First ever pictures of single proteins thanks to graphene sheet

(Image credit: Jean-Nicolas Longchamp of the University of Zurich, Switzerland)

You’d think twice about snapping a selfie if the camera flash was bright enough to burn your skin off. Biologists face a similar problem when studying proteins under the microscope, as modern imaging techniques can destroy the molecules. Now graphene – the ultra-thin form of carbon – has come to the rescue, and delivered the very first pictures of a single protein.

Taking pictures of proteins lets us understand their structure and functions. This is important for treating diseases in which proteins go wrong, such as Alzheimer’s. But imaging methods such as X-ray crystallography or cryo-electron microscopy rely on averaging readings from millions of molecules, giving us a blurry view.

Averaging is needed because illuminating molecules with X-rays or high-energy electrons can damage the protein, meaning you may not get the full picture from a single image, and also because it’s tricky to keep a single molecule in one place long enough to take its picture. Now Jean-Nicolas Longchamp of the University of Zurich, Switzerland, and his colleagues have come up with a way to do just that.

They start by spraying a solution of the proteins on to a sheet of graphene, fixing the proteins in place. Then they place this under an electron holographic microscope, which uses interference patterns between electrons to produce an image.

Handy slide

This kind of instrument relies on low-energy electrons that don’t damage the protein. The snag is that they are also less able to penetrate through to the microscope’s detector. This is where graphene comes in handy. “In optical microscopy you have a glass slide. For our electron microscopy we had to find a substrate thin enough to have the electrons passing through,” says Longchamp.

The team tested their method on a range of protein molecules, all just a few nanometres in size, such as the haemoglobin found in red blood cells. The results agreed well with molecular models derived from X-ray crystallography (see image below), suggesting the images are accurate.

(Image credit: Jean-Nicolas Longchamp of the University of Zurich, Switzerland)

Now they plan to snap pictures of other molecules that can’t be imaged with existing techniques, and hope eventually to contribute to new medical treatments. “There are some diseases which are related to the wrong structure of certain proteins,” says Longchamp. “In the future, we could image the difference in the structure of a healthy person and a person who has a disease.”

Reference: arxiv.org/abs/1512.08958

ORIGINAL: New Scientist

8 January 2016

DNA Survives Re-Entry Into Earth's Atmosphere

photo credit: Adrian Mettauer. When the TEXUS-49 sounding rocket launched it carried DNA coatings on the outside of its payload

Double-stranded DNA molecules applied to the outside of a rocket payload have survived being blasted into space: they briefly entered near total vacuum and returned through the atmosphere. At the end of this, the molecules could still transfer genetic information.

Contrary to some misunderstandings, the Rosetta mission did not find DNA on Comet Churyumov-Gerasimenko 67P. It did however find organic molecules. This revived discussion of the possibility, known as “panspermia” that life is distributed around the galaxy through molecules on comets or asteroids.

One of the challenges to this idea has been the question of whether something as complex as DNA could survive the extreme heat generated when entering the atmosphere. Exposure to cosmic rays or solar radiation while unprotected by the atmosphere represents another challenge to the theory.

However, the concept is looking more credible after a team from the University of Zurich pipetted DNA onto the outside of the TEXUS-49 sounding rocket, and collected it again after re-entry. They found the DNA could be inserted into bacteria and connective tissue cells and still function.

Dr. Cora Thiel came up with the idea of the experiment while planning to use TEXUS-49's payload to study how gene expression changes in human cells in zero gravity. She started thinking about the biosignatures, which she describes as “molecules that can prove the existence of past or present extraterrestrial life.”

The outside of the same rocket looked like a particularly tough test – DNA cocooned inside an asteroid might have a better chance of surviving than something on a rocket's metallic surface.

Reporting in PLOS ONE, Thiel used DNA carrying a green fluorescent protein and an antibiotic resistance cassette and applied the material both on the front surface of the payload and in more protected spots at the bottom and in grooves where screws were inserted.

Gas temperatures at the front of the craft reached over 1000° C. Even inside, it got to 130° C. Some of the DNA had burned off, but 53% was recovered from the payload bottom and as much as 35% was intact enough to produce both fluorescent proteins and antibiotic resistance when inserted into E. coli. Control areas had no detectable DNA, eliminating the possibility of contamination after the return to Earth. Mutation rates were low.

Thiel and her co-authors note that the findings are important for future missions to other planets or moons. “For these missions, it is essential to know whether the detected biomarkers definitely originate from the analysed site or if they could be potential contamination from “stowaways” which traveled as hitchhikers on the spacecraft or analytical equipment,” they argue. Knowing just what DNA can survive will help future projects decide what scrubbing needs to be done before launch.

The flight was only 13 minutes long, so there was no time to see how the DNA stood up to the radiation in space, but the capacity to survive the heat of re-entry could reshape thinking.

ORIGINAL: IFLScience

by Stephen Luntz

November 27, 2014

Switzerland Creates Secure Test Site for GM Crops

ORIGINAL: Science Magazine

by Jop de Vrieze

28 February 2013

Secure site. Switzerland will provide security for field trials of genetically modified crops at this research station near Zurich. Credit: Wikimedia

The Swiss government will create a permanently protected area on federal land for experiments with genetically modified (GM) crops. The goal is to enable researchers to run experimental trials without running the risk that the fields will be vandalized and to reduce costs associated with security.

In a paper published today in the journal Trends in Biotechnology, scientists from the Agroscope Reckenholz-Tänikon research station and the University of Zurich detail the plan, which was approved by the Swiss Parliament and officially announced on 7 February.

GM crops are controversial in Europe, and European law requires scientists to notify the public about the precise locations of the fields where they are running experiments. This has led to protests and sometimes vandalism at more than 100 European trials since 2010. One result is that the number of GM field experiments conducted in the European Union dropped from about 250 per year in the late 1990s to fewer than 50 in 2011, the researchers report. In Switzerland, researchers have submitted just six applications for field experiments with GM plants since the late 1990s; authorities rejected two in 1999 because "the social and environmental impacts compared to any possible economic benefits were clearly too high."

In a bid to make such experiments easier, the Swiss Federal Council approved spending €600,000 annually from 2014 to 2017 to create a protected field site of approximately three hectares at the Reckenholz research station, 10 kilometers north of Zurich. Researchers will initially use it to test GM wheat with resistance to powdery mildew, a fungal disease, but they could ultimately plant other crops such as potatoes.

The Reckenholz site is already being used for GM experiments and other types of research. In 2008, a group of more than 30 masked activists threatened researchers at a nearby field site and destroyed about one-third of their experimental plants. In 2009, the researchers used grant funds to install three surveillance cameras, build a double fence with barbed wire and motion sensors, and hire security guards who kept a day-round watch.

The study released today estimates that Swiss researchers running recent GM trials spent 78% of their research funds on security. Now, the Swiss government will carry those costs at the Reckenholz site, enabling researchers to use more of their grants for science.

The move shows that legislators believe approved GM experiments "should be protected and that the research agenda should not be determined by vandals," writes Michael Winzeler, a co-author of the paper and a senior researcher at the Reckenholz station, in an e-mail to ScienceInsider.

The plan comes 5 years after two plant scientists of the University of Leeds in the United Kingdom, Peter Urwin and Howard Atkinson, called for protection of European transgenic crop research in a letter to Nature.

Atkinson says he is pleased with the Swiss plan: "You can't have a policy based on evidence if the data cannot be collected. This site will be good for that."

The Swiss government and public do not have a pro-GM reputation. In 2005, voters approved a 5-year moratorium on the commercial use of GM products, which has been extended until 2017. The moratorium includes an exception for scientific research.

"Still, that record suggests that there is no demand among Swiss citizens for GM plants on their plates, says Marianne Kuenzle, GM specialist at the environmental group Greenpeace Switzerland, which opposes GM technologies. "This field site is a waste of money. If you look at this symbolically, the fact that these studies will happen behind fences shows that there is no public acceptation of this technology." The group says it will scrutinize applications to perform GM crop trials and consider ways to prevent the establishment of the field site.

EuropaBio, the European association for bio-industries, says the Swiss move is both good and bad news. "The biotech industry welcomes this possibility to carry out research but laments that it has to happen under such conditions," the group wrote in a statement. "The need for protected field sites is a sad reflection of the power of anti-science groups, who prevent public and private research to be done in Europe."

Anne Glover, the European Commission's chief scientific adviser, says she strongly supports controlled field trials of GM plants. "[I]t is the only way we can gather evidence on any adverse impacts they may have on humans, animals and the environment as well as gauge their efficacy," she wrote in a statement. "Citizens deserve complete transparency, but they also deserve the possibility to use the best science available to meet some of the most pressing challenges of the 21st century."

zBox4, supercomputer fabrication at ITP, University of Zurich

ORIGINAL: Institute for Theoretical Physics at the University of Zurich, Switzerland ZBox4

The fourth generation of self-made supercomputer at the ITP represents the first real design update to the original zBox1 which was built in 2002. The number of cores and amount of memory was increased substantially over zBox3 and the very aging SCI Network replaced by QDR Infiniband. From the 576 cores (Intel Core2) and 1.3 TB RAM of zBox3, we now have 3072 cores (Intel Sandy Bridge E5) and 12 TB of RAM. While zBox3 was an upgrade of the main boards, CPUs and memory without making any design changes, zBox4 involved completely redesigning the platters which now each hold 4 nodes. The special rack which houses these platters was also improved with addition of a special nozzle to improve airflow and cleaning up the way cables are routed.

Planning for zBox4 began in the Spring of 2011, but these plans were partially scrapped in the late Fall of 2011 to await the arrival the Intel Sandy Bridge E5 chip with 8 cores and 4 memory channels per chip and main boards to support it. Serious planning began again in the Spring of 2012 and construction began end of September 2012. The dismantling of zBox3 and the construction of zBox4 was performed by volunteer students, postdocs and friends of the Institute, with even a few professors lending a helping hand.

Specifications

Hardware

• CPUs: 384 Intel Xeon E5-2660 (8 cores @ 2.2 GHz, 95 W), 3072 cores in total
• Main Boards: 192 Supermicro X9DRT-IBQF (2 CPUs per node) on-board QDR Infiniband
• RAM: Hynix DDR3-1600, 4 GB/core, 64 GB/node, 12.3 TB in total
• SSD: 192 OCZ 128 GB high performance Vertex 4 drives, 24.6 TB in Total
• HPC Network: QLogic/Intel QDR Infiniband in 2:1 fat tree (9 leaf and 3 core switches)
• Gbit Ethernet and seerate dedicated 100 Mbit management networks
• Power usage (full load): 44 kW
• Dimensions (L x W x H): 1.5m x 1.5m x 1.7m
• Number of Cables: Power: 112 IB: 300 Ethernet: 388
• Cost: under 750'000 CHF (797,000 USD)

System Configuration

• OS: Scientific Linux version 6.3
• Queue System: Slurm
• Swap: 8 GB on node-local SSD drive
• Temp Files: 110 GB on node-local SSD drive
• Booting: from node-local SSD, or over Ethernet
• Storage System (existing)
• Capacity: 684 TB formatted Raid-6
• Lustre file system with 50 OSTs
• 342 x 1.5 TB HDD and 171 x 2.0 TB HDD
• Physical dimensions: 48 standard rack units
• 10 Gb Ethernet and 40 Gb (QDR) Infiniband
• 3 Controllers using Intel E5645 2.4 GHz CPUs
• Tape Robot: Capacity: 800 TB, 437 tape slots
• 4 x LTO-5 drives and 2 x LTO-3 drives
• 54 TB high speed tape cache (108 TB raw storage)
• 40 Gb (QDR) Infiniband connected

The zBox4 is the latest upgrade to the famous zBox supercomputer. Located in the Institute for Theoretical Physics at the University of Zurich, Switzerland, the zBox features a custom rack design that houses 3,072 2.2GHz Intel Xeon cores and over 12TB of RAM. Each node is connected to a high speed Infiniband network, that enables researchers to perform cutting edge parallel N-body simulations of galaxy, star, and planet formation. The GHalo simulation featured in this video has over 3 billion particles and models the formation of a dark matter halo similar to that containing our own Milky Way galaxy.

Find the full details at http://www.zBox4.com

A full length video of the simulation can be found here http://youtu.be/Ty7jN-hzb-E