Genetic basis of lazy eyes uncovered

Genetic basis of lazy eyes uncovered

The underlying gene responsible for crossed or lazy eyes has been discovered.

The condition, scientifically known as strabismus, affects 1 in 20 children and typically the first symptoms will be seen between the ages of 1 and 4. Whilst it had previously been observed to run in families the genetic factors responsible were unknown until now.

The research, carried out by an international team including scientists from Harvard, identified the faulty gene TUBB3. This gene codes for the important cellular component tubulin in nerve cells. This is essential for maintaining nerve axons and ensuring accurate transport.

The study took 15 years and looked specifically at the congenital occurrence of strabismus in a family from Victoria. “We looked at about 50 members of the family (and) about 25 of them were affected in different ways. Some of them had both eyes turning, for others it was one side,” said Dr John Ruddle, a research fellow at the University of Melbourne Centre for Eye Research Australia, and one of the lead scientists in the project.

The family members in the study portrayed particularly strong indications of hereditary strabismus. However, this is not the most common form of the condition. It is hoped that the research will help understanding of non-congenital strabismus progress. There are many theories as to what may cause “simple strabismus” including viral infection and deficiencies in eye sight. “The discovery was important because it has helped build understanding of the development of the nerves that control eye,” said Dr Ruddle.

The current recommended treatments range from wearing an eye patch to corrective surgery.  The former highlights the emotional and social distress that the condition can cause for a sufferer, whilst with the later there are risks and complications associated with the surgery.

The research also identified that other problems in the developing brain may have a link to the same defective gene. This includes intellectual and behavioural impairments and facial paralysis, the researchers have term the spectrum of disorders TUBB3 syndromes.


Autotune the Abstract: Singing in the Brain

Autotune the Abstract: Singing in the Brain

Autotuned sensation Rebecca Black is very excited about this new concept...

As a science communication student I find myself constantly coming across new and different ways people try and get across scientific data and knowledge. It can range from typical things such as news articles and blog posts to knitted representations of science. Whilst some of the crazy ways people try and get out their research may seem misguided, I think this blatant eccentricity should be applauded and encouraged.

It is with this sentiment in mind that I decided for this post to create my own oddball way of presenting research. After much deliberation I decided to autotune the abstract of a science paper. The first step in my attempt to revolutionise science publishing was to pick a lucky research paper to become the launch song. After much scouring of Google Scholar I found the following:

“Singing in the brain: Professional singers, occasional singers, and out-of-tune singers: Gottfried Schlaug; Acoustical Society of America (2009)”

Which, given its subject matter, felt like the perfect research to autotune. Now, unfortunately not every research scientist is a professional sound technician. However, this is something that can be overcome as there are plenty of apps for Iphone and Android that will do all the complicated technical stuff for you! For this first attempt I selected one called “Songify” which is an app produced by the Gregory Brothers, the band who produce the popular online series ‘Autotune the News’.

So without further ado here is the first Autotune the Abstract:

I hope that this practice will become as established in scientific publishing as peer review. I also expect to see the awesomeness of the produced songs incorporated into the impact factors of journals.

Science Hoax of the Week: Human Flavoured Tofu

Science Hoax of the Week: Human Flavoured Tofu

Hmmm fake human...

There are a lot of weird food-stuffs out there, this makes it particularly difficult to tell if an outlandish food is real or a hoax. One product in particular that sought to play with this boundary was HUFU, aka Human flavoured Tofu.

“[Hufu is] a great convenience food for cannibals. No more Friday night hunting raids! Stay home and enjoy the good healthy taste of hufu,” said the Hufu website (which ran from 2005 to 2006), which also offered a range in baby seal tofu.  The product was aimed at cannibals who want to quit their antisocial practice and anthropology students studying cannibalism.

Of course no such product exists or has existed, is was a spoof product created by Mark Nuckols, who at that point was a student at the Tuck School of Business. He claimed that the idea came to him when he was eating a tofurkey (a tofu based faux turkey) sandwich whilst reading a book on cannibalism.

If you want a good laugh and to know a bit more about Hufu then I would recommend checking out The Daily Show’s segment, featuring an interview with Mark Nuckols, below:

Scientists Engineer E.Coli to Produce Key Precursor of Spandex

Scientists Engineer E.Coli to Produce Key Precursor of Spandex

The Future: Bacteria Produced Hot Pants?

Scientists from the company Genomica have genetically engineered E.Coli to produce 1,4-Butanediol (BDO), a key chemical in the production of Spandex, clothing of choice for superheroes, glam rockers and 80’s disco enthusiasts.

The work, published in the journal Nature Chemical Biology, has the potential to drastically change the way BDO is produced. Currently one million metric tons are produced per year and all of this is derived from oil and natural gas. Almost half of the BDO produced globally is dehydrated to produce Tetrahydrofuran. This can then be polymerised to polytetramethylene oxide, the primary use of which is in fibres such as spandex.

The researchers faced several challenges whilst trying to produce their engineered bacteria. The first of which being identifying a synthesis mechanism, as there is no known naturally occurring biological synthesis pathway for BDO. Instead they had to compute all potential pathways from the typical E. coli metabolites to BDO. The computer algorithm they used  identified over 10,000 four-six step pathways that could result in synthesis of BDO from common metabolites, including acetyl-CoA, succinyl-CoA and glutamate.

These methods were then narrowed down based on theoretical yield, pathway length and thermodynamic feasibility. After this they picked out the following pathway as the best way for E.Coli to produce BDO:

The BDO synthesis pathway. Each number indicates an enzyme: (1) 2-oxoglutarate decarboxylase; (2) succinyl-CoA synthetase; (3) CoA-dependent succinate semialdehyde dehydrogenase; (4) 4-hydroxybutyrate dehydrogenase; (5) 4-hydroxybutyryl-CoA transferase; (6) 4-hydroxybutyryl-CoA reductase; (7) alcohol dehydrogenase. Steps 2 and 7 occur naturally in E. coli, whereas the others are encoded by heterologous genes introduced in this work.

With an elucidated pathway, then came the challenge of how to get a bacterium to carry it out. Not all the enzymes required for the pathway are present in the wildtype E.Coli. As a result of this, the group identified several different mechanisms for generating the intermediate 4-Hydroxybulymate (4HB) settling on; the addition of three genes sucCD (E. coli), sucD and 4hbd (P. gingivalis).

The final stage in the process, 4HB to BDO, also required some manipulation. The change requires two reduction steps, catalyzed by dehydrogenases. This can occur by the addition of exogenous 4HB to wild-type Clostridium acetobutylicum. However, for efficient production they needed to have the process contained within E.Coli. So instead  they expressed the 4-hydroxybutyryl-CoA transferase (cat2) gene from P. gingivalis for the conversion of 4HB to 4HB-CoA. The final stages then involved the action of  4-hydroxybutyryl-CoA reductase and the native alcohol dehydrogenase, finally resulting in a viable BDO product.

Whilst this discovery does not directly result in the production of spandex or other useful fibres by bacteria. This could prove to be an efficient and environmentally friendly way to produce crime-fighting and disco outfits at some point in the future!

And the Oscar goes to…Science!?

And the Oscar goes to…Science!?

"I'd just like to thank my project supervisor..."

Hollywood has never had a particularly good reputation for scientific accuracy. However, recently its science acumen has received a boost. It is currently the first time that the ‘reigning’ best actor and actress have been both been scientifically published.

Colin Firth, has taken time out from swimming in country lakes and stuttering to co-author a paper in Current Biology. The research looked into whether there are any structural differences in the brains of young adults with different political affiliations.

His co-Oscar winner Natalie Portman has been published twice. Credited as Natalie Hershlag, her family name, she published a paper on sugar chemistry whilst in high school and another entitled “Frontal Lobe Activation during Object Permanence: Data from Near-Infrared Spectroscopy” whilst completing her psychology degree at Harvard.

Figure 1. Individual Differences in Political Attitudes and Brain Structure

Both also seem to have made valuable contributions to scientific knowledge with their research. Firth’s paper showed that “Liberalism was associated with the gray matter volume of anterior cingulate cortex” and that “Conservatism was associated with increased right amygdala size” as can been seen in Figure 1.

The question of whether or not it is psychological or environmental factors that influence political stance has been debated for many years. The findings of the paper side with recent studies in twins which claims that “a substantial amount” of political opinion is influenced by genetics.

The neuroscience paper published by Natalie Portman looked into the progress of ‘object permanence’ in child development. Object permanence is the understanding that objects continue to exist even when they cannot be seen, heard, or touched. Her research used near-infrared spectroscopy to monitor the levels of oxy and deoxyhaemoglobin. The research revealed that the rise in object permanence occurs simultaneously to a rise in the levels of haemoglobin concentration in the frontal cortex.

Whilst, these two members of the Hollywood A-list have dabbled in a bit of science it seems that they aren’t going to give up on their day jobs. Portman most recently graced our screens in the decidedly unscientific Thor, whilst Colin Firth was most recently seen in the tense spy film “Tinker, Tailor, Soldier, Spy”.

Viral Science: New Caledonian Crow – Not So Bird Brained

Viral Science: New Caledonian Crow – Not So Bird Brained

Behavioural Ecology Research Group © Simon Walker

The New Caledonian Crow is a remarkably smart species of bird. They are the “only non-human species with a record of inventing new tools by modifying existing ones, then passing these innovations to other individuals in the cultural group”

This weeks viral science video part of research carried out by the Behavioural Ecology Research group in Oxford . This video below is the first time these birds were presented with this challenge:

p.s. apologies for the lack of posts recently, I shall return to regular blogging shortly.

Scientists show you can’t get drunk by placing your feet in Vodka

Scientists show you can’t get drunk by placing your feet in Vodka

Time to give up on that Jameson Jacuzzi...

This post was chosen as an Editor's Selection for ResearchBlogging.org

Scientists have tested the old Danish myth that it is possible to get drunk by submerging your feet in alcohol. Their results, indicate that unfortunately a Fosters footbath is unlikely to become the new way to consume your drinks.

Figure 1: The data on the participants

The selfless scientists from the Department of Cardiology at Hillerød Hospital became the test subjects (Figure 1), declaring themselves ‘free of chronic skin and liver disease and non-dependent on alcohol and psychoactive drugs’. The really interesting thing about this study, besides the just plain weirdness of the question being asked, is the methodology. The researchers abstained from alcohol for 24 Hrs prior to the study and also each cleaned their feet with a loofah the night before testing began.

In the study itself the researchers submerged their feet in washing bowls containing three 700mL bottles of vodka (37.5% by volume). They then recorded the level of drunkenness using the concentration of plasma ethanol and a more interesting secondary outcome for 3 hours ‘a timeframe corresponding to a medium length visit to the local pub’.  This method contains my Research Quote of The Week:

The secondary outcome was self assessment of intoxication related symptoms (self-confidence, urge to speak, and number of spontaneous hugs)”

Figure 2: Self assessed intoxication related symptoms

The results of the blood plasma ethanol levels were all below the detection limit of 2.2 mmol/L and the secondary outcome results (Figure 2) were deemed not significant. Although they did observe that after the experiment the skin on the researchers feet was ‘clean and smooth’.

This study obviously does have its weaknesses. There was no control group, only 3 participants and clearly isn’t the most revolutionary discovery science has ever made. But, I do think this research is important, if only because it shows that scientists aren’t stuffy and boring and that they do have a sense of humour. A point highlighted by the conclusion to their paper:

‘New pastimes, such as “eyeball drinking,” have emerged. The significance of this activity is unknown. Rumour has it that it makes you drunk fast . . . and may damage your eyes’

ResearchBlogging.org

Hansen CS, Faerch LH, & Kristensen PL (2010). Testing the validity of the Danish urban myth that alcohol can be absorbed through feet: open labelled self experimental study. BMJ (Clinical research ed.), 341 PMID: 21156749

Viral Science: Einstein or Monroe Optical Illusion

Viral Science: Einstein or Monroe Optical Illusion

I am now free from exams, so aim to get my writing back on track. As a way of easing myself back into this post features a very cool scientific optical illusion. Now who do you see if you look at the image below? The father of modern physics or Hollywood’s most iconic sex symbol?

At normal distance from the screen you should see the face  Albert Einstein. However, if you  squint your eyes or move away from the screen. Marylin Monroe should be visible in the image instead. It is also said that those with short sightedness will see Monroe instead of Einstein initially. However, not having short sightedness I am unable to vouch for this!

So now you have successfully changed Einstein into Marilyn. Here is her famous performance of ‘I Wanna Be Loved By You’ from Some Like it Hot (1959), if you were able to switch between the two in this I image Einstein would give a rather different performance…. 

The image was originally created for a 2007 issue of New Scientist

Research Quote of the Week: Alcohol, Nudity & Himalayan Bears

Research Quote of the Week: Alcohol, Nudity & Himalayan Bears

As a bit of a new theme I am going to each week post up an odd or fascinating quote from a peer reviewed research article. I hope that this will show how awesome science can be and publicise research is not in mainstream consciousness.

This week the quote is:

“We had no logical explanation for the fact that he was found naked in the cage”

This sentence came from an unusual piece of research  detailing what happened when a Serbian man got drunk and decided to climb inside an enclosure with some Black Himalayan Bears. He was found, naked and half eaten the next day.

The research mainly concerned itself with the unusual way in which the bears attacked the individual. In the wild their normal focus of attack is the face but, in this instance it was the individuals torso and legs that appeared to have taken the brunt of the attack.  As well as this, it was found that the bears had consumed a proportion of the individual which is not typical bear attack behaviour. They theorised that the differences in behaviour may be due to living in captivity in a major city (Belgrade).

Would you like to see what happened to the man? Well due to the rather gruesome nature of the photos, I felt I should have them a little hidden. If you want to see, click on the image of the bear below:

Click on the image to see the effects of the attack

ResearchBlogging.org

Mihailovic Z, Savic S, Damjanjuk I, Stanojevic A, & Milosevic M (2011). A Case of a Fatal Himalayan Black Bear Attack in the Zoo. Journal of forensic sciences PMID: 21361947

Amish Paradise: The use of GM crops by the Amish

Amish Paradise: The use of GM crops by the Amish

Amish at the forefront of technology!?

Now, Britain may view itself as a progressive country. With universal healthcare, a permissive attitude to stem cell research and a (usually) accepting attitude to foreign cultures, this view on the whole looks fairly correct. However, there is one area where our views are in danger of becoming prehistoric, GM food.

All over the world GM crops are being used. The US plant 42.8 million hectares of the stuff, with Canada and Argentina also producing millions of hectares of GMO crops. And whilst the “but all the other kids in school are doing it” argument isn’t a particularly strong one, the use of GM crops by one particular culture makes our absentia most shameful, the Amish.

When a country that views itself as being modern and forward thinking is being technologically overtaken by the Amish something is definitely wrong! The Amish fled religious persecution in Europe in the 1690’s to the US and have shunned technology and effectively remain living in the 1690’s. They follow a literal interpretation of the Bible and live by a set of unwritten rules of the church, the Ordnung. As each Amish district is a separate church the rules vary. The list is quite extensive but, here are a few that give good idea of the rigidity of their society:

  • Full-length mirrors are forbidden, because they are thought to promote vanity and self-admiration
  • Motorized vehicles are not to be owned or driven. The Amish may request a neighbour to drive them, or may hire a driver and rent a car
  • Women are never to shave any part of their body nor to cut their hair
  • Electricity is not allowed in the home. Electrical energy is allowed in community dairy barns, but only generator power (not grid power)

So, why do they use GM crops?

Traditional harvest of a non-traditional crop

It seems that despite not having electricity, phones in their homes or cars, GM agriculture is not against their religion. In fact, it helps them stick to it. Ironically the loss of productivity they have due to farming entirely by hand is compensated for by the increased yield of the crop. The use of GM also allows them to not use pesticides, which they see advantageous. “I myself like biotechnology,” said Amish farmer Daniel Dienner, “I feel it’s what the farmers will be using in the future.” Dienner is not alone in this view either, as of 2005, 550 Amish farmers in Pennsylvania were growing a genetically enhanced, nicotine-free tobacco plant. They sold this $3,500 per acre compared with $300 to $400 for a regular corn crop.

Nicotine-free tobacco is not the only crop grown. There are also Amish farms growing BT-Corn. This strain of corn contains a gene from Bacillus thuringiensis (a gram positive soil bacteria), Bt Delta Endotoxin. This protein is highly effective at controlling caterpillar larvae. The European Corn Borer larvae (Ostrinia nubilalis) is a big problem for farmers as it eats its way up the stem of the plant damaging it and causing the plant to wilt and the corn to die. It is a particular problem for Amish farmers given their traditional harvesting techniques.

In a very odd interview, Amish farmer Gideon ( for religious reasons he could not have his face on camera) was asked what he thinks about people who say the use of GMO crops is dangerous. He responded, “I would say they are misinformed, they don’t know what they are talking about”. This to the point view shows just how behind we are. Who is to blame is to blame for the country’s hesitance about GMOs is another matter. But, whilst the Daily Mail continues to peddle it’s pseudo-science “Frankenfood” scaremongering and scientists bemoan the public for their lack of understanding, I think it is unlikely the UK’s stance will change.

So, as it sums up the farcical nature of the situation, here is Amish Paradise by Weird Al Yankovic:

Sources:

Wired  – Welcome to LeBow Country – 2001

Council for Biotechnology Information – Amish Farmers Grow Biotech Tobacco, Potatoes – 2005

BBC 2 – Jimmy’s GM Food Fight – November 2008

FSA  – Consumer views of GM food – 2003

Wikipedia – Ordnung

Agrifood Awareness Australia – World GM Food Report – 2005