Monthly Archives: February 2018

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.

A 3D printed ‘living’ tattoo

MIT engineers have devised a 3-D printing technique that uses a new kind of ink made from genetically programmed living cells. Courtesy of the researchers [and MIT]

If that image isn’t enough, there’s also a video abstract (I don’t think I’ve seen one of these before) for the paper,

For those who’d still like to read the text, here’s more from a December 5, 2017 MIT (Massachusetts Institute of Technology) news release (also on EurekAlert),

MIT engineers have devised a 3-D printing technique that uses a new kind of ink made from genetically programmed living cells.

The cells are engineered to light up in response to a variety of stimuli. When mixed with a slurry of hydrogel and nutrients, the cells can be printed, layer by layer, to form three-dimensional, interactive structures and devices.

The team has then demonstrated its technique by printing a “living tattoo” — a thin, transparent patch patterned with live bacteria cells in the shape of a tree. Each branch of the tree is lined with cells sensitive to a different chemical or molecular compound. When the patch is adhered to skin that has been exposed to the same compounds, corresponding regions of the tree light up in response.

The researchers, led by Xuanhe Zhao, the Noyce Career Development Professor in MIT’s Department of Mechanical Engineering, and Timothy Lu, associate professor of biological engineering and of electrical engineering and computer science, say that their technique can be used to fabricate “active” materials for wearable sensors and interactive displays. Such materials can be patterned with live cells engineered to sense environmental chemicals and pollutants as well as changes in pH and temperature.

What’s more, the team developed a model to predict the interactions between cells within a given 3-D-printed structure, under a variety of conditions. The team says researchers can use the model as a guide in designing responsive living materials.

Zhao, Lu, and their colleagues have published their results today [December 5, 2017] in the journal Advanced Materials. The paper’s co-authors are graduate students Xinyue Liu, Hyunwoo Yuk, Shaoting Lin, German Alberto Parada, Tzu-Chieh Tang, Eléonore Tham, and postdoc Cesar de la Fuente-Nunez.

A hardy alternative

In recent years, scientists have explored a variety of responsive materials as the basis for 3D-printed inks. For instance, scientists have used inks made from temperature-sensitive polymers to print heat-responsive shape-shifting objects. Others have printed photoactivated structures from polymers that shrink and stretch in response to light.

Zhao’s team, working with bioengineers in Lu’s lab, realized that live cells might also serve as responsive materials for 3D-printed inks, particularly as they can be genetically engineered to respond to a variety of stimuli. The researchers are not the first to consider 3-D printing genetically engineered cells; others have attempted to do so using live mammalian cells, but with little success.

“It turns out those cells were dying during the printing process, because mammalian cells are basically lipid bilayer balloons,” Yuk says. “They are too weak, and they easily rupture.”

Instead, the team identified a hardier cell type in bacteria. Bacterial cells have tough cell walls that are able to survive relatively harsh conditions, such as the forces applied to ink as it is pushed through a printer’s nozzle. Furthermore, bacteria, unlike mammalian cells, are compatible with most hydrogels — gel-like materials that are made from a mix of mostly water and a bit of polymer. The group found that hydrogels can provide an aqueous environment that can support living bacteria.

The researchers carried out a screening test to identify the type of hydrogel that would best host bacterial cells. After an extensive search, a hydrogel with pluronic acid was found to be the most compatible material. The hydrogel also exhibited an ideal consistency for 3-D printing.

“This hydrogel has ideal flow characteristics for printing through a nozzle,” Zhao says. “It’s like squeezing out toothpaste. You need [the ink] to flow out of a nozzle like toothpaste, and it can maintain its shape after it’s printed.”

From tattoos to living computers

Lu provided the team with bacterial cells engineered to light up in response to a variety of chemical stimuli. The researchers then came up with a recipe for their 3-D ink, using a combination of bacteria, hydrogel, and nutrients to sustain the cells and maintain their functionality.

“We found this new ink formula works very well and can print at a high resolution of about 30 micrometers per feature,” Zhao says. “That means each line we print contains only a few cells. We can also print relatively large-scale structures, measuring several centimeters.”

They printed the ink using a custom 3-D printer that they built using standard elements combined with fixtures they machined themselves. To demonstrate the technique, the team printed a pattern of hydrogel with cells in the shape of a tree on an elastomer layer. After printing, they solidified, or cured, the patch by exposing it to ultraviolet radiation. They then adhere the transparent elastomer layer with the living patterns on it, to skin.

To test the patch, the researchers smeared several chemical compounds onto the back of a test subject’s hand, then pressed the hydrogel patch over the exposed skin. Over several hours, branches of the patch’s tree lit up when bacteria sensed their corresponding chemical stimuli.

The researchers also engineered bacteria to communicate with each other; for instance they programmed some cells to light up only when they receive a certain signal from another cell. To test this type of communication in a 3-D structure, they printed a thin sheet of hydrogel filaments with “input,” or signal-producing bacteria and chemicals, overlaid with another layer of filaments of an “output,” or signal-receiving bacteria. They found the output filaments lit up only when they overlapped and received input signals from corresponding bacteria .

Yuk says in the future, researchers may use the team’s technique to print “living computers” — structures with multiple types of cells that communicate with each other, passing signals back and forth, much like transistors on a microchip.

“This is very future work, but we expect to be able to print living computational platforms that could be wearable,” Yuk says.

For more near-term applications, the researchers are aiming to fabricate customized sensors, in the form of flexible patches and stickers that could be engineered to detect a variety of chemical and molecular compounds. They also envision their technique may be used to manufacture drug capsules and surgical implants, containing cells engineered produce compounds such as glucose, to be released therapeutically over time.

“We can use bacterial cells like workers in a 3-D factory,” Liu says. “They can be engineered to produce drugs within a 3-D scaffold, and applications should not be confined to epidermal devices. As long as the fabrication method and approach are viable, applications such as implants and ingestibles should be possible.”

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

3D Printing of Living Responsive Materials and Devices by Xinyue Liu, Hyunwoo Yuk, Shaoting Lin, German Alberto Parada, Tzu-Chieh Tang, Eléonore Tham, Cesar de la Fuente-Nunez, Timothy K. Lu, and Xuanhe Zhao. Advanced Materials DOI: 10.1002/adma.201704821 Version of Record online: 5 DEC 2017

© 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

This paper is behind a paywall.

Entanglement and biological systems

I think it was about five years ago thatI wrote a paper on something I called ‘cognitive entanglement’ (mentioned in my July 20,2012 posting) so the latest from Northwestern University (Chicago, Illinois, US) reignited my interest in entanglement. A December 5, 2017 news item on ScienceDaily describes the latest ‘entanglement’ research,

Nearly 75 years ago, Nobel Prize-winning physicist Erwin Schrödinger wondered if the mysterious world of quantum mechanics played a role in biology. A recent finding by Northwestern University’s Prem Kumar adds further evidence that the answer might be yes.

Kumar and his team have, for the first time, created quantum entanglement from a biological system. This finding could advance scientists’ fundamental understanding of biology and potentially open doors to exploit biological tools to enable new functions by harnessing quantum mechanics.

A December 5, 2017 Northwestern University news release (also on EurekAlert), which originated the news item, provides more detail,

“Can we apply quantum tools to learn about biology?” said Kumar, professor of electrical engineering and computer science in Northwestern’s McCormick School of Engineering and of physics and astronomy in the Weinberg College of Arts and Sciences. “People have asked this question for many, many years — dating back to the dawn of quantum mechanics. The reason we are interested in these new quantum states is because they allow applications that are otherwise impossible.”

Partially supported by the [US] Defense Advanced Research Projects Agency [DARPA], the research was published Dec. 5 [2017] in Nature Communications.

Quantum entanglement is one of quantum mechanics’ most mystifying phenomena. When two particles — such as atoms, photons, or electrons — are entangled, they experience an inexplicable link that is maintained even if the particles are on opposite sides of the universe. While entangled, the particles’ behavior is tied one another. If one particle is found spinning in one direction, for example, then the other particle instantaneously changes its spin in a corresponding manner dictated by the entanglement. Researchers, including Kumar, have been interested in harnessing quantum entanglement for several applications, including quantum communications. Because the particles can communicate without wires or cables, they could be used to send secure messages or help build an extremely fast “quantum Internet.”

“Researchers have been trying to entangle a larger and larger set of atoms or photons to develop substrates on which to design and build a quantum machine,” Kumar said. “My laboratory is asking if we can build these machines on a biological substrate.”

In the study, Kumar’s team used green fluorescent proteins, which are responsible for bioluminescence and commonly used in biomedical research. The team attempted to entangle the photons generated from the fluorescing molecules within the algae’s barrel-shaped protein structure by exposing them to spontaneous four-wave mixing, a process in which multiple wavelengths interact with one another to produce new wavelengths.

Through a series of these experiments, Kumar and his team successfully demonstrated a type of entanglement, called polarization entanglement, between photon pairs. The same feature used to make glasses for viewing 3D movies, polarization is the orientation of oscillations in light waves. A wave can oscillate vertically, horizontally, or at different angles. In Kumar’s entangled pairs, the photons’ polarizations are entangled, meaning that the oscillation directions of light waves are linked. Kumar also noticed that the barrel-shaped structure surrounding the fluorescing molecules protected the entanglement from being disrupted.

“When I measured the vertical polarization of one particle, we knew it would be the same in the other,” he said. “If we measured the horizontal polarization of one particle, we could predict the horizontal polarization in the other particle. We created an entangled state that correlated in all possibilities simultaneously.”

Now that they have demonstrated that it’s possible to create quantum entanglement from biological particles, next Kumar and his team plan to make a biological substrate of entangled particles, which could be used to build a quantum machine. Then, they will seek to understand if a biological substrate works more efficiently than a synthetic one.

Here’s an image accompanying the news release,

Featured in the cuvette on the left, green fluorescent proteins responsible for bioluninescence in jellyfish. Courtesy: Northwestern University

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

Generation of photonic entanglement in green fluorescent proteins by Siyuan Shi, Prem Kumar & Kim Fook Lee. Nature Communications 8, Article number: 1934 (2017) doi:10.1038/s41467-017-02027-9 Published online: 05 December 2017

This paper is open access.

Felted carbon nanotubes

Parachute (sculpted felt lantern). Artist and artisan felter: Chantal Cardinal. Studio: FELT à la main with LOVE

Scientists from Kiel University (Christian-Albrechts-Universität zu Kiel; Germany) and the University of Trento (Italy) claim to have developed a new method for integrating carbon nanotubes (CNTs) into new materials in a technique they describe as similar to felting according to a November 21, 2017 news item on Nanowerk,

Extremely lightweight, electrically highly conductive, and more stable than steel: due to their unique properties, carbon nanotubes would be ideal for numerous applications, from ultra-lightweight batteries to high-performance plastics, right through to medical implants. However, to date it has been difficult for science and industry to transfer the extraordinary characteristics at the nanoscale into a functional industrial application. The carbon nanotubes either cannot be combined adequately with other materials, or if they can be combined, they then lose their beneficial properties.

Scientists from the Functional Nanomaterials working group at Kiel University (CAU) and the University of Trento have now developed an alternative method, with which the tiny tubes can be combined with other materials, so that they retain their characteristic properties. As such, they “felt” the thread-like tubes into a stable 3D network that is able to withstand extreme forces.

In contrast to the ‘felted’ image which opened this posting, here’s an image of the ‘felted’ carbon nanotubes,

In this new process, the tiny, thread-like carbon nanotubes (CNTs) arrange themselves – almost like felting – to form a stable, tear-resistant layer. Photo/Copyright: Fabian Schütt Courtesy: Kiel University

A November 21, 2017 Kiel University press release (also on EurekAlert), which originated the news item, expands on the theme and adds another analogy,

Industry and science have been intensively researching the significantly less than one hundred nanometre wide carbon tubes (carbon nanotubes, CNTs), in order to make use of the extraordinary properties of rolled graphene. Yet much still remains just theory. “Although carbon nanotubes are flexible like fibre strands, they are also very sensitive to changes,” explained Professor Rainer Adelung, head of the Functional Nanomaterials working group at the CAU. “With previous attempts to chemically connect them with other materials, their molecular structure also changed. This, however, made their properties deteriorate – mostly drastically.”

In contrast, the approach of the research team from Kiel and Trento is based on a simple wet chemical infiltration process. The CNTs are mixed with water and dripped into an extremely porous ceramic material made of zinc oxide, which absorbs the liquid like a sponge. The dripped thread-like CNTs attach themselves to the ceramic scaffolding, and automatically form a stable layer together, similar to a felt. The ceramic scaffolding is coated with nanotubes, so to speak. This has fascinating effects, both for the scaffolding as well as for the coating of nanotubes.

On the one hand, the stability of the ceramic scaffold increases so massively that it can bear 100,000 times its own weight. “With the CNT coating, the ceramic material can hold around 7.5kg, and without it just 50g – as if we had fitted it with a close-fitting pullover made of carbon nanotubes, which provide mechanical support,” summarised first author Fabian Schütt. “The pressure on the material is absorbed by the tensile strength of the CNT felt. Compressive forces are transformed into tensile forces.”

The principle behind this is comparable with bamboo buildings [emphasis mine], such as those widespread in Asia. Here, bamboo stems are bound so tightly with a simple rope that the lightweight material can form extremely stable scaffolding, and even entire buildings. “We do the same at the nano-scale with the CNT threads, which wrap themselves around the ceramic material – only much, much smaller,” said Helge Krüger, co-author of the publication.

The materials scientists were able to demonstrate another major advantage of their process. In a second step, they dissolved the ceramic scaffolding by using a chemical etching process. All that remains is a fine 3D network of tubes, each of which consists of a layer of tiny CNT tubes. In this way, the researchers were able to greatly increase the felt surface, and thus create more opportunities for reactions. “We basically pack the surface of an entire beach volleyball field into a one centimetre cube,” explained Schütt. The huge hollow spaces inside the three-dimensional structure can then be filled with a polymer. As such, CNTs can be connected mechanically with plastics, without their molecular structure – and thus their properties – being modified. “We can specifically arrange the CNTs and manufacture an electrically conductive composite material. To do so only requires a fraction of the usual quantity of CNTs, in order to achieve the same conductivity,” said Schütt.

Applications for use range from battery and filter technology as a filling material for conductive plastics, implants for regenerative medicine, right through to sensors and electronic components at the nano-scale. The good electrical conductivity of the tear-resistant material could in future also be interesting for flexible electronics applications, in functional clothing or in the field of medical technology, for example. “Creating a plastic which, for example, stimulates bone or heart cells to grow is conceivable,” said Adelung. Due to its simplicity, the scientists agree that the process could also be transferred to network structures made of other nanomaterials – which will further expand the range of possible applications.

So, we have ‘felting’ and bamboo buildings. I can appreciate the temptation to use multiple analogies especially since I’ve given into it, on occasion.  But, it’s never considered good style, not even when I do it.

Getting back to the work at hand, here’s a link to and a citation for the paper,

Hierarchical self-entangled carbon nanotube tube networks by Fabian Schütt, Stefano Signetti, Helge Krüger, Sarah Röder, Daria Smazna, Sören Kaps, Stanislav N. Gorb, Yogendra Kumar Mishra, Nicola M. Pugno, & Rainer Adelung. Nature Communications 8, Article number: 1215 (2017) doi:10.1038/s41467-017-01324-7 Published online: 31 October 2017

This is an open access paper.

One final comment, I notice that one of the authors is Nicola Pugno who was last mentioned here in an August 30, 2017 posting titled: Making spider silk stronger by feeding graphene and carbon nanotubes to spiders.

A transatlantic report highlighting the risks and opportunities associated with synthetic biology and bioengineering

I love e-Life, the open access journal where its editors noted that a submitted synthetic biology and bioengineering report was replete with US and UK experts (along with a European or two) but no expert input from other parts of the world. In response the authors added ‘transatlantic’ to the title. It was a good decision since it was too late to add any new experts if the authors planned to have their paper published in the foreseeable future.

I’ve commented many times here when panels of experts include only Canadian, US, UK, and, sometimes, European or Commonwealth (Australia/New Zealand) experts that we need to broaden our perspectives and now I can add: or at least acknowledge (e.g. transatlantic) that the perspectives taken are reflective of a rather narrow range of countries.

Now getting to the report, here’s more from a November 21, 2017 University of Cambridge press release,

Human genome editing, 3D-printed replacement organs and artificial photosynthesis – the field of bioengineering offers great promise for tackling the major challenges that face our society. But as a new article out today highlights, these developments provide both opportunities and risks in the short and long term.

Rapid developments in the field of synthetic biology and its associated tools and methods, including more widely available gene editing techniques, have substantially increased our capabilities for bioengineering – the application of principles and techniques from engineering to biological systems, often with the goal of addressing ‘real-world’ problems.

In a feature article published in the open access journal eLife, an international team of experts led by Dr Bonnie Wintle and Dr Christian R. Boehm from the Centre for the Study of Existential Risk at the University of Cambridge, capture perspectives of industry, innovators, scholars, and the security community in the UK and US on what they view as the major emerging issues in the field.

Dr Wintle says: “The growth of the bio-based economy offers the promise of addressing global environmental and societal challenges, but as our paper shows, it can also present new kinds of challenges and risks. The sector needs to proceed with caution to ensure we can reap the benefits safely and securely.”

The report is intended as a summary and launching point for policy makers across a range of sectors to further explore those issues that may be relevant to them.

Among the issues highlighted by the report as being most relevant over the next five years are:

Artificial photosynthesis and carbon capture for producing biofuels

If technical hurdles can be overcome, such developments might contribute to the future adoption of carbon capture systems, and provide sustainable sources of commodity chemicals and fuel.

Enhanced photosynthesis for agricultural productivity

Synthetic biology may hold the key to increasing yields on currently farmed land – and hence helping address food security – by enhancing photosynthesis and reducing pre-harvest losses, as well as reducing post-harvest and post-consumer waste.

Synthetic gene drives

Gene drives promote the inheritance of preferred genetic traits throughout a species, for example to prevent malaria-transmitting mosquitoes from breeding. However, this technology raises questions about whether it may alter ecosystems [emphasis mine], potentially even creating niches where a new disease-carrying species or new disease organism may take hold.

Human genome editing

Genome engineering technologies such as CRISPR/Cas9 offer the possibility to improve human lifespans and health. However, their implementation poses major ethical dilemmas. It is feasible that individuals or states with the financial and technological means may elect to provide strategic advantages to future generations.

Defence agency research in biological engineering

The areas of synthetic biology in which some defence agencies invest raise the risk of ‘dual-use’. For example, one programme intends to use insects to disseminate engineered plant viruses that confer traits to the target plants they feed on, with the aim of protecting crops from potential plant pathogens – but such technologies could plausibly also be used by others to harm targets.

In the next five to ten years, the authors identified areas of interest including:

Regenerative medicine: 3D printing body parts and tissue engineering

While this technology will undoubtedly ease suffering caused by traumatic injuries and a myriad of illnesses, reversing the decay associated with age is still fraught with ethical, social and economic concerns. Healthcare systems would rapidly become overburdened by the cost of replenishing body parts of citizens as they age and could lead new socioeconomic classes, as only those who can pay for such care themselves can extend their healthy years.

Microbiome-based therapies

The human microbiome is implicated in a large number of human disorders, from Parkinson’s to colon cancer, as well as metabolic conditions such as obesity and type 2 diabetes. Synthetic biology approaches could greatly accelerate the development of more effective microbiota-based therapeutics. However, there is a risk that DNA from genetically engineered microbes may spread to other microbiota in the human microbiome or into the wider environment.

Intersection of information security and bio-automation

Advancements in automation technology combined with faster and more reliable engineering techniques have resulted in the emergence of robotic ‘cloud labs’ where digital information is transformed into DNA then expressed in some target organisms. This opens the possibility of new kinds of information security threats, which could include tampering with digital DNA sequences leading to the production of harmful organisms, and sabotaging vaccine and drug production through attacks on critical DNA sequence databases or equipment.

Over the longer term, issues identified include:

New makers disrupt pharmaceutical markets

Community bio-labs and entrepreneurial startups are customizing and sharing methods and tools for biological experiments and engineering. Combined with open business models and open source technologies, this could herald opportunities for manufacturing therapies tailored to regional diseases that multinational pharmaceutical companies might not find profitable. But this raises concerns around the potential disruption of existing manufacturing markets and raw material supply chains as well as fears about inadequate regulation, less rigorous product quality control and misuse.

Platform technologies to address emerging disease pandemics

Emerging infectious diseases—such as recent Ebola and Zika virus disease outbreaks—and potential biological weapons attacks require scalable, flexible diagnosis and treatment. New technologies could enable the rapid identification and development of vaccine candidates, and plant-based antibody production systems.

Shifting ownership models in biotechnology

The rise of off-patent, generic tools and the lowering of technical barriers for engineering biology has the potential to help those in low-resource settings, benefit from developing a sustainable bioeconomy based on local needs and priorities, particularly where new advances are made open for others to build on.

Dr Jenny Molloy comments: “One theme that emerged repeatedly was that of inequality of access to the technology and its benefits. The rise of open source, off-patent tools could enable widespread sharing of knowledge within the biological engineering field and increase access to benefits for those in developing countries.”

Professor Johnathan Napier from Rothamsted Research adds: “The challenges embodied in the Sustainable Development Goals will require all manner of ideas and innovations to deliver significant outcomes. In agriculture, we are on the cusp of new paradigms for how and what we grow, and where. Demonstrating the fairness and usefulness of such approaches is crucial to ensure public acceptance and also to delivering impact in a meaningful way.”

Dr Christian R. Boehm concludes: “As these technologies emerge and develop, we must ensure public trust and acceptance. People may be willing to accept some of the benefits, such as the shift in ownership away from big business and towards more open science, and the ability to address problems that disproportionately affect the developing world, such as food security and disease. But proceeding without the appropriate safety precautions and societal consensus—whatever the public health benefits—could damage the field for many years to come.”

The research was made possible by the Centre for the Study of Existential Risk, the Synthetic Biology Strategic Research Initiative (both at the University of Cambridge), and the Future of Humanity Institute (University of Oxford). It was based on a workshop co-funded by the Templeton World Charity Foundation and the European Research Council under the European Union’s Horizon 2020 research and innovation programme.

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

A transatlantic perspective on 20 emerging issues in biological engineering by Bonnie C Wintle, Christian R Boehm, Catherine Rhodes, Jennifer C Molloy, Piers Millett, Laura Adam, Rainer Breitling, Rob Carlson, Rocco Casagrande, Malcolm Dando, Robert Doubleday, Eric Drexler, Brett Edwards, Tom Ellis, Nicholas G Evans, Richard Hammond, Jim Haseloff, Linda Kahl, Todd Kuiken, Benjamin R Lichman, Colette A Matthewman, Johnathan A Napier, Seán S ÓhÉigeartaigh, Nicola J Patron, Edward Perello, Philip Shapira, Joyce Tait, Eriko Takano, William J Sutherland. eLife; 14 Nov 2017; DOI: 10.7554/eLife.30247

This paper is open access and the editors have included their notes to the authors and the authors’ response.

You may have noticed that I highlighted a portion of the text concerning synthetic gene drives. Coincidentally I ran across a November 16, 2017 article by Ed Yong for The Atlantic where the topic is discussed within the context of a project in New Zealand, ‘Predator Free 2050’ (Note: A link has been removed),

Until the 13th century, the only land mammals in New Zealand were bats. In this furless world, local birds evolved a docile temperament. Many of them, like the iconic kiwi and the giant kakapo parrot, lost their powers of flight. Gentle and grounded, they were easy prey for the rats, dogs, cats, stoats, weasels, and possums that were later introduced by humans. Between them, these predators devour more than 26 million chicks and eggs every year. They have already driven a quarter of the nation’s unique birds to extinction.

Many species now persist only in offshore islands where rats and their ilk have been successfully eradicated, or in small mainland sites like Zealandia where they are encircled by predator-proof fences. The songs in those sanctuaries are echoes of the New Zealand that was.

But perhaps, they also represent the New Zealand that could be.

In recent years, many of the country’s conservationists and residents have rallied behind Predator-Free 2050, an extraordinarily ambitious plan to save the country’s birds by eradicating its invasive predators. Native birds of prey will be unharmed, but Predator-Free 2050’s research strategy, which is released today, spells doom for rats, possums, and stoats (a large weasel). They are to die, every last one of them. No country, anywhere in the world, has managed such a task in an area that big. The largest island ever cleared of rats, Australia’s Macquarie Island, is just 50 square miles in size. New Zealand is 2,000 times bigger. But, the country has committed to fulfilling its ecological moonshot within three decades.

In 2014, Kevin Esvelt, a biologist at MIT, drew a Venn diagram that troubles him to this day. In it, he and his colleagues laid out several possible uses for gene drives—a nascent technology for spreading designer genes through groups of wild animals. Typically, a given gene has a 50-50 chance of being passed to the next generation. But gene drives turn that coin toss into a guarantee, allowing traits to zoom through populations in just a few generations. There are a few natural examples, but with CRISPR, scientists can deliberately engineer such drives.

Suppose you have a population of rats, roughly half of which are brown, and the other half white. Now, imagine there is a gene that affects each rat’s color. It comes in two forms, one leading to brown fur, and the other leading to white fur. A male with two brown copies mates with a female with two white copies, and all their offspring inherit one of each. Those offspring breed themselves, and the brown and white genes continue cascading through the generations in a 50-50 split. This is the usual story of inheritance. But you can subvert it with CRISPR, by programming the brown gene to cut its counterpart and replace it with another copy of itself. Now, the rats’ children are all brown-furred, as are their grandchildren, and soon the whole population is brown.

Forget fur. The same technique could spread an antimalarial gene through a mosquito population, or drought-resistance through crop plants. The applications are vast, but so are the risks. In theory, gene drives spread so quickly and relentlessly that they could rewrite an entire wild population, and once released, they would be hard to contain. If the concept of modifying the genes of organisms is already distasteful to some, gene drives magnify that distaste across national, continental, and perhaps even global scales.

These excerpts don’t do justice to this thought-provoking article. If you have time, I recommend reading it in its entirety  as it provides some insight into gene drives and, with some imagination on the reader’s part, the potential for the other technologies discussed in the report.

One last comment, I notice that Eric Drexler is cited as on the report’s authors. He’s familiar to me as K. Eric Drexler, the author of the book that popularized nanotechnology in the US and other countries, Engines of Creation (1986) .

New nanomapping technology: CRISPR-CAS9 as a programmable nanoparticle

A November 21, 2017 news item on Nanowerk describes a rather extraordinary (to me, anyway) approach to using CRRISP ( Clustered Regularly Interspaced Short Palindromic Repeats)-CAS9 (Note: A link has been removed),

A team of scientists led by Virginia Commonwealth University physicist Jason Reed, Ph.D., have developed new nanomapping technology that could transform the way disease-causing genetic mutations are diagnosed and discovered. Described in a study published today [November 21, 2017] in the journal Nature Communications (“DNA nanomapping using CRISPR-Cas9 as a programmable nanoparticle”), this novel approach uses high-speed atomic force microscopy (AFM) combined with a CRISPR-based chemical barcoding technique to map DNA nearly as accurately as DNA sequencing while processing large sections of the genome at a much faster rate. What’s more–the technology can be powered by parts found in your run-of-the-mill DVD player.

A November 21, 2017 Virginia Commonwealth University news release by John Wallace, which originated the news item, provides more detail,

The human genome is made up of billions of DNA base pairs. Unraveled, it stretches to a length of nearly six feet long. When cells divide, they must make a copy of their DNA for the new cell. However, sometimes various sections of the DNA are copied incorrectly or pasted together at the wrong location, leading to genetic mutations that cause diseases such as cancer. DNA sequencing is so precise that it can analyze individual base pairs of DNA. But in order to analyze large sections of the genome to find genetic mutations, technicians must determine millions of tiny sequences and then piece them together with computer software. In contrast, biomedical imaging techniques such as fluorescence in situ hybridization, known as FISH, can only analyze DNA at a resolution of several hundred thousand base pairs.

Reed’s new high-speed AFM method can map DNA to a resolution of tens of base pairs while creating images up to a million base pairs in size. And it does it using a fraction of the amount of specimen required for DNA sequencing.

“DNA sequencing is a powerful tool, but it is still quite expensive and has several technological and functional limitations that make it difficult to map large areas of the genome efficiently and accurately,” said Reed, principal investigator on the study. Reed is a member of the Cancer Molecular Genetics research program at VCU Massey Cancer Center and an associate professor in the Department of Physics in the College of Humanities and Sciences.

“Our approach bridges the gap between DNA sequencing and other physical mapping techniques that lack resolution,” he said. “It can be used as a stand-alone method or it can complement DNA sequencing by reducing complexity and error when piecing together the small bits of genome analyzed during the sequencing process.”

IBM scientists made headlines in 1989 when they developed AFM technology and used a related technique to rearrange molecules at the atomic level to spell out “IBM.” AFM achieves this level of detail by using a microscopic stylus — similar to a needle on a record player — that barely makes contact with the surface of the material being studied. The interaction between the stylus and the molecules creates the image. However, traditional AFM is too slow for medical applications and so it is primarily used by engineers in materials science.

“Our device works in the same fashion as AFM but we move the sample past the stylus at a much greater velocity and use optical instruments to detect the interaction between the stylus and the molecules. We can achieve the same level of detail as traditional AFM but can process material more than a thousand times faster,” said Reed, whose team proved the technology can be mainstreamed by using optical equipment found in DVD players. “High-speed AFM is ideally suited for some medical applications as it can process materials quickly and provide hundreds of times more resolution than comparable imaging methods.”

Increasing the speed of AFM was just one hurdle Reed and his colleagues had to overcome. In order to actually identify genetic mutations in DNA, they had to develop a way to place markers or labels on the surface of the DNA molecules so they could recognize patterns and irregularities. An ingenious chemical barcoding solution was developed using a form of CRISPR technology.

CRISPR has made a lot of headlines recently in regard to gene editing. CRISPR is an enzyme that scientists have been able to “program” using targeting RNA in order to cut DNA at precise locations that the cell then repairs on its own. Reed’s team altered the chemical reaction conditions of the CRISPR enzyme so that it only sticks to the DNA and does not actually cut it.

“Because the CRISPR enzyme is a protein that’s physically bigger than the DNA molecule, it’s perfect for this barcoding application,” Reed said. “We were amazed to discover this method is nearly 90 percent efficient at bonding to the DNA molecules. And because it’s easy to see the CRISPR proteins, you can spot genetic mutations among the patterns in DNA.”

To demonstrate the technique’s effectiveness, the researchers mapped genetic translocations present in lymph node biopsies of lymphoma patients. Translocations occur when one section of the DNA gets copied and pasted to the wrong place in the genome. They are especially prevalent in blood cancers such as lymphoma but occur in other cancers as well.

While there are many potential uses for this technology, Reed and his team are focusing on medical applications. They are currently developing software based on existing algorithms that can analyze patterns in sections of DNA up to and over a million base pairs in size. Once completed, it would not be hard to imagine this shoebox-sized instrument in pathology labs assisting in the diagnosis and treatment of diseases linked to genetic mutations.

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

DNA nanomapping using CRISPR-Cas9 as a programmable nanoparticle by Andrey Mikheikin, Anita Olsen, Kevin Leslie, Freddie Russell-Pavier, Andrew Yacoot, Loren Picco, Oliver Payton, Amir Toor, Alden Chesney, James K. Gimzewski, Bud Mishra, & Jason Reed. Nature Communications 8, Article number: 1665 (2017) doi:10.1038/s41467-017-01891-9 Published online: 21 November 2017

This paper is open access.

Paving the way for hardware neural networks?

I’m glad the Imperial College of London (ICL; UK) translated this research into something I can, more or less, understand because the research team’s title for their paper would have left me ‘confuzzled’ .Thank you for this November 20, 2017 ICL press release (also on EurekAlert) by Hayley Dunning,

Researchers have shown how to write any magnetic pattern desired onto nanowires, which could help computers mimic how the brain processes information.

Much current computer hardware, such as hard drives, use magnetic memory devices. These rely on magnetic states – the direction microscopic magnets are pointing – to encode and read information.

Exotic magnetic states – such as a point where three south poles meet – represent complex systems. These may act in a similar way to many complex systems found in nature, such as the way our brains process information.

Computing systems that are designed to process information in similar ways to our brains are known as ‘neural networks’. There are already powerful software-based neural networks – for example one recently beat the human champion at the game ‘Go’ – but their efficiency is limited as they run on conventional computer hardware.

Now, researchers from Imperial College London have devised a method for writing magnetic information in any pattern desired, using a very small magnetic probe called a magnetic force microscope.

With this new writing method, arrays of magnetic nanowires may be able to function as hardware neural networks – potentially more powerful and efficient than software-based approaches.

The team, from the Departments of Physics and Materials at Imperial, demonstrated their system by writing patterns that have never been seen before. They published their results today [November 20, 2017] in Nature Nanotechnology.

Interlocking hexagon patterns with complex magnetisation

‘Hexagonal artificial spin ice ground state’ – a pattern never demonstrated before. Coloured arrows show north or south polarisation

Dr Jack Gartside, first author from the Department of Physics, said: “With this new writing method, we open up research into ‘training’ these magnetic nanowires to solve useful problems. If successful, this will bring hardware neural networks a step closer to reality.”

As well as applications in computing, the method could be used to study fundamental aspects of complex systems, by creating magnetic states that are far from optimal (such as three south poles together) and seeing how the system responds.

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

Realization of ground state in artificial kagome spin ice via topological defect-driven magnetic writing by Jack C. Gartside, Daan M. Arroo, David M. Burn, Victoria L. Bemmer, Andy Moskalenko, Lesley F. Cohen & Will R. Branford. Nature Nanotechnology (2017) doi:10.1038/s41565-017-0002-1 Published online: 20 November 2017

This paper is behind a paywall.

*Odd spacing eliminated and a properly embedded video added on February 6, 2018 at 18:16 hours PT.

Colliding organic nanoparticles caught on camera for the first time

There is high excitement about this development in a November 17, 2017 news item on Nanowerk,

A Northwestern University research team is the first to capture on video organic nanoparticles colliding and fusing together. This unprecedented view of “chemistry in motion” will aid Northwestern nanoscientists developing new drug delivery methods as well as demonstrate to researchers around the globe how an emerging imaging technique opens a new window on a very tiny world.

A November 17, 2017 Northwestern University news release (also on EurekAlert) by Megan Fellman, which originated the news item, further illuminates the matter,

This is a rare example of particles in motion. The dynamics are reminiscent of two bubbles coming together and merging into one: first they join and have a membrane between them, but then they fuse and become one larger bubble.

“I had an image in my mind, but the first time I saw these fusing nanoparticles in black and white was amazing,” said professor Nathan C. Gianneschi, who led the interdisciplinary study and works at the intersection of nanotechnology and biomedicine.

“To me, it’s literally a window opening up to this world you have always known was there, but now you’ve finally got an image of it. I liken it to the first time I saw Jupiter’s moons through a telescope. Nothing compares to actually seeing,” he said.

Gianneschi is the Jacob and Rosaline Cohn Professor in the department of chemistry in the Weinberg College of Arts and Sciences and in the departments of materials science and engineering and of biomedical engineering in the McCormick School of Engineering.

The study, which includes videos of different nanoparticle fusion events, was published today (Nov. 1 [2017]7) by the Journal of the American Chemical Society.

The research team used liquid-cell transmission electron microscopy to directly image how polymer-based nanoparticles, or micelles, that Gianneschi’s lab is developing for treating cancer and heart attacks change over time. The powerful new technique enabled the scientists to directly observe the particles’ transformation and characterize their dynamics.

“We can see on the molecular level how the polymeric matter rearranges when the particles fuse into one object,” said Lucas R. Parent, first author of the paper and a National Institutes of Health Postdoctoral Fellow in Gianneschi’s research group. “This is the first study of many to come in which researchers will use this method to look at all kinds of dynamic phenomena in organic materials systems on the nanoscale.”

In the Northwestern study, organic particles in water bounce off each other, and some collide and merge, undergoing a physical transformation. The researchers capture the action by shining an electron beam through the sample. The tiny particles — the largest are only approximately 200 nanometers in diameter — cast shadows that are captured directly by a camera below.

“We’ve observed classical fusion behavior on the nanoscale,” said Gianneschi, a member of Northwestern’s International Institute for Nanotechnology. “Capturing the fundamental growth and evolution processes of these particles in motion will help us immensely in our work with synthetic materials and their interactions with biological systems.”

The National Institutes of Health, the National Science Foundation, the Air Force Office of Scientific Research and the Army Research Office supported the research.

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

Directly Observing Micelle Fusion and Growth in Solution by Liquid-Cell Transmission Electron Microscopy by Lucas R. Parent, Evangelos Bakalis, Abelardo Ramírez-Hernández, Jacquelin K. Kammeyer, Chiwoo Park, Juan de Pablo, Francesco Zerbetto, Joseph P. Patterson, and Nathan C. Gianneschi. J. Am. Chem. Soc., Article ASAP DOI: 10.1021/jacs.7b09060 Publication Date (Web): November 17, 2017

Copyright © 2017 American Chemical Society

This paper is behind a paywall.