Researchers at the Swiss Federal Institute of Technology in Lausanne (EPFL), Switzerland, are fine-tuning a technology that transforms wet algal biomass into a biogas that is compatible with today’s natural gas infrastructure.... Read more »
Mariluz Bagnoud-Velásquez, Martin Brandenberger, Frédéric Vogel, Christian Ludwiga. (2014) Continuous catalytic hydrothermal gasification of algal biomass and case study on toxicity of aluminum as a step toward effluents recycling. Catalysis Today, 35-43. DOI: 10.1016/j.cattod.2013.12.001
Pretty blossoms aren’t immune to the body-morphing, plague-spreading powers of a good microbe. Some of the flowers you admire on a spring day might only be blooming, for example, because they’re hostages of a disease. Plant diseases can’t scatter in sneeze droplets like a human virus can. But they can change the look and behavior […]The post The 5 Creepiest Ways Plant Diseases Mutate Flowers appeared first on Inkfish.... Read more »
McArt SH, Koch H, Irwin RE, & Adler LS. (2014) Arranging the bouquet of disease: floral traits and the transmission of plant and animal pathogens. Ecology letters. PMID: 24528408
In a study published last week in the journal Science, Kyoung-Shin Choi, a chemistry professor at the University of Wisconsin-Madison, and postdoctoral researcher Tae Woo Kim combined cheap, oxide-based materials to split water into hydrogen and oxygen gases using solar energy with a solar-to-hydrogen conversion efficiency of 1.7 percent, the highest reported for any oxide-based photoelectrode system.... Read more »
Tae Woo Kim, Kyoung-Shin Choi. (2014) Nanoporous BiVO4 Photoanodes with Dual-Layer Oxygen Evolution Catalysts for Solar Water Splitting. Science. DOI: 10.1126/science.1246913
Humans have been using silver for millennia – as currency, jewellery, or fine dining cutlery. In these forms, the lustrous metal is harmless. But when silver is allowed to dissolve into solution – as it does in photographic processing applications or in mining operations – the innocuous metal becomes highly toxic. That’s because the free silver ions (Ag ) present in such solutions are far more reactive than those in the solid metal.... Read more »
Pillai S, Behra R, Nestler H, Suter MJF, Sigg L . (2014) Linking toxicity and adaptive responses across the transcriptome, proteome, and phenotype ofChlamydomonas reinhardtii exposed to silver. Proceedings of the National Academy of Sciences. info:/
Using a new microscopy method, researchers at the Department of Energy’s Oak Ridge National Laboratory can image and measure electrochemical processes in batteries in real time and at nanoscale resolution.... Read more »
Robert L. Sacci, Nancy J. Dudney, Karren L. More, Lucas R. Parent, Ilke Arslan, Nigel D. Browning and Raymond R. Unocic. (2014) Direct visualization of initial SEI morphology and growth kinetics during lithium deposition by in situ electrochemical transmission electron microscopy. Chemical Communications. DOI: 10.1039/c3cc49029g
Researchers at the Georgia Institute of Technology have developed a new type of low-temperature fuel cell that directly converts biomass to electricity with assistance from a catalyst activated by solar or thermal energy.... Read more »
Wei Liu, Wei Mu, Mengjie Liu, Xiaodan Zhang, Hongli Cai . (2014) Solar-induced direct biomass-to-electricity hybrid fuel cell using polyoxometalates as photocatalyst and charge carrier. Nature Communications. DOI: 10.1038/ncomms4208
Scientists have created a microbattery that packs twice the energy compared to current microbatteries used to monitor the movements of salmon through rivers in the Pacific Northwest and around the world.... Read more »
Honghao Chen, Samuel Cartmell, Qiang Wang, Terence Lozano, Z. Daniel Deng, Huidong Li, Xilin Chen, Yong Yuan, Mark E. Gross, Thomas J. Carlson, Jie Xiao. (2014) Micro-battery development for juvenile salmon acoustic telemetry system applications. Scientific Reports. DOI: 10.1038/srep03790
Elsevier is not the only publisher with a large innovation inertia. In fact, I think many large organizations do, particularly if there are too many interdependencies, causing too long lines. Greg Laundrum made me aware that one American Chemical Society journal is now going to encourage (not require) machine readable forms of chemical structures to be included in their flagship. The reasoning by Gilson et al. is balanced. It is also 15 years too late. This question was relevant at the end of the last century. The technologies were already more advanced than what will now be adopted. 15 years!!! Seriously, that's close to the time it takes to bring a new drug on the market!Look at what they suggest and think about it. Include SMILES strings for structures in the paper. I very much welcome this, of course, despite I am not a big fan of SMILES at all. They could have said something about OpenSMILES too, which is more precise. They do say something about the InChI and InChIKey, but not that the SMILES string can more precisely reflect the drawing. I wonder why they don't go for a format that can actually capture the image, like CML or a MDL molfile. Then again, a SMILES copy/pastes so nicely. Talking about slow innovation. There is zero technical reason you could not copy/paste a MDL molfile into a spreadsheet (and you can with many tools, in fact...)Now, I still have tons of questions. What tool will be used to validate the correctness and absence of ambiguity before the publication? Will the SMILES strings be validated at all? And at what level? Will it have to be compatible with particular tools? Does it have to be compatible with OpenSMILES? Under what license will these SMILES be available (can we data mine DOI-SMILES links and openly share them)? What was the reasoning for finally adopting this? Will the journal also accept submission where both SMILES and other formats are provided? Will they accept or deny SMARTS strings (e.g. for Markush structures)?All in all, I second the others, and am happy to see this step. I do hope they do not stop here and wait again 15 years for another step. In fact, they ask for input on email@example.com. That is double promising! Gilson MK, Georg G, & Wang S (2014). Digital Chemistry in the Journal of Medicinal Chemistry. Journal of medicinal chemistry PMID: 24521446... Read more »
Gilson MK, Georg G, & Wang S. (2014) Digital Chemistry in the Journal of Medicinal Chemistry. Journal of medicinal chemistry. PMID: 24521446
To Exchange or Not to Exchange? That is the question — at least for the graduate students participating in our Proteins Journal Club this semester (my apologies to those members of the Shakespearean Journal Club — although I do like the musical version of Hamlet as performed on Gilligan’s Island). As […]... Read more »
Walters B. T., Mayne L., Hinshaw J. R., Sosnick T. R., & Englander S. W. (2013) Folding of a large protein at high structural resolution. Proceedings of the National Academy of Sciences, 110(47), 18898-18903. DOI: 10.1073/pnas.1319482110
When developing T1 MRI contrast agents one always have the goal of creating the contrast agent that will shorten T1 the most. That is, a compound with high relaxivity. It turns out that short T1 is not always desired, for other kind of agents. PARACEST contrast agents follow a different mechanism for contrast enhancement, in […]... Read more »
S. James Ratnakar, Todd C. Soesbe, Lloyd Laporca Lumata, Quyen N. Do, Subha Viswanathan, Chien-Yuan Lin, A. Dean Sherry, and Zoltan Kovacs. (2013) Modulation of CEST Images in Vivo by T1 Relaxation: A New Approach in the Design of Responsive PARACEST Agents. Journal of the American Chemical Society. DOI: 10.1021/ja406738y
An electrode designed like a pomegranate — with silicon nanoparticles clustered like seeds in a tough carbon rind — overcomes several remaining obstacles to using silicon for a new generation of lithium-ion batteries, say its inventors at Stanford University and the Department of Energy’s SLAC National Accelerator Laboratory.... Read more »
Nian Liu, Zhenda Lu, Jie Zhao, Matthew T. McDowell, Hyun-Wook Lee, Wenting Zhao . (2014) A pomegranate-inspired nanoscale design for large-volume-change lithium battery anodes. Nature Nanotechnology. DOI: 10.1038/nnano.2014.6
The paper for this week is"Hyperpolarization without persistent radical for in vivo real-time metabolic imaging"byEichhorn, Takado, Salameh, Capozzi, Cheng, Hyacinthe, Mishkovsky, Roussel and CommentPNAS 2013 110 18064http://www.ncbi.nlm.nih.gov/pubmed/24145405http://www.pnas.org/content/110/45/18064.longThere is a lot going on in this short and well-written paper. I highly recommend that you read it yourself, because I don't quite know where to start. I guess I have to start somewhere, so let's jump into metabolic imaging.For most organic chemists busy dissolving their precious compounds into 500 uL of CDCl3 and transferring to 5 mm NMR tubes, it might be a shock to learn that using high end MRI scanners, it is possible to take spatially- and temporally-resolved spectra on mice (or humans). Yes. You can lay in a (high end) MRI scanner and someone can take an NMR spectrum of a specific anatomical region, say the brain or the heart. Some organic chemist should ask the question - why doesn't my department buy an MRI scanner and let me (and all my lab mates) set up a reaction flask inside and take NMR spectra of little regions of my flask as the reaction proceeds? Frankly, the spectra are crummy relative to conventional NMR. One trick used to improve spectral quality is to use 13C-labeled material and record 13C NMR spectra. Going back to biological samples, it is possible to measure the real-time, spatially-resolved conversion of substrates into metabolites in this technique. This technique is called metabolic imaging. Sensitivity is one big problem with metabolic imaging, leading various groups (and companies, etc.) to borrow any available tools to increase signal-to-noise. One powerful tool that is all the rage in solid state NMR of biological macromolecules these days is dynamic nuclear polarization or DNP. One of the best explanations of DNP is on the website of Bridge12, a company that sells hardware to do this type of experiment.http://www.bridge12.com/learn/dynamic-nuclear-polarization-dnp-nmr By the way, I'll mention that Bridge12 maintains a nice literature blog at http://blog.bridge12.com/ To summarize briefly, a sample is mixed with persistent radicals. Because the unpaired electron has a much larger gyromagnetic ratio, the population difference between spin-down and spin-up states is larger, which explains why EPR is so much more sensitive than NMR. The trick behind DNP is to use microwave irradiation to saturate the EPR signal of the persistent radicals and transfer the polarization to the nuclei in the sample, much like the classic steady state NOE experiment. This transfer leads to an enhancement of signal.For any clinical application, though, DNP is hard to pull off. Because you cannot inject radicals into a patient, you have to filter them out after transfer. Meanwhile everything is relaxing and some of the signal enhancement that you have fought so hard (and paid so much) to get is lost. You get about a minute. But in this minute, impressive results have been collected, allowing real-time detection of metabolic intermediates in vivo. The authors assert that "most preclinical developments have focused on samples of neat pyruvic acid (PA) to which suitable persistent radicals are added." PA is important because "this molecule has a central position in the glycolytic pathyway" and "is a powerful marker for cancer metabolism." As the title of the publication suggest the authors of this paper describe a way to take advantage of the sensitivity gains of DNP without persistent radicals. They make tiny beads of neat PA and extract an electron by UV irradiation to make a radical. They do the DNP experiment to enhance the 13C signal of PA. When these beads are dissolved in water, all you get is hyperpolarized pyruvate, pyruvate hydrate and acetate (and CO2 gas). All this extra signal make it possible to record spatially and temporally resolved 13C spectra inside a mouse and watch the formation of lactate and breakdown of pyruvate! What do the authors actually do?They devise a clever experimental setup so that droplets of 2 +/- 0.5 uL of pyruvic acid are dripped one-by-one into a 3 mm EPR tube (http://www.wilmad-labglass.com/Products/705-PQ-6-25/) sitting inside a EPR dewar (http://www.wilmad-labglass.com/Products/WG-850-B-Q/) filled with liquid nitrogen. Each drop is flash frozen into a little bead ~1.5 mm in diameter. Approximately a dozen beads are collect in each EPR tube. I picture bubble tea in my head. Then each EPR tube filled with frozen beads and liquid nitrogen is irradiated for 1 hour using a high-power 365-nm LED array. What happens in this setup? First, radical are created. Figure 1B and C show the X-band EPR spectrum of natural abundance PA beads and [1-13C] PA beads at 77 K after 1 hour of UV irradiation.For readers unfamiliar with EPR, it helps to think of EPR in terms of NMR, except EPR focuses on unpaired electrons. The x-axis is magnetic field instead of frequency (or ppm) because in EPR the magnetic field is swept during the experiment. The y-axis is the first derivative of absorbance instead of absorbance. At the point on the x-axis where the signal switches from positive to negative is the maximum of the absorbance. If you study Fig 1B, you will see four such crossing. If you study the intensity of the bands you can convince yourself that the absorbance spectrum is a quartet. The reason is that a delocalized unpaired electron is coupled to three equivalent protons (the methyl group of PA). As a control, the authors also make beads with 13C enrichment at the 1 position. In this case, the unpaired electron is coupled to one 13C nuclei and 3 equivalent protons. The absorbance spectrum is a doublet of quartets. If you study the EPR spectrum in Fig 1C you can convince yourself that you see a doublet of quartets. What is actually going on in the beads upon UV irradiation in not consequential for this publication. To quote the authors "in aqueous solution, PA undergoes efficient photodecarboxylation. ... The radicals produced by the low-temperature UV irradiation of the pure acid ... are most likely related to intermediary products postulated for this photodecarboxylation mechanism." In summary it does not matter why, but the authors can produce PA radical at concentrations of 15 mM. They get the concentration from quantitative EPR. Approximately seven frozen beads of [U-13C] PA are dissolved in ~500 uL of D2O to make a 900 mM solution, which is transferred to 5 mm NMR tube. The authors record a 1D 13C NMR spectrum with no 1H decoupling on a 400 MHz NMR. The interscan delay equals 180 s and the number of scans equal 512 for a total acquisiton time ~17 hours. The result is shown in Fig. 2.The authors assign several 13C resonances to pyruvate, pyruvate hydrate, acetate and CO2. The authors interpretation of this result is that upon dissolution, PA radical decomposes to CO2 and acetate! There is no EPR signal upon dissolution and the 13C T1 are the same as non-UV irradiated PA. Together these data indicate that there is no radicals and these samples can be injected or perfused into live animals. To get hyperpolarization, though, you still have to do the microwave saturation experiment. The authors state that using their system, 13C polarization of 10% can be achieved in 2.5 h at 5 T and 1.2 K using 50 mW microwave power. I have no idea if that is impressive or not. It sounds very expensive, though. By way of comparison, using traditional persistent radicals, 13C polarization of 60% can be achieved in the same amount of time. To demonstrate the potential of their method, the authors collect in vivo metabolic images on a mouse. 80 mM hyperpolarized pyruvate solutions are prepared from UV-irradiated PA beads. A 300 uL bolus was injected into mouse femoral vein. A 13C spectrum localized in the mouse head was measured every 3 s for 75 s. Holy crap! A 13C spectrum every three seconds! Figure 4A shows thespectra. The inset spectrum is a sum projection (I assume). What is more is that the authors can collect metabolic images 5 mm^3 spatial resolution, 3 s time resolution. ... Read more »
Eichhorn TR, Takado Y, Salameh N, Capozzi A, Cheng T, Hyacinthe JN, Mishkovsky M, Roussel C, & Comment A. (2013) Hyperpolarization without persistent radicals for in vivo real-time metabolic imaging. Proceedings of the National Academy of Sciences of the United States of America, 110(45), 18064-9. PMID: 24145405
Scott MacIvor has cracked open hundreds of artificial bee nests. But two he peered inside in Toronto gave him pause. Within their containers, the bees he studies had carefully built homes for their young out of plastic debris. Mixed in with the usual construction materials of leaves and mud, MacIvor could clearly see bits of […]The post Urban Bees Build Their Nests with Plastic appeared first on Inkfish.... Read more »
J. Scott MacIvor, & Andrew E. Moore. (2013) Bees collect polyurethane and polyethylene plastics as novel nest materials. Ecosphere, 4(12). DOI: 10.1890/ES13-00308.1
After lithium-ion batteries were introduced to the public in the early 1990s, they've charged all kinds of products, from handheld cell phones to jumbo airplanes. But as their prevalence has grown, so have concerns with their safety.
In January 2013, airlines had to ground their fleets of Boeing Dreamliners due to fires linked to the "thermal runaway" of lithium-ion batteries. Likewise, lithium-ion-powered cars, such as the Tesla Model S, have caught fire "20 or so [times] in the past few years," sparking damaging viral videos (but still paling in comparison to the number of fires related to standard engines).1 Even more recently, a US teen's iPhone ignited in her back pocket because of its li-ion battery, an event the Daily Mail dutifully covered.... Read more »
Wong, D. H. C., Thelen, J. L., Fu, Y., Devaux, D., Pandya, A. A., Battaglia, V. S., Balsara, N. P., and DeSimone, J. M. (2014) Nonflammable perfluoropolyether-based electrolytes for lithium batteries. PNAS. DOI: 10.1073/pnas.1314615111
Kennedy, T., Mullane, E., Geaney, H., Osiak, M., O'Dwyer, C., Ryan, K. M. (2014) High-performance germanium nanowire-based lithium-Ion battery anodes extending over 1000 cycles through in situ formation of a continuous porous network. Nano Letters, 716-723. PMID: 24417719
In studying a material that prevents marine life from sticking to the bottom of ships, researchers led by chemist Joseph DeSimone at UNC-Chapel Hill have identified a surprising replacement for the only inherently flammable component of today’s lithium-ion batteries: the electrolyte.... Read more »
Dominica H. C. Wong, Jacob L. Thelen, Yanbao Fu, Didier Devaux, Ashish A. Pandya, Vincent S. Battaglia, Nitash P. Balsara, and Joseph M. DeSimone. (2014) Nonflammable perfluoropolyether-based electrolytes for lithium batteries. Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1314615111
While the debate over using crops for fuel continues, scientists are now reporting a new, fast approach to develop biofuel in a way that doesn’t require removing valuable farmland from the food production chain.... Read more »
Monitoring TriAcylGlycerols Accumulation by Atomic Force Microscopy Based Infrared Spectroscopy in Streptomyces Species for Biodiesel Applications. (2014) Ariane Deniset-Besseau, Craig B. Prater, Marie-Joëlle Virolle, and Alexandre Dazzi. Monitoring TriAcylGlycerols Accumulation by Atomic Force Microscopy Based Infrared Spectroscopy in Streptomyces Species for Biodiesel Applications, 654-658. DOI: 10.1021/jz402393a
Researchers at the MESA research institute at the University of Twente, Netherlands, have developed a new type of hybrid membrane that allows to separate gases from each other in an energy-saving way, even under extreme conditions.... Read more »
Michiel J. T. Raaijmakers, Mark A. Hempenius, Peter M. Schön, G. Julius Vancso, Arian Nijmeijer, Matthias Wessling, and Nieck E. Benes. (2014) Sieving of Hot Gases by Hyper-Cross-Linked Nanoscale-Hybrid Membranes. Journal of the American Chemical Society, 136(1), 330-335. DOI: 10.1021/ja410047u
Microscopy is a technique used in the lab to look at things that you can’t see with the naked eye. There are a number of different microscopes that have been developed to do this, but today I’m going to focus on fluorescence microscopy as that’s what I have experience using! It’s also (I think) pretty interesting.
This technique is actually really simple, and is based upon the principle that when you shine high energy light onto certain substances they will absorb and emit this light at different wavelengths. If you can attach one of these fluorescent substances to whatever you’re trying to visualise, then you can look at it via a microscope.... Read more »
Cowell IG, Tilby MJ, & Austin CA. (2011) An overview of the visualisation and quantitation of low and high MW DNA adducts using the trapped in agarose DNA immunostaining (TARDIS) assay. Mutagenesis, 26(2), 253-60. PMID: 21068206
Gasoline-like fuels can be produced from cellulosic materials such as farm and forestry waste using a new process invented by chemists at the University of California, Davis. ... Read more »
Mascal, M., Dutta, S. and Gandarias, I. (2014) Hydrodeoxygenation of the Angelica Lactone Dimer, a Cellulose-Based Feedstock: Simple, High-Yield Synthesis of Branched C7–C10 Gasoline-like Hydrocarbons. Angewandte Chemie International Edition, 53(7), 1854-1857. DOI: 10.1002/ange.201308143
UCLA engineers have invented a new process for manufacturing highly efficient photovoltaic materials that shows promise for low-cost industrial perovskite solar cell production.... Read more »
Qi Chen, Huanping Zhou, Ziruo Hong, Song Luo, Hsin-Sheng Duan, Hsin-Hua Wang, Yongsheng Liu, Gang Li, and Yang Yang. (2014) Planar Heterojunction Perovskite Solar Cells via Vapor-Assisted Solution Process. Journal of the American Chemical Society, 136(2), 622-625. DOI: 10.1021/ja411509g
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