Tag Archives: genome sequencing

Scientists discover why cockroaches are such good survivors

Researchers sequenced the American cockroach‘s genome for the first time, discovering what makes them such great survivors.

Periplaneta americana Via Flickr

The American cockroach, also known as Periplaneta americana, possesses widely expanded gene families related to taste and smell, detoxification and immunity, compared with other insects, found a team of researchers who published their discovery on March 20 in the journal Nature Communications.

“It makes total sense in the context of the lifestyle,” said Coby Schal, an entomologist at North Carolina State University who was part of a team that last month reported an analysis of the genome of the German cockroach (Blattella germanica). “Many of the gene families that expanded in the American cockroach were also expanded in the German cockroach”, Schal said.

That actually makes sense because both species are omnivorous scavengers that can thrive on altered food in extremely unsanitary environments — at least by human standards.

The American cockroach originally comes from Africa but was introduced to the Americas in the 1500s. Unlike the German cockroach, which is found almost exclusively in human dwellings, the American cockroach only tends to venture into the basements or bottom levels of buildings, according to Schal.

In China, the cockroach is often called “xiao qiang,” meaning “little mighty,” according to Sheng Li, an entomology professor at South China Normal University in Guangzhou and lead author of the paper. “It’s a tiny pest, but has very strong vitality,” he said.

The two species are remarkable survivors and their mysterious abilities appear to lie within their genes. In the new paper, professor Sheng Li and his team found that American cockroaches have the second-largest genome of any insect ever sequenced, right behind the migratory locust (Locusta migratoria). Curiously enough, 60% of the insect’s genome consists of repetitive segments. Gene families related to taste and smell were much larger than those of other bugs, and scientists counted 522 taste receptors in the roach. German cockroaches possess a similar number of taste receptors (545), Schal said.

“They need very elaborate smell and taste systems in order to avoid eating toxic stuff,” Schal added.

Source: Flickr

Interestingly, American cockroaches also have large gene families responsible for metabolization of toxic substances, including some chemicals found in insecticides — their ‘cousins’, the German cockroaches have them too. Schal said that both roaches evolved this way long before humans ruled the world. Resistance to toxic substances developed in roaches thanks to the abundance of toxin-producing bacteria in their environments and their tendency to eat rotten plant matter, he explained.

In addition, the American cockroach has a large number of immunity genes, perhaps another adaptation to unsanitary environments and fermenting food sources, Li and colleagues wrote.

Finally, the team discovered that the insect had a large number of genes devoted to physical development, such as genes responsible for synthesizing the insect’s juvenile hormone or the proteins in its exoskeleton. Authors were not surprised by this since American cockroaches can measure up to 2 inches (53 millimeters) long.

A greater understanding of the cockroach genome could help researchers come up with new ways to control theses pest species. One interesting research interest, Schal said, is the Asian cockroach (Blattella asahinai), a close relative of the pesky German cockroach that lives outdoors and doesn’t really bother humans. It would be interesting to see what are the differences between the Asian and German cockroach genomes.

Still, there’s a long way to go before we can see the broad picture of cockroach genetics.

“There are 5,000 described species of cockroaches, and now we have two [full] genomes,” Schal concluded. “So we need more.”

Scientist decode the largest genome so far – and it belongs to the axolotl

The Mexican axolotl Ambystoma mexicanum. Credit: IMP.

The Mexican axolotl Ambystoma mexicanum. Credit: IMP.

The axolotl (Ambystoma mexicanum), also known as the Mexican salamander, is one of the most peculiar animals on Earth. Its superpower is similar to that of Wolverine’s: extreme regeneration. Axolotl, this smily-faced amphibian, can regrow missing limbs, spinal chord segments, brain tissue, nerves, and retina.

Scientists have long been fascinated about this creature’s mysterious abilities. Now, a team composed of researchers from Vienna, Dresden, and Heidelberg has successfully decoded the entire genetic information of the axolotl. This data may help decipher the miracle of limb re-growth.

For quite some time, salamanders such as axolotl have been intensely studied because of their remarkable regeneration ability. If the amphibian loses a limb, in a few weeks, it will grow a new one, from scratch. The limb will be just like the old one, with no scar tissue whatsoever. These salamanders can also receive implants from their kin with no problems. A research team even performed axolotl head transplants in 1968. One of the animals lived up to 65 weeks with two functioning heads.

A key factor in understanding this type of regeneration is the animal’s genome (genetic material). So far, scientists couldn’t sequence all of it due to its length — at 32 billion base pairs, it is more than ten times larger than the human genome.

Male albino axolotl. Source: Pixabay/Tinwe

Researchers used the PacBio-platform, a sequencing technology that produces long reads to span large repetitive regions. A total of 72.435.954 reads were sequenced. Next, Gene Myers and Siegfried Schloissnig together with colleagues developed software systems that can assemble the genome from the 72 million pieces.

This is how they found that the uniqueness of the axolotl resides in its genes — the salamander only shares several genes expressed in regenerating limb tissue with other amphibian species. An essential developmental gene that plays key roles in neural and muscle development — PAX3 — is completely missing. Another gene, named PAX7, has taken over its functions.

“We now have the map in our hands to investigate how complicated structures such as legs can be re-grown”, says Sergej Nowoshilow, co-first author of the study. “This is a turning point for the community of scientists working with axolotl, a real milestone in a research adventure that started more than 150 years ago.”

Because of their incredible regenerative abilities, axolotls are of great interest to scientists. Because they can not only regenerate limbs and organs, but also brain tissue, many researchers hope that they might one day be able to do the same for human tissue in certain conditions. The implications in medical practice would be immensenly beneficial.  One challenging aspect has always been the axolotl’s huge genome size but now that it’s been sequenced, a whole new avenue of discoveries await.

Scientific reference: The axolotl genome and the evolution of key tissue formation regulators. Sergej Nowoshilow, Siegfried Schloissnig, Ji-Feng Fei, Andreas Dahl, Andy W.C. Pang, Martin Pippel, Sylke Winkler, Alex R. Hastie, George Young, Juliana G. Roscito, Francisco Falcon, Dunja Knapp, Sean Powell, Alfredo Cruz, Han Cao, Bianca Habermann, Michael Hiller, Elly M. Tanaka, and Eugene Myers. Nature, doi: 10.1038/nature25458.

The site from the Mota cave where the 4,500 Ethiopian man was found. Image: Kathryn and John Arthur

First ancient African genome sequenced

The complete genetic code book of a person who lived 4,500 years ago in Ethiopia was completed by US researchers. Although much older genomes have been sequenced, like those of 38,000 year-old Neanderthals, samples from African forefathers have proven difficult to sequence as the DNA is often destroyed by accelerated decay, driven by tropical conditions. As such, this is the first time a complete genome retrieval was performed from an ancient human in Africa. In this light, the findings are very important: they suggest even older DNA could be retrieved – maybe even millions of years back to the age of other species of the homo genus.

The site from the  Mota cave where the 4,500 Ethiopian man was found. Image: Kathryn and John Arthur

The site from the Mota cave where the 4,500 Ethiopian man was found. Image: Kathryn and John Arthur

After a creature dies, enzymes start breaking down the nucleotides (genetic letters) that form DNA and bacteria and other microorganisms speed the decay. If water is present – and it almost always is, especially in the soil where bodies are buried – the nucleotide bond disintegration is even faster. Previously palaeogeneticists  discovered that DNA has a half-life of 521 years, meaning after 521 years, half of the bonds between nucleotides in the backbone of a sample would have broken; after another 521 years half of the remaining bonds would have gone; and so on. Considering ideal preservation conditions like  −5 ºC temperature, DNA could be readable for 6.8 million years. In practice, it starts breaking down much faster becoming barely usable after just 1.5 million years past which the remaining strands would be too short to give meaningful information.

It wasn’t until scientists had found clever ways to stitch together DNA fragments that genome sequencing of ancient fossils really took off. Humans in Asia and Europe who lived tens of thousands of years ago had their genetic makeup analyzed, and this way scientists had been able to retrace migration patterns and understand how populations mixed together and moved from place to place. One of the most important study to do this was led by Ron Pinhasi, an archaeologist at University College Dublin, who found that the best place to look for genetic makeup is the bone surrounding the inner ear.

It’s quite remarkable how much you can tell from a person’s DNA. Case in point, you can retrieve valuable information not only of the individual himself but also his lineage. For ancient Africans, however, this has proven problematic because the tropical conditions obliterate DNA. Luckily, John W. Arthur and Kathryn Weedman Arthur, archaeologists at the University of South Florida were able to find a mint conditioned specimen at the Mota cave, in the highlands of southern Ethiopia. They sent the inner bone of the ancient Ethiopian man to Pinhasi hoping he might be able to tell them something. To everyone’s surprise, Pinhasi was able to extract the man’s full genome, who lived and died around 3,000 BCE.

“What we were able to get is a few very high quality undamaged DNA from which we could reconstruct the whole genome of the individual”, said senior author Dr. Andrea Manica from the University of Cambridge’s Department of Zoology.

Apparently the man from Mota had brown skin and brown eyes, and also bore the same genetic adaptations found in modern day Ethiopian highlanders that helped them cope better with the lower temperature and oxygen levels. What’s most interesting is that the Mota man didn’t have any trace of Indo-European DNA, despite modern day people in Nigeria have 7% Indo-European DNA and the  Mbuti pygmies who live in the rain forest in the Democratic Republic of Congo have 6%. This implies two possibilities: either the Mota man was part of a tribe who had managed to stay isolated from other tribes, local or foreign, and bred only among themselves or, more likely, Indo-Europeans hadn’t arrived in Ethiopia 4,500 years ago in what’s called a backflow. Initially, humans left Africa between 100,000 and 50,000 years ago settling in Europe and Asia. Then some populations, which became genetically distinct, came back to Africa and bred with the native African populations causing a genetic backflow. To know for sure, the Arthurs and Pinhasi should retrieve more DNA from ancient Africans.

woolly mammoth

Woolly Mammoth genome sequencing makes cloning a lot more doable

A team at University of Chicago made the most comprehensive woolly mammoth genome sequencing ever. By comparing its genome with that of its distant cousins, the Asian and African elephants, the researchers were able to determine which are the mammoth’s specific genes. These were ran with libraries and repositories to identify what these do. We now know which of mammoth’s gene shaped its uncanny skull and small ears, how it got hair to cover all its body or how the mammoth adapted a special fat metabolism and cold coping mechanism. To test their findings, the researchers transplanted a mammoth gene into a human cell. The kidney cell produced new proteins which were tolerant to heat or cold, as suspected showing their other genetic determinations are also likely correct.

woolly mammoth

Image: Technopedia

What the mammoth

This isn’t the first time a mammoth’s genome was sequenced, of course. However, these previous efforts were error-prone and yielded only limited results .This is natural after all, since we’re working with DNA from a creature which went extinct some 10,000 years ago. The last ice most likely killed off the mammoth which roamed the frigid tundra steppes of northern Asia, Europe and North America. On the bright side, the ice age helped keep mammoth specimens in the “freezer” helping preserve whole tissue and even mammoth blood. The cold, however, damages DNA and sequencing the genomic data can be a lot like retrieving data from a hard drive with “bad” sectors. You can fill in the gaps, but only so much.

Vincent Lynch, PhD, assistant professor of human genetics at the University of Chicago used new techniques to sequence the whole genomes of two woolly mammoths and three Asian elephants, which are the closest living relatives of the mammoth. The two genomes were then compared against each other. The genome of the African elephant, a more evolutionary distant relative of both species, was also added to the mix.

The researchers identified 1.4 million genetic variants unique to woolly mammoths, which caused changes in the proteins produced by 1,600 genes. Proteins are basically what signal physical growth, change and function. Thus, mammoth genes were identified that are involved in fat metabolism (including brown fat regulation), insulin signaling, skin and hair development (including genes associated with lighter hair color), temperature sensation and circadian clock biology. These are all highly important in helping the mammoth adapt to Arctic temperatures.

“This is by far the most comprehensive study to look at the genetic changes that make a a woolly mammoth,” said study author Vincent Lynch, PhD, assistant professor of human genetics at the University of Chicago. “They are an excellent model to understand how morphological evolution works, because mammoths are so closely related to living elephants, which have none of the traits they had.”

To make sure they did their job right, the researchers used ancestral sequence reconstruction techniques to “resurrect” the mammoth version of one of these genes, TRPV3, then implanted it into a human kidney cell. The TRPV3 gene produced a protein that was less responsive to temperature than the modern elephant ancestral version. So it seems likely that TRPV3 was also important for mammoth cold tolerance. Findings appeared in Cell Reports.

Resurrecting a fallen beast

Naturally, the better the genome sequencing, the better the chances of a mammoth cloning working well. Some researchers think this is total nonsense and won’t even happen, but there are research groups around the world that are working on making the very first ancient creature resurrection. The scientific challenges are quite difficult to overcome, though. For instance, Harvard University researchers are now filling the gaps in poor mammoth genome sequences with elephant DNA. The better the genome, the better the odds that a live, functional mammoth might be born alive. But will it be a mammoth in the first place? It’s hard to tell.

“We can’t know with absolute certainty the effects of these genes unless someone resurrects a complete woolly mammoth, but we can try to infer by doing experiments in the laboratory,” Lynch said.

“Eventually we’ll be technically able to do it. But the question is: if you’re technically able to do something, should you do it?” he said. “I personally think no. Mammoths are extinct and the environment in which they lived has changed. There are many animals on the edge of extinction that we should be helping instead.”

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.

 

faroeislands

Faroe Islands wants to sequence its entire population’s genome

Located in the North Atlantic, right in between Greenland and Scotland, Faroe Islands is one of the smallest countries in the world. At the same time, however, it has also remained fairly isolated for many centuries, which in time has led to the formation of a distinct language and population. You can spot a native from a mile away, and in fact, they all seem to resemble each other quite well, at least in dominant features. This is because the country has a highly homogeneous population, even by Nordic standards, which puts it at high risk of developing genetic disorders.

faroeislandsWith this in mind, the local government recently implemented a program which aims to sequence the genome of all its citizens, or at least all of them who agree.  So far,  some 30,000 citizens — about three-fifths of the total population — have already submitted blood samples to its new Genetic Biobank. According to officials, the project doesn’t have an immediate goal in mind, however armed with such a complete database, whenever scientists have a better understanding of how the genetic disorders affecting Faroese work, they can then quickly summon citizens most at risk to the hospital to commence treatment.

For instance, ever growing cases of  carnitine transporter deficiency (CTD) are reported. The disease prevents the body from maintaining adequate levels of carnitine, which plays a critical role in metabolism. The disease most often is fatal, and the largest concentration of cases are found in the Faroe Islands, hundreds of times higher than in neighboring regions.

Last year, the country’s Ministry of Health launched an extensive program aiming  to sequence the genome of every citizen who wants it, focusing most on those with CTD, along with other conditions, such as schizophrenia, cystic fibrosis and diabetes.

“I don’t call it inbreeding, but line breeding,” says Gudrid Andorsdottir, who runs the biobank. “There is the implication that you are strengthening some factors, rather than inbreeding, which is a more negative word.”

The local government takes this very seriously and currently has one of the most extensive genetic records in the world.  The Genetic Biobank has finished digitizing the past 200 years of genealogical histories, and when combined with an almost complete population genome sequence, the country might become in the future one of the first at the forefront of the medicine of the future – a future in which every citizen has his own extremely personalized treatment, with the right dosage and medication calculated to extreme precision for maximum efficiency.

Indeed, this could save countless lives, but this also means that the government has or will have at least access to the DNA of every individual in the country. In a paranoia ridden world, especially considering recent whistle-blowing in the US that alleges a massive internet spying program in the US, this might not be the right precedent to set. If successful, Faroe Islands might be the pilot program that can spur other countries to apply similar methods. Then again, we’re speaking about a country made out of 18 tiny islands, and tiny as it is the program has already gobbled $50 million and will require hundreds of millions more of funding to decipher the meanings of the genomes. It will certainly not be just as easy for other countries in the world.

via Discover

 

 

ecoli

Is evolution predictable? Research shows specialization isn’t that special after all

There are millions of species on Earth, and naturally understanding the mechanics of evolution is of great importance for understanding further on what sparks life. What sparks consciousness, well that’s a whole different ball-game. Currently, scientists are concentrating on how diversification occurs in order to better their knowledge of how so many species surfaced along the eons. Is this task impossible though? Is evolution itself predictable?

ecoli

The E. coli bacteria. (c) Food Poison Journal

A recent research by scientists at University of British Columbia seems to suggests so, after they breaded three separate populations of the popular lab pet bacteria, E. coli, for a whooping 1200 generations. What they found is that eventually each population, though separate and independent from each other, evolved in very similar and in some respects identical strains to accommodate to their new environments.

Conducted by Matthew Herron and Michael Doebeli, the experiment involved placing each of the E. coli populations in an environment with two different sources of dietary carbon – glucose and acetate. In the beginning all bacteria behaved as generalists, after some 1200 generations though the bacteria branched into two distinct species, each specialized on eating one of the two food sources. This happened in each of the three separate populations.

Simple empirical observations weren’t enough, so prudent as they are, the scientists were careful to freeze samples from each population at 16 different points during their evolution. Recent advances in sequencing technology allowed the scientists to sequence large numbers of whole bacterial genomes, so the researchers had now access to a large volume of highly valuable data.

What they found was absolutely striking similarities in how the bacteria evolved. Basically, for all populations a core set of genes were causing the two different phenotypes that they saw, and in some cases the researchers witnessed the very same exact genetic change at play.

“There are about 4.5 million nucleotides in the E. coli genome,” said co-author Matthew Herron, research assistant professor at the University of Montana. “Finding in four cases that the exact same change had happened independently in different populations was intriguing.”

The obvious conclusion: selection can be deterministic.

“Not only did similar genetic changes occur, but the temporal sequence in which the changes occur over evolutionary time was also similar between the different evolving populations. This ‘parallelism’ implies that diversification is a deterministic process driven by natural selection,” said co-author and University of British Columbia zoologist Prof. Michael Doebeli.

The authors claim that negative frequency dependence – a well known particular form of selection – plays a major role in driving diversification. Simply put, a bacteria specialized on feeding on an alternative resource will be at an advantage, and thus have greater chances of passing its genes.

Is this research flawed, however? Considering the study only focuses on only a single type of bacteria, this might be the case. Evolution is not simple, by any means, and despite it might be governed by a fixed set of laws, the fabrics of its creation can be rather startling.

Nevertheless, the authors plan on repeating the experiment and conduct other more in order to see whether these conclusions remain the same at a larger scale and with larger, more complicated organisms.

Findings were published in the  journal PLOS Biology.

A micro-fluidic device developed at MIT designed to automatically run DNA experiments on other planets. Credit: Christopher Carr | MIT

Entrepreneurs compete in audacious race after Martian DNA

The search for extraterrestrial life has always been a fascinating thought, one that has entertained the human mind for generations, sparked by the life-long question “are we alone in the Universe?” Existentialism aside, in the past decades intense efforts have been made in order to find life beyond our blue marble, the most recent of which is the now renowned Mars Curiosity rover mission, whose main objective is that of finding evidence of live on the red planet. Some people, however, who possess the necessary resources and gut, one that bounders the fine line between brilliant vision and madness, have an agenda of their own as far as extraterrestrial life is concerned.

Two high-profile entrepreneurs, Jonathan Rothberg, founder of Ion Torrent, a DNA sequencing company, and J. Craig Venter, founder of Sythentic Genomics, are each separately currently developing solutions for sequencing alien DNA directly on the Martian surface itself. Audacious claims, for sure, since neither company has any deal in place that could see their devices piggybacked on a rocket headed for Mars in the first place. The two are still keen on their ideas and have no intentions in becoming derailed.

Venter claims that his team of researchers is already conducting tests in the Mojave Desert to demonstrate that their machine is capable of autonomously isolating microbes from soil, sequencing their DNA, and then transmitting the information to a remote computer, as would be required on an unmanned Mars mission. On the other side, Rothberg’s Personal Genome Machine is being adapted for Martian conditions, part of project funded by Harvard and MIT called SET-G –  “the search for extra-terrestrial genomes.”

Either of the projects, or both, could wind up as being part of the next Mars missions. Scientists have long supported the idea of sending a probe on a return trip to Mars, so that it may retrieve a sample for study. With a DNA sequencer in place already on a Mars rover, the logistic hurdles of sending material back to Earth could be averted.

A micro-fluidic device developed at MIT designed to automatically run DNA experiments on other planets. Credit: Christopher Carr | MIT

A micro-fluidic device developed at MIT designed to automatically run DNA experiments on other planets. (c) Christopher Carr

As one might expect, there are incredibly numerous and difficult challenges. NASA doesn’t have any plans of sending another rover to Mars at least before 2018, and besides this their specifications for adding any new instruments are extremely strict. Christopher Carr, an MIT research scientist involved in the effort, says his lab is working to shrink Ion Torrent’s machine from 30 kilograms down to just 3 kilograms so that it can fit on a NASA rover. It’s not only about weight though; the Martian surface is plagued by radiation which often interferes with studies. Also, sequencing machines are extremely sensitive devices; one single germ from Earth is enough to ruin a multi-billion dollar mission.

A race that might only have losers

Studies have shown that DNA can not be preserved for longer than 1 million years, both space agencies like NASA and private ventures have to embark with the idea that life is already presented on Mars. The planet’s surface is a barren wasteland at its surface, no doubt about it, but a few meters below its surface microbial life might be present, relatively sheltered from the harsh conditions. On Earth, bacteria has been found kilometers below the crust, so the hypothesis isn’t entirely far fetched.

“The current NASA approach is to look for past life. Many people are reticent to talk about extant life,” says Carr. “We are sticking out necks out a little bit, but we want to take that leap.”

The biggest hurdle yet is of a biological nature, though. If life truly exists on Mars, what’s to say that it resembles that on Earth? It’s quite possible that alien life DNA is comprised of different building blocks than that of Earth; it might not even have a double helix. In this case, these genome sequencers would become utterly useless. And if indeed life would be detected and read, than an intense debate would ensue over the eventual discovery’s validity. Scientists would stress contamination, others would be quick to give truth to theories that hold Earth and Mars have exchanged life. Numerous meteorites of Martian origin have been found on Earth. I know I’m pocking a lot of holes in these projects, but frankly there are a myriad of obstacles in place.

Venter also said it might be feasible in the future to reconstruct Martian organisms in a super-secure laboratory on Earth, using just their DNA sequence – he calls this idea “biological teleportation”.

“People are worried about the Andromeda strain,” says Venter. “We can rebuild the Martians in a P-4 spacesuit lab, instead of having them land in the ocean.”

My instinct tells me these ventures are more of a hunt for glory and satisfying the ego than sincere scientific progress. Either way, I personally wish both of them the best of luck.

 

 

 

barley

Closer to brewing the perfect beer after scientists sequence barley genome

Barley is a key ingredient in beer, the third most popular drink in the world after water and tea, an industry which currently amounts to $300 billion a year. The quality of the barley greatly influences the savor of beer, so by growing better quality barley we might be able to brew a beer that’s closer to perfection. A worthy cause indeed for science, and with or without this exactly in mind, an international consortium of scientists have recently published a  high-resolution draft of the barley genome, allowing scientists onward to improve yields and disease resistance, and maybe equally importantly brew a better beer.

barleyBarley is  the world’s fourth most important cereal crop in terms of area of cultivation and quantity produced. Mapping its genome is a first critical step to engineering variants that can cope with the demands of climate change and are resistant to the various disease that currently plague barley and amount to billions in damage, worldwide. For instance, before the 1990′s Minnesota had millions of acres of barley. Today that has dwindled to about 120,000 acres because of an epidemic of Fusarium head blight.

“This research will streamline efforts to improve barley production through breeding for improved varieties,” said Professor Robbie Waugh, of Scotland’s James Hutton Institute, who led the research. “This could be varieties better able to withstand pests and disease, deal with adverse environmental conditions, or even provide grain better suited for beer and brewing.”

The team of researchers, , consisting of scientists from 22 organizations around the globe and called the International Barley Genome Sequencing Consortium (IBSC), published a first high-resolution draft of the barley genome, revealing structure and order for most of its 32,000 gene. Their research, however, wasn’t without obstacles. For one, the barley genome is almost twice the size of that of the human genome; moreover, the barley genome contains a large proportion of closely related sequences that are difficult to piece together into a true linear order. These challenges were overcome with success, eventually.

Their results will help scientists produce better quality and more resistant barley, indispensable to beer and whiskey production, but also to the meat and dairy industries, where barley is a principle animal feed product.

“It will accelerate research in barley, and its close relative, wheat,” Waugh said. “Armed with this information breeders and scientists will be much better placed to deal with the challenge of effectively addressing the food security agenda under the constraints of a rapidly changing environment.”

The findings were reported in the journal Nature.

As shown in this image, the nuclear genomes of bears (black outline), suggest that polar bears and brown bears diverged from one another 4 to 5 million years ago, and that occasional exchange of genes between the two species (shaded gray areas) followed. Results from maternally inherited mitochondrial DNA (dotted line) indicates extinction (marked with an "X") and replacement of polar bear mitochondrial DNA around 160,000 years ago due to interbreeding between the two species. (c) Penn State University

Polar bears interbred with brown bears during warmer climate

A new research has found after analyzing the genomes of polar bears and brown bears that the two species interbred, after the two species split some 5 million years ago, during periods of warmer climate. Recent evidence suggests this is happening today as well, as an effect of global warming.

The team of scientists from Pennsylvania State University and the University at Buffalo, sequenced the genomes of polar and brown bears and found that polar bears evolved into a distinct species some four or five million years ago. Previously polar bears were thought to be a lot younger as a species, but this new research also takes into accounts its rather complicated interbreeding history with brown and black bears as well.

“Maybe we’re seeing a hint that in really warm times, polar bears changed their life style and came into contact, and indeed interbred, with brown bears,” says Stephan Schuster of Penn State.

Schuster and colleagues sequenced the genomes of three brown bears and a black bear and compared them with the genomes of polar bears, one modern and the other obtained from remains from a 120,000-year-old polar bear. “Very few vertebrate species have such comprehensive genomic resources available,” says Schuster.

As shown in this image, the nuclear genomes of bears (black outline), suggest that polar bears and brown bears diverged from one another 4 to 5 million years ago, and that occasional exchange of genes between the two species (shaded gray areas) followed. Results from maternally inherited mitochondrial DNA (dotted line) indicates extinction (marked with an "X") and replacement of polar bear mitochondrial DNA around 160,000 years ago due to interbreeding between the two species. (c) Penn State University

As shown in this image, the nuclear genomes of bears (black outline), suggest that polar bears and brown bears diverged from one another 4 to 5 million years ago, and that occasional exchange of genes between the two species (shaded gray areas) followed. Results from maternally inherited mitochondrial DNA (dotted line) indicates extinction (marked with an “X”) and replacement of polar bear mitochondrial DNA around 160,000 years ago due to interbreeding between the two species. (c) Penn State University

Previous research, which only looked at small segments of DNA, had polar bears as being only 600,000 years old as a distinct species. Data from Schuster’s team suggests after split between polar and brown bears, the two species remained isolated for some time, allowing genetic changes to accumulate, before interbreeding more recently, their analysis indicates.

“We showed, based on a consideration of the entire DNA sequence, that earlier inferences were entirely misleading,” says Webb Miller of Penn State.

Hybridization between the two species has continued to this day. As Arctic sea ice upon which they live recedes ever more and polar bears become forced to spend increasingly more time on land, this trend is set to intensify.

“Recently, wild hybrids and even second-generation offspring have been documented in the Northern Beaufort Sea of Arctic Canada where the ranges of brown bears and [polar bears] appear to overlap, perhaps as a recent response to climatic changes,”  the researchers write.

The findings were presented in the journal PNAS.

 

Stephen Quake

Prolific inventor, Stephen Quake, awarded the Lemelson-MIT $500,000 prize

Stephen Quake

Stephen Quake is a professor of bioengineering and applied physics at Stanford University and investigator at the Howard Hughes Medical Institute. Besides his fruitful academic background however, Quake is an extremely prolific inventor, as well, his most successful one being a chip with miniature pumps and valves that incorporates complex fluid-handling steps to speed genetic research. For his contribution to the field of genetics and innovative efforts combining integrated circuitry to biology, Quake was recently awarded the prestigious Lemelson-MIT prize for outstanding innovators, worth $500,000.

“I get interested in a scientific problem and often find a way to measure the thing I’m interested in,” Quake said in an interview. “Often I find the measurement technique has different applications.”

It’s not like he needs the cash that much, though. Quake co-founded Fluidigm Corp in 1999 to commercialize his genome sequencing technology, a company which  generated sales of $10.8 million in the first quarter of 2012.

Quake first reached major headlines in 2009, when news outlets covered how he managed to sequence his own genome for under $50,000. During his personal genome research, he found a mutation that made him prone to cardiomyopathy, a disease that weakens and enlarges the heart muscles. He soon choose to be frequently monitored by a cardiologist.

Imagine an age of personalized medicine, one in which every person would be able to have his genome sequenced, easy and on the cheap, to efficiently prevent genetically transmitted or favorable diseases. We might not be that far away. Last year I reported how Ion Torrent System developed a device which would be able to sequence a person’s genome for under $1000! That may sound fantasmagoric, but sources have it that it’s indeed double. More on it in 2013, alegedly.

Back to Quake, the inventor also developed a non-invasive prenatal diagnostic test for Down Syndrome and is currently preoccupied with better understanding the human immune system; an interested sparked when one of his two children developed food allergies.

“As we started to see doctors we realized a lot is not known about how allergies work and how the immune system gets off track,” he said.

When asked about the prize money for the recently awarded Lemelson-MIT, Quake said he’ll most likely put them in his kids’ college fund. Now that’s a guy cooler than all the video games put together.

A western lowland gorilla goes eye-to-eye with the camera. (c) National Geographic

Gorillas are more related to humans than previously thought, complete genome sequence shows

A western lowland gorilla goes eye-to-eye with the camera. (c) National Geographic

A western lowland gorilla goes eye-to-eye with the camera. (c) National Geographic

Researchers have completed the great apes family’s genetic library after they sequenced the genes of a western lowland gorilla, joining the already-sequenced genomes of humans, chimpanzees and orangutans. Scientists found that gorillas, which share 98% of their genes with humans, are a lot more related to humans than previously thought, as well as surprising genetic differences which went unnoticed until recently.

“Previously, people had some sort of picture based on … probably one percent of the whole [gorilla] genome. So we now have a complete picture,” said study co-author Richard Durbin, a geneticist with the U.K.’s Wellcome Trust Sanger Institute.

“Based on the comparisons between them, it helps us explore the evolutionary origins of humans and where we separated from other great ape species in Africa between six and ten million years ago,” Durbin said.

The first step was taken in 2008, when the researchers sampled DNA from Kamilah, a 30-year old female western lowland gorilla, who was born in captivity and now lives at the San Diego Zoo Safari Park. Four years later, the researchers presented the complete genome, as seen published in this Wednesday edition of the journal Nature.

Gorillas – our close cousins

Their results show gorillas are are closer to humans than some might have thought. All of the members of the hominids family are considered to have descended from a common ancestor, some 10 million years ago. Around that time, human-chimp line split from the gorilla line, despite this however the team detected groups of gorilla genes that were surprisingly similar to human genes.

“Although [70 percent] of the human genome is indeed closer to chimpanzees, on average, a sizable minority of 15 percent is in fact closer to gorillas, and another 15 percent is where chimpanzees and gorillas are closest,” said geneticist Aylwyn Scally, a study co-author also at the Wellcome Trust.

The new data shows that humans and gorillas are 98% genetically identical – most of our genes are very similar, or even identical to, the gorilla version of the same gene. However, there are few important differences which have been observed.

Insightful genetic differences

Some illuminating genetic differences have been found by the researchers. For instance, certain genes involved in sperm formation have become inactive or have been reduced in the gorilla genome compared with the human genome. This trait has been probably developed by humans in consequence of severe mating competition. Gorilla packs however most often include only one male and several females.

A common sight is that of gorillas walking with the help of their arms, basically stepping on their fists. The researchers discovered gorillas possess a gene that helps the animal’s skin grow a tough layer of keratin, a protein found in hair and nails. This genes, the scientists suggest, lead to the development of tough knuckles.

What’s maybe the most interesting and valuable piece of information discovered thus far by the researchers is that of certain genes shared by gorillas and humans that cause disease in our species, but not in our ape cousins. Some variants are linked to dementia and heart failure in humans, and are shared by both humans and gorillas, however the latter seem to be unaffected by the conditions. Future research sparked by this find might show promising medical applications.

“If we could understand more about why those variants are so harmful in humans but not in gorillas, that would have important useful medical implications,” Tyler-Smith said.

MinION portable DNA sequencing device plugged to the USB port of a laptop

USB-powered DNA sequencer puts genetic analysis out of the lab to your laptop

Since the advent of modern DNA sequencing technology, biological research and discoveries has been dramatically accelerated. It’s absolutely instrumental to genetic research nowadays, which among other great achievements, has lead to the sequencing of the human genome. The methods and technologies involved in DNA sequencing are terribly complex, however, and usually require sophisticated research laboratories. What if you could simplify the process?

MinION portable DNA sequencing device plugged to the USB port of a laptop

Oxford Nanopore (ON) had this idea in mind for some time, and recently unveiled an extraordinary product the company has completed developing – a fast, portable, and disposable nucleotide sequencer the gets powered via USB and runs analysis on the same computer it gets plugged in. Extreme costs are promised to be alleviated once this products gets introduced on the market, eliminating the need for highly expensive facility usage for small projects and offering the possibility to perform genetic analysis on the go when needed.

The MinION, as it’s been dubbed by ON researchers, doesn’t need polymerase chain reaction (PCR) or other DNA amplification technique for optimum sensitivity, and can sequence up to 150 million base pairs within its six hour working life. The device accepts samples of  blood, plasma, and serum for an immediate analysis.

MinION’s centerpiece is its nanopore port. A nanopore is basically an organic molecule with a very narrow hole, just a few nanometers in width. This nanopore is embedded inside two molecule thick synthetic polymer membrane, which has a very high electrical resistance, such that the nanopore hole forms a path from one side of the membrane to the other. Through the nanopore hole electrophysiological fluid is inserted, which has its volume divided in half as a result of a specific geometry.

When passing through the variable geometry in the nanopore hole, the electrophysiological fluid is swept by an ionic current which causes a voltage difference. Each molecule, including DNA or RNA, has its own characteristic voltage, and thus using this technique the MinION can detect and identify the sample. Of course, the MinION’s main purpose is that of sequencing DNA, so the device is optimized to differentiate the four nucleobases (adenine, cytosine, guanine, and thymine) which encode genes in DNA. To analyze the DNA, the MiniON uses strand sequencing.

This diagram shows a protein nanopore set in an electrically resistant membrane bilayer.  An ionic current is passed through the nanopore by setting a voltage across this membrane. (c) Oxford Nanopore Technology

This diagram shows a protein nanopore set in an electrically resistant membrane bilayer. An ionic current is passed through the nanopore by setting a voltage across this membrane. (c) Oxford Nanopore Technology

The device’s sensing electronics has  512 nanopores embedded onto its sample chip, resulting in a total strand reading rate of about 7500 bases/second. During its limited 6 hours operation life time, the MinION can read 150 million bases; enough to read small chromosomes or bacteria genome. Check out this excellent video from Oxford Nanopore explain in great detail how the MinION works and how the DNA sequencing process unfolds.

Nanopore DNA sequencing from Oxford Nanopore on Vimeo.

The researchers working on the device have already tested the device successfully, after sequencing the genome of the lambda bacteriophage – 48500 base pairs in length. Clive Brown, the Chief Technology Officer of Oxford Nanopores, has been cited during the product’s announcement at AGBT 2012, that the MinION might be introduced on the market with a $900 price tag!

“The exquisite science behind nanopore sensing has taken nearly two decades to reach this point; a truly disruptive single molecule analysis technique, designed alongside new electronics to be a universal sequencing system.  GridION and MinION are poised to deliver a completely new range of benefits to researchers and clinicians,” said Dr Gordon Sanghera, CEO of Oxford Nanopore.  “Oxford Nanopore is as much an electronics company as a biotechnology company, and the development of a high-throughput electronics platform has been essential for us to design and screen a large number of new candidate nanopores and enzymes. Our toolbox is customer-ready and we will continue to develop improved nanopore devices over many years, including ongoing work in solid state devices.”

press release / via Gizmag

Ancestors of homo sapiens breeding

High-resolution genome sequence of ancient human ancestor released online

Last year, researchers at the Max Planck Institute for Evolutionary Anthropology, produced a draft of the Denisova genome, in order study in what proportion they relate to homo sapiens sapiens. The  Denisovans, are a new group of hominids, discovered just two years ago, which is believed to have lived around 30,000 years ago, alongside Neanderthals and early homo sapiens ancestors. Since they first released their draft, the researchers from Germany have now produced a highly refined version of the Denisovan genome, sequenced 30 times, which they also publicaly released on the web to help other scientists with their study.

The idea came after Max Planck paleogeneticist Svante Pääbo was at a meeting in Sweden, and noticed there that his fellow colleagues were working and studying based on year-old sequence data, and that the all the other labs in the world were probably using the same outdated material as well.

“I felt bad knowing that we had this very much better version of the same genome and that it would be a few months before it became available,” says Pääbo.

Even though Pääbo and colleagues have yet to release the paper they’ve been working on for such a long time, the researchers decided to allow their colleagues to download the sequence data for the high-resolution genome today. The sequence can be freely downloaded from  both on Max Planck website and through Amazon’s Web Services. Speaking of which,  this latest version of the genome they’ve released online and which will be presented shortly for scientific publishing, has every position sequenced an average of 30 times – all based on DNA extracted from less than 10 milligrams of the finger bone of the ancient girl found in the Denisovan caves, in Siberia.

Ancestors of homo sapiens breeding

With this higher resolution of the genome in their hands, the scientists can now more accurately determine how our hominid ancestors influenced modern man, since DNA differences can be precisely extracted from that of living humans and Neanderthals. It’s believed that early humans interbred with both Neanderthals and Denisovans. We all currently have Neanderthal genes inside our DNA, however they’re inactive; modern humans in Melanesia and other parts of Asia have inherited about 4% of their DNA from Denisovans.

A third group of extinct humans, Homo floresiensis, nicknamed “the hobbits” because they were so small, also walked the Earth until about 17,000 years ago. It is not known whether modern humans bred with them because the hot, humid climate of the Indonesian island of Flores, where their remains were found, impairs the preservation of DNA.

Of course, to protect their ability to publish a paper, the Max Planck team is releasing the sequence under a license that prohibits anyone else from doing an analysis of the complete genome, nevertheless anyone, scientist or not, is now free to analyze specific genes in the genome without having to wait for the study to pass peer review.

Ozzy Osborne’s genome reveals why he is still alive

The lead singer, rock legend bat beheader has done pretty much anything you can do in this life. He played in front of thousands, ate/drank/smoked/injected pretty much everything that can be, had motorcycle accidents, never ate right, and yet, at the proud age of 61 he’s alive and kicking just as he ever was. Researchers wanted to find out why this is happening (not that anybody would have something against it), analyzed his genome and found some interesting mutations.

Ozzy Osborne joined DNA co-discoverer James Watson and Harvard University professor Henry Louis Gates in having his genome analyzed by Cofactor Genomics, a Saint Louis–based company and Knome, Inc. At first, he said he was a bit skeptical, but after a while thought he actually has something to give to science.

[read this in his voice]”I was curious,” he wrote in his column. “Given the swimming pools of booze I’ve guzzled over the years—not to mention all of the cocaine, morphine, sleeping pills, cough syrup, LSD, Rohypnol…you name it—there’s really no plausible medical reason why I should still be alive. Maybe my DNA could say why.”

It is in fact pretty curious how he managed to survive after such a lifestyle, and researchers were interested in finding out how he metabolized things, and how this was affected by his substance use; they also found some interesting mutations regarding the way the brain processes dopamine. Here are just a few questions Scientific American asked Jorge Conde, co-founder and chief executive as Knome:

[..]

Is Ozzy the first rock star to have his full genome sequenced?

Conde: Yes, as far as I know. I can definitely tell you he’s the first prince of darkness to have his genome sequenced and analyzed.

Can we see in his genome any traces of his legendary rock-and-roll lifestyle—or evidence of his body’s efforts to repair any damage?

Conde: We cannot find the “Ozzy Osbourne” gene. But what we did see, as one of our scientists refers to it, is a lot of interesting smoke—but not any specific fire. We found many variants—novel variants—in genes associated with addiction and metabolism that are interesting but not quite definitive.

So can his genomes tell us anything about his ability to survive so many years of hard partying?

Pearson: I talked with Ozzy, and we looked at the genome with an eye toward the nerves. If you think about what makes Ozzy unusual, it’s that he’s a world-class musician, he has an addictive personality, he has a tremor, he’s dyslexic, he gets up very early in the morning. And many of these can be traced back to the nervous system.

One variant involves a gene that makes CLTCL1, which is a really interesting protein. When a cell takes in things from the outside membrane, it pulls itself in like a basket to pull things in. It does this in all kinds of cells, including nerve cells. He has two copies of an unusual variant that makes a grossly different version of the protein than most people produce. Here’s a gene that’s central to how nerve cells communicate with each other, so it’s curious to us to see a grossly different protein variant. It’s thought provoking.

We didn’t find anything that can explain to you from point A to point B why Ozzy can think up good songs or why he is so addicted to cocaine, but we found some things that would be interesting to follow up on.

Such as?

Pearson: Alcohol dehydrogenase genes. They’re involved in breaking down alcohol when you drink. Ozzy has an unusual variant near one of his alcohol dehydrogenase genes, ADH4, that help regulate how much of the protein gets made. Given his troubles with alcohol in the past, obviously we would like to clarify why his body responds differently than other people’s.

What can we learn from Ozzy’s genome?

Pearson: I think one lesson is understanding music. It’s a pretty interesting thing we do at humans—that some of us can synchronize to a beat, that we like to sing songs. But we don’t understand it well genetically, so one of the open questions is we’ll get a better understanding of what makes a good musician, what kinds of variants help us keep a beat, make a good tune. I think looking ahead, sequencing the genomes of more musicians would be a good idea.

If you could sequence any other celebrity genomes, whose would you choose?

Pearson: Ozzy suggested Keith Richards. Our partners who did the sequencing suggested we sequence Ozzie Smith, the baseball player, as a control. He’s always been a good teetotaler.

Full interview here