Crop The Wild Relatives*

* It’s not illegal!

Kew’s growth strategy: hybrid crops without the genetic modification
Plan to crossbreed crops with their wild cousins to help boost resistance to climate change

British researchers are leading an unprecedented global project to track down and store wild relatives of common crops – to help breed hybrids with higher yields that could be resistant to the effects of climate change.

Crossing staple crops such as wheat, potatoes and rice with their wild cousins offers a natural, safe alternative to the genetic modification of plants in the lab, according to experts at the Royal Botanic Gardens in Kew, which is behind the scheme.

A report by researchers at Kew found that so-called “crop wild relatives” offer a badly neglected “treasure trove” of genetic information that, if harnessed properly, could boost agricultural production and be worth up to £128bn to the global economy.

But global stocks of crop wild relatives are woefully low and many species are close to extinction, with aubergine, potato, apple, sunflower and carrot varieties most at risk, the report found.

More than half the 455 known crop wild relatives of the world’s 29 most-consumed food plants have either not been collected at all, or are badly under-represented, making it essential to build stocks as soon as possible, warns Jonas Mueller, of the Kew Millennium Seed Bank.

“Now that we have identified the gaps the next step is to collect them and make them accessible for agricultural research. We know the climate will change but we don’t know how. So we don’t yet know how it will affect the crops that have been bred in the past specifically for the climate of today,” said Dr Mueller. “It can take 15 to 20 years to breed a new crop variety, so every year we delay has a knock-on effect. It is a matter of urgency,” he added.

Locating and storing the crops will begin this summer in Italy, Cyprus and Portugal. It is a huge task that in many cases is easier said than done. Many crops lie in conflict-ridden regions such as Pakistan and Sudan, where wars can put both the species and the collectors at risk.

Some wild relatives of the faba bean – better known in this country as the broad bean – are found only in war-torn Syria and are a particular cause for concern. Bolivia, China, Ecuador, Ethiopia, India, Kenya, Mexico, Mozambique, Australia and the US also have large numbers of priority crop wild relatives that need to be collected and stored.

The Seed Bank, yesterday. Or not. It might have been Friday. Or not.

Britain could benefit tremendously from an injection of wild genes as its widely grown crops of conventional wheat, potatoes, barley, carrots, sugar cane and apples face an increasingly unpredictable climate.

A new generation of wild-domesticated crop hybrids could be more resistant to floods, droughts and extreme temperatures, using a technology which many scientists say is better understood and more effective than genetic modification. Ruth Eastwood, of Kew’s Millennium Seed Bank, said the procedure could potentially be safer than GM because their similar genetic backgrounds meant there was a “lower likelihood of unexpected interactions between genes”. “It certainly is another option that has proved to be effective already,” she said.

Andy Jarvis, of the International Centre for Tropical Agriculture in Colombia, also involved in the project, said: “Crop wild relatives are a potential treasure trove of useful characteristics that scientists can put to good use for making agriculture more resilient and improving the livelihoods of millions of people.”

Kew’s global 10-year programme with Germany’s Global Diversity Trust to identify and plug gaps in wild relative stocks is unprecedented.

Britain is also playing a leading role in the science. In May, the National Institute of Agricultural Botany in Cambridge claimed to have developed a new type of wheat that could increase its productivity by 30 per cent. It did this by recreating the original rare cross between an ancient wheat and wild grass species that happened in the Middle East 10,000 years ago, to form a “synthetic” wheat that can be crossed with modern UK varieties.

Advocates of plant breeding with crop wild relatives, which has been going on for decades, say it is a much safer and more effective way of improving plant yields than the fledgling process of genetic modification, which the Government is promoting in the face of an effective ban in Europe.

Success stories include a nutritionally enhanced variety of broccoli which contains higher levels of glucoraphanin, thought to slow down the progress of skin cancer.

An analysis of Kew’s research by the financial consultants PricewaterhouseCoopers estimates that commercial crops that have already benefited from the input of crop wild relatives will generate a total of £44bn in their lifetimes. This would rise to £128bn if the technique boosted the yield, disease resistance, and tolerance to temperature, drought and flooding of the world’s 32 most-consumed crops.

Ms Eastwood said: “Adapting agriculture to climate change is one of the most urgent challenges of our time. Crop wild relatives are already being used to improve our food crops right now and are extremely valuable economically as well. But they are underutilitised.”

The project team first identified all known wild relatives of the world’s most important crops. It then spent two years scouring gene banks, dried plant collections and museums to determine stock levels and gather data on sightings in the wild. From the data, the team identified species that are a high priority for collection.

The report comes a week after the UK Government announced plans to invest £160m setting up centres for innovation in sustainable farming and bringing new agricultural technologies to market.

The 29 crops: What’s involved?

The 29 crops covered in the project are: African rice, alfalfa, apple, eggplant (aubergine), bambara groundnut, banana, barley, wheat, lima bean (butter bean), carrot, chickpea, common bean, cowpea, faba bean (broad bean), finger millet, grasspea, lentil, oat, pea, pearl millet, pigeon pea, plantain, potato, rice, rye, sorghum, sunflower, sweet potato and vetch.

Early winners: potatoes and wheat

The breeding of staples with their “crop wild relatives” (CWRs) has already proved beneficial.

Late blight is one of the most damaging diseases for potatoes: its negative economic impact is thought to be $3.5bn per year in developed countries alone. Resistance to the condition in current European potato varieties has been exclusively derived from CWRs. Varieties of potato with CWR-derived late-blight resistance, such as the C88 potato, are also being introduced into China. In one study, it was estimated that CWR-derived resistance was responsible for preventing the loss of approximately 30 per cent of the annual yield, where conditions for blight were prevalent.

Wheat varieties such as Veery have benefited from the introduction of genes from rye, a relative of wheat. The beneficial traits inherited include tolerance to extremes of temperature and drought conditions, as well as resistance to a variety of diseases such as wheat rust. These wheat varieties have had a significant impact in the developing world, as well as in developed-world markets such as the USA.

Source: The Independent

Pandora’s… Pox!*

Giant viruses open Pandora’s box
Genome of largest viruses yet discovered hints at ‘fourth domain’ of life
By Ed Yong

* Well somebody had to say it!

The organism was initially called NLF, for “new life form”. Jean-Michel Claverie and Chantal Abergel, evolutionary biologists at Aix-Marseille University in France, found it in a water sample collected off the coast of Chile, where it seemed to be infecting and killing amoebae. Under a microscope, it appeared as a large, dark spot, about the size of a small bacterial cell.

Later, after the researchers discovered a similar organism in a pond in Australia, they realized that both are viruses — the largest yet found. Each is around 1 micrometre long and 0.5 micrometres across, and their respective genomes top out at 1.9 million and 2.5 million bases — making the viruses larger than many bacteria and even some eukaryotic cells.

But these viruses, described today in Science [1] are more than mere record-breakers — they also hint at unknown parts of the tree of life. Just 7% of their genes match those in existing databases.

“What the hell is going on with the other genes?” asks Claverie. “This opens a Pandora’s box. What kinds of discoveries are going to come from studying the contents?” The researchers call these giants Pandoraviruses.

“This is a major discovery that substantially expands the complexity of the giant viruses and confirms that viral diversity is still largely underexplored,” says Christelle Desnues, a virologist at the French National Centre for Scientific Research in Marseilles, who was not involved in the study.

Claverie and Abergel have helped to discover other giant viruses — including the first [2] called Mimivirus, in 2003, and Megavirus chilensis, until now the largest virus known [3] in 2011. Pandoravirus salinus came from the same Chilean water sample as M. chilensis. Claverie picked up the second Pandoravirus, P. dulcis, from a pond near Melbourne, where he was attending a conference.

The viruses’ presence on separate continents helped to establish that they were not artefacts of known cells. It also suggests that the Pandoraviruses are widespread, Claverie says.

Indeed, other scientists had previously mistaken them for parasitic or symbiotic bacteria. Rolf Michel, a parasitologist from the Central Institute of the Bundeswehr Medical Service in Koblenz, Germany, found one in 2008, in an amoeba living in the contact lens of a woman with keratitis4. “Reading this stunning article, I recognized that both P. salinus and P. dulcis are almost identical to what we described a few years ago,” he says. “We had no idea that those giant organisms could be viruses at all!”

The researchers showed that Pandoraviruses lack many of the hallmarks of cellular organisms such as bacteria. They do not make their own proteins, produce energy via ATP or reproduce by dividing.

They do, however, contain some of the core genes that are common to giant viruses, and they have a viral life cycle. Under an electron microscope, the researchers saw the viruses being taken up by amoeba hosts, emptying their proteins and DNA into the host cells, commandeering the host-cell nuclei, producing hundreds of new viral particles and, finally, splitting the host cells open.

The researchers are now trying to determine the viruses’ origins by characterizing the unknown genes and the proteins they encode. They have long suspected that giant viruses evolved from cells; if they are right, the ancestors of Pandoraviruses must have been very different from the bacteria, archaea and eukaryotes we have today. “We think that at some point, the dynasty on Earth was much bigger than those three domains,” says Abergel. Some cells gave rise to modern life, and others survived by parasitizing them and evolving into viruses.

The discovery suggests that scientists’ may revise their concept of what a virus looks like. “After reading the article, many people may wonder if they have something on their shelves that might be a giant virus,” says Abergel. “We still have more crazy things in store that we expect to be able to publish next year.”

Source: Nature doi:10.1038/nature.2013.13410
References:
1 Philippe, N. et al. Science 341, 281–286 (2013).
La Scola, B. et al. Science 299, 2033 (2003).
2 Arslan, D., Legendre, M., Seltzer, V., Abergel, C. & Claverie, J.-M. Proc. Natl. Acad. Sci. USA 108, 17486–17491 (2011).
3 Scheid, P., Hauröder, B. & Michel, R. Parasitol. Res. 106, 1371–1377 (2010).

Dolly The Mouse

OMG! “THEY” CLONED A MOUSE — FROM MOUSE BLOOD!

So, for those of you with the chemical smarts, here’s the original article, published by the Society for the Study of Reproduction with the assistance of HighWire Press:

Mouse Cloning Using a Drop of Peripheral Blood
Satoshi Kamimura, Kimiko Inoue, Narumi Ogonuki, Michiko Hirose, Mami Oikawa, Masahiro Yo, Osamu Ohara, Hiroyuki Miyoshi, and Atsuo Ogura
* Corresponding author; email: ogura@rtc.riken.go.jp
Abstract
Somatic cell nuclear transfer (SCNT) is a unique technology that produces cloned animals from single cells. It is desirable from a practical viewpoint that donor cells can be collected noninvasively and used readily for nuclear transfer. The present study was undertaken to determine whether peripheral blood cells freshly collected from living mice could be used for SCNT. We collected a drop of peripheral blood (15-45 µl) from the tail of a donor. A nucleated cell (leukocyte) suspension was prepared by lysing the red blood cells. Following SCNT using randomly selected leukocyte nuclei, cloned offspring were born at a 2.8% birth rate. Fluorescence-activated cell sorting revealed that granulocytes/monocytes and lymphocytes could be roughly distinguished by their sizes, the former being significantly larger. We then cloned putative granulocytes/monocytes and lymphocytes separately, and obtained 2.1% and 1.7% birth rates, respectively (P > 0.05). Because the use of lymphocyte nuclei inevitably results in the birth of offspring with DNA rearrangements, we applied granulocyte/monocyte cloning to two genetically modified strains and two recombinant inbred strains. Normal-looking offspring were obtained from all four strains tested. The present study clearly indicated that genetic copies of mice could be produced using a drop of peripheral blood from living donors. This strategy will be applied to the rescue of infertile founder animals or a “last-of-line” animal possessing invaluable genetic resources.
Biology of Reproduction 26 June 2013

For those who like it expert-style:

Unnamed Expert Drafted in by BBC Explains It All – Video!

And an explanation of application from the scientist guys though no one says why…
Seems we’re running to keep up in a world where we haven’t yet learned to crawl.

She’s behind me, isn’t she? Oh bugger!

Oooh, A Mosaic Of Ancestry!

Principal Product Scientist Mike Macpherson, former Research Scientist Chuong “Tom” Do, and Computational Biologist Eric Durand have led a team that spent many months developing an innovative and accurate tool to determine your ancestry going as far back as 500 years.

One of the stunning aspects of Ancestry Composition is that it’s based on the newest advances in machine learning and thus will get better over time. “Ancestry Composition is truly innovative. Not only does it use public-genetic databases for reference, it also uses the data set from 23andMe, so as more people join 23andMe, the more powerful and more accurate Ancestry Composition will become,” Mike said.

The feature can very accurately detail the mosaic of your ancestral background, distinguishing British and Irish ancestry, for instance, or telling you the breakdown of your Scandinavian or Italian ancestral origins. It’s also a powerful tool for finding Ashkenazi Jewish ancestry.

Right now, Ancestry Composition is particularly interesting for people of mixed ancestry: individuals who have Native American, Latino, African American or mixed European heritage. An update is planned in the near future to add more detail for people with African and Asian ancestry. This will give a finer level of detail and help customers zero in on the regions of their ancestral origins, but the feature can be enlightening for people of any background offering a view of an individual’s genetic ancestry, breaking down the mix of ancestry by percentage and putting it all into an intuitive visualisation.

There are several other bells and whistles for those who want to dive in and find a few fun surprises. One of those is the Split View, which gives great detail for customers who have at least one parent also in the 23andMe community. If at least one parent has been tested and is linked through the Family Tree feature, Ancestry Composition’s Split View will tell you what mix of your ancestry comes from your mother and what mix of your ancestry comes from your father. Another add-on to the feature is a Chromosome View, which “paints” the ancestry on each of your 23 chromosomes.

Total Blurb Bit If you’d like to see more detail on how this has done you can look both at a white paper put together by Mike or a recent poster presented at the annual meeting of the American Society of Human Genetics, which outlines the technique. The new feature replaces 23andMe’s “ancestry painting” and “global similarity,” two tools that were equally pioneering when they were first introduce, but with Ancestry Composition 23andMe breaks new ground and sets a new standard for determining genetic ancestry.

Source: 23andme.com

Macaulay Culkin face!

Walk Like An Egy… A Gorilla

As shoeless visitors strolled along a mechanized gait carpet in the Boston Museum of Science’s Living Laboratory, sensors detected pressure on the mid-outside portion of some pedestrians’ feet. That suggested a midtarsal break—a type of footprint pressure DeSilva and other scientists associated only with gorillas and chimpanzees.

“It was shocking,” said DeSilva, an assistant professor of anthropology at Boston University. “I mean, 80 years of research has argued that humans don’t do this.”

At least 80 years in DeSilva’s field… Last month, when he published his study in the American Journal of Physical Anthropology, two podiatrists said they’d seen a similar variation in patients’ feet. But they weren’t familiar with the term “midtarsal break”—suggesting, DeSilva said, the need for “collaboration with as many different disciplines as possible.”

DeSilva connected his unexpected discovery*—he was originally researching variations in the foot’s arch—to a two-million-year-old fossil human called Australopithecus sediba. DeSilva’s research suggests it moved like today’s apes, which have bendy feet unbound by bones. Chimps, for instance, tumble through the tall trees of the jungle by molding both their hands and their feet around each branch.

In contrast, modern human feet tend to be rigid, with stiff ligaments that maintain bone position and facilitate our bipedal nature. (The same is true of most ancient feet as well; Australopithecus sediba is unique in the fossil record.) With high arches and stiff feet, we spring into our next step. DeSilva says wearing shoes may have played a role in reshaping our feet over the years.

But perhaps some people’s feet can still manage ape-like feats. According to DeSilva’s study, conducted over the past two summers, about 1 in 13 humans may have the midtarsal break in their feet.

Using the gait carpet, a second footprint device, and a camera rig, DeSilva and his colleague Simone Gill, an occupational-therapy researcher, observed a midtarsal break—also known as “floppy feet”—in 32 out of 398 adult participants.

“This [opens a] floodgate of questions,” DeSilva said. “Who are these people? What is it about them that allows them to produce this motion?”**

DeSilva noted that the floppy-footed folks he watched tended to have flatter feet and higher body mass indexes than the stiff-steppers. They also rolled their feet more: Employing a motion called hyperpronation, they landed on the outside of their feet and rolled dramatically inward. That, said DeSilva, allows the foot to relax its joints and ligaments and create a midtarsal break.

But it’s all relative. Some subjects with floppier feet didn’t technically have a midtarsal break, though their walking pattern came close.

So how do you know if your feet might have a midtarsal break? Take a stroll on sand, DeSilva suggested. Here are a couple of tips:

Don’t even bother to test your feet at the beach unless they’re flat. If you have high arches, you probably have stiff muscles and ligaments—and decidedly unfloppy feet.
If you have a midtarsal break, the fold in your foot will pinch the sand upward. Look for a small ridge in the upper-mid portion of the footprint.

This summer, DeSilva and Gill will take MRIs of many foot types and create models of them with 3-D printers. DeSilva will compare that data with the bones of Australopithecus sediba, while Gill will use the models to explore the relationship between foot anatomy and body types.

Source: Nat Geo Mag
* …because we never saw that coming!
** answers on a postcard, please!

Painted Hula, Frog-Frog-A-Hula

A frog species native to Israel’s north which was declared extinct has been rediscovered and dubbed a “living fossil” — not only of its own species but of an entire genetic group, Jerusalem’s Hebrew University have announced.

Discovered in the Hula Valley in the 1940s, the Hula painted frog was thought to have disappeared following the drying up of the Hula Lake at the end of the 1950s, and was declared extinct by the International Union for Conservation of Nature in 1996.

The frog — individuals of which were found in the Hula swamp area two years ago — turned out “to be a unique ‘living fossil,’ without close relatives among other living frogs,” the university said in a statement.

© Sarig Gafny

A team of Israeli, German and French researchers authored a report in the scientific journal Nature Communications which details the results of a a genetic study of the amphibian, finding that the rediscovered Hula is actually the only living species of its kind.

“The Hula frog differs strongly from its other living relatives, the painted frogs from northern and western Africa. Instead, the Hula frog is related to a genus of fossil frogs, Latonia, which were found over much of Europe dating back to prehistoric periods and has been considered extinct for about a million years,” Hebrew University said.

The team — led by Hebrew University’s Rebecca Biton, Tel Aviv University’s Professor Rebecca Biton, Prof. Sarig Gafny of the Ruppin Academic Center and Dr. Vlad Brumfeld of the Weizmann Institute of Science – conducted “genetic analyses of rediscovered individuals” as well as “morphologic analyses of extant and fossil bones,” according to the statement.

“The results imply that the Hula painted frog is not merely another rare species of frog, but is actually the sole representative of an ancient clade of frogs (a group with a single common ancestor),” the university said.

Source: Times of Israel

Oh, This Is Big

Discovery may create dialogue about DNA and RNA data bank privacy issues

Researchers from Mount Sinai School of Medicine have developed a method to derive enough DNA information from non-DNA sources—such as RNA—to clearly identify individuals whose biological data are stored in massive research repositories. The approach may raise questions regarding the ability to protect individual identity when high-dimensional data are collected for research purposes.

DNA contains the genetic instructions used in the development and functioning of every living cell. RNA acts as a messenger that relays genetic information in the cell so that the great majority of processes needed for tissue to function properly can be carried out.

To date, access to data bases with DNA information has been restricted and protected as it has long been considered the sole genetic fingerprint for every individual. However, vast amounts of RNA data have been made publicly available via a number of databases in the United States and Europe. These databases contain thousands of genomic studies from around the world.

In this study, lead authors Eric E. Schadt, PhD, and Ke Hao, PhD, developed a technique whereby a person’s DNA could be inferred from RNA data using gene-expression levels monitored in any of a number of tissues. In contrast, most studies involving DNA and RNA begin with DNA sequences and then seek to associate expression patterns with changes in DNA between individuals in a population. This is the first time going from RNA levels to DNA sequence has been described.

“By observing RNA levels in a given tissue, we can infer a genotypic barcode that uniquely tags an individual in ways that enables matching the individual to an independently derived DNA sample,” said Dr. Schadt, Director of the Institute for Genomics and Multiscale Biology, the Jean C. and James W. Crystal Professor of Genomics, and Chair of the Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine. “The potential uses for this information are significant. Not only can genotypic barcodes be deduced from RNA, but RNA levels in some tissue can inform not only individual characteristics like age and sex, but on diseases such as Alzheimer’s and cancer, as well as the risks of developing those diseases.”

Schadt adds, “The significance of our findings goes beyond medicine. For example, barcodes derived from individuals who participated in a research study, where RNA levels were monitored and deposited into publicly available databases, could be tested against DNA samples left at a crime scene as a way of identifying persons of interest.”

Deducing a person’s DNA sequence from gene expression patterns could have repercussions in health care and privacy. While specific laws and government regulations have been written to protect DNA-based information from misuse, it is unclear whether such laws apply to RNA—even though this study shows that RNA is informative at a deeper level compared to DNA regarding the current state of health of an individual.

“Rather than developing ways to further protect an individual’s privacy given the ability to collect mountains of information on him or her, we would be better served by a society that accepts the fact that new types of high-dimensional data reflect deeply on who we are,” Dr. Schadt said. “We need to accept the reality that it is difficult—if not impossible—to shield personal information from others. It is akin to trying to protect privacy regarding appearances, for example, in a public place.”

Dr. Schadt said he hopes the research will catalyze a discussion that might ultimately help resolve privacy debates, and encourage patients to provide data that will help their doctors better diagnose and treat their conditions. Increased access to, and greater quantities of, DNA and other biological information would also contribute to the greater good of medical science.

In the Nature Genetics study, Drs. Schadt and Hao, Associate Professor of Genetics at Mount Sinai School of Medicine, together with Sangsoon Woo, PhD, from the Department of Biostatistics at the University of Washington, analyzed RNA and DNA from 378 livers donated by European-Americans for transplant, as well as liver and adipose tissues from 580 people from the same population group undergoing gastric bypass surgery. The authors found that levels of RNA across many genes correlate with age, sex, body weight, and other risk factors for diseases like diabetes and heart disease, but then they also correlate in many cases with changes in DNA that are unique to a given individual.

The investigators used an algorithm that matches patterns of gene expression to variations at 1,000 single-DNA-base sites in the genome. It is an application of integrative biology that examines multiple dimensions of data (DNA and RNA) to better inform a given dimension (RNA).

“The relationship of DNA to RNA is like that of an orchestra and the symphony it plays,” said Schadt describing the new technique. “The DNA (orchestra) remains the same, while the RNA pattern (quality of the music) changes in response to outside factors. The new technique is like hearing a symphony and deducing which instruments are in the orchestra, essentially unwinding the developmental process to trace tissue samples back to RNA and the gene that instructed it.”

Source: EurekAlert!

International Effort!

Amazon Web Services has just announced that it will be providing space for hosting and analyzing data collected by the 1,000 Genomes Project, an international effort to collect and catalog a vast amount of genetic information from anonymous donors worldwide. Amazon will be footing the bill to host the roughly 200 terabytes of information, but will charge researchers to use its cloud computers if they want to analyze specific sets of data. The company certainly stands to make money on the deal, but its computing tools may also allow greater access to groups with limited computing resources of their own.

The 1,700 DNA sequences from the Project are currently hosted by multiple institutions worldwide, including the National Institutes of Health and the European Bioinformatics Institute. However, Amazon’s service will let researchers import the data directly to Amazon Elastic Compute Cloud and Amazon Elastic MapReduce for analysis, removing the need to download the huge set to a physical computer. “Putting the data in the cloud provides a tremendous opportunity for researchers around the world who want to study large-scale human genetic variation but lack the computer capability to do so,” says Richard Durbin, the Project’s co-founder. The project is part of a larger Obama Administration plan for “Big Data” (PDF) which is meant to expand the resources currently available for accessing, organizing, and analyzing large collections of information.

Source: The Verge