It’s just over ten years since the human genome sequence has been elucidated and published and things have moved at a great pace since then. To update us on what’s been going on in the world of genetics since the landmark announcement, Prof Peter Donnelly came to talk at Science Oxford Live.

Peter Donnelly is a Professor of Statistical Science and Director of the Wellcome Trust Centre for Human Genetics at the University of Oxford. A mathematician by training, he spends a lot of time modelling data to make sense of the immense amount of information that is generated from DNA sequencing. As he said, part of the current challenge is to understand and make use of the huge amount of information which is where his mathematics and statistics background comes in handy.

Genetic disorders lie at some point of a spectrum defined at one end by illnesses that are caused by a single “broken” gene and at the other end by those for which susceptibility results from defects in a number of genes, as well as environmental effects. Of the former category, the first to be identified in 1989 was the gene involved in cystic fibrosis (CFTR, a transmembrane regulator), and a huge number of single-gene defects have been linked to diseases since. Knowledge of these single gene mutations aid early diagnosis and subsequently better care, which is one of the reasons why newborn babies are routinely tested (using blood from a heel prick) for genetic conditions.

In the latter case, we deal with common diseases where there is both a genetic component (often from numerous genes) and environmental component that determine susceptibility. Unlike single-gene disorders, very few genes in this category have been identified until around 2005, which was subsequently followed by an explosion in their numbers. This is likely related to the availability of the human genome sequence, first published after a huge publicly funded research effort in 2001, and the subsequent reduction in DNA sequencing costs, which has since enabled the comparison of diseased and healthy individuals’ genomes in comparative studies.

Since 2005, 200+ conditions (including height, weight, schizophrenia, diabetes and many others) have been associated with particular gene variants. This is done in so-called genome-wide association studies where a pool of “affected” individuals (the size of the pool being in the range of 1000s) is taken next to a pool of “healthy” individuals. Their genomes are sequenced and their genetic type compared at 500,000+ positions (these are the genetic markers or single nucleotide polymorphisms, SNPs, which occur at ~1:1000 positions in the DNA and which result in differences between individuals). In theory, certain genetic types will occur more frequently in the “affected” pool of individuals and, if statistically significant, they can be identified as markers associated with a specific condition. Crucially, unlike single-gene conditions, a specific mutation/genetic type does not guarantee that the individual in question will suffer form a particular disease, it simply means that the risk of getting the disease might increase a bit relative to the general population. (Donnelly exemplified the genome-wide association study with one of the associations they’ve identified for obesity, this being the FTO gene, which is much more frequently found in individuals who are obese). Such large-scale studies provide the computational challenge of storing (a study of 1350 healthy and 1350 sick subjects in a type II diabetes study generated 50 terabytes, that is 50,000,000,000,000 bytes, of data!) and analysing the data. Donnelly described this as an “informational bottleneck”, which has to be addressed.

One of the tangible consequences of the improvement in technology and significant reduction in DNA sequencing cost (it is now possible to sequence a genome for £7,000 and this is predicted to reduce to £1,000 soon, a fraction of the cost required to read the first human genome) is the advent of consumer genomics and personalised medicine. Already companies exist to whom you can send your sample (spit or cheek swab), and they will analyse sites in your genome for variability and e-mail you your relative risk for various conditions. Why would you want to know this, you might ask? Well, if you know you might be susceptible to cardiovascular disease, you might try and do a bit of prevention – not smoke, eat less saturated fat, do more exercise… Or if you are more susceptible to breast cancer, you might increase the frequency of screening visits to the doctor. In other instances, knowing about your genetic variation may allow your doctor to know if you’ll have serious side effects when taking certain medication – if we know a small sub-group of the population has severe life-threatening side effects but know these are associated with a specific mutation in gene X, it may be possible to administer the drug safely to the majority of the population (to whom it is beneficial) without having to take it off the market because of a small fraction of people being at risk of side-effects.

Finally, it is not just human genomes that can be sequenced and looking at bacterial genomes can also be useful. For example, during the past gastric infections by Clostridium difficile (C.diff) have caused havoc in hospitals by causing patients serious diarrhoea. There have been concerns that the bug is spread by poor hygiene and it was possible to show, by sequencing and comparing the C.diff genomes of the bugs isolated from different patients, that after strict new hygiene rules were introduced in hospitals the bug was actually of a different type in most patients. Therefore the majority of the cases were not due to the infection being transmitted within the hospital. In another application, Donnelly explained how metagenomics might be used in the identification of disease causes. If you don’t know what is causing a skin infection, for example, you can take a sample of material from the infected area and sequence all of the DNA found in the sample. This will contain human DNA from skin cells, that of the commensurate flora (the beneficial bacteria that live on our skin) and hopefully DNA of the causative organism. Following sequencing and subtraction to eliminate known sources of DNA, the treating doctor, with the help of the bioinformaticians, might be able to identify the culprit!

Of course, with technology comes responsibility and Donnelly rounded of his talk with a discussion of the challenges for us as a society in the era of personal genomics. In his view, the key questions are those of personal knowledge and responsibility, the question of privacy of genetic information (if I know I am susceptible to a certain disease, I should perhaps be telling my brothers and sisters, or children, as they may be susceptible too?), and finally the question of decimation of people with increased susceptibility to disease, perhaps by health insurance companies. We discussed the last point in the Q&A session extensively, as it is the problem that always seems to come up in discussions of personalised genomics. Of course, having susceptibility to a certain disease may lead to increased insurance premiums, but insurance companies have been using family medical history for exactly that purpose up till now, without anyone raising an eyebrow. And in some cases, such as with Huntington’s chorea, where a child of a parent suffering from the disease has a 50% chance of getting the same disease in their middle age, it may be beneficial to show the insurance company that one does not have the defective gene and have insurance premiums reduced as a result. Nevertheless, knowledge comes with responsibility, and we must be aware of this when discussing the future of personal genomics.

Overall, an informative and well presented talk – Prof Donnelly certainly knows how to make his science accessible to the lay public (i.e. us!).

Some useful links:

Peter Donnelly’s university profile pages:
http://www.ndm.ox.ac.uk/principal-investigators/researcher/peter-donnelly
http://www.stats.ox.ac.uk/people/academic_staff/peter_donnelly

Something about the CFTR gene:
http://en.wikipedia.org/wiki/Cystic_fibrosis_transmembrane_conductance_regulator

I am an enzymologist, and so study the chemistry, function and mechanisms of enzymes. For many of you, the word enzyme will probably ring a bell and take you back to school biology and the lock and key theory of substrates ‘clicking’ into a matching enzyme active site. But what exactly is an enzyme?

Basically, enzymes are proteins. Proteins in turn are long chains of amino acid monomers. There are twenty naturally occurring amino acids, all with the same backbone structure but with chemically varied side-chains. Although there are some exceptions in the remnants of what is thought to have been a chemically simpler RNA-based world prior to the evolution of protein and DNA, proteins provide the ‘machinery’ of living cells, with their roles ranging from structural support to catalysis.

Enzymes are a sub-group of proteins which are biological catalysts that help specific biochemical reactions to proceed at a faster rate. Although many biochemical reactions do occur in the absence of enzymes under extreme conditions, they would only happen very slowly at physiological pH and temperature. The half-times of the uncatalysed reactions can be millions of years, so if Nature depended on reactions taking place without catalysis, life as we know it would simply not be possible.

My research is into the activity of an enzyme called flap endonuclease, which acts a bit like a pair of molecular scissors that cut a DNA strand at a structurally defined position. Whilst DNA breakages in general are likely to be a bad thing because they can lead to mutations, it is important to remember that controlled cleavage is absolutely essential for cells to be able to replicate and repair DNA, because both damaged sites and primers initiating DNA synthesis have to be removed. This is where our particular enzyme, flap endonuclease, comes in.

So how can we go about trying to work out the cutting mechanism? In the protein world, it is the amino acid side-chains that provide the functionality of the enzyme, sometimes supplemented by co-factors such as vitamins and minerals from our diet. Using the earlier machinery analogy, the amino acid side-chains and key chemical groups of the co-factors can be likened to levers and cogs. However, unlike real machinery, proteins are too small to see so we have to design indirect experiments to work out where the levers are and what they do.

One option is to determine their structure by the use of X-ray crystallography or NMR spectroscopy. Nevertheless, such structural studies only provide a static picture, like seeing the machine stopped and not knowing how the levers move. In addition, enzyme structures are often determined in the absence of reactants and products so do not tell us how these molecules fit in. This is where enzymologists have work to do, carrying out solution studies to further develop mechanistic knowledge about the activity of enzymes. Unlike many other proteins, with enzymes there is usually a way of measuring the appearance of a product or disappearance of a reactant, thus allowing us to measure the enzyme efficiency. Subtly changing the conditions of the reactions – which may be by mutation of one or more of the amino acids to change the shape of a particular ‘lever’, or by changing the pH of the reaction to alter the level of protonation and therefore the state in which the ‘levers’ are in – and then comparing the rates at which each reaction proceeds can tell us something about how an enzyme catalyses the reaction.

Finally, you may ask yourself why we should spend time investigating how enzymes work. A better understanding could potentially provide new leads for the pharmaceutical industry. Some enzymes can be malfunctioning or missing, or conversely over-produced, in diseased as compared to healthy cells. It could be possible to play molecular Lego and fill in the missing or broken bits using small drug molecules to restore or inhibit function, a process which clearly becomes much easier if we know how the enzyme works.

It has recently been reported that one in six people in the UK today will live to see their 100th birthday. Interestingly, there was quite a loud outcry from the public who voiced their fears over reaching such a grand old age, but what do we really understand about ageing? In this article I will look at ageing from the genetic, cellular and multicellular level to find out what we know, what we don’t, and whether there’s anything we can do about it.

Growing old is one of life’s inevitabilities and we can see the symptoms of ageing all around us, in the colour of our hair, the texture of our skin, and the functionality of our mind… “What was I saying? Oh yes!” Despite its omnipresence, ageing remains one of science’s great mysteries – why do we age? Is our degenerative destiny mapped out from birth in our DNA? We all know ‘those’ stories of heavy smokers who lived to be a hundred and marathon runners who dropped dead at fifty. Or is it an effect of environment? A morbid summation of the general stresses and strains our body is exposed to during a lifetime which ultimately equals our expiration date. The truth is it is likely to be a combination of the two, but to what extent? And is the science out there which could let us stay forever young?

Geriatric Genes and Senior Cells

Evidence shows there is a heritable component of life span. “So, does this mean it’s all in our genes?” The short answer is, no. If it were “all in our genes” we would expect genetically identical individuals to die at approximately the same time. In humans, scientists have found identical twins to have very different life spans, and studies looking at large groups of animals with identical genetic backgrounds – such as honey bees – found huge variability in longevity. “So, does that mean there are no genes which determine ageing, and it’s all about lifestyle?” Well, again the answer is no. In recent years, many genes have been identified which contribute to an animal’s lifespan, however, further research found the actual contribution of these genes to the realised lifespan of the individual appeared to be very variable. Interestingly, the one result the scientists can agree on is the effect of food. Way back in 1934 Clive McCay and Mary Crowell from Cornell University found underfeeding (without malnutrition) increased a rodent’s lifespan by as much as 50%, and this result has been replicated many times since. However, more than 70 years later the “hows and whys” behind the mechanisms underlying this phenomena are still unknown – so don’t beat yourself up about that festive overindulgence.

“Ok, so the detail’s from the genetics seem to be a bit sketchy. But, what can we see in the ageing cell? How are the cells in someone who is old different from those in someone who is young?”

It was Peter Medwar who put forward the idea that overtime DNA would get worn out and damaged, a lot like the human body. He said that the probability of mutation accumulation (mistakes in the genetic code) increases over a longer period of time, and it is this deterioration of code that influences the ageing process. The genome – or the DNA that makes up your genes – is the recipe for all the proteins in your body. Proteins are like the cogs in a machine – they must be exactly the right shape and size to do their job. If they’re just a fraction off then the mechanism fails, and the machine starts to slow down as efficiency is reduced. There is evidence that such mistakes in protein production are involved in age-related degenerative diseases such as cataracts, Alzheimer’s disease and Parkinson’s disease.

“Ok, now we’re getting somewhere. But how does the body get rid of these old cells which are rusting up the cogs?” All cells come with a built in ticking time bomb in their DNA in a region called the telomere. The telomere gets shorter with every cell division, and when the code runs out, the cell has two options, either it will go into a suspended state called “senescence”, or it will initiate a “self-destruct mode” whereby intracellular proteins are released which destroys the cell. When this system breaks the cell becomes immortal, and will continue to replicate beyond its expiration date – this is how tumours arise. It is predicted that 85% of tumours are caused by a mutation in the telomere.

The Fountain of Eternal Youth

There is a multi-billion dollar cosmetic industry dedicated to anti-ageing products. Potions and lotions which promise your Grandmother the face of a teenager, and your mother a booty like Beyoncè. The unfortunate truth is, most are just re-packaged moisturisers – but science is making some major leaps forward in masking, and even reversing the effects of ageing.

A team of scientists from Harvard Medical School have managed to reverse the effects of ageing resulting in worn out old wrinkly rodents being rejuvenated into versions of their younger selves. They did this by breeding genetically engineered mice that were unable to produce the enzyme which caused the telomere to shorten during cell division – called telomerase. Mice without this enzyme aged prematurely, however, when the mice were given an injection to reactivate the telomerase enzyme, the signs of ageing were reversed. It is currently under further investigation as to whether this procedure actually increases longevity, but it might help improve the quality of life of individuals showing signs of age related degenerative diseases. This study is still in its early days and not yet safe for human testing, but it is certainly an important discovery into the secrets of the ageing body.

Who Wants to Live Forever?

There are some scientists that believe they will ‘cure’ ageing, allowing us to live… indefinitely. But, is that a good idea? For many, growing old gracefully isn’t an option– just take a look at the profits made by the anti-ageing cosmetic companies. It seems likely that within the next few decades the science behind ageing will take huge leaps forward, to places we find hard to contemplate. There will undoubtedly be companies looking to make some cash, and people willing to put some pretty toxic stuff into their bodies to cover the signs of ageing. I’m reminded of the dark comedy “Death Becomes Her” where two ladies who learn the secret of eternal youth end up, literally, in pieces. Research which carries with it such ethical responsibility is always tricky, but I do not believe in the stifling of knowledge due to fear of the unknown – just in its careful and responsible monitoring and application. However, it’s easy to get up on my high horse when I’m twenty five and the science isn’t there yet – but could I honestly say no? If fifty years from now someone offered me a magic potion which would literally take decades off, allow me to go running again, travel the world, see my great grand-children grow up, would I walk away? … Ask me in fifty years.

Sources
One in six people in the UK today will live to 100, study says; Reported in the Guardian by David Batty, 30 December 2010
Jaskelioff, M. et al. Telomerase reactivation reverses tissue degeneration in aged telomerase-deficient mice. Nature 469 (7328), 102.
Kirkwood, T. B. L. Understanding the Odd Science of Aging. Cell 120 (4), 437 (2005).
McCay, C. M. & Crowell, M. F. Prolonging the Life Span. The Scientific Monthly 39 (5), 405 (1934).
Harvard scientists reverse the ageing process in mice – now for humans; Reported in the Guardian by Ian Sample, 28 November 2010
Vijg, J. & Campisi, J. Puzzles, promises and a cure for ageing. Nature 454 (7208), 1065 (2008).

Like this? Check out my blog at http://celltoself.wordpress.com

Why human flu sufferers are far from alone. Tiny organisms, minor illness, massive influence.

In stuffy offices and classrooms dramatic stories and terrifying statistics spread like wildfire. From killer pandemics to man flu, viruses are hard to escape. In reality severity varies and human targets are not alone.

Angela McLean, professor of Mathematical Biology (University of Oxford), examines patterns underlying virus infection. As human flu suffers retreat, huddling cosy duvets and lemsip powder, it is easy to forget the world outside. Nevertheless, tiny viruses continue to have a massive effect in the animal and plant kingdoms. Dr Chris Gower (Oxford) and Dr Lawrence Kenyon (Head of Virology, AVRDC World Vegetable Centre) illustrate virus emergence in animal ecosystems and agriculture.

While scare stories abound, we are reminded that viruses are highly specific and leaps between species are unusual and limited in size. Understanding virus and earth systems interaction, and maintaining hygiene are perhaps the most effective defences. Just sometimes the best advice might really be to slow down, avoid crowded habitats, and stay home.

What?

To recap, a virus is an infectious agent, consisting of genetic material DNA, RNA wrapped up in a protein coat. One hundred times smaller than bacteria, barley visible through a light microscope, they come in many varieties and reproduce inside cells of other organisms. These tiny, relatively simple microorganisms are perhaps one of the most powerful forces on earth, present in all ecosystems, with the ability to devastate entire populations of almost all other forms of life, generating immensely complex questions for science.

How?

Professor McLean explains, viruses spread in cramped conditions where members of the same species are forced together in a small space. For animals this can happen when habitats are destroyed, even where only a few of the species survive as they crowd together in small remaining areas of habitat.

Virus pandemics emerge through a mixture of ecological and evolutionary processes. When one happens, like Swine Flu the viruses work on ‘power and competition’. From this, in June 2010 Prof McLean predicted the new H1N1 Swine Flu virus will become the regular strain, replacing the previous seasonal flu. It is entirely possibly, although as yet unconfirmed, that this is happening now, as the World Health Organisation (WHO) reports cases of Swine Flu virus alongside other strains. A case of ‘watch this space?’

“I am interested in how distribution of people such as movement from villages to towns affects how a virus spreads. The more a virus spreads the more it evolves.

In history when Europeans first went to the ‘New World’ devastating outbreaks of smallpox and measles occurred in people who had never encountered these diseases before.”
Professor Angela McLean

Prevention and Treatment

Luckily it is not all doom with preventative vaccines and anti viral medication available. Professor McLean takes a closer look.

“It is amazing how successful vaccinations for viruses have been. The same measles vaccine has been effective for over forty years and the virus has not been able to evolve resistance despite selection pressure put on it by humans. In contrast new flu vaccines are needed every year, reflecting the changing underlying biology of the microorganism, different every year whether you vaccinate or not.”

For viruses where no vaccine is yet available e.g HIV, anti viral drugs are the first line of attack. When using antiviral drugs it is important to use genetic screening in a laboratory to check for resistance and help doctors decide which to use.

“We use information encoded in the RNA extracted from a blood sample (genetic material) to make real treatment decisions in real clinics. The right combination of antiviral drugs will not cure HIV but it can nearly completely suppress the virus and stop it reproducing, so as long as the person is able to continue to take it they will remain well. Failing to screen and using treatments where a patient has natural resistance is harmful in that it delays effective treatment and resistance not previously there can develop, burning through patients options for treatment.”
Professor Angela McLean

Out in the Wild

Our four legged friends can also suffer and domestic animals such as dogs are major virus carriers. Surprisingly it is wild populations like Ethiopian wolves who are left vulnerable, Chris Gower from Oxford University talks about protecting them.

“Ethiopian wolves are smaller than the European wolves that they descended from when they migrated from Europe to Africa. They are a flagship for the Afro Alpine habitat, when they are there you know everything else is present in the habitat ecosystem, including rodents. This important region supplies water for Somali, Egypt and Sudan.” Chris Gower

These wolves are an endangered, not dangerous, with less than 500 remaining in the world. As people move into their habitat in the Ethiopian highlands with dogs and livestock the threat from the transfer of a rabies virus to such a small population is potentially devastating. Strategic vaccination creates barriers of immunised dogs to contain the outbreak. It would be quicker to inoculate the wolves directly, however the only available vaccine now uses Genetically Modified Organisms and is currently not allowed.

Feeding a Cold

What better way to beat the snuffles than vitamin C packed juicy tomatoes? Dr Lawrence Kenyon Head of Virology at the World Vegetable Centre (AVRDC) demonstrates that they too are not immune, often at the mercy of virus carrying insects.

Plant viruses are transferred from plant to plant either by insects such as whitefly or infected plants rubbing together through human and animal contact. Tomato leaf curl is an example of a major crop virus, the leaves of infected plants show symptoms first, curling up to a dry withered crunch before the entire plant dies.

“Plant viruses do have pandemics but it is not so dramatic as seen with swine flu because as a rule plants don’t get on aeroplanes, requiring insects for transmission.”
Dr Lawrence Kenyon

In Taiwan ‘power and competition’ is in action as indigenous tomato leaf curl virus is being replaced by the more aggressive Thailand leaf curl virus, affecting peppers as well as tomatoes.

Plants like cabbages can act as whitefly sources, encouraging virus spread. Measures to prevent this in crops include; careful choice of species planted together, regular clearing of dead and dying plants, and housing in net cages. Spraying can also be used with more or less toxic agents. Reflective distracts the insects’ visual systems stopping them from landing on surrounded crops, and artificial coatings can be used on fruits. Selective breeding and genetic interventions to produce disease resistance, provide an alternative where other methods are too expensive or impractical.

Commercially desirable characteristics such as sweet juicy fruits make plants more vulnerable to viruses. Insects find hairy plants less attractive to land on, increasing their resistance to infection. This principle explains why commercial thorn less roses can only be grown in glass houses.

Non native environments also increase vulnerability. Cassava or Manioc now a widely grown staple crop in Africa was introduced from South America over two hundred years ago. Cassava Mosaic virus is now a major agricultural problem in Africa.

“If you go back to the centre of origin of Cassava it is not found at all, or anything like it. Scientists think it must have come from the native African plants and found Cassava to be a better host.”
Dr Lawrence Kenyon

Making a Leap?

I asked the scientists just how big a leap can virus species make between hosts. They agree;
“Viruses can jump from dogs to wolves, pigs to people and some of the genes move between species. They get inside cells where they can grow so there needs to be enough similarity between the cell types. Every gardener knows humans don’t get sick from plant viruses, the cell receptors are too different. The biggest jump we have seen in nature is SARS, from birds to people. This is exceptional and still within vertebrates.”
Professor Angela McLean

“Plant viruses have evolved to affect plants, just a few will also affect the insect carrying vector. Animal cells produce antibodies to foreign material and a plant virus will be recognised as such so animals don’t get infected.”
Dr Lawrence Kenyon

Who’s Life is it Anyway?

Personally I consider finding acceptable mechanisms of virus prevention an example of a really difficult dilemma and wonder whether ‘natural’ gene pool conservation can be considered desirable and achievable in today’s fast moving society. I would also like to know whether human created computer viruses exhibit similar emergence patterns to human, animal and plant varieties. Certainly, migration and translation generate immensely complex evolutionary effects across the earth’s systems.

I am not a geneticist or plant scientist, with no knowledge of Mandarin or Taiwanese, so a visit to the World Vegetable Centre (AVRDC) home for the World’s largest public vegetable gene bank, in Taiwan, tested my skills of interpretation and translation to the limit.

Working especially with farmer’s co-operatives across Asia, India and Africa, AVRDC supplies crop seeds, adapted to survive whatever misfortunes an increasingly fickle climate and trails of over breeding and overcrowding throw at them.

Headquarters for the World Vegetable Centre, an international Non Governmental Organisation is located in the region of the old Taiwan capital, Tainan County. The centre attracts scientists across the world, while retaining strong ties to the local community of Shan Hua, a town with a long established agricultural tradition.
Providing the roots for the Centre’s activities, Dr Andreus Ebert from Germany and Taiwanese Mr Whan share responsibility for curating Gene Bank’s the vast collection. I had the chance to glimpse inside the heart of this real life archive and out in the fields, speak to researchers using the records to conserve rare indigenous vegetables and create hardy new varieties of familiar favourites like tomatoes.

Approaching the bank my steps fall into the sifting rhythm, transmitted from a circle of people in conical straw hats, crouching among the trees, shifting and shaking pans of seeds. Like most things in Taiwan it was important to move beyond first impressions. I was soon to learn that this was more than a musical accompaniment, and in fact an ingrediant of the scientific process of sorting and selecting seeds for preservation in the gene bank vaults.

Changing into slippers so that I don’t carry spores, viruses or other plant pests in on my shoes, I accompany Dr Ebert on a guided tour of the bank.

1. Processing – Within the walls, genetic inheritance information from over 56,000 global varieties, collected over 30 years, is identified, coded and stored. Records in this unusual library are in the form of germplasm, the genetic information that allows plants to reproduce. While most is seeds, there is also an alium store for onions, shallots and garlic and tubors like potatoes as their structure and high moisture content needs different treatment.

   Shuffling into the first space, we see seeds being processed, extracted and cleaned, mostly by hand. Seeds are selected, bad seeds, very small seeds damaged seeds or those not confirming to the standards are removed. For long term preservation, temperature and humidity must come down. In this short term storage and processing area the temperature is cooled from the average 25-30 °C outside to 15°C.

2. Storage – The door of the cavernous chamber for medium term storage, clunked shut behind us. Here, temperature is reduced to 5°C like the inside of a domestic fridge, giant fans reducing the humidity to 45%. Different species require slightly different treatment to balance the temperature and humidity levels with the viability limits of the variety. Some seed surfaces will crack at lower temperatures, affecting their ability to grow outside. Coco seeds are not suitable for long term storage as they quickly loose viability, and coffee can only be stored for a few months.

   I was lucky enough to catch a rare glimpse inside the second chamber. The long term store can’t be opened very often as this will increase the already enormous amount of energy needed to regulate its environment. The humm of fans and giant fridges became a roar as the door sealed. Temperature is below 0 °C, with humidity of -10 to 18%. Under these conditions seeds are expected to last between 50 and 70 years.
   They must not however, be forgotten, samples are grown outside at regular intervals. I am told that farmers would soon complain if the proportion of viable seeds is low and they regularly fail to germinate. First seeds must be mobilised by imbibing to take up water. Plants can then be grown outside, and their seeds harvested to maintain the variety. Wherever possible, it is best to use the originals, as each time seeds are grown outside they start to adapt to the conditions in Taiwan, losing their native characteristics.

   Care is taken to preserve indigenous crops, defined as those that are not immediately of major commercial importance world wide, in line with national programmes across the World. Examples include, egg plants, okra, loofah and bitter gourds, rich in antioxidants under investigation for treating diabetes. Older varieties may be more hardy with better resistance to disease than cultivated hybrids with desirable commercial characteristics and a narrow genetic basis.

   Dr Ebert tells me, small farmers need to use a risk management strategy of growing mixed crops together so they are less vulnerable to specialist insect attack. Failure to do this was responsible for totally wiping out coffee in Shri Lnaka which had to be replaced by tea. It was necessary to return to the origin of the crop in Etheopia to find older varieties with natural genetic resistance. The gene bank exists to help manage such eventualities.

3. Conserving Indigenous Vegetables – Out in the sunshine, heavily pregnant Mandy Li-Ju Lin took me on a tour of the indigenous vegetable garden. Here, lesser known species with promising characteristics, either for commercial development or crossing with current popular varieties are grown. Tiny wild tomatoes gleam like holy berries, inedible for humans yet more hardy and resilient than their cultivated cousins. Creamy white African egg plant nestles among lush green and purple African cassava (sweet potato leaves) and, and I spot pink tarot popular in hotpots and markets across Taiwan. I am intrigued by the thorny coriander, popular in Thailand, exotic, pungent and aromatic for humans but far less attractive to insects than the commonly available round leafed type.

   Mandy told me many of these vegetables are considered to have strong unpleasant tastes and smells making them less popular candidates for commercial development. She reminded me they have uses beyond food like washing skin and clothes and water purification. As well as climate resilience plants can also be selected for nutritional properties such as high antioxidant or beta carotene content (vitamins). This is often indicated by deep colour, greens, purples and yellows, and can help human immunity. Plants shelter in net cages to protect them from virus carrying Taiwanese whitefly and avoid cross pollination, maintaining the purity of the lines.

   Transferring the information to records library helps prevent less immediately commercially attractive crops disappearing from existence, as farmers feel pressure to replace local varieties with high yield hybrids. Plants are measured, observed and photographed, recording days to flower and fruit, and fruit size and weight. I set out to discover how to identify which ones have the real X factor.

4. New Stress Resilient Varieties – In the greenhouse scientist Rachael Symonds (UK), described how she combines indigenous genes with commercial varieties to improve survival in extreme conditions.
   ‘I have been working at an international research centre with an international community for the global public good’
   “Why we are doing the research is to help plants survive under stress, for example tomatoes with thicker skin may be more resilient. This is vital now as the climate is changing and the world is getting drier and hotter. Plants, especially vegetables won’t be able to live where they do at the moment. We need to produce high value nutritious crops for areas most affected like Sub Saharan Africa.”

   She told me, commercial varieties can be crossed with wild types that you can’t eat to help their tolerance to stress. For example some types of inedible wild tomato growing naturally near the sea may be more resistant to drought and dehydration from salty soil by having a different type of cell membrane barrier structure. These can then be bred with some of the more commercial varieties to produce food crops better able to survive.

   “We’ve got a gene bank with thousands of varieties so we select types of interest, often going back to the wild type to cross them with cultivated varieties. Seeds that don’t get selected for one experiment are returned to the bank for use at another time and place.”

   Controlled experiments are used to test this out, comparing samples of tomatoes with known characteristics with the new varieties in controlled dry and wet conditions, artificially created in pots. Water and salt level are carefully measured and the resulting crop yields dried and weighed to establish whether or not there is a significant advantage, and if so its extent.

   “ I can take many types of measurements to describe the plants and their interaction with the environment. A breeding programme for a new variety can take three years to produce vegetables to eat.”

5. Packing and Labelling – Back inside the bank, Dr Ebert explained how packing and labelling is an essential step towards distribution of identified seeds. First, in the processing area, they are weighed and stored 20 – 30 in paper packages. A barcode system is used to identify the seeds and labels are placed on them by hand. Each time the packets are labelled there is a danger that two numbers could be exchanged and the barcode system is used to reduce errors.

   In the long term store, seeds are packed into vapour proof aluminium packets. Unlike the organic paper material this doesn’t have the same interaction with moisture in the environment. Before putting in these final bags seed samples are tested for moisture content, comparing it with the baseline. Given even the slightest hint of moisture seeds could germinate, rendering them useless for storage and future planting and breeding. The aluminium packets are kept in sealed drums for future.

6. Passport Data – ‘Integrated passport data’ for seed lines is represented on a freely accessible database. This information includes, a unique number to identify the lines, and like your own birthday, their date and place of collection. Nutritional information is also stored and used to inform the breeding process, together with research information from other parts of the Centre, to produce a well documented profile. The computerised records are freely available for anyone interested enough to browse them.
7. Safety Back Up – When disaster strikes such as the 2004 Boxing Day Tsunami in Shri Lanka is, this preserved collection enabled the farmers to go back to the seeds and start production again. Just like backing up your hard drive, a safety back up is made in a secure sister site in Korea. This is reassuring given that Taiwan is prone to earthquakes, and like anywhere is not without is vulnerabilities to climate catastrophe as demonstrated by the landslides shortly after my visit in 2009. Unlike a computer the genetic information is stored in the seeds themselves. Even in long term storage viability beyond fifty to seventy years is precarious, requiring a considerable energy.
8. Distribution – There is a small charge for distribution of seeds from the gene bank, staggered according to means, lower for national programmes and higher for seed companies. Co-ordinating distribution flow is tricky, as the Rio conference on Biodiversity in 1992 gave countries of origin ownership of seeds and plant materials. They can choose whether or not to make it available to the bank, grant or refuse permission for countries beyond their own borders to use them, placing restrictions on the bank. Dr Ebert suggests the current legislation is complex to implement because plant species don’t stick to international geographical and political boundary limits making it hard for any one country to prove which plants are native.

   “Co-operation and collaboration are needed to continue with the exchange to produce new varieties and feed a still growing world population with always less and less land which is more difficult with this legislation.”

   Balancing the need for movement with ecosystem preservation is a critical challenge. As sea levels rise in response to climate change, so does demand for heat, drought, flood and salt tolerance species, accelerating global redistribution of genes. At the same time, recognition of the importance of wild and domestic varieties is higher than ever, as farmers need to incorporate characteristics from wild types, more hardy to poor soil and extreme temperatures into the higher yielding varieties. Seeds are treated for pests before leaving the bank and quarantine encouraged in the receiving country.

9. Consumer Choice – World Wide, Who’s to say what happens to the gene lines on leaving the bank, as on reaching their destination seeds will enter agricultural production as the farmers see fit exposing them to cross breeding at the discretion of local humans, animals, birds and insect behaviour. Despite best efforts, it is not possible for the gene bank to certify that seeds are virus and pest free. Post entry quarantine and growing out isolated samples in the destination country is required to check for disease that might be present but not show up in Taiwan. Success now, is dependent on local knowledge and expertise, and outcomes cannot be completely controlled.

   The gene bank is vital in countering the threat of a narrowing gene base as farmers select for specific traits, leaving commercially valuable crops with large juicy fruit crops that are both attractive to insects and vulnerable to devastation by viruses. The coffee crisis in Shri Lanka, demonstrated this threat is real. Today, thanks to consumer’s preference for flavour, taste and colour, older stronger varieties are becoming more popular, despite having lower yields. This trend for quality has allowed niche markets for unusual varieties to develop, powerful encouragement for preserving the world’s diverse genetic heritage.

For more information visit:
http://www.avrdc.org/index.php?id=13

Even for the most distractible amongst us, it would have been hard not to pick up on the recent news that researchers at the University of Cardiff have discovered a genetic component for Attention Deficit Hyperactivity Disorder (ADHD). I was woken up by this news on the Today Programme, was reminded of it in every news bulletin during the day and then heard it quipped about two days later when listening to The News Quiz.

With the announcement of this study, the timeworn debate returned between those who suggest that parents are to blame for a child’s particular problems and those who say that these issues are more likely to be caused by a hardwired malfunction in the brain. Taken at face value, the discovery of a genetic component in ADHD makes the latter explanation more plausible. But does this mean that the genetic difference is solely responsible for the problems in these children? And are those who suggest that the disorder originates with the environment created by the parents completely wrong?

This debate did not start with ADHD. Back in 1949, Austrian psychiatrist Leo Kanner suggested that a lack of maternal warmth (from so-called “refrigerator parents”) was the cause for autism. In fact, the concept of “nature versus nurture” was first coined in the late 1860s by Sir Francis Galton to describe the influence of innate characteristics as compared to environmental factors and personal experience on someone’s behaviour.

Yet I was struck listening to the heated discussion on the Today Programme between Oliver James, in the Nurture corner, and the lead author of the study Professor Anita Thapar for the Nature side, that there was actually not as much division between the supposedly polarised opinions as the tone of some of the comments implied. Both contributors acknowledged a role for both environment and genes, with the point of contention being over the relative influence of each. Indeed, my sense as a scientist, admittedly working several steps removed from the front line of this research, has been that a lot of the most interesting work focuses its attention precisely at the intersection of these two extremes: how genes and our environment interact with one another to make us who we are.

One example of such a multi-influence approach comes from a neuroimaging study conducted by researchers at the Donders Institute for Brain, Cognition and Behaviour that appeared in May of this year in Proceeding of the National Academy of Sciences1. The study showed that an evolutionarily old part of the brain called the amygdala seems to be particularly active in stressful situations in a subset of people who, compared to the majority of the population, have a slightly different form of a specific gene which codes for a receptor in the brain that responds to a neurochemical called noradrenaline. Noradrenaline plays a role in regulating arousal and where to direct attention in the world, while the amygdala is thought to be involved in working out how to respond to emotional situations and is also a critical node in a circuit of brain regions that store and remember such arousing events. Similarly, a large epidemiological study conducted at the Institute of Psychiatry in London, published in Science back in 2003, indicated that people who had a particular form of the gene which codes for the serotonin transporter in the brain were more likely to succumb to depression and suicide in the face of stressful life events2. In both these examples, a genetic component is present, but environmental conditions (in the above examples the presence of a stressful life event) ‘decide’ whether the gene is expressed.

I was reminded of this intersection between genes and environment when on the 30th September Professor Colin Blakemore gave an enjoyable and eloquent lecture on that small topic of “The Brain” at Science Oxford. Our brains, Professor Blakemore illustrated, are modular: different functions happen in different areas. To the untrained eye, these areas are more-or-less in the same place in us all. For instance, when any of us looks at another person’s face, a specific region in each and every one of our brains becomes active. This region, found in the back of the brain towards the sides of our head (and on both sides of the brain), is called the fusiform gyrus, and, because of the information it is interested in, is also sometimes referred to as the fusiform face area.

Generally, our genes ensure that our brains develop as mammalian evolution has specified. However, that does not mean that they could not develop differently. In a series of technically elegant experiments at MIT in 2000, Mriganka Sur’s research team showed that if the visual pathways in a ferret are re-routed towards the part of the brain that would customarily process sound, then this “auditory” cortex would develop maps of the visual world similar to those normally found in “visual” cortex3,4. In other words, the back of our brains is “visual” cortex not because our genes allow it to become a special visual part of the brain, but mainly because they ensure it is set up to receive visual information from our eyes.

Indeed, as Professor Blakemore pointed out, just as striking as the modularity of the brain is its profound ability to alter its structure. Professor Blakemore showed a dramatic example of such neural plasticity, as it is commonly called, in people who lost their vision later in life. He and his colleagues asked people who had become blind at a later stage in their lives, after having experienced normal vision, to explore a human-like face of a doll and a face-like non-recognisable shape with their hands. As we have seen above, when sighted people are looking at faces, the fusiform face area becomes active. The striking result of this study was that when the blind people explored the human face-like object with their hands, the same fusiform face area became active. No such activation was observed when sighted people touched the human face-like object. Thus, areas normally involved in purely visual information processing can develop this ability to process information from other sensory modalities when people are deprived of sight5.

But it is not only such circumstances of physical loss that cause structural changes within the brain to occur. They are also brought about by more mundane and everyday events such as learning and the creation of memories. In a study published in Nature Neuroscience in November 2009, a group at the Oxford Centre for Functional Magnetic Resonance Imaging of the Brain led by Dr Heidi Johansen-Berg showed quite how plastic our brains can be6. Her research group recruited a group of volunteers and scanned them in an MRI scanner to investigate the structure of their brains. Then the experiment became slightly more trying: the participants had to learn to juggle. The training regime was intense; participants practiced for half an hour every day, 5 days a week for six week, after which they again had an MRI scan. When the researchers compared the brains from before and after, they found that the brain’s white matter pathways – the connections between brain structures responsible for communication between them – had changed significantly since becoming an expert juggler in one discrete region thought to be involved linking together our visual and motor systems. Thus, Dr Johansen-Berg’s group showed for the first time a direct correlation between acquiring and practicing a new motor skill and structural changes in the human brain.

While this is of course of interest for any of us keen on learning new circus tricks, the deeper purpose of the research is to discover how the human brain can change in the face of new circumstances and how training may specifically facilitate this process. Such knowledge may be of invaluable use for understanding how to help rehabilitate patients with motor problems as a result of brain damage.

While it may seem that way, this study is by no means trying to undermine the power of genetics. We all know of people who seem to be better coordinated than others or who are more naturally physically skilled or athletic. Indeed, in the above study, there were differences in the speed with which participants learned to juggle. A recent review by Giuseppe Lippi and colleagues in the British Medical Bulletin suggests that there is increasing evidence for some genetic basis to sporting abilities, although many different genes are implicated and the precise interactions between genes and the environment and training are likely to be highly complex7.

When New Yorker writer Malcolm Gladwell’s book “Outliers, the story of success”, first came out, it received a lot of attention as it seemed to say what all of us want to hear: everyone can become a genius or a sports star, as long as enough time is dedicated to practising. Gladwell suggests that aptitude or innate talent has little to do with success and genius, but instead relies on a combination of happenstance and extraordinary persistence: around 10,000 hours of practice, to be precise8. Again, however, this should not necessarily be seen as another example sidelining the importance of genes. Instead, Gladwell argues that, rather than a particular musical aptitude or footballing skill being genetically-determined, it may instead be traits such as single-minded determination and desire – he even goes as far as to call it love – for a single topic that might be influenced by our genes. If you are interested in listening to Gladwell’s arguments, you can find him here in conversation with Robert Krulwich of the wonderful American science based radio programme Radiolab.

In line with this, behavioural genetics studies have long indicated that genes are not simply passive recipients of whatever influences are provided by the environments their host organisms should find themselves in. Instead, genes can also actively and passively “create” environmental circumstances. For instance, someone who has the genetic make-up to be outgoing may attract more social situations (i.e. may often be invited to parties or events) than someone whose genes make them more introverted in nature. And it is likely that this is just a continuation from infancy: a smiley and sociable baby is likely to evoke more socially rich responses than a shy baby. Thus, our genes seek out particular environments by influencing our behaviour (sociability leads to more party invitations) and the way in which we behave also influences our environment (sociability in a smiley baby is reinforced by more social responses from the environment).

All these examples give us a very complex picture of ourselves, our behaviour and even our environment. Genes and environment, or nature and nurture, work together in intricate ways to create not only who we are, but also what the circumstances are we find ourselves in. Thus, it seems rather pointless to focus on just the one and ignore the other. The ADHD debate could have been a lot more interesting and productive if the journalists and news producers had not just been looking for a scapegoat.

1. Cousijn H, Rijpkema M, Qin S, Shaozheng, Marle HJF, Franke B, Hermans EJ, Wingen G, Fernández, G (2010). Acute stress modulates genotype effects on amygdala processing in humans. Proceedings of the National Academy of Science 107, 9867-9872.
2. Caspi A, Sugden K, Moffitt TE, Taylor A, Craig IW, Harrington H et al., (2003). Influence of life stress on depression: moderation by a polymorphism in the 5-HTT gene, Science 301, 386–389.
3. Sharma J, Angelucci A, Sur M (2000). Induction of visual orientation modules in auditory cortex. Nature 404, 841–847.
4. Dragoi V, Sharma J, Sur M (2000). Adaptation-induced plasticity of orientation tuning in adult visual cortex. Neuron 28, 287–298.
5. Goyal MS, Hansen PJ, Blakemore CB (2006). Tactile perception recruits functionally related visual areas in the late-blind. Neuroreport 17, 1381-1384.
6. Scholz J, Klein MC, Behrens TE, Johansen-Berg H (2009). Training induces changes in white-matter architecture. Nature Neuroscience 12, 1370-1371.
7. Lippi G, Longo UG, Maffulli N (2010). Genetics and sports. British Medical Bulletin 93, 27-47.
8. Gladwell M. (2008). Outliers, the story of success. Little, Brown and Company, New York.

Researchers at the J. Craig Venter Institute (JCVI) published results today describing the successful construction of the first self-replicating, synthetic bacterial cell. The team synthesised the 1.08 million base pair chromosome of a modified Mycoplasma mycoides genome. The synthetic cell is called Mycoplasma mycoides JCVI-syn1.0 and is the proof of principle that genomes can be designed in the computer, chemically made in the laboratory and transplanted into a recipient cell to produce a new self-replicating cell controlled only by the synthetic genome.

This research will be published by Daniel Gibson et al in the 20th May edition of Science Express and will appear in an upcoming print issue of Science.

‘For nearly 15 years Ham Smith, Clyde Hutchison and the rest of our team have been working toward this publication today – the successful completion of our work to construct a bacterial cell that is fully controlled by a synthetic genome,’ said J. Craig Venter, Ph.D., founder and president, JCVI and senior author on the paper. ‘We have been consumed by this research, but we have also been equally focused on addressing the societal implications of what we believe will be one of the most powerful technologies and industrial drivers for societal good. We look forward to continued review and dialogue about the important applications of this work to ensure that it is used for the benefit of all.’

According to Dr Smith, ‘With this first synthetic bacterial cell and the new tools and technologies we developed to successfully complete this project, we now have the means to dissect the genetic instruction set of a bacterial cell to see and understand how it really works.’

To complete this final stage in the nearly 15 year process to construct and boot up a synthetic cell, JCVI scientists began with the accurate, digitised genome of the bacterium, M. mycoides. The team designed 1,078 specific cassettes of DNA that were 1,080 base pairs long. These cassettes were designed so that the ends of each DNA cassette overlapped each of its neighbours by 80bp. The cassettes were made according to JCVI’s specifications by the DNA synthesis company, Blue Heron Biotechnology.

The JCVI team employed a three stage process using their previously described yeast assembly system to build the genome using the 1,078 cassettes. The first stage involved taking 10 cassettes of DNA at a time to build 110, 10,000 bp segments. In the second stage, these 10,000 bp segments are taken 10 at a time to produce eleven, 100,000 bp segments. In the final step, all 11, 100 kb segments were assembled into the complete synthetic genome in yeast cells and grown as a yeast artificial chromosome.

The complete synthetic M. mycoides genome was isolated from the yeast cell and transplanted into Mycoplasma capricolum recipient cells that have had the genes for its restriction enzyme removed. The synthetic genome DNA was transcribed into messenger RNA, which in turn was translated into new proteins. The M. capricolum genome was either destroyed by M. mycoides restriction enzymes or was lost during cell replication. After two days viable M. mycoides cells, which contained only synthetic DNA, were clearly visible on petri dishes containing bacterial growth medium.

The initial synthesis of the synthetic genome did not result in any viable cells so the JCVI team developed an error correction method to test that each cassette they constructed was biologically functional. They did this by using a combination of 100 kb natural and synthetic segments of DNA to produce semi-synthetic genomes. This approach allowed for the testing of each synthetic segment in combination with 10 natural segments for their capacity to be transplanted and form new cells. Ten out of 11 synthetic fragments resulted in viable cells; therefore the team narrowed the issue down to a single 100 kb cassette. DNA sequencing revealed that a single base pair deletion in an essential gene was responsible for the unsuccessful transplants. Once this one base pair error was corrected, the first viable synthetic cell was produced.

Dr Gibson stated, ‘To produce a synthetic cell, our group had to learn how to sequence, synthesise, and transplant genomes. Many hurdles had to be overcome, but we are now able to combine all of these steps to produce synthetic cells in the laboratory.’ He added, ‘We can now begin working on our ultimate objective of synthesising a minimal cell containing only the genes necessary to sustain life in its simplest form. This will help us better understand how cells work.’

This publication represents the construction of the largest synthetic molecule of a defined structure; the genome is almost double the size of the previous Mycoplasma genitalium synthesis. With this successful proof of principle, the group will now work on creating a minimal genome, which has been a goal since 1995. They will do this by whittling away at the synthetic genome and repeating transplantation experiments until no more genes can be disrupted and the genome is as small as possible. This minimal cell will be a platform for analysing the function of every essential gene in a cell.

According to Dr Hutchison, ‘To me the most remarkable thing about our synthetic cell is that its genome was designed in the computer and brought to life through chemical synthesis, without using any pieces of natural DNA. This involved developing many new and useful methods along the way. We have assembled an amazing group of scientists that have made this possible.’

As in the team’s 2008 publication in which they described the successful synthesis of the M. genitalium genome, they designed and inserted into the genome what they called watermarks. These are specifically designed segments of DNA that use the ‘alphabet’ of genes and proteins that enable the researcher to spell out words and phrases. The watermarks are an essential means to prove that the genome is synthetic and not native, and to identify the laboratory of origin. Encoded in the watermarks is a new DNA code for writing words, sentences and numbers. In addition to the new code there is a web address to send emails to if you can successfully decode the new code, the names of 46 authors and other key contributors and three quotations: ‘TO LIVE, TO ERR, TO FALL, TO TRIUMPH, TO RECREATE LIFE OUT OF LIFE.’ – JAMES JOYCE; ‘SEE THINGS NOT AS THEY ARE, BUT AS THEY MIGHT BE.’ – A quote from the book, ‘American Prometheus’; ‘WHAT I CANNOT BUILD, I CANNOT UNDERSTAND.’ – RICHARD FEYNMAN.

The JCVI scientists envision that the knowledge gained by constructing this first self-replicating synthetic cell, coupled with decreasing costs for DNA synthesis, will give rise to wider use of this powerful technology. This will undoubtedly lead to the development of many important applications and products including biofuels, vaccines, pharmaceuticals, clean water and food products. The group continues to drive and support ethical discussion and review to ensure a positive outcome for society.

Funding for this research came from Synthetic Genomics Inc., a company co-founded by Drs. Venter and Smith.

A team of scientists from Columbia University, Arizona State University, the University of Michigan, and the California Institute of Technology (Caltech) have programmed an autonomous molecular “robot” made out of DNA to start, move, turn, and stop while following a DNA track.

The development could ultimately lead to molecular systems that might one day be used for medical therapeutic devices and molecular-scale reconfigurable robots—robots made of many simple units that can reposition or even rebuild themselves to accomplish different tasks.

A paper describing the work appears in the current issue of the journal Nature.

The traditional view of a robot is that it is “a machine that senses its environment, makes a decision, and then does something—it acts,” says Erik Winfree, associate professor of computer science, computation and neural systems, and bioengineering at Caltech.

Milan N. Stojanovic, a faculty member in the Division of Experimental Therapeutics at Columbia University, led the project and teamed up with Winfree and Hao Yan, professor of chemistry and biochemistry at Arizona State University and an expert in DNA nanotechnology, and with Nils G. Walter, professor of chemistry and director of the Single Molecule Analysis in Real-Time (SMART) Center at the University of Michigan in Ann Arbor, for what became a modern-day self-assembly of like-minded scientists with the complementary areas of expertise needed to tackle a tough problem.

Shrinking robots down to the molecular scale would provide, for molecular processes, the same kinds of benefits that classical robotics and automation provide at the macroscopic scale. Molecular robots, in theory, could be programmed to sense their environment (say, the presence of disease markers on a cell), make a decision (that the cell is cancerous and needs to be neutralized), and act on that decision (deliver a cargo of cancer-killing drugs).

Or, like the robots in a modern-day factory, they could be programmed to assemble complex molecular products. The power of robotics lies in the fact that once programmed, the robots can carry out their tasks autonomously, without further human intervention.

With that promise, however, comes a practical problem: how do you program a molecule to perform complex behaviors?

“In normal robotics, the robot itself contains the knowledge about the commands, but with individual molecules, you can’t store that amount of information, so the idea instead is to store information on the commands on the outside,” says Walter. And you do that, says Stojanovic, “by imbuing the molecule’s environment with informational cues.”

“We were able to create such a programmed or ‘prescribed’ environment using DNA origami,” explains Yan. DNA origami, an invention by Caltech Senior Research Associate Paul W. K. Rothemund, is a type of self-assembled structure made from DNA that can be programmed to form nearly limitless shapes and patterns (such as smiley faces or maps of the Western Hemisphere or even electrical diagrams). Exploiting the sequence-recognition properties of DNA base pairing, DNA origami are created from a long single strand of DNA and a mixture of different short synthetic DNA strands that bind to and “staple” the long DNA into the desired shape. The origami used in the Nature study was a rectangle that was 2 nanometers (nm) thick and roughly 100 nm on each side.

The researchers constructed a trail of molecular “bread crumbs” on the DNA origami track by stringing additional single-stranded DNA molecules, or oligonucleotides, off the ends of the staples. These represent the cues that tell the molecular robots what to do—start, walk, turn left, turn right, or stop, for example—akin to the commands given to traditional robots.

The molecular robot the researchers chose to use—dubbed a “spider”—was invented by Stojanovic several years ago, at which time it was shown to be capable of extended, but undirected, random walks on two-dimensional surfaces, eating through a field of bread crumbs.

To build the 4-nm-diameter molecular robot, the researchers started with a common protein called streptavidin, which has four symmetrically placed binding pockets for a chemical moiety called biotin. Each robot leg is a short biotin-labeled strand of DNA, “so this way we can bind up to four legs to the body of our robot,” Walter says. “It’s a four-legged spider,” quips Stojanovic. Three of the legs are made of enzymatic DNA, which is DNA that binds to and cuts a particular sequence of DNA. The spider also is outfitted with a “start strand”—the fourth leg—that tethers the spider to the start site (one particular oligonucleotide on the DNA origami track). “After the robot is released from its start site by a trigger strand, it follows the track by binding to and then cutting the DNA strands extending off of the staple strands on the molecular track,” Stojanovic explains.

“Once it cleaves,” adds Yan, “the product will dissociate, and the leg will start searching for the next substrate.” In this way, the spider is guided down the path laid out by the researchers. Finally, explains Yan, “the robot stops when it encounters a patch of DNA that it can bind to but that it cannot cut,” which acts as a sort of flypaper.

Although other DNA walkers have been developed before, they’ve never ventured farther than about three steps. “This one,” says Yan, “can walk up to about 100 nanometers. That’s roughly 50 steps.”

“This in itself wasn’t a surprise,” adds Winfree, “since Milan’s original work suggested that spiders can take hundreds if not thousands of processive steps. What’s exciting here is that not only can we directly confirm the spiders’ multistep movement, but we can direct the spiders to follow a specific path, and they do it all by themselves—autonomously.”

In fact, using atomic force microscopy and single-molecule fluorescence microscopy, the researchers were able to watch directly spiders crawling over the origami, showing that they were able to guide their molecular robots to follow four different paths.

“Monitoring this at a single molecule level is very challenging,” says Walter. “This is why we have an interdisciplinary, multi-institute operation. We have people constructing the spider, characterizing the basic spider. We have the capability to assemble the track, and analyze the system with single-molecule imaging. That’s the technical challenge.” The scientific challenges for the future, Yan says, “are how to make the spider walk faster and how to make it more programmable, so it can follow many commands on the track and make more decisions, implementing logical behavior.”

“In the current system,” says Stojanovic, “interactions are restricted to the walker and the environment. Our next step is to add a second walker, so the walkers can communicate with each other directly and via the environment. The spiders will work together to accomplish a goal.” Adds Winfree, “The key is how to learn to program higher-level behaviors through lower-level interactions.”

Such collaboration ultimately could be the basis for developing molecular-scale reconfigurable robots—complicated machines that are made of many simple units that can reorganize themselves into any shape—to accomplish different tasks, or fix themselves if they break. For example, it may be possible to use the robots for medical applications. “The idea is to have molecular robots build a structure or repair damaged tissues,” says Stojanovic.

“You could imagine the spider carrying a drug and bonding to a two-dimensional surface like a cell membrane, finding the receptors and, depending on the local environment,” adds Yan, “triggering the activation of this drug.”

Such applications, while intriguing, are decades or more away. “This may be 100 years in the future,” Stojanovic says. “We’re so far from that right now.”

“But,” Walter adds, “just as researchers self-assemble today to solve a tough problem, molecular nanorobots may do so in the future.”

The other coauthors on the paper, “Molecular robots guided by prescriptive landscapes,” are Kyle Lund and Jeanette Nangreave from Arizona State University; Anthony J. Manzo, Alexander Johnson-Buck, and Nicole Michelotti from the University of Michigan; Nadine Dabby from Caltech; and Steven Taylor and Renjun Pei from Columbia University. The work was supported by the National Science Foundation, the Army Research Office, the Office of Naval Research, the National Institutes of Health, the Department of Energy, the Searle Foundation, the Lymphoma and Leukemia Society, the Juvenile Diabetes Research Foundation, and a Sloan Research Fellowship.

Contact: Kathy Svitil ksvitil@caltech.edu

Image Credit: Courtesy of Paul Michelotti

Sci­en­tists are re­port­ing that they have de­cod­ed more than half the Ne­an­der­thal ge­nome, and that the da­ta sup­ports a the­o­ry that our an­cest­ors in­ter­bred with Ne­an­der­thal peo­ple a lit­tle.

The sci­en­tists de­vised a draft ge­nome se­quence, or a list of the “let­ters” in a crea­ture’s ge­ne­tic code. These “let­ters” con­sist of mo­lec­u­lar un­its called nu­cleotides that make up the DNA. An anal­y­sis of this se­quence can re­veal in­forma­t­ion about an or­gan­is­m’s an­ces­try.

Sci­en­tists used pill-sized sam­ples of pow­der from three bones of Ne­an­der­thals, a stocky an­cient breed of hu­mans that co-ex­isted wth an­ces­tors of mod­ern hu­mans. The find­ings ap­pear in the May 7 is­sue of the re­search jour­nal Sci­ence.

The re­search­ers, led by Svante Pääbo of the Max Planck In­sti­tute for Ev­o­lu­tion­ary An­thro­po­l­ogy in Leip­zig, Ger­ma­ny, com­pared the Ne­an­der­thal ge­nome with ge­nomes of five pre­s­ent-day hu­mans.

The re­sults al­so re­vealed var­i­ous genes that are un­ique to mod­ern peo­ple, the sci­en­tists said, in­clud­ing a hand­ful of genes that spread rap­idly among our spe­cies af­ter we split from a com­mon an­ces­tor we shared with Ne­an­der­thals. Among these genes are three be­lieved to af­fect men­tal and cog­ni­tive de­vel­op­ment; muta­t­ions in these genes are linked to con­di­tions such as Down syn­drome, schiz­o­phre­nia and au­tism.

“For the first time we can now iden­ti­fy ge­net­ic fea­tures that set us apart from all oth­er or­gan­isms, in­clud­ing our clos­est ev­o­lu­tion­ary rel­a­tives,” Ne­an­der­thals, said Pääbo. “This [work] really just hints at what genes one should now stu­dy, and I’m sure we and many oth­er groups will be do­ing that.”

Ne­an­der­thals first ap­peared around 400,000 years ago, ranged across Eu­rope and west­ern Asia, and died out about 30,000 years ago. The draft Ne­an­der­thal ge­nome se­quence be­ing re­ported rep­re­sents about 60 per­cent of the ge­nome; the da­ta was worked out us­ing bones found in a cave in Cro­a­tia.

Pääbo and col­leagues al­so se­quenced the ge­nomes of five pre­s­ent-day hu­mans from south­ern Af­ri­ca, West Af­ri­ca, Pap­ua New Guin­ea, Chi­na and France, to com­pare with the Ne­an­der­thal ge­nome.

The Ne­an­der­thal ge­nome proved slightly more si­m­i­lar to those of the non-Af­ri­can peo­ple than Af­ri­cans, said the in­ves­ti­ga­tors. One of the sim­plest sce­nar­i­os to ex­plain this and some pre­vi­ous da­ta, they added, is that af­ter mod­ern hu­mans mi­grat­ed out of Af­ri­ca, they en­coun­tered and in­ter­bred with Ne­an­der­thals in the Mid­dle East. The han­ky-pan­ky seems to have been fairly lim­it­ed, judg­ing from the extent of the si­m­il­ar­ities, but “it’s cool to think that some of us have a lit­tle Ne­an­der­thal DNA in us,” Pääbo said.

Article Credit: World Science

A California Institute of Technology (Caltech)-led team of researchers and clinicians has published the first proof that a targeted nanoparticle – used as an experimental therapeutic and injected directly into a patient’s bloodstream – can traffic into tumours, deliver double-stranded small interfering RNAs (siRNAs), and turn off an important cancer gene using a mechanism known as RNA interference (RNAi). Moreover, the team provided the first demonstration that this new type of therapy, infused into the bloodstream, can make its way to human tumours in a dose-dependent fashion – i.e., a higher number of nanoparticles sent into the body leads to a higher number of nanoparticles in the tumour cells.

These results, published in the March 21 advance online edition of the journal Nature, demonstrate the feasibility of using both nanoparticles and RNAi-based therapeutics in patients, and open the door for future ‘game-changing’ therapeutics that attack cancer and other diseases at the genetic level, says Mark Davis, the Warren and Katharine Schlinger Professor of Chemical Engineering at Caltech, and the research team’s leader.

The discovery of RNA interference, the mechanism by which double strands of RNA silence genes, won researchers Andrew Fire and Craig Mello the 2006 Nobel Prize in Physiology or Medicine. The scientists first reported finding this novel mechanism in worms in a 1998 Nature paper. Since then, the potential for this type of gene inhibition to lead to new therapies for diseases like cancer has been highly touted.

‘RNAi is a new way to stop the production of proteins,’ says Davis. What makes it such a potentially powerful tool, he adds, is the fact that its target is not a protein. The vulnerable areas of a protein may be hidden within its three-dimensional folds, making it difficult for many therapeutics to reach them. In contrast, RNA interference targets the messenger RNA (mRNA) that encodes the information needed to make a protein in the first place.

‘In principle,’ says Davis, ‘that means every protein now is druggable because its inhibition is accomplished by destroying the mRNA. And we can go after mRNAs in a very designed way given all the genomic data that are and will become available.’

Still, there have been numerous potential roadblocks to the application of RNAi technology as therapy in humans. One of the most problematic has been finding a way to ferry the therapeutics, which are made up of fragile siRNAs, into tumour cells after direct injection into the bloodstream. Davis, however, had a solution. Even before the discovery of RNAi, he and his team had begun working on ways to deliver nucleic acids into cells via systemic administration. They eventually created a four-component system – featuring a unique polymer – that can self-assemble into a targeted, siRNA-containing nanoparticle. The siRNA delivery system is under clinical development by Calando Pharmaceuticals, Inc., a Pasadena-based nanobiotech company.

‘These nanoparticles are able to take the siRNAs to the targeted site within the body,’ says Davis. Once they reach their target – in this case, the cancer cells within tumours – the nanoparticles enter the cells and release the siRNAs.

The scientific results described in the Nature paper are from a Phase I clinical trial of these nanoparticles that began treating patients in May 2008. Phase I trials are, by definition, safety trials; the idea is to see if and at what level the drug or other therapy turns harmful or toxic. These trials can also provide an in-human scientific proof of concept – which is exactly what is being reported in the Nature paper.

Using a new technique developed at Caltech, the team was able to detect and image nanoparticles inside cells biopsied from the tumours of several of the trial’s participants. In addition, Davis and his colleagues were able to show that the higher the nanoparticle dose administered to the patient, the higher the number of particles found inside the tumour cells – the first example of this kind of dose-dependent response using targeted nanoparticles.

Even better, Davis says, the evidence showed the siRNAs had done their job. In the tumour cells analysed by the researchers, the mRNA encoding the cell-growth protein ribonucleotide reductase had been degraded. This degradation, in turn, led to a loss of the protein.

More to the point, the mRNA fragments found were exactly the length and sequence they should be if they’d been cleaved in the spot targeted by the siRNA, notes Davis. ‘It’s the first time anyone has found an RNA fragment from a patient’s cells showing the mRNA was cut at exactly the right base via the RNAi mechanism,’ he says. ‘It proves that the RNAi mechanism can happen using siRNA in a human.’

‘There are many cancer targets that can be efficiently blocked in the laboratory using siRNA, but blocking them in the clinic has been elusive,’ says Antoni Ribas, associate professor of medicine and surgery at UCLA’s Jonsson Comprehensive Cancer Centre. ‘This is because many of these targets are not amenable to be blocked by traditionally designed anti-cancer drugs. This research provides the first evidence that what works in the lab could help patients in the future by the specific delivery of siRNA using targeted nanoparticles. We can start thinking about targeting the untargetable.’

‘Although these data are very early and more research is needed, this is a promising study of a novel cancer agent, and we are proud of our contribution to the initial clinical development of siRNA for the treatment of cancer,’ says Anthony Tolcher, director of clinical research at South Texas Accelerated Research Therapeutics (START).

‘Promising data from the clinical trials validates our years of research at City of Hope into ribonucleotide reductase as a target for novel gene-based therapies for cancer,’ adds coauthor Yun Yen, associate director for translational research at City of Hope. ‘We are seeing for the first time the utility of siRNA as a cancer therapy and how nanotechnology can target cancer cells specifically.’

The Phase I trial – sponsored by Calando Pharmaceuticals – is proceeding at START and UCLA’s Jonsson Comprehensive Cancer Centre, and the clinical results of the trial will be presented at a later time. ‘At the very least, we’ve proven that the RNAi mechanism can be used in humans for therapy and that the targeted delivery of siRNA allows for systemic administration,’ Davis says. ‘It is a very exciting time.’

Imagine if your fear of spiders, heights or flying could be cured with a simple injection. Research published in BioMed Central’s open access journal, Behavioural and Brain Functions suggests that one day this could be a reality.

The cerebellum, an area of the brain thought to be involved with the development of our fears, was studied in goldfish by researchers at the University of Hiroshima in Japan. Using classical conditioning, Masayuki Yoshida and Ruriko Hirano taught their fish to become afraid of a light flashed in their eyes. By administering a low voltage electric shock every time a light was shone, the fish were taught to associate the light with being shocked, which slowed their hearts – the typical fish reaction to a fright. Yoshida explains, ‘As you would expect, the goldfish we used in our study soon became afraid of the flash of light because, whether or not we actually gave them a shock, they had quickly learned to expect one. Fear was demonstrated by their heart beats decreasing, in a similar way to how our heart rate increases when someone gives us a fright.’

Humans can also be ‘trained’ to become afraid, and in fact, simple classical conditioning rooted in our childhood and early development can explain many of our behaviours. In this study however, the team discovered that fish that had first been injected in the cerebellum with lidocaine had stable heart rates and showed no fear when the light was shone – they were unable to learn to become afraid.

Since the brains of goldfish show many similarities with those of mammals, including humans, it is hoped that with further study it may soon be possible to understand more about the biological and chemical processes that cause us to become afraid. For the goldfish, the effect of lidocaine is only temporary – fearless fish return to being frightened fish as soon as the anaesthetic has worn off. Nevertheless, one day, our irrational phobias could become a thing of the past.

A research team led by the University of Colorado at Boulder has discovered a previously unknown cellular ‘switch’ that may provide researchers with a new means of triggering programmed cell death, findings with implications for treating cancer.

The new results are a big step forward in understanding programmed cell death, or apoptosis, a cell suicide process that involves a series of biochemical events leading to changes like cell body shrinkage, mitochondria destruction and chromosome fragmentation, said CU-Boulder Professor Ding Xue. But unlike traumatic cell death from injury, programmed cell death is a naturally occurring aspect of animal development that may help prevent human diseases like cancer and autoimmune disorders, said Xue, lead author on the new study.

In the new study, Xue and his team found that a well-known cellular molecule called caspase – known as the ‘executioner enzyme’ for apoptosis because of its primary role of cutting up and destroying cellular proteins – has an entirely different effect on a particular enzyme called Dicer. The team found that when caspase cleaves Dicer, it does not kill it but instead changes its function, causing Dicer to break up chromosomes – pieces of coiled DNA containing thousands of genes – and kill the cells that house them.

‘This finding was totally unexpected,’ said Xue of CU-Boulder’s molecular, cellular and developmental biology department. ‘We believe that by understanding this mechanism, we may be able to develop a new way to trigger cell death in a controlled manner as a way to treat disease.’

A paper on the subject appears in the March 12 issue of Science. Co-authors on the study included CU-Boulder postdoctoral researchers Akihisa Nakagawa and Yong Shi and Tokyo Women’s Medical University researchers Eriko Kage-Nakadai and Shohei Mitani.

The normal function of Dicer is to snip strands of RNA into smaller pieces that attach to messenger RNA molecules – which carry DNA’s genetic messages from the nucleus of cells to make specific proteins in cell cytoplasm – and silence their activity, said Xue. But when caspase comes in contact with Dicer, it takes away Dicer’s ability to cleave RNA and it replaces it with the ability to snip up and destroy DNA-laden chromosomes.

The experiments were undertaken on a common, eyelash-sized nematode known as Caenorhabditis elegans, a popular laboratory organism for genetic and biomedical experiments. The study of cell death in C. elegans is providing critical information to scientists trying to understand cell death mechanisms in humans and identify ways to combat human diseases caused by ‘inappropriate apoptosis,’ Xue said.

‘There are many enzymes whose job it is to cut RNA, and many unrelated enzymes whose job it is to cut DNA,’ said CU-Boulder MCD Biology Department Chair Tom Blumenthal, who studies RNA processing in C. elegans and who was not involved in the study. ‘But this is the first time that anyone has shown that it is possible to cleave an RNA-cutter enzyme and thereby convert it to a DNA-cutter enzyme.’

As part of the study, the team ‘knocked out’ the C. elegans gene that encodes the Dicer enzyme. The removal of the gene compromised the apoptosis process and blocked the fragmentation of chromosomes, said Xue.

Genetic studies of C. elegans have identified many genes that are important for the five sequential steps of programmed cell death, Xue said. They include the specification of which cells should die, the activation of the cell death program, the onset of the killing process, the engulfment of cell ‘corpses’ and the degradation of cellular debris, said Xue.

‘Our findings initially seemed too good to be true,’ said Xue, who said the team has been working on the project for five years. ‘We wound up looking at the results from a number of angles, including genetics, cell biology and biochemistry. Eventually we reached the only logical conclusions we could make.’

‘This is a completely novel finding, and all of the players in this story are well known, well studied aspects of a very important process in our lives,’ said Blumenthal. ‘The minute I saw the results, I knew it was a very, very important finding with wide implications.’

Since the failure of apoptosis is one of the main contributors to the development of tumours, many biomedical researchers believe that a better understanding of the programmed cell death process could lead to potential therapeutic agents for those suffering from a number of diseases caused by abnormal apoptosis, said Xue. ‘The biomedical potential here is for researchers to be able turn a pro-survival enzyme into an enzyme that is pro-death,’ Xue said.

The Science study by Xue and his team was funded by the Burroughs Wellcome Fund and the National Institutes of Health.

The researchers are now investigating whether human cells have the mechanisms to convert the function of Dicer enzyme in the same manner as C. elegans cells, said Xue. Nearly half of the genes found in C. elegans are believed to have functional counterparts in humans, he said.

C. elegans is a key organism for scientists to study for several reasons, according to Xue. It was the first organism whose genome was completely sequenced, and its transparency under microscopes has allowed scientists to study many aspects of cellular and developmental biology, as well as genetics. Nobel prizes for C. elegans biomedical research were awarded in 2002, 2006 and 2008.

In a world first an international team of researchers have successfully extracted ancient DNA from the eggshells of various species of extinct birds.

The research, published in scientific journal Proceedings of the Royal Society B, shows that fossil eggshell is a previously unrecognised source of ancient DNA and can provide exceptional long-term preservation of DNA in warmer climates. The findings will boost research in archaeology and biology where species identifications can add significantly to our understanding of biodiversity, evolutionary processes, past environmental change and dispersal of animal and human populations.

The study includes samples of Aepyornis sp, the giant Madagascan elephant bird collected by Dr Jean-Luc Schwenninger, a Quaternary geochronologist based at the Research Laboratory for Archaeology and the History of Art (RLAHA) at Oxford University. The bird looked like an outsized ostrich, standing about three metres high and weighing in excess of half a tonne. It was the heaviest bird to have ever existed and produced eggs with a capacity of 11L (equivalent to over two hundred chicken eggs or seven ostrich eggs). Its eggs are the largest eggs ever known.

Since 1991, Schwenninger and a team from Sheffield University, the University of Colorado, and Antananarivo’s National Museum of Art and Archaeology in Madagascar have conducted large scale archaeological surveys of the Southern region of Madagascar and studied the timing of extinction of these giant flightless birds. Whilst scouring the coastal dunes of Southern Madagascar they have found evidence of many of the bird’s former nesting sites from concentrations of eggshell debris. They have also excavated archaeological sites which document the rise and fall of a lost civilization with long-distance trade contacts to Africa’s Swahili coast, the Persian Gulf and China.

Dr Schwenninger and his colleague Professor Michael Parker Pearson, from the University of Sheffield, believe that by the time this civilization flourished, from the 11th to the 13th century, the population of elephant birds was in serious decline. The precise cause of extinction is not yet fully understood but it is probably linked to the arrival of humans.

AMS radiocarbon dating of eggshell remains, carried out at the Oxford Radiocarbon Accelerator Unit based at RLAHA, indicate that most of the birds seem to have died out at about the same time as large numbers of settlements appear in the archaeological record at around AD 1000. The French governor Etienne de Flacourt refers to indigenous sightings of the Aepyornis in 1650 which describe the bird as a ‘type of ostrich which people cannot catch and which searches out the most deserted places’.

The DNA breakthrough was achieved when Dr Schwenninger and doctoral student James Haile, based at Oxford’s Ancient Biomolecules Centre considered analysing samples of sediment for his research. Dr Shwenninger said: ‘This time last year, I gave James a few samples from several of our archaeological and subfossil sites in Madagascar to see if any plant or animal DNA could be extracted. I also mentioned to him that I had some eggshell which might be worth looking at. In fact, we had already tried this back in 1998 and again in 2003 but without success. He was very keen to give it another go and he succeeded where others, including his thesis supervisor had previously failed.’

How much do we now know about the human genome? What can genes tell us about how we, and other species, evolved? How much of our DNA actually does something, and how much is just non-functional ‘junk’? Join Professor Chris Ponting as he discusses how evolution has shaped our genes, and what we know about our own genetic makeup.

Further Information
Professor Chris Ponting was trained in particle physics before being entranced by the analysis of DNA, genes and genomes. He was a major participant in the international project that sequenced the human genome, and then performed similar roles in projects that sequenced the genomes of the lab mouse, rat, dog, opossum, chicken, and platypus genomes. Once in a while, he has unearthed a nugget of information that tells us something new about human disease. This, in itself, will not immediately help those suffering from health problems. Instead, once this information is published, it provides someone else with a missing piece in their own research puzzle which – when complete – leads to improved diagnoses, drugs or therapy. His most recent research focuses on several human diseases, including learning disability, asthma, obesity, Alzheimer’s and muscular dystrophy.

Two teams of Oxford University researchers led by Professors Judith Armitage and David Stuart have made the first steps towards being able to engineer a bacterial cell that can sense and respond to novel environmental cues. The groups demonstrated that it should be possible to design synthetic signalling circuits inside a cell, ultimately enabling the development of new biosensors.

The ability of bacteria to respond to environmental cues is a universal feature of living cells. Evolution has created a vast array of signalling mechanisms that enable cells to react in many ways to changes in their surroundings. One of the most important of these is a two-component signalling circuit which is widely used by bacteria. It comprises a protein kinase, which acts as the sensor, and its partner protein known as a response regulator. Some species of bacteria have over 150 different sensor-response regulator pairs in a single cell, so the specificity between these pairs has to be tightly controlled to prevent ‘crossed wires’ between signalling pathways.

The two Oxford groups combined their expertise in structural biology and biochemistry to address where this specificity comes from. They used extremely bright pinpoints of light produced by the UK’s national synchrotron facility, Diamond Light Source in south Oxfordshire, to carry out X-ray crystallography, a method that allows visualization of proteins at an atomic level. Using this approach, the researchers solved the three-dimensional structure of one of these two-component complexes found in the bacterium Rhodobacter sphaeroides. This complex is crucial for a process known as chemotaxis which controls the movement of a bacterium when it senses a chemical or nutrient gradient in its environment. Based on the crystallography results, the researchers were able to pinpoint the specific amino acids that are required for this molecular recognition. They found that one amino acid on the response regulator pointed out like a finger towards a pocket on the sensor, enabling the two proteins to fit snugly together. By introducing this finger into other response regulator proteins, which do not normally partner this specific sensor, they were able to change their specificity and re-engineer the chemotaxis pathway.

This is the first time that researchers have re-designed the intracellular part of the chemotaxis circuitry. This re-engineering paves the way for producing custom-designed circuits for applications in systems biology.

“This is a significant step on the road to identifying the critical amino acid interface that allows discrimination between apparently related proteins and their partners, and a step along the road to rational design of protein signalling networks.”
Professor Judith Armitage, Department of Biochemistry

“The aim is to understand the system so well that you’re able to change it in any way you like”, says Christian Bell, the postgraduate student who worked on the project in both labs. “The dream will be a synthetic cell that does exactly what you want.”

In adult fe­male mice, switch­ing off one gene seems to start turn­ing the ovaries in­to tes­ti­cles and trig­gers the pro­duct­ion of male hor­mones at nor­mal male levels, sci­en­tists say.

The cu­ri­ous find­ings have led two re­search­ers to re­mark in a pub­lished pa­per that, bi­o­log­ic­ally speak­ing, fe­males may be en­gaged in a life­long “bat­tle to sup­press their in­ner ma­le.”

Both pa­pers ap­pear in the Dec. 11 is­sue of the re­search jour­nal Cell.

The new results echo a pre­vious study that found that fe­male ovar­ian tissues in mice start to con­vert to male-like tis­sues in the ab­sence of sig­nals from es­tro­gen, a fe­male sex hor­mone. That stu­dy ap­peared in the Dec. 17, 1999 is­sue of the jour­nal Science.

In the newer re­search, N. Hen­ri­ette Uh­len­haut of the Eu­ro­pe­an Mo­lec­u­lar Bi­ol­o­gy Lab­o­r­a­to­ry in Hei­del­berg, Ger­ma­ny, and col­leagues were stu­dy­ing genes that dur­ing de­vel­op­ment are re­spon­si­ble for con­vert­ing glands called go­nads in­to ei­ther ovaries or tes­ti­cles, de­pend­ing on the sex.

Ovaries produce eggs, the fe­male sex cells, while tes­ti­cles produce sperm.

Uh­len­haut and col­leagues ge­net­ic­ally en­gi­neered mice in which the ac­ti­vity of a called Fox2L could be chem­ic­ally sup­pressed in the ovaries.

Fox2L, in turn, is a reg­u­la­tor gene that in­flu­ences the lev­el of ac­ti­vity of an ar­ray of oth­er genes. Among oth­er things, it keeps in check genes that tend to pro­mote tes­ti­cle de­vel­op­ment, ac­cord­ing to Uh­len­haut’s group.

Switch­ing off Fox2L had the im­me­di­ate ef­fect of in­creas­ing the lev­el of ac­ti­vity of some of these “tes­tis-specific” genes, the sci­en­tists re­ported. Crit­i­cal among these, they iden­ti­fied one called Sox9.

Con­com­i­tant with the boost in Sox9 ac­ti­vity was a “re­pro­gram­ming” of cer­tain ovar­i­an cell lin­eages in­to what ap­peared to be tes­tis cell lin­eages, Uh­len­haut and col­leagues found. Mean­while, the mod­i­fied ovaries be­gan pro­duc­ing nor­mal ma­le-like lev­els of the hor­mone tes­tos­ter­one.

“Our re­sults show that main­te­nance of the ovar­i­an phe­no­type [form] is an ac­tive pro­cess through­out life,” the sci­en­tists wrote.

It’s un­clear wheth­er the find­ings would trans­late to hu­mans, but be­cause mice share over 90 per­cent of their genes with hu­mans, it very of­ten hap­pens that mouse pro­cesses have par­al­lels in hu­mans.

It would seem “tes­tic­u­lar de­vel­op­ment is ac­tively re­pressed through­out the life of fe­ma­les,” added An­drew Sin­clair and Craig Smith of the Mur­doch Chil­dren’s Re­search In­sti­tute in Mel­bourne, Aus­tral­ia, in a pa­per pub­lished in the same is­sue of Cell. Sin­clair and Smith—the re­search­ers who in their ar­ti­cle metaphoric­ally sug­gested an “in­ner ma­le” may lurk with­in all fe­ma­les—also not­ed the find­ings go against “con­ven­tional wis­dom” that the ova­ry and tes­tis are “ter­mi­nally dif­fer­en­ti­ated,” or ir­re­versibly de­vel­oped to their ma­ture state.

Why does a human baby need a full year before it can start walking, while a newborn foal gets up on its legs almost directly after birth? Scientist have assumed that human motor development is unique because our brain is unusually complex and because it is particularly challenging to walk on two legs. But now a research group at Lund University in Sweden has shown that human babies in fact start walking at the same stage in brain development as most other walking mammals, from small rodents to elephants. The findings are published in the prestigious journal PNAS.

The Lund group consists of neurophysiologists Martin Garwicz and Maria Christensson and developmental psychologist Elia Psouni. Contrary to convention, they used conception and not birth as the starting point of motor development in their comparison between different mammals. This revealed astonishing similarities among species that diverged in evolution as much as 100 million years ago.
- Humans certainly have more brain cells and bigger brains than most other terrestrial mammalian species, but with respect to walking, brain development appears to be similar for us and other mammals. Our study demonstrates that the difference is quantitative, not qualitative, says Martin Garwicz.

Based on knowledge about development in other mammals it is therefore possible to actually predict with high precision when human babies will start to walk. This is a very unexpected and provocative finding. The notion that humans have a unique position among mammals is not only deeply rooted among lay people, but is also reflected in fundamental assumptions in different research fields related to human development and human brain evolution.- Our study strongly contradicts this assumption and thereby sheds new light on theories in, for instance, evolutionary and developmental biology, says Martin Garwicz
- On the other hand, our findings fit well with the substantial similarities between the genomes of different mammals. Perhaps these similarities are after all not that surprising – although the end products ‘human’ and ‘rat’ may be very different, our study suggests that the building blocks and principles for how these building blocks interact with one another during development could be the same.
The study originated in an attempt by the group to translate behavioral milestones of motor development between two distantly related species. The similarities in relative developmental time courses between the two species were so striking that the scientists started to wonder whether the regularity applied to other mammals and ultimately also to humans.

The Lund group has now compared 24 species, which together represent the majority of existing walking mammals. Some, like the great apes, are closely related to us evolutionarily while others, such as rodents, hoofed animals, and elephants, diverged from our evolutionary path about 90-100 million years ago.

Despite this, and regardless of differences in various species’ brain and body size, gestation time, and brain maturity at birth, the comparison shows that the young from all species start walking at the same relative time point in brain development. Humans may be unique, but not in this particular way. When the nervous system has reached a given level of maturity, you learn to walk, whether you are a hedgehog, a foal, or a human baby…

Article Credit: AlphaGalileo

Researchers in Japan have found that female mice produced by using genetic material from two mothers but no father live significantly longer than mice with the normal mix of maternal and paternal genes. Their findings provide the first evidence that sperm genes may have a detrimental effect on lifespan in mammals.

The research, which is published online on Wednesday 2 December in Europe’s leading reproductive medicine journal Human Reproduction [1], found that mice created from two female genomes (bi-maternal (BM) mice) lived an average of 186 days longer than control mice created from the normal combination of a male and female genome. The average lifespan for the type of mice used in the study is between about 600-700 days, meaning that the BM mice lived approximately a third longer than normal.

Professor Tomohiro Kono (PhD), from the Department of Bioscience, Tokyo University of Agriculture, and Director of the Nodai Research Institute (Tokyo, Japan), and Dr Manabu Kawahara (PhD), associate professor at the Laboratory of Animal Resource Development, Faculty of Agriculture, Saga University (Japan), carried out the research. They believe the reason for the difference in longevity could relate to a gene on chromosome 9 associated with post-natal growth.

Prof Kono said: “We have known for some time that women tend to live longer than men in almost all countries worldwide, and that these sex-related differences in longevity also occur in many other mammalian species. However, the reason for this difference was unclear and, in particular, it was not known whether longevity in mammals was controlled by the genome composition of only one or both parents.”

To answer this question, Prof Kono and Dr Kawahara set out to study the life span of mice produced without sperm. To do this, they collected non-growing oocytes (eggs) from day-old mice, manipulated the genetic material in these eggs so that the genes behaved like sperm genes, and then transplanted this manipulated genetic material into the fully grown, unfertilised oocytes of adult mice that had their nuclei removed (enucleated oocytes). These reconstructed oocytes developed into embryos, which were transferred into surrogate mother mice. The mice that were born as a result were bi-maternal, having genetic material from two mothers, but no father.

The researchers created control mice through natural mating that were genetically identical to the BM mice, apart from the fact that they were created in the normal way with genes from male and female mice.
There were 13 BM mice and 13 control mice born between October 2005 and March 2006, and Prof Kono found that the average lifespan was 186 days longer in the BM mice than in the controls (841.5 days versus 655.5 days). The longest time that any of the control mice lived was 996 days, with all but one of them dying by 800 days, while the longest time alive for the BM mice was 1045 days, with all but three of them living for more than 800 days. The researchers checked the weight of the mice at 49 days and 600 days (around 20 months after birth) and found that the BM mice were significantly lighter and smaller than the control mice. The BM mice also seemed to have better immune systems, with a significant increase in one
type of white blood cell, eosinophil.

Both sets of mice were kept in the same, infection-free environments, with free access to food, making it unlikely that some external environmental factor was the cause of the difference in life spans.
Prof Kono said: “We believe that the most likely reason for the differences in longevity relates to the repression of a gene called Rasgrf1 in the BM mice. This gene normally expresses from the paternally inherited chromosome and is an imprinted gene on chromosome 9 associated with post-natal growth. Thus far, it’s not clear whether Rasgrf1 is definitively associated with mouse longevity, but it is one of the strong candidates for a responsible gene. Furthermore, we cannot eliminate the possibility that other, unknown genes that rely on their paternal inheritance to function normally may be responsible for the extended longevity of the BM mice.”

Imprinted genes are genes that are turned on, or “expressed”, according to whether they are inherited from the mother or the father.

The researchers write: “Our results are consistent with models based on sex-specific selection of reproductive strategies, e.g. male individuals maximizing fitness by an intense investment in reproduction by way of a larger body size in order to achieve more breeding opportunities, resulting in shorter longevity…. In contrast, female individuals usually do not engage in such costly male behaviours and instead tend to optimize their reproductive output by conserving energy for delivery, providing for offspring, foraging and predator avoidance. Our results further suggested sex differences in longevity originating at the genome level, implying that the sperm genome has a detrimental effect on longevity in mammals.”

Prof Kono concluded: “The study may give an answer to the fundamental questions: that is, whether longevity in mammals is controlled by the genome composition of only one or both parents, and just maybe, why women are at an advantage over men with regard to the lifespan.”

An international group of scientists is proposing to generate whole genome sequences for 10,000 vertebrate species using technology so new it hasn’t yet been invented. But the scientists say new genome sequencing instruments that will allow them to embark on the project may be available within a year or two.

In preparation, they are identifying collaborators who can help assemble a collection of frozen or otherwise suitably preserved tissues or DNA samples from these species.

Their proposal, called “Genome 10K,” will be published this week in the Journal of Heredity.

“The idea behind the project is to prepare for this third generation of DNA sequencing technology that began with the Humane Genome Project,” said Oregon State University’s Scott Baker, who edits the Journal of Heredity. “Whereas that project took nearly 10 years at a cost of more than $3 billion, the goal now is to sequence an entire genome in less than a week, for a cost of less than $1,000.

“If that happens, the impact would be remarkable,” added Baker. “And it will happen – the only question is, how soon?”

Baker, who is associate director of OSU’s Marine Mammal Institute, is one of more than 50 scientists from around the world who is collaborating on the proposal. He is coordinating the effort to assemble DNA samples for all known species of cetaceans – whales, dolphins and porpoises – a task made more difficult because the exact number of species keeps changing.

As DNA analysis becomes more sophisticated, Baker said, molecular differences are emerging among some animals thought to belong to the same species.

“We are adding a new species every year or two,” Baker said, “and there is some disagreement about what criteria we should use to describe new species. But to date, more than 90 species have been identified and officially recognized that will require tissue or DNA samples.”

Thus far, Baker and his colleagues have viable DNA samples from 87 of those species, stored at OSU’s Hatfield Marine Science Center in Newport, Ore., at the University of Auckland in New Zealand, and at NOAA’s Southwest Fisheries Science Center in La Jolla, Calif., which holds the largest repository of cetacean tissues.

One of the challenges is to obtain samples for rare, endangered and even extinct species, Baker said.

“We have thousands of samples from humpback whales, for example,” he pointed out. “But there are a few cetacean species that are known literally from only a single skull, and it can be tough to extract DNA from that.”

The feasibility of sequencing 10,000 vertebrate genomes “requires only one more order of magnitude reduction in the cost of DNA sequencing, following the four orders of magnitude reduction we have seen in the last 10 years,” the scientists write in their article.

The variety of species identified will present different challenges for genome sequencing, Baker says, and whales, dolphins and porpoises could be among the most difficult.

“With some species of mammals, the computational assembly process is relatively simple – you start with one DNA sequence and stitch it together with an existing sequence that is similar, but not identical,” Baker said. “With whales, though, it is what’s called a ‘de-novo’ assembly. There is no template to follow.

“It’s like a gigantic jigsaw puzzle and you have to figure out where the pieces go,” he added.

Baker and his colleagues have been working for nearly 20 years on creating DNA barcodes for different cetacean species. The ability to create entire genome sequences would be of enormous benefits to conservation and basic scientific understanding of cetaceans, he said.

“It would give us tremendous new insight into a group of mammals that went through one of the most remarkable adaptations in evolutionary history,” Baker pointed out. “Cetaceans represent an incredible range of ‘extremophiles,’ including the blue whale, which can reach up to 100 feet in length, the bowhead whale, thought to live up to 200 years of age, and the sperm whales, capable of diving to more than a mile in depth.

“Yet despite this rapid adaptation in physiology and physical form, the molecular evolution of whales is 10 times slower than in other mammals,” Baked added. “This may help us find out why. The more we learn about how whales and dolphins have evolved – and how they are similar or different in genetic diversity – the better we will be able to protect species driven to the verge of extinction.”

The Genome 10K proposal is available free online at the Journal of Heredity, http://jhered.oxfordjournals.org

Further information is available from the Genome 10K Community of Scientists, http://www.genome10k.org