Now, researchers from the Okinawa Institute of Science and Technology Graduate University (OIST) have decoded the genome of the mangrove tree, Bruguiera gymnorhiza, and revealed how this species regulates its genes in order to cope with stress. Their findings, published recently in New Phytologist, could one day be used to help other plants be more tolerant to stress.

“Mangroves are an ideal model system for studying the molecular mechanism behind stress tolerance, as they naturally cope with various stress factors,” said Dr. Matin Miryeganeh, first author of the study and a researcher in the Plant Epigenetics Unit at OIST.

Mangroves are an important ecosystem for the planet, protecting coastlines from erosion, filtering out pollutants from water and serving as a nursery for fish and other species that support coastal livelihoods. They also play a crucial role in combating global warming, storing up to four times as much carbon in a given area as a rainforest.

Despite their importance, mangroves are being deforested at an unprecedented rate, and due to human pressure and rising seas, are forecast to disappear in as little as 100 years. And genomic resources that could help scientists try to conserve these ecosystems have so far been limited.

The mangrove project, which was initially suggested by Sydney Brenner, one of the founding fathers of OIST, began in 2016, with a survey of mangrove trees in Okinawa. The scientists noticed that the mangrove tree, Bruguiera gymnorhiza, showed striking differences between individuals rooted in the oceanside, with high salinity, and those in the upper riverside, where the waters were more brackish.

“The trees were amazingly different; near the ocean, the height of the trees was about one to two meters, whereas further up the river, the trees grew as high as seven meters,” said senior author, Professor Hidetoshi Saze, who leads the Plant Epigenetics Unit. “But the shorter trees were not unhealthy — they flowered and fruited normally — so we think this modification is adaptive, perhaps allowing the salt-stressed plant to invest more resources into coping with its harsh environment.”

Unlike long-term evolutionary adaptation, which involves changes to the genetic sequence, adaptations to the environment that take place over an organism’s lifespan occur via epigenetic changes. These are chemical modifications to DNA that affect the activity of different genes, adjusting how the genome responds to different environmental stimuli and stresses. Organisms like plants, which can’t move to a more comfortable environment, rely heavily on epigenetic changes to survive.

Before focusing in on how the genome was regulated, the research team first extracted DNA from the mangrove tree, Bruguiera gymnorhiza, and decoded the genome for this species. They found that the genome contained 309 million base pairs, with a predicted 34,403 genes — a much larger genome than those for other known mangrove tree species. The large size was due to, for the most part, almost half of the DNA being made up of repeating sequences.

When the research team examined the type of repetitive DNA, they found that over a quarter of the genome consisted of genetic elements called transposons, or ‘jumping genes.’

Prof. Saze explained: “Active transposons are parasitic genes that can ‘jump’ position within the genome, like cut-and paste or copy-and-paste computer functions. As more copies of themselves are inserted into the genome, repetitive DNA can build up.”

Transposons are a big driver of genome evolution, introducing genetic diversity, but they are a double-edged sword. Disruptions to the genome through the movement of transposons are more likely to cause harm than provide a benefit, particularly when a plant is already stressed, so mangrove trees generally have smaller genomes than other plants, with suppressed transposons.

However, this isn’t the case for Bruguiera gymnorhiza, with the scientists speculating that as this mangrove species is more ancestral than others, it may not have evolved to have an efficient means of suppression.

The team then examined how activity of the genes, including the transposons, varied between individuals in the oceanside location with high salinity, and individuals in the less saline, brackish waters upriver. They also compared gene activity for mangrove trees grown in the lab, under two different conditions that replicated the oceanside and upriver salinity levels.

Overall, in both the oceanside individuals and those grown in high salinity conditions in the lab, genes involved in suppressing transposon activity showed higher expression, while genes that normally promote transposon activity showed lower expression. In addition, when the team looked specifically into transposons, they found evidence of chemical modifications on their DNA that lowered their activity.

“This shows that an important means of coping with saline stress involves silencing transposons,” said Dr. Miryeganeh.

The researchers also saw increases in the activity of genes involved in stress responses in plants, including those that activate when plants are water-deprived. Gene activity also suggested the stressed plants have lower levels of photosynthesis.

In future research, the team plan to study how seasons, changes in temperature and rainfall, also affect the activity of the mangrove tree genomes.

“This study acts as a foundation, providing new insights into how mangrove trees regulate their genome in response to extreme stresses,” said Prof. Saze. “More research is needed to understand how these changes in gene activity impact molecular processes within the plant cells and tissues and could one day help scientists create new plant strains that can better cope with stress.”

Dr. Barbara Veselka: “The results from our study represent a major step forward in the fields of biological anthropology, archaeology, and palaeopathology by opening up a variety of new possibilities for the study of health and activities related to sunlight exposure of numerous past populations that practiced cremation as their funerary ritual.” The study was published in the academic journal Scientific Reports.

Burning experiments

As part of the Brussels Bioarchaeology Lab (www.bb-lab.be) and the MARI and AMGC research groups, Dr. Barbara Veselka and Prof. Christophe Snoeck conducted burning experiments using an archaeological sample of 17 paired teeth.

Veselka: “We conducted burning experiments with teeth to assess the visibility of interglobular dentine, a mineralization defect in the dentine attributed to vitamin D deficiency, in teeth burned at temperatures varying from 600 to 900°C. Our study is the first to demonstrate that this defect is still visible at temperatures up to 900°C. This enables, for the first time, the identification of vitamin D deficiency in cremated human remains.”

Sixteen pairs of molars came from the cemetery of Koekelberg, Belgium, and one pair of canines came from the cemetery of the Broerekerk Zwolle, the Netherlands. From each pair, one unburnt tooth was microscopically evaluated via thin section for interglobular dentine. The other tooth was burned at temperatures of 600, 800, or 900°C. Duration of the burning process was 2, 4, or 8 hr. Each of the burnt teeth were examined for interglobular dentine and compared to their unburnt counterparts.

Study of sunlight exposure in the past

The fact that interglobular dentine is still visible in teeth burned at temperatures of 900°C is remarkable and allows the assessment of vitamin D deficiency in past populations. Moreover, the age at which the disease occurred, the severity of the deficit, and if the disease was recurrent can also be determined. Since most of vitamin D deficient cases can be attributed to limited exposure to adequate amounts of sunlight, information on the age of occurrence aids in the reconstruction of daily activities related to sunlight exposure.

Veselka: “This innovative study stimulates more bioarchaeological research, which will increase our understanding of the influence environmental and sociocultural variables have on individuals.”

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But the control of light can also come in high-tech forms. The screen of the computer, tablet, or phone on which you are reading this is one example. Another is telecommunications, which controls light to create signals that carry data along fiber-optic cables.

Scientists also use high-tech methods to control light in the laboratory, and now, thanks to a new breakthrough that uses a specialized material only three atoms thick, they can control light more precisely than ever before.

The work was conducted in the lab of Harry Atwater, the Otis Booth Leadership Chair of the Division of Engineering and Applied Science, Howard Hughes Professor of Applied Physics and Materials Science, and director of the Liquid Sunlight Alliance (LiSA). It appears in a paper published in the October 22 issue of Science.

To understand the work, it is helpful first to remember that light exists as a wave and that it has a property known as polarization, which describes the direction in which the waves vibrate. Imagine being in a boat bobbing on the ocean: Ocean waves have a vertical polarization, which means that as the waves pass under the boat, it goes up and down. Light waves behave in much the same way, except these waves can be polarized at any angle. If a boat could ride waves of light, it might bob from side to side, or on a diagonal, or even in a spiraling fashion.

Polarization can be useful because it allows light to be controlled in specific ways. For example, the lenses in your sunglasses block glare (light often becomes polarized when it reflects off a surface, like the window of a car). The screen of a desk calculator creates legible numbers by polarizing light and blocking it in areas. Those areas where the polarized light is blocked appear dark, while areas where the light is not blocked appear light.

In the paper, Atwater and his co-authors describe how they used three layers of phosphorus atoms to create a material for polarizing light that is tunable, precise, and extremely thin.

The material is constructed from so-called black phosphorus, which is similar in many ways to graphite, or graphene, forms of carbon that consist of single-atom-thick layers. But whereas the layers of graphene are perfectly flat, black phosphorus’s layers are ribbed, like the texture of a pair of corduroy pants or corrugated cardboard. (Phosphorus also comes in red, white, and violet forms, distinct because of the arrangement of the atoms within it.)

That crystal structure, Atwater says, makes the black phosphorus have significantly anisotropic optical properties. “Anisotropy means is that it’s angle dependent,” he explains. “In a material like graphene, light is absorbed and reflected equally no matter the angle at which it’s polarized. Black phosphorus is very different in the sense that if the polarization of light is aligned along the corrugations, it has a very different response than if it’s aligned perpendicular to the corrugations.”

When polarized light is oriented across the corrugations in black phosphorus, it interacts with the material differently than when it is oriented along the corrugations — kind of like how it is easier to rub your hand along the ribs in corduroy than it is to rub your hand across them.

Many materials can polarize light, though, and that ability alone is not especially useful. What makes black phosphorus special, Atwater says, is that it is also a semiconductor, a material that conducts electricity better than an insulator, like glass, but not as well as a metal like copper. The silicon in microchips is an example of a semiconductor. And just as how tiny structures built from silicon can control the flow of electricity in a microchip, structures built from black phosphorus can control the polarization of light as an electric signal is applied to them.

“These tiny structures are doing this polarization conversion,” Atwater says, “so now I can make something that’s very thin and tunable, and at the nanometer scale. I could make an array of these little elements, each of which can convert the polarization into a different reflected polarization state.”

The liquid crystal display (LCD) technology found in phone screens and TVs already has some of those abilities, but black phosphorus tech has the potential to leap far ahead of it. The “pixels” of a black phosphorus array could be 20 times smaller than those in LCDs, yet respond to inputs a million times faster.

Such speeds are not necessary for watching a movie or reading an article online, but they could revolutionize telecommunications, Atwater says. The fiber-optic cable through which light signals are sent in telecommunications devices can transmit only so many signals before they begin to interfere with and overwhelm each other, garbling them (picture trying to hear what a friend is saying in a crowded and loud bar). But a telecommunications device based on thin layers of black phosphorus could tune the polarization of each signal so that none interfere with each other. This would allow a fiber-optic cable to carry much more data than it does now.

Atwater says the technology could also open the door to a light-based replacement for Wi-Fi, something researchers in the field refer to as Li-Fi.

“Increasingly, we’re going to be looking at light-wave communications in free space,” he says. “Lighting like this very cool-looking lamp above my desk doesn’t carry any communication signal. It just provides light. But there’s no reason that you couldn’t sit in a future Starbucks and have your laptop taking a light signal for its wireless communication rather than a radio signal. It’s not quite here yet, but when it gets here, it will be at least a hundred times faster than Wi-Fi.”

The paper describing the work is titled, “Broadband electro-optic polarization conversion with atomically thin black phosphorus.” The lead author is Souvik Biswas, graduate student in applied physics. Other co-authors are Meir Y. Grajower, postdoctoral scholar research associate in applied physics and materials science, and Kenji Watanabe and Takashi Taniguchi of the National Institute for Materials Science in Japan.

“These are exciting times for new materials discovery that can shape the future of photonic devices, and we have barely scratched the surface,” Biswas says. “It would be gratifying if some day you could buy a commercial product constructed out of such atomically thin materials, and that day might not be very far.”

Funding for the research was provided by the U.S. Department of Energy; Japan’s Ministry of Education, Culture, Sports, Science and Technology; the Japan Society for the Promotion of Science; and the Japan Science and Technology Agency.

Most of us control light all the time without even thinking about it, usually in mundane ways: we don a pair of sunglasses and put on sunscreen, and close — or open — our window blinds.

But the control of light can also come in high-tech forms. The screen of the computer, tablet, or phone on which you are reading this is one example. Another is telecommunications, which controls light to create signals that carry data along fiber-optic cables.

Scientists also use high-tech methods to control light in the laboratory, and now, thanks to a new breakthrough that uses a specialized material only three atoms thick, they can control light more precisely than ever before.

The work was conducted in the lab of Harry Atwater, the Otis Booth Leadership Chair of the Division of Engineering and Applied Science, Howard Hughes Professor of Applied Physics and Materials Science, and director of the Liquid Sunlight Alliance (LiSA). It appears in a paper published in the October 22 issue of Science.

To understand the work, it is helpful first to remember that light exists as a wave and that it has a property known as polarization, which describes the direction in which the waves vibrate. Imagine being in a boat bobbing on the ocean: Ocean waves have a vertical polarization, which means that as the waves pass under the boat, it goes up and down. Light waves behave in much the same way, except these waves can be polarized at any angle. If a boat could ride waves of light, it might bob from side to side, or on a diagonal, or even in a spiraling fashion.

Polarization can be useful because it allows light to be controlled in specific ways. For example, the lenses in your sunglasses block glare (light often becomes polarized when it reflects off a surface, like the window of a car). The screen of a desk calculator creates legible numbers by polarizing light and blocking it in areas. Those areas where the polarized light is blocked appear dark, while areas where the light is not blocked appear light.

In the paper, Atwater and his co-authors describe how they used three layers of phosphorus atoms to create a material for polarizing light that is tunable, precise, and extremely thin.

The material is constructed from so-called black phosphorus, which is similar in many ways to graphite, or graphene, forms of carbon that consist of single-atom-thick layers. But whereas the layers of graphene are perfectly flat, black phosphorus’s layers are ribbed, like the texture of a pair of corduroy pants or corrugated cardboard. (Phosphorus also comes in red, white, and violet forms, distinct because of the arrangement of the atoms within it.)

That crystal structure, Atwater says, makes the black phosphorus have significantly anisotropic optical properties. “Anisotropy means is that it’s angle dependent,” he explains. “In a material like graphene, light is absorbed and reflected equally no matter the angle at which it’s polarized. Black phosphorus is very different in the sense that if the polarization of light is aligned along the corrugations, it has a very different response than if it’s aligned perpendicular to the corrugations.”

When polarized light is oriented across the corrugations in black phosphorus, it interacts with the material differently than when it is oriented along the corrugations — kind of like how it is easier to rub your hand along the ribs in corduroy than it is to rub your hand across them.

Many materials can polarize light, though, and that ability alone is not especially useful. What makes black phosphorus special, Atwater says, is that it is also a semiconductor, a material that conducts electricity better than an insulator, like glass, but not as well as a metal like copper. The silicon in microchips is an example of a semiconductor. And just as how tiny structures built from silicon can control the flow of electricity in a microchip, structures built from black phosphorus can control the polarization of light as an electric signal is applied to them.

“These tiny structures are doing this polarization conversion,” Atwater says, “so now I can make something that’s very thin and tunable, and at the nanometer scale. I could make an array of these little elements, each of which can convert the polarization into a different reflected polarization state.”

The liquid crystal display (LCD) technology found in phone screens and TVs already has some of those abilities, but black phosphorus tech has the potential to leap far ahead of it. The “pixels” of a black phosphorus array could be 20 times smaller than those in LCDs, yet respond to inputs a million times faster.

Such speeds are not necessary for watching a movie or reading an article online, but they could revolutionize telecommunications, Atwater says. The fiber-optic cable through which light signals are sent in telecommunications devices can transmit only so many signals before they begin to interfere with and overwhelm each other, garbling them (picture trying to hear what a friend is saying in a crowded and loud bar). But a telecommunications device based on thin layers of black phosphorus could tune the polarization of each signal so that none interfere with each other. This would allow a fiber-optic cable to carry much more data than it does now.

Atwater says the technology could also open the door to a light-based replacement for Wi-Fi, something researchers in the field refer to as Li-Fi.

“Increasingly, we’re going to be looking at light-wave communications in free space,” he says. “Lighting like this very cool-looking lamp above my desk doesn’t carry any communication signal. It just provides light. But there’s no reason that you couldn’t sit in a future Starbucks and have your laptop taking a light signal for its wireless communication rather than a radio signal. It’s not quite here yet, but when it gets here, it will be at least a hundred times faster than Wi-Fi.”

The paper describing the work is titled, “Broadband electro-optic polarization conversion with atomically thin black phosphorus.” The lead author is Souvik Biswas, graduate student in applied physics. Other co-authors are Meir Y. Grajower, postdoctoral scholar research associate in applied physics and materials science, and Kenji Watanabe and Takashi Taniguchi of the National Institute for Materials Science in Japan.

“These are exciting times for new materials discovery that can shape the future of photonic devices, and we have barely scratched the surface,” Biswas says. “It would be gratifying if some day you could buy a commercial product constructed out of such atomically thin materials, and that day might not be very far.”

Funding for the research was provided by the U.S. Department of Energy; Japan’s Ministry of Education, Culture, Sports, Science and Technology; the Japan Society for the Promotion of Science; and the Japan Science and Technology Agency.