Monthly Archives: January 2017

Seeing the future with quantum computing

Researchers at the University of Sydney (Australia) have demonstrated the ability to see the ‘quantum future’ according to a Jan. 16, 2017 news item on ScienceDaily,

Scientists at the University of Sydney have demonstrated the ability to “see” the future of quantum systems, and used that knowledge to preempt their demise, in a major achievement that could help bring the strange and powerful world of quantum technology closer to reality.

The applications of quantum-enabled technologies are compelling and already demonstrating significant impacts — especially in the realm of sensing and metrology. And the potential to build exceptionally powerful quantum computers using quantum bits, or qubits, is driving investment from the world’s largest companies.

However a significant obstacle to building reliable quantum technologies has been the randomisation of quantum systems by their environments, or decoherence, which effectively destroys the useful quantum character.

The physicists have taken a technical quantum leap in addressing this, using techniques from big data to predict how quantum systems will change and then preventing the system’s breakdown from occurring.

A Jan. 14, 2017 University of Sydney press release (also on EurekAlert), which originated the news item, expands on the theme,

“Much the way the individual components in mobile phones will eventually fail, so too do quantum systems,” said the paper’s senior author Professor Michael J.  Biercuk.

“But in quantum technology the lifetime is generally measured in fractions of a second, rather than years.”

Professor Biercuk, from the University of Sydney’s School of Physics and a chief investigator at the Australian Research Council’s Centre of Excellence for Engineered Quantum Systems, said his group had demonstrated it was possible to suppress decoherence in a preventive manner. The key was to develop a technique to predict how the system would disintegrate.

Professor Biercuk highlighted the challenges of making predictions in a quantum world: “Humans routinely employ predictive techniques in our daily experience; for instance, when we play tennis we predict where the ball will end up based on observations of the airborne ball,” he said.

“This works because the rules that govern how the ball will move, like gravity, are regular and known.  But what if the rules changed randomly while the ball was on its way to you?  In that case it’s next to impossible to predict the future behavior of that ball.

“And yet this situation is exactly what we had to deal with because the disintegration of quantum systems is random. Moreover, in the quantum realm observation erases quantumness, so our team needed to be able to guess how and when the system would randomly break.

“We effectively needed to swing at the randomly moving tennis ball while blindfolded.”

The team turned to machine learning for help in keeping their quantum systems – qubits realised in trapped atoms – from breaking.

What might look like random behavior actually contained enough information for a computer program to guess how the system would change in the future. It could then predict the future without direct observation, which would otherwise erase the system’s useful characteristics.

The predictions were remarkably accurate, allowing the team to use their guesses preemptively to compensate for the anticipated changes.

Doing this in real time allowed the team to prevent the disintegration of the quantum character, extending the useful lifetime of the qubits.

“We know that building real quantum technologies will require major advances in our ability to control and stabilise qubits – to make them useful in applications,” Professor Biercuk said.

Our techniques apply to any qubit, built in any technology, including the special superconducting circuits being used by major corporations.

“We’re excited to be developing new capabilities that turn quantum systems from novelties into useful technologies. The quantum future is looking better all the time,” Professor Biercuk said.

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

Prediction and real-time compensation of qubit decoherence via machine learning by Sandeep Mavadia, Virginia Frey, Jarrah Sastrawan, Stephen Dona, & Michael J. Biercuk. Nature Communications 8, Article number: 14106 (2017) doi:10.1038/ncomms14106 Published online: 16 January 2017

This paper is open access.

Monitoring the life of bacteria in microdroplets

Trying to establish better ways to test the effect of drugs on bacteria has led the Institute of Physical Chemistry of the Polish Academy of Sciences to develop a new monitoring technique. From a Jan.  11, 2017 news item on Nanowerk,

So far, however, there has been no quick or accurate method of assessing the oxygen conditions in individual microdroplets. This key obstacle has been overcome at the Institute of Physical Chemistry of the Polish Academy of Sciences.

Not in rows of large industrial tanks, nor on shelves laden with test tubes and beakers. The future of chemistry and biology is barely visible to the eye: it’s hundreds and thousands of microdroplets, whizzing through thin tubules of microfluidic devices. The race is on to find technologies that will make it possible to carry out controlled chemical and biological experiments in microdroplets. At the Institute of Physical Chemistry of the Polish Academy of Sciences (IPC PAS) in Warsaw a method of remote, yet rapid and accurate assessment of oxygen consumption by micro-organisms living in individual microdroplets has been demonstrated for the first time.

“Devices for the cultivation of bacteria in microdroplets have the chance to revolutionize work on the development of new antibiotics and the study of mechanisms responsible for the acquisition of drug resistance by bacteria. In one small microfluidic system it is possible to accommodate several hundred or even several thousand microdroplets – and to carry out a different experiment in each of them, for example with different types of microorganisms and at different concentrations of antibiotic in each drop,” describes Prof. Piotr Garstecki (IPC PAS), then explains: “For such studies to be possible, one has to provide the bacteria with conditions for development for even a few weeks. Thus, knowledge about the flow of oxygen to the droplets and the rate of its consumption by the microorganisms becomes extremely important. In our latest system we demonstrate how to read this key information.”

A Jan. 11, 2017 IPC PAS press release on EurekAlert, which originated the  news item, describes the work in more detail,

The bioreactors of the future are water droplets with culture medium suspended in a carrier liquid with which they are immiscible (usually this is oil). In the channel of the microfluidic device each droplet is longer than it is wide and it almost completely fills its lumen; sizes matched in this manner ensure that the drops do not swop places in the channel and throughout the duration of the experiment they can be identified without any problems. At the same time, there has to be a thin layer of oil maintained continuously between each microdroplet and the wall of the channel. Without this, the bacteria would be in direct contact with the walls of the channel so they would be able to settle on them and move from drop to drop. Unfortunately, when the microdroplet is stationary, with time it pushes out the oil separating it from the walls, laying it open to contamination. For this reason the drops must be kept in constant motion – even for weeks.

Growing bacteria need culture medium, and waste products need to be removed from their environment at an appropriate rate. Information about the bacterial oxygen consumption in individual droplets is therefore crucial to the operation of microbioreactors.

“It is immediately obvious where the problem lies. In each of the hundreds of moving droplets measurements need to be carried out at a frequency corresponding to the frequency of division of the bacteria or more, in practice at least once every 15 minutes. In addition, the measurement cannot cause any interference in the microdroplets,” says PhD student Michal Horka (IPC PAS), a co-author of the publication in the journal Analytical Chemistry.

Help was at hand for the Warsaw researchers from chemists from the Austrian Institute of Analytical Chemistry and Food Chemistry at the Graz University of Technology. They provided polymer nanoparticles with a phosphorescent dye, which after excitation emit light for longer the higher the concentration of oxygen in the surrounding solution (the nanoparticles underwent tests at the IPC PAS on bacteria in order to determine their possible toxicity – none was found).

Research on monitoring oxygen consumption in the droplets commenced with the preparation of an aqueous solution with the bacteria, the culture medium and a suitable quantity of nanoparticles. The mixture was injected into the microfluidic system constructed of tubing with Teflon connectors with correspondingly shaped channels. The first module formed droplets with a volume of approx. 4 microlitres, which were directed to the incubation tube wound on a spool. In the middle of its length there was another module, with detectors for measuring oxygen and absorbance.

“In the incubation part in one phase of the cycle the droplets flowed in one direction, in the second – in another, electronically controlled by means of suitable solenoid valves. All this looks seemingly simple enough, but in practice one of the biggest challenges was to ensure a smooth transition between the detection module and the tubing, so that bacterial contamination did not occur at the connections,” explains PhD student Horka.

During their passage through the detection module the droplets flowed under an optical sensor which measured the so-called optical density, which is the standard parameter used to evaluate the number of cells (the more bacteria in the droplets, the less light passes through them). In turn, the measurement of the duration of the phosphorescence of the nanoparticles, evaluating the concentration of oxygen in the microdroplets, was carried out using the Piccolo2 optical detector, provided by the Austrian group. This detector, which looks like a big pen drive, was connected directly to the USB port on the control computer. Comparing information from both sensors, IPC PAS researchers showed that the microfluidic device they had constructed made it possible to regularly and quickly monitor the metabolic activity of bacteria in the individual microdroplets.

“We carried out our tests both with bacteria floating in water singly – this is how the common Escherichia coli bacteria behave – as well as with those having a tendency to stick together in clumps – as is the case for tuberculosis bacilli or others belonging to the same family including Mycobacterium smegmatis which we studied. Evaluation of the rate of oxygen consumption by both species of microorganisms proved to be not only possible, but also reliable,” stresses PhD student Artur Ruszczak (IPC PAS).

The results of the research, funded by the European ERC Starting Grant (Polish side) and the Maria Sklodowska-Curie grant (Austrian side) are an important step in the process of building fully functional microfluidic devices for conducting biological experiments lasting many weeks. A system for culturing bacteria in microdroplets was developed at the IPC PAS a few years ago, however it was constructed on a polycarbonate plate. The maximum dimensions of the plate did not exceed 10 cm, which greatly limited the number of droplets; in addition, as a result of interaction with the polycarbonate, after four days the channels were contaminated with bacteria. Devices of Teflon modules and tubing would not have these disadvantages, and would be suitable for practical applications.

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

Lifetime of Phosphorescence from Nanoparticles Yields Accurate Measurement of Concentration of Oxygen in Microdroplets, Allowing One To Monitor the Metabolism of Bacteria by Michał Horka, Shiwen Sun, Artur Ruszczak, Piotr Garstecki, and Torsten Mayr. Anal. Chem., 2016, 88 (24), pp 12006–12012 DOI: 10.1021/acs.analchem.6b03758 Publication Date (Web): November 23, 2016

Copyright © 2016 American Chemical Society

This paper is behind a paywall.

Novel self-assembly at 102 atoms

A Jan. 13, 2017 news item on ScienceDaily announces a discovery about self-assembly of 102-atom gold nanoclusters,

Self-assembly of matter is one of the fundamental principles of nature, directing the growth of larger ordered and functional systems from smaller building blocks. Self-assembly can be observed in all length scales from molecules to galaxies. Now, researchers at the Nanoscience Centre of the University of Jyväskylä and the HYBER Centre of Excellence of Aalto University in Finland report a novel discovery of self-assembling two- and three-dimensional materials that are formed by tiny gold nanoclusters of just a couple of nanometres in size, each having 102 gold atoms and a surface layer of 44 thiol molecules. The study, conducted with funding from the Academy of Finland and the European Research Council, has been published in Angewandte Chemie.

A Jan. 13, 2017 Academy of Finland press release, which originated the news item, provides more technical information about the work,

The atomic structure of the 102-atom gold nanocluster was first resolved by the group of Roger D Kornberg at Stanford University in 2007 (2). Since then, several further studies of its properties have been conducted in the Jyväskylä Nanoscience Centre, where it has also been used for electron microscopy imaging of virus structures (3). The thiol surface of the nanocluster has a large number of acidic groups that can form directed hydrogen bonds to neighbouring nanoclusters and initiate directed self-assembly.

The self-assembly of gold nanoclusters took place in a water-methanol mixture and produced two distinctly different superstructures that were imaged in a high-resolution electron microscope at Aalto University. In one of the structures, two-dimensional hexagonally ordered layers of gold nanoclusters were stacked together, each layer being just one nanocluster thick. Modifying the synthesis conditions, also three-dimensional spherical, hollow capsid structures were observed, where the thickness of the capsid wall corresponds again to just one nanocluster size (see figure).

While the details of the formation mechanisms of these superstructures warrant further systemic investigations, the initial observations open several new views into synthetically made self-assembling nanomaterials.

“Today, we know of several tens of different types of atomistically precise gold nanoclusters, and I believe they can exhibit a wide variety of self-assembling growth patterns that could produce a range of new meta-materials,” said Academy Professor Hannu Häkkinen, who coordinated the research at the Nanoscience Centre. “In biology, typical examples of self-assembling functional systems are viruses and vesicles. Biological self-assembled structures can also be de-assembled by gentle changes in the surrounding biochemical conditions. It’ll be of great interest to see whether these gold-based materials can be de-assembled and then re-assembled to different structures by changing something in the chemistry of the surrounding solvent.”

“The free-standing two-dimensional nanosheets will bring opportunities towards new-generation functional materials, and the hollow capsids will pave the way for highly lightweight colloidal framework materials,” Postdoctoral Researcher Nonappa (Aalto University) said.

Professor Olli Ikkala of Aalto University said: “In a broader framework, it has remained as a grand challenge to master the self-assemblies through all length scales to tune the functional properties of materials in a rational way. So far, it has been commonly considered sufficient to achieve sufficiently narrow size distributions of the constituent nanoscale structural units to achieve well-defined structures. The present findings suggest a paradigm change to pursue strictly defined nanoscale units for self-assemblies.”


(1)    Nonappa, T. Lahtinen, J.S. Haataja, T.-R. Tero, H. Häkkinen and O. Ikkala, “Template-Free Supracolloidal Self-Assembly of Atomically Precise Gold Nanoclusters: From 2D Colloidal Crystals to Spherical Capsids”, Angewandte Chemie International Edition, published online 23 November 2016, DOI: 10.1002/anie.201609036

(2)    P. Jadzinsky et al., “Structure of a thiol-monolayer protected gold nanoparticle at 1.1Å resolution”, Science 318, 430 (2007)

(3)    V. Marjomäki et al., “Site-specific targeting of enterovirus capsid by functionalized monodispersed gold nanoclusters”, PNAS 111, 1277 (2014)

Here’s the figure mentioned in the news release,

Figure: 2D hexagonal sheet-like and 3D capsid structures based on atomically precise gold nanoclusters as guided by hydrogen bonding between the ligands. The inset in the top left corner shows the atomic structure of one gold nanocluster.

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

Template-Free Supracolloidal Self-Assembly of Atomically Precise Gold Nanoclusters: From 2D Colloidal Crystals to Spherical Capsids by Dr. Nonappa, Dr. Tanja Lahtinen, M. Sc. Johannes. S. Haataja, Dr. Tiia-Riikka Tero, Prof. Hannu Häkkinen, and Prof. Olli Ikkala. Angewandte Chemie International Edition Volume 55, Issue 52, pages 16035–16038, December 23, 2016 Version of Record online: 23 NOV 2016 DOI: 10.1002/anie.201609036

© 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim

This paper is behind a paywall.

Political internship (Canada’s Liberal Party)

i don’t usually feature jobs for political parties but there appears to be a movement afoot in the US where scientists are possibly going to run for political office so it seems more à propos than usual. Before getting to the job information (for a Canadian political party), here’s more about the nascent scientists as politicians movement from a Jan. 25, 2017 article (Professor Smith Goes to Washington) by Ed Yong for The Atlantic (Note: Links have been removed),

For American science, the next four years look to be challenging. The newly inaugurated President Trump, and many of his Cabinet picks, have repeatedly cast doubt upon the reality of human-made climate change, questioned the repeatedly proven safety of vaccines. Since the inauguration, the administration has already frozen grants and contracts by the Environmental Protection Agency and gagged researchers at the US Department of Agriculture. Many scientists are asking themselves: What can I do?

And the answer from a newly formed group called 314 Action is: Get elected.

The organization, named after the first three digits of pi, is a political action committee that was created to support scientists in running for office. It’s the science version of Emily’s List, which focuses on pro-choice female candidates, or VoteVets, which backs war veterans. “A lot of scientists traditionally feel that science is above politics but we’re seeing that politics is not above getting involved in science,” says founder Shaughnessy Naughton. “We’re losing, and the only way to stop that is to get more people with scientific backgrounds at the table.”

Yong is a good writer and the article offers some insight into why scientists do or don’t involve themselves in the political process along with links for more information.

***ETA Feb. 13, 2017: has published an article by Deborah Netburn (originally written for the Los Angeles Times) which offers some insight into scientists some of whom are involving themselves in politics for the first in their lives in a Feb. 13, 2017 news item titled ‘Science entering a new frontier: Politics‘.***

Science Borealis, the Canadian science blog aggregrator/community, has chimed in on the science and politics situation in the US with two blog postings on the topic. I wish they’d used titles that more accurately reflected the content but there’s Sarah Boon’s Jan. 24, 2017 posting, The War on Science: Can the US Learn From Canada? on her Watershed Moments blog, where she notes how different the situations are and how much Americans have already done and are doing to work on the issues,

When Donald Trump was first elected president of the United States, our editorial team at  Science Borealis talked about whether or not we should write an editorial supporting US scientists in what was likely going to become a fight for science. In the end we decided not to write it, for a number of reasons. For one thing, the likely impact of Trump on science remained a huge unknown. But for another thing, we thought US scientists were already well-prepared for a war on science. …

Unfortunately, Boon goes on to offer a collection of writings on the Canadian situation. I understand it’s well meant but I can’t help recalling people who rushed to comfort me in a difficult situation by recounting their own stories, at length. It wasn’t as helpful as they might have hoped.

John Dupuis’ Jan. 25, 2017 posting, The Trump War on Science: What Can the US Learn From Canada’s Experience? on his Confessions of a Science Librarian blog, is more egregiously titled but he goes on to provide links to resources for more information on the situation in the US. Although he, too, goes on to offer links to more about the Canadian situation.

One final observation, I have an objection to the term ‘war on science’; there was never a war on science in Canada. There was/is a war on certain kinds of science. In any event, here’s getting to the point of this posting.


For those scientific (stretching past political science students) types who think they might be interested in politics,  from the 2017 Liberal Party of Canada Internship Program page,

Are you a young Canadian with a love of politics? Are you passionate about serving your community, engaging with volunteers, and talking with Canadians about the issues that matter most? The Liberal Party of Canada is looking for hardworking young leaders to join Justin Trudeau’s team this summer, to help us continue to grow Canada’s Liberal movement from coast to coast to coast.

Whether it includes marching in the Vancouver Pride Parade, knocking on doors in Halifax, getting our message out to Canadians using social media, supporting our local Liberal associations in their communities, or learning directly from our campaign experts in Ottawa, an internship with the LPC is guaranteed to be an unforgettable summer! Our interns will have the opportunity to learn the foundations of organizing and campaigning directly from the people who paved our road to victory in 2015, and those who are already hard at work planning for the next election. With less than three years until the next general election, our team is looking for talented young Canadians to bring fresh and innovative ideas to the table.

You’ll gain valuable career experience, and get to know leading members of the Liberal team.

While every individual’s tasks and projects will be different, selected Liberal interns may work in areas including:

  • Communications and Media Relations
  • National Field – Campaigns
  • Social Media
  • Email Marketing
  • Graphic and Web Design
  • Local Field and Outreach
  • Riding Services
  • Party Operations
  • Finance and Accounting

Who: You! All Registered Liberals are encouraged to apply! We are looking for talented young Canadians from coast to coast to coast to work on Justin Trudeau’s team and become the next generation of leaders in the largest, most open, and most inclusive political movement in Canadian history.

Where: Most Interns will be placed in the Liberal Party of Canada National Office in Ottawa, and there also exciting opportunities available in our Regional Offices across the country. Please indicate in your application at least one city where you would be interested in working with our team.

When: Internship positions will run from Monday, May 1 to Friday, August 25. You must be available full-time for the duration of the internship.

This is a full-time, paid internship. [emphasis mine]

All applicants will receive an email of confirmation upon the submission of their application. Interviews will be conducted throughout the month of February. Due to a high volume of applications, only those who are selected for an interview will be contacted.

Apply now

Application Deadline: 11:59pm PST on Friday, February 10, 2017. [emphasis mine]

There is a FAQs (frequently asked questions) section on the the 2017 Liberal Party of Canada Internship Program page. Good luck!

Nanomechanics for deciphering beetle exoskeletons

Beetles carry remarkably light yet strong armor in the form of their exoskeletons and a research team at Northwestern University (US) is looking to those beetle exoskeletons for inspiration according to a Jan. 11, 2017 news item on ScienceDaily,

What can a beetle tell us about good design principles? Quite a lot, actually.

Many insects and crustaceans possess hard, armor-like exoskeletons that, in theory, should weigh the creatures down. But, instead, the exoskeletons are surprisingly light — even allowing the armor-wearing insects, like the beetle, to fly.

Northwestern Engineering’s Horacio D. Espinosa and his group are working to understand the underlying design principles and mechanical properties that result in structures with these unique, ideal properties. This work could ultimately uncover information that could guide the design and manufacturing of new and improved artificial materials by emulating these time-tested natural patterns, a process known as bio-mimicry.

Supported by the Air Force Office of Scientific Research’s Multidisciplinary University Research Initiative (MURI), the research was featured on the cover of Advanced Functional Materials. Postdoctoral fellows Ruiguo Yang and Wei Gao and graduate student Alireza Zaheri, all members of Espinosa’s laboratory, were co-first authors of the paper. Cheryl Hayashi, professor of biology at the University of California, Riverside, was also a co-author.

A Jan. 11, 2017 Northwestern University news release, which originated the news item, expands on the theme,

Though there are more than a million species of beetles, the team is first studying the exoskeleton of the Cotinis mutabilis, a field crop pest beetle native to the western United States. Like all insects and crustaceans, its exoskeleton is composed of twisted plywood structures, known as Bouligand structures, which help protect against predators. Fibers in this Bouligand structure are bundles of chitin polymer chains wrapped with proteins. In this chain structure, each fiber has a higher density along the length than along the transverse.

“It is very challenging to characterize the properties of such fibers given that they are directionally dependent and have a small diameter of just 20 nanometers,” said Espinosa, the James N. and Nancy J. Farley Professor in Manufacturing and Entrepreneurship at Northwestern’s McCormick School of Engineering. “We had to develop a novel characterization method by taking advantage of the spatial distribution of fibers in the Bouligand structure.”

To meet this challenge, Espinosa and his team employed a creative way to identify the geometry and material properties of the fibers that comprise the exoskeleton. They cut the Bouligand structure along a plane, resulting in a surface composed of closely packed cross-sections of fibers with different orientations. They were then able to analyze the mechanics of the fibers.

“With more than a million species, which greatly vary from each other in taxomic relatedness, size, and ecology, the beetle is the largest group of insects,” Hayashi said. “What makes this research exciting is that the methods applied to the Cotinis mutabilis beetle exoskeleton can be extended to other beetle species.”

By correlating the mechanical properties with the exoskeleton geometries from diverse beetle species, Espinosa and his team plan to gain insight into natural selection and better understand structure-function-properties relationships.

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

AFM Identification of Beetle Exocuticle: Bouligand Structure and Nanofiber Anisotropic Elastic Properties by Ruiguo Yang, Alireza Zaheri, Wei Gao, Cheryl Hayashi, and Horacio D. Espinosa. Advanced Functional Materials DOI: 10.1002/adfm.201603993 Version of Record online: 27 DEC 2016

© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

This paper is behind a paywall.

Curcumin: a scientific literature review concludes health benefits may be overstated

Given the number of times I’ve featured ‘curcumin research’, it seems only right to include this latest work. A Jan. 11, 2017 American Chemical Society (ACS) news release (also on EurekAlert) describes the results of a review of the scientific literature on curcumin’s (a constituent of turmeric) medicinal effectiveness,

Curcumin, a compound in turmeric, continues to be hailed as a natural treatment for a wide range of health conditions, including cancer and Alzheimer’s disease. But a new review of the scientific literature on curcumin has found it’s probably not all it’s ground up to be. The report in ACS’ Journal of Medicinal Chemistry instead cites evidence that, contrary to numerous reports, the compound has limited — if any — therapeutic benefit.

Turmeric, a spice often added to curries and mustards because of its distinct flavor and color, has been used for centuries in traditional medicine. Since the early 1990’s, scientists have zeroed in on curcumin, which makes up about 3 to 5 percent of turmeric, as the potential constituent that might give turmeric its health-boosting properties. More than 120 clinical trials to test these claims have been or are in the process of being run by clinical investigators. To get to the root of curcumin’s essential medicinal chemistry, the research groups of Michael A. Walters and Guido F. Pauli teamed up to extract key findings from thousands of scientific articles on the topic.

The researchers’ review of the vast curcumin literature provides evidence that curcumin is unstable under physiological conditions and not readily absorbed by the body, properties that make it a poor therapeutic candidate. Additionally, they could find no evidence of a double-blind, placebo-controlled clinical trial on curcumin to support its status as a potential cure-all. But, the authors say, this doesn’t necessarily mean research on turmeric should halt [emphasis mine]. Turmeric extracts and preparations could have health benefits, although probably not for the number of conditions currently touted. The researchers suggest that future studies should take a more holistic approach to account for the spice’s chemically diverse constituents that may synergistically contribute to its potential benefits.

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

The Essential Medicinal Chemistry of Curcumin by Kathryn M. Nelson, Jayme L. Dahlin, Jonathan Bisson, James Graham, Guido F. Pauli, and Michael A. Walters. J. Med. Chem., Article ASAP DOI: 10.1021/acs.jmedchem.6b00975 Publication Date (Web): January 11, 2017

Copyright © 2017 American Chemical Society

This paper is open access.

Developing cortical implants for future speech neural prostheses

I’m guessing that graphene will feature in these proposed cortical implants since the project leader is a member of the Graphene Flagship’s Biomedical Technologies Work Package. (For those who don’t know, the Graphene Flagship is one of two major funding initiatives each receiving funding of 1B Euros over 10 years from the European Commission as part of their FET [Future and Emerging Technologies)] Initiative.)  A Jan. 12, 2017 news item on Nanowerk announces the new project (Note: A link has been removed),

BrainCom is a FET Proactive project, funded by the European Commission with 8.35M€ [8.3 million Euros] for the next 5 years, holding its Kick-off meeting on January 12-13 at ICN2 (Catalan Institute of Nanoscience and Nanotechnology) and the UAB [ Universitat Autònoma de Barcelona]. This project, coordinated by ICREA [Catalan Institution for Research and Advanced Studies] Research Prof. Jose A. Garrido from ICN2, will permit significant advances in understanding of cortical speech networks and the development of speech rehabilitation solutions using innovative brain-computer interfaces.

A Jan. 12, 2017 ICN2 press release, which originated the news item expands on the theme (it is a bit repetitive),

More than 5 million people worldwide suffer annually from aphasia, an extremely invalidating condition in which patients lose the ability to comprehend and formulate language after brain damage or in the course of neurodegenerative disorders. Brain-computer interfaces (BCIs), enabled by forefront technologies and materials, are a promising approach to treat patients with aphasia. The principle of BCIs is to collect neural activity at its source and decode it by means of electrodes implanted directly in the brain. However, neurorehabilitation of higher cognitive functions such as language raises serious issues. The current challenge is to design neural implants that cover sufficiently large areas of the brain to allow for reliable decoding of detailed neuronal activity distributed in various brain regions that are key for language processing.

BrainCom is a FET Proactive project funded by the European Commission with 8.35M€ for the next 5 years. This interdisciplinary initiative involves 10 partners including technologists, engineers, biologists, clinicians, and ethics experts. They aim to develop a new generation of neuroprosthetic cortical devices enabling large-scale recordings and stimulation of cortical activity to study high level cognitive functions. Ultimately, the BraimCom project will seed a novel line of knowledge and technologies aimed at developing the future generation of speech neural prostheses. It will cover different levels of the value chain: from technology and engineering to basic and language neuroscience, and from preclinical research in animals to clinical studies in humans.

This recently funded project is coordinated by ICREA Prof. Jose A. Garrido, Group Leader of the Advanced Electronic Materials and Devices Group at the Institut Català de Nanociència i Nanotecnologia (Catalan Institute of Nanoscience and Nanotechnology – ICN2) and deputy leader of the Biomedical Technologies Work Package presented last year in Barcelona by the Graphene Flagship. The BrainCom Kick-Off meeting is held on January 12-13 at ICN2 and the Universitat Autònoma de Barcelona (UAB).

Recent developments show that it is possible to record cortical signals from a small region of the motor cortex and decode them to allow tetraplegic [also known as, quadriplegic] people to activate a robotic arm to perform everyday life actions. Brain-computer interfaces have also been successfully used to help tetraplegic patients unable to speak to communicate their thoughts by selecting letters on a computer screen using non-invasive electroencephalographic (EEG) recordings. The performance of such technologies can be dramatically increased using more detailed cortical neural information.

BrainCom project proposes a radically new electrocorticography technology taking advantage of unique mechanical and electrical properties of novel nanomaterials such as graphene, 2D materials and organic semiconductors.  The consortium members will fabricate ultra-flexible cortical and intracortical implants, which will be placed right on the surface of the brain, enabling high density recording and stimulation sites over a large area. This approach will allow the parallel stimulation and decoding of cortical activity with unprecedented spatial and temporal resolution.

These technologies will help to advance the basic understanding of cortical speech networks and to develop rehabilitation solutions to restore speech using innovative brain-computer paradigms. The technology innovations developed in the project will also find applications in the study of other high cognitive functions of the brain such as learning and memory, as well as other clinical applications such as epilepsy monitoring.

The BrainCom project Consortium members are:

  • Catalan Institute of Nanoscience and Nanotechnology (ICN2) – Spain (Coordinator)
  • Institute of Microelectronics of Barcelona (CNM-IMB-CSIC) – Spain
  • University Grenoble Alpes – France
  • ARMINES/ Ecole des Mines de St. Etienne – France
  • Centre Hospitalier Universitaire de Grenoble – France
  • Multichannel Systems – Germany
  • University of Geneva – Switzerland
  • University of Oxford – United Kingdom
  • Ludwig-Maximilians-Universität München – Germany
  • Wavestone – Luxembourg

There doesn’t seem to be a website for the project but there is a BrainCom webpage on the European Commission’s CORDIS (Community Research and Development Information Service) website.

2016 report on nanomaterial reporting released by French government

Lynn L. Bergeson has announced the release of a new report from the French government in her Jan. 3, 2017 posting on Nanotechnology Now,

In November 2016, the Ministry of the Environment, Energy, and the Sea released its 2016 report, in French, Éléments issus des déclarations des substances à l’état nanoparticulaire. … The report analyzes nanomaterial declarations received in 2016 for reporting year 2015. Under Decree No. 2012-232, companies that manufacture, import, and/or distribute a “substance with nanoparticle status” in an amount of at least 100 grams per year must submit an annual report with substance identity, quantity, and use information. According to the report, while the number of declarations received in 2016 decreased from 2015, the quantity of materials produced increased (350,487 tonnes vs. 300,822 tonnes in 2015), as well as the quantity imported (125,279 tonnes vs. 114,951 tonnes in 2015).

For people with the French language skills, you can find the report here (PDF). You can also check out the R-Nano website (French language) (English language) for more information about the reporting programme in France.

In related news. the US Environmental Protection Agency announced its one-time only nanomaterial reporting requirements as highlighted in my Jan. 18, 2017 posting.

Antibiotic synthetic spider silk

I have a couple of questions, what is ‘click’ chemistry and how does a chance meeting lead to a five-year, interdisciplinary research project on synthetic spider silk? From a Jan. 4, 2017 news item on ScienceDaily,

A chance meeting between a spider expert and a chemist has led to the development of antibiotic synthetic spider silk.

After five years’ work an interdisciplinary team of scientists at The University of Nottingham has developed a technique to produce chemically functionalised spider silk that can be tailored to applications used in drug delivery, regenerative medicine and wound healing.

The Nottingham research team has shown for the first time how ‘click-chemistry’ can be used to attach molecules, such as antibiotics or fluorescent dyes, to artificially produced spider silk synthesised by E.coli bacteria. The research, funded by the Biotechnology and Biological Sciences Research Council (BBSRC) is published today in the online journal Advanced Materials.

A Jan. 3, 2016 University of Nottingham press release (also on EurekAlert), which originated the news item, provides a few more details about ‘click’ chemistry (not enough for me) and more information about the research,

The chosen molecules can be ‘clicked’ into place in soluble silk protein before it has been turned into fibres, or after the fibres have been formed. This means that the process can be easily controlled and more than one type of molecule can be used to ‘decorate’ individual silk strands.

Nottingham breakthrough

In a laboratory in the Centre of Biomolecular Sciences, Professor Neil Thomas from the School of Chemistry in collaboration with Dr Sara Goodacre from the School of Life Sciences, has led a team of BBSRC DTP-funded PhD students starting with David Harvey who was then joined by Victor Tudorica, Leah Ashley and Tom Coekin. They have developed and diversified this new approach to functionalising ‘recombinant’ — artificial — spider silk with a wide range of small molecules.

They have shown that when these ‘silk’ fibres are ‘decorated’ with the antibiotic levofloxacin it is slowly released from the silk, retaining its anti-bacterial activity for at least five days.

Neil Thomas, a Professor of Medicinal and Biological Chemistry, said: “Our technique allows the rapid generation of biocompatible, mono or multi-functionalised silk structures for use in a wide range of applications. These will be particularly useful in the fields of tissue engineering and biomedicine.”

Remarkable qualities of spider silk

Spider silk is strong, biocompatible and biodegradable. It is a protein-based material that does not appear to cause a strong immune, allergic or inflammatory reaction. With the recent development of recombinant spider silk, the race has been on to find ways of harnessing its remarkable qualities.

The Nottingham research team has shown that their technique can be used to create a biodegradable mesh which can do two jobs at once. It can replace the extra cellular matrix that our own cells generate, to accelerate growth of the new tissue. It can also be used for the slow release of antibiotics.

Professor Thomas said: “There is the possibility of using the silk in advanced dressings for the treatment of slow-healing wounds such as diabetic ulcers. Using our technique infection could be prevented over weeks or months by the controlled release of antibiotics. At the same time tissue regeneration is accelerated by silk fibres functioning as a temporary scaffold before being biodegraded.”

The medicinal properties of spider silk recognised for centuries.

The medicinal properties of spider silk have been recognised for centuries but not clearly understood. The Greeks and Romans treated wounded soldiers with spider webs to stop bleeding. It is said that soldiers would use a combination of honey and vinegar to clean deep wounds and then cover the whole thing with balled-up spider webs.

There is even a mention in Shakespeare’s Midsummer Night’s Dream: “I shall desire you of more acquaintance, good master cobweb,” the character ‘Bottom’ said. “If I cut my finger, I shall make bold of you.”

The press release goes on to describe the genesis of the project and how this multidisciplinary team was formed in more detail,

The idea came together at a discipline bridging university ‘sandpit’ meeting five years ago. Dr Goodacre says her chance meeting at that event with Professor Thomas proved to be one of the most productive afternoons of her career.

Dr Goodacre, who heads up the SpiderLab in the School of Life Sciences, said: “I got up at that meeting and showed the audience a picture of some spider silk. I said ‘I want to understand how this silk works, and then make some.’

“At the end of the session Neil came up to me and said ‘I think my group could make that.’ He also suggested that there might be more interesting ‘tweaks’ one could make so that the silk could be ‘decorated’ with different, useful, compounds either permanently or which could be released over time due to a change in the acidity of the environment.”

The approach required the production of the silk proteins in a bacterium where an amino acid not normally found in proteins was included. This amino acid contained an azide group which is widely used in ‘click’ reactions that only occur at that position in the protein. It was an approach that no-one had used before with spider silk — but the big question was — would it work?

Dr Goodacre said: “It was the start of a fascinating adventure that saw a postdoc undertake a very preliminary study to construct the synthetic silks. He was a former SpiderLab PhD student who had previously worked with our tarantulas. Thanks to his ground work we showed we could produce the silk proteins in bacteria. We were then joined by David Harvey, a new PhD student, who not only made the silk fibres, incorporating the unusual amino acid, but also decorated it and demonstrated its antibiotic activity. He has since extended those first ideas far beyond what we had thought might be possible.”

David Harvey’s work is described in this paper but Professor Thomas and Dr Goodacre say this is just the start. There are other joint SpiderLab/Thomas lab students working on uses for this technology in the hope of developing it further.

David Harvey, the lead author on this their first paper, has just been awarded his PhD and is now a postdoctoral researcher on a BBSRC follow-on grant so is still at the heart of the research. His current work is focused on driving the functionalised spider silk technology towards commercial application in wound healing and tissue regeneration.

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

Antibiotic Spider Silk: Site-Specific Functionalization of Recombinant Spider Silk Using “Click” Chemistry by David Harvey, Philip Bardelang, Sara L. Goodacre, Alan Cockayne, and Neil R. Thomas. Advanced Materials DOI: 10.1002/adma.201604245 Version of Record online: 28 DEC 2016

© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

This paper is behind a paywall.

I imagine Mr. Cockayne’s name has led to much teasing over the years. People who have names with that kind of potential tend to either change them or double down and refuse to compromise.

Clay nanosheets and world food security

This is some interesting agricultural research from Australia. From a Jan. 11, 2017 news item on,

A University of Queensland team has made a discovery that could help conquer the greatest threat to global food security – pests and diseases in plants.

Research leader Professor Neena Mitter said BioClay – an environmentally sustainable alternative to chemicals and pesticides – could be a game-changer for crop protection.

“In agriculture, the need for new control agents grows each year, driven by demand for greater production, the effects of climate change, community and regulatory demands, and toxicity and pesticide resistance,” she said.

“Our disruptive research involves a spray of nano-sized degradable clay used to release double-stranded RNA, that protects plants from specific disease-causing pathogens.”

The research, by scientists from the Queensland Alliance for Agriculture and Food Innovation (QAAFI) and UQ’s Australian Institute for Bioengineering and Nanotechnology (AIBN) is published in Nature Plants.

A Jan. 11, 2017 University of Queensland press release, which originated the news item, provides a bit more detail,

Professor Mitter said the technology reduced the use of pesticides without altering the genome of the plants.

“Once BioClay is applied, the plant ‘thinks’ it is being attacked by a disease or pest insect and responds by protecting itself from the targeted pest or disease.

“A single spray of BioClay protects the plant and then degrades, reducing the risk to the environment or human health.”

She said BioClay met consumer demands for sustainable crop protection and residue-free produce.

“The cleaner approach will value-add to the food and agri-business industry, contributing to global food security and to a cleaner, greener image of Queensland.”

AIBN’s Professor Zhiping Xu said BioClay combined nanotechnology and biotechnology.

“It will produce huge benefits for agriculture in the next several decades, and the applications will expand into a much wider field of primary agricultural production,” Professor Xu said.

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

Clay nanosheets for topical delivery of RNAi for sustained protection against plant viruses by Neena Mitter, Elizabeth A. Worrall, Karl E. Robinson, Peng Li, Ritesh G. Jain, Christelle Taochy, Stephen J. Fletcher, Bernard J. Carroll, G. Q. (Max) Lu & Zhi Ping Xu. Nature Plants 3, Article number: 16207 (2017) doi:10.1038/nplants.2016.207 Published online: 09 January 2017

This paper is behind a paywall.

I don’t usually do this but here’s the abstract for the paper,

Topical application of pathogen-specific double-stranded RNA (dsRNA) for virus resistance in plants represents an attractive alternative to transgenic RNA interference (RNAi). However, the instability of naked dsRNA sprayed on plants has been a major challenge towards its practical application. We demonstrate that dsRNA can be loaded on designer, non-toxic, degradable, layered double hydroxide (LDH) clay nanosheets. Once loaded on LDH, the dsRNA does not wash off, shows sustained release and can be detected on sprayed leaves even 30 days after application. We provide evidence for the degradation of LDH, dsRNA uptake in plant cells and silencing of homologous RNA on topical application. Significantly, a single spray of dsRNA loaded on LDH (BioClay) afforded virus protection for at least 20 days when challenged on sprayed and newly emerged unsprayed leaves. This innovation translates nanotechnology developed for delivery of RNAi for human therapeutics to use in crop protection as an environmentally sustainable and easy to adopt topical spray.

It helps a bit but I’m puzzled by the description of BioClay as an alternative to RNAi in the first sentence because the last sentence has: “This innovation translates nanotechnology developed for delivery of RNAi … .” I believe what they’re saying is that LDH clay nanosheets were developed for delivery of RNAi but have now been adapted for delivery of dsRNA. Maybe?

At any rate this paper is behind a paywall.