Friday 27 February 2009

I propose gene therapy for everyone

'Happiness' gene helps you look on the bright side
25 February 2009 by Andy Coghlan

Positive people may owe their optimism to a gene variant that helps them dwell on the good and ignore the bad.

That's the conclusion from a study examining people's subliminal preferences for happy, neutral, and threatening images.

Volunteers who had inherited two copies of the "long" variant of 5-HTTLPR – a gene that controls transport of the mood-affecting neurotransmitter serotonin – showed clear avoidance of negative images, such as fierce animals, and a clear preference for positive ones, such as puppies. People with this variant combination are dubbed "LL" carriers.

The effect wasn't seen in volunteers with at least one version of the "short" variant of the same gene – these people showed no strong preference whatever the content of the images.

Time lapse

In repeated tests, the 97 volunteers had less than a second to identify dots hidden in one or other of a pair of adjacent images. Each pair contained a neutral image alongside one that was either positive or negative.

The researchers found that LL volunteers took 18.3 milliseconds longer on average to spot the dots in a negative rather than neutral image, suggesting a subliminal aversion to bad images.

Conversely, they noticed the dots 23.5 milliseconds sooner in the positive images, such as cuddly puppies, than in the neutral ones, suggesting they were subliminally drawn to them. "It sounds very small, but in terms of attentional time, it's consistent," says team leader Elaine Fox of the University of Essex in Colchester, UK.

Optimistic streak

Fox and her colleagues conclude that the LL volunteers may be primed to seek out positive events and ignore negative events.

Earlier studies had revealed a tendency for negativity and anxiety among individuals with at least one short variant of the gene, but the study is the first to reveal an optimistic streak in LL individuals.

"A number of mechanisms may contribute to this difference, and the authors have provided good evidence that attentional bias in the processing of emotional stimuli may be one of those mechanisms," says Turhan Canli, who has studied the same phenomenon at Stony Brook University in New York.

Journal reference: Proceedings of the Royal Society B (DOI: 10.1098/rspb.2008.1788)

http://www.newscientist.com/article/dn16662-happiness-gene-helps-you-look-on-the-bright-side.html?DCMP=NLC-nletter&nsref=dn16662

Wednesday 25 February 2009

Gene for Tooth Enamel Discovered

Scientists believe they have found a way to grow teeth in the laboratory, a discovery that could put an end to fillings and dentures.

The US team from Oregon have located the gene responsible for the growth of enamel, the hard outer layer of teeth which cannot grow back naturally.

Other scientists are already growing the inner parts of teeth in animals - but they have no hard enamel coatings.

The Proceedings of the National Academy of Sciences work may plug this gap.

Experiments in mice have shown that the gene, a "transcription factor" called Ctip2, has several functions involving immune responses and the development of skin and nerves.

A lot of work would still be needed to bring this to human applications, but it should work
Lead researcher Dr Chrissa Kioussi

The work at Oregon State University made the link with enamel by studying mice bred to lack Ctip2.

Lead researcher Dr Chrissa Kioussi said: "It's not unusual for a gene to have multiple functions, but before this we didn't know what regulated the production of tooth enamel."

The scientists found that Ctip2 was crucial for the enamel-producing cells, called ameloblasts, to form and work properly.

Dr Kioussi said: "This is the first transcription factor ever found to control the formation and maturation of ameloblasts, which are the cells that secrete enamel."

Controlling the gene in conjunction with stem-cell technology could make the artificial creation of functional teeth a real possibility.

Alternatively, the knowledge could be used to strengthen existing enamel and repair damaged enamel, cutting decay and the need for fillings.

Dr Kioussi said: "A lot of work would still be needed to bring this to human applications, but it should work. It could be really cool, a whole new approach to dental health."

Paul Sharpe, an expert on tooth development at the Dental Institute at King's College London, said: "If you could find some way of growing ameloblasts that make enamel, you could find a way to repair teeth.

"Any gene like this is worth understanding. The more we learn about it the more we can use the information to make biological models of tooth repair."

http://news.bbc.co.uk/1/hi/health/7907192.stm

Friday 20 February 2009

Transgenes found in wild corn!

Everyone guessed this was going to happen eventually...

http://www.newscientist.com/article/mg20126964.200-transgenes-did-escape-into-the-wild-from-gm-farms.html?DCMP=NLC-nletter&nsref=mg20126964.200

NOW it's official: genes from genetically modified corn have escaped into wild varieties in rural Mexico. A new study resolves a long-running controversy over the spread of GM genes and suggests that detecting such escapes may be tougher than previously thought.

In 2001, when biologists David Quist and Ignacio Chapela reported finding transgenes from GM corn in traditional varieties in Oaxaca, Mexico, they faced a barrage of criticism over their techniques. Nature, which had published the research, eventually disowned their paper, while a second study by different researchers failed to back up their findings.

But now, Elena Alvarez-Buylla of the National Autonomous University in Mexico City and her team have backed Quist and Chapela's claim. They found transgenes in about 1 per cent of nearly 2000 samples they took from the region (Molecular Ecology, vol 18, p 750).

"They are out there, but it's hit-and-miss," says Paul Gepts of the University of California, Davis, a co-author of the new study. The escaped transgenes are common in a few fields and absent in others, he says, so gene-monitoring efforts must sample as broadly as possible.

What's more, not every detection method - or laboratory - identified every sample containing transgenes. Monitors should use many methods to avoid false negatives, says Gepts.

Some intersting pictures for Anatomists

Check this out! http://www.newscientist.com/gallery/dn16578-anatomy-specimens-as-art?DCMP=NLC-nletter&nsref=dn16578

Wednesday 11 February 2009

Francis Crick was high on LSD when he discovered the DNA double helix

Nobel Prize genius Crick was high on LSD when he discovered the secret of life
BY ALUN REES

Source: Mail on Sunday
Date: 8 August 2004


Francis Crick, the Nobel Prize-winning father of modern genetics, was under the influence of LSD when he first deduced the double-helix structure of DNA nearly 50 years ago.

The abrasive and unorthodox Crick and his brilliant American co-researcher James Watson famously celebrated their eureka moment in March 1953 by running from the now legendary Cavendish Laboratory in Cambridge to the nearby Eagle pub, where they announced over pints of bitter that they had discovered the secret of life.

Crick, who died ten days ago, aged 88, later told a fellow scientist that he often used small doses of LSD then an experimental drug used in psychotherapy to boost his powers of thought. He said it was LSD, not the Eagle's warm beer, that helped him to unravel the structure of DNA, the discovery that won him the Nobel Prize.

Despite his Establishment image, Crick was a devotee of novelist Aldous Huxley, whose accounts of his experiments with LSD and another hallucinogen, mescaline, in the short stories The Doors Of Perception and Heaven And Hell became cult texts for the hippies of the Sixties and Seventies. In the late Sixties, Crick was a founder member of Soma, a legalise-cannabis group named after the drug in Huxley's novel Brave New World. He even put his name to a famous letter to The Times in 1967 calling for a reform in the drugs laws.

It was through his membership of Soma that Crick inadvertently became the inspiration for the biggest LSD manufacturing conspiracy-the world has ever seen the multimillion-pound drug factory in a remote farmhouse in Wales that was smashed by the Operation Julie raids of the late Seventies.

Crick's involvement with the gang was fleeting but crucial. The revered scientist had been invited to the Cambridge home of freewheeling American writer David Solomon a friend of hippie LSD guru Timothy Leary who had come to Britain in 1967 on a quest to discover a method for manufacturing pure THC, the active ingredient of cannabis.

It was Crick's presence in Solomon's social circle that attracted a brilliant young biochemist, Richard Kemp, who soon became a convert to the attractions of both cannabis and LSD. Kemp was recruited to the THC project in 1968, but soon afterwards devised the world's first foolproof method of producing cheap, pure LSD. Solomon and Kemp went into business, manufacturing acid in a succession of rented houses before setting up their laboratory in a cottage on a hillside near Tregaron, Carmarthenshire, in 1973. It is estimated that Kemp manufactured drugs worth Pounds 2.5 million an astonishing amount in the Seventies before police stormed the building in 1977 and seized enough pure LSD and its constituent chemicals to make two million LSD 'tabs'.

The arrest and conviction of Solomon, Kemp and a string of co-conspirators dominated the headlines for months. I was covering the case as a reporter at the time and it was then that I met Kemp's close friend, Garrod Harker, whose home had been raided by police but who had not been arrest ed. Harker told me that Kemp and his girlfriend Christine Bott by then in jail were hippie idealists who were completely uninterested in the money they were making.

They gave away thousands to pet causes such as the Glastonbury pop festival and the drugs charity Release.

'They have a philosophy,' Harker told me at the time. 'They believe industrial society will collapse when the oil runs out and that the answer is to change people's mindsets using acid. They believe LSD can help people to see that a return to a natural society based on self-sufficiency is the only way to save themselves.

'Dick Kemp told me he met Francis Crick at Cambridge. Crick had told him that some Cambridge academics used LSD in tiny amounts as a thinking tool, to liberate them from preconceptions and let their genius wander freely to new ideas. Crick told him he had perceived the double-helix shape while on LSD.

'It was clear that Dick Kemp was highly impressed and probably bowled over by what Crick had told him. He told me that if a man like Crick, who had gone to the heart of human existence, had used LSD, then it was worth using. Crick was certainly Dick Kemp's inspiration.' Shortly afterwards I visited Crick at his home, Golden Helix, in Cambridge.

He listened with rapt, amused attention to what I told him about the role of LSD in his Nobel Prize-winning discovery. He gave no intimation of surprise. When I had finished, he said: 'Print a word of it and I'll sue.'

Monday 9 February 2009

Installing PHP, MySQL and Perl modules on Linux

Lately I've been doing quite a bit of work with Perl and I needed to count the number of characters in a string. Usually this is done with this command:
$len = length($string);
But what this actually does is count the number of bytes, so if you are using an encoding like UTF-8 it will not give the correct count of the letters in the string. I did a little search and discovered the existence of the Unicode::String module. I tried to follow the instructions to install it on Linux Ubuntu but both the usual and the manual method failed!

I discovered that you can use the Synaptic Package Manager to install Perl modules! If you do a search for "Unicode::String" in synaptic you can find the module and it installs so easily! So now the code is like:

#! /usr/bin/perl -w
use Unicode::String qw(utf8 latin1 utf16);

#... (some code to get the string from the file and stick it into $str)
$uStr = utf8($str);
print $uStr->length;

Another thing I was doing was messing about with the PHP module in Netbeans. They provide probably the best instructions on the Internet on how to install Apache, PHP and MySQL on Linux: http://www.netbeans.org/kb/docs/php/configure-php-environment-ubuntu.html

Sunday 8 February 2009

Baby born with 6 digits on each limb - what are the chances?!

A baby boy has been born in California with 24 perfectly formed fingers and toes - six on each hand and foot.

Being born with additional digits - or being a "polydactyl" - is not wholly uncommon, but it is unusual to see the condition on every extremity.

The Bay Area hospital said staff did not notice the extra digits on ultrasound scans - and did not even spot it when Kamani Hubbard was born.

It was his father, Kris, who realised his son had some unusual features.

Polydactylism is genetic and the father said there was a family history of the condition. However he added his son's case was unique.

"Some family members have had six fingers, not completely developed. But not the toes."

A paediatrician at St Luke's hospital, Dr Michael Treece, said: "It's merely an interesting and beautiful variation rather than a worrisome thing.

"Imagine what sort of a pianist a 12-fingered person would be. Imagine what sort of flamenco guitarist. Think of their typing skills."

Famous polydactyls have reputedly included the English music hall entertainer Little Tich and Anne Boleyn - although the latter is still disputed by historians.

Cricketer Sir Garfield Sobers was also born with an extra finger on each hand.

http://news.bbc.co.uk/2/hi/health/7870769.stm

Tuesday 3 February 2009

Software: Big File Line Reader (BFLR)

It is not uncommon in bioinformatics and in general computing to come across huge datasets, often bundled into files. The typical text editor on most operating systems is a simple program but it takes forever to open large files and often becomes unresponsive and crashes. You do not have an option to choose how much of the file you wish to see and this is a seriously annoying limitation.

So I decided to write simple text editor in Java called Big File Line Reader because it gives you the option to choose which lines of the file to view and consequently this makes it much faster than opening the whole thing with the default text editor.

BFLR has these features:
  • Choose which range of lines to see, e.g. 50 - 500
  • Choose which lines to display from, e.g. 1000 - end
  • Display the whole file, e.g. all
  • Save a file from the displayed text
  • Edit, Copy, Cut, Paste and Select All.
  • Search strings
  • Search next occurance of string
  • Line, Letter and Character numbering *
If you need more memory to open large files, for example 500MB of RAM, you should open up the executable jar file via the command line with a command like this:
java -Xmx500m -jar bigfilelinereader.jar
Here's a screenshot showing the first 7 lines (verses) from my Quran.txt file (6236 lines, 880KB):

It's not a perfect program - there's the occasional bug here and there but it does what I need it to so it should be useful to most people. You can get the source here:
http://code.google.com/p/big-file-line-reader/
You need to build the project first then run it by double clicking the executable bigfilelinereader.jar file in the dist folder.

*(line numbering includes wordwraped lines)