Biology posts
- April 27, 2013
- 07:28 AM
- 93 views
The Science of Guns and Violence in America
by Stephanie Swift in mmmbitesizescience
I read a Nature News article recently about gun control in the USA that horrified me so much that I now have to write a bit about this horrifying topic myself. It goes without saying that there is a huge … Continue reading →... Read more »
Wintemute GJ. (2013) Tragedy's legacy. The New England Journal of Medicine, 368(5), 397-9. PMID: 23268646
- April 27, 2013
- 06:37 AM
- 64 views
A vaccine for autism symptoms? Not exactly
by Paul Whiteley in Questioning Answers
"Vaccine". "Autism".I'm struggling to think of two words in combination which, in modern times, are any more likely to stir up emotion, debate and even argument. Indeed in these times of measles outbreaks and seemingly daily news reporting on the very, very strong requirement for vaccination to protect against the disease, it is coincidental that two research papers should now land in my inbox which mention both of those words in the title.Paradise in Zakynthos @ Wikipedia The first paper is by Ivan Gentile and colleagues* reporting on seropositivity rates to measles, mumps and rubella in cases of autism spectrum disorder (ASD) following MMR vaccination. The second paper, by Brittany Pequegnat and colleagues**, discusses the concept and early development of a vaccine targeting a specific type of gut bacteria which the authors speculate might have some interesting knock-on effects to some of the signs and symptoms linked to cases of autism.Although pertinent to the current measles news, I'm not on this occasions heading too far into the Gentile paper. My reasoning is two-fold: (i) the paper is fairly explanatory in that "children with ASD have a similar level and seropositivity rate of antibodies against the MMR vaccine to same-age controls" (bearing in mind the small participant numbers) and, (ii) I'm not really qualified to go into any heavy duty discussions on how this fits into the existing scientific literature on this topic; bearing in mind a similar finding previously published*** and a contrary one****. All I will say is that vaccination saves lives as per this CDC flier.The Pequegnat paper has received some media attention with headlines like: "Vaccine To Help Autism Symptoms Developed" and "Scientists develop first vaccine to help control autism symptoms". As one might expect, headlines which don't necessarily reflect the actual science reported so far...The long-and-short of the research is that based on some earlier findings of a specific gut bacterium being discovered in a group of children with autism***** - Clostridium bolteae previously called Clostridium clostridioforme (see here******) but renamed, I think, after Ellen Bolte******* - the authors applied some established know-how to begin formulating a vaccine targeting the surface sugars, polysaccharides, of C.bolteae. If you want to see the human face of the researchers involved, look no further than this article from 2012.All that talk of this research helping to 'control' autism symptoms is, at the moment, more speculation than fact. As far as I can see, the authors got no further than providing the "first description of a C.bolteae immunogen" following some initial investigation in rabbits. It is therefore a significant jump to say that this vaccine will affect the behavioural presentation of autism. Indeed, no-one really knows if it will impact on any gastrointestinal (GI) symptoms either.That being said, I am quite interested in their report and the concept that we could artificially stimulate immunity to 'undesirables' such as specific types of gut bacteria. As well as being particularly interested in all things bacteria on this blog (see here and here), a quick trawl of the scientific literature suggests that the future is now as per the paper by Sougioultzis and colleagues******** (open-access) on a C.diff toxoid vaccine. One wonders whether we might also apply similar logic to other bacterial findings related to autism such as that very interesting Sutterella work?I am also drawn to the polysaccharide bit of the Pequegnat paper and whether or not it is useful to link back to the work of Harumi Jyonouchi and colleagues on the presence of specific polysaccharide antibody deficiency (SPAD) comorbid to some cases of autism. If I am interpreting this correctly, the suggestion is that SPAD interferes with correct antibody formation to polysaccharide coated bacteria which could have implications I assume, for vaccination to/against bacteria like C.bolteae also. I could be wrong though.I'm gonna stop with this post shortly. There are other things I could say, for example, discussing the method of vaccine delivery (nanoparticle anyone?) including doing away with the big scary needle in favour of something a little more 'ouchless' (microneedles or even inhaled delivery). But that is perhaps fodder for another day.Oh, and just so you know, on purpose I posted a lovely serene picture from the beautiful island of Zakynthos instead of one of those pictures of big needles complete with crying child which, as other commentators have pointed out, might not necessarily be the best platform on which to discuss the topic of vaccination.----------* Gentile I. et al. Response to Measles-Mumps-Rubella vaccine in children with autism spectrum disorders. In Vivo. 2013; 27: 377-382.** Pequegnat B. et al. A vaccine and diagnostic target for Clostridium bolteae, an autism-associated bacterium. Vaccine. April 2013.*** Baird G. et al. Measles vaccination and antibody response in autism spectrum disorders. Arch Dis Child. 2008; 93: 832-837.**** Singh VK. et al. Abnormal measles-mumps-rubella antibodies and CNS autoimmunity in children with autism. J Biomed Sci. 2002; 9: 359-364.***** Finegold SM. et al. Gastrointestinal microflora studies in late-onset autism. Clin Infect Dis. 2002; 35 (Supplement 1): S6-S16.****** Song Y. et al. Real-time PCR quantitation of Clostridia in feces of autistic children. Appl. Environ. Microbiol. 2004; 70: 6459-6465.******* Bolte ER. Autism and Clostridium tetani. Med Hypotheses. 1998; 51: 133-144.******** Sougioultzis S. et al. Clostridium difficile toxoid vaccine in recurrent C. difficile–associated diarrhea. Gastroenterology 2005; 128: 764–770.----------... Read more »
Pequegnat B, Sagermann M, Valliani M, Toh M, Chow H, Allen-Vercoe E, & Monteiro MA. (2013) A vaccine and diagnostic target for Clostridium bolteae, an autism-associated bacterium. Vaccine. PMID: 23602537
- April 26, 2013
- 08:20 PM
- 72 views
Patenting Genes: Human Invention or Product of Nature?
Leading up to the debate on gene patenting, this week marks the 60th anniversary of the discovery of the DNA double helix. On April 25th, 1953 the work of James Watson, Francis Crick, Maurice Wilkins, Rosalind Franklin and other colleagues on the structure of DNA was published in Nature. Without this milestone achievement, we wouldn’t ...... Read more »
Hall JM, Lee MK, Newman B, Morrow JE, Anderson LA, Huey B, & King MC. (1990) Linkage of early-onset familial breast cancer to chromosome 17q21. Science (New York, N.Y.), 250(4988), 1684-9. PMID: 2270482
WATSON JD, & CRICK FH. (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature, 171(4356), 737-8. PMID: 13054692
- April 26, 2013
- 03:46 PM
- 70 views
North Korea and the USA can indeed unite: in the battle against TB.
Tuberculosis (TB) is an infectious disease caused by a bacterium. It spreads through cough or sneeze from subjects with an active infection. While in most cases the disease is asymptomatic, a minority of latent infections does become active (i.e. the subject develops symptoms), and when it does, if left untreated, the disease can be deadly. According to the CDC one third of the world's population are infected with TB, and while in the US the incidence of the disease has been declining over time, it is still a huge problem in parts of the world like Asia and sub-saharan Africa. While normally the chance of a latent TB infection becoming active is one in ten, the chance is much higher for HIV-positive subjects because their immune system is already debilitated by the HIV virus. As the CDC reports:"TB is a leading killer of people living with HIV (PLHIV)."A regimen of 3-4 drugs has been available for years to keep latent infections from becoming active. Sadly, TB infections from multidrug resistant strains (MDR) have been steadily increasing, setting back the progress made in the past decades.From the World Health Organization:"Drug resistance arises due to improper use of antibiotics in chemotherapy of drug-susceptible TB patients. This improper use is a result of a number of actions including, administration of improper treatment regimens and failure to ensure that patients complete the whole course of treatment. Essentially, drug resistance arises in areas with weak TB control programmes. A patient who develops active disease with a drug-resistant TB strain can transmit this form of TB to other individuals."One of the countries plagued by MDR TB strains is North Korea, where the incidence of TB has dramatically advanced over the past years, reaching one of the highest incidences outside sub-saharan Africa. In this week's issue, Science Magazine describes a joint effort between two countries that, according to the recent news, you'd least expect to pair up: North Korea and the United States. In collaboration with Stanford University, the Korean ministry of Public Health opened in 2010 a National Tuberculosis Reference Laboratory (NTRL). "NTRL researchers can now diagnose TB cases that are resistant to first-line drug combinations, making it possible to spot patients who need more aggressive therapy. And the lab will soon add capacity to screen for extensively drug-resistant TB, known as XDR—the worst strains, some of which are close to impossible to treat."The Science report covers stories of hope in the midst of desperation. It points to pressing issues the North Korean government has to address within its borders, and focusing on them would seem a more reasonable and logical strategy than polishing nuclear arsenals. Let's hope that the roots of this collaboration grow deeper than any political discrepancies. Let's hope that a common enemy will put an end to the empty, unfounded threats and pave the way to a broader, more civilized way of communication between countries. Stone, R. (2013). Public Enemy Number One Science, 340 (6131), 422-425 DOI: 10.1126/science.340.6131.422... Read more »
Stone, R. (2013) Public Enemy Number One. Science, 340(6131), 422-425. DOI: 10.1126/science.340.6131.422
- April 26, 2013
- 01:53 PM
- 69 views
The Curious Case of the Earworm (Part 2)
by Melissa Chernick in Science Storiented
In Part 1 of this topic, we explored the reasons why we like certain songs. But what transforms that likable melody into an earworm? Or is likability even a contributing factor? We took the biochemical/neurological route in Part 1, so now we’re gonna go all psychology for this one with a paper published in 2011 in Psychology of Music.Let’s get some terminology out of the way first. We all have internally-directed thought (all that stuff you think to yourself), and we also experience spontaneous cognitions, which are those “common, everyday experiences that occur against a backdrop of deliberate goals-directed mental processes.” Musical imagery is associated with this. Involuntary musical imagery (INMI) is when a piece of music comes unbidden into your mind and repeats outside of your conscious control. It is the “earworm”, “brain worm,” “sticky music,” “cognitive itch,” and/or “stuck song syndrome.” This 2011 study looked to see if there were any patterns in everyday life that lead to an INMI episode, basically what prompts an earworm. The researchers first wanted to catalog known instances of earworms. So they used a radio feature where listeners could contact the presenter/DJ to describe their earworm experiences, and they used an online survey on the radio’s website to collect earworms. This survey allowed people to answer questionnaires and even write descriptions of the songs stuck in their heads. Their results showed eight dominant themes to describe INMI triggering. These themes were then grouped into four abstract categories (listed from most common cause to least):Music exposure – this theme is divided into recent and repeated. Recent exposure is when you hear music and then later have an INMI experience. Repeated exposure is when you hear the music on multiple occasions before an earworm occurs.Memory triggers – this theme relates to INMI episodes that are triggered not when you hear a song but when you remember a song. This can happen through Association in which you might sight a person, situation, word, sound, or rhythm that triggers the earworm. Or it may happen through Recollection, a personal memory that acts as the trigger. It may also be the result of Anticipation, an upcoming event that is connected to a tune.Affective states – this theme is more situational. Your mood, stress level, and emotions can all cause earworms.Law attention states – this theme is abstract in that it relates to circumstances where the demands on your brain are low. These times are usually when you are dreaming or when your mind wanders.This is a psychology study and so delves into involuntary retrieval theory and states of mind. I won’t go in to all of that. I’ll simply say that this study is interesting because it categorizes the cues associated with earworms. A simple but effective exercise. If you are like me, then you probably read most or all of those and thought, “Yep, that’s how it happens with me,” or something similar.A recent study published in Applied Cognitive Psychology, looked into this question of earworms a bit more. These researchers wanted to know what gets stuck and why. This study first uses a survey designed to collect earworm experiences, focusing on the cues that cause them, the nature of re-experiencing the song, and if commonly stuck songs are liked or disliked.This survey found that a person’s connection to the song predicted which songs became earworms (you usually know your earworm well), and it is usually the result of recent exposure (supporting the "music exposure" results of the previous study). It also showed that the song itself was unique to the individual, and that people generally liked the song stuck in their heads but less so the more often it got stuck. That makes sense; the longer that song is in there the more you just go AHH! You know how you repeat only part of the song over and over, usually the chorus? This science says you aren’t alone, this is how it happens with a lot of people. However, if you are a musician or someone who listens to music constantly or for a large part of the day, you are more likely to develop an earworm. When the researchers had people keep an earworm diary, they found similar results.Next, the scientists ran a few lab experiments. The first experiment tried to induce an earworm by having participants evaluate songs, then engage in an unrelated task (solving a maze), and then report any earworms. They found no effects of music type but that song order affected both earworm duration and the likelihood that the earworm would return. The last song you hear is probably the one that will get stuck in your head. The next lab experiment investigated the role of cognitive load (how strained your brain is). They used the method of the first experiment with the exception that they made the tasks harder (Sudoku puzzles of various difficulty levels), making the brain work more (hard puzzle = large cognitive load). They found that the last song became an earworm more often regardless of cognitive load, but it played for a longer time in people with more challenging puzzles. Also, if a person reported the last song as an earworm playing during the puzzle then they were more likely to have the song return later (during a lower cognitive low) as compared to those people who didn’t have the song playing during their puzzle. The last experiment was an extension of the cognitive load experiment, this time using a verbal task (solving anagrams of various difficulties) instead of a puzzle. Here, the researchers found similar results to the second experiment in that song order was important, especially for more difficult tasks. However, the last song was experienced less when completing verbal tasks than nonverbal tasks.Whew. That was a lot of info in a small amount of space. If we sum up Part 1 and 2, what did we learn? Well, when you hear something you like your brain releases dopamine, the feel good, reward stuff. Your brain stores information about the kinds of songs you like and later uses that information to decide if it likes a song if you’ve never heard before. If it decides that you like it then it gives you your reward, making you want to hear that song again. Songs you enjoy are more likely to develop into earworms, particularly if they are the last song you hear, but there are other situational and emotional experiences that can trigger and earworm too (that whole science-is-never-simple thing again).“I’m gonna pop some tags – Only got twenty dollars in my pocket….” ....*sigh*Williamson, V., Jilka, S., Fry, J., Finkel, S., Mullensiefen, D., & Stewart, L. (2011). How do "earworms" start? Classifying the everyday circumstances of Involuntary Musical Imagery Psychology of Music, 40 (3), 259-284 DOI: 10.1177/0305735611418553Hyman, I., Burland, N., Duskin, H., Cook, M., Roy, C., McGrath, J., & Roundhill, R. (2013). Going Gaga: Investigating, Creating, and Manipulating the Song Stuck in My Head Applied Cognitive Psychology, 27 (2), 204-215 DOI: ... Read more »
Williamson, V., Jilka, S., Fry, J., Finkel, S., Mullensiefen, D., & Stewart, L. (2011) How do "earworms" start? Classifying the everyday circumstances of Involuntary Musical Imagery. Psychology of Music, 40(3), 259-284. DOI: 10.1177/0305735611418553
Hyman, I., Burland, N., Duskin, H., Cook, M., Roy, C., McGrath, J., & Roundhill, R. (2013) Going Gaga: Investigating, Creating, and Manipulating the Song Stuck in My Head. Applied Cognitive Psychology, 27(2), 204-215. DOI: 10.1002/acp.2897
- April 26, 2013
- 12:47 PM
- 70 views
This Month In Blastocystis Research
by Christen Rune Stensvold in Blastocystis Parasite Blog
The first post in a series of monthly updates on Blastocystis research mainly based on emerging papers in PubMed.... Read more »
Gould R, & Boorom K. (2013) Blastocystis surface antigen is stable in chemically preserved stool samples for at least 1 year. Parasitology research. PMID: 23609598
Dogruman-Al F, Simsek Z, Boorom K, Ekici E, Sahin M, Tuncer C, Kustimur S, & Altinbas A. (2010) Comparison of methods for detection of Blastocystis infection in routinely submitted stool samples, and also in IBS/IBD Patients in Ankara, Turkey. PloS one, 5(11). PMID: 21124983
Alfellani MA, Stensvold CR, Vidal-Lapiedra A, Onuoha ES, Fagbenro-Beyioku AF, & Clark CG. (2013) Variable geographic distribution of Blastocystis subtypes and its potential implications. Acta tropica, 126(1), 11-8. PMID: 23290980
Alfellani MA, Jacob AS, Perea NO, Krecek RC, Taner-Mulla D, Verweij JJ, Levecke B, Tannich E, Clark CG, & Stensvold CR. (2013) Diversity and distribution of Blastocystis sp. subtypes in non-human primates. Parasitology, 1-6. PMID: 23561720
Abdulsalam AM, Ithoi I, Al-Mekhlafi HM, Khan AH, Ahmed A, Surin J, & Mak JW. (2013) Prevalence, predictors and clinical significance of Blastocystis sp. in Sebha, Libya. Parasites , 86. PMID: 23566585
Clark CG, van der Giezen M, Alfellani MA, & Stensvold CR. (2013) Recent developments in blastocystis research. Advances in parasitology, 1-32. PMID: 23548084
Malheiros AF, Stensvold CR, Clark CG, Braga GB, & Shaw JJ. (2011) Short report: Molecular characterization of Blastocystis obtained from members of the indigenous Tapirapé ethnic group from the Brazilian Amazon region, Brazil. The American journal of tropical medicine and hygiene, 85(6), 1050-3. PMID: 22144442
- April 26, 2013
- 11:05 AM
- 87 views
The Shambulance: Reflexology and Other Stories
by Elizabeth Preston in Inkfish
The Shambulance is an occasional series in which I try to find the truth about bogus or overhyped health products. Helping me keep the Shambulance on course are Steven Swoap and Daniel Lynch, both biology professors at Williams College.
Sticking a Q-tip up one’s nose is not the source of many great insights. Yet it’s how an American doctor in the early 20th century developed the theory that became modern reflexology. He would be proud—though maybe a little confused—to see people today flocking to reflexology spas, where practitioners treat all their problems via the soles of their feet.
The American doctor in question was William H. Fitzgerald, an ear, nose and throat specialist. In a 1917 book, he explained the genesis of his big idea:
Six years ago I accidentally discovered that pressure with a cotton tipped probe on the muco-cutinous margin (where the skin joins the mucous membrane) of the nose gave an anesthetic result as though a cocaine solution had been applied . . . Also, that pressure exerted over any bony eminence of the hands, feet or over the joints, produces the same characteristic results in pain relief . . . This led to my ‘mapping out’ these various areas and their associated connections and also to noting the conditions influenced through them. This science I have named "Zone Therapy."
Chapter titles from Zone Therapy include "Zone Therapy for Women" (tongue depressor into the back of the throat for menstrual cramps), "Painless Childbirth" (rubber bands around the toes, among other interventions) and "Curing Lumbago with a Comb."
A nurse and physical therapist named Eunice D. Ingham extended the idea of zone therapy in the 1930s and 1940s, eventually mapping the entire body onto the soles of the feet. She called each important point on the foot a “reflex” because it reflected back to a certain organ or body part. Ingham wrote two books on the subject, now called reflexology: Stories the Feet Can Tell and Stories the Feet Have Told.
Today, the International Institute of Reflexology describes its practice as as “a science which deals with the principle that there are reflex areas in the feet and hands which correspond to all of the glands, organs and parts of the body.” Stimulating these points “can help many health problems in a natural way.” The site insists, “Reflexology…should not be confused with massage.”
There has been some confusion and blending, though, between Western reflexology and traditional Chinese medicine. Ingham and Fitzgerald's idea of "zones" is similar to the Chinese principle of "meridians." In traditional Chinese medicine, meridians are paths that carry qi through the body and connect the acupuncture points. Reflexology groups like to say that Fitzgerald "rediscovered" the science from more ancient roots. They even claim that ancient Egyptians practiced it, based on tomb paintings showing people holding each other's feet.
Whoever thought it up first, the idea that the soles of your feet hold a miniature map of the entire rest of your body defies a scientific explanation.
“The problem is communication,” says physiologist Steven Swoap. “How does the foot talk to the pancreas?”
The foot is full of sensory nerves, Swoap explains. These can detect temperature, pain or position and send that information to the spinal cord. If the signal is something urgent—say, you stepped on a nail—the spinal cord will send a quick command back to the foot (“STOP!”). If the signal from the foot is a non-painful one (“Hey, I’m walking on grass”), it will travel all the way up the spinal cord to the brain.
“But in no instance do those sensory nerves bypass either the spinal cord or the brain and go directly to the liver, or the kidney, or the colon,” Swoap says. This means your foot can’t communicate directly with any other body part except your spinal cord or brain. Whatever stories the feet have told, they’ve had a limited audience.
Daniel Lynch, a biochemist, points out that sex organs are missing from some reflexology maps. “Why aren’t the gonads on there?” he asks. Other maps label a "testes and ovaries" region around the middle of the heel, but there's variation from one chart to the next.
Setting aside the map itself, Lynch says, “Where is the evidence that it actually works?”
The evidence is slimmer than a stiletto heel. In a 2011 review paper, complementary medicine researchers at the Universities of Exeter and Plymouth dug up every scientific study of reflexology they could find. Out of 23 randomized clinical trials, only 8 “suggested positive effects.”
The quality of the studies was “variable,” the authors write, “but, in most cases, it was poor.” Only four studies that found a positive effect used a placebo control—that is, did massaging the feet without regard to “zones” give patients the same symptom relief? In general, studies tended to use small groups of subjects and not to be replicated by other researchers.
Reflexology has been tested on conditions including asthma, premenstrual syndrome, irritable bowel syndrome, multiple sclerosis, and back pain. If reflexology does have a benefit, “The most promising evidence seems to be in the realm of cancer palliation,” or making patients more comfortable, the authors write. Overall, though, they found no convincing evidence that reflexology has power beyond the placebo.
Not that we should thumb our Q-tip-free noses at the placebo effect. The body has an impressive power to make itself feel better based on our expectations. A foot rub from a professional may very well ease a person’s pain. If that professional says anything about zones, though, it’s only a story.
Image: Foot reflexology chart by Stacy Simone (Wikipedia)
Ernst, E., Posadzki, P., & Lee, M. (2011). Reflexology: An update of a systematic review of randomised clinical trials Maturitas, 68 (2), 116-120 DOI: 10.1016/j.maturitas.2010.10.011
... Read more »
Ernst, E., Posadzki, P., & Lee, M. (2011) Reflexology: An update of a systematic review of randomised clinical trials. Maturitas, 68(2), 116-120. DOI: 10.1016/j.maturitas.2010.10.011
- April 26, 2013
- 07:11 AM
- 84 views
Intelligent Whales Have Their Own Culture
by Katja Keuchenius in United Academics
Whales already were one the most fascinating and intelligent creatures we know and they now also appear to work together in adapting to their environments. Just like us, they give each other tips. Is it in their songs?... Read more »
Allen, J., Weinrich, M., Hoppitt, W., & Rendell, L. (2013) Network-Based Diffusion Analysis Reveals Cultural Transmission of Lobtail Feeding in Humpback Whales. Science, 340(6131), 485-488. DOI: 10.1126/science.1231976
- April 26, 2013
- 07:00 AM
- 58 views
April 26, 2013
by Erin Campbell in HighMag Blog
It’s Worm Week here at HighMag Blog. Worms are amazing little creatures, and the species C. elegans is an invaluable model system for studying cell and developmental biology. Their genome is sequenced, their development is precise and well-documented, and their bodies and embryos are translucent (making them photogenic under a microscope). Today’s image is from the same lab that brought Tuesday’s image…worm gonads rock!Blurb and image from Christian R. Eckmann:The image is an immuno-stained part of an extruded C. elegans hermaphrodite gonad; germ cell nuclei (magenta) and the apical membrane (green). The germ stem cells reside at the closed end of this tube like tissue. In wild type, the germ stem cells exit the mitotic zone, entering meiosis further away from the closed tip and start differentiating into sperm or oocytes. The image posted earlier this week is from the Gracida and Eckmann paper that identifies a nuclear receptor that protects germ stem cell integrity, and in turn fertility, after dietary perturbations.Gracida, X. & Eckmann, C. (2013). Fertility and Germline Stem Cell Maintenance under Different Diets Requires nhr-114/HNF4 in C. elegans Current Biology, 23 (7), 607-613 DOI: 10.1016/j.cub.2013.02.034 ... Read more »
Gracida, X., & Eckmann, C. (2013) Fertility and Germline Stem Cell Maintenance under Different Diets Requires nhr-114/HNF4 in C. elegans. Current Biology, 23(7), 607-613. DOI: 10.1016/j.cub.2013.02.034
- April 26, 2013
- 05:51 AM
- 73 views
Scientists Create Novel Approach to Find RNAs Involved in Long-term Memory Storage
by Perikis Livas in Tracing Knowledge
Despite decades of research, relatively little is known about the identity of RNA molecules that are transported as part of the molecular process underpinning learning and memory.... Read more »
Office of Communications | Press Release. (2013) Scientists Create Novel Approach to Find RNAs Involved in Long-term Memory Storage. The Scripps Research Institute. info:/
- April 26, 2013
- 03:00 AM
- 21 views
Rare diseases – new developments and initiatives
by Lizzie Perdeaux in BHD Research Blog
The aim of this year’s Rare Disease Day, Rare Disorders Without Borders, was to promote the message that international collaboration between patients, clinicians and researchers is imperative to find cures for rare diseases. Indeed, this has been the feeling of … Continue reading →... Read more »
McCormack FX, Inoue Y, Moss J, Singer LG, Strange C, Nakata K, Barker AF, Chapman JT, Brantly ML, Stocks JM.... (2011) Efficacy and safety of sirolimus in lymphangioleiomyomatosis. The New England journal of medicine, 364(17), 1595-606. PMID: 21410393
O'Connor, D. (2013) Orphan drug designation – Europe, the USA and Japan. Expert Opinion on Orphan Drugs, 1(4), 255-259. DOI: 10.1517/21678707.2013.769876
- April 25, 2013
- 05:10 PM
- 59 views
FISH-Quant: the sequel
by Gal Haimovich in Green Fluorescent Blog
As promised, I started using FISH-Quant to analyze my FISH images. I must say that I enjoy using FQ much better than the previous program that was developed by one of my lab members. I find FQ more intuitive, more informative, … Continue reading →... Read more »
Mueller, F., Senecal, A., Tantale, K., Marie-Nelly, H., Ly, N., Collin, O., Basyuk, E., Bertrand, E., Darzacq, X., & Zimmer, C. (2013) FISH-quant: automatic counting of transcripts in 3D FISH images. Nature Methods, 10(4), 277-278. DOI: 10.1038/nmeth.2406
- April 25, 2013
- 04:30 PM
- 70 views
how to shield yourself in a vacuum, sci-fi style
by Greg Fish in weird things
In a fair bit of science fiction, we see advanced alien species use some sort of shielding to walk around other planets or survive being ejected into space. Something around them flickers and a protective invisible bubble is raised, protecting them from a horrible death by dehydration as all the fluid in their bodies effectively boils away. As it turns out, that’s actually possible. [...]... Read more »
Takaku, Y., Suzuki, H., Ohta, I., Ishii, D., Muranaka, Y., Shimomura, M., & Hariyama, T. (2013) A thin polymer membrane, nano-suit, enhancing survival across the continuum between air and high vacuum. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1221341110
- April 25, 2013
- 10:00 AM
- 6 views
Novel industrial applications from salt loving extremophiles
by Clay Clark in Biochem Blogs
This blog will review two recent publications that explore environmentally friendly advances in biotechnology by exploiting halophilic organisms from the family Halobacteriaceae. Halophiles are found in all kingdoms of life. They employ two different survival mechanisms to cope with their typically inhospitable environment. … Continue reading →... Read more »
Karan Ram, Capes Melinda D, DasSarma Priya, & DasSarma Shiladitya. (2013) Cloning, overexpression, purification, and characterization of a polyextremophilic β-galactosidase from the Antarctic haloarchaeon Halorubrum lacusprofundi. BMC Biotechnology, 13(1), 3. DOI: 10.1186/1472-6750-13-3
Zhao Dahe, Cai Lei, Wu Jinhua, Li Ming, Liu Hailong, Han Jing, Zhou Jian, & Xiang Hua. (2013) Improving polyhydroxyalkanoate production by knocking out the genes involved in exopolysaccharide biosynthesis in Haloferax mediterranei. Applied Microbiology and Biotechnology, 97(7), 3027-3036. DOI: 10.1007/s00253-012-4415-3
- April 25, 2013
- 08:29 AM
- 9 views
Challenging the dogma that animal studies of spinal cord injury can’t be replaced
by Professor Sue Barnett in NC3Rs Blog
Spinal cord injuries can lead to permanent disabilities such as paralysis. Research in rats and mice for new treatments involve severing nerve fibres, which can cause moderate or severe suffering. Professor Sue Barnett, University of Glasgow, who is a 3Rs Prize 2012 runner up, writes about an in vitro technique, funded by NC3Rs, to replace the use of rodents in her laboratory.... Read more »
Boomkamp, S., Riehle, M., Wood, J., Olson, M., & Barnett, S. (2012) The development of a rat in vitro model of spinal cord injury demonstrating the additive effects of rho and ROCK inhibitors on neurite outgrowth and myelination. Glia, 60(3), 441-456. DOI: 10.1002/glia.22278
- April 25, 2013
- 05:22 AM
- 66 views
Prenatal valproate exposure and autism: reloaded
by Paul Whiteley in Questioning Answers
When does the the term 'correlation does not equal causation' become a moot point? It's a question I've often pondered, having discussed the issue quite a few times on this blog for all manner of correlations and associations linked to autism (sorry, the autisms).The weight of the heart @ Wikipedia Is there, for example, a recognised tipping point where the weight of evidence correlating A with B might actually lead to the consensus that A causes B either wholly or partially?Yes, I know that science deals with probabilities not absolutes (something which we are all guilty of forgetting from time to time) and that science is generally quite reserved about its findings. But surely as per the example of smoking and lung cancer, there must be a time when the likelihood that A causes B creeps over the 'chance' explanation to something a little more concrete and directional?The reason for the question(s) follows the publication of a study by Jakob Christensen and colleagues* (open-access) which suggested that in large and pretty well-defined Danish cohort "maternal use of valproate during pregnancy was associated with a significantly increased risk of autism spectrum disorder and childhood autism in the offspring". Regular readers might remember that quite recently there was some similar chatter on this antiepileptic medication based on the Bromley paper (see here) but on an altogether smaller scale compared with the current dataset.There has been some media attention paid to the recent trial (see here and here) which is perhaps not surprising given the suggestion that approximately 1 in 20 mothers who were using valproate during pregnancy to control epilepsy or seizure disorders subsequently had a child with autism or an autism spectrum disorder (ASD). The actual risk (absolute risk) was quoted as 2.5% and 4.4% respectively based on the 508 children exposed to valproate in-utero. Even the latest 'survey' figures of 1 in 50 children presenting with an ASD in the US are seemingly dwarfed by the Christensen findings.There are obviously caveats to all this talk about risk, and how risk is risk, not certainty. That also valproate is actually quite effective in controlling cases of epilepsy** is a point which should not get lost in any discussions on risk. Indeed when one reads such studies linking drug A to condition B, it's all too easy to forget that drug A is being taken for a reason; often a very important reason. Physicians generally do not enter lightly into such clinical decisions, particularly in light of past scandals of medication and pregnancy (see here). Not forgetting too that epilepsy can, in extreme cases kill***.Outside of the autism-valproate link (if I can call it that) the Christensen data also includes some other potentially interesting factoids, as per the suggestion that among children of mums with epilepsy who were not exposed to valproate during pregnancy (n=6152), the absolute risk of a diagnosis of autism and ASD were 1.02% and 2.44% respectively. I hasten to add that I'm not an expert on risk, absolute risk, but 2.44%, by my reckoning, equates as roundabout 1 in 40 with an ASD born to mums with epilepsy. I'm cautious not to read too much into this just in case I've got it completely wrong but if it is correctly interpreted, might imply some greater connection between offspring autism and a maternal history of epilepsy as per previous findings****.I'm not going to go through all the possible weaknesses in the Christensen paper because the manuscript does that quite well enough itself including some discussion on that folate-autism link. Likewise my previous post on valproate and offspring autism talked about some of the possible mechanisms to account for any effect, so again no need to cover all that ground. There is one tidbit to pick up on: "Valproate is a fatty acid derivative" so the authors report. I've often wondered about this point and the suggested mechanism of seizure control in some cases by use of the ketogenic diet impacting on fatty acids (see the paper by Chang and colleagues*****). Assuming the Chang findings are accurate, does this place more emphasis on the HDAC inhibition side of things when it comes to valproate and offspring autism risk?The question still remains about the 'correlation does not equal causation' mantra with prenatal valproate exposure and offspring autism in mind. The Christensen paper at the very least, makes a really strong case for a lot more detailed inspection of this potential association as once again the use of pharmacotherapy during pregnancy comes under the spotlight.Oh, and just in case you thought I was singling out valproate for special attention in relation to autism, have a look at the recent paper by Dheeraj Raj and colleagues****** (open-access) on prenatal antidepressant exposure and offspring autism risk again adding to the previous literature. Indeed it makes me wonder if that environmental exposome fish experiment carried out a while back might well be a model, albeit with revisions, we need to revisit.A song to close methinks. Something vintage and snazzy today.... Elvis and Viva Las Vegas.----------* Christensen J. et al. Prenatal valproate exposure and risk of autism spectrum disorders and childhood autism. JAMA. 2013; 309: 1696-1703.** Marson AG. et al. The SANAD study of effectiveness of valproate, lamotrigine, or topiramate for generalised and unclassifiable epilepsy: an unblinded randomised controlled trial. Lancet. 2007; 369: 1016–1026.*** Berg A. Mortality in epilepsy. Epilepsy Curr. 2001; 1: 28.**** Leonard H. et al. Maternal health in pregnancy and intellectual disability in the offspring: a population-based study. Ann Epidemiol. 2006; 16: 448-454.***** Chang P. et al. Seizure control by ketogenic diet-associated medium chain fatty acids. Neuropharmacology. 2013; 69: 105-114.****** Raj D. et al. Parental depression, maternal antidepressant use during pregnancy, and risk of autism spectrum disorders: population based case-control study. BMJ. 2013; 346: f2059----------... Read more »
Jakob Christensen, Therese Koops Grønborg, Merete Juul Sørensen, Diana Schendel, Erik Thorlund Parner, Lars Henning Pedersen, & Mogens Vestergaard. (2013) Prenatal Valproate Exposure and Risk of Autism Spectrum Disorders and Childhood Autism. JAMA. info:/
- April 25, 2013
- 12:43 AM
- 84 views
A room with a view: what do dogs want?
by Cobb & Hecht in Do You Believe In Dog?
Putting the woof in tweet! (source)Hi Julie,Wow! Thanks for sharing the amazing fun tweet-week we had posting for @realscientists on Twitter. It was great to engage with so many people about so many areas of dog (and other animal!) behaviour and research. And poo. So many questions about dog poo! Some things can be relied upon in life; it’s good to know people are always curious about dog poo.If you want to revisit any of those posts or links we exchanged as part of the Real Scientists project, check out the amazing collection of our tweets, compiled via Storify by the fabulous Sarah, genius behind Science for Life . 365. This week, they have an astrophysicist/cosmologist who studies exploding stars and dark energy tweeting – so interesting! He has a beagle named Bagel who has learned to open doors on everything – the house, the fridge, the microwave – he’s keeping himself and everyone following on Twitter entertained!Over recent weeks I have been talking to working dog industry groups and visiting a variety of kennel facilities as part of my ongoing work with the Australian Animal Welfare Strategy. It’s been great being back around the wagging tails and eager faces of working dogs again. Seeing a wide range of kennel facilities has been fantastic and has given me some good motivation to complete my PhD research in the area of kennelled working dogs.(source)Kennel facilities (including shelter, boarding/breeding and working dog kennel contexts) are often built to house as many individuals as they can in the space available and to be easily cleaned (usually via chemical wash down and hosing) in order to maintain a hygienic environment. This has historically resulted in spaces formed in concrete and metal that we (as people) readily perceive as barren and sterile. (source)Modern facilities are often built with different materials, and can seem more pleasing to our eye, but I wonder if they’re actually any different in meeting dogs’ behavioural needs? It’s been interesting while visiting the recent facilities to consider the dogs’ experience of living in them. One point of difference that I noted was that some facilities offer the dog/s a view. Others didn’t. (source)This view might be limited to the dog opposite their kennel run, or fairly open to many other dogs, people, surrounding scenery, traffic, animals, etc. especially in areas where dogs have a choice to be in- or outside. The limited research in this area suggests that in situations where dogs are housed singly and have the opportunity to view other dogs, they take it. I find it interesting that human studies have illustrated positive effects of proximity to windows with a view in hospital and workplace environments: improved recovery times and reduced job stress. A review paper by Taylor and Mills (see below) suggests that sensory overstimulation may occur in kennel environments, so what does that mean when we consider what provision should be made for dogs to see outside of their kennel?Someone thinks it's important, with a fence porthole having been launched for pet dogs a few years ago. So is this marketing to the dogs' needs or the people's perceptions? Dogs certainly seem to actively seek out visual information about the world around them.... Read more »
Wells Deborah L., & Hepper Peter G. (1998) A note on the influence of visual conspecific contact on the behaviour of sheltered dogs. Applied Animal Behaviour Science, 60(1), 83-88. DOI: 10.1016/S0168-1591(98)00146-4
Taylor K, & Mills D. (2007) The effect of the kennel environment on canine welfare: a critical review of experimental studies. Animal Welfare, 16(4), 435-447. http://www.ingentaconnect.com/content/ufaw/aw/2007/00000016/00000004/art00003
Sop Shin Won. (2007) The influence of forest view through a window on job satisfaction and job stress. Scandinavian Journal of Forest Research, 22(3), 248-253. DOI: 10.1080/02827580701262733
Verderber Stephen, & Reuman David. (1987) Windows, views, and health status in hospital therapeutic environments. Journal of Architectural and Planning Research, 4(2), 120-133. http://psycnet.apa.org/psycinfo/1988-30782-001
- April 24, 2013
- 03:25 PM
- 70 views
Video reveals cancer cells’ Achilles’ heel
by Perikis Livas in Tracing Knowledge
Scientists from the Manchester Collaborative Centre for Inflammation Research (MCCIR) have discovered why a particular cancer drug is so effective at killing cells. Their findings could be used to aid the design of future cancer treatments.... Read more »
Morwenna Grills. (2013) Video reveals cancer cells’ Achilles’ heel. The University of Manchester . info:/
- April 24, 2013
- 02:06 PM
- 57 views
A true paleo diet: dinosaurs eating fish
by Zen Faulkes in NeuroDojo
There’s been a lot of talk about “paleo diets”, but here we have the real deal. A meal caught in the middle of digestion in a dinosaur.
Microraptor gui was introduced back in 2003, and immediately attracted attention because of the its feathers, particularly lots of long, prominent feathers on its hind legs, so unlike any bird or other flying beast we know of. There is good evidence (though disputed) that it was a glossy, black animal, rather like the grackles that hang around my campus.
But behaviour is one of the trickiest things to pull from fossils. How did these animals live?
Here is the newest fossil to shed light on this question in Microraptor.
Just in front of where the hind legs meet the spine, and below the spine, there is a mass that is a little darker than the surrounding rock. There are close ups of this area in the journal article, but the reproduction is disappointingly low-resolution in the pre-print, and in any case, relatively few would immediately recognize the key feature there.
Fish bones. There is nothing but fish bones in the gut of this dinosaur. Authors Xing and colleagues say, “M. gui was an adept hunter of aquatic prey.”
Still, are there any other indications in the anatomy that Microraptor gui was a habitual fish-eater? After all, all kinds of meat eaters will pick up any meal that’s available. It is at least possible that this one individual M. gui scavenged some leftovers off someone else’s plate, so to speak.
Xing and company say that evidence against this being scavenging is that fish spoils quickly, so the window of opportunity would be small. However, other M. gui fossils have bird and mammals bones, suggesting this species may not be a picky eater.
Microraptor may not be alone in its fish-eating habits. It’s been suggested that much larger dinosaurs were fish-eaters:
When Jurassic Park 3 came out, I snickered a little bit at the use of the Spinosaurus as the “big bad” monster to up the ante over Tyrannosaurus rex. Because a quick visit to wikipedia indicated that people thought this spiny beast ate fish, based on the skull, and backward facing teeth (think of fishhooks to keep the prey in place).
Are there any anatomical features that support M. gui as an “adept aquatic predator”? This fossil gives previously unseen views of the teeth in this species. The only thing that might be related to a possible fish diet is that some of the teeth are not serrated, and some of the very frontmost teeth point forward. Both features are apparently common in fish-eaters.
Given that well-preserved Microraptor fossils seem to emerge regularly, we can probably expect still more insight into how this interesting little beast lived. Not bad for something we didn
It s wonderful to think that ten years ago, we didn’t know Microraptor gui ever existed (the genus was named in 2000, M. gui named in 2003). Now, we know what it looked like and what it ate, putting is well on the way to becoming one of the best “fleshed out” dinosaurs.
Reference
Xing L, Persons WS, Bell PR, Xu X, Zhang J, Miyashita T, Wang F, Currie PJ. 2013. Piscivory in the feathered dinosaur Microraptor. Evolution: in press. DOI: 10.1111/evo.12119
External links
There’s something fishy about Microraptor (Of course Switek beat me to this!)
Microraptor reconstruction from here.... Read more »
Xing Lida, Persons W. Scott, Bell Phil R., Xu Xing, Zhang Jianping, Miyashita Tetsuto, Wang Fengping, & Currie Philip J. (2013) Piscivory in the feathered dinosaur Microraptor . Evolution. DOI: 10.1111/evo.12119
- April 24, 2013
- 11:58 AM
- 81 views
The Dynamic Nucleus
by Perikis Livas in Tracing Knowledge
What is the Cell Picture Show?
A place to showcase striking images in cell, developmental, and molecular biology; a place to learn about cutting-edge research with beautiful images.... Read more »
Cell picture show. (2013) The Dynamic Nucleus. Cell picture show. info:/
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