How Long are your Telomeres?

The telomere is a DNA/protein complex that caps the ends of chromosomes. Everyone has seen the X shaped chromosomes but few people think about why our DNA is split into chromosomes rather than one large circular plasmid or set of plasmids like with bacteria. Furthermore, few people think about why chromosomes form that X shape and what stops the lengthening of the p and q arms. We'll be looking at the latter in this post.

One can think of the telomere as the aglet on the end of a shoe lace, the cap on the end of a length of DNA to stop it getting any longer - it's what stops chromosome legs linking up end to end. The region of DNA on either end of a chromosome is actually a length of G-rich DNA with the pattern TTAGGG repeating over and over again for a length of 5-15kb, then finishing off with a long G tail of 50 - 300b. A protein complex, sheltrin, binds to this section of DNA and helps the legth of DNA form a T loop which is a bit like a knot at the end of a shoe lace.

It is generally well known in the scientific community that the length of the telomere is related to the life span of a cell or multicellular organisms - regulating how many times cells can replicate before they stop dividing, go into senescence and eventually die. Generally a human cell will go through 40-60 cycles or thereabouts (the Hayflick limit). The length of telomeres reduces with every-other revolution of the cell cycle and it gets to critical length before the cell stops dividing.

This year's (2009) nobel prize in phyisology/medicine was awarded to Elizabeth H. Blackburn, Carol W. Greider and Jack W. Szostak for discovering how chromosomes are protected by telomeres and the enzyme telomerase. One of their key findings was that telomeres are not shortened with every cell cycle.

It is not known exactly to what level the length of telomeres or the rate of erosion affects people's life expectancy. The general rule is that if you start off with long telomeres and/or telomere shortening is slow, then your life expectancy will be longer. But life expectancy and longevity has multiple factors governing it.

Telomerase is the enzyme that keeps the telomere long. Some species even produce enough to lengthen their telomeres with every-other cycle so they live longer lives but they still die eventually. Telomerase and long telomeres may play a larger role in slowing the ageing process rather than extending life.

Because telomere erosion occurs consistantly during the cell cycle it can be used as a measurement of age of a species where it is difficult to predict the age of an animal. And intraspecies, the telomere lengths and rate of erosion is quite different. Compared to many animals the homo sapien has a really long life considering that human telomeres are only 8–12 kb in length or less at birth and reduce 2 - 4kb in a lifetime. The rate of change of telomere erosion plays a role but looking at the graph below it is not so clear cut if long telomere lengths extend life, especially when compared with our closest living relative, (Pan) the chimpanzee. And also, one wonders about trees - some trees are thousands of years old and still going! (see B.E. Falanary paper below)

Graph showing the relationship between rate of change in mean telomere length (TROC) (base pairs lost [negative numbers] or gained [positive numbers] per year) in various tissues and maximum life span for five birds shown in Table 1 (circles) and eight mammals (boxes) (see C.M. Vleck paper). Common names are: Mus spretus, western wild mouse; Ovis aries, domesticated sheep, Canis familiaris, dog; Macaca nemestrina, pigtailed macaque; Bos taurus, cattle; Macaca fascicularis, cynomolgus monkey; Pan troglodytes, chimpanzee; Homo sapiens, human. Taken from C.M. Vleck et al., The natural history of telomeres: tools for aging animals and exploring the aging process.

The role of telomeres is to maintain the chromosome package. In bacteria mutations are not a big deal but in higher organisms they can cause serious harm and even lead to cancer. The hayflick limit governed by telomere length is seen as a safety mechanism which limits the number of cycles a cell goes through in order to make sure the quality of the DNA does not deteriorate, because with age comes an increased risk of mutation and cancer development.

Recommended papers:
C.M. Vleck et al., 2003, The natural history of telomeres: tools for aging animals and exploring the aging process.
Y. Deng et al., 2008, Telomere dysfunction and tumour suppression: the senescence connection
P.M. Lansdorp, 2009, Telomeres and disease
B.E. Flanary, 2005, Analysis of telomere length and telomerase activity in tree species of various
life-spans, and with age in the bristlecone pine Pinus longaeva
T.J. Vulliami, 2009, Premature Aging
C. Auriche et al., 2007, Budding yeast with human telomeres: A puzzling structure

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

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

Cancer can spread to foetus from the mother

Scientists have established beyond doubt that in rare cases cancer can be transmitted in the womb, following the birth of a baby to a woman with leukaemia.

A team at the Institute of Cancer Research, a college of the University of London, working with colleagues in Japan, found that the cancer had defied accepted theories of biology. Leukaemia cells had crossed the placenta and spread from the 28-year-old mother to her unborn baby.

Dr Tony Ford on how cancer can pass from the woman to foetus in the womb Link to this audio

There have been suspicions for years that cancer could be passed on in the womb. About 17 cases of suspected mother-to-child transmission have been noted – usually leukaemia or melanoma. But until now researchers have been unable to establish whether it had happened and, if so, how.

If the cells did cross the placental barrier, the child's immune system should have recognised them as foreign invaders and destroyed them.

In the latest case no one knew the mother, who was Japanese, had cancer during her pregnancy. She had a normal delivery in hospital, giving birth to an apparently healthy baby girl.

But just over a month later the mother developed vaginal bleeding, which became uncontrollable. She was diagnosed with an advanced stage of leukaemia and died.

When the baby was 11 months old she was brought to hospital with a swollen right cheek. Tests showed she had a tumour in her jaw and the cancer had spread to her lungs.

Although the cancers were not the same – the baby had a lymphoma and is now in remission – the Japanese doctors suspected a link to the leukaemia that had killed her mother.

They called in the team at the Institute of Cancer Research, which has done a lot of work in recent years on the genetics of cancers of identical twins. In the journal Proceedings of the National Academy of Sciences, the researchers explain how they used genetic "fingerprinting" techniques to establish that the child's cancer cells came from the mother.

They found the cancer cells of mother and baby carried the identical mutated cancer gene (called BCR-ABL1), but the infant had not inherited this gene. This meant that the child could not have developed the cancer in isolation – the cells must have come from the mother.

To investigate how leukaemia cells could have crossed the placental barrier and survived in the baby, the scientists looked for evidence of some form of immunological acceptance or tolerance of the foreign cells by the foetus. They examined the genes of the cancer cells in the infant and found a deletion mutation – some DNA missing in the region that controls expression of the major histocompatibility locus (HLA).

This was significant because HLA molecules primarily distinguish one individual, and his or her cells, from another, so the absence of these on the cancer cells meant the infant's immune system would not have recognised that they were foreign.

Professor Mel Greaves, who led the study, said: "It appears that in this and, we presume, other cases of mother-to-offspring cancer, the maternal cancer cells did cross the placenta into the developing foetus and succeeded in implanting because they were invisible to the immune system. We are pleased to have resolved this longstanding puzzle.

"But we stress … the chances of any pregnant woman with cancer passing it on to her child are remote."

Dr David Grant, scientific director at Leukaemia Research, said: "The important message from this … is that leukaemia cells can be destroyed by the immune system. Harnessing the power of the immune system to cure and protect patients from leukaemia is one of our priority areas of research."

http://www.guardian.co.uk/science/2009/oct/12/cancer-passed-from-mother-foetus

The human genome in 3D

Scientists have worked out the 3D structure of the human genome.

Their findings, published in Science magazine, reveal how long strands of DNA code are folded and tightly packed into the nucleus of a human cell.

Unfolded, the cell's genome - those strands of DNA code - would be approximately 2m in length.

The team showed how this is organised into a tight ball to fit inside a nucleus, which is about one hundredth of a millimetre in diameter.

The US-based research team developed improved DNA sequencing and computational methods to build a model of the genome.

This is the first glimpse we're getting of a whole genome in 3D Job Dekker University of Massachusetts

Job Dekker, from the University of Massachusetts Medical School, led the research.

He explained to BBC News that, with its new approach, his team had discovered important patterns in the shape of the genome.

"For a given part of the genome, we can determine its neighbours," he said.

"And if you can do that for every gene - if you know which other genes surround it - you can work your way back computationally to calculate the structure.

"This is the first glimpse we're getting of a whole genome in 3D."

Professor Julian Parkhill visits the Wellcome Collection to unravel the science behind the genome

DNA is bundled into chromosomes. The combination of DNA and protein that makes up these chromosomes is called chromatin.

Dr Dekker explained how a 3D view showed how chromatin's complicated folding pattern was important in the regulation of genes.

"We now see that things that are far apart along the linear sequence of the genome are actually next to each other in the folded structure," he said.

"They're close together in the structure, and they're talking to each other."

This constant communication is the basis of the regulation that keeps a cell healthy and functional.

This means that a detailed view of the genome's structure could provide a new window into diseases such as cancer, which is caused by errors in the genetic code.

"Maybe we will be able to predict these [disease-causing] changes better now," said Dr Dekker.

The team also discovered that the human genome is organised into two separate compartments, keeping active genes accessible while keeping inactive DNA in a sort of storage compartment.

The chromosomes snake in and out of the two compartments - separating their active and inactive sections.

http://news.bbc.co.uk/1/hi/sci/tech/8296861.stm

IBM to announce new DNA sequencing technique

IBM will announce on Tuesday how it intends to hold DNA molecules in tiny holes in silicon in an effort to decode their genetic secrets letter by letter.

Their microelectronic approach solves one of two long-standing problems in "nanopore" DNA sequencing: how to stop it flying through too quickly.

The aim is to speed up DNA sequencing in a push toward personalised medicine.

IBM's chief executive Sam Palmisano will announce the plans to the Medical Innovation Summit in the US on Tuesday.

While sequencing the genomes of humans and animals has become relatively routine in a laboratory setting, the ability to quickly and cheaply sequence genomes of individuals remains out of reach.

That widely available genetic information will help bring about the era of "personalised medicine" - in which preventative or therapeutic approaches can be tailored to individuals based on their specific genetic makeup.

All-electronic

"There have been a number of attempts to sequence DNA much faster than it was sequenced when the first human genome was announced," said Gustavo Stolovitzky, a computational biologist from IBM.

Individual genetic information will lead to more directed therapies

"All of them use some complicated sample preparation - chopping the DNA, amplifying, reverse transcribing - and some sophisticated and labour-intensive optics," Dr Stolovitzky told BBC News.

"All this makes sequencing faster, but still slower and more expensive than it needs to be before it could be used for personalised medicine."

Instead, Dr Stolovitzky and colleagues are pursuing a method involving silicon peppered with holes just three billionths of a metre across - 20,000 times thinner than a human hair and just wide enough for one strand of DNA to pass through.

Researchers have been looking into using such nanopores for a number of years - mimicking the proteins in cell membranes that perform the same trick - because using a semiconductor offers significant advantages over biochemical and optical techniques.

"DNA nanopore sequencing continues to be one of the great candidates to do fast and cheap DNA sequencing without sample preparation or sophisticated optics, using only electronics to fetch the signal out," Dr Stolovitzky said.

Moreover, the approach could be done in a "massively parallel" way - that is, with hundreds or thousands of DNA strands passing through an array of holes on a single chip.

Trap stack

The idea is conceptually simple but devilishly difficult to carry out. Because DNA naturally carries a net electric charge, simply applying a voltage across the two sides of the chip drives the DNA strands through the holes.

However, the DNA tends to pass through too quickly to decode the identities of the individual nucleotides - letters of the genetic code - as they pass.

More than that, until they can study DNA strands moving at a more carefully controlled pace, researchers cannot develop the techniques to query the precise nucleotide they have trapped in place.

The Blue Gene supercomputer simulated the nanopores' every atom

The IBM team have now hit on the idea of a chip composed of a stack of layers, each of which can hold a precisely-controlled voltage in a thin layer inside the nanopore.

These smaller voltages trap the negatively charged chemical groups called phosphates that separate individual nucleotides.

By cycling this internal voltage, the DNA strand can be made to advance one nucleotide at a time.

The team has used IBM's Blue Gene supercomputer to simulate the process in order to ensure it would work, and the team has built prototypes of the trapping nanopore. Tuesday's announcement marks the beginning of the testing and refinement stages of the process.

What remains is to investigate the means to identify the individual nucleotides trapped inside the nanopores, which is likely to rest on measuring some electrical or electronic property of each as it passes.

Stas Polonsky, another IBM researcher working on the project, remains convinced that with the benefit of a trapping mechanism, this last problem is tractable.

"As a company we have a lot of expertise with electrical measurements," he said.

"We have nanopores plus the whole arsenal of microelectronics - we can integrate all these ultrasensitive circuits right on a chip, which will boost the sensitivity for measurements tremendously."

http://news.bbc.co.uk/1/hi/sci/tech/8291185.stm

Remove index.php from the URL in Kohana

If you read the Kohana documentation they will tell you to edit your .htaccess file in order to remove index.php from your URLs, so that

http://localhost/kohana/index.php/controller/view

becomes

http://localhost/kohana/controller/view

But it is my experience that when creating URLs using the framework's helpers, like so:

<?php echo html::anchor('controller/view', 'Title'); ?>

Even with the htaccess modification, it will show the url as

http://localhost/kohana/index.php/controller/view

What you need to do is to edit the file:

/kohana/application/config/config.php

and modify this line to:

$config['index_page'] = '';

Now your URLs will not have index.php in them and the htaccess file can do its job.