Potential HIV "cure" set back

Back in Berlin 2007, an HIV-positive man called Timothy Ray Brown was given a bone marrow transplant using cells from a donor naturally genetically resistant to the virus. Brown, known as the "Berlin Patient", has remained free of the virus since the procedure. 

This incredible result was an impressive result of chance - Brown required a bone marrow transplant to treat leukemia, and the doctors managed to find a donor who not only matched close enough for the transplant to be accepted but carried a mutation in the CCR5 gene. In Europeans, this deletion mutation occurs in both copies of the gene in 1% of the population and significantly reduces the ability of the HIV virus to enter CD4+ T cells (a type of immune cell).

Six years after this procedure, and Brown still remains virus free. The success of this procedure led to great hopes in the treatment of HIV in patients all over the world, although the difficulty of finding donor who matched close enough for transplant and had the CCR5 mutation is an enormous hurdle to overcome.

Are our methods for detecting HIV sensitive enough?

Two HIV+ patients in Boston, one in 2008 and the other in 2010, also received bone marrow transplants to treat leukemia. However their donors did not have the resistance mutation. To the surprise of many doctors, the patients appeared virus free after the procedures and remained that way for years even after discontinuing antiretroviral medication.

Unfortunately now it has been announced that the virus has rebound in both patients. As well as being devastating news to the patients and their families, it has much wider repercussions in the medical world.

After receiving the transplants, the men underwent all sorts of test to measure their viral loads and none were able to detect HIV presence. Yet now it is clear the virus was there all along. This means that the tests we have are not good enough.

There is also the disturbing realisation that people previously described as "cured" may still have the virus lurking somewhere within them. Patients such as the infant cured of HIV will have to be carefully monitored for viral resurgence and those who have seen their viral load reduced to "none" on medication should refrain from discontinuing.

This is a huge set back in research into potential cures for HIV, the virus is even more persistent than previously thought and the design of more sensitive test for viral load is required urgently.

Paper warning of dangers of GM corn retracted

Back in September of last year, a paper published in the peer-reviewed journal Food and Chemical Toxicology linked the genetically modified corn NK603 to adverse health effects in rats. Although previous long term studies had shown no ill-effects of a diet of GM crops, these two year long study disturbingly showed higher rate of cancer and reduced lifespan of rats fed on NK603 in comparison to the control groups. Publication of these findings led to further public fear and confusion over the actual risk of GM crops.

At the time, many scientists questioned the reliability of the paper "Long-term toxicity of a Roundup herbicide and a Roundup-tolerant genetically modified maize". Cited were issues with the methodology, very low statistical significance linked to small sample size and, significantly, that the strain of rats used in the study (known as Sprague-Dawley rats) are incredibly susceptible to the spontaneous growth of tumors as they age. The $1.4 million study was also plagued with accusations of bias, with conflicts of interests on both the sides of its supporters and those who petitioned for its removal from the journal.

NK603 is resistant to the herbicide glyphosate
and approved for human consumption

On the 28th November 2013 however, the journal announced the redaction of the paper, following analysis of the data and an investigation into the peer-review process it went through. In a press conference, Corinne Lepage, a Member of the European Parliament and a founding member of one of the funding bodies behind the paper, explained that the retraction of the paper "will not make these questions [about the safety of GM crops] disappear".

It is entirely necessary that further studies into the possible risks of GM crops (and the benefits that they generate too) are carried out. However it is vital that these are performed with the best scientific rigor, to prevent further confusion for the public and embarrassment to those working in these fields.

Removal of the paper is unlikely to dampen the public concern over GM crops that its initial publication generated. Like the now decades-old vaccine scares, the general media finds it much easier to promote scare stories involving small, unreliable (or, in some terrible cases, fabricated) data than to rationally and delicately explain finding to the lay-person. This means that it is on the shoulders of the scientific community to ethically and without bias report real findings in such a way that any rational person is able to determine their reliability for themselves.

Ancient life: the oldest living organisms

 I would like to begin by making it clear that Ming the clam was not killed with any malice. Scientists at Bangor University were studying the ocean quahog clams (Arctica islandica) to investigate both climate changes in the ocean and the process of aging. It was only upon Ming's unfortunate death that its remarkable age was known.

Ming (so named as it would have begun it's life at the time of the Chinese Ming dynasty) has been making headlines recently as the oldest individual animal who's age could be accurately recorded, making it to around 507 years before being dredged up off the coast of Iceland. This species of clam are notoriously long-lived, in all probability Ming's much older relatives are still living content lives on the ocean floor.

Longevity in individual animals is of great interest to scientists. As we as a species are living longer, it benefits us to see how other creatures cope with the metabolic stress of lives spanning centuries.

Adwaita the Giant Tortoise reached 255 years

Giant tortoises are probably the most well known terrestrial animals to hit the two century mark, the most famous being Adwaita the male Aldabra Giant Tortoise. When he died in the Alipore Zoological Gardens in India in 2006 his age was estimated at 255 years, putting the average Blue Peter pet to shame. A pet of Clive of India, he was moved to the zoo in 1875, over a 100 years after his initial owner's suicide.

For marine animals however a couple of centuries of life is not uncommon. Specimens of black corals (Antipatharia) have been identified as the oldest continuously living animal on the planet - 4,265 years old being the key number here. To give a sense of scale, this coral began life in the late Bronze age, a millennium before the human population even reached 50 million.

On land, individual plants have become famous for their age. The UK boasts two of the top ten oldest individual trees in the world, with the Fortingall Yew (Perthshire, Scotland) clocking in at around 2500 years and the Llangernyw Yew ( Llangernyw, North Wales) thought to be over 4000 years old. Both are Taxus baccata, an ancient yew species not uncommon in European churchyards.

The exact location of the single most ancient individual tree in the world is kept secret to protect it from overenthusiastic tourists. It is know though that there is a Great Basin Bristlecone Pine (Pinus longaeva) who's ring count put it at 5063 years old. Located somewhere in the White Mountains of California, this tree was growing at the same time the pyramids were constructed.

Once we leave the world of individual creatures, longevity is expected. The world of colonial organisms is fascinating, from the world's largest organism (an individual fungus of the species Armillaria solidipes that covers 2,384 acres beneath the Malheur National Forest) to pine colonies in Tasmania estimated at 10,000 years old (individuals within the colony living to over 3,000 years).

These colonies can be fully connected via their root systems, and whilst at any given time only a fraction of the colony is "alive" in the sense of having an active metabolism, the colony is one genetically identical system. This can make calculating the age of colonial plant systems difficult, especially as the ages get more and more extreme, due to the many climate changes that they have likely survived through.

Pando - a colonal colony of Quaking Aspen

In the Fishlake National Forest, Utah, lives a colony know as The Trembling Giant, or Pando (latin for "I spread"). This clonal colony covers 106 acres, weighs 5900 tonnes, and has over 40,000 trunks emerging from the ground. All this is interconnected by a single root system. It is this one root system that allows Pando to break the record for oldest organism, estimated at 80,000 years old (some recent debate suggests it may be even older than that).

For those of you struggling to imagine just how long those same Quaking Aspen(Populus tremuloides) roots have been living and growing, eighty thousand years ago we as a species were thinking about leaving continental Africa.

These organisms have grown and thrived through millennia of human progress and spread. Likely they will continue well after we are done on this planet - as long as we can leave them well enough alone.

@imogenwrote

The first immortal line

Henrietta Lacks

Henrietta Lacks did not lead a particularly remarkable life. Born in Roanoke, Virginia in 1920 as Loretta Pleasant, at 4 years old she moved to live in a log cabin with her grandfather and cousin, Day Lacks. By the age of 19 she had had two children with her cousin and went on to marry him shortly before her 21st birthday. 

Henrietta Lacks

That year, she moved with her family to Maryland, where her husband Day got a job at the steel mill. Henrietta and Day went on to have another three children in the next nine years. After giving birth to her last child, a boy named Joseph, Henrietta was in significant pain and bleeding profusely. A local doctor tested her for syphilis, and when that came back negative sent her to John Hopkins Hospital – the only hospital in the area that would treat black patients.

At the hospital, Dr Howard Jones examined Henrietta, performed a biopsy on a lump on her cervix and found she was suffering from a malignant epidermoid carcinoma of the cervix (cervical cancer) and treated her with radium tube inserts. During these radiation treatments, further samples of Henrietta’s cervix were taken – both from healthy and cancerous tissues – without her permission.

Eight months after her initial admission to the hospital, Henrietta Lacks died through complications caused by the cancer that had now spread throughout her body. She was buried without a headstone, near to her mother’s grave in Halifax County, Virginia at the age of 31.

The sample taken from the cancerous growth in Henrietta’s cervix was given to George Otto Gey, who was able to grow the cells in vitro. These were the first human cells ever to be successfully propagated in a laboratory and were to have a profound impact on medical research. The cells were named HeLa cells, in an attempt to maintain Henrietta Larks’ anonymity. However within a few years, she was identified in the press. Gey did not attempt to patent the cell line; instead he donated the cells and the processes necessary to grow them to researchers simple for the sake of science and to benefit medical advances.

In the early 1950s, polio epidemics were devastating the USA. In 1952, over 57, 000 cases were reported, leading to 3,145 deaths and 21, 269 cases of disabling paralysis. Dr Jonas Salk was dedicated to finding a way to prevent is horrifically debilitating virus, and required a line of cells, available in large volume, to test his new vaccine before clinical trials. HeLa cells were observed to be susceptible to poliomyelitis and are otherwise stable in culture. The National Foundation for Infantile Paralysis funded the establishment of a cell culture factory at Tuskegee University to supply Salk and other medical researchers with large quantities of the cells.

By 1955, Salk’s vaccine was declared safe and effective and rolled out across the USA, Canada Australia and Western Europe. Within two years, 100 million doses had been given throughout the USA alone, and many countries were reporting virtually no new cases of infection by poliomyslitis. Last year only 291 cases were reported across the whole world, leading to suggestions that soon polio may be eradicated completely.

HeLa cells have been used for research into many different areas of disease, with over 60,000 articles published on research performed on this cell line. From AIDS to hormone signalling to the effects of radiation, cells descended from those taken from Henrietta Lacks in 1951 have had a huge impact on science and are still being used today in research into gene changes and behaviours in cancer.

Henrietta Lacks’ cervical cancer was caused by an infection by the human papillomavirus 18 (for which there is now a vaccine). The virus transferred some of its own genome into that of the cells, causing the original HeLa line cells to have probably 82 chromosomes, rather than the normal 46. This cannot be known for sure, as due to the constant rapid and uneven division that is the nature of cancer cells, the genome of the HeLa cells in incredibly unstable. HeLa cells have also been seen to be capable of “infecting” other cell lines grown in the same laboratory, leading to the suspicion that several other established cell lines may now contain HeLa cells.

Due to the exceptional nature of the HeLa cells, in 1991 evolutionary biologist Leigh Van Valen proposed that they be defined as a new species, Helacyton gartleri. However this definition has not been accepted by the wider scientific community and HeLa cells remain considered as human.

For the Lacks’ family, since discovering in the 1970s that their mother’s cells had become an essential research tool, the continual growth of these cells (current estimates run at 20 tonnes of HeLa cells grown over the last 60 years) and the patenting of discoveries made using them have been a sore point. In the 1980s the family’s medical records were published without their consent and the complete HeLa line genome was sequenced and published on 11th March 2013, however it has since been taken down.

Whist in the 1950s, permission to harvest cells from a patient was not required, the commercialisation of one person’s cells had never occurred before. Whilst in 1990, the Supreme Court in California decreed that discarded cells or tissues are no longer a person’s property, some ethical issues remain with the use of the HeLa cell line. A ruling earlier this year had thankfully prevented the patenting of unmodified genes, stopping any one company or person profiting from all research done with these cells.

As of August this year, it was decided in a meeting with Henrietta Lacks’ surviving family that data on the HeLa cells’ genome would remain available under restricted access. Papers that utilise the HeLa cells will now recognise Henrietta and the contribution that her cells have made to the research. A committee has been formed, which includes members of the Lacks family, who will regulate access to the DNA code of the cells, hopefully allowing the cell lines to remain in medical research use for many years to come.

Henrietta Lacks has become in some way immortal. Her contribution to medicine in the last sixty years has been immense. In 2010, Dr Roland Pattilo donated a tombstone for Lacks, placed near where she is buried, reading:

“Henrietta Lacks, August 01, 1920-October 04, 1951.
In loving memory of a phenomenal woman, wife and mother who touched the lives of many.
Here lies Henrietta Lacks (HeLa). Her immortal cells will continue to help mankind forever.
Eternal Love and Admiration, From Your Family”

Later published on Nouse Online

The future is in your genes

Phenylketonuria (PKU) is a genetic disorder that causes the build-up of the amino acid phenylalanine in the blood. Although babies born with this disorder initially appear normal and healthy, after a few months the children develop permanent intellectual disability, with delayed development and seizures frequently occurring. PKU is, however, symptomless if infants are given the correct treatment and the child will grow to a normal, healthy adult.

Many serious genetic diseases are initially symptomless but benefit greatly from early intervention. This is why all newborn babies in the UK are given a blood spot screening test; this checks for diseases such as PKU, cystic fibrosis and sick cell disease. These screening programs allow families either some piece of mind or time to prepare for the future of their child who may require specialised care.

The costs of sequencing DNA have, in recent years, dropped remarkably. The newborn blood spot test costs in the region of £65 and to sequence an entire human genome in now a little under £3500. A lot of the human genome however does not code for proteins (faulty proteins being the most likely cause of genetic disorders) – a vast amount of the human, around 99%, regulates the activity of the coding 1%, plays a structural role or has a currently unknown function; it is unlikely to be all completely unnecessary “junk”. The 1% of the genome that does actually encode proteins, the exome, can be sequenced for around £650, with remarkable accuracy.

Would you like to know if you were going to get Alzheimers? ©Tom Varco; Image credit: WikimediaCommons

Whilst this focus on prices may seem cold and calculating, the cost of research plays a major role in diagnoses. A child suffering from a mysterious illness twenty years ago, say a case of inflammatory bowel disease that was causing the gut to leak into the abdomen, may well have undergone years of intensive surgery with no successful outcomes. But now, as in the case of Nicholas Volker, a full sequencing of his genome allowed the cause to be identified as a mutation in theXIAP gene, leading to a leukaemia-like disorder. One bone marrow transplant later and Nicholas is able to lead a healthy life.

Exome sequencing is allowing patients with rare disorders to finally get the diagnosis that they need, both to receive treatment and plan their lives correctly – for example the tragic case of an infant girl with late stage liver disease, that was found to be caused by a series of mutations that would soon lead to fatal neurodegeneration and heart failure, this spared the infant the further trauma of a liver transplant and meant that her family was able to simply keep her comfortable for her last days. Although these diseases are rare, each one affecting maybe a handful of people across the whole world, rare diseases add up. Taken all together, rare hereditary diseases affect 25 million people in the United States alone.

Rare hereditary diseases affect 25 million people in the United States

Sequencing, for these patients, means a diagnosis rather than just treatment of symptoms. Here is it used for an explanation, not as a forecast; but this is what it could be. With sequencing costs reducing every year, it may not be long until all newborns have their entire exomes sequenced at birth, or until you may go to your doctors and ask what your future health may hold for you.

Children of patients suffering from Huntington’s diseaseare already offered a test to see if they carry it themselves; if they are, they may wish to avoid passing it on should they also have children. In the case of Huntington’s, carrying a faulting a faulty HTT guarantees that you will suffer from the neurodegenerative disorder. However few other diseases are quite so clear cut.

When Angelina Jolie found out she had a mutation in her BRCA1 gene, increasing her risk of breast cancer to 65-87% (calculations are dependent on the details of the mutation) she decided to undergo a double mastectomy, reducing her risk to getting breast cancer to <5 able="" again="" an="" and="" being="" do="" future="" genetic="" have="" health.="" here="" impact="" incredibly="" invoke="" knowing="" may="" mutations="" on="" one="" positive="" reduce="" risk="" s="" something="" the="" they="" to="">

But would you like to know if you had a copy of a variant APOE4 gene, doubling the risk of Alzheimer’s disease? Alzheimer’s is currently incurable, and can leads to years of suffering, both to the patients and their families. Many people may feel uncomfortable knowing that such a fate is likely to await them, yet others would argue that this would allow those at high risk to prepare better for their future.

Pre-emptive treatments, from statins given to those with moderately high cholesterol to a half aspirin a day for those at risk to blood clots, have been with us a long time. Perhaps it is time that these measures become tailored to each individual, dependant in their genetic profiles. In countries with private health care however, this is a sticking point. Insurance premiums for those deemed high risk for various diseases would do through the roof, likely preventing health care access to those who actually need it most.

The NHS too, may be unable to support such a system. Lifetime treatments become incredibly expensive, especially for a disease that may or may not have come to pass. Could a “life time risk” cut-off be put in place? How high would your disease risk have to be to quality for the treatment? 40%? 80%?

Currently, however, exome sequencing is only an option for those suffering from rare diseases. The human genome contains so many variants from person to person that evaluating risk for many complicated combinations of mutations will require vast amounts of in-depth knowledge of our genetic code, as the signal-to-noise ratio of mutations is still far too high to be clear. Drugs companies too will need to change their stance. Instead of making universal treatments worth billions of dollars, every drug will have to be targeted for individuals.

Ethical issues come in to play here too. Would you counsel those carrying many risky mutations to avoid having children, and those with particularly health codes to donate sperm and eggs? These are extreme fears, and cries that exome profiling will lead to eugenics have already been made, but likewise could a doctor morally allow two people to have a child if it meant that child would suffer from a debilitating disease.

These barriers, both ethical and financial stand still stand in the way of genetic health profiling for all, and many years of debates are yet to come as we try to navigate out way through the rapidly changing landscaper of modern medicine.

Published on The Yorker Online

IT Girl - Hard drives, heavy lifting and hammocks

The more astute reader may have noticed the slight time lag between when these articles are written and when they are published. As of now, it is the first Monday of August and the weather is bloody miserable. Having spent the morning trudging around with masses of A3 paper, the IT girl resembles a drowned rat and is dripping on her keyboard.

Weather-based trauma aside, my first payday has come and my National Insurance contribution has flown off. I don't feel particularly hard done by in that respect, as I won't be paying tax on my stipend for the next four years and I really have managed to get a lot of NHS for my contributions (around £100) so far.

The task of recent days has been to scrap a large number of PCs and bits of equipment that are well past their use-by dates. Mostly, this means those beige Viglen desktops with 1GB memory and their accompanying CRT screens. There are a surprising number of these on the site, considering how a lot of the science they do here requires masses of computing power and graphic software. I suppose people just don't like change.

When machines get disposed of, the hard drives must be removed and stored (and eventually thoroughly destroyed); a horribly dirty task. Not only are the innards of most peoples' computers filled with dust and hair, but one even had a spider in it. I beg of you all, take a mini-vacuum to your desktop at least one a year...

Other than the general filth, the biggest problem with these very old machines is their sheer weight. I cannot physically lift them, or the Nokia CRT screens that have been know to accompany them (apparently Nokia made computer screens back in the day). Under the health and safety regulations, I am apparently not even allowed to lift something over 5.5kg without wearing heavy boots. I may be quite a feeble example of humanity but that does seem rather low, especially considering our pet cat weighs more than that...

There is, however, a simple solution to this problem. The easiest way I have found to move heavy object from an office to the workshop (a ground floor room in the next building along) is to bat my eyelashes and look as pathetic as possible in a room full of men. Feminist it may not be, but it saves my back and gives everyone else a chance to stretch their legs...

Official work hammock.

Working 9 to 5, throughout the entirety of the long summer hols is, quite frankly, exhausting. All I really want to do is laze around in the sun and occasionally paddle in the river. However, rents must be paid and all that, so here I am. However, a brief lunchtime-exploitation of the site with a couple of fellow summer students lead to the discovery of hammocks in a small wooded area near a wind turbine.

Who put the hammocks there, and why, we are yet to decipher. Though this week perhaps the weather is far from ideal, hopefully the occasional long lunch spent reclined in comfort in the shade of the trees will go some way to making up a holiday.

Probably not.

Follow me on Twitter: @ImogenWrote

IT Girl - Graduation, guided tours and the generation gap

Pity the poor IT Girl, she is nobly cracking on with composing a witty blog entry despite the temperature outside passing the 30°C mark. Being trapped in a powerfully air conditioned office for most of the day has prevented me from enjoying the weather, as river swimming and BBQ-ing opportunities are few and far between on the site.

Good news, I am now officially wise and knowledgeable; I can probably put letters after my name. I even have an A4 piece of cream(ish) paper to prove so. On the 10th I took some holiday time off and toddled up to York again. Kitted out in a rather dashing grey gown and stylish hat, I trotted up on stage in front of many friends, acquaintances and course-mates who I'd never seen before to have my hand shaken with alarming vigor. The (thankfully quite brief) ceremony was followed swiftly by a party in the department and many, many attempts to take jumping-in-the-air photos. I ruined most of them. I fly like a caterpillar.

Monday morning, however, I was back at work looking up coffee machines and wondering if I can put one on my desk. Preferably with an IV drip directly into my artery. However I perked up when I got an email inviting me and the other summer students on a guided tour of Vulcan. Hoping to either meet a Roman deity or see a far distant planet with a striking resemblance to a 1970s film set, I wandered around the site til I found the starting point.

The CLF’s Vulcan Petawatt laser is one of the most powerful in the world and produces pulses of super intense light that are fired at tiny solid targets.

Vulcan, it turns out, is a massive laser. A really massive laser. Several rooms worth of really massive laser.

The Vulcan Petawatt laser is one of five laser systems within The Central Laser Facility, at the STFC's Rutherford Appleton Laboratory. After the requisite physics explanations (which I bravely endeavored to follow) we all trouped around the systems, peering in through very thick coloured glass, and entered a massive lead-lined concrete bunker. This contained the chamber where the laser is used to make things explode. Which is pretty cool. The laser is used mostly for studying the behavior of plasma - the fourth state (after solid, liquid and gas) - but conversation soon turned to how effective the bunker would be as a last resort location in a zombie apocalypse. Vulcan and the other laser systems on site are used for a wide range of science, from studying organic samples to investigating nuclear fission.

I have now met quite a few summer and sandwich year students on the site, with lunchtimes now spent sitting in large circles under trees and contemplating forming a rounders team to take on the grad students. It is nice to spend time with other people younger than Microsoft, even if explaining my job and what I am doing on site is a wee bit embarrassing. It seems that "bio" degrees are really the bottom of the technology ladder.

people younger than Microsoft

That being said, I am pretty lucky. The people I am working with have the patience of saints. They happily explain what I am meant to be doing, and how to do it, without any jargon and are very forgiving when it takes me twenty minutes to find a room that is actually just down the corridor. I am now generally self-sufficient on some tasks (mainly printer repair and Windows 7 upgrades) and have got paperwork filing down pat. Over the next few weeks I'll hopefully get to see more of the site, including the Diamond Synchrotron, and actually figure out what one can do with cmd.exe.

Published on The Yorker

Bugs on the brain

Pity poor Rochelle Harris who recently returned from Peru with a mild headache that turned out to be caused by 10 maggots residing in her ear canal, grown from eggs deposited there by a rather intrepid New World screwworm fly. The maggots burrowed a hole of 12mm into her inner ear, but managed to be removed by doctors who smothered the bugs with olive oil, forcing them to come to the surface. Her story has now been reported with rather macabre glee by all branches of the online media and Harris has featured on a Discovery Channel documentary series called ‘Bugs, Bites and Parasites’.

The New World screwworm fly, or Cochliomyia, are a genus of blowflies, the most common two species being species Cochliomyia hominivorax andCochliomyia macellaria. Cochliomyia hominivorax is rather an unpleasant customer. With a preference for living flesh and the ability to dig itself in deep into humans and livestock alike, the United States Department of Agriculture led a very focused campaign to eliminate the fly from the USA. Beginning in the 1950s, huge numbers of sterlie male flies were released in Florida. This exploited the nature of female hominivorax , which are only capable of mating and reproducing once in their lifetimes. Thus reproduction rates plummeted and now Cochliomyia hominivorax could be considered to be eliminated from the USA and Mexico, though regular checks of livestock must be carried out, to prevent the species from reestablishing itself.

In general, C. macellaria are of little threat to healthy humans and livestock as they are only capable of consuming already necrotic tissue.The species had a brief career in surgical maggot therapy, however the stigma of being part of the screwworm family proved too much (that and their annoying tendency to reinfect healing wounds) and they were replaced by the more easily controlled blowfly Lucilia sericata.

stigma of being part of the screwworm family proved too much

The activity of maggots has been used to treat wounds for thousands of years, as they eat away infected and necrotic tissue, leaving the healthy flesh to heal. Although it lost popularity during the second world war due to the rise of penicillin, some hospitals still used the technique, specifically using specially sterilized Lucilia sericata maggots, to heal deep burns and abscesses right up to the 1990s before it was phased out completely.

In recent years however, maggot therapy has come back into play. As of 2005, any doctor in the USA or most of western Europe can prescribe maggot therapy to treat a patient. This is due to the massive rise in antibiotic resistant bacterial infections occurring in hospitals throughout the western world.

Lucilia sericata

Methicillin-resistant Staphylococcus aureus (MRSA) causes the formation of abscesses, wide-spread sepsis and necrosis of infected tissues. Early treatment with an arsenal of new generation antibiotics (often with terrible side-effects) can prevent the spread of the bacteria,especially protecting the patient's lungs from deep infections. However, once necrotic sores have formed and the bacteria have colonised the surrounding tissues, necrotizing fasciitis (aka "flesh-eating" skin infection) or pyomyositis (skeletal bone infection) can set in.

This is where Lucilia sericata maggots shine. Not only do they consume all rotting tissue, thus reducing further bacterial spread, research from Swansea University has identified two antibacterial compounds excreted by L. sericatawhich are effective in the disruption of growth of several species of bacteria, including 12 MRSA strains. Maggot slime extracted and tested in the lab was shown to powerful enough to exhibit strong antimicrobial properties whilst in clinical use they are capable of ridding up to 92% of Staphylococcus soft tissue infections.

Researchers are currently looking into refining larvae slime (hoping to achieve the same antimicrobial effect without the whole maggots-in-an-open-wound deal) to extract and purify the antimicrobial compounds to a clinical standard. Til then we must be grateful to our blowfly friend, not only have they treated battlefield wounds since the days of the Roman Empire, but their powerful drive not to share their lunch has meant that they have evolved to be what may become the next important species in medicine.

And please, do not self medicate with maggots at home.

@ImogenWrote

Published on The Yorker

IT Girl – Fashion, fitness and fixing things

headscarves, the whole lot. However, as a lowly IT girl, the only resemblance I have to my heroines of the silent movies is a (slightly lopsided) bob and a penchant for gin cocktails.

You see fashion, in the world of the IT girl, is rather less fun. There are no cigarette holders or strings of pearls and certainly no stockings rolled down to the knee. Clothing must be “practical” (shudder) in case desks need to be clambered over to access misbehaving printers and the like. My shoes must be comfortable and my makeup must not startle the engineers. Oh, and I am not allowed to wear my dungarees – not even my smart pair.

This has limited my wardrobe somewhat. My current working day ensembles tend to resemble pajamas (leggings, vests, baggy jumpers) which does little to improve my post-lunch napping tendencies. As for comfortable shoes, if I could get any closer to actually wearing slippers I would.

I am loath to admit it, but the comfortable shoe plays a vital, if unattractive, role in my day. My job involves rather a lot of walking about, the site is large and things must be carried from one end of it to the next. Quite often this necessitates the use of the IT girls’ natural enemy: The Yellow Trolley.

The Yellow Trolley, unloaded, appears to weigh almost as much as me, it has runners that stick out right at ankle height and four wheels, each of different sizes and each with a sense of free will rare to an inanimate object. Adventures with TYT often result in bruising and swearing and multiple sudden encounters with door-frames.

TYT and I travel around 5km a day around the site, with me doing at least another three without the sadistic thing. This is a horrific amount of exercise, but thankfully it is well balanced out by the unremitting supply of free food. Not only do I get jam doughnuts and chocolate biscuits on tap in the office, but I am frequently offered sweets, fruit and snacks on my travels to repair hardware. Unfortunately the continuous stream of junk food, combined with long distance marches in the hot sun and ridiculous levels of air con really do play havoc on an IT girl’s complexion.

Blending in with the IT crowd is turning out not to be so hard really, despite my lack of interest in Wimbledon limiting the conversation somewhat. People in the department are friendly, helpful and surprisingly forgiving of my general ineptitude. They are also very interested in what they do and incredibly keen on explaining it to me. So far I have found out what the Vulcan Laser does and have been promised a tour of the Diamond synchrotron - this is all very exciting to my little nerdy heart.

Now I have been an IT girl for a whole seven hardworking days and actually do appear to be capable of fixing things. This is quite reassuring to my line manager, who I feel was rather worried upon my arrival when I couldn't get my desktop PC to turn on. Things that I have been able to repair in one way or another include a CD drive that could no longer write CDs (I didn’t realise people still did that either) and a printer that had an annoying squeak to it (the squeaking ceased once I jammed a lolly stick between the two offending pieces of plastic).

My repair approach may be a little ad hoc, but it is effective. The greatest fix that I have managed though, is securing five days paid leave over the summer, along with a four day bank holiday weekend. This mean that they will pay me to go to my graduation. Really, being an IT girl could be much, much worse.

Published on The Yorker

IT Girl – An introduction to the rest of my summer

don’t understand computers. I should make that clear now. Not only do I not understand them, but I distrust and slightly fear the bloody things too. I am pretty sure my laptop is running a vendetta against my coursework and any university desktop I approach seems to commit hara-kiri before I can complete the most simple of tasks.

With this is mind, I am spending my last ever long summer holiday working 9-5 for 11 weeks in an IT support service. But this is not just your bog-standard IT support service; this is one that runs in a technology department within a massive campus full of engineers and physicist. When they need IT help, you know something isvery wrong.

But Imogen, I hear you ask, you are a biochemist! What would possess you to take such a job? Well, like most things I do in life, it seemed like a good idea at the time. All my previous summer jobs (almost all summer, every summer, since I was in sixth form) have been in a biochemistry lab; it is time I saw some more of the world of science before I commit the next three years of my life to just one field. The theory is quite simple, I really must learn about computers to get on and this is the perfect opportunity to get hands on experience working with the wretched things. After all, one must know one’s enemy and all that.

And so, with this in mind, I was up and out of bed at the crack of 7:30am on Monday morning and was soon being driven out of the city by my (remarkably chipper for that time of morning) mother. No, she is not my personal taxi service, she just happens to work on the site too.

On arrival at the site, I was swiftly whisked through reception, given a yellow lanyard to make clear my status as “visitor” and “not to be trusted”, dragged through a maze of buildings and into a room that smelt of stale caffeine and nervous engineering students.

a room that smelt of stale caffeine and nervous engineering students

The source of the former turned out to be a free(!) coffee machine, which I quickly got myself acquainted with whilst I surveyed the crowd that was generating the latter.

After the standard round of introductions, it was clear that we were all here for summer placements or year-out courses. Networking opportunities were mostly overlooked in favour of trying to deconstruct the coffee machine to get a stronger espresso and comparing dissertation projects. I couldn’t be sure what went over worse, my placement in IT support or the “bio” in my degree title.

However, a riveting two and a half hour health and safety lecture soon took my mind off that. All clued up to what to go in case of asbestos (don’t touch it) and klaxons sounding (enter the nearest “substantial” building - scary) I headed up to my new office. It only took three wrong rooms until I found my new boss and was set up at my massive desk, with two windows and four monitors. Logging in barely took ten minutes and soon I was kitted out with my official ID card and administrative access to an alarming amount of computing power.

Thankfully I didn't have to deal with anything involving a server yet and instead I spent the next few hours pushing a trolley full of computer parts around seemingly unending corridors, fixing mechanical faults in printers and playing with the kit in the metrology lab – they have a photopolymer 3D printer and all sorts of exciting devices.

By the end of the working day I had walked 8km around the site, eaten my lunch alone as I couldn’t find the main canteen and driven the trolley into a small brick wall that I swear wasn’t there half a second before. I am still yet to interact with anyone within two decades of my age here; all the summer students appear to be kept individually trapped in small rooms where the damage that they can do is limited.

I was shattered and, for the first time in a while, extremely grateful to be spending the whole summer living at home. Nothing quite like a massive plate of homemade spaghetti Bolognese to perk up the end of the day.

@ImogenWrote

@YorkerComment

Publish online at The Yorker 03/07/2013

Science Highlights of the Week - Sixth Edition

Stubble is Sexy.

A study in Australia has investigated how much of a man's socio-sexual standing, as perceived by woman and other men, is based around their facial hair.

Photographs of ten men were taken when they were clean shaven, after five days of stubble growth, ten days and then after six weeks of growth (full beard). These images were shown to a mixed group of volunteers who rated each photo for the qualities of sexual attractiveness, general health, masculinity and parenting abilities.

The study found that both men and woman ranked the fully bearded images as highest for masculinity, parenting abilities and health. The perception of three qualities were seen to increase linearly with facial hair growth.

However, whilst the men reckoned the fully bearded guys were also the most attractive, women ranked men with thick stubble (10 days of growth) as most sexually appealing. This perception could be linked to previous studies which have found that women tend to judge men with much thicker facial hair as more aggressive.

Gonorrhea is Getting Serious.

Antibiotic resistance is a rapidly increasing (and well documented) problem in many diseases and with over 17, 000 gonorrhea infections identified and treated in the UK last year it is no surprise that the drugs are beginning to fail.

The antibiotic ceftriaxone is the only drug used to successfully treat the common STI but cases of gonorrhea recorded in Canada, America and parts of Europe that have not responded to antibiotic treatment are on the rise. Currently, about 6% of gonorrhea infections diagnosed in Canada are not treatable with available antibiotics.

Untreated gonorrhea can lead to serious complications in both men and women as the bacteria can spread through the body, causing pelvic inflammatory disease and eventually affecting joints and heart valves. In women, long term infections can lead to infertility.

Whilst cases of resistant infections are still low, but it has been predicted that by 2015 these cases will be more common than the treatable strains. It is not likely that a new antibiotic will be developed by this time.

The Evolution of the Penis

Four researchers at the University of Georgia have published a study of how the evolution of the human penis has been affected by mate selection by females. In comparison to other closely related primates, the human penis is disproportionately large. From an evolutionary stand point, this is an interesting phenomenon as it seems selection for reproduction was precopulatory rather than post-, i. e. reproductive selection was not just dependent on sperm survival but on what the paper has described as "cryptic female choice".

There are many factors that determine mate choice and this study focused purely on the visual. The study involved the use of artificially generated images of men of varying heights, penis size and hips:shoulders ratios - in total 343 different figures were produced. These were shown to heterosexual women who rated their attractiveness as sexual partners (and before you start wondering, all the penises depicted in the study were flaccid).

Taller males with wider shoulders were consistently selected as most attractive, independent of penis size. However once individual factors were taken into account, for example, at one given hip:shoulder ratio, penis size had a small but significant increase in perceived attractiveness. Interestingly, after controlling for hip:shoulder ratio, penis size elevated relative attractiveness far more strongly for taller men than for shorter ones.

The relationship between penis size and attractiveness was not linear; a considerably larger-than-average penis (more than 2 standard deviations from the average of 8.9cm) made for a less attractive figure.

Most research into female attraction has shown that height and wide shoulders are the most important factors in mate selection but the findings in this paper does suggest that selection on penis size was potentially as strong as selection on stature back before humans began to habitually wear clothing.

Science Highlights of the Week - The Fifth Edition

Scientists Try To Make Mice Puke

Rodents are unable to vomit, a response which is seen in almost all other mammalian species. Researchers at the University of Pittsburghnoted this, and looked it to the phenomenon.

A range of rodents (from mice and rats to mountain beavers) were given chemicals that would induce vomiting in other mammals. However no retching or vomiting was seen.

It is thought that a mixture of anatomical constraints (the rodent aesophagus is very long and not fully muscled) and an absent neurological component is behind this odd trait.

An Alternative Approach Against MRSA

Antibiotic resistance is one of the greatest challenges modern medicine is going to have to face. New antibiotic drugs are expensive to develop and few have been produced in recent years.

Scientists at the Rockefeller University’s Laboratory of Bacterial Pathogenesis and Immunology have shown that the use of bacteriophages (think viruses that attack bacteria) as a means of infection control.

So far, they have seen success in curing mice infected with either MRSA or Anthrax using this approach without development of antibacterial resistance being seen. Whilst human clinical trials are a long way off at this time, this is a very promising step towards the next generation of antimicrobial drugs.

Paranoid? So is Everyone Else.

In a paper published in Current Biology, researchers observed that people would assume that the gaze of others was directed at them, especially in low lighting or when the other was wearing sunglasses.

This is possibly because we have evolved, as a species, to utilise gaze to determine if we are being faced by friend or foe. The direction of another's gaze is used to provide insight into their focus of interest, and simple ego assumes that we are the most interesting thing around.

What's wrong, honey?

Using fMRI scans, researchers have seen that men are, in fact, less able to read a woman emotional states that they are another man's. It seems that this may be due to a difference in brain activity between the genders.

Participants in the study were shown different faces and asked to judge the mood that that person was feeling as their brains was watched for activity. The function of the amygdala is thought to be key in empathy, but when men looked at women's faces, there was not as much neural activity seen in that location. Yet when they looked at men's images, activity was seen and more correct answers were given.

Careful, Your Gender Gap is Showing

When Elise Andrew, the owner of the Facebook page "I fucking love science" posted a link to her personal twitter account on the page, a lot of people got over excited. Whilst some of them, like me, were keen to expand their exposure to rather marvelous puns about transport proteins (oh come on, it is funny), an alarming number of Facebook commentators took it upon themselves to be shocked about her gender.

STEM gender gap - An unnecessary barrier ©Doctree; Image credit: Wikimedia Commons

Statements ranged from the confused: "Dude ur a chick? Wtf???!?", the confusing:"MUST BE A LESBIAN! just kidding", to the pretty insulting:"Please sell this page to a male.". And not all were, it seems, made in jest.

So why is there this alarm that an incredibly popular page focused on the wonderful world of science could be run by a woman?

Gender bias across all STEM subjects is a still a massive problem. It is a problem seen all the way from how lab partners treat each other in high school chemistry lessons to who gets what job and which pay packet well into adulthood.

The general idea that women neither like nor do well in math and science has been widely accepted by many people and for many years. Girls are meant to prefer the "arty" subjects, they like fiction and writing comprehension, let boys play with the chemicals and the machines. And yet, when interviewed and assessed in primary school, girls get higher grades and are more likely to express an interest in maths or science than boys.

The problems seem to begin in high school as girls are drip fed the idea that they are somehow under-qualified to perform scientific tasks. A study performed by Psychology Today, 72% of 11 year old girls felt that they were confident in their STEM skills, but only 55% of 15 year olds described themselves as confident. However when comparing the results of standardized test scores no loss in actual ability was seen.

This loss of self-confidence leads many to forsake the science subjects that they may have performed very well in at GSCE and choose A levels in areas where they haven't been convinced that they are innately unable to perform in.

This trend follows into higher education and post-graduate education choices. Growing up I was lucky, I come from a family of scientists across all fields and went to an all female high school, gender discrimination in the sciences wasn't something that I experienced. So it wasn't until the first year of my biochemistry undergraduate that someone suggested that "Surely doing just biology would be more girly?" and another informed me that "You don't look like enough of a nerd to do chemistry".

Whilst the male to female undergrad split in the biological sciences in the UK now lies at around 50:50, look sideways into the chemistry, physics and engineering fields and you'll find only one woman for every eight men.

The 2011 data from the Bureau of Labor Statistics (in the USA) showed the average weekly earnings of a woman in biological sciences ($853) versus that of a man in the same field ($1,117). This all adds up to a woman in the same area of work earning a little over £9000 less a year compared to her male counterparts.

You may have noticed that this study is rather general, perhaps the women are working part time (perhaps for childcare reasons) or in less well-subsidized areas and thus their average income is brought down?

Researchers at Yale in 2012 thought this too. They produced a set of CVs, each one with identical qualifications but half were identified as being from men, and half from women. They gave these CVs to 127 science faculty members (of mixed genders) at the university and asked them to rank the applicant on a scale of 1 to 7 and also suggest a mean starting salary that they would give each candidate.

Regardless of the gender of the professor, or even their field of study, the female "applicant" was consistently offered a lower starting salary and ranked lower on all accounts of competence. Over all, a woman going into this (albeit fictional) job would expect to earn over $3000 less per year than her male counterparts.

There is little to suggest that things are any different this side of the pond. If I wish to persue a career in academic science, a decade from now I can expect to be earning noticeably less than any guy in my graduation class who follows the same path. And God forbid I take time off to have children - or even suggest to a prospective employer that one day in the future I may wish to start a family.

But what can be done to address this ongoing inequality? Groups such as theWISE Campaign aim to encourage woman and girls to enter the STEM fields, but progress has been slow and any "trickle up" effect seen from encouraging girls to take science A levels has yet to make an impact. The Athena SWANaward, given in institutions to recognise their commitment to advancing women's careers in STEM academia, is helping to encourage universities to be aware of the bias that can and will affect their female STEM graduates. The Department of Chemistry here in York is the first Chemistry Department in the UK to hold an Athena SWAN gold award.

Will these groups (or any of the multitudes like them) have a positive impact on women's role in science and academic research? I do hope so. However the big change will need to come from a long overdue change in the way that "science" is seen as a boys-only club; young girls should not find themselves forced out of doing what they want to do by the opinions of others.

Published YorkerOnline 27th March

@Yorker Comment

@ImogenWrote

Science Highlights of the Week - Part Four

The Genetic Sequence of Wheat

The draft genome of bread wheat (Triticum urartu) has been completed. By using this data published in Nature, it is hoped that new strains of wheat that are tougher and giver greater yields will be produced through genetic modifications.

This has brought the debate over the use of GM crops to the surface again, as there are still many who worry that the use of GM plants will lead to the breeding of superbugs or cause adverse reactions in those that consume them. However, as the human population rapidly increases, global food shortages are a genuine threat and any process that can speed up the already intensive selective breeding of foodstuff will likely be welcomed by future generations.

Learning Makes Your Head Hurt

As anyone who has done a 16 hour library stint knows, learning gives you a headache. However all that education may also be causing physical damage, What has now been seen in mice is that exposure to a new environment causes double-strand breaks in DNA in neurons (a single molecule of DNA is broken into two). This is then associated with the movement of histones (DNA packaging proteins) and the rearrangement of other proteins around the neuron.

In a healthy brain, this damaged is quickly repaired and the neuron restored, but in transgenic mice made to mimic a human brain suffering from Alzheimer's this damage is seen to be more severe and longer lasting as the standard repair mechanisms have been disrupted.

This is no excuse to skip on the workload though, as all studies so far have seen that increased brain activity through life, especially in later years, can lessen the risk of neural decline in old age.

Scientists Spend Time Watching Cats

Most cat owners will chat with their pets, I for one have just had a very interesting conversation about the nature of gender bias in the scientific community with my feline companion.

In this vein, two researchers from the Graduate School of Arts and Sciences, The University of Tokyo and the Department of Psychology, Keio University have looked into whether or not our furry friends actually recognise the voice of their beloved owners.

In short, the research showed that, unsurprisingly, they do recognise their owners voices but they mostly choose to ignore any calls whatsoever.

Science Highlights of the Week - Part The Third

Higgs Boson Confirmed?

In a press release from CERN on the 14th March, it has been announced that two and a half times more data has been collected from the Large Hadron Collider and analysed.

This new data points towards the particle in question being confirmed as the elusive Higgs boson. However more research is needed to truly be sure what kind of boson it is.

Antibiotic Resistant Bacteria On The Rise

In the last century, we have become ever more dependent on the use of antibiotic drugs. This is not particularly news to anyone who has been following various bacterial epidemic scares across the last few year and ideas to slow the development of resistance have been around almost as long as antibiotics themselves.

A recent report in the UK lead by Sally Davies has highlighted 17 key policies that should be followed to prevent the spread of such resistant pathogens and slow down the evolution of new, even more dangerous ones.

Sex Could Be Good For The Brain

In a study involving rats, researchers in Maryland have seen that sexual experience has a positive effect in increasing neurogenesis(growth of new brain cells) in adult rats.

This is due to the effect of the hormones released during what the paper euphemistically calls a "rewarding experience" on neuron growth and the function of the hippocampus - an area important in memory.

Unfortunately, improved mental function was only seen for some time after sexual experience, if behavioral testing was left too late, little or no improvement in cognitive task was actually seen. On the other hand, frequent sex and often could very well have a strong positive effect on your brain power, at least for a short while.

Congratulations Commander Hadfield

Canadian astronaut Chris Hadfield has taken over the helm of the International Space Station (only the second leader not to be American or Russian).

Hadfield (here on Reddit...) has been part of a skeleton crew manning the station since 21st December, with cosmonaut Roman Romanenko and astronaut Thomas Marshburn. They will return to Earth on 13th May, a total of 144 days in orbit.