You’re sat at your desk, reading a journal article. You see a graph that looks like this:
the first thing that comes to mind? WHAT ON EARTH DOES IT MEAN?!
At this point many people will skip the methods section of their article and head straight to the discussion- But these graphs and techniques aren’t so scary once you understand the science behind them.
What is ITC used for?
Isothermal Titration Calorimetry, or ITC, measures a very basic interaction- how does one thing bind to another? Imagine you have a protein, and want to measure how well it binds to its substrate. ITC allows you in a single experiment to gain a huge amount of information. ... Read more »
Rajarathnam K, & Rösgen J. (2014) Isothermal titration calorimetry of membrane proteins - Progress and challenges. Biochimica et biophysica acta, 1838(1), 69-77. PMID: 23747362
Ghai R, Falconer RJ, & Collins BM. (2012) Applications of isothermal titration calorimetry in pure and applied research--survey of the literature from 2010. Journal of molecular recognition : JMR, 25(1), 32-52. PMID: 22213449
Jing M, & Bowser MT. (2011) Methods for measuring aptamer-protein equilibria: a review. Analytica chimica acta, 686(1-2), 9-18. PMID: 21237304
The amount of cow dung plopped into the world every day is almost unthinkable, but Tomas Roslin is thinking about it."We can regard it as either an immense waste problem or an enormous ecosystem service," he says. He means that what starts out as a turd in a field turns into a wealth of nutrients for plants—assuming it can make its way below ground. So understanding how dung gets broken down can help us ensure an ecosystem is running smoothly. To address such a messy, large-scale question, Roslin recruited a big mess of young volunteers.Roslin is an ecologist at the University of Helsinki, and he found his citizen scientists through the Finnish 4H Federation. In all, 79 volunteers signed up, ranging from 10 to 27 years old (most were under 20). They agreed to sample 82 cattle farms that spanned Finland nearly from end to end.From each farm, the volunteers collected 20 liters of "fresh dung" in late spring or early summer. They divided their dung into 15 pats (using an official dung measurer that had been provided to them) and put the pats back onto cow pastures. Some of the manmade cow patties were left open to the air, while others were covered with cages of coarse or fine mesh to keep out certain insects.Roslin and his coauthors were especially interested in large dung beetles called dor beetles. In some cases they prevented dor beetles from burying the dung (as the beetles enjoy doing) by putting mesh underneath the patty, and in other cases a full wire cage kept dor beetles from getting into the dung at all. Smaller insects were kept out with finer mesh cages, and earthworms were blocked from the dung by putting a layer of cloth underneath it.Volunteers weighed the dung piles periodically over the next two months to see how much was left of them. As the summer went on, the patties dried out and were broken down by whatever insects could reach them, as well as by microbes that couldn't be kept out. (Only 73 farms were left in the final analysis, since a few sites were lost to "lack of sufficient commitment by the volunteer" and others to "cows trampling on the experimental pats.")The results showed that 13 percent of dung decomposition is done by insects. Microbes and rainstorms take care of the rest. The farther north you are in Finland, the more slowly your dung will disappear, perhaps because cooler weather slows bacterial growth.Each added barrier around the dung made it decompose a little more slowly, showing that all the groups of insects were helping to break it down. But the biggest contribution came from dor beetles. This was in line with what previous, small-scale research had shown—but his network of citizen scientists let Roslin confirm that dor beetles are equally important all across Finland.It matters because "our dor beetles are not doing that well," Roslin says. Out of three species in Finland, one has gone regionally extinct and another is on the decline. Knowing how important the dor beetle is to healthy farms gives Finland more reason to keep it alive.Additionally, Roslin says, "just figuring out the basics of how the system works" is critical. In the United States, most cattle waste goes into manure lagoons, where beetles or ecosystems don't really enter the equation. But when waste is returned to the soil, Roslin says, "we need to understand who is behind it." He points out that cattle were initially brought to Northern Europe in part to fertilize the fields."We love citizen science," Roslin declares. He and his lab have previously organized citizen investigations of dung beetles and gall-wasps, and they're now working with volunteers to study the hermit beetle Osmoderma barnabita. "The volunteers involved have come to appreciate completely new aspects of their own environment," he says.There are some drawback to the approach, of course —experiments have to be kept simple, and sometimes a volunteer loses interest or flattens a cow patty. But by pairing small-scale lab research with large citizen projects, Roslin says, "we have managed to collect scientific data sets unachievable by relying on professional biologists."Riikka Kaartinen, Bess Hardwick, & Tomas Roslin (2013). Using citizen scientists to measure an ecosystem service nationwide. Ecology DOI: 10.1890/12-1165.1Images: top Timo Marttila/Satakunnan Kansa; bottom Riikka Kaartinen.
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Riikka Kaartinen, Bess Hardwick, & Tomas Roslin. (2013) Using citizen scientists to measure an ecosystem service nationwide. Ecology. DOI: 10.1890/12-1165.1
Researchers at MIT have found that genetically modified viruses can help to produce better cathodes for Li-air batteries.... Read more »
Dahyun Oh, Jifa Qi, Yi-Chun Lu, Yong Zhang, Yang Shao-Horn, Angela M. Belcher. (2013) Biologically enhanced cathode design for improved capacity and cycle life for lithium-oxygen batteries. Nature Communications, 2756. DOI: 10.1038/ncomms3756
Lignin, a complex polymer of aromatic alcohols, is an integral part of the secondary cell walls of plants and some algae. By its nature, lignin inhibits access to cellulose, reducing accessibility of plant sugars for biofuel production. Now, researchers at the Joint BioEnergy Institute (JBEI) have characterized the enzymatic activity of a rain forest microbe that breaks down lignin essentially by breathing it.... Read more »
Khudyakov J.I., D'haeseleer P., Borglin S.E., Deangelis K.M., Woo H., Lindquist E.A., Hazen T.C., Simmons B.A., & Thelen M.P. (2012) Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus. Proceedings of the National Academy of Sciences of the United States of America, 109(32), 73-82. PMID: 22586090
This week we would like to introduce you to the work of Dr Fred Menko, a consultant clinical geneticist at the Department of Clinical Genetics at VU University Medical Center in Amsterdam, the Netherlands. Dr Menko is also editor-in-chief of … Continue reading →... Read more »
Menko FH, van Steensel MA, Giraud S, Friis-Hansen L, Richard S, Ungari S, Nordenskjöld M, Hansen TV, Solly J, Maher ER.... (2009) Birt-Hogg-Dubé syndrome: diagnosis and management. The lancet oncology, 10(12), 1199-206. PMID: 19959076
With all the recent-ish chatter about dietary quality for those on the spectrum (see here), coupled with a hint of something like the mechanisms of malabsorption being linked to specific cases (see here), the potential issue of 'nutritional deficiency' in relation to autism represents a pretty constant research topic these days. Iodine @ WikipediaI've talked before about research defining a deficiency in certain vitamins and minerals in relation to cases of autism on this blog; be it in relation to the vitamin-of-the-hour, vitamin D (see here) or vitamin B12 (see here) or something like zinc (see here).The picture is a complicated one and not necessarily a universal one in terms of prevalence across the autism spectrum nor being solely due to poor eating patterns. But given the increasing understanding of the importance of nutrition to mental and physical health and wellbeing, one would expect quite a lot more to be said on this topic over the coming years.The paper by Rasha Hamza and colleagues* detailing findings in relation to iodine in cases of autism and other family members adds to the interest. Based on a relatively small participant group, the authors reported that: "Of autistic children and their mothers, 54% and 58%, respectively, were iodine deficient". This contrasted with none of the 50 control group children or mothers presenting with iodine deficiency (ID).Before progressing through the Hamza study further, I might point out that the British Dietetic Association (BDA) carries quite a detailed information sheet about iodine (see here) as does the US Office of Dietary Supplements (see here). Iodine is sourced mainly from food, and as you'll see from the links, outside of seafood and shellfish, milk and dairy products are one of the biggest dietary sources of iodine. Casein-free diet anyone?A primary use for iodine in the body is for the production of thyroid hormones. Without going over previous ground, there is some research history when it comes to thyroid hormone and autism as per discussions on the measurement of thyroid hormone levels in autism (see here) and more recent research talking about maternal thyroid levels and offspring 'autistic symptoms' (see here). Dare I even mention the possible environmental variables which have been associated with thyroid function too?Back to the Hamza paper. As well as measuring levels of urinary iodine (UI) - which apparently is quite a good way of measuring iodine intake** - the researchers also scored child participants with autism using the CARS so as to have some measure of the extent of their presented symptoms. That and examining levels of some of the various thyroid hormones, they were able to arrive at a few other preliminary, but potentially important conclusions."Childhood Autism Rating Scale (CARS) score correlated negatively with UI (r = -0.94, p <0.001)". I'm no statistician (add it to the long list of things for which I'm more amateur than professional) but a correlation (r) of -0.94 seems pretty good to me bearing in mind that (1) or (-1) indicates a perfect positive and negative correlation respectively. This data translates as a higher CARS score being generally associated with lower levels of urinary iodine. Further, when looking maternal and child UI output and other thyroid hormones, the authors reported some interesting positive correlations between child and mother values obtained.It would be easy to say that the Hamza study has some methodological issues. Outside of the quite small participant group, and their exclusive focus on Egyptian families, this was very much a snapshot study in terms of looking at participants at a particular point in time. CARS, like many other autism screening and assessment instruments, is still quite a subjective measure also and who's to say that if this study was repeated a week or a month later, whether similar results would be had with the same group. And then there is that milk-free dietary issue to also consider...But with all that in mind, this remains an interesting study. I note that other independent groups have also reported issues with iodine being related to cases of autism as per the findings by Blaurock-Busch and colleagues*** (open-access here) and a familiar name to this blog (see here) Jim Adams and his paper***. I was also drawn to an interesting communication on the topic of iodine deficiency as being related to autism from Sullivan & Maberly**** as food for thought, bearing in mind I'm less inclined to believe there is just one factor linked to the increasing numbers of cases of autism being reported.So, perhaps on that collected basis, there is a little more research to do when it comes to iodine and autism? Oh, and with my blogging caveat about no medical or clinical advice given or intended, please take some proper medical advice if you're thinking about supplementing with iodine (see here).To close, The Life of Riley by the Lightning Seeds (not to be confused with the life of Whiteley).----------* Hamza RT. et al. Iodine Deficiency in Egyptian Autistic Children and Their Mothers: Relation to Disease Severity. Arch Med Res. 2013 Oct 9. pii: S0188-4409(13)00222-1. doi: 10.1016/j.arcmed.2013.09.012.** Delange F. et al. Determining median urinary iodine concentration that indicates adequate iodine intake at population level. Bulletin of the World Health Organization. 2002; 80: 633-636.*** Blaurock-Busch E. et al. Toxic Metals and Essential Elements in Hair and Severity of Symptoms among Children with Autism. Maedica (Buchar). 2012 Jan;7(1):38-48.**** Adams JB. et al. Analyses of toxic metals and essential minerals in the hair of Arizona children with autism and associated conditions, and their mothers. Biol Trace Elem Res. 2006 Jun;110(3):193-209.***** Sullivan KM. & Maberly GF. Iodine deficiency as a cause of autism? BMJ. Rapid Response. 13 October 2004.----------... Read more »
Hamza RT, Hewedi DH, & Sallam MT. (2013) Iodine Deficiency in Egyptian Autistic Children and Their Mothers: Relation to Disease Severity. Archives of medical research. PMID: 24120386
Animals’ scent posts may be equally as short, relatively speaking, yet they convey an encyclopedia of information about the animals that left them.
In the current issue of the Proceedings of the National Academy of Sciences, a Michigan State University researcher shows that the detailed scent posts of hyenas (Figure 1) are, in part, products of symbiotic bacteria, microbes that have a mutually beneficial relationship with their hosts.
“When hyenas leave paste deposits on grass, the sour-smelling signals relay reams of information for other animals to read,” said Kevin Theis, the paper’s lead author and MSU postdoctoral researcher. ... It’s like a bulletin board of who’s around and how they’re doing.”
...A spotted hyena scent marking. (courtesy of Michigan State University)
Interestingly, it is the bacteria in pastes – more diverse than scientists had imagined – that appear to be doing the yeoman’s job of sending these messages.
“Scent posts are bulletin boards, pastes are business cards, and bacteria are the ink, shaped into letters and words that provide information about the paster to the boards’ visitors,” Theis said. “Without the ink, there is potentially just a board of blank uninformative cards.”
Theis, who co-authored the study with Kay Holekamp, MSU zoologist, studied multiple groups of male and female spotted hyenas and striped hyenas in Kenya.
By using molecular surveys, they were afforded unprecedented views of the diversity of microbes inhabiting mammals’ scent glands. The researchers were able to show that the diversity of odor-producing bacteria in spotted hyena scent glands is much greater than historical studies of mammals had suggested (Figure 2).
...Variation in the bacterial communities and volatile fatty acid (VFA) profiles of the pastes of immigrant male, lactating female, and pregnant female spotted hyenas in the Talek clan. (A and C) A plot showing variation in the structure of paste bacterial communities among Talek clan members. (B) A heat map of the mean abundances of the prominent bacteria in the pastes of Talek hyenas. (D) A heat map of the mean percent abundances of VFAs in the pastes of Talek hyenas.
...The diversity, however, still consistently varies between hyena species, and with sex and reproductive state among spotted hyenas, Theis added. Importantly, the variation in scent gland bacterial communities was strongly correlated with variation in the glands’ odor profiles, suggesting that bacteria were responsible for the variation in scent.
For the current paper, Theis’ team was the first to combine microbial surveys and complementary odor data from wild animals. The studies’ findings leave Theis anxious to return to the field.
“Now I just need to get back into the field to test new predictions generated by this study,” Theis said. “The next phase of this research will be to manipulate the bacterial communities in hyenas’ scent glands to test if their odors change in predictable ways.”
Source: Modified from materials provided by Michigan State University.
...Theis KR, Venkataraman A, Dycus JA, Koonter KD, Schmitt-Matzen EN, Wagner AP, Holekamp KE, & Schmidt TM (2013). Symbiotic bacteria appear to mediate hyena social odors. Proceedings of the National Academy of Sciences of the United States of America PMID: 24218592
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Theis KR, Venkataraman A, Dycus JA, Koonter KD, Schmitt-Matzen EN, Wagner AP, Holekamp KE, & Schmidt TM. (2013) Symbiotic bacteria appear to mediate hyena social odors. Proceedings of the National Academy of Sciences of the United States of America. PMID: 24218592
The smallest hemichordatan in the world Discovered the smallest hemichordatan: it has traits that, in other species, are found in juveniles and it reproduces in a peculiar way... Read more »
Worsaae K., Sterrer W., Kaul-Strehlow S., Hay-Schmidt A. e Giribet G. (2012) An anatomical description of a miniaturized acron worm (Hemichordata, Enteropneusta) with asexual reproduction by paratomy. PLoS ONE. DOI: 0.1371/journal.pone.0048529
The first post on Expiscor - a few blog within the SciLogs network. This post introduces three species of arthropods, each with interesting biology.... Read more »
Cushing, P. (1997) Myrmecomorphy and myrmecophily in spiders: a review. The Florida Entomologist, 165-193. DOI: 10.2307/3495552
Cushing, P. (2012) Spider-Ant Associations: An Updated Review of Myrmecomorphy, Myrmecophily, and Myrmecophagy in Spiders. Pysche. DOI: 10.1155/2012/151989
Dik, B. (2006) Erosive Stomatitis in a white pelican (Pelecanus onocrotalus) caused by Piagetiella titan (Mallophaga: Menoponidae). Journal of Veterinary Medicine, Series B. DOI: 10.1111/j.1439-0450.2006.00927.x
A method to look at chromosome structure in single cells reveals what the X chromosomes looks like and how it varies from cell to cell.... Read more »
Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, Dean W, Laue ED, Tanay A, & Fraser P. (2013) Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature, 502(7469), 59-64. PMID: 24067610
Is the ability to empathize uniquely human? This question has long been pondered by philosophers and animal behaviorists alike. Empathy depends in part on the ability to recognize the wants and hopes of others. A new study by researchers at the University of Cambridge suggests that we may not be alone with this ability. A male Eurasian jay feeds his female mate. Photo provided by Ljerka Ostojić.Ljerka Ostojić, Rachael Shaw, Lucy Cheke, and Nicky Clayton conducted a series of studies on Eurasian jays to explore whether male jays could perceive changes in what their female partners desired. Eurasian jays are a good species with which to explore this phenomenon because males routinely provide food to their female mates as a part of their courtship. The researchers wanted to know if males would adjust what food items males offered their mates depending on what food type the females wanted more. In order to make a female prefer one food type over another, the researchers fed each female one of two food types (wax moth larvae and mealworm larvae) until they were full. But being full of one type of food doesn’t mean you can’t find room for desert, right? So when the researchers then offered the females access to both wax moth larvae and mealworm larvae, those that had previously eaten wax moth larvae now preferred mealworm larvae and those that had previously eaten mealworm larvae now preferred wax moth larvae. But could their male partners tell what they preferred at that moment? In order to test whether male jays were sensitive to their partners’ desires, the researchers fed the females either wax moth larvae or mealworm larvae until they were full. They did this while their male partners watched from behind a transparent screen. They then removed the screen and gave the males 20 opportunities to choose between a single wax moth larvae or mealworm larvae to feed their partner. In this context, males usually chose to share with their mates the food that their partners preferred rather than the food their partners had already been fed! But are the males responding to their mate’s behavior or are they responding to what they saw when the females were eating earlier? This video (provided by Ljerka Ostojić) shows the experimental process in which the male chooses a food type and then shares it with his mate. The researchers repeated the study with an opaque screen so the males could not see their mates while the females gorged on one particular food type. Without the ability to see the mate eating beforehand, males chose both food types equally and did not attend to their mate’s preferences. Because the females still had a preference for the opposite food type but the males were not adjusting for that preference, this means that the males are not responding to their mate’s behavior in this experiment or the previous one. This suggests that if male Eurasian jays see what their mates are eating, then somehow they have the ability to know to give their mate the opposite food type! Whether this process involves the males having an understanding of their mate’s desires or some other mechanism is not fully known. But male Eurasian jays are certainly adjusting what they give their mates according to what she wants. Now if we can only teach human males to do that! Want to know more? Check this out:Ostojić, L., Shaw, R.C., Cheke, L.G., & Clayton, N.S. (2013). Evidence suggesting that desire-state attribution may govern food sharing in Eurasian jays PNAS, 110 (10), 4123-4128 DOI: 10.1073/pnas.1209926110 ... Read more »
Ostojić, L., Shaw, R.C., Cheke, L.G., & Clayton, N.S. (2013) Evidence suggesting that desire-state attribution may govern food sharing in Eurasian jays. PNAS, 110(10), 4123-4128. DOI: 10.1073/pnas.1209926110
Methane hydrates are a potential energy source—only the already known methane hydrate reservoirs in the U.S. are expected to contain 6,700 trillion cubic feet of natural gas—more than the largest conventional natural gas fields. They, however, are also a potential source of global warming if massive amounts of methane were released during an earthquake or by rising ocean temperatures. A pair of methane-eating microbes may play a key role in this process.... Read more »
Glass J.B., Yu H., Steele J.A., Dawson K.S., Sun S., Chourey K., Pan C., Hettich R.L., & Orphan V.J. (2013) Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulfidic marine sediments. Environmental Microbiology. PMID: 24148160
Recently we announced our newest training materials on GenoCAD. The introductory tutorial provides a great foundation for understanding the features that are available and how it could help you in the lab. But for those folks who want to take their design skills further–now you can use the GenoCAD Advanced Topics materials to do so. […]... Read more »
Wilson ML., Hertzberg R., Adam L., & Peccoud J. (2011) A step-by-step introduction to rule-based design of synthetic genetic constructs using GenoCAD. Methods Enzymol. DOI: 10.1016/B978-0-12-385120-8.00008-5
Wilson M. L., Okumoto S., Adam L., & Peccoud J. (2013) Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors. Bioinformatics. DOI: 10.1093/bioinformatics/btt646
In evolutionary theory, a fitness landscape is a map where fitness is a function of either the genotype or the phenotype. The genotype is some description of the genetic make-up of an organism. This can be the DNA or a list of the mutations/alleles, and are discrete variables. ... Read more »
Jasper Franke, Alexander Klözer, J. Arjan G. M. de Visser, & Joachim Krug. (2011) Evolutionary accessibility of mutational pathways. PLoS Computational Biology 7 (8) e1002134 (2011). arXiv: 1103.2479v2
Weissman DB, Desai MM, Fisher DS, & Feldman MW. (2009) The rate at which asexual populations cross fitness valleys. Theoretical population biology, 75(4), 286-300. PMID: 19285994
Østman B, Hintze A, & Adami C. (2012) Impact of epistasis and pleiotropy on evolutionary adaptation. Proceedings. Biological sciences / The Royal Society, 279(1727), 247-56. PMID: 21697174
You can hardly turn on the television or radio these days and not hear a discussion about rising gas prices. When most people set out to buy a new car it’s no doubt that fuel efficiency is one of the … Continue reading →... Read more »
Doebbe Anja, Rupprecht Jens, Beckmann Julia, Mussgnug Jan H., Hallmann Armin, Hankamer Ben, & Kruse Olaf. (2007) Functional integration of the HUP1 hexose symporter gene into the genome of C. reinhardtii: Impacts on biological H2 production. Journal of Biotechnology, 131(1), 27-33. DOI: 10.1016/j.jbiotec.2007.05.017
Kruse O. (2005) Improved Photobiological H2 Production in Engineered Green Algal Cells. Journal of Biological Chemistry, 280(40), 34170-34177. DOI: 10.1074/jbc.M503840200
Hankamer Ben, Lehr Florian, Rupprecht Jens, Mussgnug Jan H., Posten Clemens, & Kruse Olaf. (2007) Photosynthetic biomass and H production by green algae: from bioengineering to bioreactor scale-up . Physiologia Plantarum, 131(1), 10-21. DOI: 10.1111/j.1399-3054.2007.00924.x
We are taught and we teach that DNA codes fro the amino acid sequence of specific proteins. But the truth is that often times, the sequence of the mRNA ends of different than that coded by the DNA. In addition to mRNA processing, there is also RNA editing, which can add, subtract, or change the base sequence in a transcript.
New research is showing just how extensive RNA editing is and the powerful role it plays in cellular expression. A new algorithm has been introduced to better predict RNA editing sites in plants, for C to U as well as U to C edits.
Inosine, a nonstandard nucleoside, has functions outside nucleic acids, as new research is showing that in rodent models of hypoxia, there is an increase in extracellular accumulation of inosine and adenosine, presumably working as antioxidants.
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Paz-Yaacov N, Levanon EY, Nevo E, Kinar Y, Harmelin A, Jacob-Hirsch J, Amariglio N, Eisenberg E, & Rechavi G. (2010) Adenosine-to-inosine RNA editing shapes transcriptome diversity in primates. Proceedings of the National Academy of Sciences of the United States of America, 107(27), 12174-9. PMID: 20566853
Takahashi T, Otsuguro K, Ohta T, & Ito S. (2010) Adenosine and inosine release during hypoxia in the isolated spinal cord of neonatal rats. British journal of pharmacology, 161(8), 1806-16. PMID: 20735412
Lenz H, & Knoop V. (2013) PREPACT 2.0: Predicting C-to-U and U-to-C RNA Editing in Organelle Genome Sequences with Multiple References and Curated RNA Editing Annotation. Bioinformatics and biology insights, 1-19. PMID: 23362369
Poulsen HE, Nadal LL, Broedbaek K, Nielsen PE, & Weimann A. (2013) Detection and interpretation of 8-oxodG and 8-oxoGua in urine, plasma and cerebrospinal fluid. Biochimica et biophysica acta. PMID: 23791936
Wang P, Fisher D, Rao A, & Giese RW. (2012) Nontargeted nucleotide analysis based on benzoylhistamine labeling-MALDI-TOF/TOF-MS: discovery of putative 6-oxo-thymine in DNA. Analytical chemistry, 84(8), 3811-9. PMID: 22409256
The southern beeches used to classified in one genus (Nothofagus) and one family (Nothofagaceae). A new paper argues convincingly that the genus should be divided into four genera.... Read more »
Heenan, P.B.; Smissen, R.D. (2013) Revised circumscription of Nothofagus and recognition of the segregate genera Fuscospora, Lophozonia, and Trisyngyne (Nothofagaceae). Phytotaxa. DOI: 10.11646/phytotaxa.146.1.1
Window or aisle? Hamburger or hot dog? Bouquet of flowers or rotting flesh? Not all your preferences are up to you—some have been hammered into your genes by evolution.
If you're an average human, you avoid the smell of decay. It signals unsafe food and the threat of infection or disease. Other animals run toward the stench of a stale carcass, maybe because they're flies and it signals a place to lay their eggs.
Whether they love it or hate it, animals identify the scent of rot from two signature molecules. German doctor Ludwig Brieger discovered these molecules in the late 1900s; in English, they're rather cutely named "cadaverine" and "putrescine." Bacteria create the two culprits by breaking down down amino acids in animal bodies. Not solely the sign of a rotting carcass, cadaverine and putrescine also show up in urine and bad breath.
Despite the importance of these smells (or avoiding these smells) in animals' lives, no one had found receptors for these molecules—that is, the locks to which the molecules are keys. Scent receptors are attached to one end of a neuron inside the nose (or whichever body part an animal smells with); when a certain chemical wafts up the nose and latches onto the receptor, a signal travels along the neuron to the brain at the other end. Researchers at the University of Cologne in Germany and Harvard University think they've found one of those receptors for rot.
The authors, led by the University of Cologne's Ashiq Hussain, studied zebrafish, which are commonly used to model the sense of smell in vertebrates. First they checked to make sure zebrafish respond to the smell of decay. When they put putrescine and cadaverine into a tank, zebrafish swam to the other end, showing they feel the same way we do about these smells. When the authors plugged the zebrafishes' little nostrils with glue, the fish were no longer bothered by the odor.
The researchers searched for a receptor in a family of proteins called TAARs (trace amine-associated receptors). Related receptors in rodents are thought to detect other unpleasant odors that come from living things. Zebrafish make 112 different kinds of these receptors, but the molecules that attach to them hadn't been found yet.
After testing 93 smelly chemicals on representative zebrafish TAARs, the authors found a match: cadaverine turns on a receptor called TAAR13c. But could the receptor detect cadaverine in real life, and not only when it was dripped on in purified form by a scientist? To test it, the researchers used an extract of dead fish. When exposed to liquid made from a recently deceased zebrafish, the receptors didn't respond. Liquid from a week-old, rotten fish carcass, though, easily activated the receptor—even when diluted to 1 part in 1,000.
Finding a receptor for cadaverine means scientists have decoded one part of the brain's system for responding to awful smells. This could lead to a better understanding of how animals process all kinds of odors, whether they enjoy them or not.
Image: by Bill Gracey (via Flickr)
Ashiq Hussain, Luis R. Saraiva, David M. Ferrero, Gaurav Ahuja, Venkatesh S. Krishna, Stephen D. Liberles, & Sigrun I. Korsching (2013). High-affinity olfactory receptor for the death-associated odor cadaverine. PNAS DOI: 10.1073/pnas.1318596110
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Ashiq Hussain, Luis R. Saraiva, David M. Ferrero, Gaurav Ahuja, Venkatesh S. Krishna, Stephen D. Liberles, & Sigrun I. Korsching. (2013) High-affinity olfactory receptor for the death-associated odor cadaverine. PNAS. DOI: 10.1073/pnas.1318596110
Scientists, for the first time, found the neural mechanism of sensing high-speed motion in faint light in the visual cortex of the brain.
Neurons in the visual cortex:
A group of neurons in the primary visual cortex (V1) of the brain are luminance-contrast cells that are responsive to a uniform patch of luminance and they prefer low spatial frequencies, high temporal frequencies, high motion speeds, and they respond strongly to luminance decrements.
These luminance-contrast cells are different from many other cells in primary visual cortex, which are either “luminance-only” - cells modulated by luminance only - and “contrast-only” - cells modulated by contrast only.
In the present study, researchers worked on the responses of cat V1 cells to the changing luminance and compared the speed preferences of luminance-contrast cells and contrast cells. They found that luminance-sensitive cells in cat V1 are important in motion processing under dim conditions of light as they prefer higher motion speeds than the contrast cells and a large number of these cells give strong responses to the decreasing brightness of light as compared to the increasing brightness of light.
Researchers are of opinion that these cells would be of particular help to the animals such as cats and other animals moving in low visibility environment such as in dark night and fog.
“We are further investigating the roles of these cells in the visual presentation of objects in the early visual cortex,” Yi Wang told SayPeople.com. Yi Wang is corresponding author of the paper.
“Using artificial stimuli with carefully designed parameters is the most effective method for in advancing our understanding of visual functions,” Researchers wrote in the paper.
This research can help in designing artificial vision, as Yi Wang told me.
Ran Li, Yi Wang (2013). Neural Mechanism for Sensing Fast Motion in Dim Light Scientific Reports DOI: 10.1038/srep03159... Read more »
Ran Li, Yi Wang. (2013) Neural Mechanism for Sensing Fast Motion in Dim Light. Scientific Reports. DOI: 10.1038/srep03159
The title of this post should also have included the word 'glutathione' too based on the results reported by Richard Frye and colleagues* (open-access) describing behavioural and biochemical data from a 3-month open trial of methylcobalamin, a vitamin B12 'vitamer', and folinic acid with a group of children diagnosed with an autism spectrum disorder (ASD).Dr Frye and his various research are no stranger to this blog; ranging from mitochondrial dysfunction linked to cases of autism (see here), through to tetrahydrobiopterin (BH4) and autism (see here), and folate receptor autoantibodies and autism (see here). Indeed that last link on folate receptor autoantibodies brings into view a potential reason why folinic acid was included in their recent study. That and the inclusion of Jill James on the authorship list and her previous studies looking at combined methylcobalamin and folinic acid supplementation for autism** (open-access) discussed as part of a previous post (see here).The crux of this study was the suggestion that in the great and complex pathway which links the recycling of homocysteine (the big 'H') and the folate cycle, there is potentially enough going on in cases of autism to interfere with (a) the process of methylation (see here) and (b) that most useful of compounds, glutathione (see here), well reduced glutathione anyway. I'm also inclined to point readers the way of the very thorough analysis of glutathione and autism produced by Main and colleagues*** (open-access) a while back (see here) just in case you think I'm talking biochemical mumbo-jumbo.Readers might already have seen mention of the words 'open trial' at the top of this post. This indicating that the latest study from Frye and colleagues was a case of following 37 children who fitted the entrance criteria - including "abnormal methylation capacity (SAM/SAH < 3.0) and glutathione redox metabolism (GSH/GSSG < 6.0)" - and seeing how they went over the course of a "sterile subcutaneous injection of methylcobalamin in the fatty tissue of the buttocks" every 3 days combined with oral delivery of folinic acid twice daily mixed with food. For those wincing or furrowing their brows about those injections of methylcobalamin with children with autism, I'll just say that the issue of drug delivery has been talked about in a previous post and this study was passed through an ethics committee "at the University of Arkansas for Medical Sciences".The results are interesting. Quite a few behavioural changes were documented according to use of the VABS. This bearing in mind that (a) there was no control or placebo group and (b) VABS is a parent-report schedule which in this case merely looked at unblinded pre- and post-intervention scores. Nonetheless, the intervention resulted in "significant increases in VABS scores for all domains, including daily living, social, and communication skills, with an average effect size of 0.59, which is in the medium-to-large range." The authors even went as far to say that the VABS changes indicated something like an average 7.7 month gain over the 3 month period of study.All well and good with that open-trial caveat well and truly in place. It is however the details regarding the biochemical measure of glutathione measurement that I was more interested in. Indeed, if I had to suggest one improvement to this paper, it would have been to include a simple table showing glutathione measures - GSH/GSSG - at baseline compared with at 3 months. Instead, the glutathione results are all bundled up with the VABS results as per the example of figure 3 showing: "the change in the glutathione redox status (reduced-to-oxidized glutathione ratio) and change in subscales of the Vineland Adaptive Behavior Scale (VABS) subscales".What I did manage to glean is that: "the overall glutathione redox status was not related to VABS subscales, indicating that overall development did not appear to be related to overall glutathione redox status". Fair enough, a possible selection issue based on the group eventually included for study. It was the change in glutathione redox status after intervention which seemed to tie into the VABS results reported. Still, I would have liked to have the biochemical data presented as a stand-alone table.I'm trying not to be overly-critical of this paper and results contained within. As with many other researchers, I'm guilty of the odd open-trial forming part of my CV (see here). Whilst useful as a starting point for looking at a particular intervention or trying to get others to do a more methodologically-sound study, one has to be quite cautious of such work and the myriad of biases that they contain.I do get the impression that outside of just a more methodologically-sound trial, a lot more questions need to be asked about this intervention regime before it can be considered as something more mainstream. Outside of the 2 children who dropped out of the study because "parents were uncomfortable giving the methylcobalamin injections", there's also a question of what such an intervention is actually doing. I note the authors when discussing the previous James trial**, are quoted as saying: "The fact that the treatment [methylcobalamin and folinic acid] improved but did not normalize methionine, SAM and glutathione concentrations may reflect ongoing metabolic compensation for incompletely resolved oxidative stress". This may very well be true, but could also indicate that intervention was also working on other biological systems too.That also mention is made of the Hardan trial of N-acetlycysteine (NAC) for autism (see here) and NAC being a direct glutathione precursor, suggests to me that when it comes to glutathione production, the shortest point might be A to B bearing in mind what results have been obtained from direct glutathione supplementation**** (open-access).To close, the Clash have a question for you.... (it's the indecisions which bug me).----------* Frye RE. et al. Effectiveness of Methylcobalamin and Folinic Acid Treatment on Adaptive Behavior in Children with Autistic Disorder Is Related to Glutathione Redox Status. Autism Res Treat. 2013: 609705.** James SJ. et al. Efficacy of methylcobalamin and folinic acid treatment on glutathione redox status in children with autism. Am J Clin Nutr. 2009 January; 89(1): 425–430.*** Main PA. et al. The potential role of the antioxidant and detoxification properties of glutathione in autism spectrum disorders: a systematic review and meta-analysis. Nutr Metab (Lond). 2012 Apr 24;9:35.**** Kern JK. et al. A clinical trial of glutathione supplementation in autism spectrum disorders. Med Sci Monit. 2011 Dec;17(12):CR677-82.----------... Read more »
Richard Frye, Stepan Melnyk, George Fuchs, Tyra Reid, Stefanie Jernigan, Oleksandra Pavliv, Amanda Hubanks, David W. Gaylor, Laura Walters, S. Jill James. (2013) Effectiveness of Methylcobalamin and Folinic Acid Treatment on Adaptive Behavior in Children with Autistic Disorder Is Related to Glutathione Redox Status. Autism Research and Treatment. DOI: 10.1155/2013/609705
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