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New NASA Mission Going to the International Space Station –"To Explore Mysteries of Cosmic Rain" – The Daily Galaxy (blog)
Posted: August 13, 2017 at 1:48 am
A new experiment set for an Aug. 14 launch to the International Space Station will provide an unprecedented look at a rain of particles from deep space, called cosmic rays, that constantly showers our planet. The Cosmic Ray Energetics And Mass mission destined for the International Space Station (ISS-CREAM) is designed to measure the highest-energy particles of any detector yet flown in space.
"The CREAM balloon experiment achieved a total sky exposure of 191 days, a record for any balloon-borne astronomical experiment," said Eun-Suk Seo, a professor of physics at the University of Maryland in College Park and the experiment's principal investigator. "Operating on the space station will increase our exposure by over 10 times, taking us well beyond the traditional energy limits of direct measurements."
Sporting new instruments, as well as refurbished versions of detectors originally used on balloon flights over Antarctica, the refrigerator-sized, 1.4-ton (1,300 kilogram) ISS-CREAM experiment will be delivered to the space station as part of the 12th SpaceX commercial resupply service mission. Once there, ISS-CREAM will be moved to the Exposed Facility platform extending from Kibo, the Japanese Experiment Module.
From this orbital perch, ISS-CREAM is expected to study the "cosmic rain" for three yearstime needed to provide unparalleled direct measurements of rare high-energy cosmic rays.
At energies above about 1 billion electron volts, most cosmic rays come to us from beyond our solar system. Various lines of evidence, including observations from NASA's Fermi Gamma-ray Space Telescope, support the idea that shock waves from the expanding debris of stars that exploded as supernovas accelerate cosmic rays up to energies of 1,000 trillion electron volts (PeV). That's 10 million times the energy of medical proton beams used to treat cancer. ISS-CREAM data will allow scientists to examine how sources other than supernova remnants contribute to the population of cosmic rays.
Protons are the most common cosmic ray particles, but electrons, helium nuclei and the nuclei of heavier elements make up a small percentage. All are direct samples of matter from interstellar space. But because the particles are electrically charged, they interact with galactic magnetic fields, causing them to wander in their journey to Earth. This scrambles their paths and makes it impossible to trace cosmic ray particles back to their sources.
"An additional challenge is that the flux of particles striking any detector decreases steadily with higher energies," said ISS-CREAM co-investigator Jason Link, a researcher at NASA's Goddard Space Flight Center in Greenbelt, Maryland. "So to better explore higher energies, we either need a much bigger detector or much more observing time. Operating on the space station provides us with this extra time."
Large ground-based systems study cosmic rays at energies greater than 1 PeV by making Earth's atmosphere the detector. When a cosmic ray strikes the nucleus of a gas molecule in the atmosphere, both explode in a shower of subatomic shrapnel that triggers a wider cascade of particle collisions. Some of these secondary particles reach detectors on the ground, providing information scientists can use to infer the properties of the original cosmic ray.
Technicians lower ISS-CREAM into a chamber that simulates the space environment during system-level testing at NASA's Goddard Space Flight Center in summer 2015. Credit: University of Maryland Cosmic Ray Physics Laboratory These secondaries also produce an interfering background that limited the effectiveness of CREAM's balloon operations. Removing that background is another advantage of relocating to orbit.
With decreasing numbers of particles at increasing energies, the cosmic ray spectrum vaguely resembles the profile of a human leg. At PeV energies, this decline abruptly steepens, forming a detail scientists call the "knee." ISS-CREAM is the first space mission capable of measuring the low flux of cosmic rays at energies approaching the knee.
"The origin of the knee and other features remain longstanding mysteries," Seo said. "Many scenarios have been proposed to explain them, but we don't know which is correct."
Astronomers don't think supernova remnants are capable of powering cosmic rays beyond the PeV range, so the knee may be shaped in part by the drop-off of their cosmic rays in this region.
"High-energy cosmic rays carry a great deal of information about our interstellar neighborhood and our galaxy, but we haven't been able to read these messages very clearly," said co-investigator John Mitchell at Goddard. "ISS-CREAM represents one significant step in this direction."
ISS-CREAM detects cosmic ray particles when they slam into the matter making up its instruments. First, a silicon charge detector measures the electrical charge of incoming particles, then layers of carbon provide targets that encourage impacts, producing cascades of particles that stream into electrical and optical detectors below while a calorimeter determines their energy. Two scintillator-based detector systems provide the ability to discern between singly charged electrons and protons. All told, ISS-CREAM can distinguish electrons, protons and atomic nuclei as massive as iron as they crash through the instruments.
ISS-CREAM will join two other cosmic ray experiments already working on the space station. The Alpha Magnetic Spectrometer (AMS-02), led by an international collaboration sponsored by the U.S. Department of Energy, is mapping cosmic rays up to a trillion electron volts, and the Japan-led Calorimetric Electron Telescope (CALET), also located on the Kibo Exposed Facility, is dedicated to studying cosmic ray electrons.
Overall management of ISS-CREAM and integration for its space station application was provided by NASA's Wallops Flight Facility on Virginia's Eastern Shore. ISS-CREAM was developed as part of an international collaboration led by the University of Maryland at College Park, which includes teams from NASA Goddard, Penn State University in University Park, Pennsylvania, and Northern Kentucky University in Highland Heights, as well as collaborating institutions in the Republic of Korea, Mexico and France.
The Daily Galaxy via NASA's Goddard Space Flight Center
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New NASA Mission Going to the International Space Station --"To Explore Mysteries of Cosmic Rain" - The Daily Galaxy (blog)
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VIDEO: Research To Advance Disease Therapies Among Cargo Headed To Space Station On Dragon Monday – SpaceCoastDaily.com
Posted: at 1:48 am
By NASA // August 13, 2017
ABOVE VIDEO:The SpaceX CRS-12 mission will carry more than 20 ISS National Lab experiments to the International Space Station ranging from research on Parkinsons disease, DNA science to many others.
BREVARD COUNTY KENNEDY SPACE CENTER, FLORIDA The SpaceX Dragon cargo spacecraft is targeted for launch Monday, Aug. 14 from Kennedy Space Center for its 12th commercial resupply (CRS-12) mission to the International Space Station.
The flight will deliver investigations and instruments that study cosmic ray particles, protein crystal growth, stem cell-mediated recellularization and a nanosateliite technology demonstration.
The vehicle also will deliver supplies and equipment to crew members living aboard the station.
Here are some highlights of research that will be delivered:
Investigation studies cosmic ray particles
Cosmic ray particles reach Earth from far outside the solar system with energies well beyond what man-made accelerators can achieve. The Cosmic Ray Energetics and Mass (ISS-CREAM) instrument, attached to the Japanese Experiment Module Exposed Facility, measures the charges of cosmic ray particles ranging from hydrogen to iron nuclei.
The data collected from the CREAM instrument will be used to address fundamental science questions such as:
Do supernovae supply the bulk of cosmic ray particles?
What is the history of cosmic ray particles in the galaxy?
Can the energy spectra of cosmic rays result from a single mechanism?
Tested in several long duration balloon flights, the CREAM instrument holds the longest known exposure record for a single balloon-borne experiment at approximately 190 days of exposure. ISS-CREAMs three-year mission will help the scientific community build a stronger understanding of the fundamental structure of the universe.
Microgravity-grown protein crystals aid in understanding of Parkinsons disease
ABOVE VIDEO:The Michael J. Fox Foundation is sending an experiment to the ISS National Lab to investigate the LRRK2 protein, a key target in identifying the makeup of Parkinsons disease.
The microgravity environment of the space station allows protein crystals to grow larger and in more perfect shapes than earth-grown crystals, allowing them to be better analyzed on Earth.
Developed by the Michael J. Fox Foundation, Anatrace and Com-Pac International, the Crystallization of Leucine-rich repeat kinase 2 (LRRK2) under Microgravity Conditions (CASIS PCG 7) investigation will use the orbiting laboratorys microgravity environment to grow larger versions of this important protein, implicated in Parkinsons disease.
Defining the exact shape and morphology of LRRK2 would help scientists to better understand the pathology of Parkinsons and aid in the development of therapies against this target.
Telescope-hosting nanosatellite tests new concept
The Kestrel Eye (NanoRacks-KE IIM) investigation is a microsatellite carrying an optical imaging system payload. This investigation validates the concept of using microsatellites in low-Earth orbit to support critical operations, such as providing lower-cost Earth imagery in time-sensitive situations such as tracking severe weather and detecting natural disasters.
Sponsored by the space station U.S. National Laboratory, the overall mission goal for the investigation is to demonstrate that small satellites are viable platforms for providing critical path support to operations and hosting advanced payloads.
Growth of lung tissue in space could provide information about disease pathology
ABOVE VIDEO:The University of Texas Medical Branch will be sending human lung tissue to the ISS National Lab to better understand how lung tissue functions in microgravity in preparation for long-term spaceflight.
The Effect of Microgravity on Stem Cell Mediated Recellularization (Lung Tissue) uses the microgravity environment of space to test strategies for growing new lung tissue.
Using bioengineering techniques, the Lung Tissue investigation cultures different types of lung cells in controlled conditions aboard the space station.
The cells are grown in a specialized framework that supplies them with critical growth factors so that scientists can observe how gravity affects growth and specialization as cells become new lung tissue.
The SpaceX Dragon cargo spacecraft is targeted for launch Monday, Aug. 14 from Kennedy Space Center for its 12th commercial resupply (CRS-12) mission to the International Space Station.
Tissue mimic models such as this also have the potential to be used for assessing drug or chemical toxicity by biotechnology and pharmaceutical companies and could allow for rapid testing of new chemicals and compounds, considerably lowering the overall costs for research and development of new drugs.
The ultimate goal of this investigation is to produce bioengineered human lung tissue that can be used as a predictive model of human responses allowing for the study of lung development, lung physiology or disease pathology.
These investigations and others launching aboard CRS-12 will join many other investigations currently happening aboard the space station. Follow @ISS_Research for more information about the science happening on station.
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VIDEO: Research To Advance Disease Therapies Among Cargo Headed To Space Station On Dragon Monday - SpaceCoastDaily.com
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Local Boy Scout troop experiment about to take off for outer space … – Chicago Tribune
Posted: at 1:48 am
Wearing winter clothes, Andrew Frank entered a minus 20 degrees Celsius freezer at the Kennedy Space Center in Florida earlier this month to help insert hundreds of biological samples into a tiny device destined for a mission in space.
But the unit wouldn't quite fit into the 4-by-4-by-6-inch box required for the mission, so the 16-year-old Boy Scout with Palatine-based Troop 209 and other volunteers improvised with tinier screws and silicon tape to seal the container. After eight hours working off and on in the deep freeze, Frank was shaking from the cold, but the device was cleared for liftoff.
With that, a two-year process to build an experiment capable of testing DNA mutations in space while meeting strict NASA specifications was complete.
The project was chosen from a competition among Chicago-area troops sponsored by Boy Scouts of America and the Center for the Advancement of Science in Space, which runs the U.S. laboratory on the International Space Station. Some of the Scouts will be on hand to watch when the experiment is due to launch aboard a SpaceX rocket from the Florida space center on Monday.
"It's been a huge learning experience," said Frank, the team leader. "I had never done anything like this."
The experiment will test genetic mutations of bacteria in low gravity. Using a procedure called the Ames test, the Scouts will examine how much E. coli cultures change in space and compare that with what happens to them on Earth.
If they find changes in mutations, the Scouts said, it might suggest better ways to fight cancer or grow tissue to heal wounds.
"At the beginning, it's just really cool to do something that's going into outer space," said team mentor Norm McFarland. "By the end, the Scouts were coming up with their own solutions to problems they were finding."
Their device will take photos of each culture repeatedly throughout the flight, checking for a telltale color change from purple to yellow.
To fit a testing device into the restricted space, the Scouts tried out multiple designs, cameras and motors, finally settling on an octagon-shaped carousel that rotates the samples so they can be photographed. Sensors also track time, temperature and humidity.
The device must do all that without using more than the allotted power limit of about 2.5 watts, a small fraction of the power commonly used by lightbulbs.
When astronauts return the experiment to Earth after about a month, the Scouts will check the results, then run the same experiment under the same conditions but in normal gravity.
Some 20 Scouts, age 11 to 18, worked on the project, putting in more than 5,000 hours of meeting time.
The team had guidance from many adults including McFarland, an electrical engineer who retired from Siemens Building Technologies after helping develop numerous patents. Among those who also assisted were a microbiologist and a father who helped fabricate the aluminum parts for the device.
The Scouts themselves designed and soldered a circuit board to help make their experiment work. They even included a position sensor, so if the space station loses power temporarily, the device can reset itself.
Frank and teammate Harmon Bhasin were in Florida before the launch to explain their project at a NASA preflight news conference.
Adult volunteer Kathleen Cassady said she was impressed by how the Scouts grew during the project.
"I thought this would be a good thing to get them interested in STEM (science, technology, engineering and math)," she said, "but I never thought it would also give them the soft skills, to be able to work as a team, provide leadership and problem-solve."
Armando L. Sanchez/Chicago Tribune
Members of Palatine Boy Scout Troop 209 built this device to test genetic mutations of bacteria in low gravity. Its scheduled to launch on Monday, Aug. 14, 2017, aboard a SpaceX rocket in Florida.
Members of Palatine Boy Scout Troop 209 built this device to test genetic mutations of bacteria in low gravity. Its scheduled to launch on Monday, Aug. 14, 2017, aboard a SpaceX rocket in Florida. (Armando L. Sanchez/Chicago Tribune)
This isn't the only Scout experiment chosen for the space station. Explorer Post 2400, which includes males and females up to age 20 out of Calumet College of St. Joseph in Whiting, was chosen for the next space launch this fall, to test the effect of low gravity on peptides, which are thought to play a key role in Alzheimer's disease.
One of the faculty leaders on the project, Sandra Chimon Rogers, chairwoman of the college's department of biophysical chemistry and math, said the team developed an infrared spectrometer that fit into the tiny space allowed and cost only about $700, rather than the tens of thousands of dollars such devices often cost.
"It's an amazing opportunity for them, and more students should be aware of it," Rogers said.
In addition, a team of students from Deerfield High School won a separate competition to send their experiment on Monday's launch. They will test different materials for their ability to provide a shield from radiation, which could prove crucial to any long-range space mission, such as an expedition to Mars.
That Go For Launch! competition was sponsored by Higher Orbits, a nonprofit that promotes science and technology, and was judged in part by a former astronaut, Dorothy Metcalf-Lindenburger.
One of the students on the Deerfield team, 16-year-old Chirag Goel, said he was thrilled at the opportunity.
"To look into the night sky and to be a small part of that is humbling," Goel said. "To tell your kids I helped design an experiment to go into space ... what could be cooler than that?"
Twitter @RobertMcCoppin
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Local Boy Scout troop experiment about to take off for outer space ... - Chicago Tribune
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Primary students the first to code experiments for International Space Station – The Sydney Morning Herald
Posted: at 1:48 am
About 24 primary students are the first in the country to code science experiments that will be launched on a rocket to the International Space Station this weekand completed by astronauts.
The students from six public schoolshave spent the past three months choosing an experiment and coding the hardware necessary to complete it in space.
AbdelelahFaisal, 11, who is in year 6 at Granville East Public School, and his group havecoded a mini-computer to take photographs in space and transmit the data back to earth, where theywill use it to create an artwork.
"We wanted to see how much light is actually in space because in space videosit's always so dark up there," Abdelelah said.
"No primary schools have ever done this beforeso this was our first opportunity to experience what uni students do."
The school's assistant principal Sarah Mellish, who has worked closely with the year 6 students involved in theproject being run by Cuberider, said it has previously only been offered to high school students.
"We were initially told primary students couldn't do the experiment and we said 'no,that's not true, we have really high expectations for them'," Mrs Mellish said.
She said the students"pickedup on it really quickly" once they started working with six year 7 students at Casula High School, and completed the project over four days.
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"Coding and robotics are becoming really common in primary schoolsand the idea of sending something into space was a really cool drawing card," Mrs Mellish said.
Emily Signorini, who is head teacher of STEM at Casula High School and led the project, said other experiments include measuring the temperature at the International Space Station and comparing it toearth to look at how a farm could be set up in space.
"One of the things the teachers have really enjoyed watching is all of the discussions that have broken off," Mrs Signorini said.
"Not just about the space station but about things like the terraforming ofMars, changing it so that it's fit for us to live on.
"As teachers, we were very surprised to hear that. They're going off on their own hypothetical journeys.
"We could have the first people to ever go to Mars in our classroom right now."
The codes and hardware to carry out the experiments will be launched from the Kennedy Space Center in Florida on Tuesday in a SpaceXrocket that is delivering supplies to the International space station.
Cuberider will also conduct the experiments in the earth's stratosphere through a balloon launch scheduled in October.
Abdelelah said the project has made him much more interested in science.
"I wasn't that interested in it until I went into this," he said.
"I'm excited to see how it's actually going to be launched and whether the experiment will work.
"And my friends are also jealous."
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DNA test leads brothers to reunite with mother — after 46 years – CNN
Posted: at 1:47 am
Raymond was speechless. He glanced at his younger brother, then his eyes darted back to the entrance to the Dallas Fort Worth International Airport baggage claim.
The woman continued to walk slowly toward them -- then she froze.
"Elsie?" Anthony called out, his voice a tone higher. "Raymond?" she asked.
It was an emotional reunion between a mother and her sons that had been 46 years in the making. "I love you," she whispered, kissing both men on the cheek again and again.
As they hugged their mother, Abreu and Wiggs were surrounded by their children and girlfriends, members of the media, airport employees and curious travelers -- each perhaps trying to understand what they had just witnessed.
Many months of late-night calls -- and a DNA test -- had led to that life-changing moment. Now 64-year-old Elsie Ramirez was finally face-to-face with her sons, Raymond, 47, and Anthony, 46. She hadn't seen them since they were infants. Before the meeting, she had been anxious. "I feel the butterflies ... and felt like a new butterfly," she said as she hugged her sons.
Ramirez said she left Aguadilla, Puerto Rico, in the 1970's shortly after her relationship with her husband broke down. He was in the military and stationed at Ramey Air Force Base.
Soon after the couple's relationship soured, social services in Puerto Rico became involved and the brothers and their mother were split up. Raymond Abreu -- 10 months older than his brother -- moved in with his grandparents. Soon after that, his father took him to San Antonio, Texas.
Meanwhile, baby Anthony had been adopted by the Wiggs family. Marta Wiggs and her family called the boy "Mikey," a nod to his birth name.
She fondly recalls the morning in 1971 that her late husband called and told her about a little boy who had been dropped off at the base's social services office -- and who needed a home.
"I think my dad panicked," Anthony Wiggs told CNN. "He didn't know what to do with me and he took me to someone he knew, who happened to be his sergeant in his platoon, who (also worked) for social services."
Marta Wiggs already had an 8-month-old boy and said that at the time she felt that she had everything she needed to raise another baby. She immediately agreed to take on the child. "A couple of hours later, we had Mikey in the house too," she remembered, chuckling. "We were overjoyed." By 1973, the adoption was official and the Wiggs family moved to California.
Ramirez said she looked for her boys after she moved from Puerto Rico to Massachusetts and was devastated that she couldn't find them. She said the separation caused her years of pain.
Anthony, meanwhile, had become curious about his family history. His adoptive mother showed him his birth certificate. He searched the white pages each day and would make a few calls to Puerto Rico, New York and Florida. Eventually he connected with Raymond's ex-wife living in Texas who put the brothers in touch. Both believed their mother was dead. Everybody they knew to ask told them so. But still they weren't convinced.
"My brother found me first when I was 28 and he continued the mission to find mom," Raymond Abreu said. "He was just die hard, 'I'm going to find her.'"
In May this year they made a massive breakthrough. Anthony's girlfriend bought him a DNA test for his birthday. He was able to connect with a large database of historical records to find living relatives who shared the same DNA.
The test threw up a match for Wiggs' cousin, Elsie Ramirez' nephew, who he then tracked down. The man broke some stunning news -- Elsie was alive and living in Massachusetts. "I got on Facebook and just started typing her name," Anthony Wiggs said. "I ended up on a Facebook page with her best friend."
Wiggs got Elsie's cell phone number from her friend and left a voice message. His mother heard his voice on her phone just an hour later. "She was actually at the mall in the restroom," Wiggs said. "There was a lady in there next to her who heard her screaming and crying out of joy."
Still in shock, Elsie explained why she was so thrilled to the stranger and then stepped outside to call her son. Anthony had Raymond join the call. Abreu said his mother told them in Spanish "I always prayed, I always tried to look for you." Then all three cried together.
Four of her five Texas grandchildren were at the airport to greet Ramirez when she made her long-awaited arrival recently. They described the experience of being introduced to a new grandma as "surreal, exciting -- and nerve-racking."
Raymond and Anthony also have seven other half-brothers and sisters -- Elsie's other children. "My brother was like, you know what, let's just take it one step at a time," Abreu said. "Let's get mom here to Dallas. Let's concentrate on her. And next we will concentrate on our siblings. I think we made the right choice. It was too much to handle."
After being separated by almost 2,000 miles, they are excited about starting a relationship together, as a family. They spent their weekend hanging out at the pool, cooking, going out to dinner, and relaxing. Nobody could sleep, so they stayed up late chatting.
Elsie said she is eager to make up for missed moments and stay as close to her boys as possible. "It doesn't matter if we're older now, we're still her babies," Wiggs said as he smiled, receiving another kiss on the cheek from his mom.
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DNA test leads brothers to reunite with mother -- after 46 years - CNN
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Researchers encode malware in DNA, compromise DNA sequencing software – Ars Technica
Posted: at 1:47 am
Enlarge / This data could potentially contain malware.
With everyone from academics to Microsoft looking at the prospect of storing data using DNA, it was probably inevitable that someone would start looking at the security implications. Apparently, they're worse than most people might have expected. It turns out it's possible to encode computer malware in DNAand use it to attack vulnerabilities on the computer that analyzes the sequence of that DNA.
The researchers didn't find an actual vulnerability in DNA analysis softwareinstead, they specifically made a version of some software with an exploitable vulnerability to show that the risk is more than hypothetical. Still, an audit of some open source DNA analysis software shows that the academics who have been writing it haven't been paying much attention to security best practices.
DNA sequencing involves determining the precise order of the bases that make up a DNA strand. While the process that generates the sequence is generally some combination of biology and/or chemistry, once it's read, the sequence is typically stored as an ASCII string of As, Ts, Cs, and Gs. If handled improperly, that chunk of data could exploit vulnerable software to get it to execute arbitrary code. And DNA sequences tend to see a lot of software, which find overlapping sequences, align it to known genomes, look for key differences, and more.
To see whether this threat was more than hypothetical, the researchers started with a really simple exploit: store more data than a chunk of memory was intended to hold, and redirect program execution to the excess. In this case, said excess contained an exploit that would use a feature of the bash shell to connect into a remote server that the researchers controlled. If it worked, the server would then have full shell access to the machine running the DNA analysis software.
Actually implementing that in DNA, however, turned out to be challenging. DNA with Gs and Cs forms a stronger double-helix. Too many of them, and the strand won't open up easily for sequencing. Too few, and it'll pop open when you don't want it to. Repetitive DNA can form complex structures that get in the way of all the enzymes we normally use to manipulate DNA. The computer code they wanted to use, however, had lots of long runs of the same character, which made for a repetitive sequence that was very low in Gs and Cs. The company they were ordering DNA from couldn't even synthesize it.
In the end, they had to completely redesign their malware so that its translation into nucleic acids produced a DNA strand that could be synthesized and sequenced. The latter created another hurdle. The most common method of sequencing is currently limited to reading a few hundred bases at a time. Since each base has two bits of information, that means the malware has to be incredibly compact. That limits what can be done, and it explains why all this particular payload did was open up a remote connection.
Then, there was the matter of getting the malware executed. Since this was a proof of concept, the researchers made it easy on themselves: the modified an existing tool to create an exploitable vulnerability. They also made some changes to the system's configuration to make the execution of random memory locations easier (made the stack executable and turned off memory address randomization). While that makes the test environment less realistic, the goal was simply to demonstrate that DNA-delivered malware was possible.
With everything in place, they ordered some DNA online then sent it off to a facility for sequencing. When their sequences came back, they sent them through a software pipeline that included their vulnerable utility. Almost immediately, the computer running the software connected into their host, providing them with access to the machine. The malware worked.
Given how easy the authors made thingsa known vulnerability and a number of safeguards turned offdoes this really pose a threat? There's good news and bad news here.
On the good side, there's the complications of translating computer instructions into DNA that can be synthesized and sequenced. Plus there's the issue that most sequencing machines are limited in how long a sequence they can read. The machine used in this work maxes out at 300 bases, which is the equivalent of 600 bits, and most facilities keep things shorter than that. Longer read machines are available, but they're also error prone, and any errors will typically disable the malware.
But it's also common for the software used to analyze DNA to look for places where two short sequences overlap and use that to build up longer sequences. This has the potential to expand the size of the malware considerably, although less of the analysis software pipeline will be exposed to these longer, assembled sequences.
Similar issues exist with how the malware is encoded. While the authors used each base to encode two bits, DNA analysis software handles DNA in various ways internally. For example, if sequencing doesn't provide a clear indication of what a base is, other characters may be used (for example, N for any base, or R for G or A). Any software that handles these ambiguous bases has to have a more complex encoding scheme; many simply use ASCII characters.
As a result, different pieces of software will be vulnerable to different malware encodings. While that means some software will be immune, the size of the DNA analysis pipelines typically means that a dozen or more pieces of software will be run in succession. Chances are good that at least one of them will use the same encoding as the malware.
The research community's habits are also a major point of vulnerability. The analysis software was generally not written with security in mind. Using the Clang compiler's analysis tools and HP's Fortify compiler, the authors searched a collection of open source DNA analysis software for potential vulnerabilities. They found widespread use of functions that are prone to buffer overflows (strcat, strcpy, sprintf, vsprintf, gets, and scanf)about two instances for every 1,000 lines of code. "Our research suggests that DNA sequencing and analysis have not to date received significantif anyadversarial pressure," they conclude.
The second issue is how easy it is to infiltrate malicious code onto other machines via DNA. The sequencing machines have such a high capacity, work from several different labs is run on a single machine at the same time. As a result, some of the sequences returned from the machine will end up mixed into an unrelated sample. When the researchers checked with another group that had their sequencing performed at the same time, they found that the other group's results contained 27 instances of the malware.
Separately, lots of services simply allow you to send in any DNA for sequencing, putting their software at risk. And many public repositories allow people to upload their sequence for analysis by others. So, you wouldn't even have to synthesize any DNA to have your exploit analyzedyou can simply upload the text of the sequence you've designed to someone else's data repository.
None of this means that a DNA-based exploit is around the corner. But it's a healthy warning that the research community and commercial DNA companies should look to improve their practices before this does become a problem.
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Now, DNA sensor for quick pathogen detection – The Hindu
Posted: at 1:46 am
An ultrasensitive DNA sensor that can detect S. pyogenes, a bacterium which causes a wide range of diseases in about 30 minutes has been developed. The DNA chip is highly specific device for S. pyogenes. The conventional method of identification takes 18-24 hours and the basic culture test does not specifically help distinguish S. pyogenes.
From mild skin and throat infections to life-threatening toxic shock syndrome, S. pyogenes infections affect 700 million people every year. If not treated during early stages of the infection, S. pyogenes can even lead to rheumatic heart disease (heart valves damage).
The sensor was developed by scientists from CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB) and National Centre for Disease Control (NCDC) Delhi, and the results were published in the International Journal of Biological Macromolecules.
The DNA chip based sensor consists of a carbon electrode embedded with gold nanoparticles. By means of a bioinformatics study, the researchers were able to design probes which are specific for S. pyogenes.
The working electrode surface of the device is attached with several small-sized, single-stranded DNA probe specific to the pathogen. When patients DNA, isolated from throat swabs, are placed on the surface, they bind to the complementary single-stranded DNA on the device and an electrochemical change is seen. This is measured using a differential pulse voltammetry.
Identification of pathogen
For confirmation, traditional culture test was used and the results matched with the DNA sensor. The sensor is highly sensitive and could detect even 60-65 bacteria in a 6 microlitre sample. It could identify the pathogen even at very low concentrations of DNA. We were able to get a peak with a concentration of even 0.001nanogram per 6 microlitre, explains Swati Singh from IGIB and the first author of the paper.
The sensor was found to be stable for 12 months with only 10% loss in initial current peak on storage at 4 degree C. We are working on construction of different biosensors for different pathogens. Early and quick diagnosis can help in preventing the diseases and seek medical treatment at the early stage of infection, adds Dr. Ashok Kumar, Chief Scientist/Professor (AcSIR) at IGIB and corresponding author of the paper.
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Genome leader Illumina expands again in San Diego – The San Diego Union-Tribune
Posted: at 1:46 am
Like a fast-growing child constantly outgrowing clothes, biotech giant Illumina has trouble keeping up with its continued expansion.
So on Monday, the San Diego genome sequencing leader is scheduled to open a new addition a 7-acre, 316,000 square-foot complex called the i3 campus. Illumina considers it an extension of its headquarters, less than a mile away in the University Town Center area.
Consisting of three buildings refitted for Illuminas needs, the i3 campus emphasizes openness, with ample windows to the outside and an open-style office space inside. Amenities include a gym and a restaurant called Salt + Air.
And there are meeting rooms lots of meeting rooms. Larger rooms, for formal presentations, can be reserved. Smaller ones, where one or two people can sit, are available on the fly for the innumerable spontaneous discussions that seem to be baked into Illuminas DNA.
Employees manage their own day and calendars, so we infused the i3 workplace with open and non-bookable places for employees to work these can be visitors from the main HQ campus or employees from another site, said Jenny Durbin, the companys global facilities manager. An employee can choose to work at i3 even if their team or department is based at the main campus.
Illumina employs almost 7,000 people, nearly 3,000 of them in San Diego. Its stock is valued at more than $28 billion, making it by far the highest valued biotech in San Diego.
In January 2014, Illumina made international headlines by bringing down the cost of sequencing a human genome to below $1,000, with its HiSeq X Ten Sequencing System. And this January, the company announced machines in its NovaSeq line that can reduce the time to process a human genome to an average rate of one per hour, when many are processed in large batches.
As a result of such advances, Illumina dominates the market for DNA sequencers. It also leverages genomic technology into such fields as prenatal testing.
Since its impossible to know what scientific research will lead to new opportunities, Illumina makes sure its employees have flexibility, Durbin said. As biomedical research unveils new breakthroughs, Illumina races to translate the research into new products to serve the field, in government, academic and medical applications.
The i3 campus was developed by BioMed Realty, designed by the Seattle architectural firm of Perkins + Will, and built by McCarthy contractors. Tucked onto seven acres at the east end of Executive Drive, its cantilevered buildings perched like hawks over Interstate 805.
Theres a common theme working up and down the coast, said design principal Ryan Bussard, looking for innovation in architecture, tying together site design as well as architecture and collaboration spaces. The indoor and outdoor down here you can really take advantage of that year-round. Its pretty unique.
BioMed Realty held a design competition in 2011 that Perkins + Will won, five years before Illumina signed a lease for the property, and the architects and developers had to conceive a building before the users needs were known.
One of the first decisions was to demolish a never-occupied building and locate parking underground to gain more above-ground usable space.
The siting of the building was kind of a invert of the traditional, Bussard said.
That cost more but yielded highly valued space, including a 33,500-square-foot courtyard.
The second decision was to build three concrete-and-glass buildings and cantilever them out toward I-805 as much as 30 feet beyond the lower floors. The effect is to float above the landscaped fire lane where the company will host its first big event next month.
Its almost weightless, he said.
The local inspirations? The Salk Institute and the J. Craig Venter Institute on Torrey Pines Mesa. About 40,000 cubic yards of smooth white concrete make up the structure, rather than a more traditional steel-and-glass framework.
That eliminated the need to locate elevators, bathrooms and other core facilities in the middle of the buildings and increased the flexibility of each floors layout.
The third decision was to set aside half the building to be used for lab space on the interiors and administrative space around the exterior walls. But Illumina chose to make the entire building into office space a shift that could be reversed in the future.
We build flexible space for the infrastructure to support, Bussard said.
Inside the three buildings, the finance, marketing and other company executives will work to turn researchers inventions and findings into products and services.
Perkins + Will designers took the companys philosophy of work anywhere and created interior design layouts that decouple staff from their desktop phones, computers and potted plants.
Large and small meetings will be scheduled in a variety of ground-floor spaces in Building B, located to the right of the campus entrance. One conference room can be extended to about 120 feet in length and voice-sensitive cameras can transmit the proceedings off campus.
A smaller plaza lounge at the end of the building offers a more informal space in a midcentury modern, 60s residential look. Durbin, the global facilities manager, called the approach resimercial a mashup of residential and commercial design.
Its a blend between formal spaces and a more home-like space, she said.
To orient employees no matter where they work, the same colors are being used floor by floor the first floor is pumpkin orange, the second is blue and the third green. Abstract carpet patterns complement the color scheme.
Its important to have innovation and consistency, said Norm Fjeldheim, senior vice president, chief information officer and head of global facilities.
Some employees will have assigned desks that can be adjusted for standing or sitting, while others can move day to day, depending the task at hand. At night they can store their personal items in lockers. For private phone conversations, there are 60 phone booths in the complex but bring your own cell phone that links into the buildings WiFi network.
Those desks and phone booths will be used by people not only from San Diego, but from around the world.
Besides San Diego, Illumina has offices in Hayward, Santa Clara, San Francisco, Redwood City, Madison, Wis.; and internationally in Victoria, Australia; Shangai and Beijing; Tokyo; So Paulo; Eindhoven, the Netherlands; Chesterford and Fulbourn, United Kingdom; Singapore; and Victoria, Canada.
As a company with a worldwide presence, Illumina uses technology to bridge the gap between its widespread locations, said Durbin said.
I feel as an employee working across the globe that my team members and colleagues at the other sites feel just as close to me as my team mates here, because we make the efforts to use the technology (Jabber, message, box, video and teleconferencing) to bridge the distance, Durbin said.
In San Diego, Illuminas presence goes far beyond its direct employment. Local biomedical institutions such as Scripps Health, the J. Craig Venter Institute and Rady Childrens Hospital San Diego are Illumina customers. Illumina is also a longtime charitable supporter of Rady Childrens.
When babies show up at the hospital with unidentifiable serious illnesses, their genomes may be sequenced with Illumina products to find clues to their condition. This can save lives and prevent unneeded procedures.
Shimul Chowdhury, Rady Childrens clinical laboratory director, used to work for Illumina. As a board-certified molecular geneticist, he analyzes the genetic data from clinical reports and delivers them to physicians.
My role as a laboratory director is really to be the bridge between the laboratory who presents the reports to our physicians in a manner that they understand and that is useful for them to be able to take care of their patients, Chowdhury said.
At Illumina, he worked in the clinical laboratory, seeking to learn what information could be gleaned from a genome to make genome sequencing become routine in clinical practice. That required him to analyze patient samples and collaborate with doctors. He collaborated with Dr. Stephen Kingsmore, who heads the Rady Institute for Genomic Medicine.
As Chowdhury learned more about Rady Childrens, he decided to join the hospital to help put genomic technology into clinical practice. And his work still very much involves technology from Illumina.
Theyre providing the instruments and the reagents (supplies) to help us sequence kids, Chowdhury said. But it goes broader than that in terms of collaboration. Were taking these sequencing technologies and testing them in patients in intensive care units. So I think our feedback is valuable to them.
On a larger scale, he said Illuminas presence in San Diego draws visibility to use of the technology.
It really increases the genomics literacy of this region, which really helps us when were speaking to families, speaking to doctors, he said.
Radys uses Illuminas most advanced genomics instrument, the NovaSeq, Chowdhury said. With speed and accuracy, the instrument is important for searching for genetic causes of disease in children who may be critically ill and not have much time left.
We really view this machine as a next step in our evolution for being able to provide rapid genomes for more and more kids in San Diego and throughout the United States, he said.
Illumina expands with massive new manufacturing building
Growth slowdown sinks Illumina
Illumina's Jay Flatley named to Entrepreneur Hall of Fame
Illumina selects new CEO
Cameron's visit to Illumina continues San Diego's British biotech invasion
Illumina CEO brings entrepreneurial spirit to genomics giant
Illumina makes big push in cancer screening
Illumina's Flatley speaks of genomic future
Illumina helps doctors diagnose sick babies faster
bradley.fikes@sduniontribune.com
(619) 293-1020
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What is genome editing? – The Hindu
Posted: at 1:46 am
What is it?
In a first, researchers from the Oregon Health and Science University along with colleagues in California, China and South Korea repaired a mutation in human embryos by using a gene-editing tool called CRISPR-Cas9.
The mutation seen in the MYBPC3 gene causes a common heart condition called hypertrophic cardiomyopathy, which is marked by thickening of the heart muscle.
The mutation is seen in about one in 500 people and can lead to sudden death later in life. It is an inherited cardiac disease and the presence of even one copy of the gene can cause symptoms, which usually manifest as heart failure. Correcting the mutation in the embryo ensures that the child is born healthy and the defective gene is not passed on to future generations. There is currently no cure for the condition.
How did it come about?
CRISPR-Cas9 is a system used by bacterial cells to recognise and destroy viral DNA as a form of adaptive immunity. Using components of the CRISPR system, researchers can remove, add or alter specific DNA sequences in the genome of higher organisms.
The gene editing tool has two components a single-guide RNA (sgRNA) that contains a sequence that can bind to DNA, and the Cas9 enzyme which acts as a molecular scissor that can cleave DNA. The genetic sequence of the sgRNA matches the target sequence of the DNA that has to be edited. In order to selectively edit a desired sequence in DNA, the sgRNA is designed to find and bind to the target.
Upon finding its target, the Cas9 enzyme swings into an active form that cuts both strands of the target DNA. One of the two main DNA-repair pathways in the cell then gets activated to repair the double-stranded breaks. While one of the repair mechanisms result in changes to the DNA sequence, the other is more suitable for introducing specific sequences to enable tailored repair. In theory, the guide RNA will only bind to the target sequence and no other regions of the genome.
But the CRISPR-Cas9 system can also recognise and cleave different regions of the genome than the one that was intended to be edited. These off-target changes are very likely to take place when the gene-editing tool binds to DNA sequences that are very similar to the target one. Though many studies have found few unwanted changes suggesting that the tool is probably safe, researchers are working on safer alternatives.
Why does it matter?
Along with sperm from a man with hypertrophic cardiomyopathy, the gene-editing tool was also introduced into eggs from 12 healthy women before fertilisation. In normal conditions, a piece of DNA with the correct sequence serves as a template for the repair to work, although the efficiency can be significantly low. Instead of the repair template that was provided by the researchers, the cells used the healthy copy of the DNA from the egg as a template. This came as a big surprise.
Normally, if sperm from a father with one mutant copy of the gene is fertilized in vitro with normal eggs, 50% of the embryos would inherit the condition. When the gene-editing tool was used, 42 out of the 58 embryos did not carry the mutation. The remaining 16 embryos had unwanted additions or deletions of DNA.
Thus the probability of inheriting the healthy gene increased from 50 to 72.4%. There was no off-target snipping of the DNA. According to Nature, the edited embryos developed similarly to the control embryos, with 50% reaching an early stage of development (blastocyst). This indicates that editing does not block development.
What next?
Clinical trials are under way in China and in the U.S. to use this tool for treating cancer. In May this year, it was shown in mice that it is possible to shut down HIV-1 replication and even eliminate the virus from infected cells. In agriculture, a new breed of crops that are gene-edited will become commercially available in a few years. In February this year, the National Academy of Sciences (NAS) and the National Academy of Medicine said scientific advances make gene editing in human reproductive cells a realistic possibility that deserves serious consideration.
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Scientists edit pig genome with goal of human organ transplants – CNN
Posted: at 1:46 am
Using the genome-editing technology CRISPR, scientists deactivated a family of retroviruses within the pig genome overcoming a large hurdle in the path to the transplant of pig organs into humans.
Transplantation from one species to another -- xenotransplantation -- holds "great promise," the American and Chinese research team believes.
Retroviruses carry their genetic blueprint in the form of ribonucleic acid (or RNA) and transcribe this into deoxyribonucleic acid, commonly known as DNA. This is a reverse of the usual transcription process, which flows from DNA to RNA. This reversal makes it possible for retrovirus genes not only to infect cells but to become permanently incorporated into a cell's genome.
In particular, the pig genome is known to carry porcine endogenous retroviruses (or PERVs), which are capable of transmitting diseases, including cancers, into humans. The presence of these PERVs means pig organs cannot now be safely transplanted into humans.
But George Church of MIT's Broad Institute and Harvard, Dong Niu of Zhejiang University and their colleagues demonstrated a new method for deactivating the retroviruses in a pig cell line as a way to eliminate the transfer of PERVs to human cells.
First, the researchers proved that PERVs can be transmitted from pig to human cells and transmitted among human cells, even in conditions in which the fresh human cells have no prior exposure to pig cells.
Next, the team created a map of the PERVs in the genome of pig fibroblast (connective tissue) cells. Having identified a total of 25 PERVs, the science team used CRISPR to edit out -- or deactivate -- all those gene sites.
The scientists grew clone cells of these edited cells but were unable to cultivate one with greater than 90% of the PERVs deleted. But they added "ingredients" during the gene modification process -- including both growth factors and growth inhibitors -- and finally succeeded.
The new cells had 100% of the PERVs deactivated.
From here, the researchers produced PERV-inactivated embryos and implanted them into sows. The resulting piglets exhibited no signs of PERVs.
Dr. Ian McConnell, emeritus professor of veterinary science at the University of Cambridge, sees the research as a "promising first step." McConnell, who was not involved in the study, added that "it remains to be seen whether these results can be translated into a fully safe strategy in organ transplantation."
Formidable obstacles remain "in overcoming immunological rejection and physiological incompatibility of pig organs in humans," he said.
Scientists have been introducing human cells into animals to create models of diseases for decades, yet the 2009 policy suspended funding for chimera-based research due to ethical concerns.
With the advance of both stem cell and gene editing technologies, the ability to create more sophisticated animal-human chimeras raised concerns. Worries include human cells populating the brain of an animal thus humanizing that animal. Alternatively, human cells populating the germline of an animal could enable human genes to pass onto offspring.
The National Institutes of Health hopes a revised policy will enable research to continue -- safely.
The new research supports the value of using CRISPR to deactivate PERVs and so brings pig organs one step closer to safe transplantation, concluded the scientists.
Though more research is needed, they believe the "PERV-inactivated pig" can serve as a foundation strain that might be further engineered to "provide safe and effective organ and tissue resources" for transplantation into humans.
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