Research Blogging - Chemistry - English

Scientists Trying to Photograph Photosynthesis

2013-05-17T14:10:00Z

Photosynthetic oxidation of water is one of the central processes of life on Earth, but it is still not completely understood. Now, a German-American team of scientists has set out to observe the intermediate stages of this complex catalytic reaction using ultrashort snap shots taken at light sources including BESSY II in Berlin and the Linac Coherent Light Source at Stanford....

Kern, J., Alonso-Mori, R., Hellmich, J., Tran, R., Hattne, J., Laksmono, H., Glockner, C., Echols, N., Sierra, R., Sellberg, J.... (2012) Room temperature femtosecond X-ray diffraction of photosystem II microcrystals. Proceedings of the National Academy of Sciences, 109(25), 9721-9726. DOI: 10.1073/pnas.1204598109

Water’s secrets

2013-05-16T18:37:21Z

A team of Canadian and UK researchers has discovered what may be some of the oldest pockets of water on the planet – and they may contain life....

Kim Luke, University of Toronto, Office of Public Relations, McMaster University, Aeron Haworth, The University of Manchester, & Lancaster University, News. (2013) Water's secrets. Tracing Knowledge. info:/

Researchers Develop New Way to Produce Hydrogen From Water and Sunlight

2013-05-16T14:27:00Z

Using a combination of microanalytic techniques that at the same time image photoelectric current and chemical reaction rates across a surface on a micrometer scale, researchers at the National Institute of Standards and Technology (NIST) have shed new light on what may become a cost-effective way to generate hydrogen gas directly from water and sunlight....

Esposito, D., Levin, I., Moffat, T., & Talin, A. (2013) H2 evolution at Si-based metal–insulator–semiconductor photoelectrodes enhanced by inversion channel charge collection and H spillover. Nature Materials. DOI: 10.1038/nmat3626

"Fool Me Twice, Shame on ME," Says Sea Slug

2013-05-16T11:17:08Z

"Simple" is often a compliment in the human world, used to describe low-fuss dinners or closet solutions. When scientists use "simple" to describe an animal, they mean something more like, "That sac of goo has no business acting clever." An especially simple creature—a sea slug—recently demonstrated that despite its humble resources, it can learn from experience and form new hunting strategies. Smaller goo sacs, beware. Despite its squishy stature, the sea slug Pleurobranchaea californica is a killer. It roams the sea and swallows whatever appealing morsels are in its way. Being blind, it can't tell how tasty its prey looks—or doesn't. It can't see, for example, the flashy coloration of the "Spanish shawl" nudibranch (Flabellina iodinea). If it could, it might guess that those bright pink and orange hues are a warning: Flabellina is not nice to eat. It steals stinging cells from its own prey (such as corals and anemones) and stores those stingers in its bristles. Rhanor Gillette, a neuroscientist at the University of Illinois, Urbana-Champaign, observed that not only do Pleurobranchaea slugs spit out Spanish shawls, but they seem to remember and avoid the animals in the future. To study how well the predatory sea slugs learn their lesson after tasting Flabellina, he and graduate student Vanessa Noboa set up a meet-and-greet between the two species. In tanks, the large, hungry sea slugs encountered the smaller nudibranchs. Researchers recorded how long it took for Pleurobranchaea to take a taste, then waited for the slugs to change their minds and turn away from their potential prey. (Here's a great video of a Pleurobranchaea attempting to Hoover up a Flabellina, then spitting the animal back out. While the big slug pivots away in disgust, the little one does its "Don't eat me" dance like nobody's watching, which is true.) On the first day, this interaction happened five times. By the end, most of the Pleurobranchaea slugs were much slower to take a taste of the Spanish shawls, or were ignoring them altogether. Twenty-four hours later, the sea slugs were still reluctant to approach Flabellina. Even after 72 hours, they remembered what they'd learned. Gillette and Noboa report their results in the Journal of Experimental Biology. Since the predatory slugs seem to sniff something in the water that makes them turn away, the researchers think the noxious Spanish shawls give off a distinctive warning odor. Gillette says the sea slugs have a decent memory, considering their elementary nervous system. "In these experiments their memory is strong at 48 hours," he says, "and in unpublished work we've seen savings up to a week, so it's not bad." (Oddly, some slugs had to be removed from the experiment because they didn't mind the taste of the stinging Flabellina at all. They sucked it up just like any other food.) Learning from an unpleasant taste experience, then using that memory to change one's hunting strategy, is "a real cognitive trait," Gillette says—in other words, a "goal-directed use of knowledge." The Pleurobranchaea slugs learned to avoid the smell of Flabellina, although they continued to eat a related, non-stinging species without hesitation. Being able to change their feeding strategy is a good thing, since these slugs are generalists. Everything in the path of their oozing is a potential meal. "More specialized animals, say sea-slugs that may munch on a particular kind of sponge, may not need to employ such learning abilities," Gillette says. For a hunter like Pleurobranchaea, the decisions aren't so simple. Noboa, V., & Gillette, R. (2013). Selective prey avoidance learning in the predatory sea-slug Pleurobranchaea californica Journal of Experimental Biology DOI: 10.1242/jeb.079384 Image: Rhanor Gillette....

Noboa, V., & Gillette, R. (2013) Selective prey avoidance learning in the predatory sea-slug Pleurobranchaea californica. Journal of Experimental Biology. DOI: 10.1242/jeb.079384

Scarlet macaw genome sequenced | @GrrlScientist

2013-05-15T11:06:58Z

The newly-sequenced scarlet macaw genome will provide many important insights into avian and human biology, behaviours and genetics and will contribute to parrot conservation.After many years of research into the behaviours, diseases, genetics and life history of scarlet macaws, a team of scientists have taken their studies to the next level. Christopher Seabury, an Assistant Professor of Genetics at Texas A&M University's college of Veterinary Medicine and Biomedical Sciences, and Ian Tizard, Director of the Schubot Exotic Bird Health Center and a Professor of Microbiology & Immunology at Texas A&M University's college of Veterinary Medicine and Biomedical Sciences, spearheaded an international collaboration of scientists that sequenced the genome of the scarlet macaw, Ara macao. This work significantly expands the range and depth of research opportunities involving scarlet macaws and other parrots. In addition to important conservation applications, this research may provide insights into the genetics that contribute to key traits of parrots, such as cognitive and speech abilities as well as longevity.Scarlet macaws are large and showy parrots with brilliant red, yellow and blue plumage and long pointed tails. Endemic to Central and South America, this impressive neotropical parrot occupies a large range from southeastern Mexico throughout the Amazon basin region of Peru, Bolivia and Brazil. Easily trained to do complex tasks and to mimic human speech, wild scarlet macaws have been persecuted by the caged bird trade. Additionally, their preferred habitat of lowland evergreen rainforests makes them vulnerable to deforestation and habitat destruction. To do this work, Drs Seabury and Tizard and their team obtained a blood sample from an adult female scarlet macaw known as "Neblina" who resides at the Blank Park Zoo in Iowa. A wild-caught parrot from Brazil, Neblina had been seized in 1995 by the US Fish and Wildlife Service after she illegally entered the United States. Unlike mammals, avian red blood cells are nucleated, so a small sample of whole blood from a bird is an excellent source of DNA for molecular, chromosomal and cytological studies. Some cells were grown in cultures so the intact chromosomes could be harvested and examined whilst DNA was extracted from other cells for sequencing. These gene sequences were then assembled into the complete scarlet macaw genome by Seabury and his team.Similar to almost all vertebrates, scarlet macaws are diploid; having two copies of each chromosome type, one contributed by each parent. Like all birds except birds of prey (Falconiformes), parrot genomes contain macrochromosomes and a larger number of microchromosomes. Macrochromosomes are what most people think of when they hear the word "chromosome" and they are the type of chromosomes that are typically found in mammals. Macrochromosomes, which include autosomes and sex chromosomes, are large -- generally more than 40 megabases (Mb) in size (1 megabase is 1,000,000 nucleotide basepairs in length). Microchromosomes, on the other hand, are very small -- usually less than 20 Mb in size. Due to their small size, microchromosomes are often impossible to distinguish when creating a traditional karyotype, as you see in Figure 1 (larger view):Scarlet macaws have somewhere between 62 and 64 chromosomes; including 22 macrochromosomes (10 pairs of autosomomes and two sex chromosomes) and between 40 and 42 microchromosomes. To identify similar regions between scarlet macaw and chicken macrochromosomes, the team used chromosome painting. This method uses fluorescently labeled chromosome-specific DNA probes that hybridise to complementary DNA regions, thereby identifying macaw chromosome regions that are similar to chicken chromosomes (Figure 2; larger view):As expected, the final completed scarlet macaw genome shows similarities to that of the domestic chicken. However, there are a number of important differences, which are to be expected since parrots and chickens (taxonomic order: Galliformes) diverged approximately 122–125 million years ago. For example, several macaw macrochromosomes (1, 6 & 7) show significant rearrangements. The sex chromosome W shows no similarities at all between chicken and macaw, indicating that this chromosome is changing rapidly and thus, has not been conserved across such a large evolutionary distance. As typical for other avian genomes studied so far, scarlet macaw genomes are smaller than mammalian genomes. "The final analysis showed that there are about one billion DNA bases in the genome, which is about one-third of that found in mammals," Dr Tizard explained in a written press release. "Birds have much less DNA than mammals primarily because they do not possess nearly as much repetitive DNA."Repetitive DNA has no currently known function. The amount of repetitive DNA varies greatly between taxa: for example, more than 50 percent of the human genome is repetitive DNA [doi:10.1038/nrg3117].According to Dr Seabury, comparing the scarlet macaw genome to other avian genomes will provide scientists with a better understanding of avian biology. "The Scarlet Macaw Genome Project opens a variety of doors ranging from modern forensics to determining how the macaws utilize their natural habitat and landscape, as inferred from variable genetic markers," said Dr Seabury in a written press release.In addition to research into evolution and population genetics, and conservation biology applications, what can we learn from the scarlet macaw's genome? First, even though birds have higher metabolisms than mammals, they enjoy much longer life spans than do mammals with the same body mass. In the case of scarlet macaws, adults weigh somewhere between 1000 and 1200 grams (roughly 2.2 pounds), and they reach sexual maturity at 5 years of age, yet their life span rivals that of humans. By comparing avian genomes to those obtained from other animals, it may be possible to identify which genes contribute to birds' remarkable longevity. Other genes of interest are those involved in heart and cardiovascular fitness, and those that contribute to the risk for diabetes. But perhaps most interesting are those genes involved with cognition and brain size. "A preliminary analysis of their genome suggests that [macaws] have a lot of genes involved in brain development", said Dr Tizard in a video press release. "Which fits, knowing how smart they are."Despite differences from humans in brain development and structure, macaws are much like humans: they are very intelligent and live in highly complex social groups. Additionally, macaws' brains are twenty-one percent larger than those of zebra finches, Taeniopygia guttata, which are the model system for vertebrate learning and memory. Thus, comparing the scarlet macaw, zebra finch and human genomes could provide greater insight and understanding into important genetic differences in brain development, structure and volume. Sources:Seabury C.M., Dowd S.E., Seabury P.M., Raudsepp T., Brightsmith D.J., Liboriussen P., Halley Y., Fisher C.A., Owens E. & Viswanathan G. & Tizard, I.R. (2013). A Multi-Platform Draft de novo Genome Assembly and Comparative Analysis for the Scarlet Macaw (Ara macao), PLoS ONE, 8 (5) e62415. doi:...

Seabury Christopher M., Dowd Scot E., Seabury Paul M., Raudsepp Terje, Brightsmith Donald J., Liboriussen Poul, Halley Yvette, Fisher Colleen A., Owens Elaine, & Viswanathan Ganesh. (2013) A Multi-Platform Draft de novo Genome Assembly and Comparative Analysis for the Scarlet Macaw (Ara macao). PLoS ONE, 8(5). DOI: 10.1371/journal.pone.0062415.s019

Oleksyk Taras K, Pombert Jean-Francois, Siu Daniel, Mazo-Vargas Anyimilehidi, Ramos Brian, Guiblet Wilfried, Afanador Yashira, Ruiz-Rodriguez Christina T, Nickerson Michael L, & Logue David M. (2012) A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education. GigaScience, 1(1), 14. DOI: 10.1186/2047-217X-1-14

Ried T, Schröck E, Ning Y, & Wienberg J. (1998) Chromosome painting: a useful art. Human Molecular Genetics, 7(10), 1619-1626. DOI: 10.1093/hmg/7.10.1619

Cadmium: toxic to mammals, harmless to a bacterium, helpful to an alga

2013-05-15T08:36:27Z

Heavy metal poisoning is a major health concern across the world. Heavy metal ions frequently leak into the environment from industrial waste causing multiple health problems in humans, animals, and other organisms. While there is no universally accepted definition of … Continue reading →...

Bertin G., & Averbeck D. (2006) Cadmium: cellular effects, modifications of biomolecules, modulation of DNA repair and genotoxic consequences (a review). Biochimie, 88(11), 1549-1559. DOI: 10.1016/j.biochi.2006.10.001

Schwager Stephan, Lumjiaktase Putthapoom, Stöckli Martina, Weisskopf Laure, & Eberl Leo. (2012) The genetic basis of cadmium resistance of . Environmental Microbiology Reports, 4(5), 562-568. DOI: 10.1111/j.1758-2229.2012.00372.x

LEE JENNIFER G., ROBERTS SAMANTHA B., & MOREL FRANÇOIS M. M. (1995) Cadmium: A nutrient for the marine diatom Thalassiosira weissflogii. Limnology and Oceanography, 40(6), 1056-1063. DOI: 10.4319/lo.1995.40.6.1056

Scientists Use Cyborg Plants to Harvest Solar Energy

2013-05-10T09:32:00Z

Our star, the Sun, provides most of the energy on this planet. (Essentially, all the energy except for nuclear, comes directly or indirectly from it.) Our current methods of converting solar radiation into electricity (photovoltaics) are not very efficient in comparison with plants. Researchers at the University of Georgia looked to nature for inspiration, and they are now developing a new technology that makes it possible to use plants to generate electricity....

Calkins, J., Umasankar, Y., O'Neill, H., & Ramasamy, R. (2013) High photo-electrochemical activity of thylakoid–carbon nanotube composites for photosynthetic energy conversion. Energy . DOI: 10.1039/C3EE40634B

Scientists Get More Energy, Less Carbon Dioxide From Natural Gas

2013-05-09T17:39:00Z

As the world shifts from coal to natural gas, it is becoming more important to find ways of using natural gas efficiently and environmentally friendly. Now chemical engineering researchers have identified a new mechanism to convert natural gas into energy up to 70 times faster, while effectively capturing the greenhouse gas—carbon dioxide....

Galinsky, N., Huang, Y., Shafiefarhood, A., & Li, F. (2013) Iron Oxide with Facilitated O Transport for Facile Fuel Oxidation and CO Capture in a Chemical Looping Scheme . ACS Sustainable Chemistry , 1(3), 364-373. DOI: 10.1021/sc300177j

New Robotic Instruments to Provide Real-Time Data on Gulf of Maine Red Tide

2013-05-08T06:13:19Z

A new robotic sensor deployed by Woods Hole Oceanographic Institution (WHOI) in Gulf of Maine coastal waters may transform the way red tides or harmful algal blooms (HABs) are monitored and managed in New England. The instrument was launched at the end of last month, and a second such system will be deployed later this spring....

WHOI Media Relations Office. (2013) New Robotic Instruments to Provide Real-Time Data on Gulf of Maine Red Tide. Woods Hole Oceanographic Institution . info:/

The Black Sea is a Goldmine of Ancient Genetic Data

2013-05-08T04:31:59Z

When Woods Hole Oceanographic Institution (WHOI) marine paleoecologist Marco Coolen was mining through vast amounts of genetic data from the Black Sea sediment record, he was amazed about the variety of past plankton species that left behind their genetic makeup (i.e., the plankton paleome)....

WHOI Media Relations Office. (2013) The Black Sea is a Goldmine of Ancient Genetic Data. Woods Hole Oceanographic Institution. info:/