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  • January 4, 2013
  • 10:44 AM
  • 273 views

Cellular Recap of 2012 #2: favorites

by TheCellularScale in The Cellular Scale

As promised, here are my favorite posts from each month.January: The Human Neuron" not so special after all?Butti C, Santos M, Uppal N, & Hof PR (2011). Von Economo neurons: Clinical and evolutionary perspectives. Cortex; a journal devoted to the study of the nervous system and behavior PMID: 22130090February: If you give a mouse a placebo...Wise RA, Wang B, & You ZB (2008). Cocaine serves as a peripheral interoceptive conditioned stimulus for central glutamate and dopamine release. PloS one, 3 (8) PMID: 18682722 March: Plant neurons: Sensation and Action in the Venus FlytrapBenolken RM, & Jacobson SL (1970). Response properties of a sensory hair excised from Venus's flytrap. The Journal of general physiology, 56 (1), 64-82 PMID: 5514161Volkov AG, Adesina T, & Jovanov E (2007). Closing of venus flytrap by electrical stimulation of motor cells. Plant signaling & behavior, 2 (3), 139-45 PMID: 19516982 Forterre Y, Skotheim JM, Dumais J, & Mahadevan L (2005). How the Venus flytrap snaps. Nature, 433 (7024), 421-5 PMID: 15674293... Read more »

Butti C, Santos M, Uppal N, & Hof PR. (2011) Von Economo neurons: Clinical and evolutionary perspectives. Cortex; a journal devoted to the study of the nervous system and behavior. PMID: 22130090  

Benolken RM, & Jacobson SL. (1970) Response properties of a sensory hair excised from Venus's flytrap. The Journal of general physiology, 56(1), 64-82. PMID: 5514161  

Volkov AG, Adesina T, & Jovanov E. (2007) Closing of venus flytrap by electrical stimulation of motor cells. Plant signaling , 2(3), 139-45. PMID: 19516982  

Forterre Y, Skotheim JM, Dumais J, & Mahadevan L. (2005) How the Venus flytrap snaps. Nature, 433(7024), 421-5. PMID: 15674293  

Kindt M, Soeter M, & Vervliet B. (2009) Beyond extinction: erasing human fear responses and preventing the return of fear. Nature neuroscience, 12(3), 256-8. PMID: 19219038  

Kim IJ, Zhang Y, Yamagata M, Meister M, & Sanes JR. (2008) Molecular identification of a retinal cell type that responds to upward motion. Nature, 452(7186), 478-82. PMID: 18368118  

Kay JN, De la Huerta I, Kim IJ, Zhang Y, Yamagata M, Chu MW, Meister M, & Sanes JR. (2011) Retinal ganglion cells with distinct directional preferences differ in molecular identity, structure, and central projections. The Journal of neuroscience : the official journal of the Society for Neuroscience, 31(21), 7753-62. PMID: 21613488  

Kraskov A, Dancause N, Quallo MM, Shepherd S, & Lemon RN. (2009) Corticospinal neurons in macaque ventral premotor cortex with mirror properties: a potential mechanism for action suppression?. Neuron, 64(6), 922-30. PMID: 20064397  

Casile A, Caggiano V, & Ferrari PF. (2011) The mirror neuron system: a fresh view. The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry, 17(5), 524-38. PMID: 21467305  

Blackiston DJ, Silva Casey E, & Weiss MR. (2008) Retention of memory through metamorphosis: can a moth remember what it learned as a caterpillar?. PloS one, 3(3). PMID: 18320055  

Marx M, Günter RH, Hucko W, Radnikow G, & Feldmeyer D. (2012) Improved biocytin labeling and neuronal 3D reconstruction. Nature protocols, 7(2), 394-407. PMID: 22301777  

Finger TE, & Kinnamon SC. (2011) Taste isn't just for taste buds anymore. F1000 biology reports, 20. PMID: 21941599  

Triana-Del Rio R, Montero-Domínguez F, Cibrian-Llanderal T, Tecamachaltzi-Silvaran MB, Garcia LI, Manzo J, Hernandez ME, & Coria-Avila GA. (2011) Same-sex cohabitation under the effects of quinpirole induces a conditioned socio-sexual partner preference in males, but not in female rats. Pharmacology, biochemistry, and behavior, 99(4), 604-13. PMID: 21704064  

Labour MN, Banc A, Tourrette A, Cunin F, Verdier JM, Devoisselle JM, Marcilhac A, & Belamie E. (2012) Thick collagen-based 3D matrices including growth factors to induce neurite outgrowth. Acta biomaterialia, 8(9), 3302-12. PMID: 22617741  

Fu M, Yu X, Lu J, & Zuo Y. (2012) Repetitive motor learning induces coordinated formation of clustered dendritic spines in vivo. Nature, 483(7387), 92-5. PMID: 22343892  

  • January 3, 2013
  • 08:33 PM
  • 157 views

Below Absolute Zero temperature

by Usman Paracha in SayPeople

Researchers have achieved the record “negative temperature”, i.e. below absolute zero that was considered to be the lowest possible temperature.

This research has been published online in the journal Science.

This is a paradoxical temperature as the temperature below zero is referred to as cold but this “negative absolute temperature” can also be considered as hotter than infinity and it has “motional degrees of freedom” while at colder temperatures atoms show decreased motion or stop moving.


With positive temperatures (blue), atoms more likely occupy low-energy states than high-energy states, while the opposite is true for negative temperatures (red). (Credit: LMU / MPQ Munich)
"We have created the first negative absolute temperature state for moving particles," said researcher Simon Braun at the University of Munich in Germany.

Usually atoms like to occupy the lower energy state at positive temperatures that is known as Boltzmann distribution in physics. However, atoms can go to the higher energy states after heating. At absolute zero, atoms occupy the lowest energy state and at an infinite temperature, atoms would occupy all energy states. On the other hand, negative temperatures are opposite to the positive temperatures i.e. atoms would like to occupy high energy states than low energy states that could be considered as the “inverted Boltzmann distribution.”

"The inverted Boltzmann distribution is the hallmark of negative absolute temperature, and this is what we have achieved," said researcher Ulrich Schneider, a physicist at the University of Munich in Germany. "Yet the gas is not colder than zero kelvin, but hotter. It is even hotter than at any positive temperature — the temperature scale simply does not end at infinity, but jumps to negative values instead."

One of the oddities of the negative temperature is that the energy flows from the objects with the negative temperatures to the objects with positive temperatures i.e. negative temperatures are hotter than the positive ones. Another weird finding is that the entropy, i.e. the measure of the disorderliness of a system, is absorbed by the objects in the negative temperature, when they release energy.

The cold gas will also have the negative pressure created by researchers, which would result in collision of the atoms but the negative temperature is avoiding such happening.

This research paves the way to develop new engines with more than 100% efficiency. Those new types of engines would not only absorb energy from the hotter substances but also from the colder substances helping them to work with more than 100% efficiency.

This research could also help to understand the mysterious dark energy that is thought to be involved in the expansion of the universe.

Reference:

Braun, S., Ronzheimer, J., Schreiber, M., Hodgman, S., Rom, T., Bloch, I., & Schneider, U. (2013). Negative Absolute Temperature for Motional Degrees of Freedom Science, 339 (6115), 52-55 DOI: 10.1126/science.1227831... Read more »

Braun, S., Ronzheimer, J., Schreiber, M., Hodgman, S., Rom, T., Bloch, I., & Schneider, U. (2013) Negative Absolute Temperature for Motional Degrees of Freedom. Science, 339(6115), 52-55. DOI: 10.1126/science.1227831  

  • December 30, 2012
  • 05:23 AM
  • 224 views

Scientists Rediscover the Violence Gene, MAOA-2R

by nooffensebut in The Unsilenced Science

New research shows that MAOA-2R induces violence and delinquency far more than the so-called “warrior gene,” MAOA-3R. It is also far more common in African-American men than white men. Plus, MAOA’s designation as a cancer gene could influence the development of therapies.... Read more »

Alpini G, Invernizzi P, Gaudio E, Venter J, Kopriva S, Bernuzzi F, Onori P, Franchitto A, Coufal M, Frampton G.... (2008) Serotonin metabolism is dysregulated in cholangiocarcinoma, which has implications for tumor growth. Cancer research, 68(22), 9184-93. PMID: 19010890  

Beaver, K., Wright, J., Boutwell, B., Barnes, J., DeLisi, M., & Vaughn, M. (2013) Exploring the association between the 2-repeat allele of the MAOA gene promoter polymorphism and psychopathic personality traits, arrests, incarceration, and lifetime antisocial behavior. Personality and Individual Differences, 54(2), 164-168. DOI: 10.1016/j.paid.2012.08.014  

Brunner HG, Nelen MR, van Zandvoort P, Abeling NG, van Gennip AH, Wolters EC, Kuiper MA, Ropers HH, & van Oost BA. (1993) X-linked borderline mental retardation with prominent behavioral disturbance: phenotype, genetic localization, and evidence for disturbed monoamine metabolism. American journal of human genetics, 52(6), 1032-9. PMID: 8503438  

Cases O, Seif I, Grimsby J, Gaspar P, Chen K, Pournin S, Müller U, Aguet M, Babinet C, & Shih JC. (1995) Aggressive behavior and altered amounts of brain serotonin and norepinephrine in mice lacking MAOA. Science (New York, N.Y.), 268(5218), 1763-6. PMID: 7792602  

Caspi A, McClay J, Moffitt TE, Mill J, Martin J, Craig IW, Taylor A, & Poulton R. (2002) Role of genotype in the cycle of violence in maltreated children. Science (New York, N.Y.), 297(5582), 851-4. PMID: 12161658  

Crabtree, G. (2013) Our fragile intellect. Part II. Trends in Genetics, 29(1), 3-5. DOI: 10.1016/j.tig.2012.10.003  

Fergusson DM, Boden JM, Horwood LJ, Miller A, & Kennedy MA. (2012) Moderating role of the MAOA genotype in antisocial behaviour. The British journal of psychiatry : the journal of mental science, 200(2), 116-23. PMID: 22297589  

Gallardo-Pujol D, Andrés-Pueyo A, & Maydeu-Olivares A. (2012) MAOA genotype, social exclusion and aggression: an experimental test of a gene-environment interaction. Genes, brain, and behavior. PMID: 23067570  

Guo, G., Roettger, M., & Cai, T. (2008) The Integration of Genetic Propensities into Social-Control Models of Delinquency and Violence among Male Youths. American Sociological Review, 73(4), 543-568. DOI: 10.1177/000312240807300402  

Guo, G., Ou, X., Roettger, M., & Shih, J. (2008) The VNTR 2 repeat in MAOA and delinquent behavior in adolescence and young adulthood: associations and MAOA promoter activity. European Journal of Human Genetics, 16(5), 626-634. DOI: 10.1038/sj.ejhg.5201999  

Huang L, Frampton G, Rao A, Zhang KS, Chen W, Lai JM, Yin XY, Walker K, Culbreath B, Leyva-Illades D.... (2012) Monoamine oxidase A expression is suppressed in human cholangiocarcinoma via coordinated epigenetic and IL-6-driven events. Laboratory investigation; a journal of technical methods and pathology, 92(10), 1451-60. PMID: 22906985  

Jones, R., Brown, C., & Ship, J. (1995) Odor identification in young and elderly African-Americans and Caucasians. Special Care in Dentistry, 15(4), 138-143. DOI: 10.1111/j.1754-4505.1995.tb00501.x  

Mahmut, M., & Stevenson, R. (2012) Olfactory Abilities and Psychopathy: Higher Psychopathy Scores Are Associated with Poorer Odor Discrimination and Identification. Chemosensory Perception, 5(3-4), 300-307. DOI: 10.1007/s12078-012-9135-7  

Malorni W, Giammarioli AM, Matarrese P, Pietrangeli P, Agostinelli E, Ciaccio A, Grassilli E, & Mondovi B. (1998) Protection against apoptosis by monoamine oxidase A inhibitors. FEBS letters, 426(1), 155-9. PMID: 9598998  

McDermott R, Tingley D, Cowden J, Frazzetto G, & Johnson DD. (2009) Monoamine oxidase A gene (MAOA) predicts behavioral aggression following provocation. Proceedings of the National Academy of Sciences of the United States of America, 106(7), 2118-23. PMID: 19168625  

Moffitt, T., Caspi, A., & Rutter, M. (2006) Measured Gene-Environment Interactions in Psychopathology. Concepts, Research Strategies, and Implications for Research, Intervention, and Public Understanding of Genetics. Perspectives on Psychological Science, 1(1), 5-27. DOI: 10.1111/j.1745-6916.2006.00002.x  

Murphy SM, Puwanant A, Griggs RC, & Consortium for Clinical Investigations of Neurological Channelopathies (CINCH) and Inherited Neuropathies Consortium (INC) Consortia of the Rare Disease Clinical Research Network. (2012) Unintended effects of orphan product designation for rare neurological diseases. Annals of neurology, 72(4), 481-90. PMID: 23109143  

Pietrangeli, P. (2004) Amine Oxidases and Tumors. NeuroToxicology, 25(1-2), 317-324. DOI: 10.1016/S0161-813X(03)00109-8  

Reti IM, Xu JZ, Yanofski J, McKibben J, Uhart M, Cheng YJ, Zandi P, Bienvenu OJ, Samuels J, Willour V.... (2011) Monoamine oxidase A regulates antisocial personality in whites with no history of physical abuse. Comprehensive psychiatry, 52(2), 188-94. PMID: 21295226  

Roush, W. (1995) Conflict marks crime conference. Science, 269(5232), 1808-1809. DOI: 10.1126/science.7569909  

Scott, A., Bortolato, M., Chen, K., & Shih, J. (2008) Novel monoamine oxidase A knock out mice with human-like spontaneous mutation. NeuroReport, 19(7), 739-743. DOI: 10.1097/WNR.0b013e3282fd6e88  

Shih JC, Ridd MJ, Chen K, Meehan WP, Kung MP, Seif I, & De Maeyer E. (1999) Ketanserin and tetrabenazine abolish aggression in mice lacking monoamine oxidase A. Brain research, 835(2), 104-12. PMID: 10415365  

Sjöberg, R., Ducci, F., Barr, C., Newman, T., Dell'Osso, L., Virkkunen, M., & Goldman, D. (2007) A Non-Additive Interaction of a Functional MAO-A VNTR and Testosterone Predicts Antisocial Behavior. Neuropsychopharmacology, 33(2), 425-430. DOI: 10.1038/sj.npp.1301417  

Tuinier S, Verhoeven WMA, Scherders MJWT, Fekkes D, & Pepplinkhuizen L. (1995) Neuropsychiatric and biological characteristics of X-linked MAOA deficiency syndrome: A single-intervention case study. New Trends in Experimental and Clinical Psychiatry, 11(4), 99-107. info:/

Wong CC, Caspi A, Williams B, Craig IW, Houts R, Ambler A, Moffitt TE, & Mill J. (2010) A longitudinal study of epigenetic variation in twins. Epigenetics : official journal of the DNA Methylation Society, 5(6), 516-26. PMID: 20505345  

  • December 28, 2012
  • 05:32 PM
  • 264 views

Strange behavior: new study exposes living cells to synthetic protein

by Perikis Livas in Tracing Knowledge

One approach to understanding components in living organisms is to attempt to create them artificially, using principles of chemistry, engineering and genetics. A suite of powerful techniques—collectively referred to as synthetic biology—have been used to produce self-replicating molecules, artificial pathways in living systems and organisms bearing synthetic genomes.... Read more »

Richard Harth. (2012) Strange behavior: new study exposes living cells to synthetic protein. ASU Biodesign Institute. info:/

  • December 26, 2012
  • 05:43 PM
  • 284 views

The physics of life: one molecule at a time

by Perikis Livas in Tracing Knowledge

The esteemed physicist Erwin Schrödinger, whose name is associated with the most notorious equation of quantum mechanics, also wrote a brief essay entitled ‘What is Life?’, asking: ‘How can the events in space and time which take place within the spatial boundary of a living organism be accounted for by physics and chemistry?’ The 60 years following this seminal work have seen enormous developments in our understanding of biology on the molecular scale, with physics playing a key role in solving many central problems through the development and application of new physical science techniques, biophysical analysis and rigorous intellectual insight.... Read more »

Leake, M. (2012) The physics of life: one molecule at a time. Philosophical Transactions of the Royal Society B: Biological Sciences, 368(1611), 20120248-20120248. DOI: 10.1098/rstb.2012.0248  

  • December 21, 2012
  • 12:57 PM
  • 288 views

Fossil Scan Reveals Ghost of Lizard Past

by Elizabeth Preston in Inkfish





Peering into the past life of this fossil took an x-ray scanner powered by a particle accelerator. What scientists saw there was mysterious: an ancient lizard had left behind its skin and teeth, but none of its bones. To tell the ghost's tale, they relied on some very modern equipment.

At Stanford University, an accelerator called a synchrotron sends electrons zipping around a track fast enough that x-rays spin off of them. These x-rays are collected into an extremely bright x-ray beam that scientists can use for various projects. One application, x-ray fluorescence, lets researchers map the actual chemical elements inside on object.

Other methods of analyzing an item's chemical makeup require scientists to focus on tiny slices, destroy their samples entirely, or creep along at a rate of one square centimeter a day. But the setup at Stanford lets scientists look quickly and thoroughly at larger objects while keeping them in one piece. The synchrotron has previously been used to reveal writings of Archimedes that were scraped away and painted over, and to deduce the pattern on the feathers of the 120-million-year-old Confuciusornis.

University of Manchester paleobiologist Phillip Manning and his colleagues, who had worked on scanning Confuciusornis and other fossils, now turned the synchrotron's powerful x-ray beam onto an unusual fossil. The 50-million-year-old lizard specimen comes from Colorado. What's unusual is that the animal's skin is beautifully preserved, right down to the scales—but the skeleton is gone.

Scanning the fossil for sulfur (in the photo above) or copper produced ghostly silhouettes of the lizard's whole body, since these elements are naturally present in trace amounts throughout an organism. Tuning their scans for phosphorous brought a surprise: dots popped out of the lizard's ghostly head in the shape of a jaw.




In the image above, green is a map of sulfur in the head and neck (check out the scales!). Phosphorous and magnesium are overlaid in red and blue. The authors write that this chemistry is "typical for biomineralized structures." A close look revealed two overlapping bites: a full set of lizard teeth.

Before the synchrotron scanning, researchers thought the unusual Colorado fossil was a 50-million-year-old molted lizard skin. But even animals that shed their skin don't tend to leave behind their entire jaws when they do so. This animal died in one piece.

Although bones and teeth have similar ingredients, the authors write that the structure of teeth makes them more resistant to dissolving. But how did the delicate skin stay intact? "If the acidity of the ground waters are high, bone would be vulnerable," Manning says. "However, high acidity is often helpful in 'tanning' skin to preserve [it]. Think bog bodies from northern Europe."

As researchers continue to peer into the past with the synchrotron, Manning is narrating their progress at his blog. He doesn't anticipate running out of subjects. "We have a few million life forms to wade through," he says. In other words, there are plenty of ghosts of fossils yet to come.


Edwards, N., Wogelius, R., Bergmann, U., Larson, P., Sellers, W., & Manning, P. (2012). Mapping prehistoric ghosts in the synchrotron Applied Physics A DOI: 10.1007/s00339-012-7484-3

Images: Edwards et al.

... Read more »

Edwards, N., Wogelius, R., Bergmann, U., Larson, P., Sellers, W., & Manning, P. (2012) Mapping prehistoric ghosts in the synchrotron. Applied Physics A. DOI: 10.1007/s00339-012-7484-3  

  • December 21, 2012
  • 11:59 AM
  • 61 views

Happy Christmas Lectures (Merry “Chemist-mas” everyone)

by Duncan Hull in O'Really?

If you hate Chemistry [1] it’s probably because your Chemistry teachers weren’t up to scratch. Peter Wothers, The Modern Alchemist, is someone who might rekindle your interest in Chemistry through his delivery of the 2012 Christmas Lectures. Wothers will unpick the chemistry of the world around us, looking at Air, Water and Earth, three of the original Greek ‘elements’ that tantalised alchemists for centuries. He’ll also be exploding and burning things too.... Read more »

Lippincott, W. (1979) Why Students Hate Chemistry. Journal of Chemical Education, 56(1), 1. DOI: 10.1021/ed056p1  

  • December 18, 2012
  • 05:21 AM
  • 148 views

Scientific controversy is healthy

by Raphaël Lévy in The blog of Raphaël Lévy’s lab at the University of Liverpool

Douglas Natelson (Professor of Physics at Rice University) has posted an interesting article on his blog a few days ago about the “stripy nanoparticles” controversy. He notes that the controversy raises questions about peer review because “Lévy points out that many articles seem to be published that take the assertion of stripiness practically on faith or on very scant [...]... Read more »

Cesbron, Y., Shaw, C., Birchall, J., Free, P., & Lévy, R. (2012) Stripy Nanoparticles Revisited. Small. DOI: 10.1002/smll.201001465  

  • December 18, 2012
  • 01:44 AM
  • 170 views

Plants have a chemical defense against irritating insects

by Usman Paracha in SayPeople

Researchers have found plants may repel the “insect antagonists” after getting cues related to the odors of flies to attract female flies that may result in damage to the plants.

This research has been published online in the journal Proceedings of the National Academy of Sciences (PNAS).

"It's become increasingly clear in recent years that plants are responsive to odors," Mark Mescher, assistant professor of entomology, said in a statement. "But previous examples of this are all plant-to-plant. For example, some plants have been shown to respond to the odor of insect-damaged neighbors by priming their own defenses. What's new about this is that it seems that plants may sometimes be able to smell the insects themselves."

Researchers worked on tall goldenrod (Solidago altissima) plants. They exposed some of the plants to the odor of the male fly and observed the laying of eggs by female on exposed and unexposed plants by checking the characteristic scarring that happens when females pierce the stem to lay their eggs inside, said Mescher.

Researchers found that the plant started a defensive chemical response after the male emission of particular odors and females laid fewer eggs on exposed plants as they were four times more likely to lay eggs on the unexposed plants.

Researchers also found that the other herbivores such as beetles also resulted in very less damage to the tall goldenrod plants exposed to the fly odors.

"It seems that plants that are able to anticipate an attach by the fly and defend themselves against this damage will be more successful, producing higher quality seeds for the next generation," John Tooker, assistant professor of entomology, said. "So there must be a strong advantage for plants that can perceive the fly odor."

"I suspect that this may be happening in many plants," Tooker added. "But we don't yet know how widespread it is."

Reference:

Helms, A., De Moraes, C., Tooker, J., & Mescher, M. (2012). Exposure of Solidago altissima plants to volatile emissions of an insect antagonist (Eurosta solidaginis) deters subsequent herbivory Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1218606110... Read more »

Helms, A., De Moraes, C., Tooker, J., & Mescher, M. (2012) Exposure of Solidago altissima plants to volatile emissions of an insect antagonist (Eurosta solidaginis) deters subsequent herbivory. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1218606110  

  • December 18, 2012
  • 12:46 AM
  • 177 views

First ever seen intermediate compound between the aromatic and antiaromatic compounds

by Usman Paracha in SayPeople

Researchers have developed a stable "antiaromatic" compound that can be switched between the aromatic and anti-aromatic states and a first ever found intermediate state.

This research has been published online in the journal Nature Chemistry.

Aromatic compounds are the class of organic chemical compounds that have one or more rings of carbon atoms and undergo chemical reactions characteristic of benzene. It was found that nearly half of all organic compounds are aromatic compounds. Ring-like structure in those compounds cause the electrons to be shared between the atoms resulting in high degree of stability and no change in structure under different conditions in which the molecules would react.

"That's one of the reasons why they're so useful in industry," Jonathan Sessler, the Rowland Pettit Centennial Chair in Chemistry in the College of Natural Sciences, said in a statement. "It's also why they tend to be pro-carcinogenic. They're very hard for us to metabolize or catabolize, and the results of that are usually not benign. One of the first class of tumors ever observed was testicular cancer. It was highly prevalent among 18th century chimney sweeps, who were exposed to aromatic compounds found in coal tar."

On the other hand, antiaromatics are the compounds that have two additional or two fewer electrons than aromatic compounds. Antiaromatics are as unstable and highly reactive as the aromatics are stable in nature.

"They don't want to exist in a planar form without giving up or adding the two electrons that distinguish them from their aromatic analogues," said Sessler, "so they tend to twist around, to a lower energy state. That destroys their antiaromaticity. The net result is that bona fide antiaromatic compounds are elusive. What we have done, by rational design, is put big buttressing groups around the compounds, basically clamping them into place."

When the two electrons moved away from the antiaromatics the resulting compound was something in between the aromatics and anti-aromatics with stability of aromatics and nature of antiaromatics. This intermediate compound has been seen for the first time and therefore it has no common name yet.

"When you have to struggle for the words to describe what's being done, you know that it's cutting edge," said Christian Brueckner, a fellow porphyrin chemist and a professor at The University of Connecticut. "Twenty years ago when I was a graduate student I was told simply that you can't make large antiaromatics like this. Later the idea was that you can make them but you can't do much with them. Now you can do it, and it can switch between states, and it can exist in the intermediate state. It's just a beautiful progression of scholarship, a beautiful example of how the ability of chemists to manipulate matter is advancing."

Reference:

Ishida, M., Kim, S., Preihs, C., Ohkubo, K., Lim, J., Lee, B., Park, J., Lynch, V., Roznyatovskiy, V., Sarma, T., Panda, P., Lee, C., Fukuzumi, S., Kim, D., & Sessler, J. (2012). Protonation-coupled redox reactions in planar antiaromatic meso-pentafluorophenyl-substituted o-phenylene-bridged annulated rosarins Nature Chemistry DOI: 10.1038/nchem.1501... Read more »

Ishida, M., Kim, S., Preihs, C., Ohkubo, K., Lim, J., Lee, B., Park, J., Lynch, V., Roznyatovskiy, V., Sarma, T.... (2012) Protonation-coupled redox reactions in planar antiaromatic meso-pentafluorophenyl-substituted o-phenylene-bridged annulated rosarins. Nature Chemistry. DOI: 10.1038/nchem.1501  

  • December 15, 2012
  • 08:14 AM
  • 125 views

Microwave heating: still nothing special

by Tom Phillips in A Chemical Education

For many years there has been debate over whether there is a specific microwave effect on chemical reactions or if it’s just a thermal effect. A couple of years ago I took lecture course on microwave and ultrasound chemistry. The … Continue reading →... Read more »

Kappe C. Oliver, Pieber Bartholomäus, & Dallinger Doris. (2012) Microwave Effects in Organic Synthesis—Myth or Reality?. Angewandte Chemie International Edition. DOI: 10.1002/anie.201204103  

  • December 13, 2012
  • 07:53 PM
  • 133 views

Stripy revisited posts; where to start…

by Raphaël Lévy in The blog of Raphaël Lévy’s lab at the University of Liverpool

A round post about the stripy nanoparticles controversy... Read more »

Cesbron, Y., Shaw, C., Birchall, J., Free, P., & Lévy, R. (2012) Stripy Nanoparticles Revisited. Small. DOI: 10.1002/smll.201001465  

  • December 13, 2012
  • 08:09 AM
  • 182 views

Order in the cell maintained by a disordered protein?

by Clay Clark in Biochem Blogs

Normally proteins have a globular shape in order to be enzymatically or structurally relevant. Intrinsically disordered proteins (IDPs) broke the protein norms by maintaining their functional roles with little to no overall structure. Most proteins have regions of disorder, such … Continue reading →... Read more »

Kalkhoven Eric. (2004) CBP and p300: HATs for different occasions. Biochemical Pharmacology, 68(6), 1145-1155. DOI: 10.1016/j.bcp.2004.03.045  

Vo N, & Goodman R H. (2001) CREB-binding protein and p300 in transcriptional regulation. The Journal of biological chemistry. PMID: 11279224  

Avantaggiati M L, Ogryzko V, Gardner K, Giordano A, Levine A S, & Kelly K. (1997) Recruitment of p300/CBP in p53-dependent signal pathways. Cell, 1175-1184. PMID: 9215639  

Ferreon Josephine C, Lee Chul Won, Arai Munehito, Martinez-Yamout Maria A, Dyson H Jane, & Wright Peter E. (2009) Cooperative regulation of p53 by modulation of ternary complex formation with CBP/p300 and HDM2. Proceedings of the National Academy of Sciences of the United States of America. PMID: 19357310  

  • December 12, 2012
  • 06:54 AM
  • 100 views

Making semiconducting polymers in flow

by Tom Phillips in A Chemical Education

Organic electronics has a problem with batch-to-batch variability in the quality of materials, particularly the active semiconducting layer. A fellow PhD student in my office described to me the trouble he often experiences. He made one batch of solar cells … Continue reading →... Read more »

Bannock J. H., Krishnadasan S. H., Nightingale A. M., Yau C. P., Khaw K., Burkitt D., Halls J. J. M., Heeney M., & de Mello J. C. (2012) Continuous Synthesis of Device-Grade Semiconducting Polymers in Droplet-Based Microreactors. Advanced Functional Materials. DOI: 10.1002/adfm.201203014  

  • December 10, 2012
  • 07:57 AM
  • 183 views

Are Rocks the Key to Finding Extraterrestrial Life?

by Jason Carr in Wired Cosmos

While scientists like to bandy origin of life theories around, they seldom make the connection to astrobiological research. These theories, however, have a lot to suggest about how life may have developed on other worlds. According to recent studies, low-density vesicular volcanic rock material like pumice might have acted as something like a natural laboratory [...]... Read more »

Martin D. Brasiera, Richard Matthewmana, Sean McMahonb, Matt R. Kilburnc, & David Wacey. (2013) Pumice from the ∼3460 Ma Apex Basalt, Western Australia: A natural laboratory for the early biosphere. Precambrian Research, 1-10. info:/10.1016/j.precamres.2012.09.008

  • December 8, 2012
  • 08:24 AM
  • 231 views

New type of chemical bonding in the shining universe

by Usman Paracha in SayPeople

Scientists found new type of chemical reaction at molecular level that is thought to change the views about chemical compound formation.

This research has been published online in the July 20th issue of the journal Science.

“We discovered a new type of chemical bonding,” University of North Dakota’s computational chemist Mark Hoffmann, who is known for his work on theory and computational modeling of chemical compound synthesis, said in a statement. “That’s a pretty bold statement, but I’m not kidding you! It’s a brand new type of chemical bonding, not previously known to science.”

This new type of chemical reaction is also thought to explain the processes taking place in some of the celestial bodies such as white dwarfs, which are small extremely dense stars in the final stages of their evolution, and the formation and death of stars.

"Our discovery addresses one of the mysteries in astrophysics about the spectrum of white dwarf stars," Hoffmann said. "White dwarfs have an unusual spectrum that has been thought to result from polymerized hydrogen and helium which, of course, do not occur on Earth.

"It's possible out there because the magnetic fields on white dwarfs are several orders of magnitude larger than anything that can be generated on Earth."

In this discovery, Hoffmann and collaborators have found a magnetically induced bonding process between materials i.e. “perpendicular paramagnetic bonding”. This bonding process is “generated by the stabilization of antibonding orbitals in their perpendicular orientation relative to an external magnetic field.”

Magnetic field on the dwarf stars is very much high that could result in changing the way through which the atoms join together and resulting in altered chemical reality to that on Earth. (For comparison, Tesla is a unit of magnetic field and refrigerator magnets have one thousandth of Tesla and the maximum Tesla generated on Earth is 1000 but Sirius B has 200,000 to 400,000 Tesla of magnetic fields).

"What we had before we discovered this was basically a paper-and-pencil model of what goes on in the universe. Compared to what's out there in places such as white dwarf stars, the magnetic fields we can generate here -- even with the strongest magnets -- are pathetic."

So how did they do it?

"We computationally modeled the behavior that we theorized, based on universally applicable physical principles," Hoffmann said.

The computer model presented by the team is according to their theory and now astrophysicists have to check the model by the conventional observation of stars.

Reference:

Lange, K., Tellgren, E., Hoffmann, M., & Helgaker, T. (2012). A Paramagnetic Bonding Mechanism for Diatomics in Strong Magnetic Fields Science, 337 (6092), 327-331 DOI: 10.1126/science.1219703... Read more »

Lange, K., Tellgren, E., Hoffmann, M., & Helgaker, T. (2012) A Paramagnetic Bonding Mechanism for Diatomics in Strong Magnetic Fields. Science, 337(6092), 327-331. DOI: 10.1126/science.1219703  

  • December 6, 2012
  • 01:40 PM
  • 156 views

Cyclotides: A new ‘wave’ of discovery

by Clay Clark in Biochem Blogs

The cyclotide family is the the largest class of circular proteins with as many as 50,000 predicted members. They are currently only found in the Violaceae, Cucurbitaceae, Rubiaceae and recently (1) Fabaceae family of the plant kingdom (violets, gourds, coffee and legumes, … Continue reading →... Read more »

Poth A. G., Colgrave M. L., Lyons R. E., Daly N. L., & Craik D. J. (2011) From the Cover: Discovery of an unusual biosynthetic origin for circular proteins in legumes. Proceedings of the National Academy of Sciences, 108(25), 10127-10132. DOI: 10.1073/pnas.1103660108  

Saska I., Gillon A. D., Hatsugai N., Dietzgen R. G., Hara-Nishimura I., Anderson M. A., & Craik D. J. (2007) An Asparaginyl Endopeptidase Mediates in Vivo Protein Backbone Cyclization. Journal of Biological Chemistry, 282(40), 29721-29728. DOI: 10.1074/jbc.M705185200  

  • November 29, 2012
  • 10:30 PM
  • 319 views

Come out smelling like a rose

by Aurametrix team in Olfactics and Diagnostics

You are what you eat. And you smell like your food. Well, it's actually a bit more complicated - as we emit complex combinations of volatile chemicals produced from food by our own metabolic system as well as microbes that call us home. Same foods can be translated into a wide range of odors, depending on the individual. People exhibit a large variety of smells, much more diverse than animals or plants. Thanks to variations in our digestive enzymes, diets, supplements, medicines, perfumes, detergents, clothes, cars and a lot of other chemicals we are exposed to via different routes. And there are many ways to smell of a rose - for example, by putting a few petals in the pocket, wearing Sa Majeste La Rose or drinking rose oil.As confirmed by gas-chromatograph mass spectrometry using a thermo desorption system and a selective ion mode (Akiyama et al., 2006), linalool, citronellol and geraniol, which are the main components of rose essential oil, are emitted from our palms after an oral intake of rose oil. The aroma starts to increase 30 minutes after ingestion and reaches its peak within an hour, then slowly decreases, wearing off more than 100 times in the next 6 hours. Citronellol seems to evaporate the fastest, and linalool lingers a little longer than the other two compounds, but, of course, this may very well differ for different individuals.A new "functional food" - Deo Perfume Candy  - is an attempt to take the sciences of smells and foods to a whole new level by creating a sweet treat intended to make you smell good. The main active ingredient of this candies is Geraniol. It is extracted from rose oil, which in its turn is extracted from real rose petals - one gram of oil per two thousand petals. Small amounts of citric acid and tangerine oil are added for more flavor. An healthy food company Beneo partnered with Bulgarian candy maker, Alpi, to develop this nutricosmetics  treat. At present it is sold exclusively on Amazon and has already collected 5 reviews - ranging from a praise of the observed fresh-just-showered smell to complaints of the need to eat a buck load of candies to see some kind of effect. Does it really work? It might for some of us. With the right chemistry and metabolism, and the right combination of everything else. You can enter it in Aurametrix as Deo Perfume Candy and check back later to see how it worked for others. Or just log what you normally eat and wear to find how your body could react to Geraniol.You might want to compare it with Otoko Kaoru's chewing gum - despite a name that translates to "man smell" it also contains rose-flavored geraniol. Although one tester reported to smell like an apple-flavored soap after chewing it.  You can also experiment with the "coming soon" edible perfume from Netherlands, and its mystery ingredient. There will be more to come.The possibilities are endless and so are the human odor outcomes.REFERENCESAKIYAMA, A., IMAI, K., ISHIDA, S., ITO, K., KOBAYASHI, T., NAKAMURA, H., NOSE, K., & TSUDA, T. (2006). Determination of Aromatic Compounds in Exhalated from Human Skin by Solid-Phase Micro Extraction and GC/MS with Thermo Desorption System BUNSEKI KAGAKU, 55 (10), 787-792 DOI: 10.2116/bunsekikagaku.55.787... Read more »

AKIYAMA, A., IMAI, K., ISHIDA, S., ITO, K., KOBAYASHI, T., NAKAMURA, H., NOSE, K., & TSUDA, T. (2006) Determination of Aromatic Compounds in Exhalated from Human Skin by Solid-Phase Micro Extraction and GC/MS with Thermo Desorption System. BUNSEKI KAGAKU, 55(10), 787-792. DOI: 10.2116/bunsekikagaku.55.787  

  • November 29, 2012
  • 04:37 PM
  • 202 views

Metal measuring and autism

by Paul Whiteley in Questioning Answers

Now and again, two papers of a similar ilk are published temporally close together in the great autism research melting pot so as to cumulatively make for interesting reading.Congratulations, it's a baby T-1000 @ Wikipedia  In the case of this post, I am referring to the paper by Jim Adams and colleagues* and the paper by Yahya Al-Farsi and colleagues** which both examined the burden of metals present in cases of autism from the perspective of two very different geographical areas of the world. Both papers are published in the same journal too.I should say that I've covered metals, heavy and toxic, before on this blog with reference to the background to this whole area (see here) and some research on that most controversial of areas, mercury and autism (see here). As with just about every other instance of autism research, the message is a messy one, with no 'one-size-fits-all' finding, which often wrongly gets translated as either 'it must be a universal effect' or 'there must be no effect' with seemingly no middle ground where the autisms are concerned.Anyhow, a few details about the papers:The Adams paper:The hypotheses were: (a) "children with autism would have higher levels of some toxic metals in their blood and urine" (n=55) compared with asymptomatic controls (n=44), and (b) the severity of symptoms would be associated with the toxic metal burden.This current study formed part of a wider body of work undertaken and published by the authors*** (open-access) looking at children aged 5-16 years. This follows other work in a similar vein**** (open-access).Morning blood and urine samples were eventually analysed by an old favourite method (ICP mass spectrometry) and the severity of autistic symptoms assessed by various means including the ATEC.Results: there were quite a few of them but most notably levels of lead in red blood cells (RBC) and urine were significantly elevated in the autism group compared with the control group, alongside urinary thallium, urinary tin and urinary tungsten.In terms of the measured severity of autism correlating with the metals findings, a slightly complicated picture emerges which suggested that whole blood and RBC mercury concentrations showed "possibly" significant correlations with the three assessment instruments used.The authors conclude that their results suggest that either there is increased exposure to these metals, increased absorption of these metals or decreased (fecal) excretion of these metals or some combination of these explanations. The Al-Farsi paper:A very similar starting point by all means, testing the hypothesis that "children with ASD will show variations and deregulated levels of heavy metals and essential minerals when compared to non-ASD controls".Based in the Sultanate of Oman, hair samples from children with DSM-IV autism (n=27) were analysed again by ICP-MS for the presence of various heavy metals and compared with results from age- and sex-matched asymptomatic controls (n=27).Results: again, quite a few but generally speaking levels of heavy metals were elevated in the autism group compared to controls, and included cobalt, cadmium, chromium, aluminium and also our old friend lead.When also looking at levels of essential minerals, a slightly more mixed picture emerges with lower levels of calcium and copper to be present but higher zinc, iron and sulphur (to name but a few).OK, there are a few differences to point out between these studies outside of just the ethnicity of their autism cohorts and the possible differences in geographical exposure patterns. The Adams paper looked at blood and urine, the Al-Farsi paper looked at hair. The mean ages of the groups examined were also slightly different (Adams: autism = 5.3 years; Al-Farsi: autism = 10 years). So we are not able to directly transpose results one on top of another.That being said, there were some similarities to these results not least about those findings related to lead. Indeed, I have quite an interest in all things lead for quite a few reasons, not least that even Superman had problems with lead so why wouldn't children exposed to the stuff, and those figures from last year (2011) which listed lead reduction as being one potential candidate among many as to why the US crime figures were falling. Exposure to lead is generally speaking not a great thing for developing or developed brains/bodies.I'll admit to not being a great expert on how hair, blood and urine samples compare when looking at metals or any other kind of chemical/compound so I can't offer too much in the way of information about the functionality of these measures and the extent to which they reflect levels of these metals or indeed evidence of storage and any on-going physiological activity / effect. I am for some reason drawn back to the very recent CHARGE findings on air pollution and autism (bearing in mind that the reduction of lead in petrol we've seen over the past few decades) as an interesting variable potentially relevant to these results but will say no more than that at this time.Accepting the issue of hair analysis, the Al-Farsi findings revealed some interesting trends with reference to the trace minerals examined. Higher zinc, higher iron and higher sulphur raise questions about what this means in light of other research indicating lower hair zinc (see this post) for example, and indeed that body of research on iron levels in autism (see this post and this post). The curse of messy heterogeneous autism research?Interestingly both papers seem to wade back to similar biochemical pathways in terms of the potential significance of their findings. So glutathione pops up (see this post on where glutathione sits in the current autism research world) and how glutathione is a key component in both the processes of antioxidation-oxidative stress as well as being tied into the removal of things like metals. The feeling is that the consistently lower levels of glutathione (GSH) noted in cases of autism is probably not going to be a great thing for the biological processing of such toxic metals.Both papers end with calls for further research into this complicated (and often controversial) area. I'd like to second that call given that this is a topic which seems to be cropping up more regularly in recent years. I know that when people start talking about toxic metals and autism, specific toxic metals, some conversations instantly move into areas which make some people a little uncomfortable. Irrespective of what causes such issues to become apparent, the questions must surely be (i) what effect, if any such burdens have contributing to the presentation of autism or indeed any of its potential com... Read more »

Adams, J., Audhya, T., McDonough-Means, S., Rubin, R., Quig, D., Geis, E., Gehn, E., Loresto, M., Mitchell, J., Atwood, S.... (2012) Toxicological Status of Children with Autism vs. Neurotypical Children and the Association with Autism Severity. Biological Trace Element Research. DOI: 10.1007/s12011-012-9551-1  

Al-Farsi, Y., Waly, M., Al-Sharbati, M., Al-Shafaee, M., Al-Farsi, O., Al-Khaduri, M., Gupta, I., Ouhtit, A., Al-Adawi, S., Al-Said, M.... (2012) Levels of Heavy Metals and Essential Minerals in Hair Samples of Children with Autism in Oman: a Case–Control Study. Biological Trace Element Research. DOI: 10.1007/s12011-012-9553-z  

  • November 28, 2012
  • 10:19 AM
  • 219 views

Mr. Nanny Makes Mr. Right

by Miss Behavior in The Scorpion and the Frog

Quick! Introduce yourself to this guy before his baby-high wears off! Photo by David Castillo Dominici at FreeDigitalPhotos.net. What happens if you take a wrestler or action star and force him to babysit obnoxious but lovable kids? Well, if you’ve seen movies like The Pacifier with Vin Diesel, The Tooth Fairy with Dwayne ‘The Rock’ Johnson, Kindergarten Cop with Arnold Schwarzenegger, or The Spy Next Door with Jackie Chan, you know that he will fall madly in love both with his young charges and with the closest available woman. Hollywood is so sure of this phenomenon that they have based a whole genre of family movies on it. Now, scientists are finding that Hollywood may be on to something. Prairie voles are one of the only 3-5% of mammals that are monogamous and in which both parents help take care of young. In females, maternal care is regulated in part by the hormones associated with pregnancy, birth and lactation. The fact that males don’t do those things and they still provide paternal care is curious. The fact that male prairie voles will often provide care to offspring that aren’t even their own is even more curious. Will Kenkel, Jim Paredes, Jason Yee, Hossein Pournajafi-Nazarloo, Karen Bales, and Sue Carter at the University of Illinois at Chicago recently explored what happens to male prairie voles when they are exposed to unfamiliar vole pups. Male voles without any experience with females or pups were placed in a new clean cage. Then the researchers put either a pup (that was not related to the male), a dowel rod (an unfamiliar object), or nothing into the cage with them for 10 minutes. Afterwards, they measured oxytocin (a hormone associated with bonding between mothers and their offspring) and corticosterone (a stress hormone) in the males’ blood at different time points. In another study, they also looked at the activity of brain neurons associated with the production of these hormones. A male prairie vole is startled to find a baby in his cage... But then he takes care of it. Video by Will Kenkel. Both adult and juvenile males exposed to a pup for 10 minutes had higher oxytocin and lower corticosterone compared to the males not exposed to a pup. But this effect was short-lived, as male hormone levels quickly evened out again. Most of these males that were exposed to a pup showed alloparental care (care of a baby that is not their own), like approaching the pup, cuddling with it and grooming it. Males with higher oxytocin and lower corticosterone levels were more attentive towards the pups. Additionally, alloparental males exposed to pups had more activity of oxytocin-producing neurons and less activity of neurons associated with corticosterone-production in a specific brain region called the paraventricular nucleus (or PVN for short). Oxytocin is strongly associated with pair bonding in prairie voles, particularly in females, and corticosterone affects pair bonding too (generally increasing pair bonding in males and preventing it in females). If exposure to a pup affects these hormones, maybe it affects how the male would interact with adult females. To test this, the researchers put male voles in a new clean cage and put a pup, a dowel rod, or nothing into the cage with them for 20 minutes. Then they put the males with an unfamiliar adult female for 30 minutes. After getting acquainted with the female, the males were put in a “partner preference apparatus”, which has three connected chambers: a neutral center chamber, a connected chamber with the familiar female tethered into it, and a connected chamber with an unfamiliar female tethered into it. The researchers measured how much time the males spent in each of the three chambers and with each of the two females over the next 3 hours. A prairie vole pair snuggles. Photo from Young, Gobrogge, Liu and Wang paper in Frontiers in Neuroendocrinology (2011) Males that were exposed to a dowel rod or to nothing before they were introduced to a female spent equal amounts of time with each of the two females. But males that were exposed to a pup before they were introduced to a female spent nearly 4 times as much time with that female than with the unfamiliar one. In other words, hanging out with a random pup acted like Love Potion #9 on these bachelor males and made them fall for the next female they encountered! Interestingly, this effect was true not only for the males that acted in an alloparental way towards the pups, but it was also true of males that attacked the pups (The researchers quickly rescued the pups if this occurred). Perhaps, males that were alloparental with the pups had increased oxytocin and males that were aggressive with the pups had increased corticosterone, either of which would make it more likely for them to form a preference for the female they were with. Hmm… Got your eye on a special someone? Try volunteering him to babysit before your next date. Want to know more? Check this out:... Read more »

Kenkel, W., Paredes, J., Yee, J., Pournajafi-Nazarloo, H., Bales, K., & Carter, C. (2012) Neuroendocrine and Behavioural Responses to Exposure to an Infant in Male Prairie Voles. Journal of Neuroendocrinology, 24(6), 874-886. DOI: 10.1111/j.1365-2826.2012.02301.x  

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