Photo: Skånska Matupplevelser/Flickr.

EU’s rules on genetically improved crops a ‘threat’ to developments in agriculture, say MPs

A report out today is calling for the equivalent of Nice – the National Institute for Health and Clinical Excellence – for developments in crop technologies. The House of Commons Science and Technology Committee also says the government should encourage more public debate around developments in crop technologies

It recommends forming a ‘citizens council’ for considering the social and ethical impacts of new crops. Nice has a similar role producing advice on new medicines, which is used by the NHS to make funding decisions.

In its report, the committee criticises the model used for regulating genetically modified organisms in the European Union. The system “threatens to prevent such products from reaching the market both in the UK, in Europe and, as a result of trade issues, potentially in the developing world,” according to the committee of MPs. Continue reading

Peas in pods

150 years of Mendelian genetics

Last Sunday, the world celebrated its musicians and film stars in flashy ceremonies. But another celebration was due at the same time.

8 February 2015 marked 150 years since the first of Mendel’s lectures where he presented his results on pea breeding for the first time. These lectures, based on his paper Versuche über Pflanzen-Hybriden (Experiments on Plant Hybridisation), presented the world with a vision of genetics never seen before – and led to him gaining the title ‘The Father of Modern Genetics’.

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Mustard seeds (Dennis Wilkinson/Flickr)

Conserving our crops’ genetic diversity

More than 22 years have passed since the Convention on Biological Diversity was signed. It called for international efforts to conserve the world’s biodiversity, which had long been suffering the effects of human activities. Since then, there has been a lot of debate over what the best way of securing this biodiversity is.

But really, there isn’t a best way. There isn’t a clear consensus, one method to fit all. We can’t choose one way to preserve all the different elements that form what we call biodiversity.

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Searching for a needle in a genetic haystack

In the last year, a brand new technique for genome editing has appeared with the potential to revolutionise the way in which scientists engineer genomes. It provides the ability to make cuts in the genome at precisely controlled locations, resulting in the silencing of that particular region. This technique is known as CRISPR. To make such a precise cut, however, requires the active protein to find a unique 20 base pair region within the vast sequence space of the entire genome.

“Seek and Destroy” – Nature issue 7490 (image from Nature.com)

The CRISPR system originates from the bacterial immune system in which a segment of the bacteria’s genome contains short elements of viral DNA (protospacers), which act as guides to attack invading viruses by disrupting their genetic code [1]. This segment (known as the CRISPR array) contains so-called ‘Cas’ proteins capable of cleaving segments of DNA, that are guided into place by the protospacers stored in the array. The bacteria are able to add new stretches of foreign DNA to this array to develop immunity in future encounters with the invader.

The genome editing technology [2,3] takes this CRISPR array structure and replaces the viral DNA sections with lengths of the target genome that are intended to be silenced. This can then be inserted into the target genome by standard methods and, when transcribed, the Cas protein finds its way to the point in the genome with precise sequence complementarity to its guide. However, despite this technique’s success, the mechanism enabling the Cas-RNA complex to find its target was unknown, until now.

In this week’s nature cover article [4], Sternberg et al. show that a particular Cas protein, Cas9, can only bind to regions containing a three-nucleotide motif region, known as a PAM, that is found adjacent to protospacers. When searching for a needle in a haystack, you would not pick up every piece of hay, compare it to a picture of a needle, and then replace it when it didn’t match. Similarly, Cas9 does not try every point on the genome and compare the local sequence to its guide. It first limits the number of places to search by only binding to PAMs. This could be likened to the first step in searching for a matching phone number; you only compare the numbers with the same area code.

Of course, there are still a large number of PAM sequences in a given genome (or else the technique would be somewhat limited), but it vastly simplifies the problem. Furthermore, the PAM acts as the start point for the guide/genome sequence comparison, which proceeds one nucleotide at a time in sequence. The process is such that if the first 2-3 nucleotides do not match, then the complex rapidly disengages from that region and can move on to try a different location.  These factors combined ensure that the complex spends as little time as possible at incorrect locations.

This work is an impressive demonstration of how biological systems are able to solve difficult problems. An invading virus needs to be dealt with quickly if a bacterium is to survive. The CRISPR system therefore needed to find a rapid way of finding a target within a large search space. It achieved this by utilising a regular motif present within the target genome, choosing to only incorporate stretches of DNA adjacent to these motifs. It seems the trick to finding a needle in a haystack is to choose a smaller haystack to lose it in.

References

  1. Wiedenheft, B., Sternberg, S. H. & Doudna, J. A. RNA-guided genetic silencing systems in bacteria and archaea. Nature 482, 331-338 (2012).
  2.  Mali, P. et al. RNA-guided human genome editing via Cas9. Science 339, 823-826 (2013).
  3.  Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819-823 (2013).
  4.  Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C. & Doudna, J. A. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507, 62-67 (2014).

By Matthew Evans- a second year PhD student in the lab of Dr Richard Morris

Genetically modified foods: would you eat a purple tomato?

In the past week there has been a lot of press coverage about genetically modified foods. The first of these was a proposal made by Rothamsted Research in Hertfordshire to carry out field trials on plants engineered to produce the omega-3 oils that are usually found in fish. The second of these was a farm in Canada who had produced 1,200 litres of juice from‘purple tomatoes’ – a genetically modified tomato developed here at the John Innes Centre. With all the buzz around these genetically modified foods, it made sense to write a post about the potential that genetic modification (GM) has for increasing the benefit of our foods.

GM is a type of plant breeding that has been used to improve crops, and has been in global commercial use for 18 years. These GM organisms, or GMOs, contain a DNA sequence that does not occur naturally in its own genome and has not been created by conventional breeding. GM has been used to create more efficient and improved crops, for instance increasing food production or creating herbicide-resistant plants.

Genetic modification is usually carried out using one of two systems. Both systems begin with identification of a desired gene. The gene is then inserted into a circular piece of DNA called a plasmid. This plasmid is then transferred into a bacterium which reproduces to create several copies of the gene. The gene is then transferred to the plant by one of two ways. The first is to attach the DNA sequence to particles of gold or tungsten and firing the particles into plant tissue. The second is to use an infective soil bacterium called Agrobacterium tumefaciens which has been modified so that it takes the chosen gene into the plant tissue but does not become active once inside the plant. These processes are usually done involving an antibiotic marker to allow detection of successful GMOs, although new technologies are being developed that work without an antibiotic marker1.

The first commercial GMOs were grown in North America in the late 1990s. Globally over 12% of arable land is now used for GM crops. Soya is the world’s leading GM crop imported for both feed and human products, with GM maize, oilseed rape and cotton being other important GM crops.

Most GM crops that are commercially grown are modified to improve their yields or pest/disease resistance. However, in more recent years, the potential of GM has been directed to improving the crops to make them more beneficial to health or to provide nutrients that are more difficult to get into the diet otherwise. Here I will briefly highlight three examples of this to show the potential that this technology can have.

Golden Rice vs Normal Rice
(Image from Wikimedia Commons)

Golden Rice:
Golden rice is a strain of rice that has been engineered with higher levels of vitamin A than normal rice. It was developed to combat childhood vitamin A deficiency – a common problem in developing countries such as India, which can lead to a compromised immune system and even blindness. This golden rice was developed with the aim that it would be freely available to developing countries without the demand for payment or licences which they simply could not afford. Engineering this sort of crop could make a huge difference to the lives of children in developing countries, and golden rice has had a lot of positive publicity behind it2.

If you are more interested in Golden Rice, there is an event at JIC this week, which will be streamed online and open to questions on twitter. More information here.

purple tomatoes

Only the purple tomatoes are GM.
The rest are natural varieties

Purple tomatoes:
These tomatoes produced here at the Norwich Research Park have two new genes from the snapdragon plant. These genes increase the levelsof anthocyanins in the tomatoes. These anthocyanins are the antioxidants found in blackberries and cranberries, and it is thought that these anthocyanins offer protection against some cancers, cardiovascular disease and age-related diseases. Considering that in 2012 32% of UK deaths were caused by circulatory disease, and 29% from cancer, developing foods that could combat these diseases is a top priority3. Tomatoes and their by-products such as tomato sauce are a widely produced and consumed food in the UK, and are more commonly consumed than the berries with naturally high anthocyanins. These purple tomatoes have been shown to extend the lifespan of cancer-susceptible mice4, leading to possible application in human cancer treatment/prevention. As mentioned previously, a farm in Canada has recently grown and juiced a crop of these tomatoes. This juice can now be used for further research on its benefits, as well as used to attract new investors. To find out more about the new advances in this, check out this video or this press release
People may be put off by the purple colour of the tomatoes – but humans have been breeding to change the colour of vegetables for centuries. Ancestral carrots were once purple – but the Dutch bred them to be orange, and those are the carrots we eat today.

Many people take fish oil capsules as a supplement (Image from Wikimedia Commons)

Omega-3 oils in plants:
Some fatty acids that we need in our diet are found in oily fish – which gain these oils by consuming marine algae. Eating these fish allows the fatty acids into our diets, and there are also dietary supplements that can be bought. Increasing omega-3 oil consumption is putting pressure on rapidly diminishing fish stocks, and fish farming relies on feeding fish existing omega-3 oils rather than the marine algae that they would get them from in nature adding furtherpressure on the industry. Researchers at Rothamsted Research in Hertfordshire have inserted algal genes into oil-producing crops (such as Camelina sativa, or false flax) to enable them to produce these oils in a more sustainable setting5. The crops that they have produced are currently awaiting approval for field trials of these GM crops.

As you can see from these three examples, there is a huge potential for using genetic modification to improve the crops that we grow and improve our diets for the better (and possibly cheaper too!). GM still has its skeptics, as well as a large amount of regulation at the EU and government level. We won’t be growing any of these crops for consumption here in the UK in the near future, but as even more developments come in the science, maybe changes will be made in the regulation and we might finally get the chance to try these exciting new products. I’d certainly like to try a purple tomato – would you?

To read about our experiences talking about GM at Science Festivals, check out our post from a few months ago here

References:

  1. http://www.food.gov.uk/policy-advice/gm/gmanimal#.UhyxKxuko50
  2. Am J Clin Nutr 2009; 89:1776–83; 7. Nature Biotechnology 26, 1301 – 1308 (2008)
  3. Deaths Registered in England and Wales (Series DR), 2011, ONS
  4. Nature Biotechnology 26, 1301 – 1308 (2008)
  5. Plant Biotechnology 7: 704-716 (2009)


By Izzy Webb – a second year PhD student in Phil Poole’s group

Young Microbiologists Symposium 2013

On Monday 18th November my department at the John Innes Centre, Molecular Microbiology, hosted a day of talks from ten up-and-coming scientists in the field. The majority of these were in the middle of a post-doctoral grant, others starting their post-doctoral training while a few were coming to the end of their PhD projects. The speakers travelled from the USA, mainland Europe and the UK to present their work to the audience.

The wonderful world of microbiology (all images from Wikipedia)

It was obviously lovely to see some familiar faces giving talks and seeing what they are up to now. And at the same time, it was great to get an insight into what is happening in the research community outside of my area. A range of bacteria was spoken about from cell cycle models such as Caulobacter crescentus to previously uncultivated microbes in sea sponges. Some talks were mainly bioinformatics, which to be honest is not my strong point, and I have to admit, I did not completely understand… Others were on natural products and how to mine them from genomes – a field which is becoming increasing important. All in all, it was a good day with lots of new information learnt, as you always get from conferences!

Maybe we will see some of these scientists as project leaders one day – who knows? Or, maybe they will be joining the JIC soon possibly in more senior fellowship or group leader positions. It would be exciting to have some of their fantastic brains (and more nice people too) in our department! Or, on a more positive note, it is always nice to know that any one of the many PhD students in the JIC could be giving a talk at a symposium or at a conference, and maybe their future boss will be in that room!

By Rowena Fung, a 3rd year PhD in Jake Malone’s Group

Frederick Sanger: an inspiration to scientists everywhere

Frederick Sanger, 1918-2013

It was sadly announced that Frederick Sanger, a legendary British biochemist died on 19th November 2013 at the age of 95.

Frederick Sanger’s name may not be a household name but his name is a “lab-hold” name. Within the scientific community, especially in biology, he is someone every student will know the name of. (One of the few big names I remember from my undergraduate lectures!).

For most scientists a Nobel Prize is a far-off dream but for Sanger, his research was so exceptional that he is the only person to have won two Nobel prizes for Chemistry and one of four people to have won two Nobel prizes. Despite this success I have heard him described as one of the most humble, down-to-earth people you will ever meet, and an article in Science in 2007 described him as “the most self-effacing person you could ever hope to meet”.

But why is he so famous? What was his work?

Sanger’s research looked at two of the fundamental components of the machinery of life; Proteins and Nucleic Acids (e.g. DNA) , described as “the orchestra which plays the various expressions of life”1.  Nucleic acids are the components of our genetic information and proteins make up the machinery that ‘reads’ our genetic code, makes products required for normal functions (e.g. enzymes that break up food in our stomachs), and makes components that are ‘building- blocks’ for organisms.

Most people are familiar with the idea that protein is found in our food but specific proteins are not widely known.  A specific protein that may be familiar to many people, especially those living with diabetes, is insulin. Insulin is produced in the pancreas and is a protein which tells the body that it has lots of sugar and it needs to store it. In people with Type 1 diabetes insulin isn’t made and to regulate their sugar levels they need to take synthetic insulin. Sanger studied the structure of insulin and worked out that it was made of a specific sequence of small components, called amino acids. His work on insulin showed that proteins are not largely undefined and that they in fact have a specific structure, which is now a fundamental biological concept. This work also helped to understand what insulin is and it is thought to have possibly helped in the understanding of how DNA encodes proteins, proposed by Francis Crick in 1958. This work on Insulin earned Sanger his first Nobel Prize for Chemistry in 1958.

The sequencing of the human genome made national headlines in 2003. The sequencing of the first human genome has laid the foundations for research into the differences between individuals, disease, human development and evolution. Again Sanger’s research quietly lies in the background.  His pioneering work in DNA sequencing led to the development of the Sanger Sequencing method which was used to sequence the human genome as it was much better at ‘reading’ longer regions of DNA than the existing methods at the time. For his work on Nucleic Acids, Sanger was awarded a half Nobel Prize for Chemistry shared with Walter Gilbert in 1980.

Both his work in Proteins and Nucleic Acids were major breakthroughs and laid the foundations for years of ground-breaking research which has followed. His work has led to huge leaps in our understanding in the basic components of the machinery of life which has far from being obscure and unimportant to the non-scientific community, has led to increased understanding of human biology and medicine which influences all of us.

Fredrick Sanger (1918-2013) was and still is a true inspiration to all scientists.

1Professor G Malmström in the Nobel Prize for Chemistry speech, 1980

http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1980/presentation-speech.html

http://en.wikipedia.org/wiki/Frederick_Sanger

http://www.sciencemag.org/content/317/5840/879.5.full?sid=9a9d3d15-d13c-441e-9eeb-5ffb95d57b19

http://www.genome.gov/10001772

by Annis Richardson- a third year PhD student in the lab of Prof Enrico Coen

A few SVC members expressed their goodbyes on twitter:

RIP Sanger