I'm back

So I'm back from my break and raring to get going again with this blog. The project I was working on while I was off requires some artistic thinking time so I'm going to let it pan out without forcing any ideas and it'll get it done in my spare time bit by bit.

Anyway, in the mean time I think I'll contribute a page or two to Wikipedia... will blog about this later :)

After that I don't know what I'll do but it'll be something to do with genomes probably.

I still don't have a job. It has been almost 9 months since I graduated and I'm really wondering what to do - no-one from life sciences or the computer world is willing to give me a chance. They're throwing away a great asset and they can't seem to recognise it. Anyone want to throw me a life-line?

The government seems to want to get rid of this problem by telling us to find jobs abroad. What sort of advice or solution is that?!! It's like they're admitting complete failure. Graduates 'should try leaving UK'

Hiatus

I'm going to have a little break from blogging on bioinfornetics so that I can concentrate on a project I'm working on (nothing to do with this blog).

Making and extracting TAR archives

Here are just a few helpful hints about tar and gzip files.

The TAR file format is popular in Unix/Linux and the TAR program is used to stick many files together into an archive - one file. That file can then be gzipped to become compressed.

To extract a TAR archive:

tar -xvf example_file.tar

The 'x' argument means eXtract, 'v' is for verbose (information about what is happening is displayed) and 'f' stands for filename which you provide after the arguments.

To TAR a folder:

tar -cvf example_name.tar ./folder_to_tar

The 'c' argument means create. This command will tar the folder "folder_to_tar" into the archive (file) "example_name.tar".

A good way to remember these tar commands is to realise that the argument letters are all next to each other - the C, V and F form a triangle on your keyboard (qwerty). And X stands for extract. Simples.

On another point, you can compress the tar archive on the fly by adding the argument 'x' within the argument list like so: -xzvf. Just don't put any argument after the 'f' flag or it will think that letter is the filename and cause you errors.

Tars are good to gzip if you forget to use the 'z' flag in the argument list. To gzip, compress, the tar file if you want using this command:

gzip example_name.tar

This will replace the tar in the directory with the popular .tar.gz file type: example_name.tar.gz.

To extract the .tar.gz archive:

gunzip example_name.tar.gz

This will put the tar file back in the directory as it was before.

There you go. Have fun in your console.

Vegetarians more likely to get colorectal cancer?!

A recent BBC article concerning a recent research into cancer epidemiology was titled: Vegetarians 'get fewer cancers'. While this is well known and universally accepted, the BBC neglected to clearly inform the general public of a more important discovery: Although vegetarians are less likely to get cancer in general, they are significantly more likely to get colorectal cancer!

All those who ever did a module on cancer are left sratching their heads saying WTF?!! What we were taught back in Uni was that carnivorous humans were more likely to get colorectal cancer (amongst other related health issues), but this discovery sheds new light on the subject. The thing we all must be wondering is WHY?

We all know why-not - beneficial phytochemicals, anti-oxidants, the effect on the bacterial flora (positive), lots of fibre promotes healthy bowel movement and reduces cancer-promoting irritation... but now we are wondering - why does it highten the risk of colorectal cancer? Could it be the insecticides - doubtful. Could it be the more dangerous phytochemicals - maybe? Could it be the effect on the bacterial flora (negative)? We just don't know and it really is a shock to be honest. However, there's still the inkling that the data might not be right, that further research may turn this discovery on its head again, or that what was discovered is not a universal response... we shall see in due time.

Anyway, the best advice is to stick to a mostly vegetarian diet as it will help save you from a whole load of problems the heavy meat eaters deal with. Getting just colorectal cancer rather than a whole slew of other cancers and other diseases should be worth it. Your 5 fruit and veg a day target is well worth it so stick to it. Keep Healthy :)

Highlighting Perl code using PHP

The grand majority of highlighting (coloring) scripts that exist on the web today ignore the Perl language, but if you have the PEAR extension installed on your PHP-enabled webserver you can use the Text_Highlighter package to highlight many programming languages including Perl. But what if you don’t have PEAR installed and are unable to install it for one reason or another?

You may be aware of PHP’s in-build highlight functions:highlight_string() and highlight_file(). They both return or output highlighted PHP code. In order to get your code to be highlighted as PHP you have to stick the PHP opening and closing tags around it.

But did you know you can use these functions to highlight Perl code if you trick it into thinking it is PHP? Perl code is quite similar to PHP code so it does a reasonable job but it’s not perfect. In fact you have to do some pre and post processing. In my example below I have a Perl file which I want to highlight... Continue reading the article here: http://www.islamic-dictionary.com/blog/?p=59

(Copying and pasting didn't work - Blogger's code handling is worse than Wordpress's so that's why I'm linking to the other article)

Gene therapy by Nanotechnology

Nano-treatment to torpedo cancer

Nanotechnology has been used for the first time to destroy cancer cells with a highly targeted package of "tumour busting" genes.

The technique, which leaves healthy cells unaffected, could potentially offer hope to people with hard-to-treat cancers where surgery is not possible.

Although it has only been tested in mice so far, the researchers hope for human trials in two years.

The UK study is published online by the journal Cancer Research.

We hope this therapy will be used to treat cancer patients in clinical trials in a couple of years Dr Andreas Schatzlein School of Pharmacy, London

The genes were wrapped up in microscopic nano-particles, 80,000 times smaller than the width of a human hair, which were taken up by cancer cells, but not their healthy neighbours.

Once inside, the genes stimulated production of a protein which destroys the cancer.

The researchers say the technology could potentially be particularly relevant for people with cancers that are inoperable because they are close to vital organs.

They hope it will eventually also be used to treat cancer that has spread.

'Exciting step'

Lead researcher Dr Andreas Schatzlein, from the School of Pharmacy in London, said: "Gene therapy has a great potential to create safe and effective cancer treatments but getting the genes into cancer cells remains one of the big challenges in this area.

"This is the first time that nanoparticles have been shown to target tumours in such a selective way, and this is an exciting step forward in the field.

"Once inside the cell, the gene enclosed in the particle recognises the cancerous environment and switches on. The result is toxic, but only to the offending cells, leaving healthy tissue unaffected.

"We hope this therapy will be used to treat cancer patients in clinical trials in a couple of years."

Traditional chemotherapy indiscriminately kills cells in the affected area of the body, which can cause side effects like fatigue, hair loss or nausea.

It is hoped that gene therapy will have fewer associated side effects by targeting cancer cells.

Dr Lesley Walker, of the charity Cancer Research UK, said: "These results are encouraging, and we look forward to seeing if this method can be used to treat cancer in people.

"Gene therapy is an exciting area of research, but targeting genetic changes to cancer cells has been a major challenge.

"This is the first time a solution has been proposed, so it's exciting news."

Italian doctor says he has cloned three babies

A controversial Italian doctor known for his work allowing post-menopausal women to have children has claimed in an interview to have cloned three babies who are now living in eastern Europe.

"I helped give birth to three children with the human cloning technique," Severino Antinori, a prominent gynaecologist, told Oggi weekly in an interview to appear Wednesday.

"It involved two boys and a girl who are nine years old today. They were born healthy and they are in excellent health now."

He did not provide proof of his claims, but said cells from the three fathers, who were sterile, allowed the cloning to be carried out.

The women's egg cells were impregnated in a laboratory through a method called "nuclear transfer," he said.

Antinori, who became famous after allowing a 63-year-old woman to have a child in 1994, said "respect for the families' privacy does not allow me to go further."

He added that the method used was "an improvement" over the technique used to clone Dolly the sheep in 1996.

Reminded by the journalist that such cloning is prohibited in heavily Catholic Italy, the doctor said he preferred to "speak of innovative therapies" or "genetic recoding" rather than cloning.

Two weeks ago, Antinori sparked controversy by announcing that he would artificially impregnate a woman whose husband is in an irreversible coma following a brain tumour.

It would be the first procedure of its kind in Italy if successful.

Source.

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

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