Ionic issue 3 by Yalda Javadi

Issue 3. March 2013

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IONIC Issue 3 - MESSAGE FROM THE EDITOR

Message from the editor Ionic Magazine 03.13 Today is a good day, for two reasons. The first reason is that winter is over and March is here. The second reason is that with that comes Issue 3 of Ionic Magazine, which means fresh science and fresh art. Read about batteries that run on sound, complexities in diagnosing prostate cancer, how to make made bird flu airborne, and some facts about Whey protein, to mention a few. Think you got the message? Think again. Alongside each article add an artists perspective to the scientifically wrapped message. Some striking, some beautiful and some will make you smile. I hope you all enjoy Issue 3 as much as me. Share the love and keep up-to-date with Ionic Magazine on Facebook and Twitter. And to get involved with Issue 4 just get in touch www.ionicmagazine.co.uk/getinvolved Much love,

Yalda Javadi Ph.D. Editor

@IonicMagazine facebook.com/ionicmagazine

IONIC Issue 3 - CONTENTS

Contents How to make an airborne virus… CENSORED

‘No batteries required’ Running on sound

By Yalda Javadi - Illustration by Dan Lucas

By Lux Fatimathas - Illustration by Alfie Christiansen

The Explosive Evolution of the Grandmother

A catalogue for “spelling mistakes” in cancer

By Emily Head - Illustration by Sara Kapadia

By Klodiana Jani - Illustration by David Purnell

STEALING DNA: AN ASEXUAL ANIMAL’S SECRET FOR SURVIVAL

Why the whey?

By Beth Atkinson - Illustration by Angela Brew

Complexities of detecting prostate cancer By Rugina Ali - Illustration by Mita Brahma

By Xavier Roeseler - Illustration by Lewis Stipic

IONIC Issue 3 - HOW TO MAKE AN AIRBORNE VIRUS… CENSORED

How to make an airborne virus… CENSORED By Dan Lucas

By Yalda Javadi - twitter.com/yjavadi

ow does highly pathogenic avian influenza (bird flu) H5N1, become airborne? Ron Fouchier and his team of virologists from Erasmus MC, in Rotterdam, set out to answer that very question. Along the way however, they would face attempts at full-scale censorship and fuel worldwide regulation debates that developed into a twelve-month suspension on influenza research. Why such a reaction? Because they did it, they made bird flu airborne, proving that it could potentially pose a pandemic threat and then published it for the whole world to see. The group changed the DNA code of H5N1 so that it bared similarities to previous airborne human flu pandemics. This mutant H5N1 virus was injected intranasally (up the nasal passage) to a group of ferrets. Ferrets? Yes ferrets, the group chose ferrets in their studies as they share many similarities to humans in terms of their respiratory system and how they respond to influenza viruses. Through natural selection, the virus was allowed to adapt to the animal through a process known as virus passaging. Here, ferret number one, whose been injected with the virus, has its lungs and specific nasal bones homogenized (all blended together into a mixture that is consistent throughout) and injected intranasally into ferret number two. This process was repeated ten times, before these ‘passage-10 ferrets’ had DNA from their nasal swabs analysed to reveal the genetic makeup of the resulting virus mixture. With a potentially airborne virus produced, the next step was to determine whether the viral mixture was indeed airborne transmissible. To test this, the scientists set up an experiment; healthy ferrets were placed in cages near ferrets injected with the virus mixture. Nasal and throat swabs from the ‘healthy’ ferrets confirmed successful bird flu transmission.

www.lunchtimedoodles.co.uk

Bird flu has been responsible for the deaths of tens of millions of birds worldwide, and to-date, taken 359 human lives too. Changes to the DNA composition of the virus – mutations – can lead to a virus that is airborne in mammals and the results of this study suggest that a few mutations are enough for this to happen. Great work, right? Time to publish the results. Not everybody agreed. The group faced hours of interrogation by the National Science Advisory Board for Biosecurity (NSABB), who didn’t want the results published. The censorship attempts were primarily in the interest of preventing serious bioterrorism threats, or misuse of their methods by ‘rogue’ countries, careless or DIY scientists. The group fought and presented their motives clearly; it was in the interest of public health, and preventing or in fact limiting the impact if prevention fails, of a human pandemic threat of H5N1 virus. And as such all findings, including full methodology disclosure should be included. The paper was finally published in Science in June 2012 and in January 2013; the twelve-month ban on influenza research was finally lifted. In a recent ‘Science and Censorship’ lecture at the University of Cambridge, UK, Fouchier stated that ‘science should never be censored’. He believes that scientists working on projects such as this airborne H5N1 virus, all follow a code of conduct. And much of the rules and regulations, while in place to prevent misconduct, do nothing to prevent ‘bad guys from doing what they’re already going to do. All they do is slow down the good guys’.

http://www.sciencemag.org/content/336/6088/1534.abstract

IONIC Issue 3 - The Explosive Evolution of the Grandmother

The Explosive Evolution of the Grandmother

By Sara Kapadia

By Emily Head - http://scienceandshoes.wordpress.com

www.sara.kapadia.com

hough our Grandmothers may be protective (or perhaps even territorial) over us at times, not many of us would expect them to engage in a physical fight to defend us. However, the more mature, female members of a particular termite species do even more than that…

and preventing attack upon their dependent and defenceless grandchildren, whilst their mother seeks the opportunity to have more children. Meanwhile, ‘grandmothering’ behaviour is also known to increase one’s lifespan, by reducing the amount of labourintensive childcare that is bared by the mother.

The workers (those that forage for food and tidy and maintain the nest) of the Neocapritermes taracua species develop the self-sacrificing tactic of ‘bombing’ foreign nest-invading termites as they age, with older workers taking on a larger share of the defence. So much for retiring and indulging in your pension pot!

To test this idea of loving Grandmas increasing our lifespan, a collaboration of mathematicians and scientists created a computerised model of the behaviour. Using chimpanzee lifespan, they discovered that grandmothering can double a lifespan in less than 60,000 years (in evolutionary terms, a much shorter phase than it seems!)

This explosive ability starts to develop as the worker’s food intake, and thus their survival, diminishes. As they begin to starve, a specialist pair of glands develops to help the ladies with their ‘final mission’. Residing on the termite’s back, these ‘backpack-like’ glands hold the copper-containing protein which causes the formation of blue crystals within the glands. When bitten into by attackers, the puncturing of these backpacks causes its contents to be explosively released. Outside of the termite’s system, and as the blue colour of the crystals fades, the released substance becomes a ‘sticky trap’ for the termite’s predator. This hampers invaders and saves the nest, all thanks to Grandma! And it’s not just these termite grandmothers that act in such an altruistic way. Evolutionarily it is believed that human grandmothers looking after their grandkids have increased human lifespan by protecting

But why do our grandmothers adopt such a caring attitude? Put simply, menopause. It’s thought that the menopause results in a ‘change of tactic’ for females. While initially females focus on producing offspring to ensure that their genes are passed on, following menopause and unable to produce babies, Grandmothers assume a position of care thought to protect their offspring. This mechanism of protecting ones genetic line is rife within the natural kingdom and applies equally within the termite species, whereby their exploding behaviour prevents the attack of their siblings and parents who hold a proportion of Grandmother’s genes. This natural response to protecting the family may come as a result of the evolutionary raison d’être of ‘passing on’ one’s genes, where it becomes just

as important to nurture and protect your ‘additional genetic investments’ (AKA your existing family and offspring). Much similar behaviour is believed to have evolved to ensure the survival of the all-important genetic lineage. So whilst Grandmothers may seem kind and caring, an underlying evolutionary cause could be the reason for their loving behaviour!

Hawkes, K., Nature. 428, 128-129 (2004). Kim, P.S., Coxworth, J.E., Hawkes, K., Proceedings of the Royal Society Biological Sciences. doi:10.1098/rspb.2012.1751 (2012). Šobotník, J.,Bourguignon, T., Hanus, R., Demianová, Z., Pytelková, J., Mareš, M., Foltynová, P., Preisler, J., Cvacˇka, J., Krasulová, J., Roisin, Y., Science. 337, 436 (2012). Williams, G.C., Evolution. 11, 398-411 (1957)

IONIC Issue 3 - Stealing DNA: An asexual animal’s secret for survival

Stealing DNA: An asexual animal’s secret for survival

By Angela Brew

By Beth Atkinson - http://www.bristol.ac.uk/biology/people/beth-atkinson/

http://pinterest.com/brewdrawing/

tiny invertebrate, that has lost the ability to have sex, can steal DNA from its food. Bdelloid rotifers are microscopic creatures found throughout the world in fresh water and damp soil. They are also all female and only reproduce asexually, having lost sex and males millions of years ago. However, they can inherit new genes from other non-animal species such as bacteria and fungi. Researchers studied the rotifers’ mRNA, a molecule similar to DNA that only contains genes used to make proteins1. The mRNA was compared to a database containing the mRNA of thousands of other species. When a section of mRNA from the rotifers matched a section in the database, scientists looked up where the genes came from. Using this method they found that about 10% of the genes were alien – coming from nonrotifer species that included bacteria, fungi and algae. Scientists suspect that the rotifers acquire these genes from the organic debris they eat. Even more unusual is that because this method only looked at genes being expressed, we know that this alien DNA is not just sitting in cells, it is being used to make proteins. Most of these proteins are enzymes, molecules that enable chemical reactions to occur. These acquired enzymes may explain the amazing capabilities of bdelloid rotifers. Despite living in aquatic and damp environments bdelloid rotifers can survive drying out. The dehydrated rotifers lie dormant until they’re rehydrated when the environment gets wetter. The enzymes made, using foreign genes, enable the rotifers to use otherwise unusable substances as food, and to manufacture protective molecules. This could be important for surviving dehydration.

The consumption of DNA may also account for the number of bdelloid rotifer species. Bdelloid rotifers reproduce without sex. This is not unusual as many organisms reproduce asexually, but bdelloid rotifers are the only animals to exclusively reproduce this way. Theory predicts that this lack of sex should limit their ability to adapt to changing conditions, and therefore limit their evolution into new species. However, there are over 300 species of bdelloid rotifer. Sex mixes genes from different individuals creating new combinations that might be useful. This mixing also creates variety within a species, helping species to evolve by increasing the chance of some individuals being adapted to current conditions. Bdelloid rotifers can create new combinations of genes without sex by horizontal gene transfer – where genes are transferred between two rotifers. But horizontal gene transfer alone, between rotifers, isn’t expected to have resulted in the diversity of bdelloid rotifers seen throughout the world. The introduction of new genes from other life forms increases the variation between bdelloid rotifers, and may explain the large number species seen. So not only does stealing genes from their food add to the weirdness of these already unique creatures, it may explain their millennia of survival and evolution.

Boschetti C. et al. PLoS Genet 8(11) e1003035 (2012)

IONIC Issue 3 - Complexities of detecting prostate cancer

Complexities of detecting prostate cancer By Rugina Ali https://www.facebook.com/rugina.ali

rostate cancer (PC) is the most common cancer in men and the third leading cause of cancer in the European Union. Men with a family history of prostate cancer are advised to start screening at the age of 40-45, whilst others are advised after 50. Screening for the cancer involves detection of Prostate Specific Antigens (PSA), which is a protein produced exclusively by the prostate and released into the blood in small quantities. Normal PSA levels are considered to be 4 ng/mL, whilst levels greater than 10 ng/mL indicate a high risk of prostate cancer. In the 1980s, PSA was approved as a test to help manage patients diagnosed with prostate cancer, and was later approved as a diagnostic tool. The testing allows for early detection of a disease that is so often undiagnosed due to its symptomless progression. Interpretation of the PSA tests can be complicated and cut-off values differ between laboratories. PSA levels change over time depending on the size of the tumour and how fast it grows. For non-aggressive cancers “watching-waiting” can be employed, whereby PSA levels are tested every 6-12 months and an increase in PSA levels is indicative of disease progression. Surgical removal of the prostate will result in a decrease in PSA levels. Unless of course, the gland isn’t completely removed, the cancer has recurred or indeed metastasized. However, increases in PSA levels don’t always suggest prostate cancer, and the PSA test can frequently give false positive reads. Since its introduction as a screening tool, PSA testing has led to the discovery of non-fatal cancers, or those, which would not have been detected in the absence of screening, which has led to over-diagnosis. This has inevitably led to overtreatment.

As what man would choose to live with an unpredictable cancer? Whether falsely diagnosed or not, various courses of treatment is their likely choice to escape the mental anguish of uncertainty, and who can blame them? PSA screening has certainly lead to increased prostate cancer awareness since its introduction as a screening tool but due to the unspecific nature of the PSA test, it has increased problems with overdiagnosis. Advancements are being made with investigating different biomarkers and variations of PSA testing for early detection of prostate cancer. However, in spite of its failings, the PSA test still remains the best screening tool currently available. An advanced approach may be to implement individualised interval screening based on results after first round of PSA screening. Those men with lower PSA may benefit from lengthened screening intervals, while men with higher levels should be screened more often.

Barqawi AB, Krughoff KJ and Eid K. Current Challenges in Prostate Cancer Management and the Rationale behind Targeted Focal Therapy. Advances in Urology. 2012;May 10. Brett T. Prostate specific antigen. Australian Family Physician. Vol. 40, NO. 7, July 2011. Stamey TA, Caldwell M, McNeal JE, Nolley R, Hemenz M, and Downs J. The prostate specific antigen era in the United States is over for prostate cancer: what happened in the last 20 years. Journal of Urology. Vol 172, no 41, 1297-1301, 2004. Rove KO and Crawford ED. Randomized controlled screening trials for prostate cancer using prostate-specific antigen: a tale of contrasts. World J Urol (2012) 30:137-142. Colloca G. Prostate-specific antigen kinetics as a surrogate endpoint in clinical trials of metastatic castration-resistant cancer: A review. Cancer Treatment Reviews. 2012 April 12. Klotz L. Active Surveillance for Favourable-risk Prostate Cancer: Background, Patient Selection, Triggers for Intervention, and Outcomes. Curr Urol Rep (2012) 13:153-159.

By Mita Brahma

www.mitabrahma.com

IONIC Issue 3 - No batteries required: Running on sound

No batteries required: Running on sound By Lux Fatimathas - https://www.facebook.com/l.fatimathas

op culture is littered with imaginary futures where man and machine have fused together as one – from the plugged-in urbanites of the Matrix to the infamous villains of Star Trek, the Borg. A future where human biology is wired into machine is not as far-fetched as it may sound. Surgical implants from titanium hip replacements to carbon heart valves are already commonplace. These stalwarts of prosthetic medicine are sturdy but static. Human ingenuity has also engineered machines that actively interact with our bodies, such as the artificial pacemaker that delivers electrical impulses to the heart to keep it beating in rhythm. This life-saving device is powered by the humble battery and so is destined, at some point, to run flat. The next step in the evolution of medical machines is therefore to forego the need for batteries, and tap into an energy source closer to home – namely the human body. Forget Robocop and think more Robo-guinea pig. Though this furry critter may seem far removed from a human being, when it comes to our ability to hear, we have lots in common. Scientists have therefore developed a prototype device, no bigger than a peanut, which draws energy from electrical impulses generated by the inner ear of a guinea pig. This remarkable piece of kit also measures these electrical impulses, called endocochlear potentials, and transmits this information across the airwaves. The device, called an endoelectronics board, is more affectionately referred to as an energy harvester. So how does it work? Sound is the key. More specifically, the apparatus mammals have evolved to detect sound. The inner ear is the business end of the mammalian hearing system, responsible for the physical detection of sound as well as balance.

Within the inner ear lies the cochlea - Greek for snail owing to its spiral shape. The cochlea picks up sound waves that enter the ear and converts them to changes in electrical impulses. When it comes to electrical activity, whether from a bolt of lightning, a pylon or even from an ear, it can be captured, collected and used to power any number of devices. The energy produced by the inner ear of the guinea pig was harvested by hooking up a small electronics board to the cochlea, using electrodes. The board contained a capacitor to store the energy and a radio transmitter to wirelessly send out information on the electrical potentials being generated. Initial experiments managed to keep this set-up running for five hours, sending wireless data feeds every minute or so, while leaving the hearing of these furry fellows intact. There is still much to troubleshoot, develop and importantly miniaturise, before testing in humans is possible. However should these devices prove successful the world of medical implants will be set to change. Be it pacemakers or hearing aids, without the need for cumbersome batteries the ‘nano’ tag synonymous with Apple may find itself hitched onto the end of many a medical device.

http://www.nature.com/nbt/journal/v30/n12/full/nbt.2394.html

By Alfie Christiansen

http://heyalfie.blogspot.com/

IONIC Issue 3 - A catalogue for “spelling mistakes” in cancer

A catalogue for “spelling mistakes” in cancer By Klodiana Jani - https://www.facebook.com/iidolk

lickety clack, clickety clack, clickety clack, ping…… ziiip. Who has never experienced the unique metallic sounds of a manual typewriter? With the tick of each key on the keyboard the typewriter leaves permanent impressions of letters upon a sheet of paper. Clickety clack, clickety clack, clickety clack, ping… pshsht. The sound of the hauled sheet out of the typewriter anticipates the verdict. The evidence displays the flow of incorruptible thoughts and the ever-present typing slips and spelling errors. There are no ways to rectify the meaningless words and phrases; they are eternally engraved onto that piece of paper. Whereas the repertoire of misspelled words produces titters of amusements, in contrast, the errors generated through the addition of incorrect DNA building blocks (nucleotides) during DNA replication (i.e., generation of near perfect copies of themselves) in cells lead to mutagenesis and possibly cancer. Within this cellular typewriter, the “typist”, so-called DNA polymerase, “spells out” the code imprinted on the template DNA and simultaneously matches it adding one nucleotide at a time building the new DNA strand. The end result is a newly synthesized, precise impression of the template’s code. In contrast to a typist in a hurry who might simply X-out the typos, the little “spelling” imperfections of DNA replication are monitored and corrected by multiple and complex repair processes. Yet, even these flawless cellular “proofreaders and editors” miss out errors, and thus generate sequence alterations known as mutations. When you displace T for N your “Tasty” dish becomes strangely “Nasty”. Instead, for example, the swapping of one nucleotide (DNA building blocks) during DNA replication, such as TTC to TTA, introduces a premature stop signal causing any resulting protein from the particular gene to be incomplete.

These abnormal products can have a damaging effect on cells and represent an underlying cause of cancer. Currently, scientists have catalogued the mutations that occur in 21 breast cancers, in essence mapping the cancers’ life history. By applying mathematical models they estimated that accumulation of the mutational processes within a cancer cell over time plays a crucial role in expansion of the breast cancer. The interplay between the DNA repair defects and nucleotide substitutions can increase the mutation rate of cancers as well as generate variation between them. They pinpointed five independent single- and double-nucleotide substitution processes that occur either simultaneously or during different phases of cancer progression. The substitution events also seem to be common within regions of the cancer genome that have undergone many mutations, known as ‘‘kataegis’’. Regions of kataegis seemingly vary between cancers but bear similarities in the pattern of nucleotide substitutions. The information on mutation variants presented in this study may allow scientists to assess the type of cancer, what stage it is at, and ultimately determine the specific mode of action. This may well be the beginning of wide-ranging opportunities for personalized treatment of patients with cancer.

Nik-Zainal, S., et al., The life history of 21 breast cancers. Cell, 2012. 149(5): p. 994-1007. Nik-Zainal, S., et al., Mutational processes molding the genomes of 21 breast cancers. Cell, 2012. 149(5): p. 979-93.

By David R Purnell MA

http://www.behance.net/ davidrpurnell

IONIC Issue 3 - Why the whey?

Why the whey? By Xavier Roeseler

can’t tell you how many times I’ve spotted a huge tub of WHEY protein on a friend’s kitchen shelf. What’s the deal with these vanilla, banana or cookies and cream flavoured protein shakes? We all know that eating or drinking anything to excess is not good. So I wonder, do these people really know how much protein they are ingesting? Whey protein – a by-product of the cheese industry – is processed and sold as a protein supplement commonly used by body-builders and, more recently, by teenagers wanting to buff-up quickly. Muscles are, for the most part, made up of protein. If a muscle is to get bigger, besides the importance of exercise, it will need protein. However, this is where the marketing of protein shakes wins and a misunderstanding creeps in: supplementing a diet with whey protein is not a prerequisite for building muscle. It’s obvious that someone who exercises many hours a week is likely to need more protein – and energy – than someone who barely does any exercise, but research indicates that protein supplements do not significantly help increase muscle build-up . In effect, the average diet provides enough protein to fuel the growing muscles of exercising individuals. The importance here is not which flavour you prefer, but how much protein you consume. The gastrointestinal tract can absorb about 6 grams of protein per hour , while the average scoop of whey – a standard dose – contains about 25 grams of protein.

As the shake takes about 1.5 hours to pass through the gastrointestinal tract, this means that only a maximum of roughly 9 grams of protein can be absorbed – less than half the protein contained in the drink.

By Lewis Stipic

Furthermore, the kidneys and liver are responsible for eliminating the toxic component (nitrogen) from proteins, which ends up in the urine. As such, any excessive protein in your system is broken down and makes both organs work harder. Considering that the average diet supplies enough protein to achieve exercise results, unnecessarily loading more protein in the form of shakes should be avoided unless you are properly monitoring your intake of protein, and – not to forget – fancy peeing half of your money down the drain. The UK’s Department of Health advises against consuming more than double the recommended daily intake of protein – 55.5g for men and 45g for women – which is not only derived from meat and dairy products, but from virtually all common foods and drinks. Another essential requirement for effective muscle build-up (in fact, the most important) is satisfying the energy needs of a hungry muscle. Energy stores in the muscle are often depleted after exercise and the body reacts quickly to restore them. Indeed, evidence indicates that the energy requirement of muscle after exercise exceeds the need for extra protein . So in effect, ensuring the diet provides enough energy – in the form of carbohydrates – should be the main priority when attempting to become Van Damme, and he is strong.

The key message here is that if buffing up is the goal: eat energy-rich foods and monitor your protein intake.

S. Bilsborough and N. Mann International Journal of Sport Nutrition and Exercise Metabolism 16 129-152 (2006).

In reality you probably won’t even need to drink that cookies and cream shake, despite it being super tasty – and boy, I love those flavourings.

Position of the American Dietetic Association, Dietitians of Canada, and the American College of Sports Medicine: Nutrition and Athletic Performance (2009)

Alert: Protein drinks (July 2010), Consumer Reports Magazine.

IONIC Issue 1 - Contents

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