Biology posts
- May 8, 2013
- 04:31 AM
- 36 views
The Black Sea is a Goldmine of Ancient Genetic Data
by Perikis Livas in Tracing Knowledge
When Woods Hole Oceanographic Institution (WHOI) marine paleoecologist Marco Coolen was mining through vast amounts of genetic data from the Black Sea sediment record, he was amazed about the variety of past plankton species that left behind their genetic makeup (i.e., the plankton paleome).... Read more »
WHOI Media Relations Office. (2013) The Black Sea is a Goldmine of Ancient Genetic Data. Woods Hole Oceanographic Institution. info:/
- May 8, 2013
- 01:30 AM
- 23 views
Atmospheric Conditions Influence Outbreaks of Disease in Europe
by Rebecca Kreston in BODY HORRORS
A recently published paper in Scientific Reports has found that climate variability in the form of the North Atlantic Oscillation (NAO) has had a significant impact on the occurrence of disease outbreaks in Europe over the past fifty years. Researchers in France and the United Kingdom studied 2,058 outbreaks occurring in 36 countries from 114 infectious diseases from 1950 to 2009 and found that climatic variations and seasonal changes in air pressure across the continent attributed to the NAO influenced the outbreak occurrences of eleven diseases. ... Read more »
Morand S, Owers KA, Waret-Szkuta A, McIntyre KM, & Baylis M. (2013) Climate variability and outbreaks of infectious diseases in Europe. Scientific reports, 1774. PMID: 23639950
- May 7, 2013
- 08:59 PM
- 17 views
Orexin and Insomnia
by Dirk Hanson in Addiction Inbox
If Valium makes you groggy, and Ambien makes you sleepwalk…
A compound that blocks a brain receptor you probably have never heard of may hold the key to the next generation of sleeping pills—and there is always a next generation of sleeping pills.
A new class of hypnotic compounds that serve as antagonists for the neurotransmitter orexin may combat insomnia without the “confusional arousals” that have come to plague some users of zolpidem, otherwise known as Ambien. Sleepwalking, sleep driving, and sleep sex are common among the reports. Orexin is involved in central nervous system arousal. So-called DORAs, or dual orexin receptor antagonists, discovered in 1998, are being seen as potential therapies for insomnia, without the daytime drowsiness and rebound insomnia typical of existing treatments. The sleep disorder narcolepsy, which is in many ways the exact opposite of insomnia, is caused by “an autoimmune attack against neurons that express orexin,” according to Emmanuel Mignot of Stanford’s Center for Sleep Sciences, in an article for Science magazine.
If these drugs are already being thought of as potential insomnia therapies, their addiction potential will have to be much lower than that of earlier generations of sleep medications. But that just might be the case, since DORA-style drugs don’t appear to promote sleep by inhibiting brain activity through neurotransmitter systems for GABA, as most existing treatments do. A study last month in Science Translational Medicine by J.M. Uslaner and coworkers asserted that DORA-type drugs caused less cognition and memory impairment in rats than Valium or Ambien, and are effective at lower doses. With drugs that modulate the orexin system, the hope is that there would be less rebound insomnia, less memory loss, less addiction, and less weird wandering around like a zombie in the middle of the night.
The search for safer sleep drugs was recently given a shot in the arm by a disturbing report from the U.S. Substance Abuse & Mental Health Services Administration (SAMHSA). Emergency room visits caused by Ambien more than doubled from 2005 to 2010, and patients 45 years and up accounted for 74% of adverse zolpidem reactions. Overall, male ER visits went up by 144%, whereas female ER visits went up almost twice as much. Overall, women made up two-thirds of all Ambien-related emergency visits—a bald fact that led the Food & Drug Administration (FDA) in January 2013 to cut the recommended dose for females in half. Lower doses were also recommended for men as well.
But a closer look at the report shows the typical confusion of polydrug use: 50% of emergency department visits for Ambien involved its use in combination with other drugs. And in 37% of cases, Ambien was used specifically in combination with other central nervous system depressants. “Although short-term medications can help patients,” SAMSHA Administrator Pamela Hyde said in a prepared statement, “it is exceedingly important that they be carefully used and monitored.”
A new class of medications based on orexin-active drugs would follow three earlier generations of sleeping pills. And each new generation of sleeping pills seems to bring its own history of unintended consequences.
In the beginning, there was meprobamate, the postwar tranquilizer known as Miltown. In additional, powerful barbiturates like phenobarbital were marketed as miracle drugs for the anxious insomniac. By the 1950s, it had become clear that these drugs were seriously addictive, and dangerous in overdose. Emmanuel Mignot noted that in high doses, barbiturates “lead to pulmonary arrest and death, outcomes that gained further notoriety with the deaths of celebrities Marilyn Monroe and Jimi Hendrix.” Barbiturates do their work by activating chloride channel receptors for the inhibitory neurotransmitter GABA. In addition, strong sedatives were increasingly being used on psychotic patients in the 1950s, and found their way into the treatment of insomnia.
The continued promise of a safe and effective hypnotic for insomnia drove research that led to the development of the first benzodiazepines, and eventually to Valium. The benzodiazepines like Valium were safer in overdose, came in a bewildering variety of flavors, and found widespread use for sleep induction—but also as anticonvulsants, anti-anxiety agents, and muscle relaxers. The benzos bound to GABA receptor sites just like the barbiturates, but the effects were less extensive. Still, it was not long before Valium, another “perfect” drug, showed it’s adverse side, in the form of sedation, memory problems, and addiction.
Then, in 2007 came the 3rd generation, in the form of the now wildly popular “Z-drugs”—zolpidem, (Ambien) zopiclone (used overseas), and zaleplon (Sonata). And again, the side effect profiles looked better in testing, the effective dose was lower, and the binding site—GABA again—looked like the right place to bring on slower brain activity and more inclination toward sleep without the “knockout effect” of earlier barbiturates and benzos. These drugs are now the default treatment for insomnia. But over time, predictably, problems revealed themselves: “Occasional problems with dependence, tolerance, and ‘confusional arousals’ are still reported with Z-drugs…. And viewed with some suspicion by doctors and patients,” writes Mignot.
Put simply, any sleep treatment that relies on the broad-brush inhibition of GABA will likely produce a range of unwelcome side effects. There are only about 70,000 orexin-producing neurons in the hypothalamus, researchers have found. But this small band of neurons has projections to histamine systems, as well as “the adrenergic locus coeruleus, and various cholinergic and aminergic cell groups,” as Mignot sums up the research. “Blocking orexin may thus be closer to treating the underlying issue of excess alertness in insomnia compared to promoting sleep by inhibiting brain activity.”
That’s the idea, at least. And it may represent a change in thinking. Researchers are no longer looking for a better knockout drug by bludgeoning the brain into inactivity. Instead, they are looking for ways to combat hyper-alertness as a key component of insomnia.
Uslaner J.M., Tye S.J., Eddins D.M., Wang X., Fox S.V., Savitz A.T., Binns J., Cannon C.E., Garson S.L. & Yao L. & (2013). Orexin Receptor Antagonists Differ from Standard Sleep Drugs by Promoting Sleep at Doses That Do Not Disrupt Cognition, Science Translational Medicine, 5 (179) 179ra44-179ra44. DOI: 10.1126/scitranslmed.3005213
Photo Credit: F Delventhal under license from Creative Commons.
... Read more »
Uslaner J. M., Tye S. J., Eddins D. M., Wang X., Fox S. V., Savitz A. T., Binns J., Cannon C. E., Garson S. L., & Yao L. (2013) Orexin Receptor Antagonists Differ from Standard Sleep Drugs by Promoting Sleep at Doses That Do Not Disrupt Cognition. Science Translational Medicine, 5(179), 179-179. DOI: 10.1126/scitranslmed.3005213
- May 7, 2013
- 07:01 PM
- 48 views
In Your Face: soldiers' faces predict aggression, military rank and number of children | @GrrlScientist
by GrrlScientist in GrrlScientist
New research demonstrates that male soldiers' faces may predict their military rank and how many children they ultimately father... Read more »
Carré J. M, & McCormick C. M. (2008) In your face: facial metrics predict aggressive behaviour in the laboratory and in varsity and professional hockey players. Proceedings of the Royal Society B: Biological Sciences, 275(1651), 2651-2656. DOI: 10.1098/rspb.2008.0873
Wong E. M., Ormiston M. E., & Haselhuhn M. P. (2011) A Face Only an Investor Could Love: CEOs' Facial Structure Predicts Their Firms' Financial Performance. Psychological Science, 22(12), 1478-1483. DOI: 10.1177/0956797611418838
Tsujimura H., & Banissy M. J. (2013) Human face structure correlates with professional baseball performance: insights from professional Japanese baseball players. Biology Letters, 9(3), 20130140-20130140. DOI: 10.1098/rsbl.2013.0140
Stirrat Michael, Stulp Gert, & Pollet Thomas V. (2012) Male facial width is associated with death by contact violence: narrow-faced males are more likely to die from contact violence. Evolution and Human Behavior, 33(5), 551-556. DOI: 10.1016/j.evolhumbehav.2012.02.002
Stirrat M., & Perrett D. I. (2012) Face Structure Predicts Cooperation: Men With Wider Faces Are More Generous to Their In-Group When Out-Group Competition Is Salient. Psychological Science, 23(7), 718-722. DOI: 10.1177/0956797611435133
- May 7, 2013
- 10:55 AM
- 50 views
What's the Point of Making This Face When We're Scared?
by Elizabeth Preston in Inkfish
If cartoonists ever pause in their sketching to ponder human evolution, they must feel grateful to the forces that shaped our fear expression. All it takes is a pair of extra-wide eyes to show that a character is freaking out. There may be a point to this expression beyond making artists' lives easier: widening our eyes expands our peripheral vision, and might even help other people spot the cause of our alarm.
"Our lab is interested in the evolutionary origins of emotional expressions," says Daniel Lee, a graduate student in psychology at the University of Toronto—in other words, "why they look the way they do." When we feel afraid, for example, is there a point to stretching out our eyelids and raising our eyebrows to the ceiling?
To explore this question, Lee and his coauthors first asked whether widening our eyes helps us see better. They had 28 volunteers look at a fixed spot on a computer screen while holding their eyes in a neutral expression, an expression of fear, or one of disgust. (Subjects acted out these expressions rather than, say, having a chair pulled out from under them before each trial. Lee points out that emotions themselves may also change our perception, but he wanted to study the effects of widened eyes separate from any psychological effects of fear on the brain. "We coached each participant on how to make fear and disgust expressions based on the Facial Action Coding System," he says.)
Subjects were tested with flashing images on the screen in their peripheral vision. Lee found that people making a disgusted expression—with the eyelids narrowed as in "Ew, get that out of my face"—scored the worst. People making a wide-eyed fear expression scored the best, with a useful field of vision 9% larger than that of people with a neutral expression.
Being afraid, then, may help us gather more visual information about whatever's threatening us in our environment. But does it also help us communicate that threat to our companions?
The researchers next used pictures of models' eyes expressing different emotions to create simplified, graphic eye images. (They didn't use real eyes because those might have conveyed extra emotional information, instead of only varying in wideness.) Subjects saw these eye images flash briefly on a screen, looking toward the right or left by varying degrees. Lee found that when the eyes were wider, subjects had an easier time telling which way they were looking. The results are reported in Psychological Science.
"We believe the widening eyes of fear...[are] a functional response for vigilance toward threat," Lee says. When we're scared, he thinks, widening our eyes helps us to see threats and to communicate their location to our group.
The researchers point out that human eyes are uniquely suited for this kind of communication: we're the only primate with a white sclera (the area outside the iris). In other apes and monkeys, this part of the eye is dark. It's yet another factor that cartoonists, no doubt, appreciate.
Lee, D., Susskind, J., & Anderson, A. (2013). Social Transmission of the Sensory Benefits of Eye Widening in Fear Expressions Psychological Science DOI: 10.1177/0956797612464500
Image: by Tom Check (via Flickr)
... Read more »
Lee, D., Susskind, J., & Anderson, A. (2013) Social Transmission of the Sensory Benefits of Eye Widening in Fear Expressions. Psychological Science. DOI: 10.1177/0956797612464500
- May 7, 2013
- 10:41 AM
- 29 views
Detecting picograms of protein in the secretome
by Kasra Hassani in The Parasite Diary
Posted by Kasra When designing experiments in the lab, we usually say we cannot check for everything. Well, what if we could?! Meissner et al. used only 150,000 macrophages per sample to analyze their secretome. They have been able to detect and quantify protein abundances at the picogram level in a label-free system. Picogram detection [...]... Read more »
Meissner F, Scheltema RA, Mollenkopf HJ, & Mann M. (2013) Direct proteomic quantification of the secretome of activated immune cells. Science (New York, N.Y.), 340(6131), 475-8. PMID: 23620052
- May 7, 2013
- 08:15 AM
- 23 views
No Bacterium Is An Island
by Moselio Schaechter in Small Things Considered
To paraphrase an old adage, no bacterium is an island. Indeed, bacteria in nature exist as polymicrobial communities where interactions between individuals influence activities of the entire population. This is especially true of pathogenic bacteria, although it has been mostly ignored because we frequently isolate a single species from an infection site and prescribe antibiotic therapy based upon this information. A recent paper by Korgaonkar and coworkers highlights that this practice is somewhat akin to burying ones head in the sand and results in an incomplete picture of the infection dynamics. By studying co-infection systems, these researchers discovered interesting details of how synergy with neighboring organisms can contribute to a pathogen’s virulence.... Read more »
Korgaonkar A, Trivedi U, Rumbaugh KP, & Whiteley M. (2013) Community surveillance enhances Pseudomonas aeruginosa virulence during polymicrobial infection. Proceedings of the National Academy of Sciences of the United States of America, 110(3), 1059-64. PMID: 23277552
- May 7, 2013
- 03:38 AM
- 28 views
Genome Patterns of Selection and Introgression of Haplotypes in Natural Populations of the House Mouse (Mus musculus)
by Martha Serrano in genome ecology evolution etc
1. How genomes evolve in natural populations? is a question that, despite to be a long-standing search for geneticists, recent molecular genomic approaches may help to understand. Their evolution among natural populations may be shaped by forces derived from … Continuer la lecture →... Read more »
Staubach F, Lorenc A, Messer PW, Tang K, Petrov DA, & Tautz D. (2012) Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus). PLoS genetics, 8(8). PMID: 22956910
- May 7, 2013
- 03:38 AM
- 45 views
Music and Cannabis; What’s the Connection?
by Mark Fonseca Rendeiro in United Academics
When you bring up the subject of listening to music while stoned, you get a range of responses, almost all of them positive. While you might enjoy a song in a non-altered state, under the influence of Cannabis, it has been established that listening to and creating music is somehow a deeper and more intense experience. The disputed issue that arises is why this happens and if the feeling is real.... Read more »
Webster, P. (2001) Marijuana and Music. Journal of Cannabis Therapeutics, 1(2), 93-105. DOI: 10.1300/J175v01n02_05
- May 6, 2013
- 01:04 PM
- 52 views
The Aspens that were left behind
by Jes in Biogeography Bits
When climates change, species move. It’s a fact of life on Earth and probably has been for the past 542 million years, even when species don’t have legs or wings or fins to get them from place to place.
Quaking aspen is one example of a seemingly stationary species that has managed in just the past 20,000 years to expand into the largest range of any native North American tree.... Read more »
Callahan, C., Rowe, C., Ryel, R., Shaw, J., Madritch, M., & Mock, K. (2013) Continental-scale assessment of genetic diversity and population structure in quaking aspen (Populus tremuloides) . Journal of Biogeography. DOI: 10.1111/jbi.12115
- May 6, 2013
- 08:21 AM
- 10 views
The Art of Microbial Alchemy
by Moselio Schaechter in Small Things Considered
In 2001, Kashefi and collaborators published an article in Applied and Environmental Microbiology reporting the surprising finding that several iron-reducing microbes can use gold as an electron acceptor for their respiration. These microbial alchemists included both mesophilic and thermophilic bacteria as well as hyperthermophilic archaea. The beauty of this process is that the oxidized form of gold provided to the microbes, Au(III), is soluble, whereas its reduced form, Au(0), is insoluble. Hence, the microbes respire soluble gold and precipitate it as gold nanoparticles on their outer surface plus, in the case of the Gram-negative bacteria, in the periplasmic space as well. These studies provided the first experimental evidence supporting the role of microbes in the formation of gold deposits in both hydrothermal and cooler environments, thus challenging the prevailing view that gold mineralization was an abiotic process. ... Read more »
Kashefi K, Tor JM, Nevin KP, & Lovley DR. (2001) Reductive precipitation of gold by dissimilatory Fe(III)-reducing bacteria and archaea. Applied and environmental microbiology, 67(7), 3275-9. PMID: 11425752
- May 6, 2013
- 08:20 AM
- 18 views
A Good Defense Is Worth Stealing
by Moselio Schaechter in Small Things Considered
One widely-used tactic for defense against phage and other mobile genetic elements is to deploy a CRISPR-Cas system (click here and here) to recognize and chop them into pieces. Based on sequenced genomes, 60% of Bacteria and 90% of Archaea have the wherewithal to dispatch invaders this way. But phages also have to protect themselves against enemies, including other mobile elements. Knowing a good thing when they see it—and they have seen it from the receiving end often—some phages have stolen the entire CRISPR-Cas structure and use it to inactivate genetic elements that would interfere with their replication.... Read more »
Seed KD, Lazinski DW, Calderwood SB, & Camilli A. (2013) A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity. Nature, 494(7438), 489-91. PMID: 23446421
- May 6, 2013
- 07:00 AM
- 37 views
May 6, 2013
by Erin Campbell in HighMag Blog
Our bodies have multiple fronts for battling viruses, and it’s impressive that any of those suckers manage to invade our bodies at all. When virus particles do make their way into a cell, it’s important for biologists to understand their pathway through a cell in order to create drug therapies and vaccines. Today’s image is from a paper describing the use of high resolution imaging to understand this process.The polarized cells that line our digestive and respiratory tracts form a tight barrier that protects our bodies from viruses. Understanding how viruses are able to breach these polarized epithelial cells is important in guiding the development of therapeutics and vaccines, yet previous research has focused mainly on in vitro studies of virus entry into nonpolarized cells. Microscopy advances have recently allowed the high-resolution imaging of virus entry in polarized epithelial cells. Boulant and colleagues used live-cell spinning-disk confocal microscopy to follow the uptake of single mammalian reovirus (MRV) virions and infectious subvirion particles (ISVPs) in polarized Madin–Darby canine kidney cells. Both virus particles were internalized by clathrin-mediated endocytosis at the apical surface. MRV virions reached early and late endosomes, while ISVPs escaped the endocytic pathway prior to reaching early endosomes. In the images above, the tight-junction protein ZO-1 (red, left) shows the typical belt pattern surrounding the polarized cells (side views are also shown in the top and side strips). The MRV cell surface receptor JAM-A (red, right) is localized near tight junctions and on the apical side of the cells.Boulant, S., Stanifer, M., Kural, C., Cureton, D., Massol, R., Nibert, M., & Kirchhausen, T. (2013). Similar uptake but different trafficking and escape routes of reovirus virions and infectious subvirion particles imaged in polarized Madin-Darby canine kidney cells Molecular Biology of the Cell, 24 (8), 1196-1207 DOI: 10.1091/mbc.E12-12-0852... Read more »
Boulant, S., Stanifer, M., Kural, C., Cureton, D., Massol, R., Nibert, M., & Kirchhausen, T. (2013) Similar uptake but different trafficking and escape routes of reovirus virions and infectious subvirion particles imaged in polarized Madin-Darby canine kidney cells. Molecular Biology of the Cell, 24(8), 1196-1207. DOI: 10.1091/mbc.E12-12-0852
- May 6, 2013
- 04:36 AM
- 53 views
The ESSENCE of autism comorbidity?
by Paul Whiteley in Questioning Answers
Like Charlie Bucket looking through the sweet shop window at the delicious chocolates produced by the workforce of a certain Mr Willy Wonka (the candyman no less), I am always quite interested in the goings-on at the IMFAR autism research conference. The candyman can... @ Wikipedia This year (2013) proved to be a bit of a vintage, as once again the great and the good presented their Wonka bars of autism research; thus hinting at the direction of future autism research and what you can expect to read on this blog in the coming months. Oh, and something about poodles(?) (thanks Carol).I've been hearing quite a bit of chatter about the keynote speech given by Prof. Christopher Gillberg which seemed to quite strongly hint that the autism research community should be paying rather more attention to the add-ons which seem to accompany a diagnosis of autism, rather than seeing autism as just existing stand-alone in a diagnostic vacuum.Far be it from me to say 'I told you so', but comorbidity and overlap, and the often far-reaching effects on quality of life of certain comorbidity, has been a theme running through many posts on this blog and not just the more behaviourally-defined type of comorbidity. So for example the question of 'significantly over-represented' and all that autism's' chatter (note the plural) immediately come to mind. Indeed I don't actually believe that many people in the know would view the autisms as just being the total sum of the triad (very soon to be dyad). Or would they?Mention of the word ESSENCE - Early Symptomatic Syndromes Eliciting Neurodevelopmental Clinical Examinations* - has apparently been made in Prof. Gillberg's address denoting "the reality of children (and their parents) presenting in clinical settings with impairing child symptoms before age 3 (-5) years in the fields of (a) general development, (b) communication and language, (c) social inter-relatedness, (d) motor coordination, (e) attention, (f) activity, (g) behaviour, (h) mood, and/or (i) sleep". Before proceeding, I would perhaps suggest that Gillberg seems to have some interest in the use of acronyms in autism research and beyond as per the example of DAMP and MBD**.Anyhow, a quick scan of the peer-reviewed research literature does indeed see a small but growing body of work discussing ESSENCE and its use in autism research circles. I note for example this paper by Prof. Brian Neville*** who highlights an essential part of the use of ESSENCE: that the presentation of behaviour in infants and young children is often complex, and the "problems are their multiplicity". Common sense perhaps?Perhaps one of the best (so far) papers discussing the concept of ESSENCE in a real-world clinical setting is this one from Lotta Höglund Carlsson and colleagues**** (open-access) (which includes Gillberg as part of the authorship team). The paper is free for all to read so no great dissection required from me. That being said, I would highlight the fact that based on examination of just over 100 children diagnosed with an autism spectrum disorder (ASD), "a mean of 3.2 coexisting disorders or problems" were reported, including a third of children presenting with "severe hyperactivity/ADHD".I was particularly interested in this autism-ADHD link given some other recent research on the overlap*****. That and the fact that additional reports have indicated even higher levels of overlap between autism and ADHD (see this post) calls into question whether the two labels may intersect even more than we perhaps have appreciated.One of the potential implications of the co-occurrence of autism and ADHD is with regards to intervention and therapeutic options. Without trying to hijack the association with my dietary mumbo-jumbo, I would draw your attention to a previous post I published a while back on food and ADHD and some potential lesson for autism (see here). The suggestion there - and it was only a suggestion - was that some of the observations made when looking at the impact of a dietary intervention for autism actually working on some of the symptoms associated with ADHD might imply that targeting such comorbidity might eventually impact on more core autism presentation. A shocker I know that children being described as less impulsive and attending better might actually have better outcome.I'm finishing shortly but before I do, I want to draw your attention to another ESSENCE mention in the paper by Stephanie Plenty and colleagues****** (open-access) who looked at the retrospective application of the concept in cases of adult ASD and ADHD. They similarly reported: "Although differences were observed between ADHD and ASD patients in the core diagnostic areas, these syndromes also shared a number of childhood difficulties".The wave of research and opinion which is seemingly directing everyone to this idea that autism is not a stand-alone label is growing. Add into the mix the recent announcement that even before the introduction of DSM-V the NIMH prefer an even broader view of behaviour and psychiatry (RDoC) ('reorienting' apparently) and that autism-ADHD-[insert other] spectrum is starting to feel more and more like a giant tapestry.To close, for the second time in this post I'm going to direct you to the genius of Sammy Davis Jnr - the Candyman can y'know.---------* Gillberg C. The ESSENCE in child psychiatry: Early Symptomatic Syndromes Eliciting Neurodevelopmental Clinical Examinations. Res Dev Disabil. 2010; 31: 1543-1551.** Gillberg C. Deficits in attention, motor control, and perception: a brief review. Arch Dis Child 2003; 88: 904-910.*** Neville B. Role of ESSENCE for preschool children with neurodevelopmental disorders. Brain Dev. 2013; 35: 128-132.**** Höglund Carlsson L. et al. Coexisting disorders and problems in preschool children with autism spectrum disorders. Scientific World Journal. 2013: 213979.***** Cooper M. et al. Autistic traits in children with ADHD index clinical and cognitive problems. Eur Child Adolesc Psychiatry. April 2013.****** Plenty S. et al. Applying an ESSENCE Framework to Understanding Adult Autism Spectrum Disorder and ADHD: Retrospective Parent Reports of Childhood Problems. Scientific World Journal. 2013: 469594.----------... Read more »
Höglund Carlsson, L., Norrelgen, F., Kjellmer, L., Westerlund, J., Gillberg, C., & Fernell, E. (2013) Coexisting Disorders and Problems in Preschool Children with Autism Spectrum Disorders. The Scientific World Journal, 1-6. DOI: 10.1155/2013/213979
- May 5, 2013
- 11:44 AM
- 47 views
Pumping fuel from bacteria
In my last post I discussed a bioengineered E. coli strain capable of producing an engine compatible biofuel. I hailed the finding as more efficient than ordinary biofuels because this technique has less environmental impact than biofuels from crops, for example, or cellulose, which instead use great amounts of water and forest land. I did some more reading on the topic and found out that, surprise surprise, there are some costs in harvesting biofuels from bacteria as well, so my discussion was incomplete. However, there are good news at the horizon. When I first read the Howard et al. paper, I imagined a petri dish of E. coli sitting in a slime of oil-like substance. I think I got confused with making yogurt. :-) In reality, the biofuel molecules are stored inside the cells (bacteria, in this case) and need to be taken out without harming the cells. Biofuel secretion strategies have been dubbed "milking." The difference, though, is that contrary to milk and cows, biofuels are generally toxic to the bacteria that produce them.Several methods have been investigated to efficiently "milk" biofuel molecules out of bacteria without harming them. To understand these strategies, we need to learn a new concept: an efflux pump is a membrane transporter protein that carries a substance toxic to the cell outside the cell itself. These proteins remove all kinds of toxic substances, including antibiotics, for example, and they may be specific to one in particular, or carry a whole range. In [1], Dunlop et al. discuss the use of efflux pumps in "milking" biofuels out of bacteria and reduce their toxicity to the cells:"Many compounds being considered as candidates for advanced biofuels are toxic to microorganisms. This introduces an undesirable trade-off when engineering metabolic pathways for biofuel production because the engineered microbes must balance production against survival. Cellular export systems, such as efflux pumps, provide a direct mechanism for reducing biofuel toxicity."The researchers first looked at the whole genome of E. coli to identify all genes encoding efflux pumps. They found 43 different pumps expressed in the E. coli genome, and tested them against a range of possible biofuels. Their strategy was as follows: the grew a culture of pooled bacteria with different subpopluations, each subpopulation expressing a different pump. In the absence of toxic biofuel-like substances, all subpopulations grew in equal proportions, and none had an advantage over the others. When a substance was introduced, the subpopulations with the most advantageous pumps with respect to that particular substance outgrew the rest. This is what happened, for example, when they introduced geranyl acetate:"When the pooled culture was grown in the presence of an inhibitory biofuel such as geranyl acetate, some efflux pumps conferred a distinct advantage. Although all strains started out with equal representation, after 38 h the population composition changed, with cells containing the advantageous pumps becoming an increasingly large proportion of the population. The efflux pumps that enhanced tolerance to geranyl acetate originated from a variety of hosts and include both known and previously uncharacterized pumps."In their study, Dunlop et al. used a type of membrane transporters called "RND," which are made of big molecules and are only found in Gram-negative bacteria. In a more recent paper [2], Doshi et al. studied a broader set of pumps called ABC, ATP-binding cassette:"Unlike RND proteins, transporters belonging to the ATP- binding cassette (ABC) protein family are widely found in all five kingdoms of life. They share a conserved structural architecture and specifically import or export a wide variety of molecules and ions across cellular membranes."Doshi et al. tested whether this family of broadly specific pumps could efficiently mediate the secretion of four different biofuel molecules. Similarly to the Howard et al. paper, they used a bioengineered strain of E. coli and noticed that "the secretion process was sustained for at least 6 days without the need to replenish the growth medium or culture. Thus, for the same quantity of biofuel produced conventionally, we have a dramatic reduction in biomass scale and significant gain in the ease of recovering the biofuel."Though my understanding is that work still needs to be done to improve this technique and make it feasible for different types of biofuels, the fact that these transporters are spread across different species makes it potentially translatable to other organisms and therefore of broader use. On a completely different note, can you guess what the macro picture is? :-)[1] Dunlop, M., Dossani, Z., Szmidt, H., Chu, H., Lee, T., Keasling, J., Hadi, M., & Mukhopadhyay, A. (2011). Engineering microbial biofuel tolerance and export using efflux pumps Molecular Systems Biology, 7 DOI: 10.1038/msb.2011.21[2] Doshi, R., Nguyen, T., & Chang, G. (2013). Transporter-mediated biofuel secretion Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1301358110... Read more »
Dunlop, M., Dossani, Z., Szmidt, H., Chu, H., Lee, T., Keasling, J., Hadi, M., & Mukhopadhyay, A. (2011) Engineering microbial biofuel tolerance and export using efflux pumps. Molecular Systems Biology. DOI: 10.1038/msb.2011.21
Doshi, R., Nguyen, T., & Chang, G. (2013) Transporter-mediated biofuel secretion. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1301358110
- May 5, 2013
- 05:57 AM
- 53 views
More on 'Bugs as Drugs'
by Christen Rune Stensvold in Blastocystis Parasite Blog
A follow-up on Carl Zimmer's post in "Phenomena" (National Geographic) on 'Bugs as Drugs'.... Read more »
Hyman P, Atterbury R, & Barrow P. (2013) Fleas and smaller fleas: virotherapy for parasite infections. Trends in microbiology. PMID: 23540830
van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, Visser CE, Kuijper EJ, Bartelsman JF, Tijssen JG.... (2013) Duodenal infusion of donor feces for recurrent Clostridium difficile. The New England journal of medicine, 368(5), 407-15. PMID: 23323867
Weinstock JV. (2012) Autoimmunity: The worm returns. Nature, 491(7423), 183-5. PMID: 23135449
- May 5, 2013
- 05:22 AM
- 71 views
The (Lack of) Changes in Ecological Research
by gunnardw in The Beast, the Bard and the Bot
Ecology is a rapidly changing, dynamic field of research. In recent decades, there’s been a major shift from considering ecosystems as stable and poised to seeing them as systems that are in constant flux. At least, that’s what ecologists want (us) to believe. But how much of this claimed change has been able to seep [...]... Read more »
Carmel, Y., Kent, R., Bar-Massada, A., Blank, L., Liberzon, J., Nezer, O., Sapir, G., & Federman, R. (2013) Trends in Ecological Research during the Last Three Decades – A Systematic Review. PLoS ONE, 8(4). DOI: 10.1371/journal.pone.0059813
- May 4, 2013
- 12:40 AM
- 56 views
Help: My freaky protein doesn’t have structure. And it aggregates!
by Vicky Doronina in Protein Solubility Blog
A biochemist about to attempt membrane protein purification knows that she is in the beginning of a difficult time in her career. However, there is another wide class of proteins, which are also difficult to purify, because they readily form protein aggregates or are plain insoluble. These are so called intrinsically disordered proteins (IDPs); but just a disordered domain within an otherwise nicely folded globular protein can be enough for the overexpressed protein to aggregate.... Read more »
Dunker, A., Silman, I., Uversky, V., & Sussman, J. (2008) Function and structure of inherently disordered proteins. Current Opinion in Structural Biology, 18(6), 756-764. DOI: 10.1016/j.sbi.2008.10.002
Uversky, V. (2013) Unusual biophysics of intrinsically disordered proteins. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1834(5), 932-951. DOI: 10.1016/j.bbapap.2012.12.008
- May 3, 2013
- 11:00 PM
- 60 views
Evolutionary economics and game theory
by Artem Kaznatcheev in Evolutionary Games Group
Like the agents they study, evolutionary economics is highly heterogeneous. Models are ad-hoc and serve as heuristic guides to specific problems. This is similar to theoretical biology, where evolutionary models are independent of each other. Even the general theory of inclusive fitness does not provide a non-controversial unifying framework. Although there is no single framework, evolutionary economists are united by four main assumptions about the world:... Read more »
Hodgson, G., & Huang, K. (2010) Evolutionary game theory and evolutionary economics: are they different species?. Journal of Evolutionary Economics, 22(2), 345-366. DOI: 10.1007/s00191-010-0203-3
- May 3, 2013
- 05:48 PM
- 2 views
Scatological Scents
by Mini Watsa in SurroundScience
Ever since tamarins were first captured from the wild to serve as research models in laboratories, we have been curious about their use of odour for communication. These miniature monkeys … Continue reading →... Read more »
Threlfall C., Law B., & Banks P. B. (2013) Odour cues influence predation risk at artificial bat roosts in urban bushland. Biology Letters, 9(3), 20121144-20121144. DOI: 10.1098/rsbl.2012.1144
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