Tag Archives: Duke University

Doing math in a test tube using analog DNA

Basically, scientists at Duke University (US) have created an analog computer at the nanoscale, which can perform basic arithmetic. From an Aug. 23, 2016 news item on ScienceDaily,

Often described as the blueprint of life, DNA contains the instructions for making every living thing from a human to a house fly.

But in recent decades, some researchers have been putting the letters of the genetic code to a different use: making tiny nanoscale computers.

In a new study, a Duke University team led by professor John Reif created strands of synthetic DNA that, when mixed together in a test tube in the right concentrations, form an analog circuit that can add, subtract and multiply as they form and break bonds.

Rather than voltage, DNA circuits use the concentrations of specific DNA strands as signals.

An Aug. 23, 2016 Duke University news release (also on EurekAlert), which originated the news item, describes how most DNA-based circuits operate and what makes the one from Duke different,

Other teams have designed DNA-based circuits that can solve problems ranging from calculating square roots to playing tic-tac-toe. But most DNA circuits are digital, where information is encoded as a sequence of zeroes and ones.

Instead, the new Duke device performs calculations in an analog fashion by measuring the varying concentrations of specific DNA molecules directly, without requiring special circuitry to convert them to zeroes and ones first.

Unlike the silicon-based circuits used in most modern day electronics, commercial applications of DNA circuits are still a long way off, Reif said.

For one, the test tube calculations are slow. It can take hours to get an answer.

“We can do some limited computing, but we can’t even begin to think of competing with modern-day PCs or other conventional computing devices,” Reif said.

But DNA circuits can be far tinier than those made of silicon. And unlike electronic circuits, DNA circuits work in wet environments, which might make them useful for computing inside the bloodstream or the soupy, cramped quarters of the cell.

The technology takes advantage of DNA’s natural ability to zip and unzip to perform computations. Just like Velcro and magnets have complementary hooks or poles, the nucleotide bases of DNA pair up and bind in a predictable way.

The researchers first create short pieces of synthetic DNA, some single-stranded and some double-stranded with single-stranded ends, and mix them in a test tube.

When a single strand encounters a perfect match at the end of one of the partially double-stranded ones, it latches on and binds, displacing the previously bound strand and causing it to detach, like someone cutting in on a dancing couple.

The newly released strand can in turn pair up with other complementary DNA molecules downstream in the circuit, creating a domino effect.

The researchers solve math problems by measuring the concentrations of specific outgoing strands as the reaction reaches equilibrium.

To see how their circuit would perform over time as the reactions proceeded, Reif and Duke graduate student Tianqi Song used computer software to simulate the reactions over a range of input concentrations. They have also been testing the circuit experimentally in the lab.

Besides addition, subtraction and multiplication, the researchers are also designing more sophisticated analog DNA circuits that can do a wider range of calculations, such as logarithms and exponentials.

Conventional computers went digital decades ago. But for DNA computing, the analog approach has its advantages, the researchers say. For one, analog DNA circuits require fewer strands of DNA than digital ones, Song said.

Analog circuits are also better suited for sensing signals that don’t lend themselves to simple on-off, all-or-none values, such as vital signs and other physiological measurements involved in diagnosing and treating disease.

The hope is that, in the distant future, such devices could be programmed to sense whether particular blood chemicals lie inside or outside the range of values considered normal, and release a specific DNA or RNA — DNA’s chemical cousin — that has a drug-like effect.

Reif’s lab is also beginning to work on DNA-based devices that could detect molecular signatures of particular types of cancer cells, and release substances that spur the immune system to fight back.

“Even very simple DNA computing could still have huge impacts in medicine or science,” Reif said.

Here’s a link to and a citation for the paper,

Analog Computation by DNA Strand Displacement Circuits by Tianqi Song, Sudhanshu Garg, Reem Mokhtar, Hieu Bui, and John Reif. ACS Synth. Biol., 2016, 5 (8), pp 898–912 DOI: 10.1021/acssynbio.6b00144 Publication Date (Web): July 01, 2016

Copyright © 2016 American Chemical Society

This paper is behind a paywall.

Being solid and liquid over a range of 1000 degrees Fahrenheit means it’s perpetual ice

Duke University researchers along with their international collaborators have made an extraordinary observation. From an Aug. 3, 2016 news item on ScienceDaily,

Imagine pouring a glass of ice water and having the ice cubes remain unchanged hours later, even under a broiler’s heat or in the very back corner of the freezer.

That’s fundamentally the surprising discovery recently made by an international group of researchers led by an electrical engineering professor at Duke University in a paper published online in Nature Matter on July 25, 2016. But instead of a refreshing mixture of H2O in a pint glass, the researchers were working with the chemical element gallium on a nanoscopic scale.

This image shows a single gallium nanoparticle sitting on top of a sapphire base. The black sphere in the center reveals the presence of solid gallium within the liquid drop exterior. The sapphire base is important, as it is rigid with a relatively high surface energy. As the nanoparticle and sapphire try to minimize their total energy, this combination of properties drives the formation and coexistence of the two phases. Courtesy: Duke University

This image shows a single gallium nanoparticle sitting on top of a sapphire base. The black sphere in the center reveals the presence of solid gallium within the liquid drop exterior. The sapphire base is important, as it is rigid with a relatively high surface energy. As the nanoparticle and sapphire try to minimize their total energy, this combination of properties drives the formation and coexistence of the two phases. Courtesy: Duke University

An Aug. 3, 2016 Duke University news release (also on EurekAlert), which originated the news item, explains more about gallium and about this new state,

Gallium is a soft, silvery bluish metal at room temperature. Raise the heat to 86 degrees Fahrenheit, however, and it melts. Drop the temperature to subzero levels, and it becomes hard and brittle. But when gallium nanoparticles sit on top of a sapphire surface, they form a solid core surrounded by a liquid outer layer. The discovery marks the first time that this stable phase coexistence phenomenon at the nanoscale has ever been directly observed.

“This odd combination of a liquid and solid state existing together has been predicted theoretically and observed indirectly in other materials in narrow bands of specific temperatures,” said April Brown, the John Cocke Professor of Electrical and Computer Engineering at Duke. “But this finding was very unexpected, especially because of its stability over such a large temperature range.”

The temperature range Brown is referring to covers more than 1,000 degrees Fahrenheit, all the way from -135 to 980 degrees.

“At a fundamental level, this finding reveals the need to reconsider all our presumptions about solid–liquid equilibrium,” wrote Andrés Aguado, professor of theoretical, atomic and optical physics at the University of Valladolid in Spain, in a News and Views piece appearing in the same edition of Nature Matter. “At a more applied level, the results hold much promise for future nanotechnology applications.”

Gallium is an important element in electronics and is used in microwave circuits, high-speed switching circuits and infrared circuits. The discovery of this novel part-solid, part-liquid nanoparticle phase could be useful in ultraviolet sensors, molecular sensing devices and enhanced photodetectors.

Brown hopes this work is just the tip of the iceberg, as she is planning on creating a facility at Duke to investigate what other nanoparticles might have similar unexpected phase qualities.

The research was conducted in conjunction with researchers at the Institute of Nanotechnology-CNR-Italy, the University of Western Australia, the University of Melbourne and Johannes Kepler University Linz.

This is an atomic view of liquid and solid gallium coexisting in a single nanoparticle taken by a transmission electron microscope. The circular shape on the left-hand side shows gallium atoms in an organized, crystalline, solid structure, while the atoms on the right are in liquid form, showing no organized structure at all. Courtesy: Duke University

This is an atomic view of liquid and solid gallium coexisting in a single nanoparticle taken by a transmission electron microscope. The circular shape on the left-hand side shows gallium atoms in an organized, crystalline, solid structure, while the atoms on the right are in liquid form, showing no organized structure at all. Courtesy: Duke University

Here’s a link to and a citation for the paper,

Thermally stable coexistence of liquid and solid phases in gallium nanoparticles by Maria Losurdo, Alexandra Suvorova, Sergey Rubanov, Kurt Hingerl, & April S. Brown.  Nature Materials (2016) doi:10.1038/nmat4705 Published online 25 July 2016

This paper is behind a paywall.

Korea Advanced Institute of Science and Technology (KAIST) at summer 2016 World Economic Forum in China

From the Ideas Lab at the 2016 World Economic Forum at Davos to offering expertise at the 2016 World Economic Forum in Tanjin, China that is taking place from June 26 – 28, 2016.

Here’s more from a June 24, 2016 KAIST news release on EurekAlert,

Scientific and technological breakthroughs are more important than ever as a key agent to drive social, economic, and political changes and advancements in today’s world. The World Economic Forum (WEF), an international organization that provides one of the broadest engagement platforms to address issues of major concern to the global community, will discuss the effects of these breakthroughs at its 10th Annual Meeting of the New Champions, a.k.a., the Summer Davos Forum, in Tianjin, China, June 26-28, 2016.

Three professors from the Korea Advanced Institute of Science and Technology (KAIST) will join the Annual Meeting and offer their expertise in the fields of biotechnology, artificial intelligence, and robotics to explore the conference theme, “The Fourth Industrial Revolution and Its Transformational Impact.” The Fourth Industrial Revolution, a term coined by WEF founder, Klaus Schwab, is characterized by a range of new technologies that fuse the physical, digital, and biological worlds, such as the Internet of Things, cloud computing, and automation.

Distinguished Professor Sang Yup Lee of the Chemical and Biomolecular Engineering Department will speak at the Experts Reception to be held on June 25, 2016 on the topic of “The Summer Davos Forum and Science and Technology in Asia.” On June 27, 2016, he will participate in two separate discussion sessions.

In the first session entitled “What If Drugs Are Printed from the Internet?” Professor Lee will discuss the future of medicine being impacted by advancements in biotechnology and 3D printing technology with Nita A. Farahany, a Duke University professor, under the moderation of Clare Matterson, the Director of Strategy at Wellcome Trust in the United Kingdom. The discussants will note recent developments made in the way patients receive their medicine, for example, downloading drugs directly from the internet and the production of yeast strains to make opioids for pain treatment through systems metabolic engineering, and predicting how these emerging technologies will transform the landscape of the pharmaceutical industry in the years to come.

In the second session, “Lessons for Life,” Professor Lee will talk about how to nurture life-long learning and creativity to support personal and professional growth necessary in an era of the new industrial revolution.

During the Annual Meeting, Professors Jong-Hwan Kim of the Electrical Engineering School and David Hyunchul Shim of the Aerospace Department will host, together with researchers from Carnegie Mellon University and AnthroTronix, an engineering research and development company, a technological exhibition on robotics. Professor Kim, the founder of the internally renowned Robot World Cup, will showcase his humanoid micro-robots that play soccer, displaying their various cutting-edge technologies such as imaging processing, artificial intelligence, walking, and balancing. Professor Shim will present a human-like robotic piloting system, PIBOT, which autonomously operates a simulated flight program, grabbing control sticks and guiding an airplane from take offs to landings.

In addition, the two professors will join Professor Lee, who is also a moderator, to host a KAIST-led session on June 26, 2016, entitled “Science in Depth: From Deep Learning to Autonomous Machines.” Professors Kim and Shim will explore new opportunities and challenges in their fields from machine learning to autonomous robotics including unmanned vehicles and drones.

Since 2011, KAIST has been participating in the World Economic Forum’s two flagship conferences, the January and June Davos Forums, to introduce outstanding talents, share their latest research achievements, and interact with global leaders.

KAIST President Steve Kang said, “It is important for KAIST to be involved in global talks that identify issues critical to humanity and seek answers to solve them, where our skills and knowledge in science and technology could play a meaningful role. The Annual Meeting in China will become another venue to accomplish this.”

I mentioned KAIST and the Ideas Lab at the 2016 Davos meeting in this Nov. 20, 2015 posting and was able to clear up my (and possible other people’s) confusion as to what the Fourth Industrial revolution might be in my Dec. 3, 2015 posting.

Frankenstein and Switzerland in 2016

The Frankenstein Bicentennial celebration is in process as various events and projects are now being launched. In a Nov. 12, 2015 posting I made mention of the Frankenstein Bicentennial Project 1818-2018 at Arizona State University (ASU; scroll down about 15% of the way),

… the Transmedia Museum (Frankenstein Bicentennial Project 1818-2018).  This project is being hosted by Arizona State University. From the project homepage,

No work of literature has done more to shape the way people imagine science and its moral consequences than Frankenstein; or The Modern Prometheus, Mary Shelley’s enduring tale of creation and responsibility. The novel’s themes and tropes—such as the complex dynamic between creator and creation—continue to resonate with contemporary audiences. Frankenstein continues to influence the way we confront emerging technologies, conceptualize the process of scientific research, imagine the motivations and ethical struggles of scientists, and weigh the benefits of innovation with its unforeseen pitfalls.

The Frankenstein Bicentennial Project will infuse science and engineering endeavors with considerations of ethics. It will use the power of storytelling and art to shape processes of innovation and empower public appraisal of techno-scientific research and creation. It will offer humanists and artists a new set of concerns around research, public policy, and the ramifications of exploration and invention. And it will inspire new scientific and technological advances inspired by Shelley’s exploration of our inspiring and terrifying ability to bring new life into the world. Frankenstein represents a landmark fusion of science, ethics, and literary expression.

The bicentennial provides an opportunity for vivid reflection on how science is culturally framed and understood by the public, as well as our ethical limitations and responsibility for nurturing the products of our creativity. It is also a moment to unveil new scientific and technological marvels, especially in the areas of synthetic biology and artificial intelligence. Engaging with Frankenstein allows scholars and educators, artists and writers, and the public at large to consider the history of scientific invention, reflect on contemporary research, and question the future of our technological society. Acting as a network hub for the bicentennial celebration, ASU will encourage and coordinate collaboration across institutions and among diverse groups worldwide.

2016 Frankenstein events

Now, there’s an exhibition in Switzerland where Frankenstein was ‘born’ according to a May 12, 2016 news item on phys.org,

Frankenstein, the story of a scientist who brings to life a cadaver and causes his own downfall, has for two centuries given voice to anxiety surrounding the unrelenting advance of science.

To mark the 200 years since England’s Mary Shelley first imagined the ultimate horror story during a visit to a frigid, rain-drenched Switzerland, an exhibit opens in Geneva Friday called “Frankenstein, Creation of Darkness”.

In the dimly-lit, expansive basement at the Martin Bodmer Foundation, a long row of glass cases holds 15 hand-written, yellowed pages from a notebook where Shelley in 1816 wrote the first version of what is considered a masterpiece of romantic literature.

The idea for her “miserable monster” came when at just 18 she and her future husband, English poet Percy Bysshe Shelley, went to a summer home—the Villa Diodati—rented by literary great Lord Byron on the outskirts of Geneva.

The current private owners of the picturesque manor overlooking Lake Geneva will also open their lush gardens to guided tours during the nearby exhibit which runs to October 9 [May 13 – Oct. 9, 2016].

While the spot today is lovely, with pink and purple lilacs spilling from the terraces and gravel walkways winding through rose-covered arches, in the summer of 1816 the atmosphere was more somber.

A massive eruption from the Tambora volcano in Indonesia wreaked havoc with the global climate that year, and a weather report for Geneva in June on display at the exhibit mentions “not a single leaf” had yet appeared on the oak trees.

To pass the time, poet Lord Byron challenged the band of literary bohemians gathered at the villa to each invent a ghost story, resulting in several famous pieces of writing.

English doctor and author John Polidori came up with the idea for “The Vampyre”, which was published three years later and is considered to have pioneered the romantic vampyre genre, including works like Bram Stoker’s “Dracula”.

That book figures among a multitude of first editions at the Geneva exhibit, including three of Mary Shelley’s “Frankenstein, or the Modern Prometheus”—the most famous story to emerge from the competition.

Here’s a description of the exhibit, from the Martin Bodmer Foundation’s Frankenstein webpage,

To celebrate the 200th anniversary of the writing of this historically influential work of literature, the Martin Bodmer Foundation presents a major exhibition on the origins of Frankenstein, the perspectives it opens and the questions it raises.

A best seller since its first publication in 1818, Mary Shelley’s novel continues to demand attention. The questions it raises remain at the heart of literary and philosophical concerns: the ethics of science, climate change, the technologisation of the human body, the unconscious, human otherness, the plight of the homeless and the dispossessed.

The exposition Frankenstein: Creation of Darkness recreates the beginnings of the novel in its first manuscript and printed forms, along with paintings and engravings that evoke the world of 1816. A variety of literary and scientific works are presented as sources of the novel’s ideas. While exploring the novel’s origins, the exhibition also evokes the social and scientific themes of the novel that remain important in our own day.

For what it’s worth, I have come across analyses which suggest science and technology may not have been the primary concern at the time. There are interpretations which suggest issues around childbirth (very dangerous until modern times) and fear of disfigurement and disfigured individuals. What makes Frankenstein and the book so fascinating is how flexible interpretations can be. (For more about Frankenstein and flexibility, read Susan Tyler Hitchcock’s 2009 book, Frankenstein: a cultural history.)

There’s one more upcoming Frankenstein event, from The Frankenstein Bicentennial announcement webpage,

On June 14 and 15, 2016, the Brocher Foundation, Arizona State University, Duke University, and the University of Lausanne will host “Frankenstein’s Shadow,” a symposium in Geneva, Switzerland to commemorate the origin of Frankenstein and assess its influence in different times and cultures, particularly its resonance in debates about public policy governing biotechnology and medicine. These dates place the symposium almost exactly 200 years after Mary Shelley initially conceived the idea for Frankenstein on June 16, 1816, and in almost exactly the same geographical location on the shores of Lake Geneva.

If you’re interested in details such as the programme schedule, there’s this PDF,

Frankenstein¹s_ShadowConference

Enjoy!

Molecular ‘lightbulb’ could mean new form of magnetic resonance imaging (MRI)

A new technique promises to show body chemistry in action according to a March 25, 2016 news item on phys.org,

Duke University researchers have taken a major step towards realizing a new form of MRI that could record biochemical reactions in the body as they happen.

In the March 25 issue of Science Advances, they report the discovery of a new class of molecular tags that enhance MRI signals by 10,000-fold and generate detectable signals that last over an hour. The tags are biocompatible and inexpensive to produce, paving the way for widespread use of magnetic resonance imaging (MRI) to monitor metabolic processes of conditions like cancer and heart disease in real time.

“This represents a completely new class of molecules that doesn’t look anything at all like what people thought could be made into MRI tags,” said Warren S. Warren, James B. Duke Professor and Chair of Physics at Duke, and senior author on the study. “We envision it could provide a whole new way to use MRI to learn about the biochemistry of disease.”

A March 25, 2016 Duke University news release (also on EurekAlert), which originated the news item, offers more information about the new technique,

MRI takes advantage of a property called spin, which makes the nuclei in hydrogen atoms act like tiny magnets. Applying a strong magnetic field, followed by a series of radio waves, induces these hydrogen magnets to broadcast their locations. Since most of the hydrogen atoms in the body are bound up in water, the technique is used in clinical settings to create detailed images of soft tissues like organs, blood vessels and tumors inside the body.

But the technique also has the potential to show body chemistry in action, said Thomas Theis, assistant research professor of chemistry at Duke and co-lead author on the paper. “With magnetic resonance in general, you have this unique sensitivity to chemical transformations. You can see them and track them in real time,” Theis said.

MRI’s ability to track chemical transformations in the body has been limited by the low sensitivity of the technique, which makes small numbers of molecules impossible to detect without using unattainably massive magnetic fields.

For the past decade, researchers have been developing methods to “hyperpolarize” biologically important molecules, converting them into what Warren calls magnetic resonance “lightbulbs.”

With this boosted signal, these “lightbulbs” can be detected even in low numbers. “Hyperpolarization gives them 10,000 times more signal than they would normally have if they had just been magnetized in an ordinary magnetic field,” Warren said.

While promising, Warren says these hyperpolarization techniques face two fundamental problems: incredibly expensive equipment — around 3 million dollars for one machine — and most of these molecular lightbulbs burn out in a matter of seconds.

“It’s hard to take an image with an agent that is only visible for seconds, and there are a lot of biological processes you could never hope to see,” said Warren. “We wanted to try to figure out what molecules could give extremely long-lived signals so that you could look at slower processes.”

Jerry Ortiz Jr., a graduate student at Duke and co-lead author on the paper, synthesized a series of molecules containing diazarines, a chemical structure which is composed of two nitrogen atoms bound together in a ring. Diazirines were a promising target for screening because their geometry traps hyperpolarization in a “hidden state” where it cannot relax quickly.

Using a simple and inexpensive approach to hyperpolarization called SABRE-SHEATH, in which the molecular tags are mixed with a spin-polarized form of hydrogen and a catalyst, the researchers were able to rapidly hyperpolarize one of the diazirine-containing molecules, greatly enhancing its magnetic resonance signals for over an hour.

Qiu Wang, assistant professor of chemistry at Duke and co-author on the paper, said this structure is a particularly exciting target for hyperpolarization because it has already been demonstrated as a tag for other types of biomedical imaging.

“It can be tagged on small molecules, macro molecules, amino acids, without changing the intrinsic properties of the original compound,” said Wang. “We are really interested to see if it would be possible to use it as a general imaging tag.”

The scientists believe their SABRE-SHEATH catalyst could be used to hyperpolarize a wide variety of chemical structures at a fraction of the cost of other methods.

“You could envision, in five or ten years, you’ve got the container with the catalyst, you’ve got the bulb with the hydrogen gas. In a minute, you’ve made the hyperpolarized agent, and on the fly you could actually take an image,” Warren said. “That is something that is simply inconceivable by any other method.”

The researchers have provided an artistic representation of the molecular ‘lightbulbs’,

Caption: Duke scientists have discovered a new class of inexpensive and long-lived molecular tags that enhance MRI signals by 10,000-fold. To activate the tags, the researchers mix them with a newly developed catalyst (center) and a special form of hydrogen (gray), converting them into long-lived magnetic resonance 'lightbulbs' that might be used to track disease metabolism in real time. Credit: Thomas Theis, Duke University

Caption: Duke scientists have discovered a new class of inexpensive and long-lived molecular tags that enhance MRI signals by 10,000-fold. To activate the tags, the researchers mix them with a newly developed catalyst (center) and a special form of hydrogen (gray), converting them into long-lived magnetic resonance ‘lightbulbs’ that might be used to track disease metabolism in real time. Credit: Thomas Theis, Duke University

Here’s a link to and a citation for the paper,

Direct and cost-efficient hyperpolarization of long-lived nuclear spin states on universal 15N2-diazirine molecular tags by Thomas Theis, Gerardo X. Ortiz Jr, Angus W. J. Logan, Kevin E. Claytor, Yesu Feng, William P. Huhn, Volker Blum, Steven J. Malcolmson, Eduard Y. Chekmenev, Qiu Wang, and Warren S. Warren. Science Advances  25 Mar 2016: Vol. 2, no. 3, e1501438 DOI: 10.1126/sciadv.1501438

This paper appears to be open access.

Structural colo(u)r with a twist

There’s a nice essay about structural colour on the Duke University website (h/t Nanowerk). Long time readers know my favourite piece of writing on the subject is by Cristina Luiggi for The Scientist magazine which I profiled here in a Feb. 7, 2013 posting.

This latest piece seems to have been written by Beverley Glover and Anika Radiya-Dixit and it is very good. From the Oct. 27, 2015 Duke University blog posting titled, Iridescent Beauty: Development, function and evolution of plant nanostructures that influence animal behavior,

Iridescent wings of a Morpho butterfly

Creatures like the Morpho butterfly on the leaf above appear to be covered in shimmering blue and green metallic colors. This phenomenon is called “iridescence,” meaning that color appears to change as the angle changes, much like soap bubbles and sea shells.

In animals, the physical mechanisms and function of structural color have been studied significantly as a signal for recognition or mate choice.

Glover, one of the post’s authors, is a scientist who believes there may be another reason for iridescence,

On the other hand, Beverley Glover believes that such shimmering in plants can actually influence animal behavior by attracting pollinators better than their non-iridescent counterparts. Glover,Director of Cambridge University Botanic Garden,  presented her study during the Biology Seminar Series in the French Family Science Center on Monday [Oct. 26, 2015] earlier this week.

Hibiscus Trionum

The metallic property of flowers like the Hibiscus Trionum above are generated by diffraction grating – similar to the way CD shines – to create color from transparent material.

In order to observe the effects of the iridescence on pollinators like bees, Glover created artificial materials with a surface structure of nanoscale ridges, similar to the microscopic view of a petal’s epidermal surface below.

Nanoscale ridges on a petal's epidermal surface.

In the first set of experiments, Glover and her team marked bees with paint to follow their behavior as they set the insects to explore iridescent flowers. Some were covered in a red grating – containing a sweet solution as a reward – and others with a blue iridescent grating – containing a sour solution as deterrent. The experiment demonstrated that the bees were able to detect the iridescent signal produced by the petal’s nanoridges, and – as a result – correctly identified the rewarding flowers.

It’s worth reading the Oct. 27, 2015 Duke University blog posting to just to see the pictures used to illustrate the ideas and to find out about the second experiment.

$81M for US National Nanotechnology Coordinated Infrastructure (NNCI)

Academics, small business, and industry researchers are the big winners in a US National Science Foundation bonanza according to a Sept. 16, 2015 news item on Nanowerk,

To advance research in nanoscale science, engineering and technology, the National Science Foundation (NSF) will provide a total of $81 million over five years to support 16 sites and a coordinating office as part of a new National Nanotechnology Coordinated Infrastructure (NNCI).

The NNCI sites will provide researchers from academia, government, and companies large and small with access to university user facilities with leading-edge fabrication and characterization tools, instrumentation, and expertise within all disciplines of nanoscale science, engineering and technology.

A Sept. 16, 2015 NSF news release provides a brief history of US nanotechnology infrastructures and describes this latest effort in slightly more detail (Note: Links have been removed),

The NNCI framework builds on the National Nanotechnology Infrastructure Network (NNIN), which enabled major discoveries, innovations, and contributions to education and commerce for more than 10 years.

“NSF’s long-standing investments in nanotechnology infrastructure have helped the research community to make great progress by making research facilities available,” said Pramod Khargonekar, assistant director for engineering. “NNCI will serve as a nationwide backbone for nanoscale research, which will lead to continuing innovations and economic and societal benefits.”

The awards are up to five years and range from $500,000 to $1.6 million each per year. Nine of the sites have at least one regional partner institution. These 16 sites are located in 15 states and involve 27 universities across the nation.

Through a fiscal year 2016 competition, one of the newly awarded sites will be chosen to coordinate the facilities. This coordinating office will enhance the sites’ impact as a national nanotechnology infrastructure and establish a web portal to link the individual facilities’ websites to provide a unified entry point to the user community of overall capabilities, tools and instrumentation. The office will also help to coordinate and disseminate best practices for national-level education and outreach programs across sites.

New NNCI awards:

Mid-Atlantic Nanotechnology Hub for Research, Education and Innovation, University of Pennsylvania with partner Community College of Philadelphia, principal investigator (PI): Mark Allen
Texas Nanofabrication Facility, University of Texas at Austin, PI: Sanjay Banerjee

Northwest Nanotechnology Infrastructure, University of Washington with partner Oregon State University, PI: Karl Bohringer

Southeastern Nanotechnology Infrastructure Corridor, Georgia Institute of Technology with partners North Carolina A&T State University and University of North Carolina-Greensboro, PI: Oliver Brand

Midwest Nano Infrastructure Corridor, University of  Minnesota Twin Cities with partner North Dakota State University, PI: Stephen Campbell

Montana Nanotechnology Facility, Montana State University with partner Carlton College, PI: David Dickensheets
Soft and Hybrid Nanotechnology Experimental Resource,

Northwestern University with partner University of Chicago, PI: Vinayak Dravid

The Virginia Tech National Center for Earth and Environmental Nanotechnology Infrastructure, Virginia Polytechnic Institute and State University, PI: Michael Hochella

North Carolina Research Triangle Nanotechnology Network, North Carolina State University with partners Duke University and University of North Carolina-Chapel Hill, PI: Jacob Jones

San Diego Nanotechnology Infrastructure, University of California, San Diego, PI: Yu-Hwa Lo

Stanford Site, Stanford University, PI: Kathryn Moler

Cornell Nanoscale Science and Technology Facility, Cornell University, PI: Daniel Ralph

Nebraska Nanoscale Facility, University of Nebraska-Lincoln, PI: David Sellmyer

Nanotechnology Collaborative Infrastructure Southwest, Arizona State University with partners Maricopa County Community College District and Science Foundation Arizona, PI: Trevor Thornton

The Kentucky Multi-scale Manufacturing and Nano Integration Node, University of Louisville with partner University of Kentucky, PI: Kevin Walsh

The Center for Nanoscale Systems at Harvard University, Harvard University, PI: Robert Westervelt

The universities are trumpeting this latest nanotechnology funding,

NSF-funded network set to help businesses, educators pursue nanotechnology innovation (North Carolina State University, Duke University, and University of North Carolina at Chapel Hill)

Nanotech expertise earns Virginia Tech a spot in National Science Foundation network

ASU [Arizona State University] chosen to lead national nanotechnology site

UChicago, Northwestern awarded $5 million nanotechnology infrastructure grant

That is a lot of excitement.

Nanotechnology takes the big data dive

Duke University’s (North Carolina, US) Center for Environmental Implications of Nano Technology (CEINT) is back in the news. An August 18, 2015 news item on Nanotechnology Now  highlights two new projects intended to launch the field of nanoinformatics,

In two new studies, researchers from across the country spearheaded by Duke University faculty have begun to design the framework on which to build the emerging field of nanoinformatics.

An August 18, 2015 Duke University news release on EurekAlert, which originated the news item, describes the notion of nanoinformatics and how Duke is playing a key role in establishing this field,

Nanoinformatics is, as the name implies, the combination of nanoscale research and informatics. It attempts to determine which information is relevant to the field and then develop effective ways to collect, validate, store, share, analyze, model and apply that information — with the ultimate goal of helping scientists gain new insights into human health, the environment and more.

In the first paper, published on August 10, 2015, in the Beilstein Journal of Nanotechnology, researchers begin the conversation of how to standardize the way nanotechnology data are curated.

Because the field is young and yet extremely diverse, data are collected and reported in different ways in different studies, making it difficult to compare apples to apples. Silver nanoparticles in a Florida swamp could behave entirely differently if studied in the Amazon River. And even if two studies are both looking at their effects in humans, slight variations like body temperature, blood pH levels or nanoparticles only a few nanometers larger can give different results. For future studies to combine multiple datasets to explore more complex questions, researchers must agree on what they need to know when curating nanomaterial data.

“We chose curation as the focus of this first paper because there are so many disparate efforts that are all over the road in terms of their missions, and the only thing they all have in common is that somehow they have to enter data into their resources,” said Christine Hendren, a research scientist at Duke and executive director of the Center for the Environmental Implications of NanoTechnology (CEINT). “So we chose that as the kernel of this effort to be as broad as possible in defining a baseline for the nanoinformatics community.”

The paper is the first in a series of six that will explore what people mean — their vocabulary, definitions, assumptions, research environments, etc. — when they talk about gathering data on nanomaterials in digital form. And to get everyone on the same page, the researchers are seeking input from all stakeholders, including those conducting basic research, studying environmental implications, harnessing nanomaterial properties for applications, developing products and writing government regulations.

The daunting task is being undertaken by the Nanomaterial Data Curation Initiative (NDCI), a project of the National Cancer Informatics Nanotechnology Working Group (NCIP NanoWG) lead by a diverse team of nanomaterial data stakeholders. If successful, not only will these disparate interests be able to combine their data, the project will highlight what data are missing and help drive the research priorities of the field.

In the second paper, published on July 16, 2015, in Science of The Total Environment, Hendren and her colleagues at CEINT propose a new, standardized way of studying the properties of nanomaterials.

“If we’re going to move the field forward, we have to be able to agree on what measurements are going to be useful, which systems they should be measured in and what data gets reported, so that we can make comparisons,” said Hendren.

The proposed strategy uses functional assays — relatively simple tests carried out in standardized, well-described environments — to measure nanomaterial behavior in actual systems.

For some time, the nanomaterial research community has been trying to use measured nanomaterial properties to predict outcomes. For example, what size and composition of a nanoparticle is most likely to cause cancer? The problem, argues Mark Wiesner, director of CEINT, is that this question is far too complex to answer.

“Environmental researchers use a parameter called biological oxygen demand to predict how much oxygen a body of water needs to support its ecosystem,” explains Wiesner. “What we’re basically trying to do with nanomaterials is the equivalent of trying to predict the oxygen level in a lake by taking an inventory of every living organism, mathematically map all of their living mechanisms and interactions, add up all of the oxygen each would take, and use that number as an estimate. But that’s obviously ridiculous and impossible. So instead, you take a jar of water, shake it up, see how much oxygen is taken and extrapolate that. Our functional assay paper is saying do that for nanomaterials.”

The paper makes suggestions as to what nanomaterials’ “jar of water” should be. It identifies what parameters should be noted when studying a specific environmental system, like digestive fluids or wastewater, so that they can be compared down the road.

It also suggests two meaningful processes for nanoparticles that should be measured by functional assays: attachment efficiency (does it stick to surfaces or not) and dissolution rate (does it release ions).

In describing how a nanoinformatics approach informs the implementation of a functional assay testing strategy, Hendren said “We’re trying to anticipate what we want to ask the data down the road. If we’re banking all of this comparable data while doing our near-term research projects, we should eventually be able to support more mechanistic investigations to make predictions about how untested nanomaterials will behave in a given scenario.”

Here are links to and citations for the papers,

The Nanomaterial Data Curation Initiative: A collaborative approach to assessing, evaluating, and advancing the state of the field by Christine Ogilvie Hendren, Christina M. Powers, Mark D. Hoover, and Stacey L. Harper.  Beilstein J. Nanotechnol. 2015, 6, 1752–1762. doi:10.3762/bjnano.6.179 Published 18 Aug 2015

A functional assay-based strategy for nanomaterial risk forecasting by Christine Ogilvie Hendren, Gregory V. Lowry, Jason M. Unrine, and Mark R. Wiesner. Science of The Total Environment Available online 16 July 2015 In Press, Corrected Proof  DOI: 10.1016/j.scitotenv.2015.06.100.

The first paper listed in open access while the second paper is behind a paywall.

I’m (mostly) giving the final comments to Dexter Johnson who in an August 20, 2015 posting on his Nanoclast blog (on the IEEE [Institute of Electrical and Electronics Engineers] website) had this to say (Note: Links have been removed),

It can take days for a supercomputer to unravel all the data contained in a single human genome. So it wasn’t long after mapping the first human genome that researchers coined the umbrella term “bioinformatics” in which a variety of methods and computer technologies are used for organizing and analyzing all that data.

Now teams of researchers led by scientists at Duke University believe that the field of nanotechnology has reached a critical mass of data and that a new field needs to be established, dubbed “nanoinformatics.

While being able to better organize and analyze data to study the impact of nanomaterials on the environment should benefit the field, what seems to remain a more pressing concern is having the tools for measuring nanomaterials outside of a vacuum and in water and air environments.”

I gather Christine Hendren has succeeded Mark Weisner as CEINT’s executive director.

Silver nanoparticles and wormwood tackle plant-killing fungus

I’m back in Florida (US), so to speak. Last mentioned here in an April 7, 2015 post about citrus canker and zinkicide, a story about a disease which endangers citrus production in the US, this latest story concerns a possible solution to the problem of a fungus, which attacks ornamental horticultural plants in Florida. From a May 5, 2015 news item on Azonano,

Deep in the soil, underneath more than 400 plant and tree species, lurks a lethal fungus threatening Florida’s $15 billion a year ornamental horticulture industry.

But University of Florida plant pathologist G. Shad Ali has found an economical and eco-friendly way to combat the plant destroyer known as phytophthora before it attacks the leaves and roots of everything from tomato plants to oak trees.

Ali and a team of researchers with UF’s Institute of Food and Agricultural Sciences, along with the University of Central Florida and the New Jersey Institute of Technology, have found that silver nanoparticles produced with an extract of wormwood, an herb with strong antioxidant properties, can stop several strains of the deadly fungus.

A May 4, 2015 University of Florida news release, which originated the news item, describes the work in more detail,

“The silver nanoparticles are extremely effective in eliminating the fungus in all stages of its life cycle,” Ali said. “In addition, it has no adverse effects on plant growth.” [emphasis mine]

The silver nanoparticles measure 5 to 100 nanometers in diameter – about one one-thousandth the width of a human hair. Once the nanoparticles are sprayed onto a plant, they shield it from fungus. Since the nanoparticles display multiple ways of inhibiting fungus growth, the chances of pathogens developing resistance to them are minimized, Ali said. Because of that, they may be used for controlling fungicide-resistant plant pathogens more effectively.

That’s good news for the horticulture industry. Worldwide crop losses due to phytophthora fungus diseases are estimated to be in the multibillion dollar range, with $6.7 billion in losses in potato crops due to late blight – the cause of the Irish Potato Famine in the mid-1800s when more than 1 million people died – and $1 billion to $2 billion in soybean loss.

Silver nanoparticles are being investigated for applications in various industries, including medicine, diagnostics, cosmetics and food processing.  They already are used in wound dressings, food packaging and in consumer products such as textiles and footwear for fighting odor-causing microorganisms.

Other members of the UF research team were Mohammad Ali, a visiting doctoral student from the Quaid-i-Azam University, Islamabad, Pakistan; David Norman and Mary Brennan with the University of Florida’s Plant Pathology-Mid Florida Research and Education Center; Bosung Kim with the University of Central Florida’s chemistry department; Kevin Belfield with the College of Science and Liberal Arts at the New Jersey Institute of Technology and the University of Central Florida’s chemistry department.

Ali’s comment about silver nanoparticles not having any adverse effects on plant growth is in contrast to findings by Mark Wiesner and other researchers at  Duke University (North Carolina, US). From my Feb. 28, 2013 posting (which also features a Finnish-Estonia study showing no adverse effects from silver nanoparticles  in crustaceans),

… there’s a study from Duke University suggests that silver nanoparticles in wastewater which is later put to agricultural use may cause problems. From the Feb. 27, 2013 news release on EurekAlert,

In experiments mimicking a natural environment, Duke University researchers have demonstrated that the silver nanoparticles used in many consumer products can have an adverse effect on plants and microorganisms.

The main route by which these particles enter the environment is as a by-product of water and sewage treatment plants. [emphasis] The nanoparticles are too small to be filtered out, so they and other materials end up in the resulting “sludge,” which is then spread on the land surface as a fertilizer.

The researchers found that one of the plants studied, a common annual grass known as Microstegium vimeneum, had 32 percent less biomass in the mesocosms treated with the nanoparticles. Microbes were also affected by the nanoparticles, Colman [Benjamin Colman, a post-doctoral fellow in Duke’s biology department and a member of the Center for the Environmental Implications of Nanotechnology (CEINT)] said. One enzyme associated with helping microbes deal with external stresses was 52 percent less active, while another enzyme that helps regulate processes within the cell was 27 percent less active. The overall biomass of the microbes was also 35 percent lower, he said.

“Our field studies show adverse responses of plants and microorganisms following a single low dose of silver nanoparticles applied by a sewage biosolid,” Colman said. “An estimated 60 percent of the average 5.6 million tons of biosolids produced each year is applied to the land for various reasons, and this practice represents an important and understudied route of exposure of natural ecosystems to engineered nanoparticles.”

“Our results show that silver nanoparticles in the biosolids, added at concentrations that would be expected, caused ecosystem-level impacts,” Colman said. “Specifically, the nanoparticles led to an increase in nitrous oxide fluxes, changes in microbial community composition, biomass, and extracellular enzyme activity, as well as species-specific effects on the above-ground vegetation.”

Getting back to Florida, you can find Ali’s abstract here,

Inhibition of Phytophthora parasitica and P. capsici by silver nanoparticles synthesized using aqueous extract of Artemisia absinthium by Mohammad Ali, Bosung Kim, Kevin Belfield, David J. Norman, Mary Brennan, & Gul Shad Ali. Phytopathology  http://dx.doi.org/10.1094/PHYTO-01-15-0006-R Published online April 14, 2015

This paper is behind a paywall.

For anyone who recognized that wormwood is a constituent of Absinthe, a liquor that is banned in many parts of the world due to possible side effects associated with the wormwood, here’s more about it from the Wormwood overview page on WebMD (Note: Links have been removed),

Wormwood is an herb. The above-ground plant parts and oil are used for medicine.

Wormwood is used in some alcoholic beverages. Vermouth, for example, is a wine beverage flavored with extracts of wormwood. Absinthe is another well-known alcoholic beverage made with wormwood. It is an emerald-green alcoholic drink that is prepared from wormwood oil, often along with other dried herbs such as anise and fennel. Absinthe was popularized by famous artists and writers such as Toulouse-Lautrec, Degas, Manet, van Gogh, Picasso, Hemingway, and Oscar Wilde. It is now banned in many countries, including the U.S. But it is still allowed in European Union countries as long as the thujone content is less than 35 mg/kg. Thujone is a potentially poisonous chemical found in wormwood. Distilling wormwood in alcohol increases the thujone concentration.

Returning to the matter at hand, as I’ve noted previously elsewhere, research into the toxic effects associated with nanomaterials (e.g. silver nanoparticles) is a complex process.

Of airborne nanomaterials, bacterial microbiomes, viral microbiomes, and paper sensors

There’s a Jan. 14, 2015 news item on Nanowerk from the Virginia Polytechnic Institute (Virginia Tech) which is largely a personal profile featuring some basic information (useful for those new to the topic) about airborne nanoparticles (Note: A link has been removed),

The Harvard educated undergraduate [Linsey Marr,  professor of civil and environmental engineering, Virginia Tech] who obtained her Ph.D. from University of California at Berkeley and trained as a postdoctoral researcher with a Nobel laureate of chemistry at MIT is now among a handful of researchers in the world who are addressing concerns about engineered nanomaterials in the atmosphere.

Marr is part of the National Science Foundation’s Center for the Environmental Implications of Nanotechnology and her research group has characterized airborne nanoparticles at every point of their life cycle. This cycle includes production at a commercial manufacturing facility, use by consumers in the home, and disposal via incineration.

A Jan. 14, 2015 Virginia Tech news release, which originated the news item, quotes Marr on the current thinking about airborne nanoparticles,

“Results have shown that engineered nanomaterials released into the air are often aggregated with other particulate matter, such as combustion soot or ingredients in consumer spray products, and that the size of such aggregates may range from smaller than 10 nanometers to larger than 10 microns,” Marr revealed. She was referring to studies completed by research group members Marina Quadros Vance of Florianopolis, Brazil, a research scientist with the Virginia Tech Institute of Critical Technology and Applied Science, and Eric Vejerano, of Ligao, Philippines, a post-doctoral associate in civil and environmental engineering.

Size matters if these aggregates are inhaled.

Another concern is the reaction of a nanomaterial such as a fullerene with ozone at environmentally relevant concentration levels. Marr’s graduate student, Andrea Tiwari, of Mankato, Minnesota, said the resulting changes in fullerene could lead to enhanced toxicity.

The story then segues into airborne pathogens and viruses eventually honing in on virus microbiomes and bacterial microbiomes (from the news release),

Marr is a former Ironman triathlete who obviously has strong interests in what she is breathing into her own body. So it would be natural for her to expand her study of engineered nanoparticles traveling in the atmosphere to focus on airborne pathogens.

She did so by starting to consider the influenza virus as an airborne pollutant. She applied the same concepts and tools used for studying environmental contaminants and ambient aerosols to the examination of the virus.

She looked at viruses as “essentially self-assembled nanoparticles that are capable of self-replication.”

Her research team became the first to measure influenza virus concentrations in ambient air in a children’s day care center and on airplanes. When they conducted their studies, the Virginia Tech researchers collected samples from a waiting room of a health care center, two toddlers’ rooms and one babies’ area of a childcare center, as well as three cross-country flights between Roanoke, Virginia., and San Francisco. They collected 16 samples between Dec. 10, 2009 and Apr. 22, 2010.

“Half of the samples were confirmed to contain aerosolized influenza A viruses,” Marr said. The childcare samples were the most infected at 75 percent. Next, airplane samples reached 67 percent contamination, and health center numbers came in at 33 percent.

This study serves as a foundation for new work started about a year ago in her lab.

Marr collaborated with Aaron J. Prussin II, of Blacksburg, Virginia, and they successfully secured for him a postdoctoral fellowship from the Alfred P. Sloan Foundation to characterize the bacterial and viral microbiome — the ecological community of microorganisms — of the air in a daycare center.

They are now attempting to determine seasonal changes of both the viral microbiome and the bacterial microbiome in a daycare setting, and examine how changes in the microbiome are related to naturally occurring changes in the indoor environment.

“Little is known about the viral component of the microbiome and it is important because viruses are approximately 10 times more abundant than bacteria, and they help shape the bacterial community. Research suggests that viruses do have both beneficial and harmful interactions with bacteria,” Prussin said.

With Prussin and Marr working together they hope to verify their hypothesis that daycare centers harbor unique, dynamic microbiomes with plentiful bacteria and viruses. They are also looking at what seasonal changes might bring to a daycare setting.

They pointed to the effect of seasonal changes because in previous work, Marr, her former graduate student Wan Yang, of Shantou, China, and Elankumaran Subbiah, a virologist in the biomedical sciences and pathobiology department of the Virginia-Maryland College of Veterinary Medicine, measured the influenza A virus survival rate at various levels of humidity.

Their 2012 study presented for the first time the relationship between the influenza A virus viability in human mucus and humidity over a large range of relative humidities, from 17 percent to 100 percent. They found the viability of the virus was highest when the relative humidity was either close to 100 percent or below 50 percent. The results in human mucus may help explain influenza’s seasonality in different regions.

According to the news release Marr and her colleagues have developed a fast and cheap technology for detection of airborne pathogens (Note: A link has been removed),

With the urgent need to understand the dynamics of airborne pathogens, especially as one considers the threats of bioterrorism, pandemic influenza, and other emerging infectious diseases, Marr said “a breakthrough technology is required to enable rapid, low-cost detection of pathogens in air.”

Along with Subbiah and Peter Vikesland,  professor of civil and environmental engineering, they want to develop readily deployable, inexpensive, paper-based sensors for airborne pathogen detection.

In 2013 they received funding of almost $250,000 from Virginia Tech’s Institute for Critical Technology and Applied Science, a supporter of the clustering of research groups, to support their idea of creating paper-based sensors based on their various successes to date.

Marr explained the sensors “would use a sandwich approach. The bottom layer is paper containing specialized DNA that will immobilize the virus. The middle layer is the virus, which sticks to the specialized DNA on the bottom layer. The top layer is additional specialized DNA that sticks to the virus. This DNA is attached to gold nanoparticles that are easily detectable using a technique known as Raman microscopy.”

They key to their approach is that it combines high-tech with low-tech in the hopes of keeping the assay costs low. Their sampling method will use a bicycle pump, and low cost paper substrates. They hope that they will be able to incorporate smart-phone based signal transduction for the detection. Using this approach, they believe “even remote corners of the world” would be able to use the technique.

Vikesland previously received funding from the Gates Foundation to detect the polio virus via paper-based diagnostics. Polio is still found in countries on the continents of Asia and Africa.

I have previously mentioned Linsey Marr in an Oct. 18, 2013 post about the revival of the Nanotechnology Consumer Products Inventory (originally developed by the Project for Emerging Nanotechnologies) by academics at Virginia Tech and first mentioned CEINT in an Aug. 15, 2011 post about a special project featuring a mesocosm at Duke University (North Carolina).