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News Article | February 1, 2016
Site: http://www.fastcompany.com

A team of engineering students from MIT has won the Best Overall Design Award at the SpaceX’s Hyperloop Pod Competition Design Weekend contest at Texas A&M University in College Station, Texas. The MIT Hyperloop Team won for their design for pods that could travel via Hyperloop, a conceptual transportation system described in 2013 by SpaceX CEO Elon Musk as a series of tubes that shuttle passengers in pods at up to 700 miles an hour. The MIT design beat out more than 115 student engineering teams from across the globe, reports the Texas A&M Engineering blog. The winning team said the philosophy behind their design "is to demonstrate high-speed, low-drag levitation technology. We aim to build a light pod to allow us to achieve the highest cruise speed." The design relies on a magnetic levitation system that keeps the pod 15 millimeters above the Hyperloop tube’s surface. The pod’s shell will be constructed of woven carbon fiber and polycarbonate sheets. In case of emergency, the pod design includes a braking system that will automatically activate if any system in the pod fails, and, if necessary, the pod would be able to drive itself forward or backward using physical wheels. Twenty-one other teams participating in the competition also won awards for innovation and technical excellence. All 22 teams will get the chance to actually test their designs on a real Hyperloop test track at SpaceX's Hawthorne, California headquarters this summer. Musk, who is also CEO of electric car company Tesla, made an appearance at the awards event, where he praised all the teams involved. "I'm starting to think this is really gonna happen. It’s clear that the public and the world wants something new, and I think you guys are going to bring it to them," Musk said. He added, "As soon as [the Hyperloop] happens somewhere, and people see it really work out, I think it will quickly spread throughout the world." Indeed, though public Hyperloop tracks are years away from being built, there are now plenty of companies looking to lay the groundwork for the future transportation system. However, Musk noted that SpaceX itself is focused on space travel right now. "We don't have any specific plans to back Hyperloop companies," Musk said. "It's possible that we would back a [Hyperloop team], but we're trying not to favor one organization over another."

« Volvo Cars plans to launch large-scale autonomous driving experiment in China; 100 cars on public roads | Main | NASA, Boeing designing truss-braced wing expected to reduce aircraft fuel consumption and emissions by 50% » The green microalga Botryococcus braunii is considered a promising biofuel feedstock producer due to its prodigious accumulation of hydrocarbon oils that can be converted into fuels. Now, a team led by researchers from Texas A&M AgriLife Research has identified the first committed step in the biosynthesis of hydrocarbon oil in B. braunii and has described a new enzyme which carries out this reaction. The study, published as an open-access paper in the current issue of the journal Nature Communications, could enable scientists to use the enzyme in a plant to make large amounts of fuel-grade oil, according to Dr. Tim Devarenne, AgriLife Research biochemist in College Station and lead scientist on the team. Devarenne’s lab has been studying the concept of making fuel from algae on a $2-million National Science Foundation grant for four years. The colony-forming green microalga B. braunii is an exciting candidate for biofuel feedstock production, as it produces up to 61% of its dry weight as liquid hydrocarbon oils. These hydrocarbons are produced inside the cells of the colony, seen as intracellular oil bodies and secreted into the colony extracellular matrix where the majority of the hydrocarbons are stored. Most importantly, catalytic hydrocracking of hydrocarbons from this alga results in petroleum-equivalent fuels of gasoline, kerosene and diesel. Intriguingly, geologic evidence also shows a direct contribution of this alga to the formation of currently used fossil fuel deposits around the globe. Despite the aforementioned advantages of B. braunii, its use for biofuel feedstock production is hindered by a slow growth rate and the lack of transformation systems to achieve targeted genetic modification. Thus, the identification of B. braunii hydrocarbon biosynthetic pathways and associated genes/enzymes can provide options for metabolically engineering these pathways into heterologous hosts with better growth characteristics and the ability to be genetically manipulated. This would then allow the development of improved versions of hydrocarbon biosynthetic enzymes, to direct production towards the most commercially desirable products. Devarenne’s lab has been trying to understand how Botryococcus braunii makes the liquid hydrocarbons—i.e., what genes and pathways are involved—so the genes can be manipulated to make more oil, possibly by transferring those genes into a land plant such as tobacco, or maybe other algae that grow very quickly. It takes about a week for one Botryococcus cell to double into two cells, whereas a faster growing algae—but one that doesn't make a lot of oil—can double in about six hours, Devarenne said. The researchers targeted deciphering the biochemical pathway for making the hydrocarbon oil, which is called lycopadiene. They discovered a gene called lycopaoctaene synthase (LOS). The enzyme encoded by the LOS gene is able to initiate the production of the oil. A closer look at the LOS enzyme revealed that the enzyme is “promiscuous” in that it is capable of mixing several substrates to make different products. Devarenne explained that’s not only different from other enzymes that are similar to LOS, but it’s important because most enzymes like LOS only use a 15-carbon substrate. In terms of fuel, it's better to start with a higher carbon number molecule. The team determined the sequence of all the actively working genes of the organism under hydrocarbon producing conditions. Bioinformatic analysis of this sequence information was then able to pinpoint a gene that might have the appropriate activity to initiate hydrocarbon biosynthesis. Even when the genes are more fully understood, scientists will have to find the right host organism to express the genes, optimize that expression and try to get them to produce as much of the oil as possible. The project included Devarenne’s graduate student Hem Thapa and colleague Mandar Naik at Texas A&M University in College Station, along with Shigeru Okada and Kentaro Takada from the University of Tokyo in Japan, Istvan Molnar from the University of Arizona’s College of Agriculture and Life Sciences and Yuquan Xu from the Chinese Academy of Agricultural Sciences.

News Article
Site: http://phys.org/biology-news/

Rush is beginning a new project looking at high-value vegetable crop production under high tunnels, particularly tomatoes this year. High tunnels are Quonset hut-type structures similar to greenhouses in appearance but lacking artificial heat. As water concerns continue to rise, the potential for making more money with the available water is really good, he said, so that's one of the reasons to look at this new production system with high tunnels and high-value vegetable crops. "One of the reasons we're doing this research is because the Ogallala Aquifer is certainly limited and in most cases the water level is dropping," Rush said. "In areas south of Amarillo particularly, the water availability is becoming scarcer every year." It's more difficult for farmers to pump due to the depth of water and the cost involved, he said. "So obviously it's really important that everybody make the most out of every inch of water they apply that they can," Rush said. "We strongly believe that in some of the areas where they are running out of water, they're no longer going to be able to grow high-value crops like peanuts or potatoes and even corn, because these all require a lot of water. "Whereas, if you had a high tunnel, you could grow tomatoes and the amount of money you could make for every inch of water vastly outpaces what you could make on any other crop we're currently growing in the Panhandle." Rush said he has multiple research projects to conduct under the high tunnels with a growing interest being expressed by retailers. H-E-B is currently supporting one project with the Texas Department of Agriculture and United Supermarkets also expressed interest in collaborating. "The potential for retail grocers to increase availability of high quality vegetables by purchasing from local growers is quite high," he said. So far, the frames of four individual high tunnels have been erected with a target date for having tomato seedlings planted by the first week of May, Rush said. Rush said the tomato cultivars have already been selected and are growing in a greenhouse setting. The seed came from Dr. Kevin Crosby, AgriLife Research vegetable breeder in College Station, and also from some commercial tomato breeders in California. "The little seedlings are growing and looking great," Rush said. "They'll be ready to go by the middle of April, and then it just depends on when we are able to get everything we want done out at the high tunnels as to when we plant the tomatoes there." Each high tunnel is 96 feet long, 30 feet wide and 12 feet tall, said Jimmy Gray, AgriLife Research technician in Amarillo. Each will have six, 60-inch beds that will be plowed and shaped up prior to completion of the tunnel building in preparation for planting. The high tunnel metal frames will be covered with a fiberglass impregnated tarp to allow sunshine in and keep most of the weather out, Gray said. The sides will roll up about 5 feet. The end walls have a 20-foot by 10-foot door that will roll all the way up to allow a breezeway through the high tunnel. "We are also installing drip tape – both subsurface drip irrigation and root-demand irrigation – along the length of each 5-foot bed," he said. "We will have three beds per zone and four zones per tunnel, so about 40 foot lengthwise by three 5-foot beds will be one irrigation management zone. And those will be controlled individually with RDI on two of the zones and SDI on two of the zones." A similar irrigation setup will be developed in the open field, Rush said. This way researchers and engineers involved in the project can compare vegetable production and water use inside the tunnels and in the open fields. Rush said this will allow them to conduct precision irrigation and fertilizer practices as they grow tomato plants, and develop best management practices to pass on to producers who adopt high tunnels in the future. "Eventually, we will look at more than just tomatoes; we will look at all sorts of other specialty crops including vegetables to be grown under high tunnels," he said. "We're going to have to work out a cropping system because you can't grow one vegetable every year inside the entire tunnel, so you need to do just like you would in a field and have rotation schedules." Rush said some of the management techniques they will study concern irrigation frequency and method. "We are excited to look at the new root-demand irrigation," he said. "Instead of having our traditional subsurface drip or drip tape on top of the bed, root-demand irrigation tape is buried in the bed around the root zone, and as the root grows into contact with that, the roots are actually able to extract water directly from the tape when they need it." Once it is installed, Rush said, theoretically producers should not have to worry about irrigation scheduling and the plant should never be exposed to stress because water is always available.

News Article | February 2, 2016
Site: http://motherboard.vice.com/

Members of the rLoop team holding up an award they got from the competition as well as a warning for the party they threw. Image: Jason Koebler Nearly all of the teams trying to build a “pod” that will work in Elon Musk’s futuristic hyperloop transportation tubes spent months toiling away together in university classrooms engineering their designs. One of the teams, however, only met each other for the first time a few hours before I met them. In 2013, Musk, the SpaceX founder, pitched the “fifth mode of transportation,” which creates a partial vacuum in a tube in order to shoot human-carrying pods down them at speeds of over 700 mph. In summer of 2015, SpaceX announced it would build a hyperloop test track at its Hawthorne, California headquarters and would hold a “pod design competition” for university students in order to spur research into the feasibility of the technology. Immediately after that announcement, members of the SpaceX subreddit floated the idea of entering the competition themselves. “There was a slow realization that we are professionals, or at least students in the field and that together we had the collective ability to actually create a competitive pod for this,” Brent Lessard, an engineer from Toronto who is the project manager of the 140-member rLoop team, told me. Brent Lessard and Gabriel Korgood of rLoop, at the Airbnb they rented. Image: Jason Koebler Team members quickly fell into roles—the leaders accepted applications for “jobs” managing the teams that would design several of the pod’s subsystems—and soon the core members of the team were spending every moment not dedicated to their day jobs working on the pod’s design. “A lot of sleepless nights,” Lessard said. “For me, it’s every waking minute, basically. And then some—I have dreams about it, too.” The team’s initial goal was to put together a pod proposal for the SpaceX design weekend, a precursor to a final competition at the test track. The design weekend was held last weekend at Texas A&M University, where SpaceX and Tesla employees judged the entries of 180 teams, most of them made up of university undergrad students. rLoop was one of 22 teams invited to the final competition, and it was the only non-university team that made it through. Now there’s more work to do. “So far, everything was doable over the internet using Google Docs or Slack or Trello,” Thomas Lambot, a NASA Ames propulsion researcher and the team’s engineering lead, told me. “Our strength, which was having a lot of brains from a lot of different countries has now become a weakness—how are we going to build this thing? Where are we going to do it?” Seven months after rLoop formed, Eric Matzner, a nootropics entrepreneur from San Francisco, met Amir Hasan Khan, a simulations expert from New Delhi, India, at the Houston airport. It was the first time anyone on rLoop had ever seen each other in real life. Naturally, the two took a selfie and sent it to everyone else on the team. “When I got that picture, I was tearing up almost, like, ‘Here we go,’” Lessard said. Lessard, Matzner, Khan, and six other members of the rLoop team rented an Airbnb in College Station, Texas to propose their design to SpaceX judges and to get to know each other. “We’ve been going nonstop. We have the opportunity this weekend to show off what we’ve done, show how we’ve worked together,” Lessard said. “I think we’re going to go home and have some beer and not worry about the engineering related issues.” The team fell into an easy friendship thanks to all the time they spent talking online, and the fact that they had all met on Reddit was a constant source of conversation among the other teams at the competition. “Even though we’ve never met before, we’ve spent so much time working late at night on reports and deadlines that it feels like we’ve known each other for a long time,” Lambot said. “It feels really natural.” The team also quickly made friends with all the other competitors, who were intrigued by the fact that the team had met on Reddit. After the competition closed, rLoop threw a small gathering at their rented Airbnb. It quickly became a full-fledged party made up of other hyperloop teams—not a rager, but definitely a party, nonetheless. It was almost immediately busted by overzealous cops who apparently didn’t realize—some of the partygoers joked—that they were interrupting some potentially world-changing engineering talk that was being fueled by a few beers. Getting to this point wasn’t easy—most teams had, at most, a couple dozen members. rLoop has had more than 300 people sign up, with about 140 making some sort of contribution. “No one was fighting, there were no power struggles, but there was a lot of confusion,” Lambot said. “There are a lot of ‘shooting stars,’ as I call them. People who join excited, start doing great work and take on responsibilities. Within a week they say, ‘I can’t do that anymore, I got a girlfriend, work is crazy.’ They just disappear. That happens all the time—people joining, helping, and disappearing. It was like herding cats trying to get people focused over the internet. But I can’t take them by the shirt and say ‘focus’ or threaten to fire them.” Matzner, who is the team’s livestreamer—a job that sound frivolous until you realize that, with only nine team members able to attend the design weekend at Texas A&M, most of rLoop relied on Matzner to keep up—says the team’s open-source ethos has allowed it to roll with the punches. Matzner meets Khan, the first meeting of any rLoop members. Image: Eric Matzner “It’s like a river—the water always changes but you still call it the same river,” Matzner said. “We carry along the ideas and skills that have come through and keep going on.” The team calls itself “the world’s first non-profit, open source, online think tank,” and it’s hard to argue with the fact that already it has done some very serious engineering work. Under Lambot's and Lessard’s lead, the team managed to scrape together a 200-page pod proposal that sufficiently impressed SpaceX judges. It will be one of 22 teams that actually builds a pod for the June competition at SpaceX. The team says it has managed to find members who have manufacturing experience, and have scored a manufacturing space in the Sacramento, California area. Still, there’s not yet a firm plan for when it will actually build the pod or how it’s going to pay for it (SpaceX is building the test track but isn’t paying the schools to build pods). The tentative plan to fund it for now, of course, is to appeal to the Reddit community for help crowdfunding the $80,000 they suspect building the pod and getting it to Hawthorne will cost. The team is hell bent on scraping together the money and says their friendship has really just begun. “You spend all your time on the internet, and you meet these people and you look around and wonder, ‘Are these your real friends?’" Matzner said. “Well now we’re here and it’s like ‘Look, we exist in the real world too.’ I like to think we’re kind of an outgrowth of the internet.”

News Article
Site: http://phys.org/biology-news/

The research team found a group of DNA sequences in pine trees, spruces and other conifers had been transferred to an ancestor of those trees from insects about 340 million years ago, said Dr. Claudio Casola, an AgriLife Research forest genomics assistant professor in the Texas A&M University ecosystem science and management department in College Station. "Loblolly pine is an important economic resource across the southeastern U.S., including Texas," Casola said. "We are just now starting to understand the different parts that form the very large genome of this pine tree and other conifers. Xuan Lin, one of Casola's doctoral students, and Dr. Nurul Faridi, leader of the U.S. Department of Agriculture Forest Service's Molecular Cytogenetics Laboratory and a collaborating faculty member, were other members of the team. Their work, "An Ancient Trans-Kingdom Horizontal Transfer of Penelope-like Retroelements from Arthropods to Conifers," was published recently in the Genome Biology and Evolution journal. "We called these conifer DNA sequences 'Dryads' after the Greek mythological nymphs that inhabit trees," Casola said. "Dryads are one of the many groups of DNA sequences known as DNA repeats." He said DNA repeats, also known as transposable elements, are particularly good at making new copies of themselves. As a result, they ended up forming more than half of the genome in some species, including conifers and other plants. "We know from studies in other plants that transposable elements affect both the activity and the structure of genes, and ultimately have a role in shaping certain traits, from the color of some grape varieties to the oval shape of some tomatoes." He said because transposable elements make up a lot of the conifers' DNA, it is important to gather a better understanding of what they are and how they influence conifer genes and phenotypic traits. "You can think of transposable elements as 'genomic parasites,'" Casola explained. "They spread into new genomes kind of like viruses spread between people. Unlike flu and other viral disease, these 'genomic infections' occur rarely, but once established, they can persist for millions of years." The similarities between some transposable elements and viruses are not only superficial, he said. For example retroviruses, the group of viruses that includes the HIV, evolved from transposable elements long ago. On the other hand, Casola said, many transposable elements known as endogenous retroviruses, or ERVs, represent "DNA fossils" of retroviruses that once infected primates and other mammals. "No less than 8 percent of our own genome is made of ERVs," he said. "Retroviruses, ERVs and other DNA repeats such as Penelope-like sequences share a unique way to make new copies of themselves." In this process, a single DNA repeat acts as a template to make many molecules called RNAs, and these RNAs are then transformed back into just as many DNA copies that are sort of stitched back in the host genome, he explained. Because the generation of new DNA copies from RNAs is called retroposition, transposable elements that amplify through this mechanism are known as retroelements, Casola said. By looking at some specific features in the DNA of retroelements, it is possible to classify them into different families and subfamilies. "Dryads represent a conifer-specific subfamily within the larger family of Penelope-like retroelements, hence the manuscript's title," Casola said. "Before we described Dryads, Penelope-like retroelements were known only in animals. "We thought that Dryads could have derived from Penelope-like retroelements that were somehow introduced into conifer genomes long ago," he said. "To confirm that, we computationally analyzed the genome sequences from 1,029 species that were neither animals nor conifers. "Some of these other species seemed to contain Penelope-like retroelements; however, after thorough inspections of these DNA sequences, we concluded that they were due to DNA contamination from either animals or conifers." Casola said they also did a lot of other analyses to confirm that Dryads are not artifacts and to show they are likely derived from insect Penelope-like retroelements. "One of the techniques used is called fluorescence in situ hybridization, or FISH, and allowed to visualize the position of Dryad DNA sequences on the loblolly pine chromosomes," Faridi said. Other lab experiments showed that Dryads do not occur in plants closely related to conifers, such as cycads and ginkgo, he said. "This helped us in timing the origin of Dryads between the separation of conifers' ancestors from other plants and the radiation of modern conifer groups known to have occurred about 340 million years ago," Casola said. The consequences of Dryads invasion for conifers evolution remain unclear, he said. When DNA repeats like Dryads amplify in a genome, they can change the structure of chromosomes and alter the activity of genes, with potential negative consequences for the organism, Casola said. Most species have evolved genetic mechanisms that slow down the amplification of DNA repeats, but when they jump into new host genomes, these defense mechanisms are not in place yet and a new cycle of amplification ensues, he said. The same likely happened in Dryads, which generated hundreds of thousands of new copies in the past 340 million years but now seem to have a relatively low activity, at least in loblolly pine, Casola said. "We think that Dryads changed significantly the genome landscape of ancestral conifers and possibly are still introducing important changes into the DNA of these trees," he said. "The next step in our research will be to understand how conifer chromosomes, and especially genes, were affected by the amplification of Dryads since their invasion of these plants," Casola said. "Additionally, we want to know if Dryads and other DNA repeats show differences between loblolly pine trees that are associated with trait differences, for example drought tolerance and pest resistance. Both these aspects will be the focus of future research in our labs." Explore further: Huge DNA code of the Christmas tree being revealed More information: Xuan Lin et al. An Ancient Trans-Kingdom Horizontal Transfer of -like Retroelements from Arthropods to Conifers , Genome Biology and Evolution (2016). DOI: 10.1093/gbe/evw076

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