Chemistry posts
- May 17, 2012
- 08:48 AM
- 539 views
Autoimmune hydrolytic antibodies
by SS in Scientific scrutiny
A discussion of the chromatographic procedures done to purify antibodies from sera of rheumatoid arthritis patients and the study design described. ... Read more »
Kamalanathan AS, Goulvestre C, Weill B, & Vijayalakshmi MA. (2010) Proteolysis activity of IgM antibodies from rheumatoid arthritis patients' sera: evidence of atypical catalytic site. Journal of molecular recognition : JMR, 23(6), 577-82. PMID: 21031477
Kamalanathan A. S., & Vijayalakshmi M. A. (2009) Molecular studies of rheumatoid factor using pseudobioaffinity membrane chromatography. Journal of Molecular Recognition, 22(2), 153. DOI: 10.1002/jmr.921
- May 16, 2012
- 05:15 PM
- 315 views
Feeling the curves of biology: How the advances in atomic force microscopy are opening new techniques to microbiology
by Clay Clark in Biochem Blogs
Traditional light microscopes are not able to resolve images small enough to explore the details of cells. One of the techniques used to investigate nanoscale samples is atomic force microscopy (AFM). AFM uses a very fine tip (atoms in … Continue reading →... Read more »
Fantner, G., Barbero, R., Gray, D., & Belcher, A. (2010) Kinetics of antimicrobial peptide activity measured on individual bacterial cells using high-speed atomic force microscopy. Nature Nanotechnology, 5(4), 280-285. DOI: 10.1038/nnano.2010.29
Carvalho, F., Carneiro, F., Martins, I., Assuncao-Miranda, I., Faustino, A., Pereira, R., Bozza, P., Castanho, M., Mohana-Borges, R., Da Poian, A.... (2011) Dengue Virus Capsid Protein Binding to Hepatic Lipid Droplets (LD) Is Potassium Ion Dependent and Is Mediated by LD Surface Proteins. Journal of Virology, 86(4), 2096-2108. DOI: 10.1128/JVI.06796-11
- May 16, 2012
- 08:40 AM
- 450 views
Mixed opinions, disturbed flow
by SS in Scientific scrutiny
Analysis of the flaws in study design for the comparison of different sorbents in their interactions with antibodies. ... Read more »
Ranjini S. Shiva, Bimal Devla, Dhivya A.P., & Vijayalakshmi M.A. (2010) Study of the mechanism of interaction of antibody (IgG) on two mixed mode sorbents. Journal of Chromatography B, 878(15-16), 1037. DOI: 10.1016/j.jchromb.2010.03.005
- May 16, 2012
- 01:16 AM
- 382 views
Are Invisible Extraterrestrials Out There?
by Jason Carr in Wired Cosmos
I recently watched The Darkest Hour, a film about invisible aliens that invade and terrorize Earth. While the movie itself leaves much to be desired, the concept of invisible aliens is one that I find noteworthy. As we search for alien lifeforms, could we be missing them due to their invisibility? While invisibility has been [...]... Read more »
Johnsen, S., & Widder, E. (1999) The Physical Basis of Transparency in Biological Tissue: Ultrastructure and the Minimization of Light Scattering. Journal of Theoretical Biology, 199(2), 181-198. DOI: 10.1006/jtbi.1999.0948
Johnsen, S. (2000) Transparent Animals. Scientific American, 282(2), 80-89. DOI: 10.1038/scientificamerican0200-80
Johnsen, S. (2001) Hidden in Plain Sight: The Ecology and Physiology of Organismal Transparency. Biological Bulletin, 201(3), 301. DOI: 10.2307/1543609
Zylinski, S., & Johnsen, S. (2011) Mesopelagic Cephalopods Switch between Transparency and Pigmentation to Optimize Camouflage in the Deep. Current Biology, 21(22), 1937-1941. DOI: 10.1016/j.cub.2011.10.014
Nikolopoulos, D. (2002) The Relationship between Anatomy and Photosynthetic Performance of Heterobaric Leaves. PLANT PHYSIOLOGY, 129(1), 235-243. DOI: 10.1104/pp.010943
- May 12, 2012
- 10:34 AM
- 484 views
Nice use of PacBio sequencing to characterize methyltransferase specificity
by Jonathan Eisen in The Tree of Life
Figure 1.
Rich Roberts just pointed me to this cool paper on which he is a co-author: Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. The paper was published in Nucleic Acids Research and is from Robert's group at New England Biolabs and Jonas Korlach's and others at Pacific Biosciences. What is cool is that they used the timing of the real time DNA sequencing to identify bases in particular DNA fragments that were methylated. And this then allowed them to determine the specificity of particular methyltransferases (first tested on ones with known activity and then on ones with unknown activity). This highlights one of the unique features of PacBio sequencing - because the method watches DNA replication in real time - if something alters the timing of the replication process - this can possibly be leveraged to detect alterations in DNA chemistry (e.g., methylation, DNA damage, etc). Folks at PacBio have been promoting the methylation detection capabilities of their system for some time but I guess I did not get that interested in it because I viewed it is analogous to many other tools to quantify methylation. But with this paper I now realize that the PacBio approach (and perhaps those of other methylation detection systems) are not just about quantifying methylation status on average across a set of DNA pieces, but can also be very specific as to exactly which bases are methylated. And this in turn can be used to define specificity for a variety of unknown methyltransferases.
Clark, T., Murray, I., Morgan, R., Kislyuk, A., Spittle, K., Boitano, M., Fomenkov, A., Roberts, R., & Korlach, J. (2011). Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing Nucleic Acids Research, 40 (4) DOI: 10.1093/nar/gkr1146
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This is from the "Tree of Life Blog"
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.
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... Read more »
Clark, T., Murray, I., Morgan, R., Kislyuk, A., Spittle, K., Boitano, M., Fomenkov, A., Roberts, R., & Korlach, J. (2011) Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Research, 40(4). DOI: 10.1093/nar/gkr1146
- May 10, 2012
- 05:10 PM
- 572 views
The Lovelock Laboratory: A fantasy workplace in the West Country
by Duncan Hull in O'Really?
Former Mancunian James Lovelock runs the kind of a laboratory most scientists can only fantasise about working in as they grind through the humdrum bureaucracy of peer-review and never-ending grant applications. Lovelock is fortunate enough to run a completely independent, self-funded lab located in the beautiful West Country. There’s a fascinating interview with him on The Life Scientific with Jim Al-Khalili where he says lots of interesting things about elocution lessons, nuclear power, climate change and his grand theory of planet earth, Gaia.... Read more »
Watson, A. (2009) Final warning from a sceptical prophet. Nature, 458(7241), 970-971. DOI: 10.1038/458970a
- May 10, 2012
- 09:59 AM
- 396 views
Life, Bit by Bit
by gunnardw in The Beast, the Bard and the Bot
In a previous post, I’ve alluded to the issues we’re facing in defining (the conditions for) life. Also, the question of how to look for it was raised. After all, it might be substantially different from what we know. Now, … Continue reading →... Read more »
Joyce, G. (2012) Bit by Bit: The Darwinian Basis of Life. PLoS Biology, 10(5). DOI: 10.1371/journal.pbio.1001323
- May 8, 2012
- 08:04 PM
- 460 views
Of wild carrots and the death of Socrates
by aewills in A Bouquet From Mendel
There is a plant I keep encountering, both on foraging trips and while out running, and for a long time I had been entertaining the hope that it was wild carrot (Daucus carota), while secretly suspecting that it was actually … Continue reading →... Read more »
Schep LJ, Slaughter RJ, & Beasley DM. (2009) Nicotinic plant poisoning. Clinical toxicology (Philadelphia, Pa.), 47(8), 771-81. PMID: 19778187
Radulović N, Dorđević N, Denić M, Pinheiro MM, Fernandes PD, & Boylan F. (2012) A novel toxic alkaloid from poison hemlock (Conium maculatum L., Apiaceae): identification, synthesis and antinociceptive activity. Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association, 50(2), 274-9. PMID: 22063758
- May 8, 2012
- 10:17 AM
- 394 views
The epigenetic crystal ball
by Clay Clark in Biochem Blogs
What if I told you there may be a new way of determining whether non-cancerous cells have the potential to form malignancies. If this were possible, it may lead to earlier diagnosis and treatment. The method may sound like … Continue reading →... Read more »
Kobayashi, Y., Absher, D., Gulzar, Z., Young, S., McKenney, J., Peehl, D., Brooks, J., Myers, R., & Sherlock, G. (2011) DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer. Genome Research, 21(7), 1017-1027. DOI: 10.1101/gr.119487.110
Yi, J., Dhir, M., Guzzetta, A., Iacobuzio-Donahue, C., Heo, K., Yang, K., Suzuki, H., Toyota, M., Kim, H., & Ahuja, N. (2012) DNA methylation biomarker candidates for early detection of colon cancer. Tumor Biology, 33(2), 363-372. DOI: 10.1007/s13277-011-0302-2
Marta Kulis, Manel Esteller. (2010) DNA methylation and cancer. Advances in Genetics, 27-56. DOI: 10.1016/B978-0-12-380866-0.60002-2
- May 3, 2012
- 04:30 PM
- 353 views
Putting the Squeeze on Microfluidics
by Hector Munoz in Microfluidic Future
Microfluidic devices are able to process small volumes of liquid and are comprised of microscale components, but the devices themselves are not often small themselves. These labs-on-chips are often limited to lives in labs instead of the remote areas that could really benefit from their use. The limitation comes in the form of support equipment used to process or analyze assays that are expensive, bulky, energy consuming and/or require trained professional operators. Syringe pumps are often used in labs to drive liquids used in assays at specific flow rates and to ensure that the right volume is used. The need for complicated, external flow equipment was recently addressed by a group from Peking University. The group’s paper, “Squeeze-chip: a finger-controlled microfluidic flow network device and its application to biochemical assays” was recently featured on the cover of Lab on a Chip.... Read more »
Li, W., Chen, T., Chen, Z., Fei, P., Yu, Z., Pang, Y., & Huang, Y. (2012) Squeeze-chip: a finger-controlled microfluidic flow network device and its application to biochemical assays. Lab on a Chip, 12(9), 1587. DOI: 10.1039/C2LC40125H
- May 2, 2012
- 02:08 PM
- 401 views
Recipe for a Roman Diet
by Kristina Killgrove in Powered By Osteons
Humans evolved to be omnivores. We'll eat anything we can get our hands on - fruit, vegetables, beans, grains, meat - and we've invented innumerable ways to cultivate and refine those basic ingredients, particularly in the last 10,000 years or so since the agricultural revolution.
But diet in the past was limited, primarily by geography but also by social class or culture. Before the New World was discovered, Italian food had no tomatoes. Before the industrialization of food production, many items we think of as dirt cheap today, like salt, were too expensive for the poor to purchase. If you didn't live on the coast, you probably weren't eating seafood.
When we talk about ancient diets, then, we're looking primarily at commonalities - what the average person was eating - while at the same time understanding that omnivores make for a dietarily heterogeneous population. There is no singular "American" diet, but we can agree that most of us likely consume a large amount of corn-based products, which are cheap and ubiquitous in the form of corn syrup, tortilla chips, popcorn, etc. This reliance on corn, a crop native to the New World, means that the average American diet differs from the average European, African, or Asian diet. Biochemically, we can see this difference in carbon isotopes, and we can show that their value increased following the transition to maize agriculture in the Americas (see, for example, Tykot 2006). My carbon isotope value is almost certainly higher than that of most contemporary Europeans.
Roman-era Mosaic
Similarly, there is no singular "Roman" diet, particularly in the Empire when goods were moving around at astounding rates, although researchers agree that a heck of a lot of wheat was consumed by all social classes and that olives and olive oil contributed a number of calories and fat to most people's diets. Ancient historical sources also seem to agree that no one really liked barley and that millet was only consumed in times of struggle, as both of these grains make inferior bread compared to wheat (Garnsey 1988). Yet dried millet tended to keep longer than other grains, making it good for storage along with dry legumes like chickpeas, lupin beans, and lentils, the latter another food that was most often consumed in times of shortage.
Ordinary Romans - that is, small farmers, peasants, and rural slaves who made up the majority of the ancient Italian population - likely got a large chunk of their diet from their non-cash crops like millet, legumes, and turnips, at least based on what writers such as Columella, Strabo, and Galen tell us (Garnsey 1988). Their daily diet would have been a far cry from the exotic foodstuffs found at elite banquets. But, as Horace writes, "Ieiunus raro stomachus volgaria temnit" (Satires II, 2, xxxviii). A hungry stomach rarely scorns plain food.
In order to find out what kinds of plain food the ancient Italians were eating, bioarchaeologists are starting to perform carbon and nitrogen isotope analyses of skeletons (e.g., Prowse et al. 2004, Prowse et al. 2005, Craig et al. 2009, Rutgers et al. 2009, Killgrove 2010). Biochemical analysis isn't perfect, as it only yields a very macro-view of the diet. That is, the carbon isotope ratio can provide information about the kinds of plants and grains consumed, and the nitrogen isotope ratio can provide information on the relative amount of legumes and fish consumed. But depending on the rate of bone turnover, which can be different in different people because of age or disease status, the C and N isotopes represent an average of the last perhaps 5-10 years of a person's diet. With that in mind, here's what the skeletons are telling us about what people were eating in the Roman suburbs and down along the coast during the Empire:
The carbon axis shows that the people living in the Roman suburbs and along the coast were eating mostly wheat and barley (C3 foods, which have lower carbon isotope values) rather than millet (C4 food, which has a much higher carbon isotope value, starting around -13.0 permil). But their carbon values are higher than a purely C3-based diet, so those could be affected by marine resources and/or consumption of animals that were foddered on millet. The nitrogen axis shows that most people were eating a terrestrial, fairly omnivorous diet, with the coastal population of Velia eating a surprisingly little amount of fish. The pure vegetarians would be at the low end of the N axis, and the pure pescatarians would be at the high end (along with breastfeeding infants).
So what is the recipe for a Roman diet? Well, it's a little bit of everything, really. But you wouldn't know that from reading the half dozen or so cookbooks that contemporary authors have written to approximate Roman cuisine. For example, my copy of A Taste of Ancient Rome, while it has much to recommend it, has just two recipes that include lentils and none that include millet.
In his Historia Naturalis, Pliny notes that Campania in particular is full of millet and that peasants often mixed bean-meal (lomentum) with millet flour. Since cooking and chemistry are two sides of the same coin, I decided to remedy this omission by creating an historically-accurate dish that a Roman peasant might have eaten but also one that would show up isotopically in the skeleton (if eaten in large enough quantities).
Roman Millet and Lentil Salad
Simmer 1/2 cup of lentils in 1 cup of water for 20 minutes, or until soft. Separately, simmer 1/2 cup of millet in 1 cup of water with a bit of butter for 15 minutes. Put aside to cool.
Mince 1/2 cup of onion, 1/4 cup of parsley, 2 tablespoons of fresh mint, and 1 clove of garlic. Add to grains.
In a separate bowl, mix 1/4 cup of lemon juice, 1 tablespoon of balsamic vinegar, and 1 teaspoon salt. Pour over the salad and toss well.
Top with freshly cracked pepper.
Delicious!
I served myself up a bunch of this salad for lunch, and I garnished it with some other Roman staples to make it a balanced meal: a bit of cheese, olives, and dried apricots. It's delicious. Kind of like tahbouli, which coincidentally is my go-to dish on 90-degree weeks like this in North Carolina.
On Monday, I'll be serving this to my friend Sarah Bond's Roman history class at Washington & Lee, while I tell them about the information skeletons can give us that histories can't. Let's hope the students like it (and that it helps them remember something about isotopes and ancient diets)!
Bonum appetitionum!
References
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Craig, O., Biazzo, M., O'Connell, T., Garnsey, P., Martinez-Labarga, C., Lelli, R., Salvadei, L., Tartaglia, G., Nava, A., Renò, L.... (2009) Stable isotopic evidence for diet at the Imperial Roman coastal site of Velia (1st and 2nd Centuries AD) in Southern Italy. American Journal of Physical Anthropology, 139(4), 572-583. DOI: 10.1002/ajpa.21021
Prowse, T., Schwarcz, H., Saunders, S., Macchiarelli, R., & Bondioli, L. (2005) Isotopic evidence for age-related variation in diet from Isola Sacra, Italy. American Journal of Physical Anthropology, 128(1), 2-13. DOI: 10.1002/ajpa.20094
Prowse, T., Schwarcz, H., Saunders, S., Macchiarelli, R., & Bondioli, L. (2004) Isotopic paleodiet studies of skeletons from the Imperial Roman-age cemetery of Isola Sacra, Rome, Italy. Journal of Archaeological Science, 31(3), 259-272. DOI: 10.1016/j.jas.2003.08.008
Rutgers, L., van Strydonck, M., Boudin, M., & van der Linde, C. (2009) Stable isotope data from the early Christian catacombs of ancient Rome: new insights into the dietary habits of Rome's early Christians. Journal of Archaeological Science, 36(5), 1127-1134. DOI: 10.1016/j.jas.2008.12.015
R. Tykot. (2006) Isotope Analyses and the Histories of Maize. Histories of Maize: Multidisciplinary Approaches to the Prehistory, Linguistics, Biogeography, Domestication, and Evolution of Maize, 131-142. DOI: 10.1016/B978-012369364-8/50262-X
- May 1, 2012
- 12:27 PM
- 329 views
Finding biomarkers for human cancer: miRNA profiling
by Clay Clark in Biochem Blogs
A newly developed technique using miRNA profiling to characterize human cancer cells... Read more »
Guo, H., Ingolia, N., Weissman, J., & Bartel, D. (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature, 466(7308), 835-840. DOI: 10.1038/nature09267
Sato, F., Tsuchiya, S., Meltzer, S., & Shimizu, K. (2011) MicroRNAs and epigenetics. FEBS Journal, 278(10), 1598-1609. DOI: 10.1111/j.1742-4658.2011.08089.x
Liu, J., Zheng, M., Tang, Y., Liang, X., & Yang, Q. (2011) microRNAs, an active and versatile group in cancers. International Journal of Oral Science, 3(4), 165-175. DOI: 10.4248/IJOS11063
Lu, J., Getz, G., Miska, E., Alvarez-Saavedra, E., Lamb, J., Peck, D., Sweet-Cordero, A., Ebert, B., Mak, R., Ferrando, A.... (2005) MicroRNA expression profiles classify human cancers. Nature, 435(7043), 834-838. DOI: 10.1038/nature03702
Ramaswamy, S. (2001) Multiclass cancer diagnosis using tumor gene expression signatures. Proceedings of the National Academy of Sciences, 98(26), 15149-15154. DOI: 10.1073/pnas.211566398
- May 1, 2012
- 07:20 AM
- 467 views
Why do old books smell? [video]
by GrrlScientist in Maniraptora
SUMMARY: That old book smell brings back so many memories, but what creates that smell? ... Read more »
Strlič, M., Thomas, J., Trafela, T., Cséfalvayová, L., Kralj Cigić, I., Kolar, J., & Cassar, M. (2009) Material Degradomics: On the Smell of Old Books. . Analytical Chemistry, 81(20), 8617-8622. DOI: 10.1021/ac9016049
- April 30, 2012
- 07:57 AM
- 602 views
Rare, Medium or Well done? The science of a perfect steak
by Stuart Farrimond in Dr Stu's Science Blog
Vegetarians, look away now. Today’s post is distinctly carnivorous. Read on, you red meat eaters, as we are discussing an issue of upmost culinary importance… You can’t beat a good steak, I say. Quality medium-rare beef fillet; served with fries and salad is true feel-good food. I know I’m not the only one: it is … Continue reading »... Read more »
Koebnick, C., Strassner, C., Hoffmann, I., & Leitzmann, C. (1999) Consequences of a Long-Term Raw Food Diet on Body Weight and Menstruation: Results of a Questionnaire Survey. Annals of Nutrition and Metabolism, 43(2), 69-79. DOI: 10.1159/000012770
Faller, A., & Fialho, E. (2009) The antioxidant capacity and polyphenol content of organic and conventional retail vegetables after domestic cooking. Food Research International, 42(1), 210-215. DOI: 10.1016/j.foodres.2008.10.009
Gerber N, Scheeder MR, & Wenk C. (2009) The influence of cooking and fat trimming on the actual nutrient intake from meat. Meat science, 81(1), 148-54. PMID: 22063975
Obuz E, & Dikeman ME. (2003) Effects of cooking beef muscles from frozen or thawed states on cooking traits and palatability. Meat science, 65(3), 993-7. PMID: 22063680
- April 27, 2012
- 11:35 AM
- 954 views
Baby Corn Plants Recruit Helpful Bacteria Posse
by Elizabeth Preston in Inkfish
When you're a newly sprouted corn seedling, all alone in the dirt, you need any advantage you can get. After all, you can't pick up your roots and travel to find resources or avoid pests. That's why corn plants emit toxic chemicals that keep away hungry insects aboveground and harmful microbes below. But to at least one kind of bacteria, this poison is more of a beacon. They follow the toxic trail back to the corn plant, set up camp in its roots, and help the vulnerable seedling grow.
A plant's roots are the center of a miniature ecosystem called the rhizosphere. Local bacteria feed on sugars and proteins that trickle out of the roots, like antelopes at a watering hole. Symbiotic fungi enmesh themselves in the plant's roots. Helpless as it may appear, the plant can even release chemicals that encourage certain microbes to live there and discourage others, or prevent competing plant species from growing nearby.
Researchers in the United Kingdom studied one of the toxic chemicals released by the roots of corn plants. The compound is a benzoxazinoid, mercifully abbreviated as BX. Seedlings of corn and other grasses secrete BX molecules to protect themselves from pests and harmful microbes.
But the team, led by Andrew Neal at Rothamsted Research, suspected that certain bacteria weren't bothered by the toxin at all. Neal says this was a bit of a "leap of faith." Many bacteria that are used to clean pollutants from soil are closely related to bacteria that colonize plant roots. And some of the toxins that plant roots produce are similar to these pollutants. So the team asked whether Pseudomonas putida--"one of the best root colonizers we know of," Neal says--might be resistant to plant toxins.
The researchers first took both the plants and bacteria out of the soil to see what was going on. They found that corn seedlings produce the most poison at one week old, protecting themselves at their most vulnerable stage of growth. Over the next couple of weeks, production drops off.
Testing P. putida bacteria, they saw that the concentration of BX molecules around a seedling's roots didn't hurt the bacteria at all. But another common soil bacterium had serious trouble growing, even at a much lower concentration of the toxin. The chemical also broke down more quickly in the presence of P. putida, suggesting that the bacteria might not only tolerate the poison, but eat it.
Next Neal and his coauthors turned to the genes of P. putida to see which ones are most active when the toxic chemical is around. A few dozen genes popped up. Some of these had to do with "chemotaxis," a trick in which bacteria use their wiggly arms to travel toward a high concentration of a chemical they like. Were P. putida bacteria actively seeking out the toxin and the corn roots that released it?
Further experiments showed that the bacteria do, in fact, travel toward areas with more BX molecules. And in the soil, corn seedlings making the toxin attract more P. putida to their roots. (Genetic mutants that can't make BX molecules attract fewer bacteria.) The effect fades by the time the plant is three weeks old.
This is the first time scientists have seen an otherwise toxic root chemical attracting helpful bacteria. A corn plant that has successfully recruited P. putida has a leg up--or a root up--in its development. These bacteria and other friendly microbes keep harmful bacteria away by crowding them out and producing antibiotics against them. They also help the plant reach nutrients such as iron and phosphorous in the soil. The bacteria, too, have an advantage over other microorganisms in the area because they can tolerate the plant's toxin and may even eat it.
Neal says that through breeding, some crops have lost their ability to generate this chemical. "Modern varieties of cereals such as corn, wheat, barley, etc., now produce widely varying amounts of the benzoxazinones we studied," he writes. "Some produce quite a lot, others produce none." Neal hopes this research has shown why BX production is a helpful trait for plants to have.
Today's breeders, better informed about what goes on beneath the soil than their predecessors, may want to create new crop varieties that can once again make their own toxins. Plants that generate BX molecules can inhibit pests and diseases--and call friendly bacteria to their aid. We might be able to use fewer pesticides and fertilizers if we let our crops' bacterial helpers help us, too.
Neal, A., Ahmad, S., Gordon-Weeks, R., & Ton, J. (2012). Benzoxazinoids in Root Exudates of Maize Attract Pseudomonas putida to the Rhizosphere PLoS ONE, 7 (4) DOI: 10.1371/journal.pone.0035498
Image: Noël Zia Lee/Flickr
... Read more »
Neal, A., Ahmad, S., Gordon-Weeks, R., & Ton, J. (2012) Benzoxazinoids in Root Exudates of Maize Attract Pseudomonas putida to the Rhizosphere. PLoS ONE, 7(4). DOI: 10.1371/journal.pone.0035498
- April 26, 2012
- 10:43 PM
- 682 views
Phthalates–why you should care about these plastic additives
by Cath in Basal Science (BS) Clarified
Aside from cost, aesthetics, and functionality, materials selection is now a topic priority for many consumers when they make a purchase. Consumers are becoming more aware of their choices for sustainable and reusable materials—even the potential health risks/toxicity associated with materials. This is especially true for products containing plastics, particularly the additives used to make [...]... Read more »
Saravanabhavan, G., & Murray, J. (2012) Human Biological Monitoring of Diisononyl Phthalate and Diisodecyl Phthalate: A Review. Journal of Environmental and Public Health, 1-11. DOI: 10.1155/2012/810501
RAHMAN, M., & BRAZEL, C. (2004) The plasticizer market: an assessment of traditional plasticizers and research trends to meet new challenges. Progress in Polymer Science, 29(12), 1223-1248. DOI: 10.1016/j.progpolymsci.2004.10.001
- April 23, 2012
- 05:04 PM
- 363 views
Will Tamiflu save the world from the avian flu?
by Clay Clark in Biochem Blogs
No one wants to catch the flu! At the very least, it will put you out of commission for a week, and it can also cause life-threatening infections – pneumonia is the most common, although other bacterial diseases like … Continue reading →... Read more »
Monto, A., McKimm-Breschkin, J., Macken, C., Hampson, A., Hay, A., Klimov, A., Tashiro, M., Webster, R., Aymard, M., Hayden, F.... (2006) Detection of Influenza Viruses Resistant to Neuraminidase Inhibitors in Global Surveillance during the First 3 Years of Their Use. Antimicrobial Agents and Chemotherapy, 50(7), 2395-2402. DOI: 10.1128/AAC.01339-05
Yen, H., Herlocher, L., Hoffmann, E., Matrosovich, M., Monto, A., Webster, R., & Govorkova, E. (2005) Neuraminidase Inhibitor-Resistant Influenza Viruses May Differ Substantially in Fitness and Transmissibility. Antimicrobial Agents and Chemotherapy, 49(10), 4075-4084. DOI: 10.1128/AAC.49.10.4075-4084.2005
Hurt, A., Holien, J., & Barr, I. (2009) In Vitro Generation of Neuraminidase Inhibitor Resistance in A(H5N1) Influenza Viruses. Antimicrobial Agents and Chemotherapy, 53(10), 4433-4440. DOI: 10.1128/AAC.00334-09
Yen, H., Hoffmann, E., Taylor, G., Scholtissek, C., Monto, A., Webster, R., & Govorkova, E. (2006) Importance of Neuraminidase Active-Site Residues to the Neuraminidase Inhibitor Resistance of Influenza Viruses. Journal of Virology, 80(17), 8787-8795. DOI: 10.1128/jvi.00477-06
- April 20, 2012
- 03:12 PM
- 653 views
Newsworthy: Banned antibiotics found in feather meal at Johns Hopkins - How did they get there, and why does your press release contain different conclusions?
by Austin Bouck in Animal Science Review
An article recently published in Environmental Science and Technology details a study conducted at Johns Hopkins where when examining samples of commercially available feather meal (used as a protein supplement feed or fertilizer) they found trace amounts of fluoroquinolones, a class of antibiotics that have been banned for use in animal feed for 6 years. This is an interesting find, and definitely warrants further research before any broad sweeping conclusions can be made. You know...unless you publish a press release condemning the entire industry for breaking the law and trying to kill us all (question, if all the chicken consumers are dead, how does that lead to higher profits?)...... Read more »
D.C. Love, R.U. Halden, M.F. Davis, & K.E. Nachman. (2012) Feather Meal: A Previously Unrecognized Route for Reentry into the Food Supply of Multiple Pharmaceuticals and Personal Care Products (PPCPs). Environmental Science and Technology, 3795-3802. info:/
Kolpin, D., Furlong, E., Meyer, M., Thurman, E., Zaugg, S., Barber, L., & Buxton, H. (2002) Pharmaceuticals, Hormones, and Other Organic Wastewater Contaminants in U.S. Streams, 1999−2000: A National Reconnaissance. Environmental Science , 36(6), 1202-1211. DOI: 10.1021/es011055j
- April 17, 2012
- 02:47 PM
- 630 views
Human Dung Wins Interspecies Taste Test
by Elizabeth Preston in Inkfish
A panel of experts in Nebraska has declared human dung more appealing than that of several other species. These experts didn't so much announce their decision as fall headfirst into baited poop traps while looking for a meal. Still, you won't find a more discerning group of judges than nine thousand dung beetles.
The various species of dung beetle that live together in the Great Plains region have evolved to consume, and share peacefully, its turd piles.* Some species are specialists, preferring one animal's feces to any others. Others will eat anything that falls their way. Two entomologists--Sean Whipple at the University of Nebraska, Lincoln, and W. Wyatt Hoback at the University of Nebraska, Kearney--set out to mess with the balance between these dung beetle species.
The researchers set traps all over a large organic cattle ranch. Each trap consisted of a large bucket sunken into the ground with a pile of dung at the bottom. The bait came from 11 different species that included carnivores, herbivores, and omnivores. Some of these dung flavors were ones the beetles might encounter regularly: bison, moose, cougar. Others were "exotic," from animals that don't normally leave their excrement around Nebraska: zebra, lion, human.
(The animal feces came fresh from a local zoo. As for the human specimens? "I will say this much," Sean Whipple said when I asked. "It is difficult to find volunteers for a study such as this.")
Human and chimpanzee feces were the clear winners of the popularity contest. Almost 9,100 dung beetles stumbled into the authors' traps, belonging to 15 different species. The beetles in the human and chimp dung buckets far outnumbered any of the rest.
Different beetle species preferred different types of dung, which explains how they can all share resources normally. But overall, omnivores were a favorite. Pig dung, while not as wildly popular as human or chimpanzee, still attracted a lot of beetles.
Whipple says the scent of omnivore dung is especially alluring. "Previous research has shown that the dung of omnivores is generally more attractive than that of herbivores, likely as a result of odor," he wrote in an email.
Incidentally, if the dung beetles had gotten a chance to eat all that sweet-smelling human dung, it would have been a good choice nutritionally. Chemical analysis showed that the human dung had the highest nitrogen content, a measure of "dung quality," Whipple says.
Herbivore dung wasn't only less popular than omnivore dung. It was also beaten out by carnivore dung. And the most widely ignored droppings came from bison--a species that local dung beetles evolved alongside, and that would have provided much of their diet just a century and a half ago.
Like five-year-olds who are bored with their green beans and would like some dessert already, please, most dung beetle species in this study were eager to switch from their usual plant-based poops to something new and exciting. They're not likely to start encountering a lot of human or chimpanzee feces on their Nebraska ranch. But a non-native animal that's introduced to an area where dung beetles live (and they live all over the world) could upset the balance between its native inhabitants. Beetles might start competing for the exotic food source, for example, or ignoring piles of poop they would ordinarily clean up.
If you're wondering what makes our own species' dung so appealing, the authors say diet doesn't seem to be a factor. Among the zoo animals whose dung they used, all the carnivores were fed the same diet, and so were the herbivores. But the dung beetles preferred some carnivore or herbivore dung to others, suggesting there's more to poop flavor than the food it started out as.
Though the human subjects may have eaten different diets, their specimens were "thoroughly mixed to ensure homogeneity," Whipple says. Now that's appetizing.
Whipple, S., & Hoback, W. (2012). A Comparison of Dung Beetle (Coleoptera: Scarabaeidae) Attraction to Native and Exotic Mammal Dung Environmental Entomology, 41 (2), 238-244 DOI: 10.1603/EN11285
Image: icadrews/Flickr
*Yes, I realize that three out of the last four posts here have involved poop (hyena, penguin, and that eaten by dung beetles). Apparently I'm in a dung rut. At least it's not a dung bucket.
... Read more »
Whipple, S., & Hoback, W. (2012) A Comparison of Dung Beetle (Coleoptera: Scarabaeidae) Attraction to Native and Exotic Mammal Dung. Environmental Entomology, 41(2), 238-244. DOI: 10.1603/EN11285
- April 13, 2012
- 01:39 AM
- 856 views
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