Tag Archives: University of Washington (state)

Some amusements in the time of COVID-19

Gold stars for everyone who recognized the loose paraphrasing of the title, Love in the Time of Cholera, for Gabrial Garcia Marquez’s 1985 novel.

I wrote my headline and first paragraph yesterday and found this in my email box this morning, from a March 25, 2020 University of British Columbia news release, which compares times, diseases, and scares of the past with today’s COVID-19 (Perhaps politicians and others could read this piece and stop using the word ‘unprecedented’ when discussing COVID-19?),

How globalization stoked fear of disease during the Romantic era

In the late 18th and early 19th centuries, the word “communication” had several meanings. People used it to talk about both media and the spread of disease, as we do today, but also to describe transport—via carriages, canals and shipping.

Miranda Burgess, an associate professor in UBC’s English department, is working on a book called Romantic Transport that covers these forms of communication in the Romantic era and invites some interesting comparisons to what the world is going through today.

We spoke with her about the project.

What is your book about?

It’s about global infrastructure at the dawn of globalization—in particular the extension of ocean navigation through man-made inland waterways like canals and ship’s canals. These canals of the late 18th and early 19th century were like today’s airline routes, in that they brought together places that were formerly understood as far apart, and shrunk time because they made it faster to get from one place to another.

This book is about that history, about the fears that ordinary people felt in response to these modernizations, and about the way early 19th-century poets and novelists expressed and responded to those fears.

What connections did those writers make between transportation and disease?

In the 1810s, they don’t have germ theory yet, so there’s all kinds of speculation about how disease happens. Works of tropical medicine, which is rising as a discipline, liken the human body to the surface of the earth. They talk about nerves as canals that convey information from the surface to the depths, and the idea that somehow disease spreads along those pathways.

When the canals were being built, some writers opposed them on the grounds that they could bring “strangers” through the heart of the city, and that standing water would become a breeding ground for disease. Now we worry about people bringing disease on airplanes. It’s very similar to that.

What was the COVID-19 of that time?

Probably epidemic cholera [emphasis mine], from about the 1820s onward. The Quarterly Review, a journal that novelist Walter Scott was involved in editing, ran long articles that sought to trace the map of cholera along rivers from South Asia, to Southeast Asia, across Europe and finally to Britain. And in the way that its spread is described, many of the same fears that people are evincing now about COVID-19 were visible then, like the fear of clothes. Is it in your clothes? Do we have to burn our clothes? People were concerned.

What other comparisons can be drawn between those times and what is going on now?

Now we worry about the internet and “fake news.” In the 19th century, they worried about what William Wordsworth called “the rapid communication of intelligence,” which was the daily newspaper. Not everybody had access to newspapers, but each newspaper was read by multiple families and newspapers were available in taverns and coffee shops. So if you were male and literate, you had access to a newspaper, and quite a lot of women did, too.

Paper was made out of rags—discarded underwear. Because of the French Revolution and Napoleonic Wars that followed, France blockaded Britain’s coast and there was a desperate shortage of rags to make paper, which had formerly come from Europe. And so Britain started to import rags from the Caribbean that had been worn by enslaved people.

Papers of the time are full of descriptions of the high cost of rags, how they’re getting their rags from prisons, from prisoners’ underwear, and fear about the kinds of sweat and germs that would have been harboured in those rags—and also discussions of scarcity, as people stole and hoarded those rags. It rings very well with what the internet is telling us now about a bunch of things around COVID-19.

Plus ça change, n’est-ce pas?

And now for something completely different

Kudos to all who recognized the Monty Python reference. Now, onto the frogfish,

Thank you to the Monterey Bay Aquarium (in California, US).

A March 22, 2020 University of Washington (state) news release features an interview with the author of a new book on frogfishes,

Any old fish can swim. But what fish can walk, scoot, clamber over rocks, change color or pattern and even fight? That would be the frogfish.

The latest book by Ted Pietsch, UW professor emeritus of aquatic and fishery sciences, explores the lives and habits of these unusual marine shorefishes. “Frogfishes: Biodiversity, Zoogeography, and Behavioral Ecology” was published in March [2020] by Johns Hopkins University Press.

Pietsch, who is also curator emeritus of fishes at the Burke Museum of Natural History and Culture, has published over 200 articles and a dozen books on the biology and behavior of marine fishes. He wrote this book with Rachel J. Arnold, a faculty member at Northwest Indian College in Bellingham and its Salish Sea Research Center.

These walking fishes have stepped into the spotlight lately, with interest growing in recent decades. And though these predatory fishes “will almost certainly devour anything else that moves in a home aquarium,” Pietsch writes, “a cadre of frogfish aficionados around the world has grown within the dive community and among aquarists.” In fact, Pietsch said, there are three frogfish public groups on Facebook, with more than 6,000 members.

First, what is a frogfish?

Ted Pietsch: A member of a family of bony fishes, containing 52 species, all of which are highly camouflaged and whose feeding strategy consists of mimicking the immobile, inert, and benign appearance of a sponge or an algae-encrusted rock, while wiggling a highly conspicuous lure to attract prey.

This is a fish that “walks” and “hops” across the sea bottom, and clambers about over rocks and coral like a four-legged terrestrial animal but, at the same time, can jet-propel itself through open water. Some lay their eggs encapsulated in a complex, floating, mucus mass, called an “egg raft,” while some employ elaborate forms of parental care, carrying their eggs around until they hatch.

They are among the most colorful of nature’s productions, existing in nearly every imaginable color and color pattern, with an ability to completely alter their color and pattern in a matter of days or seconds. All these attributes combined make them one of the most intriguing groups of aquatic vertebrates for the aquarist, diver, and underwater photographer as well as the professional zoologist.

I couldn’t resist the ‘frog’ reference and I’m glad since this is a good read with a number of fascinating photographs and illustrations.,

An illustration of the frogfish Antennarius pictus, published by George Shaw in 1794. From a new book by Ted Pietsch, UW professor of emeritus of aquatic and fishery sciences. Courtesy: University of Washington (state)

h/t phys.org March 24, 2020 news item

Building with bacteria

A block of sand particles held together by living cells. Credit: The University of Colorado Boulder College of Engineering and Applied Science

A March 24, 2020 news item on phys.org features the future of building construction as perceived by synthetic biologists,

Buildings are not unlike a human body. They have bones and skin; they breathe. Electrified, they consume energy, regulate temperature and generate waste. Buildings are organisms—albeit inanimate ones.

But what if buildings—walls, roofs, floors, windows—were actually alive—grown, maintained and healed by living materials? Imagine architects using genetic tools that encode the architecture of a building right into the DNA of organisms, which then grow buildings that self-repair, interact with their inhabitants and adapt to the environment.

A March 23, 2020 essay by Wil Srubar (Professor of Architectural Engineering and Materials Science, University of Colorado Boulder), which originated the news item, provides more insight,

Living architecture is moving from the realm of science fiction into the laboratory as interdisciplinary teams of researchers turn living cells into microscopic factories. At the University of Colorado Boulder, I lead the Living Materials Laboratory. Together with collaborators in biochemistry, microbiology, materials science and structural engineering, we use synthetic biology toolkits to engineer bacteria to create useful minerals and polymers and form them into living building blocks that could, one day, bring buildings to life.

In one study published in Scientific Reports, my colleagues and I genetically programmed E. coli to create limestone particles with different shapes, sizes, stiffnesses and toughness. In another study, we showed that E. coli can be genetically programmed to produce styrene – the chemical used to make polystyrene foam, commonly known as Styrofoam.

Green cells for green building

In our most recent work, published in Matter, we used photosynthetic cyanobacteria to help us grow a structural building material – and we kept it alive. Similar to algae, cyanobacteria are green microorganisms found throughout the environment but best known for growing on the walls in your fish tank. Instead of emitting CO2, cyanobacteria use CO2 and sunlight to grow and, in the right conditions, create a biocement, which we used to help us bind sand particles together to make a living brick.

By keeping the cyanobacteria alive, we were able to manufacture building materials exponentially. We took one living brick, split it in half and grew two full bricks from the halves. The two full bricks grew into four, and four grew into eight. Instead of creating one brick at a time, we harnessed the exponential growth of bacteria to grow many bricks at once – demonstrating a brand new method of manufacturing materials.

Researchers have only scratched the surface of the potential of engineered living materials. Other organisms could impart other living functions to material building blocks. For example, different bacteria could produce materials that heal themselves, sense and respond to external stimuli like pressure and temperature, or even light up. If nature can do it, living materials can be engineered to do it, too.

It also take less energy to produce living buildings than standard ones. Making and transporting today’s building materials uses a lot of energy and emits a lot of CO2. For example, limestone is burned to make cement for concrete. Metals and sand are mined and melted to make steel and glass. The manufacture, transport and assembly of building materials account for 11% of global CO2 emissions. Cement production alone accounts for 8%. In contrast, some living materials, like our cyanobacteria bricks, could actually sequester CO2.

The field of engineered living materials is in its infancy, and further research and development is needed to bridge the gap between laboratory research and commercial availability. Challenges include cost, testing, certification and scaling up production. Consumer acceptance is another issue. For example, the construction industry has a negative perception of living organisms. Think mold, mildew, spiders, ants and termites. We’re hoping to shift that perception. Researchers working on living materials also need to address concerns about safety and biocontamination.

The [US] National Science Foundation recently named engineered living materials one of the country’s key research priorities. Synthetic biology and engineered living materials will play a critical role in tackling the challenges humans will face in the 2020s and beyond: climate change, disaster resilience, aging and overburdened infrastructure, and space exploration.

If you have time and interest, this is fascinating. Strubar is a little exuberant and, at this point, I welcome it.

Fitness

The Lithuanians are here for us. Scientists from the Kaunas University of Technology have just published a paper on better exercises for lower back pain in our increasingly sedentary times, from a March 23, 2020 Kaunas University of Technology press release (also on EurekAlert) Note: There are a few minor grammatical issues,

With the significant part of the global population forced to work from home, the occurrence of lower back pain may increase. Lithuanian scientists have devised a spinal stabilisation exercise programme for managing lower back pain for people who perform a sedentary job. After testing the programme with 70 volunteers, the researchers have found that the exercises are not only efficient in diminishing the non-specific lower back pain, but their effect lasts 3 times longer than that of a usual muscle strengthening exercise programme.

According to the World Health Organisation, lower back pain is among the top 10 diseases and injuries that are decreasing the quality of life across the global population. It is estimated that non-specific low back pain is experienced by 60% to 70% of people in industrialised societies. Moreover, it is the leading cause of activity limitation and work absence throughout much of the world. For example, in the United Kingdom, low back pain causes more than 100 million workdays lost per year, in the United States – an estimated 149 million.

Chronic lower back pain, which starts from long-term irritation or nerve injury affects the emotions of the afflicted. Anxiety, bad mood and even depression, also the malfunctioning of the other bodily systems – nausea, tachycardia, elevated arterial blood pressure – are among the conditions, which may be caused by lower back pain.

During the coronavirus disease (COVID-19) outbreak, with a significant part of the global population working from home and not always having a properly designed office space, the occurrence of lower back pain may increase.

“Lower back pain is reaching epidemic proportions. Although it is usually clear what is causing the pain and its chronic nature, people tend to ignore these circumstances and are not willing to change their lifestyle. Lower back pain usually comes away itself, however, the chances of the recurring pain are very high”, says Dr Irina Klizienė, a researcher at Kaunas University of Technology (KTU) Faculty of Social Sciences, Humanities and Arts.

Dr Klizienė, together with colleagues from KTU and from Lithuanian Sports University has designed a set of stabilisation exercises aimed at strengthening the muscles which support the spine at the lower back, i.e. lumbar area. The exercise programme is based on Pilates methodology.

According to Dr Klizienė, the stability of lumbar segments is an essential element of body biomechanics. Previous research evidence shows that in order to avoid the lower back pain it is crucial to strengthen the deep muscles, which are stabilising the lumbar area of the spine. One of these muscles is multifidus muscle.

“Human central nervous system is using several strategies, such as preparing for keeping the posture, preliminary adjustment to the posture, correcting the mistakes of the posture, which need to be rectified by specific stabilising exercises. Our aim was to design a set of exercises for this purpose”, explains Dr Klizienė.

The programme, designed by Dr Klizienė and her colleagues is comprised of static and dynamic exercises, which train the muscle strength and endurance. The static positions are to be held from 6 to 20 seconds; each exercise to be repeated 8 to 16 times.

Caption: The static positions are to be held from 6 to 20 seconds; each exercise to be repeated 8 to 16 times. Credit: KTU

The previous set is a little puzzling but perhaps you’ll find these ones below easier to follow,

Caption: The exercises are aimed at strengthening the muscles which support the spine at the lower back. Credit: KTU

I think more pictures of intervening moves would have been useful. Now. getting back to the press release,

In order to check the efficiency of the programme, 70 female volunteers were randomly enrolled either to the lumbar stabilisation exercise programme or to a usual muscle strengthening exercise programme. Both groups were exercising twice a week for 45 minutes for 20 weeks. During the experiment, ultrasound scanning of the muscles was carried out.

As soon as 4 weeks in lumbar stabilisation programme, it was observed that the cross-section area of the multifidus muscle of the subjects of the stabilisation group has increased; after completing the programme, this increase was statistically significant (p < 0,05). This change was not observed in the strengthening group.

Moreover, although both sets of exercises were efficient in eliminating lower back pain and strengthening the muscles of the lower back area, the effect of stabilisation exercises lasted 3 times longer – 12 weeks after the completion of the stabilisation programme against 4 weeks after the completion of the muscle strengthening programme.

“There are only a handful of studies, which have directly compared the efficiency of stabilisation exercises against other exercises in eliminating lower back pain”, says Dr Klizienė, “however, there are studies proving that after a year, lower back pain returned only to 30% of people who have completed a stabilisation exercise programme, and to 84% of people who haven’t taken these exercises. After three years these proportions are 35% and 75%.”

According to her, research shows that the spine stabilisation exercises are more efficient than medical intervention or usual physical activities in curing the lower back pain and avoiding the recurrence of the symptoms in the future.

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

Effect of different exercise programs on non-specific chronic low back pain and disability in people who perform sedentary work by Saule Sipavicienea, Irina Klizieneb. Clinical Biomechanics March 2020 Volume 73, Pages 17–27 DOI: https://doi.org/10.1016/j.clinbiomech.2019.12.028

This paper is behind a paywall.

University of Washington (state) is accelerating nanoscale research with Institute for Nano-Engineered Systems

A December 5, 2017 news item on Nanowerk announced a new research institute at the University of Washington (state),

The University of Washington [UW} has launched a new institute aimed at accelerating research at the nanoscale: the Institute for Nano-Engineered Systems, or NanoES. Housed in a new, multimillion-dollar facility on the UW’s Seattle campus, the institute will pursue impactful advancements in a variety of disciplines — including energy, materials science, computation and medicine. Yet these advancements will be at a technological scale a thousand times smaller than the width of a human hair.

The institute was launched at a reception Dec. 4 [2017] at its headquarters in the $87.8-million Nano Engineering and Sciences Building. During the event, speakers including UW officials and NanoES partners celebrated the NanoES mission to capitalize on the university’s strong record of research at the nanoscale and engage partners in industry at the onset of new projects.

A December 5, 2017 UW news release, which originated the news item, somewhat clarifies the declarations in the two excerpted paragraphs in the above,

The vision of the NanoES, which is part of the UW’s College of Engineering, is to act as a magnet for researchers in nanoscale science and engineering, with a focus on enabling industry partnership and entrepreneurship at the earliest stages of research projects. According to Karl Böhringer, director of the NanoES and a UW professor of electrical engineering and bioengineering, this unique approach will hasten the development of solutions to the field’s most pressing challenges: the manufacturing of scalable, high-yield nano-engineered systems for applications in information processing, energy, health and interconnected life.

“The University of Washington is well known for its expertise in nanoscale materials, processing, physics and biology — as well as its cutting-edge nanofabrication, characterization and testing facilities,” said Böhringer, who stepped down as director of the UW-based Washington Nanofabrication Facility to lead the NanoES. “NanoES will build on these strengths, bringing together people, tools and opportunities to develop nanoscale devices and systems.”

The centerpiece of the NanoES is its headquarters, the Nano Engineering and Sciences Building. The building houses 90,300 square feet of research and learning space, and was funded largely by the College of Engineering and Sound Transit. It contains an active learning classroom, a teaching laboratory and a 3,000-square-foot common area designed expressly to promote the sharing and exchanging of ideas. The remainder includes “incubator-style” office space and more than 40,000 square feet of flexible multipurpose laboratory and instrumentation space. The building’s location and design elements are intended to limit vibrations and electromagnetic interference so it can house sensitive experiments.

NanoES will house research in nanotechnology fields that hold promise for high impact, such as:

  • Augmented humanity, which includes technology to both aid and replace human capability in a way that joins user and machine as one – and foresees portable, wearable, implantable and networked technology for applications such as personalized medical care, among others.
  • Integrated photonics, which ranges from single-photon sensors for health care diagnostic tests to large-scale, integrated networks of photonic devices.
  • Scalable nanomanufacturing, which aims to develop low-cost, high-volume manufacturing processes. These would translate device prototypes constructed in research laboratories into system- and network-level nanomanufacturing methods for applications ranging from the 3-D printing of cell and tissue scaffolds to ultrathin solar cells.

A ribbon cutting ceremony.

Cutting the ribbon for the NanoES on Dec. 4. Left-to-right: Karl Böhringer, director of the NanoES and a UW professor of electrical engineering and bioengineering; Nena Golubovic, physical sciences director for IP Group; Mike Bragg, Dean of the UW College of Engineering; Jevne Micheau-Cunningham, deputy director of the NanoES.Kathryn Sauber/University of Washington

Collaborations with other UW-based institutions will provide additional resources for the NanoES. Endeavors in scalable nanomanufacturing, for example, will rely on the roll-to-roll processing facility at the UW Clean Energy Institute‘s Washington Clean Energy Testbeds or on advanced surface characterization capabilities at the Molecular Analysis Facility. In addition, the Washington Nanofabrication Facility recently completed a three-year, $37 million upgrade to raise it to an ISO Class 5 nanofabrication facility.

UW faculty and outside collaborators will build new research programs in the Nano Engineering and Sciences Building. Eric Klavins, a UW professor of electrical engineering, recently moved part of his synthetic biology research team to the building, adjacent to his collaborators in the Molecular Engineering & Sciences Institute and the Institute for Protein Design.

“We are extremely excited about the interdisciplinary and collaborative potential of the new space,” said Klavins.

The NanoES also has already produced its first spin-out company, Tunoptix, which was co-founded by Böhringer and recently received startup funding from IP Group, a U.K.-based venture capital firm.

“IP Group is very excited to work with the University of Washington,” said Nena Golubovic, physical sciences director for IP Group. “We are looking forward to the new collaborations and developments in science and technology that will grow from this new partnership.”

A woman speaking at a podium.

Nena Golubovic, physical sciences director for IP Group, delivering remarks at the Dec. 4 opening of NanoES.Kathryn Sauber/University of Washington

“We are eager to work with our partners at the IP Group to bring our technology to the market, and we appreciate their vision and investment in the NanoES Integrated Photonics Initiative,” said Tunoptix entrepreneurial lead Mike Robinson. “NanoES was the ideal environment in which to start our company.”

The NanoES leaders hope to forge similar partnerships with researchers, investors and industry leaders to develop technologies for portable, wearable, implantable and networked nanotechnologies for personalized medical care, a more efficient interconnected life and interconnected mobility. In addition to expertise, personnel and state-of-the-art research space and equipment, the NanoES will provide training, research support and key connections to capital and corporate partners.

“We believe this unique approach is the best way to drive innovations from idea to fabrication to scale-up and testing,” said Böhringer. “Some of the most promising solutions to these huge challenges are rooted in nanotechnology.”

The NanoES is supported by funds from the College of Engineering and the National Science Foundation, as well as capital investments from investors and industry partners.

You can find out more about Nano ES here.

World heritage music stored in DNA

It seems a Swiss team from the École Polytechnique de Lausanne (EPFL) have collaborated with American companies Twist Bioscience and Microsoft, as well as, the University of Washington (state) to preserve two iconic jazz pieces on DNA (deoxyribonucleic acid) according to a Sept. 29, 2017 news item on phys.org,,

Thanks to an innovative technology for encoding data in DNA strands, two items of world heritage – songs recorded at the Montreux Jazz Festival [held in Switzerland] and digitized by EPFL – have been safeguarded for eternity. This marks the first time that cultural artifacts granted UNESCO heritage status have been saved in such a manner, ensuring they are preserved for thousands of years. The method was developed by US company Twist Bioscience and is being unveiled today in a demonstrator created at the EPFL+ECAL Lab.

“Tutu” by Miles Davis and “Smoke on the Water” by Deep Purple have already made their mark on music history. Now they have entered the annals of science, for eternity. Recordings of these two legendary songs were digitized by the Ecole Polytechnique Fédérale de Lausanne (EPFL) as part of the Montreux Jazz Digital Project, and they are the first to be stored in the form of a DNA sequence that can be subsequently decoded and listened to without any reduction in quality.

A Sept. 29, 2017 EPFL press release by Emmanuel Barraud, which originated the news item, provides more details,

This feat was achieved by US company Twist Bioscience working in association with Microsoft Research and the University of Washington. The pioneering technology is actually based on a mechanism that has been at work on Earth for billions of years: storing information in the form of DNA strands. This fundamental process is what has allowed all living species, plants and animals alike, to live on from generation to generation.

The entire world wide web in a shoe box

All electronic data storage involves encoding data in binary format – a series of zeros and ones – and then recording it on a physical medium. DNA works in a similar way, but is composed of long strands of series of four nucleotides (A, T, C and G) that make up a “code.” While the basic principle may be the same, the two methods differ greatly in terms of efficiency: if all the information currently on the internet was stored in the form of DNA, it would fit in a shoe box!

Recent advances in biotechnology now make it possible for humans to do what Mother Nature has always done. Today’s scientists can create artificial DNA strands, “record” any kind of genetic code on them and then analyze them using a sequencer to reconstruct the original data. What’s more, DNA is extraordinarily stable, as evidenced by prehistoric fragments that have been preserved in amber. Artificial strands created by scientists and carefully encapsulated should likewise last for millennia.

To help demonstrate the feasibility of this new method, EPFL’s Metamedia Center provided recordings of two famous songs played at the Montreux Jazz Festival: “Tutu” by Miles Davis, and “Smoke on the Water” by Deep Purple. Twist Bioscience and its research partners encoded the recordings, transformed them into DNA strands and then sequenced and decoded them and played them again – without any reduction in quality.

The amount of artificial DNA strands needed to record the two songs is invisible to the naked eye, and the amount needed to record all 50 years of the Festival’s archives, which have been included in UNESCO’s [United Nations Educational, Scientific and Cultural Organization] Memory of the World Register, would be equal in size to a grain of sand. “Our partnership with EPFL in digitizing our archives aims not only at their positive exploration, but also at their preservation for the next generations,” says Thierry Amsallem, president of the Claude Nobs Foundation. “By taking part in this pioneering experiment which writes the songs into DNA strands, we can be certain that they will be saved on a medium that will never become obsolete!”

A new concept of time

At EPFL’s first-ever ArtTech forum, attendees got to hear the two songs played after being stored in DNA, using a demonstrator developed at the EPFL+ECAL Lab. The system shows that being able to store data for thousands of years is a revolutionary breakthrough that can completely change our relationship with data, memory and time. “For us, it means looking into radically new ways of interacting with cultural heritage that can potentially cut across civilizations,” says Nicolas Henchoz, head of the EPFL+ECAL Lab.

Quincy Jones, a longstanding Festival supporter, is particularly enthusiastic about this technological breakthrough: “With advancements in nanotechnology, I believe we can expect to see people living prolonged lives, and with that, we can also expect to see more developments in the enhancement of how we live. For me, life is all about learning where you came from in order to get where you want to go, but in order to do so, you need access to history! And with the unreliability of how archives are often stored, I sometimes worry that our future generations will be left without such access… So, it absolutely makes my soul smile to know that EPFL, Twist Bioscience and their partners are coming together to preserve the beauty and history of the Montreux Jazz Festival for our future generations, on DNA! I’ve been a part of this festival for decades and it truly is a magnificent representation of what happens when different cultures unite for the sake of music. Absolute magic. And I’m proud to know that the memory of this special place will never be lost.

A Sept. 29, 2017 Twist Bioscience news release is repetitive in some ways but interesting nonetheless,

Twist Bioscience, a company accelerating science and innovation through rapid, high-quality DNA synthesis, today announced that, working with Microsoft and University of Washington researchers, they have successfully stored archival-quality audio recordings of two important music performances from the archives of the world-renowned Montreux Jazz Festival.
These selections are encoded and stored in nature’s preferred storage medium, DNA, for the first time. These tiny specks of DNA will preserve a part of UNESCO’s Memory of the World Archive, where valuable cultural heritage collections are recorded. This is the first time DNA has been used as a long-term archival-quality storage medium.
Quincy Jones, world-renowned Entertainment Executive, Music Composer and Arranger, Musician and Music Producer said, “With advancements in nanotechnology, I believe we can expect to see people living prolonged lives, and with that, we can also expect to see more developments in the enhancement of how we live. For me, life is all about learning where you came from in order to get where you want to go, but in order to do so, you need access to history! And with the unreliability of how archives are often stored, I sometimes worry that our future generations will be left without such access…So, it absolutely makes my soul smile to know that EPFL, Twist Bioscience and others are coming together to preserve the beauty and history of the Montreux Jazz Festival for our future generations, on DNA!…I’ve been a part of this festival for decades and it truly is a magnificent representation of what happens when different cultures unite for the sake of music. Absolute magic. And I’m proud to know that the memory of this special place will never be lost.”
“Our partnership with EPFL in digitizing our archives aims not only at their positive exploration, but also at their preservation for the next generations,” says Thierry Amsallem, president of the Claude Nobs Foundation. “By taking part in this pioneering experiment which writes the songs into DNA strands, we can be certain that they will be saved on a medium that will never become obsolete!”
The Montreux Jazz Digital Project is a collaboration between the Claude Nobs Foundation, curator of the Montreux Jazz Festival audio-visual collection and the École Polytechnique Fédérale de Lausanne (EPFL) to digitize, enrich, store, show, and preserve this notable legacy created by Claude Nobs, the Festival’s founder.
In this proof-of-principle project, two quintessential music performances from the Montreux Jazz Festival – Smoke on the Water, performed by Deep Purple and Tutu, performed by Miles Davis – have been encoded onto DNA and read back with 100 percent accuracy. After being decoded, the songs were played on September 29th [2017] at the ArtTech Forum (see below) in Lausanne, Switzerland. Smoke on the Water was selected as a tribute to Claude Nobs, the Montreux Jazz Festival’s founder. The song memorializes a fire and Funky Claude’s rescue efforts at the Casino Barrière de Montreux during a Frank Zappa concert promoted by Claude Nobs. Miles Davis’ Tutu was selected for the role he played in music history and the Montreux Jazz Festival’s success. Miles Davis died in 1991.
“We archived two magical musical pieces on DNA of this historic collection, equating to 140MB of stored data in DNA,” said Karin Strauss, Ph.D., a Senior Researcher at Microsoft, and one of the project’s leaders.  “The amount of DNA used to store these songs is much smaller than one grain of sand. Amazingly, storing the entire six petabyte Montreux Jazz Festival’s collection would result in DNA smaller than one grain of rice.”
Luis Ceze, Ph.D., a professor in the Paul G. Allen School of Computer Science & Engineering at the University of Washington, said, “DNA, nature’s preferred information storage medium, is an ideal fit for digital archives because of its durability, density and eternal relevance. Storing items from the Montreux Jazz Festival is a perfect way to show how fast DNA digital data storage is becoming real.”
Nature’s Preferred Storage Medium
Nature selected DNA as its hard drive billions of years ago to encode all the genetic instructions necessary for life. These instructions include all the information necessary for survival. DNA molecules encode information with sequences of discrete units. In computers, these discrete units are the 0s and 1s of “binary code,” whereas in DNA molecules, the units are the four distinct nucleotide bases: adenine (A), cytosine (C), guanine (G) and thymine (T).
“DNA is a remarkably efficient molecule that can remain stable for millennia,” said Bill Peck, Ph.D., chief technology officer of Twist Bioscience.  “This is a very exciting project: we are now in an age where we can use the remarkable efficiencies of nature to archive master copies of our cultural heritage in DNA.   As we develop the economies of this process new performances can be added any time.  Unlike current storage technologies, nature’s media will not change and will remain readable through time. There will be no new technology to replace DNA, nature has already optimized the format.”
DNA: Far More Efficient Than a Computer 
Each cell within the human body contains approximately three billion base pairs of DNA. With 75 trillion cells in the human body, this equates to the storage of 150 zettabytes (1021) of information within each body. By comparison, the largest data centers can be hundreds of thousands to even millions of square feet to hold a comparable amount of stored data.
The Elegance of DNA as a Storage Medium
Like music, which can be widely varied with a finite number of notes, DNA encodes individuality with only four different letters in varied combinations. When using DNA as a storage medium, there are several advantages in addition to the universality of the format and incredible storage density. DNA can be stable for thousands of years when stored in a cool dry place and is easy to copy using polymerase chain reaction to create back-up copies of archived material. In addition, because of PCR, small data sets can be targeted and recovered quickly from a large dataset without needing to read the entire file.
How to Store Digital Data in DNA
To encode the music performances into archival storage copies in DNA, Twist Bioscience worked with Microsoft and University of Washington researchers to complete four steps: Coding, synthesis/storage, retrieval and decoding. First, the digital files were converted from the binary code using 0s and 1s into sequences of A, C, T and G. For purposes of the example, 00 represents A, 10 represents C, 01 represents G and 11 represents T. Twist Bioscience then synthesizes the DNA in short segments in the sequence order provided. The short DNA segments each contain about 12 bytes of data as well as a sequence number to indicate their place within the overall sequence. This is the process of storage. And finally, to ensure that the file is stored accurately, the sequence is read back to ensure 100 percent accuracy, and then decoded from A, C, T or G into a two-digit binary representation.
Importantly, to encapsulate and preserve encoded DNA, the collaborators are working with Professor Dr. Robert Grass of ETH Zurich. Grass has developed an innovative technology inspired by preservation of DNA within prehistoric fossils.  With this technology, digital data encoded in DNA remains preserved for millennia.
About UNESCO’s Memory of the World Register
UNESCO established the Memory of the World Register in 1992 in response to a growing awareness of the perilous state of preservation of, and access to, documentary heritage in various parts of the world.  Through its National Commissions, UNESCO prepared a list of endangered library and archive holdings and a world list of national cinematic heritage.
A range of pilot projects employing contemporary technology to reproduce original documentary heritage on other media began. These included, for example, a CD-ROM of the 13th Century Radzivill Chronicle, tracing the origins of the peoples of Europe, and Memoria de Iberoamerica, a joint newspaper microfilming project involving seven Latin American countries. These projects enhanced access to this documentary heritage and contributed to its preservation.
“We are incredibly proud to be a part of this momentous event, with the first archived songs placed into the UNESCO Memory of the World Register,” said Emily Leproust, Ph.D., CEO of Twist Bioscience.
About ArtTech
The ArtTech Foundation, created by renowned scientists and dignitaries from Crans-Montana, Switzerland, wishes to stimulate reflection and support pioneering and innovative projects beyond the known boundaries of culture and science.
Benefitting from the establishment of a favorable environment for the creation of technology companies, the Foundation aims to position itself as key promoter of ideas and innovative endeavors within a landscape of “Culture and Science” that is still being shaped.
Several initiatives, including our annual global platform launched in the spring of 2017, are helping to create a community that brings together researchers, celebrities in the world of culture and the arts, as well as investors and entrepreneurs from Switzerland and across the globe.
 
About EPFL
EPFL, one of the two Swiss Federal Institutes of Technology, based in Lausanne, is Europe’s most cosmopolitan technical university with students, professors and staff from over 120 nations. A dynamic environment, open to Switzerland and the world, EPFL is centered on its three missions: teaching, research and technology transfer. EPFL works together with an extensive network of partners including other universities and institutes of technology, developing and emerging countries, secondary schools and colleges, industry and economy, political circles and the general public, to bring about real impact for society.
About Twist Bioscience
At Twist Bioscience, our expertise is accelerating science and innovation by leveraging the power of scale. We have developed a proprietary semiconductor-based synthetic DNA manufacturing process featuring a high throughput silicon platform capable of producing synthetic biology tools, including genes, oligonucleotide pools and variant libraries. By synthesizing DNA on silicon instead of on traditional 96-well plastic plates, our platform overcomes the current inefficiencies of synthetic DNA production, and enables cost-effective, rapid, high-quality and high throughput synthetic gene production, which in turn, expedites the design, build and test cycle to enable personalized medicines, pharmaceuticals, sustainable chemical production, improved agriculture production, diagnostics and biodetection. We are also developing new technologies to address large scale data storage. For more information, please visit www.twistbioscience.com. Twist Bioscience is on Twitter. Sign up to follow our Twitter feed @TwistBioscience at https://twitter.com/TwistBioscience.

If you hadn’t read the EPFL press release first, it might have taken a minute to figure out why EPFL is being mentioned in the Twist Bioscience news release. Presumably someone was rushing to make a deadline. Ah well, I’ve seen and written worse.

I haven’t been able to find any video or audio recordings of the DNA-preserved performances but there is an informational video (originally published July 7, 2016) from Microsoft and the University of Washington describing the DNA-based technology,

I also found this description of listening to the DNA-preserved music in an Oct. 6, 2017 blog posting for the Canadian Broadcasting Corporation’s (CBC) Day 6 radio programme,

To listen to them, one must first suspend the DNA holding the songs in a solution. Next, one can use a DNA sequencer to read the letters of the bases forming the molecules. Then, algorithms can determine the digital code those letters form. From that code, comes the music.

It’s complicated but Ceze says his team performed this process without error.

You can find out more about UNESCO’s Memory of the World and its register here , more about the EPFL+ECAL Lab here, and more about Twist Bioscience here.

Growing shells atom-by-atom

The University of California at Davis (UC Davis) and the University of Washington (state) collaborated in research into fundamental questions on how aquatic animals grow. From an Oct. 24, 2016 news item on ScienceDaily,

For the first time scientists can see how the shells of tiny marine organisms grow atom-by-atom, a new study reports. The advance provides new insights into the mechanisms of biomineralization and will improve our understanding of environmental change in Earth’s past.

An Oct. 24, 2016 UC Davis news release by Becky Oskin, which originated the news item, provides more detail,

Led by researchers from the University of California, Davis and the University of Washington, with key support from the U.S. Department of Energy’s Pacific Northwest National Laboratory, the team examined an organic-mineral interface where the first calcium carbonate crystals start to appear in the shells of foraminifera, a type of plankton.

“We’ve gotten the first glimpse of the biological event horizon,” said Howard Spero, a study co-author and UC Davis geochemistry professor. …

Foraminifera’s Final Frontier

The researchers zoomed into shells at the atomic level to better understand how growth processes may influence the levels of trace impurities in shells. The team looked at a key stage — the interaction between the biological ‘template’ and the initiation of shell growth. The scientists produced an atom-scale map of the chemistry at this crucial interface in the foraminifera Orbulina universa. This is the first-ever measurement of the chemistry of a calcium carbonate biomineralization template, Spero said.

Among the new findings are elevated levels of sodium and magnesium in the organic layer. This is surprising because the two elements are not considered important architects in building shells, said lead study author Oscar Branson, a former postdoctoral researcher at UC Davis who is now at the Australian National University in Canberra. Also, the greater concentrations of magnesium and sodium in the organic template may need to be considered when investigating past climate with foraminifera shells.

Calibrating Earth’s Climate

Most of what we know about past climate (beyond ice core records) comes from chemical analyses of shells made by the tiny, one-celled creatures called foraminifera, or “forams.” When forams die, their shells sink and are preserved in seafloor mud. The chemistry preserved in ancient shells chronicles climate change on Earth, an archive that stretches back nearly 200 million years.

The calcium carbonate shells incorporate elements from seawater — such as calcium, magnesium and sodium — as the shells grow. The amount of trace impurities in a shell depends on both the surrounding environmental conditions and how the shells are made. For example, the more magnesium a shell has, the warmer the ocean was where that shell grew.

“Finding out how much magnesium there is in a shell can allow us to find out the temperature of seawater going back up to 150 million years,” Branson said.

But magnesium levels also vary within a shell, because of nanometer-scale growth bands. Each band is one day’s growth (similar to the seasonal variations in tree rings). Branson said considerable gaps persist in understanding what exactly causes the daily bands in the shells.

“We know that shell formation processes are important for shell chemistry, but we don’t know much about these processes or how they might have changed through time,” he said. “This adds considerable uncertainty to climate reconstructions.”

Atomic Maps

The researchers used two cutting-edge techniques: Time-of-Flight Secondary Ionization Mass Spectrometry (ToF-SIMS) and Laser-Assisted Atom Probe Tomography (APT). ToF-SIMS is a two-dimensional chemical mapping technique which shows the elemental composition of the surface of a polished sample. The technique was developed for the elemental analysis of complex polymer materials, and is just starting to be applied to natural samples like shells.

APT is an atomic-scale three-dimensional mapping technique, developed for looking at internal structures in advanced alloys, silicon chips and superconductors. The APT imaging was performed at the Environmental Molecular Sciences Laboratory, a U.S. Department of Energy Office of Science User Facility at the Pacific Northwest National Laboratory.

This foraminifera is just starting to form its adult spherical shell. The calcium carbonate spherical shell first forms on a thin organic template, shown here in white, around the dark juvenile skeleton. Calcium carbonate spines then extend from the juvenile skeleton through the new sphere and outward. The bright flecks are algae that the foraminifera “farm” for sustenance.Howard Spero/University of California, Davis

This foraminifera is just starting to form its adult spherical shell. The calcium carbonate spherical shell first forms on a thin organic template, shown here in white, around the dark juvenile skeleton. Calcium carbonate spines then extend from the juvenile skeleton through the new sphere and outward. The bright flecks are algae that the foraminifera “farm” for sustenance.Howard Spero/University of California, Davis

An Oct. 24, 2016 University of Washington (state) news release (also on EurekAlert) adds more information (there is a little repetition),

Unseen out in the ocean, countless single-celled organisms grow protective shells to keep them safe as they drift along, living off other tiny marine plants and animals. Taken together, the shells are so plentiful that when they sink they provide one of the best records for the history of ocean chemistry.

Oceanographers at the University of Washington and the University of California, Davis, have used modern tools to provide an atomic-scale look at how that shell first forms. Results could help answer fundamental questions about how these creatures grow under different ocean conditions, in the past and in the future. …

“There’s this debate among scientists about whether shelled organisms are slaves to the chemistry of the ocean, or whether they have the physiological capacity to adapt to changing environmental conditions,” said senior author Alex Gagnon, a UW assistant professor of oceanography.

The new work shows, he said, that they do exert some biologically-based control over shell formation.

“I think it’s just incredible that we were able to peer into the intricate details of those first moments that set how a seashell forms,” Gagnon said. “And that’s what sets how much of the rest of the skeleton will grow.”

The results could eventually help understand how organisms at the base of the marine food chain will respond to more acidic waters. And while the study looked at one organism, Orbulina universa, which is important for understanding past climate, the same method could be used for other plankton, corals and shellfish.

The study used tools developed for materials science and semiconductor research to view the shell formation in the most detail yet to see how the organisms turn seawater into solid mineral.

“We’re interested more broadly in the question ‘How do organisms make shells?'” said first author Oscar Branson, a former postdoctoral researcher at the University of California, Davis who is now at Australian National University in Canberra. “We’ve focused on a key stage in mineral formation — the interaction between biological template materials and the initiation of shell growth by an organism.”

These tiny single-celled animals, called foraminifera, can’t reproduce anywhere but in their natural surroundings, which prevents breeding them in captivity. The researchers caught juvenile foraminifera by diving in deep water off Southern California. Then they then raised them in the lab, using tiny pipettes to feed them brine shrimp during their weeklong lives.

Marine shells are made from calcium carbonate, drawing the calcium and carbon from surrounding seawater. But the animal first grows a soft template for the mineral to grow over. Because this template is trapped within the growing skeleton, it acts as a snapshot of the chemical conditions during the first part of skeletal growth.

To see this chemical picture, the authors analyzed tiny sections of foraminifera template with a technique called atom probe tomography at the Pacific Northwest National Laboratory. This tool creates an atom-by-atom picture of the organic template, which was located using a chemical tag.

Results show that the template contains more magnesium and sodium atoms than expected, and that this could influence how the mineral in the shell begins to grow around it.

“One of the key stages in growing a skeleton is when you make that first bit, when you build that first bit of structure. Anything that changes that process is a key control point,” Gagnon said.

The clumping suggests that magnesium and sodium play a role in the first stages of shell growth. If their availability changes for any reason, that could influence how the shell grows beyond what simple chemistry would predict.

“We can say who the players are — further experiments will have to tell us exactly how important each of them is,” Gagnon said.

Follow-up work will try to grow the shells and create models of their formation to see how the template affects growth under different conditions, such as more acidic water.

“Translating that into, ‘Can these forams survive ocean acidification?’ is still many steps down the line,” Gagnon cautioned. “But you can’t do that until you have a picture of what that surface actually looks like.”

The researchers also hope that by better understanding the exact mechanism of shell growth they could tease apart different aspects of seafloor remains so the shells can be used to reconstruct more than just the ocean’s past temperature. In the study, they showed that the template was responsible for causing fine lines in the shells — one example of the rich chemical information encoded in fossil shells.

“There are ways that you could separate the effects of temperature from other things and learn much more about the past ocean,” Gagnon said.

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

Nanometer-Scale Chemistry of a Calcite Biomineralization Template: Implications for Skeletal Composition and Nucleation, Proceedings of the National Academy of Sciences, www.pnas.org/cgi/doi/10.1073/pnas.1522864113

This paper is behind a paywall.

‘Seamless’ bioeletronics made possible with protein bridge

For some years now I’ve been tagging certain posts with ‘machine/flesh’ as more bioelectronic devices are being invented for use as implants of various kinds.

Researchers at the University of Washington (state) have found a means of making bioelectronics implants a more comfortable fit in the body according to an Oct. 4, 2016 news item on phys.org,

Life has always played by its own set of molecular rules. From the biochemistry behind the first cells, evolution has constructed wonders like hard bone, rough bark and plant enzymes that harvest light to make food.

But our tools for manipulating life—to treat disease, repair damaged tissue and replace lost limbs—come from the nonliving realm: metals, plastics and the like. Though these save and preserve lives, our synthetic treatments are rooted in a chemical language ill-suited to our organic elegance. Implanted electrodes scar, wires overheat and our bodies struggle against ill-fitting pumps, pipes or valves.

A solution lies in bridging this gap where artificial meets biological—harnessing biological rules to exchange information between the biochemistry of our bodies and the chemistry of our devices. In a paper published Sept. 22 [2016] in Scientific Reports, engineers at the University of Washington unveiled peptides—small proteins which carry out countless essential tasks in our cells—that can provide just such a link.

An Oct. 3, 2016 University of Washington (state) news release (also on EurekAlert), which originated the news item, expands on the theme,

The team, led by UW professor Mehmet Sarikaya in the Departments of Materials Science & Engineering, shows how a genetically engineered peptide can assemble into nanowires atop 2-D, solid surfaces that are just a single layer of atoms thick. These nanowire assemblages are critical because the peptides relay information across the bio/nano interface through molecular recognition — the same principles that underlie biochemical interactions such as an antibody binding to its specific antigen or protein binding to DNA.

Since this communication is two-way, with peptides understanding the “language” of technology and vice versa, their approach essentially enables a coherent bioelectronic interface.

“Bridging this divide would be the key to building the genetically engineered biomolecular solid-state devices of the future,” said Sarikaya, who is also a professor of chemical engineering and oral health sciences.

His team in the UW Genetically Engineered Materials Science and Engineering Center studies how to coopt the chemistry of life to synthesize materials with technologically significant physical, electronic and photonic properties. To Sarikaya, the biochemical “language” of life is a logical emulation.

“Nature must constantly make materials to do many of the same tasks we seek,” he said.

The UW team wants to find genetically engineered peptides with specific chemical and structural properties. They sought out a peptide that could interact with materials such as gold, titanium and even a mineral in bone and teeth. These could all form the basis of future biomedical and electro-optical devices. Their ideal peptide should also change the physical properties of synthetic materials and respond to that change. That way, it would transmit “information” from the synthetic material to other biomolecules — bridging the chemical divide between biology and technology.

In exploring the properties of 80 genetically selected peptides — which are not found in nature but have the same chemical components of all proteins — they discovered that one, GrBP5, showed promising interactions with the semimetal graphene. They then tested GrBP5’s interactions with several 2-D nanomaterials which, Sarikaya said, “could serve as the metals or semiconductors of the future.”

“We needed to know the specific molecular interactions between this peptide and these inorganic solid surfaces,” he added.

Their experiments revealed that GrBP5 spontaneously organized into ordered nanowire patterns on graphene. With a few mutations, GrBP5 also altered the electrical conductivity of a graphene-based device, the first step toward transmitting electrical information from graphene to cells via peptides.

In parallel, Sarikaya’s team modified GrBP5 to produce similar results on a semiconductor material — molybdenum disulfide — by converting a chemical signal to an optical signal. They also computationally predicted how different arrangements of GrBP5 nanowires would affect the electrical conduction or optical signal of each material, showing additional potential within GrBP5’s physical properties.

“In a way, we’re at the flood gates,” said Sarikaya. “Now we need to explore the basic properties of this bridge and how we can modify it to permit the flow of ‘information’ from electronic and photonic devices to biological systems.”

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

Bioelectronic interfaces by spontaneously organized peptides on 2D atomic single layer materials by Yuhei Hayamizu, Christopher R. So, Sefa Dag, Tamon S. Page, David Starkebaum, & Mehmet Sarikaya. Scientific Reports 6, Article number: 33778 (2016) doi:10.1038/srep33778 Published online: 22 September 2016

This paper is open access.

This image illustrates the GrBP5 nanowires,

A top view image of GrBP5 nanowires on a 2-D surface of molybdenum disulfide.Mehmet Sarikaya/Scientific Reports

A top view image of GrBP5 nanowires on a 2-D surface of molybdenum disulfide.Mehmet Sarikaya/Scientific Reports

Ferroelectric switching in the lung, heart, and arteries

A June 23, 2014 University of Washington (state) news release (also on EurekAlert) describes how the human body (and other biological tissue) is capable of generating ferroelectricity,

University of Washington researchers have shown that a favorable electrical property is present in a type of protein found in organs that repeatedly stretch and retract, such as the lungs, heart and arteries. These findings are the first that clearly track this phenomenon, called ferroelectricity, occurring at the molecular level in biological tissues.

The news release gives a brief description of ferroelectricity and describes the research team’s latest work with biological tissues,

Ferroelectricity is a response to an electric field in which a molecule switches from having a positive to a negative charge. This switching process in synthetic materials serves as a way to power computer memory chips, display screens and sensors. This property only recently has been discovered in animal tissues and researchers think it may help build and support healthy connective tissues in mammals.

A research team led by Li first discovered ferroelectric properties in biological tissues in 2012, then in 2013 found that glucose can suppress this property in the body’s connective tissues, wherever the protein elastin is present. But while ferroelectricity is a proven entity in synthetic materials and has long been thought to be important in biological functions, its actual existence in biology hasn’t been firmly established.

This study proves that ferroelectric switching happens in the biological protein elastin. When the researchers looked at the base structures within the protein, they saw similar behavior to the unit cells of solid-state materials, where ferroelectricity is well understood.

“When we looked at the smallest structural unit of the biological tissue and how it was organized into a larger protein fiber, we then were able to see similarities to the classic ferroelectric model found in solids,” Li said.

The researchers wanted to establish a more concrete, precise way of verifying ferroelectricity in biological tissues. They used small samples of elastin taken from a pig’s aorta and poled the tissues using an electric field at high temperatures. They then measured the current with the poling field removed and found that the current switched direction when the poling electric field was switched, a sign of ferroelectricity.

They did the same thing at room temperature using a laser as the heat source, and the current also switched directions.

Then, the researchers tested for this behavior on the smallest-possible unit of elastin, called tropoelastin, and again observed the phenomenon. They concluded that this switching property is “intrinsic” to the molecular make-up of elastin.

The next step is to understand the biological and physiological significance of this property, Li said. One hypothesis is that if ferroelectricity helps elastin stay flexible and functional in the body, a lack of it could directly affect the hardening of arteries.

“We may be able to use this as a very sensitive technique to detect the initiation of the hardening process at a very early stage when no other imaging technique will be able to see it,” Li said.

The team also is looking at whether this property plays a role in normal biological functions, perhaps in regulating the growth of tissue.

Co-authors are Pradeep Sharma at the University of Houston, Yanhang Zhang at Boston University, and collaborators at Nanjing University and the Chinese Academy of Sciences.

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

Ferroelectric switching of elastin by Yuanming Liu, Hong-Ling Cai, Matthew Zelisko, Yunjie Wang, Jinglan Sun, Fei Yan, Feiyue Ma, Peiqi Wang, Qian Nataly Chen, Hairong Zheng, Xiangjian Meng, Pradeep Sharma, Yanhang Zhang, and Jiangyu Li. Proceedings of the National Academy of Sciences (PNAS) doi: 10.1073/pnas.1402909111

This paper is behind a paywall.

I think this is a new practice. There is a paragraph on the significance of this work (follow the link to the paper),

Ferroelectricity has long been speculated to have important biological functions, although its very existence in biology has never been firmly established. Here, we present, to our knowledge, the first macroscopic observation of ferroelectric switching in a biological system, and we elucidate the origin and mechanism underpinning ferroelectric switching of elastin. It is discovered that the polarization in elastin is intrinsic at the monomer level, analogous to the unit cell level polarization in classical perovskite ferroelectrics. Our findings settle a long-standing question on ferroelectric switching in biology and establish ferroelectricity as an important biophysical property of proteins. We believe this is a critical first step toward resolving its physiological significance and pathological implications.

Protein nanomachines at the University of Washington

Scouring pad or protein nanomachine?

Caption: This is a computational model of a successfully designed two-component protein nanocage with tetrahedral symmetry. Credit: Dr. Vikram Mulligan

Caption: This is a computational model of a successfully designed two-component protein nanocage with tetrahedral symmetry.
Credit: Dr. Vikram Mulligan

This illustration of a protein nanocage reminded me of a type of scouring pad, which come to think of it, I haven’t seen in any stores for some years. Getting back on topic, this nanocage is a first step to building nanomachines according to a June 5, 2014 news item on Nanowerk,

A route for constructing protein nanomachines engineered for specific applications may be closer to reality.

Biological systems produce an incredible array of self-assembling, functional protein tools. Some examples of these nanoscale protein materials are scaffolds to anchor cellular activities, molecular motors to drive physiological events, and capsules for delivering viruses into host cells.

Scientists inspired by these sophisticated molecular machines want to build their own, with forms and functions customized to tackle modern-day challenges. The ability to design new protein nanostructures could have useful implications in targeted delivery of drugs, in vaccine development and in plasmonics, which is manipulating electromagnetic signals to guide light diffraction for information technologies, energy production or other uses.

A recently developed computational method may be an important step toward that goal. The project was led by the University of Washington’s [Washington state] Neil King, translational investigator; Jacob Bale, graduate student in Molecular and Cellular Biology; and William Sheffler in David Baker’s laboratory at the University of Washington Institute for Protein Design, in collaboration with colleagues at UCLA [University of California at Los Angeles] and Janelia Farm.

The work is based in the Rosetta macromolecular modeling package developed by Baker and his colleagues. The program was originally created to predict natural protein structures from amino acid sequences. Researchers in the Baker lab and around the world are increasingly using Rosetta to design new protein structures and sequences aimed at solving real-world problems.

A June 4 (?), 2014 University of Washington news release by Leila Gray (also on EurekAlert), which originated the news item, provides more detail about the models and what the scientists hope to accomplish,

“Proteins are amazing structures that can do remarkable things,” King said, “they can respond to changes in their environment. Exposure to a particular metabolite or a rise in temperature, for example, can trigger an alteration in a particular protein’s shape and function.” People often call proteins the building blocks of life.

“But unlike, say, a PVC pipe,” King said, “they are not simply construction material.” They are also construction (and demolition) workers — speeding up chemical reactions, breaking down food, carrying messages, interacting with each other, and performing countless other duties vital to life.

With the new software the scientists were able to create five novel, 24-subunit cage-like protein nanomaterials. Importantly, the actual structures, the researchers observed, were in very close agreement with their computer modeling.

Their method depends on encoding pairs of protein amino acid sequences with the information needed to direct molecular assembly through protein-protein interfaces. The interfaces not only provide the energetic forces that drive the assembly process, they also precisely orient the pairs of protein building blocks with the geometry required to yield the desired cage-like symmetric architectures.

Creating this cage-shaped protein, the scientists said, may be a first step towards building nano-scale containers. [emphasis mine] King said he looks forward to a time when cancer-drug molecules will be packaged inside of designed nanocages and delivered directly to tumor cells, sparing healthy cells.

“The problem today with cancer chemotherapy is that it hits every cell and makes the patient feel sick,” King said. Packaging the drugs inside customized nanovehicles with parking options restricted to cancer sites might circumvent the side effects.

The scientists note that combining just two types of symmetry elements, as in this study, can in theory give rise to a range of symmetrical shapes, such as cubic point groups, helices, layers, and crystals.

King explained that the immune system responds to repetitive, symmetric patterns, such as those on the surface of a virus or disease bacteria. Building nano-decoys may be a way train the immune system to attack certain types of pathogens.

“This concept may become the foundation for vaccines based on engineered nanomaterials,” King said. Further down the road, he and Bale anticipate that these design methods might also be useful for developing new clean energy technologies.

The scientists added in their report, “The precise control over interface geometry offered by our method enables the design of two-component protein nanomaterials with diverse nanoscale features, such as surfaces, pores, and internal volumes, with high accuracy.”

They went on to say that the combinations possible with two-component materials greatly expand the number and variety of potential nanomaterials that could be designed.

It may be possible to produce nanomaterials in a variety of sizes, shapes and arrangements, and also move on to construct increasingly more complex materials from more than two components.

The researchers emphasized that the long-term goal of such structures is not to be static. The hope is that they will mimic or go beyond the dynamic performance of naturally occurring protein assemblies, and that eventually novel molecular protein machines could be manufactured with programmable functions. [emphasis mine]

The researchers pointed out that although designing proteins and protein-based nanomaterials is very challenging due to the relative complexity of protein structures and interactions, there are now more than a handful of laboratories around the world making major strides in this field. Each of the leading contributors have key strengths, they said. The strengths of the UW team is in the accuracy of the match of the designed proteins to the computational models and the predictability of the results.

It seems like it’s going to be several years before we have protein nanomachines. Here’s a link to and a citation for the research paper,

Accurate design of co-assembling multi-component protein nanomaterials by Neil P. King, Jacob B. Bale, William Sheffler, Dan E. McNamara, Shane Gonen, Tamir Gonen, Todd O. Yeates, & David Baker. Nature 510, 103–108 (05 June 2014) doi:10.1038/nature13404 Published online 25 May 2014

This paper is behind a paywall but there is a free preview via ReadCube Access.

For anyone curious about the Rosetta macromolecular modeling package used in this work, you can find out more here at the Rosetta Commons website.  As for Janelia Farm, it is a research center in Virginia and is part of the Howard Hughes Medical Institute.

Saving the frogs (and other amphibians)

Given this blog’s name, I couldn’t pass up this May 1, 2014 news release from Simon Fraser University (located in Vancouver, Canada),

An ecological strategy developed by four researchers, including two from Simon Fraser University, aims to abate the grim future that the combination of two factors could inflict on many amphibians, including frogs and salamanders.

A warming climate and the introduction of non-native fish in the American West’s mountainous areas are combining to threaten the habitat that this ecologically critical group of species needs to thrive.

Previous studies predict the combined effect of climate change and non-native fish could cause amphibian populations to decline and even become locally extinct.

In their newly published study in the journal Frontiers in Ecology and the Environment, researchers examine this challenge and propose several new climate adaptation tools to reduce threats to amphibians.

The researchers say the novel suite of tools could help prioritize the restoration of amphibian habitats in Western North America’s mountainous regions.

Wendy Palen, an SFU ecologist, Maureen Ryan, a postdoctoral fellow at SFU and the University of Washington (UW), Michael Adams, a research ecologist at the U.S. Geological Survey and Regina Rochefort, a science advisor at Washington State’s North Cascades National Park, co-authored the paper.

Many amphibians in the American West’s mountainous areas need predator-free wetlands and lakes during their aquatic life stages. “Amphibians predominantly use mountainous areas’ small, shallow ponds to breed and feed,” explains Ryan, the study’s lead author.

“These kinds of wetlands are at the highest risk of drying up under climate change due to reduced snowpack and longer summer droughts. Non-native fish, such as brook and rainbow trout, were introduced for recreational fishing almost a century ago. They remove amphibians from the biggest and most stable lakes in the environment. Fish eat most amphibians and even at low densities can devour a lake’s whole amphibian population.”

Mindful of an opportunity to help amphibians, the researchers collaborated with UW colleagues to develop new maps and hydrological models of climate impacts specific to mountainous regions.

They are using these tools along with biological survey data to identify regions where native species are most threatened by the combined effects of climate change and fish. They then hope to work with area managers who would implement fish removals.

“Our work suggests that removing fish from strategic sites may restore resilience to landscapes where inaction might lead to tipping points of species loss,” says Palen.

The SFU Earth to Ocean Research Group member has been collaborating with Adams since 1999 to evaluate threats to amphibians in mountainous regions.

“We hope newly developed wetland modeling tools can improve climate adaptation action plans so that intact ecosystems persist in the face of a changing climate,” says Palen.

Hydrologists and remote sensors helped the researchers develop models that project a substantial loss of wetlands in America’s western mountains over the next 40 to 80 years.

They note the combined threat of climate change and fish to amphibian survival also exists in B.C. but records of where fish have been introduced are scarce.

The researchers remind us that 95 per cent of the American West’s lakes are currently stocked with non-native fish, so removing them from a few sites doesn’t threaten recreational fishing opportunities.

Let’s save some frogs

Sing a song of science literacy

Let’s applaud the American Educational Research Association for its plan to livestream part of its 2014 conference being held April 3 – 6, 2014 for free (you do have to register; pause for applause). Unfortunately, the one session I’d really like to hear is not one of the chosen ones. It’s the “Sing about Science: Leveraging the Power of Music to Improve Science Education” session being delivered by two researchers from the University of Washington (UW; state). From the April 2, 2014 UW news release (also on EurekAlert),

As the United States puts ever-greater emphasis on science, technology, engineering and mathematics education to keep competitive in the global economy, schools are trying to figure out how to improve student learning in science.

University of Washington researchers Katie Davis and Greg Crowther think music may be the answer for some kids. They studied the ability of music videos to enhance students’ understanding of scientific concepts.

Davis will present “Sing about Science: Leveraging the Power of Music to Improve Science Education” on Friday (April 4) at the American Educational Research Association’s annual conference.

Davis and Crowther aren’t just talking about music as a mnemonic device to help students memorize facts. Previous research has shown that music can reduce stress and increase student engagement in the learning process, so the researchers theorized that music videos could help some students process and retain information better.

“It makes sense that we shouldn’t teach all kids in the same way; we should individualize,” said Davis, an assistant professor in the UW’s Information School. “We need to provide multiple entry points in all subject matters. Music is a different entry point into scientific concepts.”

Crowther is a biologist but is so interested in music that 10 years ago he created a website with a database of songs about science and math; SingAboutScience.org now has links to more than 7,000 of them (the majority do not have video). Teachers can type in a topic and find music relevant to what they are teaching.

For their current research, they set up laptop computers at five science-related outreach events in Washington state. Most targeted students in K-12, but adults also participated. Participants in the study ranged from 3 to 76 years old, with a median age of 12. Each person sat in front of a laptop and selected a science-based music video to watch.

For instance, one video is titled “Fossil Rock Anthem,” and is a parody of the hip-hop song “Party Rock Anthem.” It shows a dancing archaeologist, graphics of fossils and ground striations and continental plates drifting. It’s a catchy tune with fun, colorful graphics.

Participants took a pre-video quiz of four questions related to information in the video, plus a bonus question not covered by the video. They were also asked to rate their confidence in their answers. They were randomly assigned to watch either a visually-rich music video or a music video that showed only the lyrics on screen. Then they took a post-video quiz that included the same content and confidence questions.

In two-thirds of the music videos (10 out of 15), participants had more correct answers after watching the videos. Quiz scores rose by an average of one more correct answer after watching the videos. The lyrics-only music videos were as beneficial to improving quiz scores as the visually-rich videos.

Participants improved their scores not only on factoid-type questions, but also the more complex comprehension questions, which shows that the videos improved people’s scientific understanding and not just memorization.

Pre- and post-quiz scores were no different for the bonus questions, which did not cover material from the videos. This finding suggests that the boost in quiz scores was due to watching the video, and not by some other variable.

The researchers say everyone learns in different ways, and past research has shown that students learn best with hands-on, personally relevant tools that utilize powers of observation and audio-visuals. They also note that a person’s memories can change based on an emotionally charged atmosphere. Since music is an emotional medium, it makes sense that our educational memory could be enhanced by it.

“We’re not saying this is the only way you should teach science, it’s just a different way,” Davis said. “We’re hoping it can engage a broader array of students, to help them find success and create identities as science learners.”

Added Crowther, “There wasn’t a teacher breathing down students’ necks telling them they had to learn this for a test. People voluntarily watched these videos for fun. This is exactly the type of opportunity we should be creating more of. Students will seek it out just because it’s fun and interesting.”

I went to Crowther’s website, Sing About Science (be careful, you may spend more time on the website than you planned), and picked this video from the listing,

It makes me think of protest songs from the 1960s. Here’s more about the video from its YouTube home,

Uploaded on Feb 25, 2011

NIMBioS Songwriter-in-Residence RB Morris performs his song “Science for the People.” For more information about the Songwriter-in-Residence program at the National Institute for Mathematical and Biological Synthesis (NIMBioS), visit http://www.nimbios.org/songwriter

I most recently mentioned NIMBioS in a November 1, 2013 interview with Canadian rapper and science afficionado, Baba Brinkman who has also been one of their artists-in-residence.