The neocortex is a mammalian invention, not present in birds, reptiles, or any other vertebrates. It's associated with the increases in intelligence seen in mammals since the end of the Cretaceous, especially in primates, and more especially in humans. While there are dozens (probably hundreds) of discussions of the neocortex available on the Web, I haven't been able to find one that meets my needs (for linking to in detailed discussions), so I'm going to produce my own, in the process discussing a recent paper which reflects on it.The neocortex develops from a part of the developing neural tube called the telencephalic pallium. This is the part of the telencephalon that is towards the back (dorsal) and upper side (dorso-lateral), while the part towards the middle of the body (medial) develops into the hippocampus, including the dentate gyrus and some other parts of the brain associated with memory (especially spacial memory) and navigation. The bottom (ventral) part of the telencephalon develops into the basal nuclei, which "are associated with a variety of functions: motor control, cognition, emotions, and learning. [Wiki]" (The telencephalon is split into two parts, one on each side, a feature not visible in Figure 1.)Figure 1: Parts of the neural tube. (From Wiki)We'll come back to the neural tube, but for the moment let's take a look at the structure of the neocortex, by comparison with other structures: ... those that develop from the medial and ventro-lateral part of the pallium, and those in reptiles such as turtles and lizards (crocodilians are too closely related to dinosaurs and birds, and will not be considered) that have been shown to be almost certainly homologous to the neocortex: the dorsal and dorso-lateral cortex. These latter structures develop from the same part of the pallium in these reptiles as the neocortex does in mammals, and they share many similar connections, so it's worthwhile drawing parallels.Most sites discussing the neocortex will tell you that it has six layers rather than the three found in these other structures, and that the cells mature from the outside in rather than the opposite. Many will also tell you that incoming axons arrive from the bottom rather than the top: that is from the direction of the inside of the neural tube rather than the outside. All these facts are generally true, although some details are often left out and the language is often obscured by the use of various anatomical terms. Let's go over it in detail.The first difference has to do with the direction of maturity, the fact that cells mature from the outside in. Neurons in this part of the neural tube are created by cell divisions in the very inner part of the neural tube, called the ventricular zone. From there, they migrate radially, towards the outer part of the tube (called the pial surface). In turtles and lizards, these cells begin by settling in the outer part of what will become the dorsal cortex, and later cells settle inwards of them, closer to the center of the nerual tube. This is what is meant by outside-in maturation, since once they settle, these cells begin to mature.What most sites discussing the neocortex don't mention is that in the mammalian hippocampus (except for the dentate gyrus) the first cells settle on the inside, closest to the middle of the neural tube, and later cells settle farther out. This is exactly what they do in the developing neocortex, which means that this change is not limited to the neocortex, but is somewhat more general to the mammalian pallium. It's a good guess that it came first, and it allows for a greater thickness of cortex with interconnections, even without the other changes, as is shown by the structure of the hippocampus.The next change is the six-layered structure, which arises in the upper dorsal pallium and the dorsal part of the lateral pallium. This structure probably derives from the more primitive three-layered structure found in turtles, lizards, and the mammalian hippocampus, although the latter has evolved a much thicker outer layer and a characteristic "double-C pattern" with the dentate gyrus curved around the hippocampal gyrus. The three-layered structure in general is called the "allocortex": this word specifically stands for the parts of the "cerebral cortex" with a three-layered structure, although it's often used for other areas with the same cortical structure. (The "cerebral cortex" technically refers to the entire cortical area formed from the pallium, but is often instead mistakenly identified with the neocortex.)We need to start by describing the three-layered structure, then, before we can compare it with the six-layered. The three layers are like a sandwich, with areas of mostly neurites (axons, dendrites, synapses, and glial cells) making up the bread, while the filling is densely filled with neural cell bodies (somas). Most of the neural connections come from the outside (the side away from the center of the primitive neural tube), while in this area most of the axons leaving do so out the bottom (the side towards the center of the neural tube). This provides for a simple "pass-through" system, in which the nerve cells process the incoming information and produce an output which goes to another brain region.The disadvantage of this system is that the incoming axons are growing along the top of this layer, and trying to make synaptic connections with any cells they encounter. Since most of these cells don't want any specific connection, most of these attempts are refused, which constitutes a major waste of resources. Which leads us to the third difference, which is that many incoming axons from other parts of the brain come from below in mammals, in more evolved mammals, such as primates and carnivores, virtually all. We'll discuss this shortly.Before we do so, we need to consider the layers of the neocortex, which are very different from the allocortex. The layers of the neocortex are usually numbered I through VI (usually using Roman numerals, although many websites use Arabic). Layer I is almost completely free of neuron somas, being mostly made up of neuropil, along with blood vessels and other support structures. Layers II and III have many neuron somas, a good mix of pyramidal cells (see below) and interneurons, the latter usually making local connections with their axons as well as their dendrites. Layer IV is composed of a mix of stellate cells, which like interneurons make local connections, in the sense that they typically don't extend their axons out of the area they reside, but they extend much farther than interneurons, and they tend to be exitory rather than inhibitory (see below). Layers V and VI contain mostly pyramidal cells, although with some interneurons, and the lower part of layer VI often contains a large proportion of neurites, especially axon branches.In the allocortex, the majority of the interconnections are in the upper layer, although the lower layer (the one closest to the middle of the... Read more »
Alessandra Pierani, & Marion Wassef. (2009) Cerebral cortex development: From progenitors patterning to neocortical size during evolution. Development, Growth and Differentiation, 51(3), 325-342. DOI: 10.1111/j.1440-169X.2009.01095.x
Eben Alsberg (Case Western Reserve University, Ohio) and coworkers have applied biodegradable hydrogels for the sustained and local release of interfering RNA, a possible tool for gene silencing. This news feature was written on July 18, 2009.... Read more »
Krebs, M. D., Jeon, O., & Alsberg, E. (2009) Localized and Sustained Delivery of Silencing RNA from Macroscopic Biopolymer Hydrogels. Journal of the American Chemical Society, 131(26), 9204-9206. DOI: 10.1021/ja9037615
We think of spiders as fearsome hunters, spinners of webs and treacherous mates, but construction workers? Yes, that too. Some groups of spiders - trapdoor and wolf spiders - dig tunnels that they use to ambush passing insects. But these tunnels can also provide shelter and accommodation for other animals, including one of the rarest of Australia's lizards - the pygmy blue-tongue lizard. It seems that the lizard's survival depends entirely on the spiders.
The pygmy blue-tongue is a native of South Australia. It's so rare that zoologists thought it extinct for over 30 years and it re-emerged in the public eye in the most unlikely way. In 1992, a dead specimen of this supposedly extinct animal was found in the stomach of a brown snake, found dead on the side of a road. That unexpected discovery prompted intensive surveys of the surrounding area, which found several lizards living in spider burrows.
Like the spiders, the lizards use the burrows for ambush but they also act as nurseries, cooling stations and defensive forts. To understand the relationship between lizards and spiders, Michael Bull from Adelaide's Flinders University studied the fates of both species in a single hectare of South Australian land. Over two years, his team spent bursts of two weeks, intensively searching the plot of land for signs of burrows. Each one was probed with a fibre optic camera to see who lay inside.
Earlier studies have found that lizards readily accept artificial burrows and adding these to the local area will halt the decline of the lizard populations. That's all very good, but as Bull writes, "a sustainable supply of natural burrows would be a better option in the longer term".
Read the rest of this post... | Read the comments on this post...... Read more »
Fellows, H., Fenner, A., & Bull, C. (2009) Spiders provide important resources for an endangered lizard. Journal of Zoology. DOI: 10.1111/j.1469-7998.2009.00600.x
The determination of the ß-adrenergic receptor GPCR structure in 2007 was a breakthrough in structural biology. Combined with the earlier structure of rhodopsin, this provided a template for structure-based design for GPCRs. However, there was a lurking mystery in the structure, a mystery which was not always discussed but which has started to come to light recently.Th mystery is exemplified by a recent paper in which authors from D E Shaw Research in New York use extremely long molecular dynamics simulations to uncover a peculiar conformational characteristic of the ß2 AR. The original structure was crystallized bound to an inverse agonist named carazolol. The receptor as crystallized was thought to be in an inactive state. In this state, two helices of the receptor were at some distance from each other. However, this observation did not square with biochemical experiments that indicated proximity of the two helices mediated by a crucial ionic lock, a salt bridge between a glutamate and arginine. This lock however was absent in the crystal structure, raising questions about the exact role of the lock in activating the receptor and the nature of the inactive state.In the present study, the authors used extremely long, microsecond MD simulations on the crystal structure. They used the DESMOND program recently introduced by Schrodinger and D E Shaw to perform simulations of the GPCR in a lipid bilayer.All they really had to do was wait. The first 150 ns were not very interesting from the perspective of the salt bridge. However, the salt bridge spontaneously formed after 150 ns and then stayed put like a fly on fly paper. Notice the N-O distance (blue) and how it stabilizes after 150 ns.The bridge also involved local movement of the helices and some important residues. The authors also did the simulation in the presence and absence of the ligand and found that this lock forms irrespective of the presence of the ligand. They follow up with some mutagenesis experiments that reconcile the conformational changes with experimental observations. Interestingly, they mutate an aspartate that is also proximal to the arginine in the salt bridge. Mutation of this aspartate would be expected to "free up" the arginine and further encourage its interaction with the glutamate. However, the opposite seemed to happen, indicating an interesting role for the aspartate as a something of lock itself in holding the aspartate fixed.The overall conclusion is that there are probably two inactive states, one in which the salt bridge is formed (the dominant one) and one in which it's broken (not high populated) and the receptor recycles between the two. This kind of observation is clearly important for further structure-based design since it implies that one could encourage GPCR activation if the "right" conformation of the receptor could be preferentially stabilized.The thing to note here is the time. Nothing interesting would have been observed had the simulation been run for less than 150 ns. Researchers who ran the simulation for less than 150 ns may not have had something worth reporting. 150 ns is a reasonably long amount of time for any MD program or simulation. The fact that such simulations can be run for microseconds attests to the rapid development of hardware and software exemplified by D E Shaw's program DESMOND and their processor named ANTON.Sometimes simply waiting long enough can lead to productive results. Echoing an unpleasant man's ominous pronouncement, "Quantity has a quality of its own".Dror, R., Arlow, D., Borhani, D., Jensen, M., Piana, S., & Shaw, D. (2009). Identification of two distinct inactive conformations of the ß2-adrenergic receptor reconciles structural and biochemical observations Proceedings of the National Academy of Sciences, 106 (12), 4689-4694 DOI: 10.1073/pnas.0811065106... Read more »
Dror, R., Arlow, D., Borhani, D., Jensen, M., Piana, S., & Shaw, D. (2009) Identification of two distinct inactive conformations of the 2-adrenergic receptor reconciles structural and biochemical observations. Proceedings of the National Academy of Sciences, 106(12), 4689-4694. DOI: 10.1073/pnas.0811065106
by Vincent Racaniello in virology blog
Dispensers of alcohol-based rubs are appearing in public places in an attempt to reduce the spread of pandemic influenza. Are these effective at removing virus from hands?
In a recent study, the hands of twenty vaccinated, antibody-positive volunteers were contaminated with 10,000,000 TCID50 of a 1999 seasonal H1N1 influenza virus strain (see this post for an [...]... Read more »
Grayson, M., Melvani, S., Druce, J., Barr, I., Ballard, S., Johnson, P., Mastorakos, T., & Birch, C. (2009) Efficacy of Soap and Water and Alcohol‐Based Hand‐Rub Preparations against Live H1N1 Influenza Virus on the Hands of Human Volunteers. Clinical Infectious Diseases, 48(3), 285-291. DOI: 10.1086/595845
How do antidepressants work? Some people will tell you that it’s all about neurogenesis. The theory goes that antidepressants increase the rate at which new neurones are created in a region called the dentate gyrus of the hippocampus, and that, somehow, this boom in the number of new hippocampal cells alleviates depression.To date, however, all of the research linking antidepressants and neurogenesis has involved animals. It was generally assumed that if drugs altered neurogenesis in mice, the same thing happened in humans – but this was an assumption, and clearly a pretty big one. Now a new report from a New York-based team claims that antidepressants do enhance neurogenesis in people - Antidepressants increase neural progenitor cells in the human hippocampus. The authors took post-mortem brain samples from three groups of people – those with no history of depression, those with depression who were not on antidepressants when they died, and depressed people who were on antidepressants. They counted the number of neural progenitor cells (NPCs) in the hippocampus using a stain which specifically marks these cells (anti-nestin).Although like all post-mortem studies the sample size was small (n=19 total), depressed people taking antidepressants when they died had much higher NPC numbers, indicating greater neurogenesis, compared to the other two groups. (Control: 360±246; untreated: 1119±752; treated: 17229±3443).The picture above illustrates this; the brown cells are NPCs, and there are evidently more of them in the antidepressant-taking person on the right compared to the control on the left. The authors presumably picked these images because they look different, so, pinch of salt. But still, as an antidepressant user myself, it's nice to see what might well be going on inside my skull at this moment.The dentate gyrus of the hippocampus, the area where neurogenesis happens, was also larger in the antidepressant-treated group.Is this evidence for the neurogenesis theory? Not exactly. It’s fairly good evidence that some antidepressants do boost hippocampal neurogenesis in humans, in accordance with the animal data. But we really don’t know what that means. It could just be a side effect, and nothing to do with how they work. I’ve previously written about some recent animal experiments finding that antidepressants have effects on behaviour even when neurogenesis is completely blocked. And notably, five of the seven antidepressant-treated patients in this study died from suicide. So, to put it bluntly, the drugs didn’t work very well, despite sending neurogenesis through the roof...Boldrini, M., Underwood, M., Hen, R., Rosoklija, G., Dwork, A., John Mann, J., & Arango, V. (2009). Antidepressants increase neural progenitor cells in the human hippocampus Neuropsychopharmacology DOI: 10.1038/npp.2009.75... Read more »
Boldrini, M., Underwood, M., Hen, R., Rosoklija, G., Dwork, A., John Mann, J., & Arango, V. (2009) Antidepressants increase neural progenitor cells in the human hippocampus. Neuropsychopharmacology. DOI: 10.1038/npp.2009.75
It's an interesting question, when did photosynthetic life first invade dry land, and what type was it? The tradition is that green plants first invaded the land in the Ordovician or Silurian, if not later, sometime after 500 MYA, well after the Cambrian, when we first see fossils of animals developing in the ocean (there are actually some from earlier, but those may not be animals, and we know little about them). However, there are various lines of evidence that there was already extensive land-based photosynthesis going on a good deal earlier,  including a very recent paper: The late Precambrian greening of the Earth (by L. Paul Knauth and Martin J. Kennedy, unfortunately behind a paywall), which examined the correspondence of ratios of carbon isotopes and oxygen isotopes in precambrian deposits, specifically from areas influenced by runoff from continents: Here we compile all published oxygen and carbon isotope data for Neoproterozoic marine carbonates, and consider them in terms of processes known to alter the isotopic composition during transformation of the initial precipitate into limestone/dolostone. We show that the combined oxygen and carbon isotope systematics are identical to those of well-understood Phanerozoic examples that lithified in coastal pore fluids, receiving a large groundwater influx of photosynthetic carbon from terrestrial phytomass. Rather than being perturbations to the carbon cycle, widely reported decreases in 13C/12C in Neoproterozoic carbonates are more easily interpreted in the same way as is done for Phanerozoic examples. This influx of terrestrial carbon is not apparent in carbonates older than ~850 Myr, so we infer an explosion of photosynthesizing communities on late Precambrian land surfaces. As a result, biotically enhanced weathering generated carbon-bearing soils on a large scale and their detrital sedimentation sequestered carbon. This facilitated a rise in O2 necessary for the expansion of multicellular life. This analysis basically plotted the isotope ratios from thousands of observations on a two-dimensional axis, and observed that those from after about 850MYA fell into the same groups whether they were after the beginning of the Cambrian or before. This leads to the very plausible conclusion that photosynthesizers had colonized the land and were producing large amounts of carbon-rich detritus that was then oxidized and deposited.This has some interesting implications: ... The contrasting isotope data between 850 Myr ago and the Neoproterozoic suggest that the terrestrial expansion of photosynthesizing communities preceded the significant climate perturbations of the late Precambrian glaciations, and was followed by a rise of O2 ([ref]) and a secular change in terrestrial sediment composition. The onset of significant biotically enhanced terrestrial weathering would have increased the flux of lithophile nutrient elements and clay minerals to continental margins. This would have increased production and burial preservation of organic C towards modern values and consequently facilitated the stepwise rise in atmospheric O2 necessary to support multicellularity. The terrestrial expansion of an extensive, simple land biota indicated by the isotope data may thus have been a critical step in the transition from the Precambrian to the Phanerozoic world. The biggest problem with this is the lack of fossils identifiable as from plants, although the "squishier" plants leave few fossils.There is one very important feature of plants that allowed them to colonize the land: the invention of mixtures of lignin and cellulose that protects them against the "soft" ultraviolet radiation (UV) that makes it through the ozone layer. This mixture, in turn, depends on a synthesis pathway that begins with an enzyme called Phenylalanine Ammonia Lyase (PAL), "which catalyses the first and essential step of the general phenylpropanoid pathway, leading from phenylalanine to p-Coumaric acid and p-Coumaroyl-CoA, the entry points of the flavonoids and lignin routes."Another very recent paper, A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land (by Giovanni Emiliani, Marco Fondi, Renato Fani, and Simonetta Gribaldo) reports an intriguing discovery: that the gene for this enzyme was almost certainly acquired via horizontal gene transfer from a soil bacterium, or perhaps from a fungus that had in turn acquired it from a soil bacterium. What they did was to examine the phylogenetic tree of "160 representative sequences" from various species, discovering that all the genes in plants and fungi are descended from a single ancestor related to those of one bacterial lineage. This gene "is homologous to histidine ammonia lyase (HAL), which is involved in the catabolism of histidine and is widespread in prokaryotes and eukaryotes [refs]. It has been proposed that "PAL developed from HAL when fungi and plants diverged from the other kingdoms" [ref]. However, the current view of eukaryotic evolution based on phylogenetic analyses indicates that fungi and plants do not share an exclusive ancestor [refs]. In fact, Fungi are more related to Animals than to land plants. Moreover, land plants belong to the phylum Plantae, which also includes Glaucocystophytes, red algae, and green algae [refs]."Figure 1: Phylogenetic tree of HAL/PAL gene. Click on image to see original with caption. (From Ref 8 Figure 2)This, combined with the observations of Knauth et al., brings us to an interesting suggestion: is it possible that, before green plants invaded the land, it was covered with lichens? Lichens, even today, often grow in areas that are heavily exposed to sunlight (UV) but lack the soil necessary for plant roots (and their symbiotic association with certain fungi). Absent plants, they may well have been able to colonize just about any area with sufficient rainfall to provide the water they needed. Lichens are known to invade rock for nutrients, and even cyanobacteria, one of the groups of algae that for symbiotic relationships with fungi to create lichens can chemically erode rocks. The possibility that there was a coating of lichens over most of the Earth's surface as long as 850MYA is quite intriguing.An obvious question is: what, if anything, ate these lichens? Here I want to hark back to a suggestion I made a while back, regarding the origin of multi-celled animals, and probably other forms of life: Could it be that the common ancestor of fungi and animals was actually multinucleate, an amoeba-like creature with lots of nuclei, a flexible shape, and a feeding pattern based on engulfing its food?Such a creature would be well positioned to evolve into both fungi and metazoans, with the latter branch having lots of collared flagelli. The question is, why evolve multiple cells? The answer could well be an explosive adaptive radiation of invasive, intracellular predators. Such an explosion would explain the sudden acquisition of multicellularity by many lineages. It isn't just animals and fungi that would be so descended, and it's quite possible that a variety of multinucleate amoeboids were present in these early times that fed on the early lichens I've proposed. (Indeed, there are many such today. These may well have lived in small, shaded tunnels during the day (when solar UV may well have threatened them), and come out at night to feed on the upper levels o... Read more »
Emiliani, G., Fondi, M., Fani, R., & Gribaldo, S. (2009) A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land. Biology Direct, 4(1), 7. DOI: 10.1186/1745-6150-4-7
How genes for altruism can benefit strangers as well as kin
The generosity of adoption has long been considered a unique human hallmark.
Image: Shadows of Forgotten AncestorsFor decades it was conventional dogma that humans were the only species that used tools. "Man the Toolmaker" was our celebrated designation. The hominin fossil Homo habilis (or "handy" man) was even defined within our genera primarily because the skeleton was associated with stone implements. However, when Jane Goodall discovered chimpanzees using modified sticks at Gombe to "fish" for termites, Louis Leakey famously cabled her that:
Now we must redefine man, redefine tool - or accept chimpanzees as human.
By now people should stop insisting on singling out specific human behaviors and declaring them to be unique in the natural world. Invariably, whatever special attributes humans possess, other primates do in some form as well. For many years it's been argued that humans are the only primates that will adopt unrelated individuals to care for as their own. This has been conventional wisdom because it doesn't make intuitive sense according to the rigid definition of biological fitness. Read the rest of this post... | Read the comments on this post...... Read more »
Cäsar, C., & Young, R. (2007) A case of adoption in a wild group of black-fronted titi monkeys (Callicebus nigrifrons). Primates, 49(2), 146-148. DOI: 10.1007/s10329-007-0066-x
Yesterday our group discussed the recent Nature paper from Lynda Chin’s lab that identified GOLPH3 as a “first-in-class” Golgi oncogene. The study began where most cancer genomics efforts end up: with the identification of a genomic region (5p13) that’s amplified in numerous solid tumours. The authors reasoned that the amplified region likely contains a gene [...]... Read more »
Scott, K., Kabbarah, O., Liang, M., Ivanova, E., Anagnostou, V., Wu, J., Dhakal, S., Wu, M., Chen, S., Feinberg, T.... (2009) GOLPH3 modulates mTOR signalling and rapamycin sensitivity in cancer. Nature, 459(7250), 1085-1090. DOI: 10.1038/nature08109
Here we estimated the evolutionary history and inferred date of introduction to humans of each of the genes for all 20th century pandemic influenza strains. Our results indicate that genetic components of the 1918 H1N1 pandemic virus circulated in mammalian hosts, i.e., swine and humans, as early as 1911 and was not likely to be [...]... Read more »
Smith, G., Bahl, J., Vijaykrishna, D., Zhang, J., Poon, L., Chen, H., Webster, R., Peiris, J., & Guan, Y. (2009) From the Cover: Dating the emergence of pandemic influenza viruses. Proceedings of the National Academy of Sciences, 106(28), 11709-11712. DOI: 10.1073/pnas.0904991106
People accept the idea of echinoderm predation on shallow reef building corals. The voracious Crown of Thorns seastar Acanthaster planci is a familiar coral antagonist on the Great Barrier Reef, part of a natural process that may or may not be amplified by anthropogenic disturbance. Asteroid predation on deep-sea corals is more difficult to demonstrate. [...]... Read more »
Etnoyer, P. (2008) A new species of Isidella bamboo coral (Octocorallia: Alcyonacea: Isididae) from northeast Pacific Seamounts. Proceedings of the Biological Society of Washington, 121(4), 541-553. DOI: 10.2988/08-16.1
Mosher, C., & Watling, L. (2009) Partners for life: a brittle star and its octocoral host. Marine Ecology Progress Series. DOI: 10.3354/meps08113
Purcell et al. (2009). Common polygenic variation contributes to risk of schizophrenia and bipolar disorder Nature DOI: 10.1038/nature08185Neil Walker has been doing a spectacular job of serving up useful information in the comments recently, so I asked him to write the first ever guest post on Genetic Future - something that (as I will be announcing shortly) I intend to do fairly regularly over the next couple of months.The topic is a paper that has created a rather perplexed buzz recently in the complex disease genetics community: the genome-wide association study (GWAS) for schizophrenia published in Nature last week. This paper takes a novel and (at first glance) rather alarming approach to exploring the genetic basis of this complex disease, so I asked Neil to provide some insight into what he thought about the approach used in this paper and what it means for complex disease genetics.Without further comment, I present Neil's post: Read the rest of this post... | Read the comments on this post...... Read more »
Purcell, S., Wray, N., Stone, J., Visscher, P., O'Donovan, M., Sullivan, P., Sklar, P., Purcell (Leader), S., Stone, J., Sullivan, P.... (2009) Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature. DOI: 10.1038/nature08185
In old Disney comics, Scrooge McDuck would often be shown swimming in his money bin, diving through the coins like an exuberant dolphin. Leading many young minds to wonder, “How does he do that?” Coins don’t move like water; they’re arguably closer to something like dry sand.A new paper shows that one lizard may not be able to get through McDuck’s nine cubic acres of money, but it comes a lot closer than anything else we know about so far. Scincus scincus is a cute little lizard a few winches long, whose common name, “sandfish,” tells you a lot about its behaviour. These lizards dive through sand like Unca Scrooge dives through silver dollars. Previously, people had suspected they paddled though the sand using their legs, much like some fish might use their pectoral fins in addition to their trunk. The problem with testing an hypothesis like this is that sand has this irritating property of being opaque – a problem I had significant personal experience with, I might add. I solved it using wires and recording from muscles.Maladen and colleagues went to high speed X-ray videography. I suspect that they probably spent a long time trying to find a combination of materials with the right combination of transparencies to X-rays, but they did it. And they found that the sandfish might better be described as a sand eel. The swimming that these lizards did (rather fast, about 10 cm per second) was entirely driven by the trunk. The legs were simply held in position and didn’t play a part after the animal got under the sand. There are some fantastic movies of this in the supplemental material.From here, the paper looks into the physics of the situation. To be entirely honest, it’s fairly difficult stuff for me. When they write:It is remarkable that η does not change significantlyfor different φ...I have to take their word for the remarkable nature of those Greek letters. I am rather hoping that some physics blogger out there can walk through the granular materials math in this paper.Maladen and company end by noting that they have helped to show how organisms can exploit the alternately solid-like and fluid-like properties of sand to move through it. And this is indeed a substantial achievement, but what if you turn that around? If animals can do this, why haven’t more done so? To the best of my knowledge, no animals besides other lizards swim through sand like sandfish do. And I doubt that this is due to visibility problems; I think it is just that digging organisms are relatively rare.There is so much nice stuff in this paper that I might forgive them for citing a sand crab digging paper from the 1970s instead of more recent and more detailed articles.ReferenceRyan D. Maladen, Yang Ding, Chen Li, & Daniel I. Goldman (2009). Undulatory Swimming in Sand: Subsurface Locomotion of the Sandfish Lizard Science, 325 (5938), 314-318 DOI: 10.1126/science.1172490Sandfish photo by user thew...g's on Flickr. Used under Creative Commons license.... Read more »
Ryan D. Maladen, Yang Ding, Chen Li, & Daniel I. Goldman. (2009) Undulatory Swimming in Sand: Subsurface Locomotion of the Sandfish Lizard. Science, 325(5938), 314-318. DOI: 10.1126/science.1172490
If you live in a temperate deciduous climate, you probably know what a maple tree is. And if you’ve been in a maple forest during spring or fall—or, really, any time of year—you’ve probably seen maple seeds. They look a bit like badminton birdies, only flattened: a heavy, solid "nut" at the bottom, with a single "wing" above. The wing helps the seed fly relatively long distances (for a plant)—up to a few kilometers in some cases. A maple seed. From http://commons.wikimedia.org/wiki/File:Maple-seed.jpg. Watching a maple seed fly is an interesting experience—they flutter and twist very rapidly. Because they twist and spin as they fall, scientists say they autorotate. In fact, they autorotate quite stably—a factor that allows the wind to carry them far from their parent trees. Maples aren't the only trees with autorotating seeds—hornbeams, for example, have similar winged seeds. In all of these seeds, the autorotation is thought to help create extra lift on the seed, enabling it to travel farther from the parent tree. (Rambling offspring are a benefit for plants, because plant seedlings compete with surrounding plants for soil nutrients, sunlight, and water. If they land too close to the parent tree, they end up competing with their own parents—which benefits neither parent nor offspring, and therefore is detrimental to the survival of the species.) Maple seeds and other autorotating seeds produce surprisingly large amounts of lift as they fall, considering how small and relatively slow they are. This is similar to the wings of many insects, which can produce a lot of lift from a relatively small surface area. Insect wings create this lift through the production of a leading edge vortex (LEV)—that is, a maelstrom of disrupted air along the edge of the seed that is "cutting through" the air as the seed falls. (Think of a wing—one edge of it is pushing through the air as it moves forward. The other edge trails along behind. The edge cutting through the air is the leading edge.) In the 12 June issue of Science, Lentink et al report results of an investigation into the motions of maple seeds as they fall. Because the LEVs generated by insect wings help the insects produce significant lift, the researchers reasoned that maple seeds might produce similar LEVs. Maple seeds are relatively small, and studying them while they fall can be challenging. This is especially true if one is interested in observing the flow of air over and around the seed as it falls. Therefore, as an initial test, Lentink et al built a scale model of a maple seed that was somewhat larger than a real seed. To make studying the movement of the air over the seed easier, they attached the model seed to a large arm inside a tank of mineral oil. It may not be immediately clear how putting a model seed in mineral oil can be used to study the flow of air around a real seed. It turns out that this works because air and mineral oil are both fluids—substances that can flow in response to stress (pressure). As it happens, all fluids behave pretty much the same way under specific kinds of stress, provided that their differences in viscosity (resistance to flow, or thickness) are taken into account. The main difference viscosity makes is in the force required to move through the fluid—as you know if you've ever tried to walk under water. The more viscous the fluid, the more force is required to push through it, and the more slowly it returns to its original position. This latter property is the reason that many fluid dynamics studies are performed in oil or water, rather than air: the higher viscosity of a liquid makes observing its flow paths much easier. The path the liquid follows around the object is the same as the path that air would follow, so the results of the study are easily transferred to air. Lentink et al used digital particle image velocimetry (DPIV) to make an image of the fluid flow around the model seed as it "fell" through the oil. DPIV is a technique that uses laser light, high-speed cameras, and computer integration to determine the velocity (speed and direction) of the fluid moving around an object in various locations. In DPIV, tiny particles are suspended in the fluid. During the experiment, as the fluid is moving, rapid flashes of laser light shine on the fluid, making the suspended particles visible for brief instances. A high-speed camera photographs the particles during each flash. The images are fed into a computer, which analyzes the locations of the particles during each instant. Because the computer knows the location of each particle at specific instances in time, it can calculate the velocity of each particle over time. Once the computer has calculated the velocities of the particles, it can create a three-dimensional image of how they move (and, by extension, how the fluid moves). Using DPIV, Lentink et al identified a very pronounced LEV along the model seed. To confirm that their model seed accurately represents real seeds, they placed real maple seeds in a vertical wind tunnel. They adjusted the wind speed in the tunnel so that it matched the air speed the seeds would experience as they fell. As a result, the seeds hovered in place, but still spun the same way they would if they were actually falling. They recorded the motions of the seeds as they rotated. They were also able to create images of the flow of air around the seeds. The experiments with the real seeds confirmed the results seen in the model studies: maple seeds do, indeed, produce significant LEVs as they fall. By comparing the maple seeds to other plant seeds, Lentink et al showed that the rotation of the maple seeds, and the resulting development of the LEVs, allows maple seeds to fall more slowly than non-rotating seeds of a similar wing loading (wing loading is the ratio of seed weight to surface area). Therefore, maple trees (or hornbeam trees, or other trees with rotating seeds) can produce heavier seeds (which can contain more food for the embryonic tree), but those seeds can still travel far enough from the parent trees to avoid competition. Maple and hornbeam trees are not the only organisms to make use of the extra lift provided by LEVs, though. Hovering insects, bats, and possibly some birds also benefit from the production of LEVs along their wing edges. It makes me wonder whether "winged" marine organisms might generate similar vortices along their wings as they "fly" through the water. Lentink, D., Dickson, W., van Leeuwen, J., & Dickinson, M. (2009). Leading-Edge Vortices Elevate Lift of Autorotating Plant Seeds Science, 324 (5933), 1438-1440 DOI: 10.1126/science.1174196... Read more »
Lentink, D., Dickson, W., van Leeuwen, J., & Dickinson, M. (2009) Leading-Edge Vortices Elevate Lift of Autorotating Plant Seeds. Science, 324(5933), 1438-1440. DOI: 10.1126/science.1174196
Because, as busy as I am, I can always stop and bring you news of a celebrity-insect nexus.
I don’t watch much TV–and so I REALLY had no plans to watch “I’m a Celebrity, Get Me Out of Here!” (although if Rob Blagojevich had been on, that might have been worth it, just to see what [...]... Read more »
Marty, Francisco M., Whiteside, Kristen R. (2005) Myiasis Due to Dermatobia hominis (Human Botfly). New England Journal of Medicine, 352(23), 21. DOI: http://content.nejm.org/cgi/content/short/352/23/e21
Photographs and comments on the discovery of the rare longhorned beetle, Typocerus deceptus (Coleoptera: Cerambycidae) in Missouri.... Read more »
McDowell, W., & MacRae, T. (2008) First record of Typocerus deceptus Knull, 1929 (Coleoptera: Cerambycidae) in Missouri, with notes on additional species from the state. The Pan-Pacific Entomologist, 84(4), 341-343. DOI: 10.3956/2008-23.1
I know everyone is going to jump at once to talk about this mind-blowing research by some of the greatest scientists that have ever been associated with ecology, and I hate just writing about papers that everyone will talk about anyhow, but I decided I still had to comment on this paper. It may very well be the most important paper of the year, even more influential and ground-breaking than Ida (though I wouldn't mention that to her directly). Of course, I'm talking about the newest paper published in Marine Biology's "Online First", Fiddler crab burrowing affects growth and production of the white mangrove (Laguncularia racemosa) in a restored Florida coastal marsh.This paper, written by three, top-notch biologists out of Eckerd College, explores the relationship between fiddler crab burrowing activity and the growth of young white mangroves through two different pathways. The first was a transect study, where mangrove growth variables were compared to burrow density and other plant density in a natural setting. The other used mesh cages to selectively reduce or allow burrowing activity around seedlings to study not only the growth differences but changes in the soil chemistry without the affects of other plants in the area. The sum results of the two were clear - fiddler crabs had a big impact. By digging burrows, they increased mangrove growth and proliferation by ~25%, and dramatically changed the soil chemistry. Their presence decreased salinity from over 44.2 to 32.4 and changed the oxidation potential, meaning they made the soils far more mangrove-friendly. While this might seem like a small study, it's actually quite important. Mangroves are some of the most important ecosystems in the tropics, providing food and shelter for many commercially and ecologically important species. And, most importantly, we've done a fantastic job of destroying them as humans have decided that treed, swampy coasts are far less pretty to build a house on than just pristine, bulldozed sand. Now, millions of dollars are being pumped into restoration efforts, and the more we know about how to cultivate and encourage the growth of these fickle but critical trees, the better.There might also be one other reason that I think this paper is so damned important... but I'll let you figure that one out for yourselves.Smith, N., Wilcox, C., & Lessmann, J. (2009). Fiddler crab burrowing affects growth and production of the white mangrove (Laguncularia racemosa) in a restored Florida coastal marsh Marine Biology DOI: 10.1007/s00227-009-1253-7... Read more »
Smith, N., Wilcox, C., & Lessmann, J. (2009) Fiddler crab burrowing affects growth and production of the white mangrove (Laguncularia racemosa) in a restored Florida coastal marsh. Marine Biology. DOI: 10.1007/s00227-009-1253-7
If you know a little bit about neurons, even really basic stuff, you probably know that neurons send signals with action potentials (a.k.a. spikes). What fewer people know is that there is great diversity in how neurons signal. There are many sensory neurons and interneurons that work entirely without action potentials. I once asked my Ph.D. supervisor, Dorothy Paul, “Is there such a thing as a non-spiking motor neuron?” Dorothy did most of her research working on non-spiking sensory neurons in the west coast mole crab, Emerita analoga. She didn’t give me the answer, but told me it was an excellent question and I should think about it. Some time later, I heard another student asking the same question to another researcher at a poster at a Society for Neuroscience poster, and the person said, “No.”This paper says the answer is, “Yes.” There are non-spiking motor neurons. Qiang Liu and colleagues did their research on the little nematode worm, Caenorhabditis elegans, and were able to take advantage of the huge knowledge of the genetics of this beast, and our ability to manipulate this animal’s genes. They recorded the output of muscle cells using standard electrical recordings, but instead of using electricity to stimulate the motor neurons controlling those muscles – the classical way of doing things – they genetically engineered the worm.The authors were able to make the worms express a protein called channelrhodopsin in certain neurons. Rhodopsin is a visual pigment that responds to light. When you flash a light on these worms (did I mention they’re transparent?), the channelrhodopsin opens up a channel that allows electrical current to flow into the neuron. Thus, you can use a flash of light to fire neurons of your choosing.In neurons with action potentials, activity is like a light switch: flipping the switch harder doesn’t make the light from the bulb any brighter. A key set of data is to increase the light intensity stimulating the motor neurons (shown by different line colours in the figure here), and record the response of the motor neurons. If there was a classic action potential in the motor neuron, you’d expect there to be no response until you hit a threshold, and always the same response in the muscle. But the effect is more like a dimmer than a switch: the greater the light intensity to the motor neurons, the more the muscles responded. This is just what you would as expect for a non-spiking neuron.There rest of this paper revolves around characterizing the synaptic connections between motor neuron and muscle in much more detail. It mainly looks at how the strength of connections between the cells change with repeated stimulation of the motor neurons.This is not the first demonstration of non-spiking motor neurons. Another nematode, Ascaris, probably claimed that honor two decades ago (Stretton and Davis 1989). So while I did learn quite a bit from this paper (I didn’t know about the Ascaris work) and am impressed with the techniques in this paper, I am still a bit puzzled as to why it’s in Proceedings of the National Academy of Science (PNAS). PNAS is one of those exclusive high profile journals, sometimes disparagingly called a “glamour mag,” that publishes on what it considers to be “high impact” science. I guess this paper made it in because C. elegans has become such an important model organism, because this paper doesn’t show any previously unknown or unexpected kind of phenomenon.But considering that the Ascaris work was published before I asked my supervisor about non-spiking motor neurons, I suppose that the phenomenon could stand to be much better known in the neurobiology community.ReferencesLiu, Q., Hollopeter, G., & Jorgensen, E. (2009). Graded synaptic transmission at the Caenorhabditis elegans neuromuscular junction Proceedings of the National Academy of Sciences, 106 (26), 10823-10828 DOI: 10.1073/pnas.0903570106Davis RE, Stretton AO. 1989. Signaling properties of Ascaris motorneurons: graded active responses, graded synaptic transmission, and tonic transmitter release. J Neurosci 9(2):415-425. http://www.jneurosci.org/cgi/content/abstract/9/2/415... Read more »
Liu, Q., Hollopeter, G., & Jorgensen, E. (2009) Graded synaptic transmission at the Caenorhabditis elegans neuromuscular junction. Proceedings of the National Academy of Sciences, 106(26), 10823-10828. DOI: 10.1073/pnas.0903570106
One aspect we’ve discussed before about cancer development is the requirement that the cells (more specifically cancer stem cells) become immortal, able to replicate into daughter cells indefinitely. This is seen most prominently in HeLa cells, cervical cancer cells taken from Henrietta Lacks, who died in 1951. These cells have an overactive telomerase enzyme and [...]... Read more »
Park, J., Venteicher, A., Hong, J., Choi, J., Jun, S., Shkreli, M., Chang, W., Meng, Z., Cheung, P., Ji, H.... (2009) Telomerase modulates Wnt signalling by association with target gene chromatin. Nature, 460(7251), 66-72. DOI: 10.1038/nature08137
Our weekly compilation of science news for the week of July 12, 2009.... Read more »
Bluher, M., Bashan, N., Shai, I., Harman-Boehm, I., Tarnovscki, T., Avinaoch, E., Stumvoll, M., Dietrich, A., Kloting, N., & Rudich, A. (2009) Activated Ask1-MKK4-p38MAPK/JNK Stress Signaling Pathway in Human Omental Fat Tissue May Link Macrophage Infiltration to Whole-Body Insulin Sensitivity. Journal of Clinical Endocrinology , 94(7), 2507-2515. DOI: 10.1210/jc.2009-0002
Tsang, V., Yacoub, M., Sridharan, S., Burch, M., Radley-Smith, R., Khaghani, A., Savoldo, B., & Amrolia, P. (2009) Late donor cardiectomy after paediatric heterotopic cardiac transplantation. The Lancet. DOI: 10.1016/S0140-6736(09)61201-0
Rex, C., Chen, L., Sharma, A., Liu, J., Babayan, A., Gall, C., & Lynch, G. (2009) Different Rho GTPase-dependent signaling pathways initiate sequential steps in the consolidation of long-term potentiation. The Journal of Cell Biology, 186(1), 85-97. DOI: 10.1083/jcb.200901084
Bonneville, S., Smits, M., Brown, A., Harrington, J., Leake, J., Brydson, R., & Benning, L. (2009) Plant-driven fungal weathering: Early stages of mineral alteration at the nanometer scale. Geology, 37(7), 615-618. DOI: 10.1130/G25699A.1
Kritzer, J., Hamamichi, S., McCaffery, J., Santagata, S., Naumann, T., Caldwell, K., Caldwell, G., & Lindquist, S. (2009) Rapid selection of cyclic peptides that reduce α-synuclein toxicity in yeast and animal models. Nature Chemical Biology. DOI: 10.1038/nchembio.193
Edelman, A., Carlson, N., Cherala, G., Munar, M., Stouffer, R., Cameron, J., Stanczyk, F., & Jensen, J. (2009) Impact of obesity on oral contraceptive pharmacokinetics and hypothalamic–pituitary–ovarian activity☆. Contraception. DOI: 10.1016/j.contraception.2009.04.011
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