An episode of the BBC program Horizon on 'Big Data' recently caught my attention. The content was a fascinating insight into how we are living in a data-rich age and how trawling/mining/dredging such data has the ability to advance medicine, predict crime and even make someone a few quid/dollars/euros on the stock market.Gone (data) fishing @ Wikipedia I'm a big believer in big data. In particular how, with the right sources, technology, techniques and people, big data might be able to open up some real insights into many important areas including mental health research* and very possibly autism research with a specific focus on the science of biomarkers to aid things like early diagnosis. Indeed, I'm not the only one talking about this (see here).I've spoken before on this blog about biomarkers for autism and other conditions - the promises, the problems, the future - and how alongside the various autism research banks (genes, brains, etc.) and systems biology chatter, we are just starting to understand the value of those big data resources such as the archived bloodspot samples which so many neonates provide these days.Indeed with the greatest appreciation for pioneers like Robert Guthrie, I offer a post on an interesting paper by Gerald Mizejewski and colleagues** discussing results suggestive of potential candidate biomarkers for autism based on archived bloodspot samples. I should point out that this is not the first time that Dr Mizejewski has talked about the feasability of biomarkers for autism as per this article*** (open-access) as part of quite a distinguished research career it has to be said (see here) with a specific focus on an interesting molecule called alpha-fetoprotein****.The most recent paper is unfortunately not at the time of writing open-access, so I'll just go through a few summary points about the work:This was a retrospective study based on that tantalising resource of archived bloodspot cards which sit in many a hospital basement. Out of a total case group of 200 families with a child with autism, 40 families with children aged between 3-5 years old were initially contacted for participation. This was eventually whittled down to 16 participants (all diagnosed with autism by the same clinician with the same diagnostic manual) for whom archived neonatal bloodspot cards were available. Two age-matched control specimens located immediately before and after the dried bloodspot card in question in the filing system were also chosen.A small 3mm punch of the Guthrie cards was analysed by immunoassay which in this case, probed for 90 potential biomarkers covering everything from neurotrophins to cytokines, immunoglobulins to more direct inflammatory markers (including C-reactive protein).Some fancy statistical modelling was applied to the obtained results - including Bayesian information criterion (BIC) - which eventually resulted in three models of best-fit based on findings from the bloodspots of those who went to be diagnosed with an autism spectrum disorder (ASD). The 'best model' of five compounds included some familiar names to this blog: glutathione-S-transferase (GST), IL-7, IL-5, TNF-beta and something called Lp(a) (lipoprotein a). Most were increased in quantity in the autism samples aside from GST which was decreased.There is a very nice illustration in the paper (Figure 3) showing how the potential connections between the biomarkers identified and some of the more biomedical themes of autism research might fit. So we have methionine metabolism mentioned (see here and here), oxidative stress (see here), gastrointestinal comorbidity (see here) and immune activation (see here) to name a few. It's all very systems biology.The authors caution that their results are preliminary and that although said biomarkers were modelled as being related to autism they "have not been confirmed to be causative with autism".Before I get too carried away with this research, there are a few issues worth mentioning. Yes, the sample size was small in this preliminary communication and indeed very little information is provided about participants outside of just them fulfilling the DSM-IV criteria for autism in terms of things like comorbidity. Also why out of 200 families such a small number of participants were eventually included for study.Indeed there is also an assumption from this study that a biomarker for autism is present in the neonatal phase which for example, might not take into account the issue of behavioural regression that seems to cover quite a percentage of cases.Whilst the identified best-fit biomarkers are of potentially real interest to autism research as per other similar studies (see here), it is the method and resources used in this paper which is the real 'big data' story allied to all those lovely -omics which reign supreme these days. Parents in many countries will be acquainted with that bloodspot taken during the earliest days of infancy to test for various inborn errors of metabolism such as phenylketonuria (PKU). Many people don't however give a second thought to what happens to those bloodspot cards, and how valuable a resource they might constitute. Although not usually in the business of crystal-ball gazing, I would hazard a guess that we are one day going to hear big news about the big data from those archived bloodspot cards; if not with autism in mind, then something else. ----------* Ayers JW. et al. Seasonality in seeking mental health information on Google. Am JPrev Med. April 2013.** Mizejewski GJ. et al. Newborn screening for autism: in search of candidate biomarkers. Biomark Med. 2013; 7: 247-260.*** Mizejewski GJ. Biomarker testing for suspected autism spectrum disorder in early childhood: is such testing now feasible? Biomark Med. 2012; 6: 503-506.**** Mizejewski GJ. Biological roles of alpha-fetoprotein during pregnancy and perinatal development. Exp Biol... Read more »
Mizejewski GJ, Lindau-Shepard B, & Pass KA. (2013) Newborn screening for autism: in search of candidate biomarkers. Biomarkers in medicine, 7(2), 247-60. PMID: 23547820
Offshore drilling is often discussed in terms of its positive effect on the economy and the potential risks it carries for the environment. There’s, however, another side to offshore drilling, one that is less often talked about.... Read more »
Parnell, J., Boyce, A., Hurst, A., Davidheiser-Kroll, B., & Ponicka, J. (2013) Long term geological record of a global deep subsurface microbial habitat in sand injection complexes. Scientific Reports. DOI: 10.1038/srep01828
Teasing out the insulin effect.
On the face of it, the study seems to come out of left field: A group of researchers claimed that marijuana smokers showed 16 per cent lower fasting insulin levels than non-smokers. The study, called “The Impact of Marijuana Use on Glucose, Insulin, and Insulin Resistance among US Adults,” is in press for The American Journal of Medicine. The authors are a diverse group of medical researchers from Harvard, Beth Israel Deaconess Medical Center, and the University of Nebraska College of Medicine. The study concluded: “We found that marijuana use was associated with lower levels of fasting insulin and HOMA-IR [a measure of insulin resistance], and smaller waist circumference.”
Of course, it was that last tidbit about waist circumference that was picked up by the media. “Why Pot Smokers Are Skinnier,” headlined the Atlantic. However, the important implications are not so much for weight control, or the discovery of some built-in offsetting mechanism for the marijuana munchies, but rather for insulin control and the treatment of diabetes.
But in a clinical study, remarkable observations require remarkable documentation. What does the research actually say?
There are problems with the study worth noting. While researchers took blood samples after a 9-hour fast to determine insulin and glucose levels, they relied on self-reporting for marijuana use data. And self-reporting for alcohol and drug use has its limitations as an investigative tool. Namely, lack of honesty. But let’s get beyond that for a moment: From a database of 4, 657 men and women who participated in the National Health and Nutrition Examination Survey, the researchers determined that 579 were current marijuana users, while 1, 975 were pot smokers in the past.
The marijuana-smoking cohort tended to be young males who also smoked cigarettes. After running everything through a series of complicated multivariable-adjusted models, marijuana came out associated with lower insulin levels, and “lower waist circumference” than those who reported never using marijuana. And the results didn’t change much after adjusting for BMI numbers and excluding participants who actually had diabetes. Furthermore, the association was strongest in current smokers, “suggesting that the impact of marijuana use on insulin and insulin resistance exists during periods of recent use.” (It should also be noted that other health habits can effect glucose and insulin activity, including cigarettes, alcohol, and lack of physical activity.)
The investigators don’t offer a solution to the increased appetite/decreased waistline conundrum they claim to have identified. “We did not find any significant associations between marijuana use, and triglyceride levels, systolic blood pressure, or diastolic blood pressure,” they concluded.
We know marijuana has a complicated relationship with appetite mechanisms, as evidence by its use with chemotherapy patients who need to eat. The theory is that the metabolic effects are mediated by a complex mix of cannabinoid type 1 and type 2 receptor interactions, since type 1 receptor antagonists like rimonabant improve insulin resistance in humans, and type 1 knockout mice also show resistance to diet-induced obesity.
Does marijuana smoking protect against diabetes? Wisely, the researchers don’t go that far, on the basis of this one uncontrolled study. The researchers’ conclusions neatly hedge the bets, suggesting that with recent trends in the direction of marijuana legalization, “physicians will increasingly encounter patients who use marijuana and should therefore be aware of the effects it can have on common disease processes, such as diabetes mellitus.”
As it happens, the findings aren’t entirely new. Anecdotal reports abound. Back in 2010, on the Diabetes Daily support board, there was a long discussion of marijuana’s effect on blood glucose levels in diabetics. And there are several mouse models showing the same effects. In a prepared statement, lead investigator Murray A. Mittleman of Beth Israel Deaconess Medical Center in Boston conceded that previous epidemiological studies have found “lower prevalence rates of obesity and diabetes mellitus in marijuana users compared to people who have never used marijuana, suggesting a relationship between cannabinoids and peripheral metabolic processes.” However, he believes that “ours is the first study to investigate the relationship between marijuana use and fasting insulin, glucose, and insulin resistance.”
Perhaps so. A 2011 study in the American Journal of Epidemiology concluded that “the prevalence of obesity is lower in cannabis users than in nonusers.” And the British Medical Journal featured a finding in 2012 by Los Angeles researchers that marijuana use was “independently associated with a lower prevalence of diabetes mellitus.” But the online patient guide for marijuana offered by Mayo Clinic says without equivocation that “cannabis may lower blood sugar. Caution is advised in patients with diabetes or hypoglycemia, and in those taking drugs, herbs, or supplements that affect blood sugar.” In fact, Mayo Clinic advises that patients may want to monitor their blood glucose levels if they smoke medical marijuana.
Regarding the current study, the editor-in-chief of the American Journal of Medicine said in a statement that there is a need for “a great deal more basic and clinical research into the short- and long-term effects of marijuana in a variety of clinical settings such as cancer, diabetes, and frailty of the elderly.” Editor Joseph S. Alpert also called on the National Institutes of Health (NIH) and the Drug Enforcement Administration (DEA) to collaborate in “developing policies to implement solid scientific investigations that would lead to information assisting physicians in the proper use and prescription of THC in its synthetic or herbal form.”
Penner E.A., Buettner H. & Mittleman M.A. (2013). The Impact of Marijuana Use on Glucose, Insulin, and Insulin Resistance among US Adults, The American Journal of Medicine, DOI: 10.1016/j.amjmed.2013.03.002
Photo Credit: http://www.herbalmission.org/
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Penner Elizabeth A., Buettner Hannah, & Mittleman Murray A. (2013) The Impact of Marijuana Use on Glucose, Insulin, and Insulin Resistance among US Adults. The American Journal of Medicine. DOI: 10.1016/j.amjmed.2013.03.002
Scientists have found that the complex biochemical changes through RNA may have been occurred in the start of the life on early Earth.
RNA (full form: ribonucleic acid) is a nucleic acid that has the sugar ribose, is found in all living cells, and is essential for the manufacture of proteins according to the instructions carried by genes. RNA also acts instead of DNA as the genetic material in certain viruses.
RNA is thought to play an important role in the start of life on Earth more than 3 billion years ago, when environment had less oxygen and a huge amount of soluble iron, and the complex biochemical transformations were thought to be rare.
Researchers worked on the 23S ribosomal RNA and transfer RNA, two most important and plentiful types of RNA, and found their ability to catalyze electron transfer in the presence of iron and lack of oxygen.
“Our study shows that when RNA teams up with iron in an oxygen-free environment, RNA displays the powerful ability to catalyze single electron transfer, a process involved in the most sophisticated biochemistry, yet previously uncharacterized for RNA,” said Loren Williams, a professor in the School of Chemistry and Biochemistry at the Georgia Institute of Technology.
Based on these findings researchers noted that RNA may have some yet-to-be-discovered abilities in the living beings on ancient Earth.
“Our findings suggest that the catalytic competence of RNA may have been greater in early Earth conditions than in present conditions, and our experiments may have revived a latent function of RNA,” added Williams, who is also director of the Ribo Evo Center.
Hsiao, C., Chou, I., Okafor, C., Bowman, J., O'Neill, E., Athavale, S., Petrov, A., Hud, N., Wartell, R., Harvey, S., & Williams, L. (2013). RNA with iron(II) as a cofactor catalyses electron transfer Nature Chemistry, 5 (6), 525-528 DOI: 10.1038/nchem.1649... Read more »
Hsiao, C., Chou, I., Okafor, C., Bowman, J., O'Neill, E., Athavale, S., Petrov, A., Hud, N., Wartell, R., Harvey, S.... (2013) RNA with iron(II) as a cofactor catalyses electron transfer. Nature Chemistry, 5(6), 525-528. DOI: 10.1038/nchem.1649
Recently we attended the Medical Library Association conference (#MLAnet13). Librarians are working so hard to wrangle information into usable forms, and to generate new connections among data types to reveal new information and leads for further studies. I ♥ librarians. In one of the sessions I attended on Medical Informatics, I heard several great talks. One [...]... Read more »
Rabinowitz, P., Scotch, M., & Conti, L. (2010) Animals as Sentinels: Using Comparative Medicine To Move Beyond the Laboratory. ILAR Journal, 51(3), 262-267. DOI: 10.1093/ilar.51.3.262
Rabinowitz, P., Gordon, Z., Holmes, R., Taylor, B., Wilcox, M., Chudnov, D., Nadkarni, P., & Dein, F. (2005) Animals as Sentinels of Human Environmental Health Hazards: An Evidence-Based Analysis. EcoHealth, 2(1), 26-37. DOI: 10.1007/s10393-004-0151-1
Rabinowitz, P., Cullen, M., & Lake, H. (1999) Wildlife as sentinels for human health hazards: a review of study designs. Journal of Environmental Medicine, 1(4), 217-223. DOI: 10.1002/jem.33
It’s no secret that carnivorous plants are just way cool. Yet despite all the attention, there is still a lot we don’t know about them. Recent studies have expanded the view we have of these plants so that we now recognize more and more of them – like tomatoes and potatoes. Yes, our vegetables are insectivores!
New research has show that pitcher plants possess anti-microbial peptides in their pitchers, that some sundews can catapult insects into their traps in just a few milliseconds, and that underwater carnivorous plants use a vacuum-packed trap door to suck prey into a trap. Or how about that pitcher plant that hopes a tree shrew will use it for a toilet?!
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Poppinga, S., Hartmeyer, S., Seidel, R., Masselter, T., Hartmeyer, I., & Speck, T. (2012) Catapulting Tentacles in a Sticky Carnivorous Plant. PLoS ONE, 7(9). DOI: 10.1371/journal.pone.0045735
Buch, F., Rott, M., Rottloff, S., Paetz, C., Hilke, I., Raessler, M., & Mithofer, A. (2012) Secreted pitfall-trap fluid of carnivorous Nepenthes plants is unsuitable for microbial growth. Annals of Botany, 111(3), 375-383. DOI: 10.1093/aob/mcs287
Schulze, W., Sanggaard, K., Kreuzer, I., Knudsen, A., Bemm, F., Thogersen, I., Brautigam, A., Thomsen, L., Schliesky, S., Dyrlund, T.... (2012) The Protein Composition of the Digestive Fluid from the Venus Flytrap Sheds Light on Prey Digestion Mechanisms. Molecular , 11(11), 1306-1319. DOI: 10.1074/mcp.M112.021006
When animals live caves full time, their descendents often lose their eyes. It has happened over and over and over and over again, in all different kinds of animals. But how this happens is not obvious. Stephen Jay Gould wrote that some people would use cave fish as an argument that “Lamarck must have been on to something” with his idea that acquired characteristics can be inherited. Well, no, that’s not that case, but it is a good example of how tricky thinking about losses can be.
The latest paper to try to sort out eye loss uses small amphipod crustaceans (Gammarus minus). An advantage of working with this particular species is that some populations live out in the sunshine with us, but several populations have gone down in the underground. In this case, Carlini and colleagues have three separate populations that went into caves, and they have their closest relatives, which are not cave dwellers. Each pair of populations acts as a natural experiment.
The eyes do change with the habita, as expected. The amphipods that live “above” in springs have eyes with about 40 facets (ommatidia), while the cave dwellers’eyes have about 5 ommatidia.
Using genetic tests, the team found that the genes for making visual pigments, the opsins, were still intact. They had not turned into non-working genes (“pseudogenes”). The genes for the opsins were extremely similar, and in no way as different as the eyes of these little guys were.
What they did find was that the expression of these genes was dialed way down compared to their surface dwelling relatives:
Carlini and colleagues note that this could be related to the overall reduction of the eye, but they attempted to control for this by scaling expression to the size of the eyes.
Carlini and colleagues suggest that the opsin genes are under some sort of pressure to stay “intact” in this species (contrary to suggestion here that there is an advantage to blindness in caves). But the team doesn’t have a suggestion for what the opsin genes might be needed for, although they suggest it might be a non-visual function.
This doesn’t solve the matter of how the animals are reducing the amount of opsins they make. Presumably there is some mutation in a regulatory gene, perhaps even a gene one specific to the visual system.
They should keep an eye out for that.
Carlini DB, Satish S, Fong DW. 2013. Parallel reduction in expression, but no loss of functional constraint, in two opsin paralogs within cave populations of Gammarus minus (Crustacea: Amphipoda). BMC Evolutionary Biology 13(1): 89. DOI: 10.1186/1471-2148-13-89
“What big eyes you have!”
Turning light and going blind: A tale of caves and genes
Once more into the cave
Better off blind
Picture from here.... Read more »
Carlini David B, Satish Suma, & Fong Daniel W. (2013) Parallel reduction in expression, but no loss of functional constraint, in two opsin paralogs within cave populations of Gammarus minus (Crustacea: Amphipoda). BMC Evolutionary Biology, 13(1), 89. DOI: 10.1186/1471-2148-13-89
If you’ve seen March of the Penguins, you probably understand the question. Many penguins live a shitty life, walking miles and miles without any food and spending months apart from their families. This would be over with if they just flew from one place to the other. So why did they stop doing that?... Read more »
Elliott, K., Ricklefs, R., Gaston, A., Hatch, S., Speakman, J., & Davoren, G. (2013) High flight costs, but low dive costs, in auks support the biomechanical hypothesis for flightlessness in penguins. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1304838110
Scientists must ensure that they take the lead in the ethical debate surrounding the therapeutic use of stem cells derived from human clones.... Read more »
It’s something you learn in high school – there are two basic approaches to cellular life – prokaryotes (bacteria and archaea) and eukaryotes (the rest of us – aardvarks, amoebae, apricots, etc.). Prokaryotes have an open-plan office, with all biological …... Read more »
Santarella-Mellwig, R., Pruggnaller, S., Roos, N., Mattaj, I., & Devos, D. (2013) Three-Dimensional Reconstruction of Bacteria with a Complex Endomembrane System. PLoS Biology, 11(5). DOI: 10.1371/journal.pbio.1001565
“LET THERE BE LIGHT!” said the microscopist. Light plays a crucial role in microscopy and cell biology, and a recent paper describes the use of light to understand protein secretion.Light is used in microscopy in countless ways—to illuminate a sample, excite a fluorophore, and signal the localization or dynamics of a protein. Light can also be used to manipulate cellular events through the use of “caged” compounds that become active after illumination by certain wavelengths of light. This technology gives biologists the ability to spatially and temporally control cellular events in order to understand them better. Recent advances in this technology use illumination of plant photoreceptors to control protein-protein interactions, but some cellular processes such as protein secretion have been difficult to manipulate. A recent paper describes the use of the plant photoreceptor UVR8 in the first light-triggered protein secretion system developed. Chen and colleagues have shown that the recently described UVR8 can conditionally sequester proteins bound for secretion in the ER, and then upon illumination with UV light releases these proteins to the plasma membrane. In the images above, a neuron before (left) and after (right) UV illumination with this UVR8 system shows the movement of proteins known to be secreted from the soma and dendritic processes (arrowheads), where the ER is distributed, and into the Golgi (arrow), a necessary step in protein secretion.Chen, D., Gibson, E., & Kennedy, M. (2013). A light-triggered protein secretion system originally published in the Journal of Cell Biology, 201 (4), 631-640 DOI: 10.1083/jcb.201210119... Read more »
Newly discovered papers have shed light on a fascinating episode in the history of neuroscience: Weighing brain activity with the balance The story of the early Italian neuroscientist Dr Angelo Mosso and his ‘human circulation balance’ is an old one – I remember reading about it as a student, in the introductory bit of a [...]... Read more »
Sandrone S, Bacigaluppi M, Galloni MR, Cappa SF, Moro A, Catani M, Filippi M, Monti MM, Perani D, & Martino G. (2013) Weighing brain activity with the balance: Angelo Mosso's original manuscripts come to light. Brain : a journal of neurology. PMID: 23687118
A new study shows how complex biochemical transformations may have been possible under conditions that existed when life began on the early Earth.... Read more »
Georgia Institute of Technology. (2013) RNA was capable of catalyzing electron transfer on early earth with iron's help, study shows. Georgia Institute of Technology. info:/
It’s time to stop scoffing at the synesthetes: linking music to colors is totally normal. It’s not really about the notes, though. Researchers say the colors we find in music are actually the colors of the emotions the music makes us feel.
Synesthetes are people whose sensory experiences overlap; they most often link letters or numbers to certain colors. Music-color synesthesia, in which hearing music triggers the colors, is rarer. In fact, when Stephen Palmer and Karen Schloss at the University of California, Berkeley, set out to do a pilot study of music-color synesthetes, they couldn’t find any. So instead they began looking at the connections between music and colors in everybody else.
As part of a larger study called the Berkeley Color Project, Palmer and Schloss included questions about music. Participants saw a grid of colors while listening to 18 brief clips of classical pieces, and chose the colors that were “most consistent” and "least consistent" with each selection.
The researchers suspected that a connection between music and color, if there was one, might be emotional. So they separately asked their 48 subjects how happy, sad, angry, calm, strong, weak, lively and dreary each piece of music was. Subjects answered the same emotional questions about each color. (If you’re the kind of person who hates attributing personality traits to color swatches, you would not have enjoyed this study.)
There were 18 music samples, representing every possible combination of 3 composers (Bach, Mozart, Brahms), 3 tempi (fast, medium, slow), and 2 modes (major or minor). The Andante movement of Bach's Brandenburg concerto in F major, for example, was Bach/major/slow.
What emerged from this sea of lively Mozart and sad burnt-orange was a clear pattern. People linked uptempo and major-key music to colors that were warmer (yellower), lighter, and more vivid. Pieces with a slower tempo or in a minor key provoked the opposite colors: cooler (bluer), darker, and less saturated.
Additionally, music that was both slow and in a major key tended to be greener. And although there wasn’t a difference between Mozart and Bach, Brahms—a Romantic composer who wrote the most recently of the three—leaned more to the slow and minor colors.
To learn whether this consistency was strictly cultural, Palmer and Schloss found a collaborator at the University of Guadalajara who wanted to repeat the experiments with Mexican subjects.
The researcher, Lilia Prada-León, “initially complained that she didn’t want to study classical music because her Mexican participants don’t listen to that music much,” Parker recalls. “She wanted to do it with mariachi bands, which we may still do sometime later.”
Despite Prada-León's hesitation, the results from her Mexican subjects fit snugly with the results from Americans. “The pattern of results for tempo, mode, and composer were remarkably similar,” the authors write.
Also similar were the emotional ratings that Mexican and American subjects gave the musical selections, as well as the colors themselves. The emotions linked to each piece of music matched the emotions linked to that music's colors. This suggests that music itself doesn't make most people think of color. Instead, music triggers emotion—and that emotion is linked to a certain set of colors in the mind. The results are published in PNAS.
Out of the eight emotions in the original list, only four were needed to explain the results: happy, sad, strong and weak. Happier and stronger colors were associated with upbeat, major-key tunes, while weaker and sadder colors were tied to slower, minor-key pieces.
So what does all this tell us about actual synesthesia?
Palmer says his group has now repeated a version of their experiments with real music-color synesthetes (after finally rounding some up). The results looked different. While non-synesthetes chose different colors depending on the tempo of a piece of music—even if it was the same musical line artificially sped up or slowed down—synesthetes didn't.
"My current opinion is that synesthetes’ color experiences arise from direct mappings from sound to color," Palmer says. In their minds, emotions don't act as the middleman. However, "non-synesthetes’ color associations are indirect and do involve emotional mediation."
But when researchers asked synesthetes to choose the colors that were most "emotionally consistent" with the music, rather than the colors they experienced in their minds, the synesthetes picked out the same colors as everyone else. Additionally, when researchers altered melodies just enough to change them from minor to major, synesthetes—like everyone else—"chose happier colors," Palmer says.
There may be some common ground after all between synesthetes and others. The two groups probably won't agree, though, on the color of the mariachi music playing there.
Images: top by tanakawho (via Flickr); bottom Palmer et al.
Palmer, S., Schloss, K., Xu, Z., & Prado-Leon, L. (2013). Music-color associations are mediated by emotion Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1212562110
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Scientists at Oregon Health & Science University and the Oregon National Primate Research Center (ONPRC) have successfully reprogrammed human skin cells to become embryonic stem cells capable of transforming into any other cell type in the body. It is believed that stem cell therapies hold the promise of replacing cells damaged through injury or illness. Diseases or conditions that might be treated through stem cell therapy include Parkinson’s disease, multiple sclerosis, cardiac disease and spinal cord injuries.... Read more »
The New York Stem Cell Foundation, Laboratory for Stem Cells and Tissue Engineering, Columbia University, Oregon Health , & NCBI. (2013) Major Advance For Stem Cell Research. Tracing Knowledge. info:/
A Science publications is one of the best ways to launch your career, especially if it is based on your undergraduate work, part of which you carried out with makeshift equipment in your dorm! That is the story of Thomas M.S. Chang, who in 1956 started experiments (partially carried out in his residence room in […]... Read more »
Pais, D., & Leonard, N. (2013) Adaptive network dynamics and evolution of leadership in collective migration. Physica D: Nonlinear Phenomena. DOI: 10.1016/j.physd.2013.04.014
Men might have found themselves an excuse not to listen to women. New research suggests that men have twice more difficulty reading emotions in women than in men. This may not sound surprising, but evidence that men have trouble understanding women is, at best, scarce.Being able to guess someone else’s thoughts, feelings and intentions is an instinctive social skill that develops in early childhood. We might take it for granted, but people who struggle or are unable to read other people, like people with autism spectrum disorders, have serious problems in communicating and interacting socially. This important ‘mindreading’ trait, so far thought to be unique to our species, recruits a complex brain network. Different, but partially overlapping, brain regions are activated when we perceive mental states like beliefs, intentions or desires (mentalizing) and when we ‘feel’ the emotions of another person (empathy). In a new PLoSONE study, Boris Schiffer’s research group at the University of Duisburg-Essen, Germany, investigates whether there are differences in neural activation when men recognise emotions in women when compared to men. The researchers asked 22 healthy adult men to do a modified version of the ‘Reading the Mind in the Eyes’ (RME) test while their brain activity was measured using functional magnetic resonance imaging (fMRI). The RME test has been used in countless studies to measure mentalizing and empathy (you can take the test here). In this study, each participant had to guess what either a man or a woman in a photo was thinking or feeling from looking only at his or her eyes. For each of the 36 pairs of eyes, there was a choice of two mental states, for instance ‘terrified’ or ‘upset’. The participants performed better in the test when the eyes belonged to men, suggesting that men have greater difficulty in recognising mental states in women than in their own gender. But the question is… why? The fMRI readings shed some light into this.Schiffer and colleagues predicted that recognising mental states in male or female eyes would activate brain areas involved in mentalizing and empathy, and this is what they found. But there was more. Some areas were more active when the participants were guessing emotions in men, and others when they were recognising emotions in women. It isn't clear what these results mean though. As these differently activated brain regions have in one way or another previously been involved in memory, the authors speculate that they are recruited to retrieve either autobiographical emotional memories (when the participants look at male eyes) or memories of past encounters with women (when they look at female eyes). But this doesn’t explain why men have more difficulty in perceiving women’s emotions. There was, however, another clue in the fMRI readings. Just looking at male eyes, without having to do any particular task, activated the amygdala, which is a brain region associated with processing of emotions and empathy. The authors suggest that when men respond to their own gender, emotion and empathy brain networks are recruited (because men can more easily relate to other men), and this might enhance their ability to perceive mental states. A few studies support this idea. For instance, one study showed that men are better than women at recognising angry faces in men. Schiffer and colleagues further speculate that in evolutionary terms, ‘it makes more sense’, they claim, that we should be better at mentalizing about people that are most similar to us. This would have been particularly important for men in the ‘ancient times’, the authors add, as men were hunting and fighting for territory and it was advantageous for them to predict the intentions of their male rivals. But while this is an attractive hypothesis, it remains rather speculative.And what about women? The main lingering question from this research is perhaps whether women are also better at reading mental states in individuals of their own gender. According to the authors, the prediction is that they should. So men should not be too quick to blame their gender for not understanding the opposite sex- this may backfire. Reference:... Read more »
Schiffer Boris, Pawliczek Christina, Müller Bernhard W., Gizewski Elke R., Walter Henrik, & Krueger Frank. (2013) Why Don't Men Understand Women? Altered Neural Networks for Reading the Language of Male and Female Eyes. PLoS ONE, 8(4). DOI: 10.1371/journal.pone.0060278.g003
A new species of green palm-pitviper of the genus Bothriechis is described from a seriously threatened cloud forest reserve in northern Honduras. Because of similarity in color pattern and scalation, the new species (Bothriechis guifarroi) was previously confused with other Honduran palm pitvipers. Genetic analysis revealed that the closest relatives of the new species are actually found over 600 km to the south, in the mountains of Costa Rica. The study was published in the open access journal Zookeys.... Read more »
Pensoft News. (2013) When green means danger A stunning new species of palm-pitviper from Honduras. Pensoft News. info:/
I have vague memories of the first time I counted to a hundred. It felt like one of those landmarks like tying your shoes for yourself the first time, or riding the bicycle more than a few feet without the training wheels or dad holding you up.
Of course, I don't come anywhere near Adam Spencer:
Once when I was about 7, I counted to 10,000 just to check the numbers didn't run out before then #NerdConfessions
Counting large numbers is not something that comes easily for us humans. A new paper claims this little guy, a baby guppy, may be a superior number cruncher as soon as it pops out of mama’s belly:
A couple of years ago, I reported on a paper that looked at the development of “counting” ability in guppies. In that paper, they claimed that it took about 40 days for guppies to develop the sort of ability to distinguish numbers that they had as adults. Now, the same team is back, testing very young guppies again, but this time using new methods.
The team asked these tiny guppies if they recognized numbers of things by showing animals dots while they have them food. Here are the three stimuli the team used.
Both A and B differ in the number of spots, but A also differs in the average sizes of those spots (which the authors call a “continuous variable). C differs in size, but not in the number. This is try to control for the fact that when you change number of things, you also change many other factors, like amount of area reflecting light, etc.
The authors then measured the amount of time the guppies spent near each set of dots as an indication of “preference”, on the assumption that the guppies are more likely to spend time near the dots where they got food if they learned certain dots meant food. If animals don’t learn where the food is, they may well not be able to tell the stimuli apart.
The authors place these pairs of dots at the end of the tank while fish are feeding when they were four and five days old. As a control, they either feed the fish food or just in a little water without food. On day six, they placed the babies in the tank to see which set of dots they gravitate to. On day seven, they repeat this, but flip the positions of the dots.
The fish were significantly more likely to be around the set of dots that promised food when they differed by number (A and B, above), but not when the dots varied in size. That said, the guppies were not great at this. The guppies got it right only 60% of the time, which is only a slight improvement on a coin toss.
However, the authors themselves admit that this paper is hard to compare with their previous one because the stimuli are so different. The previous paper used other live fish as the stimulus, not just static dots. They also note that this test is slightly different from other training tests, which generally ask the animal to do something even more specific than “hang out at one end of an aquarium.”
It is an interesting suggestion, though, that animals so small and so young can cope with differences in number. But I still think I’ll beat them at counting to a hundred.
Piffer L, Miletto Petrazzini ME, Agrillo C. 2013. Large number discrimination in newborn fish. PLOS ONE 8(4): e62466 DOI: 10.1371/journal.pone.0062466
One fish, two fish... can fish count?
Picture by Shaojung on Flickr; used under a Creative Commons license.... Read more »
I'm gonna try and be fairly brief in this post on the paper by Valerio Napolioni and colleagues* (open-access) looking at plasma cytokine profiles in cases of autism and their asymptomatic siblings. Brief because (a) the paper is open-access and (b) the participant groups (autism: n=25; sibling controls n=25) were relatively small so one has to be quite careful in extrapolating the findings with any large degree of confidence.Siblings by Paul Klee @ WikiPaintings Just in case you are new to cytokines, we are talking biological signalling and communication, and in particular, the language of inflammation both pro- and anti-inflammatory (see this post).With the autism spectrum conditions in mind, research into cytokines has filled quite a few peer-reviewed papers** from lots of different perspectives (see here and here for example). The main message so far is that it is complicated as per everything about autism and immune function.Despite the quite small participant group, the Napolioni paper does seem to be an important paper for a few reasons:They report no overall difference in cytokine profiles - measuring 40 cytokines - between cases of autism and their asymptomatic siblings. This despite the fact that autism symptoms and total IQ measures were different. That was the paper's headline.But.... "the cytokine/chemokine levels in our subjects did correlate with the quantitative clinical traits" or in other words, certain analysed parameters seemed to match with level of severity of autistic traits as measured by schedules such as VABS and SRS. "IL-1β appears to be the cytokine most involved in the quantitative traits".When looking at the children with autism according to various clinical subgroups - non-verbal, functional gastrointestinal (GI) issues, history of regression, history of allergies - a few correlations were noted. So, children who were non-verbal seemed to show higher levels of cytokines such as IL-10, one of the more anti-inflammatory cytokines. Children with accompanying GI issues seemed to show higher levels of more pro-inflammatory cytokines like IL-1β and IL-6 compared with those without GI problems. Reported regression as part and parcel of symptom onset also seemed to show some correlation with specific cytokines too.As the authors point out correlation does not imply causation. Such that just because they reported connections between cytokines and functioning and other factors does not necessarily mean that these observations are causative of autism (or anything else). That being said, as I hinted before, this is not the first time that cytokines and their connection to immune function have been discussed in the autism research literature (see yet another example of this here***); many correlations in similar directions makes for some interesting discussions at least.That headline that children with autism and their siblings did not significantly differ in their cytokine profile carries a few possibilities for interpretation. The authors suggest that this could be evidence of "an ‘autism endophenotype’ that expands immune dysfunction to family members who are seemingly unaffected by the core symptoms of autism". One might also say the same thing about the Gondalia paper**** on gut bacteria in cases of autism and siblings (see here).Assuming that the broader autism phenotype (BAP) does not come into play here, one might speculate that (a) cytokine profiles are not related to the presence of autism, or (b) that the manifestation of autism, some autism, is representative of cytokine involvement but in addition to other factors in terms of the affected sibling - "when an environmental stress (for example, prenatal exposure to environmental toxins, viral and bacterial infections, parental microchimerism, etc.) occurs during development". This last point takes me back to that 1971 John Money study on the appearance of familial autoimmune related conditions 'round about' the presence of autism and a similar correlation. Part of a predisposition to autism?I note from Figure 4 of the paper, that when it came to summarising the various associations across the groups (and sub-groups), quite a few of the very significant differences seemed to be due to differences in IQ, which was tested using the Stanford-Binet Intelligence Scales (fifth edition). Aside from previous messages of caution on the use of this measure in autism research*****, one has to wonder whether this might be a more pertinent variable when it comes to cytokines and autism. I don't know enough about cytokine profiles in intellectual disability in children for example, to make any novel claims about this, but certainly intellectual development has been mentioned in the research literature with certain cytokines in mind******.OK I said I would try and be brief with this post and have failed miserably. The Napolioni paper has though been worth it though for the potential insights that it might provide into the complex world of cytokines and immune function in relation to the presentation of autism.To close, and following yet more 'we'll win it next year' commentary with regards to the UK entry in the event that is the Eurovision Song Content, might I suggest a group for your serious consideration as a contender next year?-----------* Napolioni V. et al. Plasma cytokine profiling in sibling pairs discordant for autism spectrum disorder. Journal of Neuroinflammation 2013; 10: 38.** Goines PE. & Ashwood P. Cytokine dysregulation in autism spectrum disorders (ASD): Possible role of the environment. Neurotoxicol Teratol. 2013; 36: 67-81.*** Ricci S. et al. Altered cytokine and BDNF levels in autism spectrum disorder. Neurotox Res. April 2013.**** Gondalia SV. et al. Molecular characterisation of gastrointestinal microbiota of children with autism (with and without gastrointestinal dysfunction) and their neurotypical siblings. Autism Research. 2012; 5: 419-427.***** Coolican J. et al. Brief report: data on the Stanford-Binet Intelligence Scales (5th ed.) in children with autism spectrum disorder. J Autism Dev Disord. 2008; 38: 190-197.****** von Ehrenstein OS. et al. Child intellectual development in relation to cytokine levels in umbilical cord blood. Am J Epidemiol. 2012; 175: 1191-1199. ----------... Read more »
Napolioni V, Ober-Reynolds B, Szelinger S, Corneveaux JJ, Pawlowski T, Ober-Reynolds S, Kirwan J, Persico AM, Melmed RD, Craig DW.... (2013) Plasma cytokine profiling in sibling pairs discordant for autism spectrum disorder. Journal of neuroinflammation, 38. PMID: 23497090
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