Thursday 19 November 2009

Cancer protein 'can be disarmed'

Scientists have found a way to disarm a protein thought to play a key role in leukaemia and other cancers.

The breakthrough raises hopes of a new type of therapy that could treat cancer and other diseases.

Previous attempts to neutralise the protein had failed, leading experts to conclude it was effectively "undruggable".

The study, carried out by the US Dana-Farber Cancer Institute, features in the journal Nature.

The protein is one of the body's transcription factors, which turn genes on or off and set in motion genetic cascades that control how cells grow and develop. They also help fuel the growth of tumours.

The transcription factor targeted in the latest study is a protein called Notch.

The gene responsible for manufacturing the protein is often damaged or mutated in patients with a form of blood cancer known as T-cell acute lymphoblastic leukaemia (ALL).

Stapled peptides promise to significantly expand the range of what's considered 'druggable'
Professor Greg Verdine
Dana-Farber Cancer Institute

As a result the gene is switched on all the time, driving the uncontrolled cell growth characteristic of cancer.

Similar abnormalities in Notch also underlie other cancers, including lung, ovarian, pancreatic and gastrointestinal tumours.

Examining the structure of Notch closely, the researchers isolated a potential weak spot in its structure.

They employed a state-of-the-art technique using chemical braces to mould protein snippets called peptides into specific three dimensional shapes.

These "stapled" peptides are readily absorbed by cells, and are so tiny they can be deployed to alter gene regulation at specific sites.

After designing and testing several synthetic stapled peptides, the researchers identified one that was able to disrupt Notch's function.

When tested in mice it was found to limit the growth of cancer cells.

It may lead to alternative drugs and better treatments for this kind of leukaemia and maybe other cancers
Dr David Ish-Horowicz
Cancer Research UK

Analysis showed that activity was depressed in genes both directly and indirectly controlled by Notch.

The researchers hope the technique could also be used to target other transcription factors with a similar structure.

Researcher Professor Greg Verdine said: "Stapled peptides promise to significantly expand the range of what's considered 'druggable'.

"With our discovery, we've declared open season on transcription factors and other intractable drug targets."

Dr David Ish-Horowicz, head of developmental genetics at Cancer Research UK's London Research Institute, described the research as "very interesting".

He said: "There is already considerable work by scientists into ways to block Notch to try and reverse the effects of ALL, but the current drugs have some serious side-effects.

"This study describes the design of a new chemical that blocks the mechanism in a different way.

"The new chemical has only been tested in mice so far, and so we don't know how it will behave in humans.

"But, long term, it may lead to alternative drugs and better treatments for this kind of leukaemia and maybe other cancers."

http://news.bbc.co.uk/1/hi/health/8353229.stm

Master-switch Gene FOXP2 is the reason why we can speak and chimps can't

(* speak the same way)

One gene 'prevents chimps talking'

A single gene that is dramatically different in chimpanzees and humans may explain why apes cannot talk.

The FOXP2 gene underwent rapid changes around the time that language emerged in people.

Scientists in the US have now learned that human and chimp versions of the gene not only look different but also function in very different ways. FOXP2 acts as a "master switch" for other genes, turning them on or off.

Scientists at the University of California at Los Angeles (UCLA) scoured human DNA to see which areas are targeted by the gene. They then looked at what effect human and chimp forms of FOXP2 had on human cell lines. To their surprise, the two FOXP2 versions triggered different patterns of activity in the human genes.

"We found that a significant number of the newly-identified targets are expressed differently in human and chimpanzee brains," said study leader Dr Daniel Geschwind. "This suggests that FOXP2 drives these genes to behave differently in the two species."

Previous research has shown a close link between FOXP2 and the power of speech. The amino acid composition of the human version of the gene mutated and changed rapidly around the time language first developed.

The findings, reported in the journal Nature, may also help scientists understand how certain brain disorders such as autism and schizophrenia disrupt speech.

Co-author Dr Genevieve Konopka, also from UCLA, said: "Genetic changes between the human and chimp species hold the clues for how our brains developed their capacity for language.

"By pinpointing the genes influenced by FOXP2, we have identified a new set of tools for studying how human speech could be regulated at the molecular level."

http://uk.news.yahoo.com/21/20091111/tsc-one-gene-prevents-chimps-talking-4b158bc.html

Wednesday 11 November 2009

Software: Bounded Queue, a PHP Class

I wrote a PHP class called the Bounded Queue that might be of use to people. It is released under the New BSD license so go ahead and use it freely if you want.

The guys at PHPClasses.org gave it this description: This class can be used to manage a queue with a limited number of elements. It can push and pop items of any type into a queue array. If the queue already contains the limit number of items when a new item is pushed, the item at the bottom of the queue is popped (shifted) out.

Technically, this queue is bidirectional and you can even insert or remove items from the middle of the queue and even change its size dynamically. Here it is:

http://www.phpclasses.org/bounded-queue

PHPClasses.org have considered the class to be "Noteable". "This means that the site users interested in packages that have something special, are being notified to pay special attention to your package." Cool :)

If you do decide to use it then please tell me what for and warn me about any bugs. Thanks.

Update of news

Here's a few things of interest that happened lately:

A critically ill Turkish boy has had his life saved after scientists were able to read his genome quickly and work out that he had a wrong diagnosis. http://news.bbc.co.uk/1/hi/health/8315258.stm (I want to see much more of this sort of thing)

Twitter has signed deals to put messages sent via the microblogging service into the Microsoft and Google search indexes. http://news.bbc.co.uk/1/hi/technology/8310716.stm (This is highly important because it means that flash trends and spreading of diseases/viruses (biological & Comutational) can be identified globally within a very short period of time and without overburdening twitter - they're infamous for crashing regularly... data mining ftw)

Scientists say they have discovered an antibody that could minimise the major internal bleeding seen in traumas like bullet wounds and car crashes. http://news.bbc.co.uk/1/hi/health/8322454.stm

A South Korean court has convicted the disgraced cloning scientist Hwang Woo-suk of embezzlement over his stem cell research. He was given a two-year sentence suspended for three years. The 56-year-old scientist's work had raised hopes of finding cures for diseases such as Alzheimer's. But his research was declared bogus in 2005, and he was put on trial the following year for embezzlement and accepting money under false pretences. Hwang's research made him a South Korean hero until revelations that it was false shocked the nation. http://news.bbc.co.uk/1/hi/world/asia-pacific/8325377.stm (I know this is old news but it's interesting how long it's taken them to finally convict him... but NOT jail him!)

I like bears :) http://news.bbc.co.uk/earth/hi/earth_news/newsid_8321000/8321102.stm

Tiny metal particles have been shown to cause changes to DNA across a cellular barrier - without having to cross it. The nanometre and micrometre scale particles resulted in an increase of damage to DNA across the barrier via a never-before-seen cell signal process. http://news.bbc.co.uk/1/hi/sci/tech/8344815.stm (Be afraid, be VERY afraid!)

The man who pioneered life-saving treatment for tuberculosis sufferers has died in Edinburgh at the age of 97. http://news.bbc.co.uk/1/hi/scotland/edinburgh_and_east/8342593.stm

Nearly 40% of breast cancer tumours change form when they spread, a UK study shows... AND ...Women treated for breast cancer are at a higher risk of a relapse if they have "dense" breasts, say researchers. http://news.bbc.co.uk/1/hi/health/8337795.stm http://news.bbc.co.uk/1/hi/health/8345245.stm (You could imagine a doctor talking to his patient one day: You're dense! Just like your breasts.)

Hundreds of experts from 50 nations are set to agree on a "DNA barcode" system that gives every plant on Earth a unique genetic fingerprint. http://news.bbc.co.uk/1/hi/sci/tech/8346635.stm

Scientists have identified a drug which may offer hope to patients with a particularly lethal form of lung cancer. The drug eliminated small cell lung cancer tumours in 50% of mice, and blocked the cells' ability to resist standard chemotherapy treatment. http://news.bbc.co.uk/1/hi/health/8350220.stm