Monthly Archives: June 2016

Replicating brain’s neural networks with 3D nanoprinting

An announcement about European Union funding for a project to reproduce neural networks by 3D nanoprinting can be found in a June 10, 2016 news item on Nanowerk,

The MESO-BRAIN consortium has received a prestigious award of €3.3million in funding from the European Commission as part of its Future and Emerging Technology (FET) scheme. The project aims to develop three-dimensional (3D) human neural networks with specific biological architecture, and the inherent ability to interrogate the network’s brain-like activity both electrophysiologically and optically. It is expected that the MESO-BRAIN will facilitate a better understanding of human disease progression, neuronal growth and enable the development of large-scale human cell-based assays to test the modulatory effects of pharmacological and toxicological compounds on neural network activity. The use of more physiologically relevant human models will increase drug screening efficiency and reduce the need for animal testing.

A June 9, 2016 Institute of Photonic Sciences (ICFO) press release (also on EurekAlert), which originated the news item, provides more detail,

About the MESO-BRAIN project

The MESO-BRAIN project’s cornerstone will use human induced pluripotent stem cells (iPSCs) that have been differentiated into neurons upon a defined and reproducible 3D scaffold to support the development of human neural networks that emulate brain activity. The structure will be based on a brain cortical module and will be unique in that it will be designed and produced using nanoscale 3D-laser-printed structures incorporating nano-electrodes to enable downstream electrophysiological analysis of neural network function. Optical analysis will be conducted using cutting-edge light sheet-based, fast volumetric imaging technology to enable cellular resolution throughout the 3D network. The MESO-BRAIN project will allow for a comprehensive and detailed investigation of neural network development in health and disease.

Prof Edik Rafailov, Head of the MESO-BRAIN project (Aston University) said: “What we’re proposing to achieve with this project has, until recently, been the stuff of science fiction. Being able to extract and replicate neural networks from the brain through 3D nanoprinting promises to change this. The MESO-BRAIN project has the potential to revolutionise the way we are able to understand the onset and development of disease and discover treatments for those with dementia or brain injuries. We cannot wait to get started!”

The MESO-BRAIN project will launch in September 2016 and research will be conducted over three years.

About the MESO-BRAIN consortium

Each of the consortium partners have been chosen for the highly specific skills & knowledge that they bring to this project. These include technologies and expertise in stem cells, photonics, physics, 3D nanoprinting, electrophysiology, molecular biology, imaging and commercialisation.

Aston University (UK) Aston Institute of Photonic Technologies (School of Engineering and Applied Science) is one of the largest photonic groups in UK and an internationally recognised research centre in the fields of lasers, fibre-optics, high-speed optical communications, nonlinear and biomedical photonics. The Cell & Tissue Biomedical Research Group (Aston Research Centre for Healthy Ageing) combines collective expertise in genetic manipulation, tissue engineering and neuronal modelling with the electrophysiological and optical analysis of human iPSC-derived neural networks. Axol Bioscience Ltd. (UK) was founded to fulfil the unmet demand for high quality, clinically relevant human iPSC-derived cells for use in biomedical research and drug discovery. The Laser Zentrum Hannover (Germany) is a leading research organisation in the fields of laser development, material processing, laser medicine, and laser-based nanotechnologies. The Neurophysics Group (Physics Department) at University of Barcelona (Spain) are experts in combing experiments with theoretical and computational modelling to infer functional connectivity in neuronal circuits. The Institute of Photonic Sciences (ICFO) (Spain) is a world-leading research centre in photonics with expertise in several microscopy techniques including light sheet imaging. KITE Innovation (UK) helps to bridge the gap between the academic and business sectors in supporting collaboration, enterprise, and knowledge-based business development.

For anyone curious about the FET funding scheme, there’s this from the press release,

Horizon 2020 aims to ensure Europe produces world-class science by removing barriers to innovation through funding programmes such as the FET. The FET (Open) funds forward-looking collaborations between advanced multidisciplinary science and cutting-edge engineering for radically new future technologies. The published success rate is below 1.4%, making it amongst the toughest in the Horizon 2020 suite of funding schemes. The MESO-BRAIN proposal scored a perfect 5/5.

You can find out more about the MESO-BRAIN project on its ICFO webpage.

They don’t say anything about it but I can’t help wondering if the scientists aren’t also considering the possibility of creating an artificial brain.

X-ray of a butterfly’s wing reveals structural colour secrets

Over millions of years, butterflies evolved sophisticated cellular mechanisms to produce brightly colored wings for mating and camouflage. iStock photo by Borut Trdina

Over millions of years, butterflies evolved sophisticated cellular mechanisms to produce brightly colored wings for mating and camouflage. iStock photo by Borut Trdina

A June 13, 2016 news item on Nanowerk announced a discovery about the physics of colour,

A team of physicists that visualized the internal nanostructure of an intact butterfly wing has discovered two physical attributes that make those structures so bright and colorful.

“Over millions of years, butterflies have evolved sophisticated cellular mechanisms to grow brightly colored structures, normally for the purpose of camouflage as well as mating,” says Oleg Shpyrko, an associate professor of physics at UC San Diego, who headed the research effort. “It’s been known for a century that the wings of these beautiful creatures contain what are called photonic crystals, which can reflect light of only a particular color.”

But exactly how these complex optical structures are assembled in a way that make them so bright and colorful remained a mystery.

A June 10, 2016 University of California at San Diego news release (also on EurekAlert), which originated the news item, describes how the mystery was solved,

In an effort to answer that question, Shpyrko and Andrej Singer, a postdoctoral researcher in his laboratory, went to the Advanced Photon Source at the Argonne National Laboratory in Illinois, which produces coherent x-rays very much like an optical laser

By combining these laser-like x-rays with an advanced imaging technique called “ptychography,” the UC San Diego physicists, in collaboration with physicists at Yale University and the Argonne National Laboratory, developed a new microscopy method to visualize the internal nanostructure of the tiny “scales” that make up the butterfly wing without the need to cut them apart.

The researchers report in the current issue of the journal Science Advances that their examination of the scales of the Emperor of India butterfly, Teinopalpus imperialis, revealed that these tiny wing structures consist of “highly oriented” photonic crystals.

“This explains why the scales appear to have a single color,” says Singer, the first author of the paper. “We also found through careful study of the high-resolution micrographs tiny crystal irregularities that may enhance light-scattering properties, making the butterfly wings appear brighter.”

These crystal dislocations or defects occur, the researchers say, when an otherwise perfectly periodic crystal lattice slips by one row of atoms. “Defects may have a negative connotation, but they are actually very useful in improving materials,” explains Singer. “For example, blacksmiths have learned over centuries how to purposefully induce defects into metals to make them stronger. ‘Defect engineering’ is also a focus for many research teams and companies working in the semiconductor field. In photonic crystals, defects can enhance light-scattering properties through an effect called light localization.”

“In the evolution of butterfly wings,” he adds, “it appears nature learned how to engineer these defects on purpose.”

The researchers have made this image illustrating their work available,

Scales from the wings of the Emperor of India butterfly consist of “highly oriented” photonic crystals. Photos by Andrej Singer, UC San Diego

Scales from the wings of the Emperor of India butterfly consist of “highly oriented” photonic crystals. Photos by Andrej Singer, UC San Diego

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

Domain morphology, boundaries, and topological defects in biophotonic gyroid nanostructures of butterfly wing scales by Andrej Singer, Leandra Boucheron, Sebastian H. Dietze, Katharine E. Jensen, David Vine, Ian McNulty, Eric R. Dufresne, Richard O. Prum, Simon G. J. Mochrie, and Oleg G. Shpyrko. Science Advances  10 Jun 2016: Vol. 2, no. 6, e1600149 DOI: 10.1126/sciadv.1600149

This paper is open access.

Cleaning up nuclear waste gases with nanotechnology-enabled materials

Swiss and US scientists have developed a nanoporous crystal that could be used to clean up nuclear waste gases according to a June 13, 2016 news item on Nanowerk (Note: A link has been removed),

An international team of scientists at EPFL [École polytechnique fédérale de Lausanne in Switzerland] and the US have discovered a material that can clear out radioactive waste from nuclear plants more efficiently, cheaply, and safely than current methods.

Nuclear energy is one of the cheapest alternatives to carbon-based fossil fuels. But nuclear-fuel reprocessing plants generate waste gas that is currently too expensive and dangerous to deal with. Scanning hundreds of thousands of materials, scientists led by EPFL and their US colleagues have now discovered a material that can absorb nuclear waste gases much more efficiently, cheaply and safely. The work is published in Nature Communications (“Metal–organic framework with optimally selective xenon adsorption and separation”).

A June 14, 2016 EPFL press release (also on EurekAlert), which originated the news item, explains further,

Nuclear-fuel reprocessing plants generate volatile radionuclides such as xenon and krypton, which escape in the so-called “off-gas” of these facilities – the gases emitted as byproducts of the chemical process. Current ways of capturing and clearing out these gases involve distillation at very low temperatures, which is expensive in both terms of energy and capital costs, and poses a risk of explosion.

Scientists led by Berend Smit’s lab at EPFL (Sion) and colleagues in the US, have now identified a material that can be used as an efficient, cheaper, and safer alternative to separate xenon and krypton – and at room temperature. The material, abbreviated as SBMOF-1, is a nanoporous crystal and belongs a class of materials that are currently used to clear out CO2 emissions and other dangerous pollutants. These materials are also very versatile, and scientists can tweak them to self-assemble into ordered, pre-determined crystal structures. In this way, they can synthesize millions of tailor-made materials that can be optimized for gas storage separation, catalysis, chemical sensing and optics.

The scientists carried out high-throughput screening of large material databases of over 125,000 candidates. To do this, they used molecular simulations to find structures that can separate xenon and krypton, and under conditions that match those involved in reprocessing nuclear waste.

Because xenon has a much shorter half-life than krypton – a month versus a decade – the scientists had to find a material that would be selective for both but would capture them separately. As xenon is used in commercial lighting, propulsion, imaging, anesthesia and insulation, it can also be sold back into the chemical market to offset costs.

The scientists identified and confirmed that SBMOF-1 shows remarkable xenon capturing capacity and xenon/krypton selectivity under nuclear-plant conditions and at room temperature.

The US partners have also made an announcement with this June 13, 2016 Pacific Northwest National Laboratory (PNNL) news release (also on EurekAlert), Note: It is a little repetitive but there’s good additional information,

Researchers are investigating a new material that might help in nuclear fuel recycling and waste reduction by capturing certain gases released during reprocessing. Conventional technologies to remove these radioactive gases operate at extremely low, energy-intensive temperatures. By working at ambient temperature, the new material has the potential to save energy, make reprocessing cleaner and less expensive. The reclaimed materials can also be reused commercially.

Appearing in Nature Communications, the work is a collaboration between experimentalists and computer modelers exploring the characteristics of materials known as metal-organic frameworks.

“This is a great example of computer-inspired material discovery,” said materials scientist Praveen Thallapally of the Department of Energy’s Pacific Northwest National Laboratory. “Usually the experimental results are more realistic than computational ones. This time, the computer modeling showed us something the experiments weren’t telling us.”

Waste avoidance

Recycling nuclear fuel can reuse uranium and plutonium — the majority of the used fuel — that would otherwise be destined for waste. Researchers are exploring technologies that enable safe, efficient, and reliable recycling of nuclear fuel for use in the future.

A multi-institutional, international collaboration is studying materials to replace costly, inefficient recycling steps. One important step is collecting radioactive gases xenon and krypton, which arise during reprocessing. To capture xenon and krypton, conventional technologies use cryogenic methods in which entire gas streams are brought to a temperature far below where water freezes — such methods are energy intensive and expensive.

Thallapally, working with Maciej Haranczyk and Berend Smit of Lawrence Berkeley National Laboratory [LBNL] and others, has been studying materials called metal-organic frameworks, also known as MOFs, that could potentially trap xenon and krypton without having to use cryogenics.

These materials have tiny pores inside, so small that often only a single molecule can fit inside each pore. When one gas species has a higher affinity for the pore walls than other gas species, metal-organic frameworks can be used to separate gaseous mixtures by selectively adsorbing.

To find the best MOF for xenon and krypton separation, computational chemists led by Haranczyk and Smit screened 125,000 possible MOFs for their ability to trap the gases. Although these gases can come in radioactive varieties, they are part of a group of chemically inert elements called “noble gases.” The team used computing resources at NERSC, the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility at LBNL.

“Identifying the optimal material for a given process, out of thousands of possible structures, is a challenge due to the sheer number of materials. Given that the characterization of each material can take up to a few hours of simulations, the entire screening process may fill a supercomputer for weeks,” said Haranczyk. “Instead, we developed an approach to assess the performance of materials based on their easily computable characteristics. In this case, seven different characteristics were necessary for predicting how the materials behaved, and our team’s grad student Cory Simon’s application of machine learning techniques greatly sped up the material discovery process by eliminating those that didn’t meet the criteria.”

The team’s models identified the MOF that trapped xenon most selectively and had a pore size close to the size of a xenon atom — SBMOF-1, which they then tested in the lab at PNNL.

After optimizing the preparation of SBMOF-1, Thallapally and his team at PNNL tested the material by running a mixture of gases through it — including a non-radioactive form of xenon and krypton — and measuring what came out the other end. Oxygen, helium, nitrogen, krypton, and carbon dioxide all beat xenon out. This indicated that xenon becomes trapped within SBMOF-1’s pores until the gas saturates the material.

Other tests also showed that in the absence of xenon, SBMOF-1 captures krypton. During actual separations, then, operators would pass the gas streams through SBMOF-1 twice to capture both gases.

The team also tested SBMOF-1’s ability to hang onto xenon in conditions of high humidity. Humidity interferes with cryogenics, and gases must be dehydrated before putting them through the ultra-cold method, another time-consuming expense. SBMOF-1, however, performed quite admirably, retaining more than 85 percent of the amount of xenon in high humidity as it did in dry conditions.

The final step in collecting xenon or krypton gas would be to put the MOF material under a vacuum, which sucks the gas out of the molecular cages for safe storage. A last laboratory test examined how stable the material was by repeatedly filling it up with xenon gas and then vacuuming out the xenon. After 10 cycles of this, SBMOF-1 collected just as much xenon as the first cycle, indicating a high degree of stability for long-term use.

Thallapally attributes this stability to the manner in which SBMOF-1 interacts with xenon. Rather than chemical reactions between the molecular cages and the gases, the relationship is purely physical. The material can last a lot longer without constantly going through chemical reactions, he said.

A model finding

Although the researchers showed that SBMOF-1 is a good candidate for nuclear fuel reprocessing, getting these results wasn’t smooth sailing. In the lab, the researchers had followed a previously worked out protocol from Stony Brook University to prepare SBMOF-1. Part of that protocol requires them to “activate” SBMOF-1 by heating it up to 300 degrees Celsius, three times the temperature of boiling water.

Activation cleans out material left in the pores from MOF synthesis. Laboratory tests of the activated SBMOF-1, however, showed the material didn’t behave as well as it should, based on the computer modeling results.

The researchers at PNNL repeated the lab experiments. This time, however, they activated SBMOF-1 at a lower temperature, 100 degrees Celsius, or the actual temperature of boiling water. Subjecting the material to the same lab tests, the researchers found SBMOF-1 behaving as expected, and better than at the higher activation temperature.

But why? To figure out where the discrepancy came from, the researchers modeled what happened to SBMOF-1 at 300 degrees Celsius. Unexpectedly, the pores squeezed in on themselves.

“When we heated the crystal that high, atoms within the pore tilted and partially blocked the pores,” said Thallapally. “The xenon doesn’t fit.”

Armed with these new computational and experimental insights, the researchers can explore SBMOF-1 and other MOFs further for nuclear fuel recycling. These MOFs might also be able to capture other noble gases such as radon, a gas known to pool in some basements.

Researchers hailed from several other institutions as well as those listed earlier, including University of California, Berkeley, Ecole Polytechnique Fédérale de Lausanne (EPFL) in Switzerland, Brookhaven National Laboratory, and IMDEA Materials Institute in Spain. This work was supported by the [US] Department of Energy Offices of Nuclear Energy and Science.

Here’s an image the researchers have provided to illustrate their work,

Caption: The crystal structure of SBMOF-1 (green = Ca, yellow = S, red = O, gray = C, white = H). The light blue surface is a visualization of the one-dimensional channel that SBMOF-1 creates for the gas molecules to move through. The darker blue surface illustrates where a Xe atom sits in the pores of SBMOF-1 when it adsorbs. Credit: Berend Smit/EPFL/University of California Berkley

Caption: The crystal structure of SBMOF-1 (green = Ca, yellow = S, red = O, gray = C, white = H). The light blue surface is a visualization of the one-dimensional channel that SBMOF-1 creates for the gas molecules to move through. The darker blue surface illustrates where a Xe atom sits in the pores of SBMOF-1 when it adsorbs. Credit: Berend Smit/EPFL/University of California Berkley

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

Metal–organic framework with optimally selective xenon adsorption and separation by Debasis Banerjee, Cory M. Simon, Anna M. Plonka, Radha K. Motkuri, Jian Liu, Xianyin Chen, Berend Smit, John B. Parise, Maciej Haranczyk, & Praveen K. Thallapally. Nature Communications 7, Article number: ncomms11831  doi:10.1038/ncomms11831 Published 13 June 2016

This paper is open access.

Final comment, this is the second time in the last month I’ve stumbled across more positive approaches to nuclear energy. The first time was a talk (Why Nuclear Power is Necessary) held in Vancouver, Canada in May 2016 (details here). I’m not trying to suggest anything unduly sinister but it is interesting since most of my adult life nuclear power has been viewed with fear and suspicion.

Café Scientifique (Vancouver, Canada) June 28, 2016 talk: Why Online Dating Doesn’t Work

Vancouver’s (Canada) Café Scientifique seems to be roaming around;  Shebeen Whiskey House (212 Carrall St) is hosting the next Café Scientifique talk. From the June 6, 2016 notice received via email,

Our next café will happen on Tuesday June 28th [2016], 7:30pm at the Shebeen Whiskey House (212 Carrall St). Our speaker for the evening will be Dr. Martin Graff, a Professor in the Department of Psychology at the University of South Wales, UK. The title of his talk is:

Why Online Dating Doesn’t Work

There is much evidence that being in a good relationship can be beneficial to our health, happiness and general well-being.  However, should we resort to online dating in the pursuit of a happy relationship?  Psychological research would seem to suggest that online dating may not be the easy answer.

This talk focuses on the reasons why we should be cautious in our online dating pursuits.  For example, people make bad decisions in online dating.  Furthermore, those we contact are often not what they appear to be.  Additionally, there is no evidence that the algorithms employed by dating sites and which purport to match us with a desirable partner actually work in reality.

Finally, this talk will also give some tips on how to at least maximize our chances in an online dating environment.

Dr. Martin Graff is Reader and Head of Research in Psychology at the University of South Wales, UK, an associate fellow of the British Psychological Society and a Chartered Psychologist.  He has researched cognitive processes in web-based learning, the formation and dissolution of romantic relationships online and offline, online persuasion and disinhibition. He has written over 50 scientific articles, published widely in the field of Internet behaviour, and presented his work at numerous International Conferences. He writes for Psychology Today magazine and regularly speaks at events in the UK and Internationally.

Happy dating!

Lungs: EU SmartNanoTox and Pneumo NP

I have three news bits about lungs one concerning relatively new techniques for testing the impact nanomaterials may have on lungs and two concerning developments at PneumoNP; the first regarding a new technique for getting antibiotics to a lung infected with pneumonia and the second, a new antibiotic.

Predicting nanotoxicity in the lungs

From a June 13, 2016 news item on Nanowerk,

Scientists at the Helmholtz Zentrum München [German Research Centre for Environmental Health] have received more than one million euros in the framework of the European Horizon 2020 Initiative [a major European Commission science funding initiative successor to the Framework Programme 7 initiative]. Dr. Tobias Stöger and Dr. Otmar Schmid from the Institute of Lung Biology and Disease and the Comprehensive Pneumology Center (CPC) will be using the funds to develop new tests to assess risks posed by nanomaterials in the airways. This could contribute to reducing the need for complex toxicity tests.

A June 13, 2016 Helmholtz Zentrum München (German Research Centre for Environmental Health) press release, which originated the news item, expands on the theme,

Nanoparticles are extremely small particles that can penetrate into remote parts of the body. While researchers are investigating various strategies for harvesting the potential of nanoparticles for medical applications, they could also pose inherent health risks*. Currently the hazard assessment of nanomaterials necessitates a complex and laborious procedure. In addition to complete material characterization, controlled exposure studies are needed for each nanomaterial in order to guarantee the toxicological safety.

As a part of the EU SmartNanoTox project, which has now been funded with a total of eight million euros, eleven European research partners, including the Helmholtz Zentrum München, want to develop a new concept for the toxicological assessment of nanomaterials.

Reference database for hazardous substances

Biologist Tobias Stöger and physicist Otmar Schmid, both research group heads at the Institute of Lung Biology and Disease, hope that the use of modern methods will help to advance the assessment procedure. “We hope to make more reliable nanotoxicity predictions by using modern approaches involving systems biology, computer modelling, and appropriate statistical methods,” states Stöger.

The lung experts are concentrating primarily on the respiratory tract. The approach involves defining a representative selection of toxic nanomaterials and conducting an in-depth examination of their structure and the various molecular modes of action that lead to their toxicity. These data are then digitalized and transferred to a reference database for new nanomaterials. Economical tests that are easy to conduct should then make it possible to assess the toxicological potential of these new nanomaterials by comparing the test results s with what is already known from the database. “This should make it possible to predict whether or not a newly developed nanomaterial poses a health risk,” Otmar Schmid says.

* Review: Schmid, O. and Stoeger, T. (2016). Surface area is the biologically most effective dose metric for acute nanoparticle toxicity in the lung. Journal of Aerosol Science, DOI:10.1016/j.jaerosci.2015.12.006

The SmartNanoTox webpage is here on the European Commission’s Cordis website.

Carrying antibiotics into lungs (PneumoNP)

I received this news from the European Commission’s PneumoNP project (I wrote about PneumoNP in a June 26, 2014 posting when it was first announced). This latest development is from a March 21, 2016 email (the original can be found here on the How to pack antibiotics in nanocarriers webpage on the PneumoNP website),

PneumoNP researchers work on a complex task: attach or encapsulate antibiotics with nanocarriers that are stable enough to be included in an aerosol formulation, to pass through respiratory tracts and finally deliver antibiotics on areas of lungs affected by pneumonia infections. The good news is that they finally identify two promising methods to generate nanocarriers.

So far, compacting polymer coils into single-chain nanoparticles in water and mild conditions was an unsolved issue. But in Spain, IK4-CIDETEC scientists developed a covalent-based method that produces nanocarriers with remarkable stability under those particular conditions. Cherry on the cake, the preparation is scalable for more industrial production. IK4-CIDETEC patented the process.

Fig.: A polymer coil (step 1) compacts into a nanocarrier with cross-linkers (step 2). Then, antibiotics get attached to the nanocarrier (step 3).

Fig.: A polymer coil (step 1) compacts into a nanocarrier with cross-linkers (step 2). Then, antibiotics get attached to the nanocarrier (step 3).

At the same time, another route to produce lipidic nanocarriers have been developed by researchers from Utrecht University. In particular, they optimized the method consisting in assembling lipids directly around a drug. As a result, generated lipidic nanocarriers show encouraging stability properties and are able to carry sufficient quantity of antibiotics.

Fig.: On presence of antibiotics, the lipidic layer (step 1) aggregates the the drug (step 2) until the lipids forms a capsule around the antibiotics (step 3).

Fig.: On presence of antibiotics, a lipidic layer (step 1) aggregates the drug (step 2) until the lipids forms a capsule around antibiotics (step 3).

Assays of both polymeric and lipidic nanocarriers are currently performed by ITEM Fraunhofer Institute in Germany, Ingeniatrics Tecnologias in Spain and Erasmus Medical Centre in the Netherlands. Part of these tests allows to make sure that the nanocarriers are not toxic to cells. Other tests are also done to verify that the efficiency of antibiotics on Klebsiella Pneumoniae bacteria when they are attached to nanocarriers.

A new antibiotic for pneumonia (PneumoNP)

A June 14, 2016 PneumoNP press release (received via email) announces work on a promising new approach to an antibiotic for pneumonia,

The antimicrobial peptide M33 may be the long-sought substitute to treat difficult lung infections, like multi-drug resistant pneumonia.

In 2013, the European Respiratory Society predicted 3 millions cases of pneumonia in Europe every year [1]. The standard treatment for pneumonia is an intravenous administration of a combination of drugs. This leads to the development of antibiotic resistance in the population. Gradually, doctors are running out of solutions to cure patients. An Italian company suggests a new option: the M33 peptide.

Few years ago, the Italian company SetLance SRL decided to investigate the M33 peptide. The antimicrobial peptide is an optimized version of an artificial peptide sequence selected for its efficacy and stability. So far, it showed encouraging in-vitro results against multidrug-resistant Gram-negative bacteria, including Klebsiella Pneumoniae. With the support of EU funding to the PneumoNP project, SetLance SRL had the opportunity to develop a new formulation of M33 that enhances its antimicrobial activity.

The new formulation of M33 fights Gram-negative bacteria in three steps. First of all, the M33 binds with the lipopolysaccharides (LPS) on the outer membrane of bacteria. Then, the molecule forms a helix and finally disrupts the membrane provoking cytoplasm leaking. The peptide enabled up to 80% of mices to survive Pseudomonas Aeruginosa-based lung infections. Beyond these encouraging results, toxicity to the new M33 formulation seems to be much lower than antimicrobial peptides currently used in clinical practice like colistin [2].

Lately, SetLance scaled-up the synthesis route and is now able to produce several hundred milligrams per batch. The molecule is robust enough for industrial production. We may expect this drug to go on clinical development and validation at the beginning of 2018.

[1] http://www.erswhitebook.org/chapters/acute-lower-respiratory-infections/pneumonia/
[2] Ceccherini et al., Antimicrobial activity of levofloxacin-M33 peptide conjugation or combination, Chem Med Comm. 2016; Brunetti et al., In vitro and in vivo efficacy, toxicity, bio-distribution and resistance selection of a novel antibacterial drug candidate. Scientific Reports 2016

I believe all the references are open access.

Brief final comment

The only element linking these news bits together is that they concern the lungs.

Nanoremediation to be combined with bioremediation for soil decontamination

There’s a very interesting proposal to combine nanoremediation with bioremediatiion (also known as, phytoremediation) techniques to decontaminate soil. From a June 10, 2016 news item on Nanowerk,

The Basque Institute of Agricultural Research and Development Neiker-Tecnalia is currently exploring a strategy to remedy soils contaminated by organic compounds containing chlorine (organochlorine compounds). The innovative process consists of combining the application of zero-iron nanoparticles with bioremediation techniques. The companies Ekotek and Dinam, the UPV/EHU-University of the Basque Country and Gaiker-IK4 are also participating in this project known as NANOBIOR.

A June 10, 2016 Elhuyar Fundazioa news release, which originated the news item, provides more detail about the proposed integration of the two techniques,

Soils affected by organochlorine compounds are very difficult to decontaminate. Among these organochlorine compounds feature some insecticides mainly used to control insect pests, such as DDT, aldrin, dieldrin, endosulfan, hexachlorocyclohexane, toxaphene, chlordecone, mirex, etc. It is a well-known fact that the use of many of these insecticides is currently banned owing to their environmental impact and the risk they pose for human health.

To degrade organochlorine compounds (organic compounds whose molecules contain chlorine atoms) present in the soil, the organisations participating in the project are proposing a strategy based on the application, initially, of zero-iron nanoparticles [also known as nano zero valent iron] that help to eliminate the chlorine atoms in these compounds. Once these atoms have been eliminated, the bioremediation is carried out (a process in which microorganisms, fungi, plants or enzymes derived from them are used to restore an environment altered by contaminants to its natural state).

The bioremediation process being developed by Neiker-Tecnalia comprises two main strategies: biostimulation and bioaugmentation. The first consists of stimulating the bacteria already present in the soil by adding nutrients, humidity, oxygen, etc. Bioaugmentation is based on applying bacteria with the desired degrading capability to the soil. As part of this process, Neiker-Tecnalia collects samples of soils contaminated by organochlorine compounds and in the laboratory isolates the species of bacteria that display a greater capacity for degrading these contaminants. Once the most interesting strains have been isolated, the quantity of these bacteria are then augmented in the laboratory and the soil needing to be decontaminated is then inoculated with them.

Bank of effective strains to combat organochlorines

The first step for Neiker-Tecnalia is to identify bacterial species capable of degrading organochlorine compounds in order to have available a bank of species of interest for use in bioremediation. This bank will be gathering strains collected in the Basque Country and will allow bacteria that can be used as a decontaminating element of soils to be made available.

The combining of the application of zero-iron nanoparticles and bioremediation constitutes a significant step forward in the matter of soil decontamination; it offers the added advantage of potentially being able to apply them in situ. So this methodology, which is currently in the exploratory phase, could replace other processes such as the excavation of contaminated soils so that they can be contained and/or treated. What is more, the combination of the two techniques makes it possible to reduce the decontamination times, which would take much longer if bioremediation is used on its own.

There is a NANOBIOR webpage here.

For the curious I have two 2012 posts that provide some very nice explanations by Joe Martin, then a Master’s student in the University of Michigan’s Public Health program,: Phyto and nano soil remediation (part 1: phyto/plant) and Phyto and nano soil remediation (part 2: nano).

A new, stable open-shell carbon molecule from Oregon

This discovery could one day make organic solar cells more efficient than silicon ones. Researchers at the University of Oregon announced their discovery in a June 9, 2016 news item on ScienceDaily,

University of Oregon chemists have synthesized a stable and long-lasting carbon-based molecule that, they say, potentially could be applicable in solar cells and electronic devices.

The molecule changes its bonding patterns to a magnetic biradical state when heated; it then returns to a fully bonded non-magnetic closed state at room temperature. That transition, they report, can be done repeatedly without decomposition. It remains stable in the presence of both heat and oxygen.

A June 9, 2016 University of Oregon news release on EurekAlert, which originated the news item, provides more detail,

 

Biradical refers to organic compounds, known as open-shell molecules, that have two free-flowing, non-bonding electrons. Producing them using techniques to control their electron spin, and thus provide semiconducting properties, in a heated state has been hampered by instability since the first synthetic biradical hydrocarbon was made in 1907.

“Potentially our approach could help to make organic solar cells more efficient than silicon solar cells, but that’s probably far in the future,” said UO doctoral student Gabriel E. Rudebusch, the paper’s lead author. “Our synthesis is rapid and efficient. We easily can make a gram of this compound, which is very stable when exposed to oxygen and heat. This stability has been almost unheard of in the literature about biradical compounds.”

The four-step synthesis of the compound — diindenoanthracene, or DIAn — and how it held up when tested in superconducting materials were detailed in a proof-of-principle paper published online May 23 by the journal Nature Chemistry. The UO team collaborated with experts in Japan, Spain and Sweden.

The molecular framework for the new molecule involves the hydrocarbon anthracene, which has three linearly fused hexagonal benzene rings, in combination with two five-membered pentagonal rings.

“The big difference between our new molecule and a lot of other biradical molecules that have been produced is those five-membered rings,” said co-author Michael M. Haley, who holds the UO’s Richard M. and Patricia H. Noyes Professorship in Chemistry. “They have the inherent ability to accept electrons or give up electrons. This means DIAn can move both negative and positive charges, which is an essential property for useful devices such as transistors and solar cells. Also, we can heat up our molecule to 150 degrees Celsius, bring it back to room temperature and heat it up again, repeatedly, and we see no decomposition in its reaction to oxygen. The unique features of DIAn are essential if these molecules are to have a use in the real world.”

Haley’s lab is now seeking to develop derivatives of the new molecule to help move the technology forward into potential applications.

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

Diindeno-fusion of an anthracene as a design strategy for stable organic biradicals by Gabriel E. Rudebusch, José L. Zafra, Kjell Jorner, Kotaro Fukuda, Jonathan L. Marshall, Iratxe Arrechea-Marcos, Guzmán L. Espejo, Rocío Ponce Ortiz, Carlos J. Gómez-García, Lev N. Zakharov, Masayoshi Nakano, Henrik Ottosson, Juan Casado & Michael M. Haley. Nature Chemistry (2016)  doi:10.1038/nchem.2518 Published online 23 May 2016

This paper is behind a paywall.

There is another June 9, 2016 University of Oregon news release by Jim Barlow about this discovery. It covers much of the same material but focuses more closely on Rudebusch’s perspective.

Weather@Home citizen science project

It’s been a while since I’ve featured a citizen science story here. So, here’s more about Weather@Home from a June 9, 2016 Oregon State University news release on EurekAlert,

Tens of thousands of “citizen scientists” have volunteered some use of their personal computer time to help researchers create one of the most detailed, high resolution simulations of weather ever done in the Western United States.

The data, obtained through a project called Weather@Home, is an important step forward for scientifically sound, societally relevant climate science, researchers say in a an article published in the Bulletin of the American Meteorological Society. The analysis covered the years 1960-2009 and future projections of 2030-49.

Caption: The elevation of areas of the American West that were part of recent climate modeling as part of the Weather@Home Program. Credit: Graphic courtesy of Oregon State University

Caption: The elevation of areas of the American West that were part of recent climate modeling as part of the Weather@Home Program. Credit: Graphic courtesy of Oregon State University

The news release expands on the theme,

“When you have 30,000 modern laptop computers at work, you can transcend even what a supercomputer can do,” said Philip Mote, professor and director of the Oregon Climate Change Research Institute at Oregon State University, and lead author on the study.

“With this analysis we have 140,000 one-year simulations that show all of the impacts that mountains, valleys, coasts and other aspects of terrain can have on local weather,” he said. “We can drill into local areas, ask more specific questions about management implications, and understand the physical and biological climate changes in the West in a way never before possible.”

The sheer number of simulations tends to improve accuracy and reduce the uncertainty associated with this type of computer analysis, experts say. The high resolution also makes it possible to better consider the multiple climate forces at work in the West – coastal breezes, fog, cold air in valleys, sunlight being reflected off snow – and vegetation that ranges from wet, coastal rain forests to ice-covered mountains and arid scrublands within a comparatively short distance.

Although more accurate than previous simulations, improvements are still necessary, researchers say. Weather@Home tends to be too cool in a few mountain ranges and too warm in some arid plains, such as the Snake River plain and Columbia plateau, especially in summer. While other models have similar errors, Weather@Home offers the unique capability to improve simulations by improving the physics in the model.

Ultimately, this approach will help improve future predictions of regional climate. The social awareness of these issues has “matured to the point that numerous public agencies, businesses and investors are asking detailed questions about the future impacts of climate change,” the researchers wrote in their report.

This has led to a skyrocketing demand for detailed answers to specific questions – what’s the risk of a flood in a particular area, what will be future wind speeds as wind farms are developed, how should roads and bridges be built to handle extremely intense rainfall? There will be questions about heat stress on humans, the frequency of droughts, future sea levels and the height of local storm surges.

This type of analysis, and more like it, will help answer some of those questions, researchers say.

New participants in this ongoing research are always welcome, officials said. If interested in participating, anyone can go online to “climateprediction.net” and click on “join.” They should then follow the instructions to download and install BOINC, a program that manages the tasks; create an account; and select a project. Participation in climateprediction.net is available, as well as many others.

I checked out the About page on the climateprediction.net website, which hosts the Weather@Home project,

Climateprediction.net is a volunteer computing, climate modelling project based at the University of Oxford in the Environmental Change Institute, the Oxford e-Research Centre and Atmospheric, Oceanic and Planetary Physics.

We have a team of 13 climate scientists, computing experts and graduate students working on this project, as well as our partners and collaborators working at other universities, research and non-profit organisations around the world.

What we do

We run climate modelling experiments using the home computers of thousands of volunteers. This allows us to answer important and difficult questions about how climate change is affecting our world now and how it will affect our world in the future.

Climateprediction.net is a not-for-profit project.

Why we need your help

We run hundreds of thousands of state-of-the-art climate models, each very slightly different from the others, but still plausibly representing the real world.

This technique, known as ensemble modelling, requires an enormous amount of computing power.

Climate models are large and resource-intensive to run and it is not possible to run the large number of models we need on supercomputers.

Our solution is to appeal to volunteer computing, which combines the power of thousands of ordinary computers, each of which tackles one small part of the larger modelling task.

By using your computers, we can improve our understanding of, and confidence in, climate change predictions more than would ever be possible using the supercomputers currently available to scientists.

Please join our project and help us model the climate.

Our Experiments

When climateprediction.net first started, we were running very large, global models to answer questions about how climate change will pan out in the 21st century.

In addition, we are now running a number of smaller, regional experiments, under the umbrella of weather@home.

BOINC

Climateprediction.net uses a volunteer computing platform called BOINC (The Berkeley Open Infrastructure for Network Computing).

BOINC was originally developed to support SETI@home, which uses people’s home computers to analyse radio signals, searching for signs of extra-terrestrial intelligence.

BOINC is now used on over 70 projects covering a wide range of scientific areas, including mathematics, medicine, molecular biology, climatology, environmental science, and astrophysics.

Getting back to Oregon State University and its regional project research, here’s a link to and a citation for the paper,

Superensemble Regional Climate Modeling for the Western United States by Philip W. Mote, Myles R. Allen, Richard G. Jones, Sihan Li, Roberto Mera, David E. Rupp, Ahmed Salahuddin, and Dean Vickers. Bulletin of the American Meteorological Society February 2016, Vol. 97, No. 2 DOI: http://dx.doi.org/10.1175/BAMS-D-14-00090.1 Published online 14 March 2016

This is an open access paper.

‘Getting into’ cellulose walls at the University of Cambridge (UK) and University of Melbourne (Australia)

“Getting into” as used in the headline is slang for exploring a topic in more depth which is what an international team of researchers did when they ‘got into’ cellulose. From a June 9, 2016 news item on phys.org (Note: Links have been removed),

In the search for low emission plant-based fuels, new research may help avoid having to choose between growing crops for food or fuel.

Scientists have identified new steps in the way plants produce cellulose, the component of plant cell walls that provides strength, and forms insoluble fibre in the human diet.

The findings could lead to improved production of cellulose and guide plant breeding for specific uses such as wood products and ethanol fuel, which are sustainable alternatives to fossil fuel-based products.

Published in the journal Nature Communications today, the work was conducted by an international team of scientists, led by the University of Cambridge and the University of Melbourne.

A June 9, 2016 University of Cambridge press release, which originated the news item, provides more detail,

“Our research identified several proteins that are essential in the assembly of the protein machinery that makes cellulose”, said Melbourne’s Prof Staffan Persson.

“We found that these assembly factors control how much cellulose is made, and so plants without them can not produce cellulose very well and the defect substantially impairs plant biomass production. The ultimate aim of this research would be breed plants that have altered activity of these proteins so that cellulose production can be improved for the range of applications that use cellulose including paper, timber and ethanol fuels.”

The newly discovered proteins are located in an intracellular compartment called the Golgi where proteins are sorted and modified.

“If the function of this protein family is abolished the cellulose synthesizing complexes become stuck in the Golgi and have problems reaching the cell surface where they normally are active” said the lead authors of the study, Drs. Yi Zhang (Max-Planck Institute for Molecular Plant Physiology) and Nino Nikolovski (University of Cambridge).

“We therefore named the new proteins STELLO, which is Greek for to set in place, and deliver.”

“The findings are important to understand how plants produce their biomass”, said Professor Paul Dupree from the University of Cambridge’s Department of Biochemistry.

“Greenhouse-gas emissions from cellulosic ethanol, which is derived from the biomass of plants, are estimated to be roughly 85 percent less than from fossil fuel sources. Research to understand cellulose production in plants is therefore an important part of climate change mitigation.”

“In addition, by using cellulosic plant materials we get around the problem of food-versus-fuel scenario that is problematic when using corn as a basis for bioethanol.”

“It is therefore of great importance to find genes and mechanisms that can improve cellulose production in plants so that we can tailor cellulose production for various needs.”

Previous studies by Profs. Persson’s and Dupree’s research groups have, together with other scientists, identified many proteins that are important for cellulose synthesis and for other cell wall polymers.

With the newly presented research they substantially increase our understanding for how the bulk of a plant’s biomass is produced and is therefore of vast importance to industrial applications.

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

Golgi-localized STELLO proteins regulate the assembly and trafficking of cellulose synthase complexes in Arabidopsis by Yi Zhang, Nino Nikolovski, Mathias Sorieul, Tamara Vellosillo, Heather E. McFarlane, Ray Dupree, Christopher Kesten, René Schneider, Carlos Driemeier, Rahul Lathe, Edwin Lampugnani, Xiaolan Yu, Alexander Ivakov, Monika S. Doblin, Jenny C. Mortimer, Steven P. Brown, Staffan Persson, & Paul Dupree. Nature Communications 7,
Article number: 11656 doi:10.1038/ncomms11656 Published  09 June 2016

This paper is open access.

Introducing the LIFE project NanoMONITOR

I believe LIFE in the project title refers to life cycle. Here’s more from a June 9, 2016 news item from Nanowerk (Note: A link has been removed),

The newly started European Commission LIFE project NanoMONITOR addresses the challenges of supporting the risk assessment of nanomaterials under REACH by development of a real-time information and monitoring system. At the project’s kickoff meeting held on the 19th January 2016 in Valencia (Spain) participants discussed how this goal could be achieved.

Despite the growing number of engineered nanomaterials (ENMs) already available on the market and in contract to their benefits the use, production, and disposal of ENMs raises concerns about their environmental impact.

A REACH Centre June 8, 2016 press release, which originated the news item, expands on the theme,

Within this context, the overall aim of LIFE NanoMONITOR is to improve the use of environmental monitoring data to support the implementation of REACH regulation and promote the protection of human health and the environment when dealing with ENMs. Within the EU REACH Regulation, a chemical safety assessment report, including risk characterisation ratio (RCR), must be provided for any registered ENMs. In order to address these objectives, the project partners have developed a rigorous methodology encompassing the following aims:

  • Develop a novel software application to support the acquisition, management and processing of data on the concentration of ENMs.
  • Develop an on-line environmental monitoring database (EMD) to support the sharing of information.
  • Design and develop a proven monitoring station prototype for continuous monitoring of particles below 100 nm in air (PM0.1).
  • Design and develop standardized sampling and data analysis procedures to ensure the quality, comparability and reliability of the monitoring data used for risk assessment.
  • Support the calculation of the predicted environmental concentration (PEC) of ENMs in the context of REACH.

Throughout the project’s kick off meeting, participants discussed the status of the research area, project goals, and expectations of the different stakeholders with respect to the project outcome.

The project has made this graphic available,

LIFE_NanoMONITOR

You can find the LIFE project NanoMONITOR website here.