Category Archives: synthetic biology

UK’s National Physical Laboratory reaches out to ‘BioTouch’ MIT and UCL

This March 27, 2014 news item on Azonano is an announcement for a new project featuring haptics and self-assembly,

NPL (UK’s National Physical Laboratory) has started a new strategic research partnership with UCL (University College of London) and MIT (Massachusetts Institute of Technology) focused on haptic-enabled sensing and micromanipulation of biological self-assembly – BioTouch.

The NPL March 27, 2014 news release, which originated the news item, is accompanied by a rather interesting image,

A computer operated dexterous robotic hand holding a microscope slide with a fluorescent human cell (not to scale) embedded into a synthetic extracellular matrix. Courtesy: NPL

A computer operated dexterous
robotic hand holding a microscope
slide with a fluorescent human cell
(not to scale) embedded into a
synthetic extracellular matrix. Courtesy: NPL

The news release goes on to describe the BioTouch project in more detail (Note: A link has been removed),

The project will probe sensing and application of force and related vectors specific to biological self-assembly as a means of synthetic biology and nanoscale construction. The overarching objective is to enable the re-programming of self-assembled patterns and objects by directed micro-to-nano manipulation with compliant robotic haptic control.

This joint venture, funded by the European Research Council, EPSRC and NPL’s Strategic Research Programme, is a rare blend of interdisciplinary research bringing together expertise in robotics, haptics and machine vision with synthetic and cell biology, protein design, and super- and high-resolution microscopy. The research builds on the NPL’s pioneering developments in bioengineering and imaging and world-leading haptics technologies from UCL and MIT.

Haptics is an emerging enabling tool for sensing and manipulation through touch, which holds particular promise for the development of autonomous robots that need to perform human-like functions in unstructured environments. However, the path to all such applications is hampered by the lack of a compliant interface between a predictably assembled biological system and a human user. This research will enable human directed micro-manipulation of experimental biological systems using cutting-edge robotic systems and haptic feedback.

Recently the UK government has announced ‘eight great technologies’ in which Britain is to become a world leader. Robotics, synthetic biology, regenerative medicine and advanced materials are four of these technologies for which this project serves as a merging point providing thus an excellent example of how multidisciplinary collaborative research can shape our future.

If it read this rightly, it means they’re trying to design systems where robots will work directly with materials in the labs while humans direct the robots’ actions from a remote location. My best example of this (it’s not a laboratory example) would be of a surgery where a robot actually performs the work while a human directs the robot’s actions based on haptic (touch) information the human receives from the robot. Surgeons don’t necessarily see what they’re dealing with, they may be feeling it with their fingers (haptic information). In effect, the robot’s hands become an extension of the surgeon’s hands. I imagine using a robot’s ‘hands’ would allow for less invasive procedures to be performed.

Learn to love slime; it may help you to compute in the future

Eeeewww! Slime or slime mold is not well loved and yet scientists seem to retain a certain affection for it, if their efforts at researching ways to make it useful could be termed affection. A March 27, 2014 news item on Nanowerk highlights a project where scientists have used slime and nanoparticles to create logic units (precursors to computers; Note: A link has been removed),

A future computer might be a lot slimier than the solid silicon devices we have today. In a study published in the journal Materials Today (“Slime mold microfluidic logical gates”), European researchers reveal details of logic units built using living slime molds, which might act as the building blocks for computing devices and sensors.

The March 27, 2014 Elsevier press release, which originated the news item, describes the researchers and their work in more detail,

Andrew Adamatzky (University of the West of England, Bristol, UK) and Theresa Schubert (Bauhaus-University Weimar, Germany) have constructed logical circuits that exploit networks of interconnected slime mold tubes to process information.

One is more likely to find the slime mold Physarum polycephalum living somewhere dark and damp rather than in a computer science lab. In its “plasmodium” or vegetative state, the organism spans its environment with a network of tubes that absorb nutrients. The tubes also allow the organism to respond to light and changing environmental conditions that trigger the release of reproductive spores.

In earlier work, the team demonstrated that such a tube network could absorb and transport different colored dyes. They then fed it edible nutrients – oat flakes – to attract tube growth and common salt to repel them, so that they could grow a network with a particular structure. They then demonstrated how this system could mix two dyes to make a third color as an “output”.

Using the dyes with magnetic nanoparticles and tiny fluorescent beads, allowed them to use the slime mold network as a biological “lab-on-a-chip” device. This represents a new way to build microfluidic devices for processing environmental or medical samples on the very small scale for testing and diagnostics, the work suggests. The extension to a much larger network of slime mold tubes could process nanoparticles and carry out sophisticated Boolean logic operations of the kind used by computer circuitry. The team has so far demonstrated that a slime mold network can carry out XOR or NOR Boolean operations. Chaining together arrays of such logic gates might allow a slime mold computer to carry out binary operations for computation.

“The slime mold based gates are non-electronic, simple and inexpensive, and several gates can be realized simultaneously at the sites where protoplasmic tubes merge,” conclude Adamatzky and Schubert.

Are we entering the age of the biological computer? Stewart Bland, Editor of Materials Today, believes that “although more traditional electronic materials are here to stay, research such as this is helping to push and blur the boundaries of materials science, computer science and biology, and represents an exciting prospect for the future.

I did look at the researchers’ paper and it is fascinating even to someone (me) who doesn’t understand the science very well. Here’s a link to and a citation for the paper,

Slime mold microfluidic logical gates by Andrew Adamatzky and Theresa Schubert. Materials Today, Volume 17, Issue 2, March 2014, Pages 86–91 (2014) published by Elsevier. http://dx.doi.org/10.1016/j.mattod.2014.01.018 The article is available for free at www.materialstoday.com

Yes, it’s an open access paper published by Elsevier, good on them!

An entire chemistry lab (nanofactory) in a droplet

I love the blue in this image, which illustrates the thousand-droplets test, research suggesting the possibility of a nanofactory or laboratory within a droplet ,

Droplets with a diameter of only a few micrometers act as the reaction vessels for a complex oscillating reaction - Photo: Maximilian Weitz / TUM

Droplets with a diameter of only a few micrometers act as the reaction vessels for a complex oscillating reaction – Photo: Maximilian Weitz / TUM

A Feb. 19, 2014 news item on Azonano reveals more,

An almost infinite number of complex and interlinked reactions take place in a biological cell. In order to be able to better investigate these networks, scientists led by Professor Friedrich Simmel, Chair of Systems Biophysics and Nano Biophysics at the Technische Universitaet Muenchen (TUM) try to replicate them with the necessary components in a kind of artificial cell.

This is also motivated by the thought of one day using such single-cell systems for example as “nanofactories” for the production of complex organic substances or biomaterials.

All such experiments have so far predominantly worked with very simple reactions, however. NIM Professor Friedrich Simmel and his team have now for the first time managed to let a more complex biochemical reaction take place in tiny droplets of only a few micrometers in size. Together with co-authors from the University of California Riverside and the California Institute of Technology in Pasadena, USA, the scientists are presenting their findings in the current edition of Nature Chemistry.

The Feb. 18, 2014 TUM press release, which originated the news item, details the experiements,

Shaking once – investigating thousands of times

The experiment is conducted by putting an aqueous reaction solution into oil and shaking the mixture vigorously. The result is an emulsion consisting of thousands of droplets. Employing only a tiny amount of material, the scientists have thus found a cost-efficient and quick way of setting up an extremely large number of experiments simultaneously.

As a test system, the researchers chose a so-called biochemical oscillator. This involves several reactions with DNA and RNA, which take place repetitively one after the other. Their rhythm becomes visible because in one step two DNA strands bind to each other in such a way that a fluorescent dye shines. This regular blinking is then recorded with special cameras.

Small droplets – huge differences

In the first instance, Friedrich Simmel and his colleagues intended to investigate the principal behavior of a complex reaction system if scaled down to the size of a cell. In addition, they specifically wondered if all droplet systems displayed an identical behavior and what factors would cause possible differences.

Their experiments showed that the oscillations in the individual droplets differed strongly, that is to say, much stronger than might have been expected from a simple statistical model. It was above all evident that small drops display stronger variations than large ones. “It is indeed surprising that we could witness a similar variability and individuality in a comparatively simple chemical system as is known from biological cells”, explains Friedrich Simmel the results.

Thus, it is currently not possible to realize systems which are absolutely identical. This de facto means that researchers have to either search for ways to correct these variations or factor them in from the start. On the other hand, the numerous slightly differing systems could also be used specifically to pick out the one desired, optimally running set-up from thousands of systems.

Investigating complex biosynthetic systems in artificial cells opens up many other questions, as well. In a next step, Friedrich Simmel plans to address the underlying theoretical models: “The highly parallel recording of the emulsion droplets enabled us to acquire plenty of interesting data. Our goal is to use these data to review and improve the theoretical models of biochemical reaction networks at small molecule numbers.”

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

Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator by Maximilian Weitz, Jongmin Kim, Korbinian Kapsner, Erik Winfree, Elisa Franco, & Friedrich C. Simmel. Nature Chemistry (2014) doi:10.1038/nchem.1869 Published online 16 February 2014

This paper is behind a paywall.

*2700th posting: new generation of hybird memristive nanodevices and an update of HP labs and its memristive products

Hard to believe this is the *2700th posting but yay! To commemorate this special occasion I’m featuring two items about memristors, work on protein-based memristors and an update of my Feb. 7, 2013 posting on the HP Labs and its promises of memristor-based products.

Michael Berger’s Dec. 16, 2013 issue of Nanowerk Spotlight focused on memristor research from bioengineers at Singapore’s Nanyang Technological University (Note: Links have been removed),

 Based on the rapid development of synthetic chemistry and bioengineering, researchers have begun to build hybrid nanostructures with various biomolecules to fulfill the functional requirements of advanced nanocircuits. Proteins already perform functions such as signalling, charge transport or storage, in all biochemical processes.

“Although the diversity of these natural molecules is vast – for instance, more than a million variants of an individual protein may be created via genetic engineering – tailoring their structures to fit the variable and complex requirements of both the biological and non-biological world is achievable by leveraging on the rapidly developing bioengineering field,” Xiaodong Chen, an Associate Professor in the School of Materials Science & Engineering at Nanyang Technological University, tells Nanowerk. “On a parallel note, bioengineering may provide an alternative approach to tune the structural and electronic properties of functional molecules leading to further development in the field of molecular electronics.”

Berger provides more context on this work by way of a 2011 Spotlight about the research (featured in my Sept. 19, 2011 posting) and then describes Chen’s latest work,

In new work, reported in a recent edition of Small (“Bioengineered Tunable Memristor Based on Protein Nanocage”) Chen and his team demonstrate a strategy for the fabrication of memristive nanodevices with stable and tunable performance by assembling ferritin monolayer inside a on-wire lithography-generated ∼12 nm gap.

Whereas the protein-based memristor devices in the previous work were fabricated from the commercial horse spleen ferritin, the new work uses the unique high iron loading capacity of Archaeoglobus fulgidus ferritin (AfFtn).

“We hypothesized that if the composition of this iron complex core can be modulated, the switching performance of the protein-based device can be controlled accordingly,” says Chen.

They found that the (tunable) iron loading in the AfFtn nanocages drastically impacts the performance of the memristive devices. The higher iron loading amount contributes to better memristive performance due to higher electrochemical activity of the ferric complex core.

This work is not going to be found in any applications for molecular devices at any time soon but it seems promising at this stage. For those who’d like more information, there’s Berger’s article or this link and a citation to the researchers’ paper,

Bioengineered Tunable Memristor Based on Protein Nanocage by Fanben Meng, Barindra Sana, Yuangang Li, Yuanjun Liu, Sierin Lim, & Xiaodong Chen. Article first published online: 19 AUG 2013 DOI: 10.1002/smll.201300810
© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

This paper is behind a paywall but Wiley does offer a number of viewing options at different price points.

HP Labs and its memristor-based products

Following on last year’s Feb. 7, 2013 update (scroll down about 1/2 way), it seems like another annual update is in order unfortunately, the news seems like a retread. Memristor’-based devices from HP Labs will not be launched (in the marketplace or even to show at technology shows) this year either. In fact, any sort of launch is much further in the future according to Chris Mellor’s Nov. 1, 2013 article for The Register; Note: Links have been removed),

HP has warned El Reg not to get its hopes up too high after the tech titan’s CTO Martin Fink suggested StoreServ arrays could be packed with 100TB Memristor drives come 2018.

In five years, according to Fink, DRAM and NAND scaling will hit a wall, limiting the maximum capacity of the technologies: process shrinks will come to a shuddering halt when the memories’ reliability drops off a cliff as a side effect of reducing the size of electronics on the silicon dies.

The HP answer to this scaling wall is Memristor, its flavour of resistive RAM technology that is supposed to have DRAM-like speed and better-than-NAND storage density. Fink claimed at an HP Discover event in Las Vegas that Memristor devices will be ready by the time flash NAND hits its limit in five years. He also showed off a Memristor wafer, adding that it could have a 1.5PB capacity by the end of the decade.

Fink spoke about the tech in June, but this week a HP spokesperson clarified to The Reg:

As with many other ground-breaking technologies being developed at HP Labs, HP has not yet committed to a specific product roadmap for Memristor-based products. HP does have internal milestones that are subject to change, depending on shifting market, technology and business conditions.

Every time I read about it HP Labs’ memristor-based products  they keep receding further into the future. Compare this latest announcement with what was being said at the time of my Feb.7, 2013 posting,

… Stanley Williams’ presence in the video reminded me of the memristor and an announcement (mentioned in my April 19, 2012 posting) that HP Labs would be rolling out some memristor-enabled products in 2013. Sadly, later in the year I missed this announcement, from a July 9, 2012 posting by Chris Mellor for TheRegister.co.uk,

Previously he (Stanley Williams) has said that HP and fab partner Hynix would launch a memristor product in the summer of 2013. At the Kavli do [Kavli Foundation Roundtable, June 2012], Williams said: “In terms of commercialisation, we’ll have something technologically viable by the end of next year [2014].”

To be fair, it seems HP Labs had abandoned plans for a commercial launch of memristor-based products even in 2013 but now it seems there is no roadmap of any kind.

* Corrected from ’3000′ to ’2700′.

Nov. 19, 2013: Myths & Realities of the DIYbio Movement event at Woodrow Wilson Center (Washington, DC)

The Synthetic Biology Project at the Woodrow Wilson International Center for Scholars is releasing a report tomorrow (Tuesday, Nov. 19, 2013) titled: Myths & Realities of the DIYbio Movement. If you’re lucky enough to be in Washington, DC, you can attend the live event,

As the Do-It-Yourself Biology (DIYbio) community has grown, so have concerns among media and policymakers about these science enthusiasts’ ability to wield DNA and manipulate life. In the words of one Wall Street Journal headline, “In Attics and Closets, ‘Biohackers’ Discover their Inner Frankenstein.”

The realities of DIYbio, however, contradict the media myths. In its first-ever survey of DIYbio practitioners, the Synthetic Biology Project at the Woodrow Wilson International Center for Scholars finds the community to be far different from these fearful and often sensationalist representations.

The report challenges seven widely held beliefs about DIYbio practitioners, particularly about their labs, capabilities and goals. The survey finds that the science they practice is far more benign than described in the popular press. In fact, the report suggests that the DIYbio community offers national education and entrepreneurship opportunities, rather than over-inflated risks. The report concludes with six policy recommendations based on the survey results.

What: Join us at the Wilson Center on Nov. 19 for the release of the survey results and analysis, followed by a panel discussion.

Copies of the report will be available at the event and online on Nov. 19 here: http://www.synbioproject.org/events/archive/6673/

You must register to attend the event. Please RSVP here: http://bit.ly/1gGZZLd [there will possibly be a webcast posted at a later date]

More information can be found here: http://www.wilsoncenter.org/event/myths-realities-the-diybio-movement

When: Nov. 19, 2013 from noon – 2:00 p.m. EST (Light lunch available at 11:30 am.)

Who: Daniel Grushkin, co-founder of Genspace and Wilson Center Fellow
Jason Bobe, co-founder of DIYbio.org
Todd Kuiken, Synthetic Biology Project

Where: Woodrow Wilson International Center for Scholars
5th Floor Conference Room
Ronald Reagan Building
1300 Pennsylvania Ave NW
Washington, D.C.

For directions, visit: http://www.wilsoncenter.org/directions

To learn more about the Synthetic Biology Project, visit: http://www.synbioproject.org/about/

According to the Center’s event webpage, there may be a webcast of the event available but it seems they won’t be livestreaming so you will have to wait until it’s posted.

I have mentioned Genspace here in a Sept. 21, 2012 posting titled: A tooth and art installation in Vancouver (Canada) and bodyhacking and DIY (do-it-yourself) culture in the US. Scroll down about 1/2 way to find the mention of Genspace (New York’s Community Biolab) and its activities. (At the time, I was focused on the bodyhacking aspect of DIYbio.)

Jason Bobe’s DIYbio.org is new to me. Here’s a little more about the organization from the homepage (Note: Links have been removed),

DIYbio.org was founded in 2008 with the mission of establishing a vibrant, productive and safe community of DIY biologists.  Central to our mission is the belief that biotechnology and greater public understanding about it has the potential to benefit everyone.

Join the global discussion
Find local groups, people and events near you
Read the diybio blog
Ask a biosafety expert your safety question
Subscribe to the quarterly postcard update
Browse the library of DIY lab hardware
Get the diybio logo and contact info

I checked out the organization’s Local Groups webpage and found three groups in Canada,,

DIYbio Toronto (this is the only city that has any current activity listed on its site)

Welcome to DIYbio Vancouver!

Biospace (Victoria, BC)

Mixing and matching your nanoparticles

An Oct. 20, 2013 Brookhaven National Laboratory (BNL; US Dept. of Energy) news release (also on EurekAlert) describes a technique for combining different kinds of nanoparticles into a single nanocomposite,

Scientists at the U.S. Department of Energy’s Brookhaven National Laboratory have developed a general approach for combining different types of nanoparticles to produce large-scale composite materials. The technique, described in a paper published online by Nature Nanotechnology on October 20, 2013, opens many opportunities for mixing and matching particles with different magnetic, optical, or chemical properties to form new, multifunctional materials or materials with enhanced performance for a wide range of potential applications.

The approach takes advantage of the attractive pairing of complementary strands of synthetic DNA—based on the molecule that carries the genetic code in its sequence of matched bases known by the letters A, T, G, and C. After coating the nanoparticles with a chemically standardized “construction platform” and adding extender molecules to which DNA can easily bind, the scientists attach complementary lab-designed DNA strands to the two different kinds of nanoparticles they want to link up. The natural pairing of the matching strands then “self-assembles” the particles into a three-dimensional array consisting of billions of particles. Varying the length of the DNA linkers, their surface density on particles, and other factors gives scientists the ability to control and optimize different types of newly formed materials and their properties.

The news release details some of the challenges the researchers faced,

… the scientists explored the effect of particle shape. “In principle, differently shaped particles don’t want to coexist in one lattice,” said Gang [Brookhaven physicist Oleg Gang]. “They either tend to separate into different phases like oil and water refusing to mix or form disordered structures.” The scientists discovered that DNA not only helps the particles mix, but it can also improve order for such systems when a thicker DNA shell around the particles is used.

They also investigated how the DNA-pairing mechanism and other intrinsic physical forces, such as magnetic attraction among particles, might compete during the assembly process. For example, magnetic particles tend to clump to form aggregates that can hinder the binding of DNA from another type of particle. “We show that shorter DNA strands are more effective at competing against magnetic attraction,” Gang said.

For the particular composite of gold and magnetic nanoparticles they created, the scientists discovered that applying an external magnetic field could “switch” the material’s phase and affect the ordering of the particles. “This was just a demonstration that it can be done, but it could have an application—perhaps magnetic switches, or materials that might be able to change shape on demand,” said Zhang [[Yugang Zhang, first author of the paper].

The third fundamental factor the scientists explored was how the particles were ordered in the superlattice arrays: Does one type of particle always occupy the same position relative to the other type—like boys and girls sitting in alternating seats in a movie theater—or are they interspersed more randomly? “This is what we call a compositional order, which is important for example for quantum dots because their optical properties—e.g., their ability to glow—depend on how many gold nanoparticles are in the surrounding environment,” said Gang. “If you have compositional disorder, the optical properties would be different.” In the experiments, increasing the thickness of the soft DNA shells around the particles increased compositional disorder.

These fundamental principles give scientists a framework for designing new materials. The specific conditions required for a particular application will be dependent on the particles being used, Zhang emphasized, but the general assembly approach would be the same.

Said Gang, “We can vary the lengths of the DNA strands to change the distance between particles from about 10 nanometers to under 100 nanometers—which is important for applications because many optical, magnetic, and other properties of nanoparticles depend on the positioning at this scale. We are excited by the avenues this research opens up in terms of future directions for engineering novel classes of materials that exploit collective effects and multifunctionality.”

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

A general strategy for the DNA-mediated self-assembly of functional nanoparticles into heterogeneous systems by Yugang Zhang, Fang Lu, Kevin G. Yager, Daniel van der Lelie, & Oleg Gang. Nature Nanotechnology (2013) doi:10.1038/nnano.2013.209 Published online 20 October 2013.

This article can be viewed/previewed on ReadCube or purchased.

Bioprospecting yields sunscreen ingredient fromTrondheim Fjord microorganism

Norwegian business, Promar, has taken out patents based on research showing that a bacterium living in the Trondheim Flord has a trait much prized by makers of sunscreens, from an Aug. 6, 2013 news item on ScienceDaily,

Norwegian researchers have recently discovered a microorganism with very special properties — a bacteria living in Trondheim Fjord with the Latin name Micrococcus luteus. It possesses a trait which is rare and highly sought-after by medical science and the cosmetics industry — a pigment which can absorb long-wavelength UV radiation (in the range 350-475 nanometres).

The researchers are from SINTEF (Norwegian: Stiftelsen for industriell og teknisk forskning), which bills itself as the largest independent research organization in Scandinavia. Their July 25, 2013 news release by Christina Benjaminsen, which originated the news item, explains why this discovery is causing some excitement,

Long-wavelength UV radiation is linked to many forms of skin cancer and malignant melanomas. Currently, there are no sunscreens on the market able to filter out this type of radiation.

However, the Norwegian company Promar AS has taken out patents for both the manufacture and use in future sunscreens of a light-filtering substance extracted from this bacterium. This has been achieved with the help of researchers at SINTEF.

Researchers at SINTEF have what amounts to a library of microorganisms after years of bioprospecting (exploring for organisms with traits useful in industrial applications), from the SINTEF nrews release,

The backdrop to this project involved activities taking place at SINTEF and NTNU [Norwegian University of Science and Technology] by which we collected a variety of different microorganisms from the water surface in Trondheim Fjord. These organisms had one thing in common. They possessed a variety of naturally-occurring light-absorbing pigments. “This is why they are very colourful”, says Trygve Brautaset, Project and Research Manager at SINTEF. The end result was an entire “library” of such microorganisms.

At about the same time, the Norwegian company Promar AS had been working on the idea of manufacturing a substance with a property lacking in sunscreen products currently on the market – the ability to filter out long-wavelength UV radiation.

This is why SINTEF and NTNU were contracted to look for a pigment with this trait. After investigating hundreds of different bacteria, the researchers found Mirococcus luteus in “the library”. It ticked all the boxes. The microscopic organism, no bigger than 1-2 micrometres across, was found to contain a particular carotenoid, known to organic chemists as sarcinaxanthin. This pigment absorbs sunlight at just the wavelength which Promar wanted to provide protection against. By adding sarcinaxanthin to sunscreen, harmful solar radiation is absorbed by the cream before it reaches the skin. However, commercial production of the carotenoid required some tricky genetic engineering.

The process of isolating the particular pigment took two years, from the SINTEF news release,

Firstly, the pigments produced by the bacteria had to be characterized using a variety of chemical techniques designed to identify the desired sarcinaxanthin carotenoid. Subsequently, the genes used by the bacterium to synthesise sarcinaxanthin had to be isolated. Finally, the research team had to transfer all the genes into a host bacterium. The aim was to create an artificial bacterium able to produce sarcinaxanthin sufficiently effectively to be of commercial interest.

“After about two years’ intensive work SINTEF had the first examples of this bacterium ready”, says Brautaset. “We have now synthesised a sarcinaxanthin-producing bacterium which can be cultivated.

We will now be carrying out tests to see if we can produce it in so-called fermenters (cultivation tanks) in the laboratory. This represents an excellent method for the effective production of sarcinaxanthin in volumes large enough to make industrial applications possible”, he says.

UVAblue is the commercial name that’s been given to this new synthetically derived version of sarcinaxanthi. This new substance has aroused much interest,

… “We have been in France talking to many of the world’s largest cosmetics manufacturers”, he says. “Everyone we talked to was very interested in making use of this type of sunscreen factor in their products”, says Goksøyr [Managing Director Audun Goksøyr at Promar AS].

Among the reasons for this is that the cells which generate malignant melanomas are located deep in the skin. It is primarily long-wavelength UV radiation which penetrates to these cells when we sunbathe. By preventing this radiation from penetrating the skin will be an excellent way of averting the development of this highly lethal form of cancer. It will also act as an anti-wrinkle agent.

You can find out more about UVAblue at its eponymous website. ETA Aug. 13, 2013 1230 pm PDT: I’ve removed a citation for and a link to a paper that was incorrectly placed here.

Nano, agriculture, and water

Surprisingly, the Council of Canadian Academies’ (CCA) Water and Agriculture in Canada: Towards Sustainable Management of Water Resources assessment (published Feb. 2013) had very little to with regard to how emerging technologies such as synthetic biology and nanotechnology are having and will have an impact on water and agriculture. Here’s the bit on synthetic biology,

Synthetic Biology

Synthetic biology is defined as the design and construction of new biological parts, devices, and systems and the re-design of existing natural biological systems for useful purposes (RAE, 2009). It is an emerging technology that is expected to have wide-ranging implications for agriculture in the future (RAE, 2009). The agricultural technology sector anticipates that synthetic biology will lead to greater productivity, profitability, and sustainability by increasing, for example: crop water productivity; nitrogen use efficiency; yields; pest, disease, and drought resistance; and the quality, quantity, and processing characteristics of agricultural products Dunbar, 2011). However, as with current methods of transgenic manipulation, concerns relating to the safety and health impacts of synthetic biology will need to be responsibly and carefully addressed (RAE, 2009). (print version pp. 134-5)

Surely they could have found a more recent reference than 2009. I don’t disagree with the overall assessment of synthetic biology but I think they were a bit miserly to confine themselves to a single paragraph.

As for nanotechnologies,

5.11 Nanotechnologies

Nanotechnology applications are being developed for different agricultural uses including: the detection of pathogenic and parasitic organisms; sensing of environmental conditions and properties (such as humidity, soil moisture, and soil and groundwater contaminants); the controlled release of fertilizers and pesticides; improved water retention in soils and uptake by plants; drug delivery and improved nutrient utilization in livestock; degradation of organic contaminants; and water treatment (Kabiri et al., 2011; Knauer & Bucheli, 2009; Manimegalai et al., 2011; Thornton, 2010). Wireless nanosensors, for example, can be used in combination
with remote sensing and precision irrigation systems to greatly enhance WUE.

Nanoscale technologies for fertilizer and pesticide application can greatly reduce runoff and water contamination. Most nanotechnologies are still in their infancy, and associated risks and benefits must be carefully evaluated. Nonetheless, they represent a promising approach towards greater improvements in WUE (OECD, 2010). However, the potential for negative impacts of nanotechnologies on the environment and health needs to be researched (Knauer & Bucheli, 2009) and their application supported by risk assessment. (pp. 144-5; print version)

Not much attention paid to nanotechnology either, although they did manage to find some more recent references. I wonder why they didn’t organize the information about synthetic biology and nanotechnology  in a section on emerging technologies and discuss some of the implications and research  at more length. Certainly there’s a lot of interest and concern regarding nanotechnology impacts on agriculture and water.

I have two more items for this posting (to prove my point at least in part), one is about nanomaterials and fertilizer and the other one is about two UN organizations and their nanotechnology and water purification initiative.

The Institute for Agriculture and Trade Policy (IATP) has released a report about nanomaterials in soil fertilizers according to an April 26, 2013 news item on Nanowerk (Note: A link has been removed),

Nanomaterials added to soil via fertilizers and treated sewage waste used to fertilize fields could threaten soil health necessary to keep land productive, says a new report released today by the Institute for Agriculture and Trade Policy (IATP). Peer-reviewed scientific research also indicates possible negative impacts of nano-fertilizers on public health and the food supply.

IATP’s report, Nanomaterials in Soil: Our Future Food Chain? (pdf), draws attention to the delicate soil food chain, including microbes and microfauna, that enable plant growth and produce new soil. Laboratory experiments have indicated that sub-molecular nanoparticles could damage beneficial soil microbes and the digestive systems of earthworms, essential engineers in maintaining soil health.

The IATP April 24, 2013 news release, which originated the news item,

Nanomaterials are advertised as a component of market-available fertilizers—designed to increase the effectiveness of fertilizers by making them the same size as plant and root pores—but because nanotechnology is an unregulated global industry, there is no pre-market safety assessment. Several researchers assume that nanomaterials are increasingly present in biosolids (also known as sewage sludge) used as fertilizer on about 60 percent of U.S. agricultural land. [emphasis mine]

“In light of published research, the Obama administration should institute an immediate moratorium on fertilizing with biosolids from sewage treatment plants near nanomaterial fabrication facilities. A moratorium would give researchers time to determine whether nanomaterials in soil can be made safe and to research alternatives to building soil heath, rather than depending on fertilization with biosolids.” says IATP’s Dr. Steve Suppan.

Over time, the report explains, nanomaterials in these agricultural inputs can accumulate and harm soil health. More research is urgently needed to adequately understand possible long-term impacts of nanotechnology.

“As agri-nanotechnology rapidly enters the market, can soil health and everything that depends on it can be sustained without regulation?” asks Suppan. “That’s the question regulators, researchers and anyone involved in our food system should be asking themselves.”

The report also details risks specific to farmers and farmworkers applying dried biosolids that incorporate nanomaterials, including inflammation of the lungs, fibrosis and other toxicological impacts.

With no regulatory system in place—in the U.S. or elsewhere—for producing, and selling nano-fertilizers, IATP’s report concludes by asking for governments to require robust technology assessments involving biological engineers, soil scientists, public health professionals, farmers and concerned citizens before allowing indiscriminate application by industry.

It seems to me IATP could have cited some facts, rather than assumptions,  in the news release, and perhaps even referenced a study or two relative to their claim of risks “specific to farmers and farmworkers applying dried biosolids that incorporate nanomaterials, including inflammation of the lungs, fibrosis and other toxicological impacts.” I have looked at the report briefly and there is some interesting and valuable research in there although I haven’t looked closely enough to see if any of it supports the claims in their news release.  I suspect not since they usually trumpet those findings and numbers loudly.

As for the two UN agencies and their water purification and nanotechnology initiative, this May 31, 2013 UNESCO (United Nations Educational, Scientific, and Culture Organization) news release explains,

Providing access to clean water is one of the most pressing challenges in developing countries. Lack of access to safe drinking water impacts the lives and well-being of millions of people, whereas non-existent, or inadequate, wastewater treatment is threatening the quality of water resources, as well as ecosystems that we depend on.  Conventional water purification and wastewater treatment technologies often require large infrastructure, high initial capital investment, and considerable operating costs associated with the use of energy and chemicals.

What is the potential that nanotechnology holds to address these water problems?   What nanotechnologies offer the most immediate promise in water purification and wastewater treatment? Which areas of water use are in the largest need of a technological upgrade and innovation?

These were the main questions raised by a joint UNESCO-UNIDO  session on “Nanotechnology Applications in Water Purification and Wastewater Treatment”, which was the kick-off event of cooperation between UNESCO and the United Nations Industrial Development Organization (UNIDO), which the two organizations have recently embarked on in the area of nanotechnology for clean water in developing countries.

Under this cooperation, the two organizations will work together on a number of joint activities to explore the potential of nanotechnology in water purification and wastewater treatment, as an emerging technology that may provide sustainable and innovative solutions to reach the Millennium Development Goals on safe drinking water and basic sanitation, as well as to contribute towards the post-2015 development agenda and future Sustainable Development Goals.  Complementing ongoing activities of UNESCO’s International Hydrological Programme aimed at promoting water sciences, the cooperation with the Investment and Technology Unit of UNIDO brings a perspective on how advances in emerging technological developments, such as those in nanotechnology, can be utilized to enhance existing solutions to water problems and make a paradigm shift in water treatment systems, as industrial applications of nanotechnology are expanding rapidly.

Experts participating in the session presented research findings on promising nanotechnology applications in water such as improved membrane technologies, removal of bacteria and other pollutants, including pharmaceuticals and trace contaminants, water quality monitoring, remediation of polluted water systems, greater wastewater reuse, desalinization, as well as less-water intensive agriculture.  The session did not focus on the optimistic technological aspect alone.   Discussions touched upon also on how to draw the line between opportunities and challenges that limit nanotechnology applications in water.

The session emphasized the need for a balanced approach to nanotechnology applications in water and underlined the risks associated with toxicology and wider impacts on human health and the environment as of importance for further deliberations given that water is a basic human need and integral to health and well-being.  Another issue of consideration was ethical issues of nanotechnology applications in water that arise from uncertainties related to environmental and health risks. Participants of the session also shared experiences on community engagement in making nanotechnologies relevant to local needs by presenting an example of using nanotechnology to provide clean water in a school in a developing country village.

Given these recent doings with IATP and UNIDO/UNESCO, I was truly surprised at how little attention the CCA paid to nanotechnologies and, by extension, the other emerging technologies.

Stranger Visions at Woodrow Wilson International Center for Scholars June 3, 2013 in Washington, DC

I got a notice from the Woodrow Wilson International Center for Scholars Science and Technology Innovation Program about an art/science presentation taking place on June 3, 2013 in Washington, DC. From their May 30, 2013 announcement,

Stranger Visions: The DNA You Leave Behind

Heather Dewey-Hagborg is an information artist who is interested in exploring art as research and public inquiry. In her recent project Stranger Visions she creates literal figurative portrait sculptures from analyses of genetic material collected in public places. Working with the traces strangers unwittingly leave behind, Dewey-Hagborg calls attention to the impulse toward genetic determinism and the potential for a culture of genetic surveillance. The project raises questions about the DNA we leave behind, privacy, and numerous legal and bioethical issues.

Designed as a provocation, Stranger Visions has been featured in the international news media, including Smithsonian, CNN, the New York Times, and National Public Radio.

In this exhibit and policy discussion, Dewey-Hagborg will discuss her process and progress on Stranger Visions. She will join Professor Sonia Suter of the George Washington University Law School and Dr. Todd Kuiken and Eleonore Pauwels of the Synthetic Biology Project  in a discussion and public Q&A about the bioethical, legal, and policy dimensions of the work.

You must register to attend the event. No RSVP is required to view the webcast.

Click here to RSVP. [If you are attending in person; viewing the webcast does not require an RSVP]

*** Webcast LIVE at [http://www.wilsoncenter.org/event/stranger-visions-the-dna-you-leave-behind]***

 

What: Stranger Visions: The DNA You Leave Behind

When: June 3, 2013 from 3:00 p.m. – 5:00 p.m.

Who:Heather Dewey-Hagborg, Information Artist and Ph.D. Candidate at Rensselaer Polytechnic Institute; Professor Sonia M. Suter, George Washington University Law SchoolNancy J. Kelley, JD, MPP; Founding Executive Director of the New York Genome Center; a representative from the FBI is tentatively scheduled to discuss their methods and protocols surrounding DNA collectionand analysis.

Dr. Todd Kuiken and Eleonore Pauwels of the Synthetic Biology Project will moderate the session.

Where: Woodrow Wilson International Center for Scholars

6th Floor Board Room

Ronald Reagan Building

1300 Pennsylvania Ave NW

Washington, D.C.

For directions, visit: http://www.wilsoncenter.org/directions

To learn more about the Synthetic Biology Project, visit: http://www.synbioproject.org/about/

It was not immediately apparent to me that this event is being held as part of the Center’s Synthetic Biology Project event series. Interesting approach to bioethical and other issues.

ETA June 3, 2013: Eleanore Pauwels, one of the Wilson Center researchers on the panel, wrote a May 31, 2013 commentary on some of the issues raised by Dewey-Hagborg’s work on Slate.com (Note: Links have been removed),

… Heather Dewey-Hagborg, a 30-year-old Ph.D. student studying electronic arts at Rensselaer Polytechnic Institute in Troy, N.Y., has the weird habit of gathering the DNA people leave behind, from cigarette butts and fingernails to used coffee cups and chewing gum. She comes to Genspace to extract DNA from the detritus she collects and sequence specific genomic regions from her samples. The data are then fed into a computer program, which churns out a facial model of the person who left the hair, fingernail, cigarette, or gum behind. Using a 3-D printer, she creates life-sized masks that offer a depiction of what the anonymous DNA donor might look like. And they may be coming to a gallery wall near you, with a show at the New York Public Library slated for early 2014.

Such a process might seem artistically cutting edge to some. But, for most of us, the “Yuck!” factor kicks in quickly. Whether you find it cool or creepy, though, this DNA-profiling experiment raises a number of legal and ethical questions that no one knows how to handle. To what degree does the DNA we leave behind in public spaces belong to us? Does a facial mask without a name raise the same issues as a photo? In either case, what exactly is our expectation of privacy?

Just because an individual sheds DNA in a public space does not mean that he or she does not care about preserving the privacy of the genetic material. There was no informed consent given to access that data. On the other hand, some might say the major problem is not unauthorized access to data but misuse of data. It is easy to imagine a scenario in which someone sequences the genome of an acquaintance (or rival) who left a cigarette behind. If the person who tested the cigarette found a risk gene for a mental disorder and posted the results on Facebook with the smoker’s name, the information could affect his social and professional life.

…  To what extent do genetic traits (such as ancestry) tell you about how a person looks? Based on the analysis of these genetic traits, how accurate is the 3-D facial model produced by the computer? At the request of a Delaware forensic practice, Dewey-Hagborg has been working on a sculpture from a DNA sample to identify the remains of an unidentified woman. This opens another black box at the connection between law enforcement and what we might call “DIY forensic science”: Here, what is the role of the state versus that of the individual?

I recommend reading the commentary in its entirety. As for the questions Pauwels raises, I’m wondering how I’d feel if I saw a mask that l00ked like me at the New York Public Library in 2014. Of course, that begs the next question, would I recognize myself?

Plants that glow in the dark; Kickstarter campaign or public relations campaign?

Synthetic biologists have set up a Kickstarter campaign, Glowing Plants: Natural Lighting with no Electricity, designed to raise funds for a specific project and enthusiasm for  synthetic biology in the form of plants that glow in the dark. As of this morning (May 7, 2013, 9:50 am PDT), the campaign has raised $248, 600. They’ve met their initial goal of $60,000 and are now working towards their stretch goal of $400,000 with 30 days left.

Glowing Arabidopsis

Glowing Arabidopsis

Ariel Schwartz in her May 7, 2013 article for Fast Company describes the project this way,

Based on research from the University of Cambridge and the State University of New York, the Glowing Plants campaign promises backers that they’ll receive seeds to grow their own glowing Arabidopsis plants at home. If the campaign reaches its $400,000 stretch goal, glowing rose plants will also become available.

“We wanted to test the idea of whether there is demand for synthetic biology projects,” explains project co-founder Antony Evans. …

Kickstarter backers will get seeds created using particle bombardment. Gold nano-particles coated with a DNA construct developed by the team are fired at plant cells at a high-velocity. A small number of those particles make it into the Arabidopsis plant cells, where they’re absorbed into the plant chromosomes.

Arabidopsis was chosen for a number of reasons: it’s not native to the U.S., so there is little risk of cross-pollination; it doesn’t survive well in the wild (again, reducing risk of cross-pollination), it self-pollinates, and up until recently, it was thought to have the shortest genome of any plant. That means the protocols for Arabidopsis plant transformation work are well-established. Roses (the stretch goal plant) have also been studied extensively, and they carry little risk of cross-pollination, according to Evans.

As Schwartz notes, the project has potential for future applications,

In the meantime, Evans and his team plan on spending the next year on the campaign. Eventually, Evans imagines that the Glowing Plants creators will work on bigger glowing plant species, so one day they could even be used for street lighting.

Here’s more about the team behind this Kickstarter campaign (from the project page, click on Antony Evans),

Omri Amirav-Drory, PhD, is the founder and CEO of Genome Compiler, a synthetic biology venture. Prior to starting his company, Omri was a Fulbright postdoctoral research fellow at Stanford University School of Medicine and HHMI, performing neuroscience research using structural and synthetic biology methods. Omri received his PhD in biochemistry from Tel-Aviv University for biochemical and structural studies of membrane protein complexes involved in bio-energetics.

Antony Evans has an MBA with Distinction from INSEAD, an MA in Maths from the University of Cambridge and is a graduate of Singularity University’s GSP program. He is both a Louis Frank and Oppidan scholar and worked for six years as a management consultant and project manager at Oliver Wyman and Bain & Company. Prior to this project he co-founded the world’s first pure mobile microfinance bank in the Philippines and launched a mobile app in partnership with Harvard Medical School.

Kyle Taylor was born and raised in the great state of Kansas, where his love of plants evolved out of an interest in the agriculture all around him. This lead him to major in Agriculture Biochemistry and minor in Agronomy at Iowa State University and then pursue a PhD in Cell and Molecular Biology at Stanford University. Not too bad for a rural country boy! Since a lot of people helped him get to this point, he’s driven to share his passion and excitement by making what he does more accessible. Kyle teaches Introduction to Molecular Cell Biology at Biocurious and is our resident plant expert.

This project reminded me of artist Eduardo Kac (pronounced Katz) and his transgenic bunny, Alba. She glows/ed green in the dark. Here’s more from Kac’s ‘transgenic bunny’ webpage,

My transgenic artwork “GFP Bunny” comprises the creation of a green fluorescent rabbit, the public dialogue generated by the project, and the social integration of the rabbit. GFP stands for green fluorescent protein. “GFP Bunny” was realized in 2000 and first presented publicly in Avignon, France. Transgenic art, I proposed elsewhere [1], is a new art form based on the use of genetic engineering to transfer natural or synthetic genes to an organism, to create unique living beings. This must be done with great care, with acknowledgment of the complex issues thus raised and, above all, with a commitment to respect, nurture, and love the life thus created.

Alba, the fluorescent bunny. Photo: Chrystelle Fontaine

Alba, the fluorescent bunny. Photo: Chrystelle Fontaine

She never looks quite real to me. Under a standard light, she’s a white rabbit but glows when illuminated by a blue  light.  From Kac’s transgenic bunny page,

She was created with EGFP, an enhanced version (i.e., a synthetic mutation) of the original wild-type green fluorescent gene found in the jellyfish Aequorea Victoria. EGFP gives about two orders of magnitude greater fluorescence in mammalian cells (including human cells) than the original jellyfish gene

I don’t know if she still lives but Kac was creating work based on her up until 2011. You can find more here.

ETA June 12, 2013:  Anya Kamenetz has written a followup June 12, 2013 article for Fast Company about this Kickstarter project (Note: A link has been removed),

Though the project is technically legal, its sheer hubris has kickstarted some serious from scientists and environmental groups that object to the release of these seeds to the public, with the chance that the DNA will get into the natural gene pool with unknown consequences. An anti-synthetic bio group called ETC has started a fundraising drive of their own, dubbed a “Kickstopper.”

There’s also an online petition according to Kamenetz. One comment, her description of ‘ETC’ as an anti-synthetic bio group doesn’t quite convey the group’s scope or depth. It’s name is the ETC Group (Action group on Erosion, Technology and Concentration) and its tag line is ‘monitoring power, tracking technology, strengthening diversity.