all-new MSc in Public Engagement with Science degree, in conjunction with the Centre for Life. Science is finally becoming more than just old men in white coats – it’s mainstream.

Raspberry Pi / programming for fun

Carla Washbourne

I left Maker Faire UK with a 20 computer. This was somewhat unprecedented. This tiny gadget, known as the ‘Raspberry Pi’, appeared throughout the Maker Faire exhibits controlling all kinds of crafty projects, from lasers to remote controlled cars. The idea had me hooked. Originally designed and marketed as a low-cost unit to allow kids to learn programming skills in a fun and immediately applicable way, the Pi has permeated the minds of makers across the world. This pocket-sized unit has significantly more processing power than my family’s first PC (and once you pop a 4GB SD card in to the pre-allocated slot, more hard drive storage space too!) and can be used to develop programming-based projects on many scales. It can run a number of different processes at any one time and sports a vast array of features which make it amazingly integrate-able with other pieces of electronic hardware.

I should say at this juncture that I am by no means a seasoned programmer, computer whizz, or electronics genius. I am a field-scientist, geoscientist and writer who occasionally still manages to irrevocably confuse Microsoft Excel. The greatest part of my experience in the field of programming was supplied by a ‘toy’ laptop I owned as a child (like this – although mine wasn’t cool / modern enough to have a mouse), which sported a number of strategically dull educational applications alongside the opportunity to learn to programme in BASIC. BASIC is a long-established programming language which gives you the power to develop your own little programmes and games. Amazingly BASIC won out over the ‘spelling bee’ and ‘word jumble’ applications, leading to the creation of a multitude of ‘quizzes’ which would predict such important events as the amount of time it would take my mum to get ready to leave the house and which boys my friends would marry (always brilliantly skewed to the hilariously screech-inducing – oh the joys of being in control of the results!) It also resulted in a number of massive disappointments, mostly where relatives of advanced years vastly overestimated both the computing power of the mid 1990′s and my skill as a programmer. Generally this resulted in said relative assuming that they could speak directly to the computer, and becoming frustrated when it seemed unwilling to accept their responses. I’d like to think that my Great Uncle Laurie was the real inspiration behind voice recognition software.

Now computers really can do some amazing things, and like many of us I have completely lost touch with much of the ingenuity behind both the hardware and software that make this possible. Through fleeting encounters with HTML and visual basic, I am now here, older, wiser, and holding a piece of simple hardware with so much more potential than I can really comprehend. I guess the point of my writing this article (and there is a point, I assure you!) is to convince both myself and you, dear readers, that a relative novice can pick up something like the Raspberry Pi without being daunted. That we can, in some small way, go back to being makers of technology rather than just users.

Where on Earth am I going to start? Well I realise that before I do anything much with my Pi I will have to learn to programme in Python – essentially tackling a new language – and that’s actually pretty exciting. I am so used to being a consumer of technology, and especially of software, that I’m actually really looking forward to learning a little bit more about what is going on in the background. I will also need to give myself a crash-course in some pretty rudimentary electronics. Soldering has already been ticked off the list, as the lovely people at MadLab (http://www.madlab.org/) agreed to let me loose with a soldering iron at the Maker Faire. Despite being a very hands-on person in my work, combining the phrases ‘electricity’ and ‘hands on’ in the same sentence does still make me wince. Perhaps the Pi will help to alleviate my fear a little, or at least prove too well-designed to allow me to accidentally melt anything particularly expensive.

A few lines of code and a bit of jiggery-pokery and the gang at the Raspberry Pi Foundation (http://www.raspberrypi.org/about) assure me that I can do anything from turning on my coffee-maker via Twitter to booby trapping my house with hidden cameras and light beam based trip-wires (which I am sure my housemates will love). What have I really got to lose?

React featured on the Newcastle Researchers’ Blog!

We’ve been featured on the Newcastle Researchers’ Blog. Check out the article here.

Cafe Waste

By Eleanor Swain

Our planet is reaching breaking point, with billions of tons of greenhouse gasses billowing into our skies, landfills at bursting point, waterways polluted and our resources grossly exploited, all while population continues to rise. Something needs to be done to reduce our burden on the planet. A relatively new concept which could help reduce this burden whilst allowing continued growth is up-cycling, currently defined as “the process of converting an industrial nutrient (material) into something of similar or greater value, in its second life” (1). So, is up-cycling another buzz word du jour, or a revolution that will change not only our attitudes to waste and resources, but ultimately save our planet?

With waste generation closely linked to population, urbanisation and affluence, post consumer waste is expected increase to 1.7 billion tons of CO2 equivalent emissions by 2020 (2) (where CO2 equivalent is the total climate change impact of all greenhouse gases, expressed in terms of the amount of carbon dioxide that would have the same impact). To put this into perspective, the total global greenhouse gas emissions in 2005 was 44 billion tons of CO2 (3). However, despite efforts to reduce the amount of waste produced (the most favoured waste solution according to the DEFRA waste hierarchy (Fig. 1)), the continued population increase means an ever-increasing generation of waste is unavoidable.

Nonetheless, there is some positive news; last year the UK saw the proportion of local authority waste entering landfill dropping below that recycled, composted or reused for the first time since records began (the second and third most favourable waste treatments). However, the rate of recycling has started to plateau, and often the process required results in down-cycled goods, in which either massive amounts of resources and energy are required to process the new material increasing the new products embedded energy, or the material quality is reduced, making them suitable for use only in lower value applications. For example, during many so-called recycling processes involved with plastics, different plastics are mixed resulting in a hybrid material that has decreased physical, mechanical and aesthetic properties. This highlights the waste hierarchy as set out by DEFRA is in need of clearer definitions of recycling (Fig. 1), as well as the introduction of down-cycling and of course up-cycling.

The popular science book ‘How Bad Are Bananas’ by Mike Berners-Lee, beautifully encapsulates the importance of calculating the embedded carbon footprint of everyday items, not merely taking emissions and energy usage as an indication of your impact on the planet. For example, less than 10g of CO2 is released producing a pint of tap water, unlike the bottled alternative which has around 1000 times the impact, which requires additional processing including purification, transportation and packaging.
“It takes 17 million barrels of oil a year to produce water bottles for the USA only, not including the energy for transportation, and it takes three times the water to make the bottle as it does to fill it”.
In addition, the global consumption of bottled water is increasing year on year, while there remains a minimal recycling of these bottles. There is an urgent need to rethink how our waste is treated, and how to define when packaging has reached the end of its useful life. Underlying these questions are a set of broader concerns, which can only be examined by positioning human attitudes to waste within certain social, cultural, and economic contexts. How for example, can we explain this rise in bottled water consumption, and to what extent will behaviour change be necessary to undermine a throwaway mind-set, and hence play a significant role in creating for us all, a more sustainable future?

There is no doubt that the waste hierarchy starts off well with reduce and reuse, however as identified, recycling really isn’t the next best step, it is simply ‘not as bad’ as landfill, and is more often more accurately labelled down-cycling. Up-cycling however fills in the gap between reuse and recycle, in which materials from used products are utilized in the the manufacturing of new products of increased value with minimal additional energy (i.e. minimal embedded energy) (Fig. 2). The concept has been welcomed by the textiles industry, in which both zero-waste patterns and zero-waste manufacture are now commonplace. In addition, companies such as Worn Again, utilise existing textiles from large companies to create new products (Fig. 3).

Researchers at Newcastle University are exploring the potential of design-led up-cycling, where products are engineered at the production stage to have a range of ‘potential’ uses during their lifetime. However, the concept of up-cycling is recognised as only successful if the general public not only recognise these new potentials in waste material, but are also motivated to do something with them too. So for example, plastic bottles, cartons, and other packaging, once regarded as worthless waste, may become more valuable if people identify these as components with a range of creative possibilities. One exciting potential is for people to take ownership of these new materials and use them in innovative ways, to create new products, and hence develop for themselves new entrepreneurial opportunities. If for example, the value of such materials increases, is there likely to be a range of new ‘grass-root’ types of business opportunities created?

What is not currently known, is the willingness of people to own a handbag made from materials once regarded as rubbish or waste, or live in a building insulated with material of a similar origin. How, and why would people of very different social, economic and cultural backgrounds choose to engage with up-cycled products, if at all? To gauge a range of possible perceptions around notions of waste, value and utility, an interdisciplinary team of academics and students from Newcastle University are constructing a Cafe made from materials described as rubbish or waste. The structure of ‘Cafe Waste’ will be cardboard and plastic, and has been designed to function as a working cafe. This is intended as a space where people of different ages, and from different neighbourhoods of Newcastle, will be invited to participate in a research dialogue with members of the project team. It is hoped that, by encouraging research participants to experience waste materials in new ways, it will be possible to explore the potential value of up-cycled products and components.

Cafe Waste will be open for business between Tuesday 16 and Thursday 18 April, and we invite students to come along and get involved. All ‘customers’ will get a free cup of coffee, but only if they bring their own disposable coffee cup. You will find Cafe Waste in the new glass reception area of Fine Arts; adjacent to The Northern Stage.

(1) Dictionary of Sustainable Management
(2) IPCC, in, Cambridge University Press, Cambridge, UK and New York, USA. pp 996, 2007.
(3) K. Baumert, T. Herzog and J. Pershing, in, World Resources Institute Working Paper 2005, p. 132.

Video from the launch party

Check out this video from our launch party for the very first edition of REACT! Meet the editors and find out how you can get involved.

 

Sea Urchins help to understand how we can reduce CO2 emissions

By Clare Tweedy

The key to understanding how we can reduce carbon dioxide emissions in the atmosphere could lie in the CO2-reacting properties of sea urchins. Newcastle University have discovered that sea urchins are able to capture CO2 from the sea via the use of Nickel particles. The carbon dioxide is then converted into harmless calcium carbonate. The carbonic acid reaction occurs when carbon dioxide reacts with water, a process which usually takes too long to carry out naturally. High amounts of Nickel were found on the exoskeleton of the sea urchin, and this effect can be recreated with the use of Nickel nanoparticles.

Current proposals to remove CO2 from the atmosphere include pumping it into the ground, though this process is expensive and could lead to the gas escaping from the ground again. Alternatively, CO2 can be converted into calcium or magnesium carbonate via an enzyme called carbonic anhydrase. This enzyme depends on the conditions not being acidic however, and the carbonic acid produced means the enzyme quickly stops working. Nickel, on the other hand, is not just able to work despite the acid but is also much cheaper than the enzyme. This process would see CO2 passed through a column of water containing Nickel, with calcium carbonate (or chalk) being produced at the end.
This discovery could help us to combat climate change and produce more efficient methods of CO2 capture. While it would not be effective in the case of vehicular pollution, fossil fuel-burning power stations could revolutionise their CO2 emissions using this method.

Pollution can decrease a baby’s birth weight

By Clare Tweedy

Pollution emitted from vehicles and the use of coal in power plants has been found to increase the chance of pregnant women having smaller babies. The worldwide study included a UK division headed by a team at Newcastle University, but also included data from nine other nations around the world. More than three million births were analysed over the course of the study with factors like socioeconomic status taken into account. It was found that in areas with higher pollution it was significantly more likely for smaller weight babies to be born. While low birth weight (defined as less than 5lbs 8oz) is harmless for some babies, it can carry with it the risk of health problems later in life.

The pollution in question is often referred to as PM (particulate matter) and levels are considerably higher in larger cities around the world. Despite tight regulations in many countries over the recent years, PM levels are clearly still having a hazardous effect on health. While the European Union currently limit PM levels to 25 micrograms per meter cubed, other nations such as the US and Scotland have set their annual limits at 12 micrograms per meter cubed. It is hoped that this worldwide study may convince countries with higher PM limits to lower them in order to combat the health problems of low birth weight children.

Earlier Diagnosis for Parkinson’s Disease

By Clare Tweedy

Researchers from Newcastle University have raised the hope of an earlier diagnosis of Parkinson’s Disease in the near future. It was long thought that the symptoms of Parkinson’s don’t tend to manifest until the later stages of the disease. However, new research suggests that the non-movement related symptoms of the disease may appear in patients earlier than was previously thought. Drooling and excessive saliva production, along with bowel problems and anxiety, have been observed in patients still in the early stages of the disease.

The chance of an earlier diagnosis can lead to treatment for the disease starting earlier, and the patient’s quality of life therefore improving. The non-motor symptoms of Parkinson’s often go unreported, though this early diagnosis could lead to these issues being treated long before the movement-related symptoms set in. On average, a Parkinson’s sufferer will experience eight of the non-movement related symptoms of the disease. The study itself was carried out as a part of Newcastle’s Initiative on Changing Age, a project intending to tackle the issue of ageing and its associated challenges.

L-forms: the naked bacteria?

by Laura Domicevica

As my first blog post for the Homo biomedicus, I wanted to start with something small. Microscopic, actually. They can talk, sense, warn others of their kin about danger and even cooperate for greater purpose. And yet we cannot see them with a naked eye. World of bacteria is wrongly accused of being dull and simplistic with nothing of interest to offer. However, among many surprising features that we already know of another one has emerged.

Most bacteria have a cell wall that shields them from outer world and allows them to keep a characteristic form and interact with environment. It is also their weak point, exploited by our immune system and antibiotics such as penicillin. Surprisingly, evidence has been found that these organisms can lose their cell wall and transform into L-forms. Such bacteria are often associated with chronic infections, with the most recognizable members from genus Mycoplasma which are often found in pneumonia patients. These bacteria are not recognised by our immune system and cannot be destroyed by most antibiotics used in traditional therapy. Antibiotic resistance is a widespread problem in healthcare. For example, the epidemics of MRSA (Methicillin resistant staphylococcus aureus) in hospitals around the world.

Researchers in Centre for Bacterial Cell Biology were able to make a Bacillus subtilis strain that could be induced to rapidly lose its cell wall and become a stable L-form and back. This is a great success and an extremely useful tool for L-form research. Although we know that cell wall can be lost naturally, it is a difficult process to repeat in a laboratory environment and even after decades of research, the changes that drive this conversion are mysteries to the microbiologists. L-form cells are fragile and sensitive to osmosis, as there is no cell wall that could guard them from the influx and efflux of metabolites – salts and nutrients.

With the modifiable strain at their disposal, insight of the manner of L-form emergence could be obtained. It soon became apparent that the protoplast, i.e. the inner parts of a cell, including cell membrane, emerges from a bulge in cell membrane and eventually separates as L-form, leaving now empty cell wall behind. This process can also happen at the sites of cell division.

Researchers predict that their method could be used to make similar strains and eventually underpin the molecular mechanisms in organisms like staphylococci and streptococci – well known human disease-causing agents. Deeper insight in the formation of L-forms might lead to new designs for antibiotics and novel therapies.

Reference

Underground Antarctic lake to be explored

By Clare Tweedy

Hidden beneath a sheet of ice at least two miles thick, Lake Ellsworth will soon be explored for the first time. The lake, in western Antarctica, is thought to have been buried under the ice around half a million years ago. Despite the lack of sunlight reaching the sub-glacial world, it is expected that microbes will be found in the waters, and these will provide information on how life can survive in extreme conditions. The lake itself is estimated to be around the size of England’s Lake Windermere.

The project, which is estimated to cost around 8 million pounds, will soon begin by drilling down through the ice. Combined with water heated to 90 degrees C, the ice will be melted and a sampling machine will be passed down into the lake. Years of planning have gone into the mere six day timeframe that the project is expected to last for, but the results are expected to be analysed in a much shorter time.

 

Diet is able to change our genes

By Clare Tweedy

Changes that we acquire in genes during our lifetime have long been linked with how we age. Yet recent research by Newcastle University has concluded that these changes can be affected by our diet. The choice of what we eat can have effects not just on our body weight and general health, but also on ageing. The changes to our genes, also known as epigenetic markers, were found to be altered depending on which diet the person followed. It has been found that selenium and vitamin D were able to reduce these changes, whereas high folate levels increased them.

Other studies complement these findings, as high folate levels have previously been linked to the epigenetic changes that lead to bowel cancer. While this particular study focused on the link of bowel cancer and our diet, it will be possible in the future to link many diseases with epigenetic markers. The research highlights how we can possibly protect ourselves from a range of diseases by something as simple as our diet.

 

Cancer patients to have DNA mapped

By Clare Tweedy

As many as 100,000 patients suffering from cancer are set to have their DNA mapped over the next five years. News of the project comes as Prime Minister David Cameron announces 100 million pounds to be spent on sequencing the genomes of those currently living with cancer. It is hoped that a map of these patient’s DNA will give some clues to the causes and treatments that could best work for the individual patient. This project will therefore bring hope to the 1 in 3 people in the UK that will develop some form of cancer in their lives.

It is currently not known how the patients will be selected to have their genome mapped, or who will be contracted to carry the sequencing out. The use of DNA sequencing in the treatment of cancer has long been hoped to allow personalised medicine depending on a person’s genome. It seems that tailored treatments are one step closer thanks to the government’s investment in the project.

Why do we need mitochondria?

By Laura Domicevica

This seemingly easy question has proved to be a rather tough nut to crack. It is well known that mitochondria produce power in the form of ATP which is the main energy currency in a cell. That seems really important, since without the energy the cell would stop dividing or die. In either case, the consequences of loosing mitochondria function are quite serious. In humans, problems in mitochondria function cause devastating disorders affecting muscles and brain the most, as these cells use great amount of energy.

What came first – the nucleus or the mitochondrion?

The way eukaryotes acquired mitochondria reminds something from Star Wars. The ancestor of mitochondrion was an ancient bacterium that lived in symbiosis with the early eukaryote. As the part of the cell that produces most of the energy, it sounds to me like a midichlorian – bacterium channelling the Force in Jedi.

The structure of mitochondria shows some proof of its bacterial ancestry, as it has double membraneinstead of the single lipid bilayer present in other subunits of the cell and even separate genome, encoding many important proteins.

Even with the extensive research done in this field, it is still impossible to tell when exactly the mitochondrion was acquired. For some time it was thought that eukaryotes formed endosymbiosis at some stage of their evolution. Consequently, this could be proved by finding a cell with a nucleus and without mitochondria. So far, no luck here.

Simple parasitic cells, for example, well known disease causing microbe Trichomonas vaginalis, do not have mitochondria in the traditional sense. They were found to have extremely reduced organelles with double membrane and some functions characteristic to mitochondria.

Elements we cannot live without – iron and sulphur

Researchers from Newcastle University looked at a parasites called Microsporidia that have lost many features common to a eukaryotic cell. Nevertheless, these obligate intracellular parasites that cannot live outside of a host cell have mitosomes – a reduced form of mitochondria. The question they were trying to answer was what is the ultimate role of the mitosome i.e. mitochondria in essence. Surprisingly, the parasite did not need it for the production of energy, as it was possible to steal it from the host.

Actually, the one of the main features still present in this organelle was the production of iron-sulphur (Fe/S) clusters. For those who do not know, Fe/S clusters are essential for all cellular life, as they keep maintenance of the protein production. They are themselves a part of integral proteins, such as polymerases replicating DNA and RNA and proteins involved in transcription and translation. This study provides more evidence of the importance of this process that now seems to be required in all forms of nuclear life.

In the end, the question I proposed in the title is not easy to answer, but looking at the simplest cells that try to lose as much as they can in order to survive might just give a few hints.

Reference

 

Public Engagement: School Kids and Science

By Sarah Rice

There’s no doubt about it: public engagement at Newcastle University has really been taking off. With the British Science Festival set to take place in 2013, science institutes university-wide are eager to jump on board. Students and professors alike are emerging from their laboratories and endeavouring to introduce their research to the public in an interesting and relatable manner. On Wednesday 5th December, one group of researchers at the Institute of Genetic Medicine, based at Newcastle’s Centre for Life, invited A-level students from eight schools across the region into their labs to find out exactly what a career as a scientist entails. I went along to see what the fuss about public engagement is all about.

The day kicked off with a series of short talks from both Professors and Clinicians based at the Institute of Genetic Medicine. The aim was to provide the students with an insight into their research, which laid the foundations for the seven interactive demonstrations they would participate in throughout the course of the day.
The eighty students moved around various workstations across the institute, manned by lab technicians, PhD students, and research assistants. In the “Patient Experience”, students were given the opportunity to meet a patient with a degenerative condition, retinitis pigmentosa, which may result in impaired vision or even blindness, to raise awareness of some of the social stigmas surrounding blindness. The highlight of this session for many was the provision of goggles that simulated one of the four types of visual impairment, which allowed the audience to truly empathise with the difficulties faced by sufferers of this condition. This session highlighted the strong relationships between the institute’s clinicians working and their patients, and related the research to its impact on the lives of patients.

In the microscopy room, students were given access to different types of microscopes, under which they could view sections of mouse muscle and cartilage, and zebrafish embryos stained with fluorescent dyes.
In school, as a part of the A-level curriculum, students learn the theory behind PCR (polymerase chain reaction) and gel electrophoresis, common techniques used in biomedical sciences to amplify particular genes from DNA samples and visualise them. One teacher from Westfield High School, Gosforth was delighted that the students had been given the opportunity to see this technique in practice. She also commented on the “enthusiasm” and “positive attitude” of the organisers, and was thrilled that the students had been given access to the institute at such a critical time in their academic careers.
This was also very much appreciated by the visiting students. Two A-level students from Sacred Heart Catholic High School, Fenham, agreed that one of their favourite aspects of the day was hearing a talk from two undergraduate students about the realities of university life and the transition from college to becoming an undergraduate student.

Unfazed by a long and activity-packed day, the students continued to work late into the afternoon, as the open day climaxed with an ethical debate regarding the use of animals in medical research. In groups, the students were assigned a role such as that of a university researcher, or an animal rights activist and asked to debate from their respective viewpoints. For many, this lively and interactive debate was the highlight of the day and staff at the institute felt the students adopted these roles with passion, maturity and insightfulness. The session was concluded by an animated talk from Sir John Burn, Professor of Clinical Genetics.

The open day at the institute was a complete success: everybody in attendance, staff and students alike, fully-enjoyed and benefited from the experience. Personally, I found the success of the open day encouraging for my own future attempts at “public engagement” and would like to thank the organisers for allowing me access to their event. With many more upcoming events across the university , Newcastle is well on-track with introducing and familiarising its research with the local community.

Image1: Research Assistant, Jon Ingledew, demonstrates PCR to one group of students, who were able to run DNA samples they were provided with on a gel, by electrophoresis, and visualise the results to idenitfy them.

Image 2: Students received a 25 minute talk from Susan Lindsay, Professor of Human Developmental Genetics, entitled “What do genes do during development?”.

Image 3: Lab Technician and PhD Student, Morten Ritso, demonstrated Tissue Culture to the visiting students. This included how to split cells and how to digest them for analysis.

Cosmic rays for measuring CO2 levels

By Clare Tweedy

The potential use of cosmic rays to monitor carbon dioxide (CO2) levels in storage sites is being investigated by a number of British universities, including Newcastle. Once carbon dioxide has been produced as a waste product in power stations, it is transported to a storage site and captured there to reduce global warming and the acidification of the ocean. Current methods to monitor levels of carbon dioxide in storage are expensive and cannot be performed continuously.

Muons, particles from cosmic rays, are able to penetrate rocks deep in the ground and can therefore measure levels of carbon dioxide in a carbon store. The use of muons from cosmic rays allows a monitoring system that can be used over longer periods of time, and therefore give long-term analysis of CO2 storage. It is hoped that the research, funded by The Department of Energy and Climate Change, will help monitor carbon dioxide storage and its effect on the prevention of global warming.

Second largest black hole ever spotted

By Clare Tweedy

The second largest black hole ever has been recorded in a galaxy a quarter the size of our own. Large galaxies usually have a supermassive black hole at the centre, and typically its size should reflect the size of the galaxy it is found in. However, the black hole found at the centre of galaxy NGC 1277 has a mass seventeen billion times larger than our Sun. The team, from the Max Planck Institute for Astronomy in Germany, also described five other galaxies of a similar size to NGC 1277. It is anticipated that these may also contain an extremely dense black hole. This peculiar discovery may force scientists to rethink their current explanations for how black holes form and expand.

(image source)

 

Reducing Vitamin D deficiency by supplements

By Clare Tweedy

A lack of sunlight during the winter months can lead to vitamin D deficiency, a problem that is particularly widespread amongst the elderly. The vitamin is responsible for increasing bone density, and therefore reduces the risk of fractures. It is thought that during the winter there is a 30% reduction in vitamin D made by the body, commonly caused by a lack of time spent outdoors.

Researchers at Newcastle University are investigating whether vitamin D supplementation can reduce the risks associated with this deficiency. Different doses of the vitamin will be given daily to participants over the age of 75. Currently, 400 iu (international units) of vitamin D per day is recommended in the UK. The study will also investigate the effect of higher doses and the possibility that more vitamin D than the current recommendation is required to avoid deficiency. The study, funded by Arthritis UK, will begin in the autumn and a change in participant’s bone density (and therefore their risk of fracture) is anticipated by the end of the two years.

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