Tag Archives: genetically modified organism

Genetically modified grass saves soils destroyed by military target practice

A common species of prairie grass can help clean soils of dangerous chemicals released by military-grade compounds, a new paper reports. The only catch (at least, in the eyes of some), is that we need to genetically modify it for the task.

A plot of switchgrass. Image credits Great Lakes Bioenergy Research Center / Flickr.

Genetically modified (GM) switchgrass (Panicum virgatum) can be used to purge soils of RDX residues, according to new research. RDX belongs to the nitramide chemical family, is flavorless, odorless, and extremely explosive. Pound for pound, it’s more powerful than dynamite. Given its high stability and ability to explode hard, RDX was in use in military-grade munitions during (and since) WW2. You’ve probably heard of C-4; RDX is its main component, alongside some plasticizing agents.

One downside of using RDX on a wide scale (that, admittedly, wouldn’t factor in very much during an active conflict) is that it can be quite damaging to the environment. In particular, compounds produced by RDX after it detonates (in combat or in firing ranges) spread around the point of impact and accumulate in groundwater, where they can pose a very real threat to any humans or wildlife they come into contact with. RDX stored in munition dumps, buried in minefields, or in rounds discarded improperly will also leech such compounds into their environment.

Genetically modified help

However, one species that’s traditionally employed against soil erosion can be modified to remove these compounds from the soil. The study, led by members at the University of York, has shown that this approach has promise at least when talking about the land on live-fire training ranges, munitions dumps, and minefields. Theoretically, however, it should be applicable wherever switchgrass can grow.

“The removal of the toxic RDX from training ranges is logistically challenging and there is currently a lack of cost-effective and sustainable solutions,” explains Dr. Liz Rylott from the Department of Biology and Director of the Centre for Novel Agricultural Products (CNAP), co-author of the study.

“Our research demonstrates how the expression, in switchgrass, of two bacterial genes that have evolved specifically to degrade RDX gives the plants the ability to remove and metabolize RDX in the field at concentrations relevant to live-fire military ranges. We demonstrated that by inserting these genes into switchgrass, the plant then had the ability to degrade RDX to non-detectable levels in the plant tissue.”

RDX-bearing ammo is still commonly used at firing ranges for training purposes, and has been for several decades already. This has led to high and widespread levels of groundwater contamination around such sites, which is never good news.

The authors explain that their approach involved grafting two genes from bacteria that are known to break down RDX into switchgrass. These plants — essentially GMOs at this point — were then grown on contaminated soil at one US military site. The plants grew well and had degraded the targeted compounds below detectable in their own tissues levels by the end of the experiment.

All in all, the grass degraded RDX at a rate of 27 kgs per hectare, which isn’t bad at all. According to the team, this is the most successful attempt to use plants to clean organic pollutants in the field to date. Processes that use plants for this purpose are collectively known as phytoremediation, and they’re a subset of the greater field of bioremediation, which involves the use of any type of organism or biological process for this task.

The findings here are of particular interest as organic pollutants, in general, tend to interact heavily with their environment (meaning they cause quite a lot of damage) while also being resistant to natural degradation processes (meaning they last for a long time in the wild). RDX in particular is of growing concern in the US. The Environmental Protection Agency (EPA) has it designated as a priority pollutant, with more than 10 million hectares of military land in the US being contaminated with weapons-associated compounds, RDX making up a sizable chunk of that contamination.

“The recalcitrance of RDX to degradation in the environment, combined with its high mobility through soil and groundwater, mean that plumes of toxic RDX continue to spread below these military sites, threatening drinking water supplies,” explains Professor Neil Bruce, also from CNAP, the study’s corresponding author.

One example the paper cites is that plumes of RDX pollution were found in groundwater and aquifers beneath the Massachusetts Military Reservation training range in Cape Cod back in 1997. This aquifer was, in effect, the only source of drinking water for half a million people, and the discovery prompted the EPA to ban the use of all live ammo during training at this site.

The paper “Field trial demonstrating phytoremediation of the military explosive RDX by XplA/XplB-expressing switchgrass” has been published in the journal Nature Biotechnology.

Are GMOs bad? Science says they’re safe

Credit: CIAT, Flickr.

Credit: CIAT, Flickr.

Genetically modified organisms (GMOs) are hotly debated all around the world. Many people are very concerned about engineering crops and animals because of the long-term effect this might have on our planet and our bodies. It’s no wonder then that the opinions people have about GMOs are so polarizing.

The majority of foods in the United States can be classed as genetically modified food because they contain at least one genetically modified ingredient. The genetic modification most often involves introducing a desirable trait to a plant, such as increased resistance to pests, by inserting genes from a foreign organism, such as a bacteria. Many crops grown in the U.S., like most of the soybean, corn, cotton, and canola, are grown from genetically engineered seeds.

According to a 2016 survey conducted by the Pew Research Center, “about half of Americans (48%) say the health effects of GM foods are no different than other foods, 39% say GM foods are worse for one’s health and one-in-ten (10%) say such foods are better for one’s health.” About one in six Americans are deeply concerned with GMOs and predominantly believe GM foods pose health risks.

What genetic modification is and how it works

Genes are bits of DNA which determine all sorts of traits and characteristics in any organism, from size to what chemicals certain cells express. Some genes offer traits that allow certain animals or plants to thrive in their environment, so these genes will be passed along. In time, with many generations, these genes will become common in the population. Our ancestors unwittingly sped up this process when they saved the seeds of the best crop plants to grow them next time, and the next, and the next.

That’s how tiny kernels on tall grass were turned into the juicy corn on the cob over 10,000 years of selection. With animals, we’ve “improved” or domesticated various species by selecting those individuals that had the best desirable qualities, from being compliant to our commands to yielding more milk. Here are a couple examples of wild vs selected crops.

Carrots were biennial plants, meaning they took two years to complete their biological cycle. They also used to be very thin and frail. Today, carrots are tasty orange roots that are an annual winter crop. Credit: Flickr, macleaygrassman / Flickr, adactio. 

Bananas were some of the first fruit that humans domesticated at around 8,000 B.C. Before human modification, bananas were tiny and filled with seeds. Credit: Wikipedia / Flickr, keepon.

Cabbage, broccoli, and kale all come from the same species, originally a wild mustard plant that is now often referred to as wild cabbage. The images speak for themselves. Credit: Wikipedia / Flickr, akaitor.

It’s hard to find someone who doesn’t love plump, juicy tomatoes. It’s even harder to picture how pathetic ancient tomatoes looked in comparison. These unmodified tomatoes were a lot smaller and darker, and resembled berries rather than the apple-shaped delight we all know today. Credit: Flickr, aris_gionis / Flickr, jeepersmedia.

So ever since the first hunter-gathers transitioned to a sedentary lifestyle, humans have been genetically modifying plants and animals around them by cross-breeding and selecting the most desirable traits in organisms.

However, the kind of modern genetic modification taking place today is different, in the sense that scientists can precisely target genes or set of genes. With selective breedings,  all the traits of the desirable animal or plant are passed on to the new offspring. But this also means you get a lot of ‘junk’ — traits that you don’t really need —  and the process takes a long time, over many breeding iterations, until you come up with the desired traits. Selective breeding also only works with organisms that are closely related, such as two varieties of corn.

To make a GM plant, scientists first isolate DNA from different organisms, which can be totally unrelated, such as bacteria, viruses, or even humans. Then, these genes are biochemically recombined in the lab to make a “gene construct”, which can consist of DNA from five to fifteen different organisms. The gene construct is then closed in bacteria so scientists have a lot of copies to work with. The isolated copies are inserted into embryonic plant tissue or migrated directly into plant tissue via a bacterium that acts as a vector. Ultimately, only a few plants out of hundreds will grow normally and exhibit the desired traits, like herbicide resistance, for instance.

Are GMOs safe?

Despite the public having polarized opinions on the safety of GMOs, scientists overwhelmingly agree that GMOs pose no hazard to consumers. In sharp contrast to public views about GMOs, 89% of scientists from the American Association for the Advancement of Science (AAAS) believe genetically modified foods are safe, the Pew Research Center study found.

The AAAS scientists say that media hype can explain the huge gap in opinion about GMOs between their views and that of the public. About 79% of the scientists surveyed by Pew Research said that the media doesn’t distinguish between “well-founded” and “not well-founded” science. What’s more, 52% of the questioned scientists think that the media oversimplifies the science.

“There are several current efforts to require labeling of foods containing products derived from genetically modified crop plants, commonly known as GM crops or GMOs. These efforts are not driven by evidence that GM foods are actually dangerous. Indeed, the science is quite clear: crop improvement by the modern molecular techniques of biotechnology is safe. Rather, these initiatives are driven by a variety of factors, ranging from the persistent perception that such foods are somehow “unnatural” and potentially dangerous to the desire to gain competitive advantage by legislating attachment of a label meant to alarm. Another misconception used as a rationale for labeling is that GM crops are untested,” reads an AAAS statement.

The AAAS also signed a joint statement that debunks claims from anti-GMO advocacy groups that suggest GM foods are less tested or nutritious than non-GM foods.

“Contrary to popular misconceptions, GM crops are the most extensively tested crops ever added to our food supply. There are occasional claims that feeding GM foods to animals causes aberrations ranging from digestive disorders, to sterility, tumors and premature death. Although such claims are often sensationalized and receive a great deal of media attention, none have stood up to rigorous scientific scrutiny. Indeed, a recent review of a dozen well-designed long-term animal feeding studies comparing GM and non-GM potatoes, soy, rice, corn and triticale found that the GM and their non-GM counterparts are nutritionally equivalent,” the AAAS said.

About 170.3 million hectares have been planted with genetically-engineered crops. Map by: National Academy of Sciences.

About 170.3 million hectares have been planted with genetically-engineered crops. Map by: National Academy of Sciences.

According to an exhaustive analysis of the current scientific literature on the subject (over 900 studies published in the last two decades), there is “no substantiated evidence of a difference in risks to human health between current commercially available genetically engineered (GE) crops and conventionally bred crops.” The 2016 study published in the National Academies of Science, Engineering, and Medicine, also concludes that there is no conclusive evidence linking GMOs to environmental problems. 

The main takeaways from what’s perhaps the most comprehensive report so far are:

  • Genetically engineered (GE) crops are safe to consume. That’s to say, there is no evidence that suggests GM food harms human health, increases food allergies, affects the gastrointestinal tract, or poses any risk for horizontal gene transfer.
  • GE crops introduced in the food system today don’t increase crop yields directly. However, they protect yields from insects and weeds.
  • Herbicide-tolerant crops and those with Bt pesticide built in require less pesticide use.
  • Glyphosate use, the herbicide which GE crops can tolerate, has caused the adaptation of glyphosate-resistant weeds, which can cause farmers a lot of expensive problems.
  • There is no evidence pointing to adverse effects or danger to biodiversity from interbreeding GE crops with wild counterparts.
  • Farmers largely earn more from GE crops, but individual results vary.
  • Small-scale farmers may not see economic gains due to the price of seeds and difficulty accessing credit.
  • Regulation of food crops should be mandatory, but based on the characteristics of the crop, rather than the technique used to develop it, be it GE or non-GE.
  • GE debate should be transparent and with public participation.

While the committee concludes that “no differences have been found that implicate a higher risk to human health and safety from these GE foods than from their non-GE counterparts,” it did include a caveat in the report stating any food, GE or otherwise, “may have some subtle favorable or adverse health effects that are not detected even with careful scrutiny and that health effects can develop over time.”

GE crops are the most researched and tested agricultural products in history. In the United States, such products are tested time and time again for consumer and environmental safety by the U.S. Department of Agriculture, the Environmental Protection Agency and the Food and Drug Administration. The same goes for the European Union which conducts tests through its own regulatory bodies. Every major scientific body in the world that has reviewed research on GMOs state that GMO production and sale is safe.

But despite this body of evidence, genetic engineering in agriculture will continue to be a topic debate for decades to come — and that might actually be a very good thing. Even though progress might be hindered, if GE foods are indeed harmful in some way, either to human health or the environment, they deserve the utmost scrutiny. However, at the end of the day, if you’re skeptical of GE food, you should also have this skepticism rooted in scientific consensus, rather than some debunked myth.  

 

gm_arctic_Apples

Genetically modified apples don’t turn brown when sliced or bruised

The US government approved a genetically modified apple that doesn’t turn brown when bruised or sliced. While most genetic alterations of plants involve making these more resilient to pests or yield more, the non-browning apples were made out of cosmetic considerations. Of course, the apples will still  rot and eventually get brown, but in time and not so easily when stressed (cell rupture). But despite the government approval, voices run rampant against the genetically modified fruit from behalf of anti-GMO groups, as well as rivaling food companies.

These apples keep their colour

gm_arctic_Apples

Left, a normal sliced apple left to oxidize; right, genetically modified Arctic apples. Image: Okanagan Specialty Fruits

Okanagan Specialty Fruits, a rather small Canadian company, is behind the new product. An oddity in itself considering the GM space is dominated by giants like Monsanto and DuPont Pioneer. Their intention is to address both consumer and food companies who might benefit from apples that don’t turn brown, which hardly sell in super markets. During harvest and shipping, tons and tons of apples get bruised, turn brown and end up in the gutter. As reported earlier, so-called ugly fruit and veggies get thrown away at a massive scale just because they don’t appeal to the market’s aesthetic standards – between 20 and 40 percent of all fresh food is thus thrown away by farmers. Companies that process apples, like sliced apples, may also greatly benefit. It’s believed that 30% of the cost for sliced apples goes into tainting these with anti-oxidants so they don’t go brown, so consumers will get to buy these 30% cheaper.

When you cut an apple in half – or a banana or potato for that matter – you’ll notice it starts getting brown within a couple of minutes. This is caused by the reaction between an enzyme found in the apples, as well as in other foods, called  polyphenol oxidase or tyrosinase with oxygen and  iron-containing phenols. The fruit starts to oxidize, when electrons are lost to another molecule (in this case the air), and the food turns brown. Basically, an edible rusty crust is formed on your food. You see the browning when the fruit is cut or bruised because these actions damage the cells in the fruit, allowing oxygen in the air to react with the enzyme and other chemicals. To keep your sliced apples as fresh as possible, you need to reduce the amount of oxygen that gets to react with the tyrosinase. Putting the apples under water or vacuum packing are just a few effective ways to do this, but you can also try adding lemon juice (acidic) to reduce the pH of the exposed surface. Or, you can buy Okanagan’s apples and be done with it.

To fix the oxidation problem, the Okanagan researchers engineered their apples – called Arctic apples – so these make less of the polyphenol oxidase. What’s interesting though is that rather than snipping out the genetic code responsible for producing the enzyme, the researchers actually added more copies of the enzyme’s gene, causing the fruit to switch off the whole lot.

Neal Carter, the president of Okanagan, said the apple had “a lot of silent supporters” and would be popular with the food service business.

“I can’t believe how many requests we’ve had just this morning to our website from people who want to buy trees,” he said.

Already, one grower is allegedly planting  20,000 trees this spring, which should yield 5,000 to 10,000 pounds of apples by the fall of 2016, that’s if nothing happens in the meantime. A lot of people are critical of the Arctic apples, which come in two varieties, Granny Smith and Golden Delicious.

“This G.M.O. apple is simply unnecessary,” Wenonah Hauter, executive director of Food & Water Watch, said in a statement, using the initials for “genetically modified organism.” “Apple browning is a small cosmetic issue that consumers and the industry have dealt with successfully for generations.”

Carter argues, however, that his apples aren’t technically genetically modified organisms, not in the traditional sense at least. In the lab, plants are typically altered by adding a gene from some foreign organism, but Carter’s apples were made by internal tweaking of its genes – there’s nothing “alien” inside. But consumer groups say shutting off the browning mechanism could have unintended effects. The Agriculture Department, however, said the Arctic apples seemed to be nutritionally equivalent to other apples. In November, the Agriculture Department approved a genetically engineered potato developed by the J.R. Simplot Company that uses a similar technique to prevent browning.

 

GMO leash

GMOs on a leash: scientists engineer bacteria that can’t survive in the wild uncontrolled

Though GMOs are generally believed to be safe, they’re still shrouded in controversy. Partly because the general public is misinformed on what GMOs are (they’ve been around for thousands of years, we’re only tweaking them much better now in the lab – see artificial selection), but also because there are some genuine and reasonable ethical issues surrounding them. A stronger, pest-resistant GMO crop can spread and put wild strains “out of business”. Controlling them can be a very challenging issue, since life is very good at overcoming obstacles. After all, replication and survival are the most fundamental guides hard-coded in the DNA. But two teams of researchers from the US may have found an elegant solution. Each team independently recoded the genome of the E. coli bacteria such that it dies when it runs out of synthetic chemical, unavailable in nature. This way, it’s impossible for the bacteria to spread into the wild uncontrolled. Effectively, this self-destruct measure puts GMOs on a tight leash!

Controlling GMOs

GMO leash

Genetically engineered micro-organisms are used in Europe, the US and China to produce drugs or fuels under contained industrial conditions. As for plants, much research has focused on making enhanced crops that are more resistant to pests, have greater nutrient content or contain a new nutrient altogether such as the case of Golden Rice, which was engineered to yield Vitamin A.

Genetically modified micro-organisms are the most worrisome since they might  outcompete native strains, with unintended ripple effects on the environment. For instance, engineered bacteria have been tested with very good results for cleaning oil spills, but while they might prove useful in averting an instance of an ecological disaster, they might trigger another one.

“I view us right now at the beginning of the biotech century, where I think a lot of solutions to defining global challenges . . . are in large part going to result from advances in biotechnology,” said Farren Isaacs, assistant professor of molecular, cellular, and developmental biology at Yale, who led one of the studies. “In many ways, what we are doing is trying to be a step ahead of any challenges we might face.”

The Harvard and Yale scientists grew about one trillion bacteria and found that not one could survive without the essential synthetic amino acid.

“We’re changing the whole genome,” Church said. “So all genes, including the ones involved in producing whatever chemical you’re interested in, all those genes get changed. None of these can go in or out functionally.”

genetically modified crop

Source: Gizmodo

The US researchers describe their research, published in Nature journal (1 and 2), as a “milestone” in synthetic biology.

“This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites,” Church says.

Yet, not everybody is convinced by the two studies.

“The problem is that we cannot quickly determine if every single GMO that is produced is absolutely safe or absolutely unsafe to people and the environment. The last thing we want to have happen is to figure out that something is dangerous through accidental release, after it is too late,” said Karmella Haynes, an assistant professor in the School of Biological and Health Systems Engineering at Arizona State University. “I feel that this research represents a step-change towards building reliable control switches for GMOs.”

Jaydee Hanson, policy director of the International Center for Technology Assessment, said that the research was limited because these first tests were done in traditional laboratory environments.

“The basic idea in them is that can we engineer something so that if it gets out into the environment, or in the case of probiotics — when it’s in your body — so it doesn’t morph into something else,” Hanson said.

“I hope their next step would be to run the experiment longer, and to make sure that you’re not having any problems after multiple generations.”

This plant may look like an ordinary tobacco plant, but on the inside it was engineered to express bacteria proteins which helps it perform more efficient photosynthesis. Photo: Rothamsted Research

Tobacco plants borrowing bacteria genes achieve more efficient photosynthesis

This plant may look like an ordinary tobacco plant, but on the inside it was engineered to express bacteria proteins which helps it perform more efficient photosynthesis. Photo: Rothamsted Research

This plant may look like an ordinary tobacco plant, but on the inside it was engineered to express bacteria proteins which helps it perform more efficient photosynthesis. Photo: Rothamsted Research

It wouldn’t be an understatement to say we owe all the wonders of life to photosynthesis – the ability of plants and certain bacteria to convert CO2 into energy (sugars) and food. Scientists have for some time attempted to enhance photosynthesis through genetic manipulation, but it’s only recently that we’re beginning to see these efforts take form. The most recent breakthrough was made by a team of British and American biologists  who report they’ve  successfully infused tobacco plants with bacterial genes – a first step towards engineering crops that grow faster, offer higher yields and use less fertilizers.

Better photosynthesis, more food

Cyanobacteria – single-celled organisms also known as blue algae – are far more better at converting CO2 to useful energy than plants. Part of the reason is that the bacteria use an upgraded version of an enzyme called  rubisco, which is the protein that converts CO2 into sugar, and is possibly the most abundant protein on Earth. About half of all the soluble proteins found in leaves are rubisco.

In plants, however, rubisco isn’t that efficient and scientists have been trying to find ways to boost it for some time. If such an attempt were to be proven entirely successful, then crops with the equivalent bacterial photosynthesis ability would cut fertilizer needs and increase crop production by 35 and 60 percent. But researchers at Cornell University, USA and Rothamsted Research, UK claim they’ve managed to solve one piece of the puzzle: they’ve modified tobacco plants that produce functional rubisco from the cyanobacterium Synechococcus elongatus.

This wasn’t an easy job, though. While previous attempts focused on swapping bacterial genes that code for the turbocharged rubisco, the team also made other genetic substitutions  that encode proteins that manufacture the rubisco. The modified plants confer CO2 into sugar faster than normal tobacco, a sign that photosynthesis had been sped up and that the researchers are heading in the right direction.

Yet they still have their work cut out for them. While the photosynthesis is more efficient, the plants themselves grew significantly slower. The researchers report:

“We grew our [genetically engineered] plants in a CO2 elevated environment” with more 22 times the amount of normal amount of the gas, “and they still were growing slightly slower than the normal type plants.”

 

While the algal rubisco makes the photosynthesis more efficient, the tobacco plant wasn’t completely engineered to mimic the whole process the bacteria use. Namely, cyanobacteria employ β-carboxysome shell proteins that ward off oxygen, creating a tiny, CO2-rich environments for their rubisco. Normal plants on the other hand lack this shell and consequently adapted by using a form of rubisco that is slower and less efficient, but which none the less is also capable of picking CO2 in favor of O2. In the case of our modified tobacco plant, the Rubisco is bacterial, but without the shell, a lot of energy is wasted on reacting with oxygen.

Obviously, researchers are concentrating on how to integrate the shell with the bacterial rubisco. So far, developments have been promising since the same team engineered tobacco plants that could generate carboxysome-like structures a while back. Integrating the findings of the two bodies of research might finally take food production to a new level.

While genetically modified plants, fertilizers and pesticides have made crop yields go a long way, the momentum sparked a couple of decades ago is steadily running out. Soon enough, we’ll have to find new ways to increase food production per unit area to keep up with an ever expanding population. Tweaking photosynthesis may be just one in many such efforts.

Findings appeared in Nature.

The Family Tree of Beer: A Team of Geneticists is creating the Beer Yeast Genome Project

In a lab in San Diego, Troels Prahl, a brewer and microbiologist at the Southern California yeast distributor White Labs sits at the tasting bar in front of 4 open half pints of beer. Each of them is different, in color and flavor, ranging from a crisp body of raspberry, rosemary and banana to a dry and subtle blend of nutmeg and fresh straw. But with the single exception of the yeast they were brewed from, all the beers are identical.

Tw0 organizations, White Labs and a Belgian genetics laboratory have teamed up to create the first genetic family tree for brewing yeasts and the beers they make, by analyzing more than 2,000 batches of beer. So far, they’ve sequenced the DNA of more than 240 strains of brewing yeasts from around the world. Alongside samples from breweries like Sierra Nevada, Duvel Moortgat and Stone, “we’ve thrown in a few wine, bakers, bio-ethanol and sake yeasts to compare,” said Kevin Verstrepen, director of the lab in Belgium.

“Yeasts can make over 500 flavor and aroma compounds,” said Chris White, the founder of White Labs, affecting not only a beer’s alcohol level, but also its taste, clarity and texture.

But while this study will provide valuable scientific information, showing which yeasts are related to which and how they evolved, it also has an economic significance, allowing researchers to create new types of beer.

“With this information, we’ll be able to select different properties in yeasts and breed them together to generate new ones,” Dr. Verstrepen said. “In a few years we might be drinking beers that are far different and more interesting than those that currently exist.”

For brewers today, yeast options are very limited. Nowadays, most yeasts are highly specialized, so mixing them together to make new drinks is almost never usable (it’s like mixing a family and a sports car to get something in between – doesn’t really work). Even genetic attempts to mix them rarely yield successes.

Also, while the technology of developing new yeasts by splicing new genes in a lab exists, consumers are highly reluctant when it comes to consuming genetically modified products. In other words, GMOs are not attractive – even beer’s GMOs.

“Right now we have a few hundred genetically modified yeast strains patiently waiting in our laboratory’s freezer,” said Jan Steensels, a microbiologist with the Belgian lab, “but most brewers and consumers don’t want anything to do with them.”

This is where this Yeast Genetic Tree steps it – the knowledge from this genome could enable researchers and companies to brew new beers without resorting to genetic modification. If you want to obtain a specific mix of tastes, flavors and alcohol content, you first have to know where to look in the genetic tree. Then, by knowing exactly which genes to track, using specialized software and computers, they will be able to mix different yeasts until they obtain the exactly properties they want.

“So let’s say there’s a yeast that produces an amazing fruity aroma in beer, but can’t ferment past 3 percent alcohol,” said Chris E. Baugh, a microbiologist at Sierra Nevada Brewing Company in Chico, Calif., who is not involved in the project. A scientist who understood the genetics, he continued, “could then breed it with a more alcohol-tolerant strain.”

Still, this will almost certainly not phase brewing giants, which for decades have clinged to their recipes, but it may lead to a boom of smaller, specialized, and more tasty beers.

“Where this is really going to take off is in the craft brewing scene,” Dr. Baugh said. The number of craft breweries and microbreweries has exploded in recent decades, to roughly 2,500 today from fewer than a dozen in 1980 (in the US).

Interestingly enough, the cost of sequencing yeast genome is not that high. As a matter of fact, the technology is so inexpensive that the first 96 strains at White Labs were sequenced free of charge by the biotechnology company Illumina, to assess one of its new sequencing machines. The real challenge lies in the immense work volume required to finish the project.

 “This project strikes me as sort of an inevitable thing that one can do,” said Randy W. Schekman, a yeast geneticist at the University of California, Berkeley, who shared the 2013 Nobel Prize in Physiology or Medicine. With the falling costs and rising speed, he added, “the sequencing is almost trivial at this point.”

This, he believes, is an important step for an industry that has long been way of genetic modifications:

“Until recently, the brewing industry has been remarkably resistant to using the techniques of genetics and molecular biology to improve their brewing strains,” Dr. Schekman said. “It’s long overdue that someone has actually delved into the molecular basis between the differences in brewing strains.”

Via NY Times.

 

yeast

Yeast chromosome engineered from scratch: creating cretures in a lab

In a huge breakthrough in synthetic biology, scientists at Johns Hopkins University have engineered from scratch a yeast chromosome. This is the first time scientists have been able to assemble a chromosome from a creature as complicated as a yeast, namely a prokaryrite. The implications of this research are far and wide. For one, the developments at Johns Hopkins provide an invaluable learning tool and launching platform for future research in synthetic biology. More immediate applications include the biofuel industry and of course beer.

Humans have been growing yeast for practical purposes ever since they figured out how to brew beer and bake bread thousands of years ago. Through selective breeding and close manipulation, mankind has been essentially engineering yeast for a long time. This time, however, the researchers led by Jef Boeke have gone the extra mile and genetically engineering an entire organism (the yeast) from scratch.

Yeast 2.0

Their work involved designing and writting a code made up of roughly 11 million letters of DNA—the As, Cs, Gs, and Ts that write the book of life. This code was synthesized and subbed in for a yeast’s natural DNA, thus obtaining a brewer’s yeast’s DNA with a completely altered  chromosome. Chromosomes are organized structures of DNA and proteins that are found in cells. A chromosome is a singular piece of DNA, which contains many genes, regulatory elements and other nucleotide sequences. Chromosomes vary extensively between different organisms. The DNA molecule may be circular or linear, and can contain anything from tens of kilobase pairs to hundreds of megabase pairs. Typically eukaryotic cells (cells with nuclei) have large linear chromosomes and prokaryotic cells (cells without defined nuclei) have smaller circular chromosomes, although there are many exceptions to this rule.

For instance, each human cell contains 23 chromosome pairs, for a total of 46. The man-made yeast chromosome represents about three percent of all of the DNA that makes a yeast.

“Yeasts have 16 chromosomes, and we’ve just completed chromosome 3,” Boeke says. “Now it’s just a matter of money and time.”

In 2010, the J. Craig Venter Institute reported a landmark advancement in synthetic biology, after scientists there built all of the DNA for a bacteria from scratch. Yeasts are one level up bacteria, however. While they’re both single-celled organisms, yeasts are eukaryotic, in the same group as plants and humans, while bacteria are eukaryotic, similar to the very first living things that formed on Earth billions of years ago.

“The synthesis and design of the first eukaryotic chromosome is obviously an exciting milestone,” says Farren Isaacs, a cell biologist at Yale University who was not involved in Boeke’s team. “Eukaryotic” refers to the grouping of life that yeast belong to.

Genetically modified organisms have come a long way in recent years, but while researchers have concentrated their efforts on designing organisms marginally similar to those born from pure evolution, adding or deleting just a couple of genes here and there, the new yeast is proof of an entirely new organism, engineered from scratch.

yeast

So their beer yeast isn’t just some carbon copy of nature, but an entirely new one – an improved version, some may say. A lot of DNA was trimmed down, parts of redundant or unnecessary segments of code called “junk DNA”. The researchers even added some stretches of DNA that give the chromosome a latent superpower that doesn’t come into play unless it’s triggered.  “It’s almost akin to being able to trigger evolution,” Isaacs says.

To test if the synthetic version with the cut out chromosome III can support yeast life, the researchers simply added the chromosome back into the yeast from which the natural version was removed. In the lab, the hybrid grew and reproduced just like its cousins.  “It looks like it, it behaves like it, it smells like it,” Boeke says. “Basically, you wouldn’t know the difference unless you take the next step and introduce what we call the genome scrambling system into it.”

There’s been a lot of talk about junk DNA, however. For instance, it’s been found before that what scientists used to call redundant genetic code turned out to be pretty useful. It’s just that some code becomes active only in particular situations. It could be that if yeast is subjected to particular environmental stimuli, like a specific temperature or pressure, it may not survive or behave differently than its natural brethren. If this happens, then it may be for the better since it would show that the cut-out genes actually do something providing an excellent learning tool.

“So what we’re doing is, in some sense, a risky business,” Boeke says. “There’s not a flag on each segment saying ‘this one’s not important’. It’s really a judgment call at a certain stage.” Luckily, yeasts, like fruit flies and mice, are one of the best-understood organisms in all biology, so the scientists relied on a huge genetic database to guide them. “But if we make a mistake, as we’ve found in some of our unpublished work, the penalty could be a dead yeast,” he says. “So we were pretty conservative.”

The future of beer

Yeast is an important component in brewing and in most beers, it’s responsible for the dominant flavour. Some yeasts make for a good flavour, but they ferment too little alcohol, which can be frustrating for research scientists at breweries. A modified synethic yeast could solve many issues. But would you drink a genetically modified beer? Some brands stay away from GMO hops because they offer their consumers all-natural flavour. So a more likely candidate for synethic yeast may be the biofuel industry where GMO corn ethanol is widely produced.

Findings appeared in the journal Science.

 

(c) PETE RICHES/DEMOTIX/CORBIS

Monsanto pulls GMO crops out of Europe, for now at least

(c) PETE RICHES/DEMOTIX/CORBIS

(c) PETE RICHES/DEMOTIX/CORBIS

Biotech giant, Monsanto, has been met with a wave of furious protests during the past year in Europe, as the company intended on introducing genetically modified seed crops in the EU. As opposed to the US, where despite the general public is nearly or just as adverse in the face of genetically modified crops, politicians in the EU actually adhered to their people’s wishes and have blocked Monsanto efforts to introduce GM crops in the EU. In response, Monsanto made a sensible business decision and  announced it will no longer be seeking approvals for genetically modified (GM) crops now under review for cultivation in the European Union (EU).

“As long as there’s not enough demand from farmers for these products and the public at large doesn’t accept the technology, it makes no sense to fight against windmills,” explained Ursula Luettmer-Ouazane, Monsanto’s German spokeswoman.

This doesn’t mean that Monsanto has given up on GM Europe, though. Instead, the company believes that Europe still needs time to get used to the idea of GMOs, and are certainly leaving their door open for when that time comes. Until then, Monsanto is still operating in the EU with business catering to conventional seed crops and agriculture.

Until recently when the company gave up on all but one of them, Monsanto sought approval from the European commission for a variety of genetically modified crops (maize, soya etc). In such cases, the regulatory path is rather clear. First, the GMO must be analyzed  by the European Food Safety Authority (EFSA) in Parma, Italy and deemed safe before it can pass a draft decision by the European Commission following three months. The red tape surrounding these procedures has proven to be much more cumbersome than Monsanto had projected it seems, despite intense lobbying.

Since 2005, the EFSA has deemed eight crops as safe, however public dismay (some countries banned GMO crops altogether) has mandated the commission not to move forward on any of them. Four crops out of these are Monsanto, while five GM crops were still under review by the EFSA. The company has chosen to withdraw all but one crop from the approval board –  one GM maize, MON810 which is already grown in the EU, but is now up for its ten-year re­approval review.

While anti-GMO advocates are thrilled at the news, others are frightened this is a step down for Europe as other regions of the world are increasingly adopting the technology.

“It’s bad news for Europe, for European farmers and for global food security,” says Jonathan Jones, who uses both GM and conventional approaches to study disease resistance in plants at the Sainsbury Laboratory in Norwich, UK. “Europe has to get its act together.”

As the GMO stigma becomes ever more bearing, even a small patch of GMO crop can cause turmoil. Increasingly, researchers are looking for the chance to do their work in more accepting countries in the Far East, Africa and Latin America, says Denis Murphy, a plant biotechnologist at the University of South Wales near Pontypridd, UK. “I do a lot of my work now overseas,” he says. “I’ve almost given up on Europe.”

11 year old gives remarkable TED talk about GMO foods

Birke Baehr is only 11 years old, but he gave one of the best TED talks I’ve seen in a while. Here’s “What’s Wrong With Our Food System? And How Can We Make A Difference?”

At age 9, while traveling with his family and being “roadschooled,” Birke Baehr began studying sustainable and organic farming practices such as composting, vermiculture, canning and food preservation. As he explains, he also found his other passion – educating others.

birke baehr