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By Megan Gambino Smithsonian.com

 

(Courtesy of Antony Evans) 

San Francisco-based entrepreneur Antony Evans has come up with a radical idea for curbing power usage: “What if we use trees to light our streets instead of electric street lamps?”

Evans and his colleagues, biologists Omri Amirav-Drory and Kyle Taylor, want to create plants that literally glow. Evans was inspired by transgenic organisms, plants or animals with genes of other species in their own DNA, which have been used to fill many human needs. A gene from the bacteriaBacillus thuringiensis is routinely introduced to corn and cotton, for instance, to make the crops insect-resistant. In one method called “pharming,” scientists have inserted human genes into plants and animals so that these hosts can produce proteins for pharmaceuticals. Others have added a gene from the crystal jelly responsible for creating green fluorescent protein to animals such as cats and pigs; this way, they can determine if a disease has been transmitted from one generation to another, just by seeing if the offspring glows in the dark.

This spring, Evans’ team posted a video to Kickstarter, explaining how they plan to insert genes from bioluminescent bacteria into a species of flora as a first step to creating glowing trees. To feed viewers’ imaginations, the video included an image of Pandora, the luminous, mid-22nd century setting from the movie Avatar. In a raucously successful 46-day campaign the group raised nearly $500,000 to fund the effort. I spoke with Evans about his project.

Scientists genetically engineered the very first glow-in-the-dark plant in the 1980s, a tobacco plant with a firefly gene inserted into it. Historically, what has been the purpose of doing this?

The first time, I think, was just a demonstration project. But scientists have used it since to study things like root growth. They really use it for basic research purposes.

Traditionally, what they’ve done is insert the gene for luciferase [an enzyme from a luminescent organism] along with a promoter [a region at the beginning of a gene that tells a cell to start transcription, the first step to producing a protein] and then add the luciferin [a chemical that produces light when oxidized] manually. They have even had these glowing plants up on the International Space Station, so it is a pretty well established technique.

For your glowing plant project, you have chosen to use a flowering species calledArabidopsis thaliana. Why this plant?

We chose this plant because it has been extremely well studied by the academic community. It is the fruit fly of plant biology. The reason it has been studied so much is because it has the shortest genome of any [flowering] plant.

What gene are you adding to create the glow?

We are using genes from Vibrio fischeri. It is marine bacteria.

How is this done? Can you take me through the process of creating a glowing plant?

We start with software called Genome Compiler. Genome Compiler allows us to search for gene sequences and then modify those gene sequences in a nice graphical user interface. We use that software to look up the Vibrio fischeri genes, and then we do something called code and optimization, which basically adjusts the sequences so that they [work] in plants instead of in bacteria. We then synthesize the DNA. There is a “print” button, and we “print” that DNA. That emails the file to a company, who makes the DNA for us. They FedEx that back to us, and then we do two things.

First, we insert the DNA into some bacteria called agrobacterium. That bacterium is very clever, it has figured out how to do genetic engineering on its own. [The bacterium] inserts the DNA into the female gametes of the plant. We can grow the seeds that come from those flowers, and we’ll have the DNA that we designed on the computer in the plant. The second thing we are doing is using a gene gun, which is a piece of equipment that fires the DNA at high velocity into the cells of the plant. Some of those cells will absorb the DNA and start to express it.

You are doing your end of the work at BioCurious, a community bio lab in Sunnyville, California, in Silicon Valley. But how DIY is this? Is this something that a garage tinkerer can manage? 

As part of the Kickstarter campaign, we have a kit, which you can use to make one of these plants. The tough part is designing the sequences, but once someone has figured them out, you can follow the recipe. 

All told, you had 8,433 Kickstarter backers pledge $484,013. Did this reaction surprise you?

We were targeting $65,000, so it is great that we got so much. With Kickstarter, you never know. We knew we had something interesting, because everyone wanted to talk about it. But, we didn’t know it would get this big. 

How realistic is it to think that one day we could have glow-in-the-dark trees lining streets instead of streetlights?

We do think it should be viable, but it is definitely a long-term goal. The big challenge with the trees is that trees take a long time to grow. Doing experiments on trees and testing different promoters will take a long time. We really need one of a few different technologies to come out. One would be a better simulation technology, so that we could simulate the gene sequences on a computer. Two would be a bio printer or something similar, so that we could print a leaf and test realistically the sequences on the leaf [instead of having to wait for a whole tree to grow]. Or, third would be some way of doing gene therapy on trees and adjusting them in situ and using that to change their DNA. We do need some developments in one of those before we will be able to really take on big trees.

In preliminary calculations, you figure that a glowing tree that covers about 1,000 square feet would cast as much light as a streetlight.

It will be a very different type of lighting effect. If you think about the way that the day is lit, the light comes from the whole sky; it doesn’t just come from a point, whereas light bulbs come from a point. Our lighting will be much more diffused and we think much more beautiful.

What are your sights set on now?

We are focused on executing on the things that we promised our Kickstarter backers. So, we are doing the work, getting the lab set up, ordering the DNA and starting to transform the [Arabidopsis] plants.

You and your colleagues promised to send each supporter, of a certain donation level, a glowing plant. What can people expect? How strong will the light be and how long lasting?

The light will be on at night as long as the plant is alive, but it won’t be super bright. We are aiming for something like glow-in-the-dark paint. You need to be in a dark room, and then you can see it dimly glowing. From there, we will work on optimizing and boosting the light output.

In the campaign video, you say, “the glowing plant is a symbol of the future.” What does this future look like to you?

The future we are referring to there is a synthetic biology future. We think that this kind of technology is going to become democratized; it will be accessible to many people. I’d like to see a future where teenagers and amateurs are genetically engineering things at home or in DIY bio labs. We want to represent that future, to tell people that it’s coming and to start a discussion around this technology—what it means and what it means for us. 

This technology is rapidly being adopted. It is going to be very transformational, and I think that it’s time that people sort of became aware of it and the potential of it, to take an interest in it. There are going to be some fantastic opportunities in it, so if people look at the project and think “I’d like to do that,” I think the answer is “You can.” Just go to your local DIY bio lab and start playing around, start learning.

Are there other transgenic organisms being created that you find promising?

There are tons of people working on stuff, tons and tons and tons. If you look at the iGEM [International Genetically Engineered Machine] Foundation projects, you can see some of the breadth and variety of things that are being done. The spider silk is cool. I think the guys working on new versions of meat are cool. There is some interesting stuff happening with algae in the bio lab down in South Bay [San Francisco], BioCurious. Engineering algae so that we can use it for energy production—I think there is a lot of work to be done on that, but it’s very promising.

Are there any projects that worry you?

Not for now. But, I think some scary stuff will happen eventually.

Some people have expressed concern with you distributing glowing plants and releasing synthetic plants into the wild. What do you have to say to those who fear this?

People have been genetically engineering plants for many decades now. We are just following in the footsteps of all of the other plants that have already been released in the last 20 years. We don’t think we are doing anything radically different. What is different about this project is how it’s been funded and that the work is taking place in a DIY bio lab rather than in a professional research institution.

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Nong You-hui’s teachers and parents claim he can see in the dark.

According to a news reel from China, a young boy there possesses the ability to see in the dark. Like a Siamese cat’s, his sky-blue eyes flash neon green when illuminated by a flashlight, and his night vision is good enough to enable him to fill out questionnaires while sitting in a pitch black room — or so say the reporters who visited Nong Yousui in his hometown of Dahua three years ago.

The footage of Nong and his strange-looking eyes originally surfaced in 2009; it got little attention at the time, but is now making a splash all over the Web. If the boy really does have a genetic mutation that confers night vision, then he would be an interesting subject for analysis by vision scientists, evolutionary biologists, and genetic engineers alike — but does he? 

The experts we shared the video with say Nong does have unusually colored irises considering his ethnicity, but he’s not the next step in human evolution.

Night vision is made possible by a layer of cells, called the tapetum lucidum, in the eyes of cats and other nocturnal animals. This thin layer is a “retroreflector” — when a beam of light hits it, it reflects the light directly back along its incoming path. The reflected beam constructively interferes with the incoming light beam, amplifying the overall signal that hits the retina and enabling the animal to see in very low-light conditions. Retroreflection also causes cat eyes to flash when they are lit upon at night, and experts say Nong’s eyes, if they are truly catlike, should do the same.

“It would be easy to test the boy’s eyes for retroreflection (eyeshine), which would be indicative of a tapetum lucidum,” said Nathaniel Greene, a physicist at Bloomsburg University of Pennsylvania who has studied retroreflection.

In fact, such a test is run in the video.

In the footage, Nong’s teacher claims the boy’s eyes flash when shined with a flashlight in the dark, but the reporters don’t seem to be able to catch the effect on camera. When Nong’s eyes are illuminated in the dark, they appear normal. James Reynolds, a pediatric ophthalmologist at State University of New York in Buffalo, noted, “A video could capture [eyeshine] easily, just like in nature films of leopards at night.”

Furthermore, there is no single genetic mutation that could produce a fully formed and functioning tapetum lucidum, Reynolds explained; such an ability would require multiple mutations, which don’t just happen all at once. Evolution happens incrementally, he said, not by leaps and bounds. “Evolutionarily, mutations can result in differences that allow for new environmental niche exploitation. But such mutations are modified over long periods. A functional tapetum in a human would be just as absurd as a human born with wings. It can’t happen,” he told Life’s Little Mysteries.

On the other hand, in the footage, the reporters gave Nong a questionnaire to fill out while sitting in a dark room, and they acted surprised by his ability to see and complete the fill-in-the-blank form. Even if he doesn’t have cat eyes, he may nevertheless have unusually good night vision, Reynolds said. He could have a rod-rich retina, for example — a retina that contains a higher than usual number of cells involved in light detection. Or the video could be a total hoax.

“It is hard to say what the truth is about this boy,” said Dennis Brooks, professor of ophthalmology at the University of Florida’s College of Veterinary Medicine. “A good ophthalmic examination by a physician ophthalmologist is in order, I think.”

Editor’s Note: Adam Hickenbotham, an optometrist and clinical researcher at the University of California, Berkeley, contacted us to say he believes Nong has a mild case of ocular albinism. This would explain the boy’s lightly-pigmented irises, and would also cause him to have a lower than usual amount of pigment in his retinas. this would make them appear slightly reflective, and would cause Nong to have difficulty seeing in bright light.

 

Natalie Wolchover

 

A team of international researchers has completed a study that suggests we will probably never find a ‘gay gene.’ Sexual orientation is not about genetics, say the researchers, it’s about epigenetics. This is the process where DNA expression is influenced by any number of external factors in the environment. And in the case of homosexuality, the researchers argue, the environment is the womb itself.

The Epigenetic Key

Writing in The Quarterly Review of Biology, researchers William Rice, a professor at the University of California, Santa Barbara, and Urban Friberg, a professor at Uppsala University in Sweden, believe that homosexuality can be explained by the presence of epi-marks — temporary switches that control how our genes are expressed during gestation and after we’re born.

Specifically, the researchers discovered sex-specific epi-marks which, unlike most genetic switches, get passed down from father to daughter or mother to son. Most epi-marks don’t normally pass between generations and are essentially “erased.” Rice and Friberg say this explains why homosexuality appears to run in families, yet has no real genetic underpinning.

Epigenetic mechanisms can be seen as an added layer of information that clings to our DNA. Epi-marks regulate the expression of genes according to the strength of external cues. Genes are basically the instruction book, while epi-marks direct how those instructions get carried out. For example, they can determine when, where, and how much of a gene gets expressed.

Moreover, epi-marks are usually produced from scratch with each generation — but new evidence is showing that they can sometimes carryover from parent to child. It’s this phenomenon that gives the impression of having shared genes with relatives.

Masculinization and Feminization

To reach this conclusion, Rice and Friberg created a biological and mathematical model that charted the role of epigenetics in homosexuality. They did so by applying evolutionary theory to recent advances in the molecular regulation of gene expression and androgen-dependent sexual development.

This data was integrated with recent findings from the epigenetic control of gene expression, especially in embryonic stem cells. This allowed the researchers to develop and empirically support a mathematical model of epigenetic-based canalization of sexual development, or the tendency of heredity to restrict the development of some characteristics to just one or a few traits. Their model successfully predicted the evolution of homosexuality in both sexes when canalizing epi-marks carry over across generations with nonzero probability.

In their study, the team writes that they “tracked changes in chromatin structure that influence the transcription rate of genes (coding and noncoding, such as miRNAs), including nucleosome repositioning, DNA methylation, and/or modification of histone tails, but not including changes in DNA sequence.”

The resulting model predicted that homosexuality can be produced by transgenerational epigenetic inheritance.

Normally, sex-specific marks that are triggered during early fetal development work to protect boys and girls in the womb from undergoing too much natural variation in testosterone, which should normally happen later in a pregnancy. Epigenetic processes prevent female fetuses from becoming masculinized when testosterone exposure gets too high, and vice versa for males.

Moreover, epi-marks also protect different sex-specific traits from swinging in the opposite direction; some affect the genitals, and others may affect sexual orientation. These epi-marks can be transmitted across generations from fathers to daughters, or mothers to sons.

Essentially, Rice and Friberg believe they have discovered the presence of “sexually antagonistic” epi-marks — which sometimes carry over to the next generation and cause homosexuality in opposite-sex offspring.

And importantly — in order to satisfy the rules of Darwinian selection — the researchers noted through their mathematical modeling that these epigenetic characteristics can easily proliferate in the population because they increase the fitness of the parent; these epi-marks normally protect parents from natural variation in sex hormone levels during fetal development. They only rarely reduce the fitness of offspring.

The entire study is online at The Quarterly Review of Biology: “Homosexuality as a consequence of epigenetically canalized sexual development.”

Genetic “first mother” and “father” of modern humanity redefined: Probably they lived 99000-200000 years ago in Africa

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   According to the DNA of 1204 Sardinians (pictured a traditional fishing) lived “Y-chromosome Adam” 180,000 years ago.

For creationists, so followers of the biblical story of creation, the thing is clear: the man – or better: Adam and Eve – was created exactly 4004 years before our era of God and then lived the same time as Tyrannosaurus Rex among others. This version of human history can be admired among others in the Creation Museum in the USA.

For science, the question of the “Great Mother” and after the “father” of humanity today is much more difficult to answer, but not impossible. The starting point are two gender-specific features of the genome: DNA in the mitochondria (mDNA), ie, the power plants of cells, is inherited exclusively from mothers to their children, and the Y chromosome exclusively from father to son.

Comparing to people living today, the variations in the mDNA and those of the Y chromosome, then can be calculated back when the woman and the man must have lived that gave the respective genes of the crucial figure.

Origin 99000-200000 years ago

So far, the researchers assumed that the “mitochondrial Eve” is much older than the “Y-chromosomal Adam.” But now two studies “Science” come in the journal to a new estimate, which suggest that our Urelternteile lived around the same time: geneticists Carlos Bustamante of Stanford University calculated by comparative genome analysis of 69 people from nine different regions of the planet, that our “father” who lived sometime 120000-156000 years ago in Africa and have our “first mother” 99000-148000 years ago.

To an even higher age for “Y-chromosome Adam” Italian researchers came up with a slightly different DNA sample: The team of Paolo Francalacci came in DNA comparisons of 1204 male inhabitants of the island of Sardinia to the conclusion that all the paternal lines in front of 180,000 to 200,000 years converged to a point.

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A dolmen (called “Coveccada”), from the late Neolithic. This picture represents the archaeological context of the peopling of the island, the main topic of this genetic research.period.

Mitochondrial Eve and Y-chromosomal Adam—two individuals who passed down a portion of their genomes to the vast expanse of humanity—are known as our most recent common ancestors, or MRCAs. But many aspects of their existence, including when they lived, are shrouded in mystery.

Now, a study led by the Stanford University School of Medicine indicates the two roughly overlapped during evolutionary time: from between 120,000 to 156,000 years ago for the man, and between 99,000 and 148,000 years ago for the woman.

“Previous research has indicated that the male MRCA lived much more recently than the female MRCA,” said Carlos Bustamante, PhD, a professor of genetics at Stanford. “But now our research shows that there’s no discrepancy.” Previous estimates for the male MRCA ranged from between 50,000 to 115,000 years ago.

Bustamante is senior author of the new study, which will be published Aug. 2 inScience. Graduate student David Poznik is the lead author.

Despite the Adam and Eve monikers, which evoke a single couple whose children peopled the world, it is extremely unlikely that the male and female MRCAs were exact contemporaries. And they weren’t the only man and woman alive at the time, or the only people to have present-day descendants. These two individuals simply had the good fortune of successfully passing on specific portions of their DNA, called the Y chromosome and the mitochondrial genome, through the millennia to most of us, while the corresponding sequences of others have largely died out due to natural selection or a random process called genetic drift.

The DNA sequences traced by the researchers were chosen because of the unique way they are inherited: the Y chromosome is passed only from father to son, and the mitochondrial genome is passed from a mother to her children. Each can serve as a useful tool for determining ancestral relationships because they don’t undergo the shuffling and swapping of genetic material that occurs routinely in most human chromosomes.

 

The researchers made their discovery by comparing Y-chromosome sequences among 69 men from nine globally distinct regions, including some that have only recently been available for study. Regions represented included Namibia, the Democratic Republic of Congo, Gabon, Algeria, Pakistan, Cambodia, Siberia and Mexico.

New, high-throughput sequencing technologies allowed the researchers to identify about 11,000 differences among the sequences. These variants enabled them to establish phylogenetic relationships and timelines among the sequences with unprecedented accuracy.

“Essentially, we’ve constructed a family tree for the Y chromosome,” said Poznik. “Prior to high-throughput sequencing, the tree was based on just a few hundred variants. Although these variants had revealed the main topology, we couldn’t say much about the length of any branch—the number of variants shared by all of its descendants. We now have a more complete structure, including meaningful branch lengths, which are proxies for the periods of time between specific branching events.”

Bustamante and Poznik obtained highly accurate sequencing results over a length of about 10 megabases of Y chromosome DNA (or 10 million nucleotides) for each of the 69 individuals. They then estimated the yearly mutation rate on the Y chromosome by calibrating it with a known event: the human settlement of the Americas that occurred about 15,000 years ago. Mutations shared by all Native Americans today must have existed prior to the peopling of the continents, whereas many of those that vary among indigenous American populations arose during the past 15,000 years. They repeated their analysis with the individuals’ mitochondrial DNA to generate the two estimates of MRCA timing, showing for the first time that they overlap.

But the Y chromosome tree they constructed did more than just identify a time period for the MRCA. It also clarified some previously unknown relationships that occurred among populations as humans expanded out of Africa into Eurasia. “We can now date certain events very precisely,” said Bustamante. “We found a single variant that shows how three ancient lineages came together about 48,000 years ago, plus or minus only a couple of hundred years. The accuracy is exquisite.” The tree also exemplifies the extraordinary depth of genetic diversity present among modern Africans.

It’s difficult to say what the apparent overlap between the male and female MRCA sequences may represent, if anything. The vagaries of inheritance are easy to see even within individual human families, and the timing could simply be a fluke. But it’s also possible that it represents a time when only a few sequences were passed on and many died out due to an external event that’s not yet been identified. “For the most part, it’s a random process,” said Poznik. “Some lineages die out, some are successful. But it’s also possible that there may be elements of human demographic history that predispose these lineages to coalesce at certain times.”