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  • April 18, 2011
  • 07:00 AM
  • 916 views

April 18, 2011

by Erin Campbell in HighMag Blog

It’s no secret, but I’ll say it anyway…I love microtubules. Really, several qualities of microtubules are ones we all inspire to have ourselves…dynamic, elegant, organized, photogenic, and essential. The image above is from a recent paper discussing how different tubulin isotypes may play bigger roles in microtubule behavior than once believed.Microtubules are hollow tubes of linear protofilaments that are composed of α- and β-tubulin heterodimers. Most organisms have multiple isotypes of α- and β-tubulin, some of which are expressed in the same cells. It was not clear if some of these isotypes could be used interchangeably in the assembly and function of microtubules, but a recent paper describes how one specific β-tubulin isotype affects microtubule behavior. The altered dynamics of microtubules when this isotype, called β5-tubulin, is either overexpressed or reduced results in cell division defects. In seen in the images above, mammalian cells with too much β5-tubulin (left) had many short microtubules (arrowheads) and indicators of cell division defects (compare fragmented nucleus to neighboring cell’s nucleus). Cells with reduced levels of β5-tubulin (right) had normal looking microtubules despite defects in cell division.Bhattacharya, R., Yang, H., & Cabral, F. (2011). Class V -tubulin alters dynamic instability and stimulates microtubule detachment from centrosomes Molecular Biology of the Cell, 22 (7), 1025-1034 DOI: 10.1091/mbc.E10-10-0822... Read more »

  • April 18, 2011
  • 03:22 AM
  • 1,288 views

Evolution in higher dimensions

by Razib Khan in Gene Expression


Ornithomimosaurian dinosaur and ostrich, image credit Nobu Tamura & James G. Howes

Imagine if you will a portal to another universe which you have access to. By fiat let’s give you a “pod” which allows you to move freely throughout this universe, and also let’s assume that you can travel fast enough to go from planet to planet. What if you see that on all the planets there’s a sludgy living “goo” of some sort? To complexify the issue imagine that upon further inspection the goo is divided between a predominant photosynthetic element, and “parasitic” heterotrophs. But aside from these two niches there’s little diversity to be seen in this cosmos. The “climax ecology” of all the planets resemble each other, in case after case convergent evolution toward the one-morphology-to-out-fit-them-all. We could from these observations construct a general theory of evolution which deemphasizes the role of contingency. In other words, there are broad general dynamics which shape and prune the tree of life in this hypothetical universe so that there is always a final terminal steady-state of the most fit morphology.
... Read more »

Salverda ML, Dellus E, Gorter FA, Debets AJ, van der Oost J, Hoekstra RF, Tawfik DS, & de Visser JA. (2011) Initial mutations direct alternative pathways of protein evolution. PLoS genetics, 7(3). PMID: 21408208  

  • April 18, 2011
  • 01:00 AM
  • 1,833 views

Rediscovery of Cicindela scabrosa floridana

by Ted MacRae in Beetles in the Bush

In refreshing contrast to the more usually heard reports of declining and extinct species, a new paper by Dave Brzoska, Barry Knisley, and Jeffrey Slotten (Brzoska et al. 2011) announces the rediscovery of a tiger beetle previously regarded as probably extinct.  Cicindela scabrosa floridana was described from a series of unusually greenish specimens collected in Miami, Florida in 1934; however, no additional specimens [...]... Read more »

Brzoska, D., C. B. Knisley, and J. Slotten. (2011) Rediscovery of Cicindela scabrosa floridana Cartwright (Coleoptera: Cicindelidae) and its elevation to species level. Insecta Mundi, 1-7. info:/

  • April 17, 2011
  • 07:59 PM
  • 1,089 views

Using flies to sniff out a new theory of smell

by aatishb in Empirical Zeal

Our sense of smell is really quite incredible. Every time we take in a breath or taste food, countless molecules swarm into our nasal passages. As they move up the nasal tract, these visitors arrive at a patch of cells on which there are over 10,000 different kinds of docking stations. These cells are odor receptors, and each of them can register a different odor. Together they make up a chemical detector that is much more sensitive and versatile that anything we can come close to building.

In a paper published in the journal PNAS in February, the authors demonstrate through a series of ingenious experiments that smell can be sensitive enough to pick up on tiny differences in atomic vibrations.... Read more »

Franco MI, Turin L, Mershin A, & Skoulakis EM. (2011) Molecular vibration-sensing component in Drosophila melanogaster olfaction. Proceedings of the National Academy of Sciences of the United States of America, 108(9), 3797-802. PMID: 21321219  

  • April 17, 2011
  • 06:46 PM
  • 1,090 views

Why Do Leafcutter Bees Cut Leafs?

by KerstinH in The Viable Blog

Because pollen sucks. It does! But if you prefer the smart word: it’s hygroscopic. It attracts water. And where is water, there is rot. Which is a problem when you are an insect that relies on pollen to feed its brood and therefore needs to store pollen for weeks, if not months. You may be [...]... Read more »

Litman JR, Danforth BN, Eardley CD, & Praz CJ. (2011) Why do leafcutter bees cut leaves? New insights into the early evolution of bees. Proceedings. Biological sciences / The Royal Society. PMID: 21490010  

  • April 17, 2011
  • 04:38 PM
  • 1,401 views

Dropping aphids and their alarm pheromones

by Africa Gomez in BugBlog

Fortunately for the organic gardener, aphids have many predators: hoverfly larvae, lacewings, ladybirds, shield bugs and spiders eat them in numbers. Although aphids appear defenceless against their predators, they have evolved a suite of antipredator responses. Some aphids have warning coloration and sequester chemicals from their feeding plants that are distasteful or toxic to their predators, other release toxic chemicals or waxes and a few have a hard-skinned soldier caste to defend the colony, yet others maintain an army of ants that defend them. The most common form of defence - both against predators or parasitoids - is however, behavioural: the aphids move away or drop from the leaf they are feeding on when they sense an approaching predator. Dropping is very effective in reducing immediate risk: aphids fall away from the approaching danger onto the ground. Once there other costs become apparent: the aphid may be far from the host plant and is exposed to ground predators or to desiccation. The orange tree in my conservatory is infested with aphids. I took advantage of the abundance of 7 spot ladybirds in the garden and brought a few onto the tree, placing them on particularly infested branches. I was pleasantly surprised by the eagerness with which the ladybirds took to the intended job. They started munching aphids straight away, clearing whole shoots in a few minutes. After a little observation, however, it became apparent that it was the aphid's behaviour which was mostly responsible for the shoots being cleared. The undisturbed aphids sat motionless, on a living carpet feeding on the tender leaf sap nearby. In contrast, as soon as a ladybird attacked, the aphids on the same leaf came alive and some started to move away, going into another leaf, while many aphids dropped to the ground as the ladybird fed on their unfortunate siblings. The following two photos illustrate this. They were taken about 27 seconds apart. In the first one, notice the three aphids on the tip of the leaf. In the second photo, these aphids have dropped to the ground, leaving just a couple of aphid molts stuck to the leaf tip, while the ladybird is still feeding on an aphid, motionless. Ladybirds are very effective at eliciting the drop response from aphids, especially when compared to smaller, less energetic feeders, as demonstrated in experiments by John Losey and Robert Denno on pea aphids feeding on alfalfa exposed to a predator insect.This means that on average 60% of aphids feeding on a plant stem dropped to the ground when a 7 spot ladybird (Coccinella septempunctata) was introduced, in sharp contrast to the lower dropping response to the bugs and the control. Given the higher mortality of aphids on the ground, it follows that ladybirds would be very effective clearing aphid infestations through direct predation, and their indirect effect on aphids dropping from the plant. What mechanisms are responsible for this dropping behaviour? or, put differently, how do aphids sense that a predator is approaching? Dropping behaviour happens in response to predator contact, vibrations generated by the predator, or in response to an alarm pheromone secreted by individual aphids when attacked. This chemical signal, (E)-ß-farnesene (EBF), is secreted in dropplets by the cornicles, little tubes at the rear of the aphid, and they may impregnate the predator, which in its next move will elicit the dropping response before actually attacking another aphid. The release of an alarm pheromone by an individual that is likely to be eaten by a predator seems paradoxical. What benefit can this individual gain from its production? An alarm pheromone can be adaptive when the benefit is shared by relatives. This is indeed the case in aphids: groups of aphids feeding in close contact are likely to be members of the same clone, that is, they are genetically identical, as aphids often reproduce parthenogenetically. The alarm pheromone also has longer lasting effects benefiting the individual relatives, as the aphids that have been exposed to the chemical tend to produce winged offspring, which will likely disperse away from predators, in the case of the ladybird attacker, they will be likely to avoid the following generation of ladybird larvae.ReferencesLOSEY, J., & DENNO, R. (1998). The escape response of pea aphids to foliar-foraging predators: factors affecting dropping behaviour. Ecological Entomology, 23 (1), 53-61 DOI: 10.1046/j.1365-2311.1998.00102.xSchwartzberg, E., Kunert, G., Stephan, C., David, A., Röse, U., Gershenzon, J., Boland, W. & Weisser, W. (2007). Real-Time Analysis of Alarm Pheromone Emission by the Pea Aphid (Acyrthosiphon pisum) Under Predation. Journal of Chemical Ecology, 34 (1), 76-81 DOI: 10.1007/s10886-007-9397-8... Read more »

  • April 16, 2011
  • 09:18 PM
  • 1,980 views

Pokéwalker more accurate than other pedometers on a treadmill (study)

by Stephen Yang in ExerGame Lab

Study Finds Pokéwalker More Accurate Than Other Pedometers: "
Nintendo’s  HeartGold and SoulSilver Pokémon Pokéwalker, is a more accurate pedometer than regular pedometers, according to Lorraine Lanningham-Foster (Iowa State University). 

Image via WikipediaAt the 2011 Experimental Biology conference in DC, she presented the accuracies of several pedometers of children and adults while walking on a treadmill at four different speeds.   
Kotaku points out that the research isn’t being funded by Nintendo, but by Iowa State’s Nutrition and Wellness Research Center.(The Cedar Rapids Gazette via Kotaku)

Study details:Participants: 22 children, 8 adultsWalking speeds:  (1.5, 1.8, 2.1, and 2.5 mph for children, 1.5, 2, 2.5, and 3 mph for adults)Results: With the Pokewalker, the faster the treadmill speeds = lower amount of error. However, looking at the mean percent error is a little disconcerting (32% ± 23 at 1.5 mph, 12% ± 20 at 1.8 mph, 3.2% ± 5.6 at 2.1 mph, and 2.4% ± 4.2 at 2.5 mph). 
Points to Ponder (P2P)Something I'll ask Lorraine is the placement of the PokeWalker.  I know it comes with a belt clip but I also know alot of kids put it in their pocket or back pack.  
It would also be interesting to see the results of free-living assessments or longer periods of time. 
Is the Pokewalker a piezoelectric device or an accelerometer?
The SenseWear Armband actually uses an accelerometer to assess steps and is placed on the back of the upper arm.  Given the discrepancies in the placement of each product - how does this impact the findings?


Lanningham-Foster, L, Foster, R, Barnes, M, Kracke, E, Kling, S, & Vik, M (2011). Step counts from two new systems during treadmill walking in children and adults The FASEB Journal, 25 (April)
Abstract included below:
Step counts from two new systems during treadmill walking in children and adultsLorraine Lanningham-Foster, Randal Foster, Megan Barnes, Elsa Kracke, Samantha Kling and Maren VikFood Science and Human Nutrition, Iowa State University, Ames, IA... Read more »

Lanningham-Foster, L, Foster, R, Barnes, M, Kracke, E, Kling, S, & Vik, M. (2011) Step counts from two new systems during treadmill walking in children and adults. The FASEB Journal, 25(April), 606. info:/

  • April 16, 2011
  • 08:36 PM
  • 1,595 views

Evolution may explain why baby comes early

by Razib Khan in Gene Expression


Image credit

The Pith: In this post I review a paper which covers the evolutionary dimension of human childbirth. Specifically, the traits and tendencies peculiar to our species, the genes which may underpin those traits and tendencies, and how that may relate to broader public health considerations.
Human babies are special. Unlike the offspring of organisms such as lizards or snakes human babies are exceedingly helpless, and exhibit an incredible amount of neoteny in relation to adults. This is true to some extent for all mammals, but obviously there’s still a difference between a newborn foal and a newborn human. One presumes that the closest analogs to human babies are those of our closest relatives, the “Great Apes.” And certainly the young of chimpanzees exhibit the same element of “cuteness” which is appealing to human adults. Still there is a difference of degree here. As a childophobic friend observed human infants resemble “larvae.” The ultimate and proximate reason for this relative underdevelopment of human newborns is usually attributed to our huge brains, which run up against the limiting factor of the pelvic opening of women. If a ...... Read more »

Plunkett J, Doniger S, Orabona G, Morgan T, Haataja R, & et al. (2011) An Evolutionary Genomic Approach to Identify Genes Involved in Human Birth Timing. PLoS Genetics. info:/10.1371/journal.pgen.1001365

  • April 16, 2011
  • 02:51 PM
  • 1,779 views

Tricksters, Selfishness & Altruism

by Cris Campbell in Genealogy of Religion

In evolutionary biology, few issues have caused more debate than altruism or what appears to be altruism. It is generally accepted that selection operates on individual organisms and that these organisms are selfishly interested in their own survival and reproduction. Another way of stating this is that individual organisms are interested solely in passing along [...]... Read more »

  • April 16, 2011
  • 09:54 AM
  • 1,875 views

PI(3)P and Exocytosis

by Dave Bridges in Dave's Blog



The classic opinion regarding PI(3)P’s role in intracellular trafficking is that it is synthesized and functions primarily on early endosomes. Several recent publications have highlighted a potential second role for this lipid in exocytosis. Extending previous work by this group and others on the positive role of PI3K-C2a in neurosecretory pathways (1,2) and GLUT4 exoctyosis (3,4) this paper from Tania Maffucci's group interrogates the role of this lipid kinase in insulin secretion in INS1 cells. Combined these results suggest a general role for PI3K-C2a and its product, PI(3)P in exocytotic events.

This group has been investigating the role of the class II PI3K isoforms in exocytosis in a variety of systems. In this paper they investigate the role of PI3K-C2a in insulin secretion using INS1 rat insulinoma cells as a model. Stable knockdown cells did not show any defects in proliferation, calcium signaling, intracellular insulin levels or the expression levels and sub-cellular localization of exocytotic proteins. The PI3K-C2a knockdown cells did however show significant defects in insulin secretion, stimulated by either a secretagogue cocktail or potassium chloride.

Mechanistically, the authors show that there is no defect in insulin granules proximal to the plasma membrane at the resting state. They do detect a decrease in the amount of SNAP25 hydrolysis induced by the secretagogue cocktail. SNAP25 hydrolysis has been proposed to be an important step in the fusion of exocytic vesicles (5). This proteolytic event has not been established as a major mechanism in exocytosis, and it may only correlate with defects in PI3K-C2a signaling. However if reduced SNAP25 proteolysis is the mechanistic defect resulting from PI3K-C2a knockdown, then this suggests a role in protease regulation by PI(3)P or another PI(3)P-derived molecule as a key part of the general exocytotic machinery. It is also possible that there is another, as of yet unstudied role of PI3K-C2a and PI(3)P in exocytosis.



Dominguez, V., Raimondi, C., Somanath, S., Bugliani, M., Loder, M., Edling, C., Divecha, N., da Silva-Xavier, G., Marselli, L., Persaud, S., Turner, M., Rutter, G., Marchetti, P., Falasca, M., & Maffucci, T. (2010). Class II Phosphoinositide 3-Kinase Regulates Exocytosis of Insulin Granules in Pancreatic Cells Journal of Biological Chemistry, 286 (6), 4216-4225 DOI: 10.1074/jbc.M110.200295

References
(1) Meunier, Frederic, Shona Osborne, Gerald Hammond, Frank Cooke, Peter Parker, Jan Domin, and Giampietro Schiavo. “Phosphatidylinositol 3-Kinase C2{alpha} Is Essential for ATP-dependent Priming of Neurosecretory Granule Exocytosis.” Molecular Biology of the Cell 16, no. 10 (2005): 4841-4851. PubMed, DOI.

(2) Wen, Peter J, Shona L Osborne, Isabel C Morrow, Robert G Parton, Jan Domin, and Frederic A Meunier. “Ca2+-regulated pool of phosphatidylinositol-3-phosphate produced by phosphatidylinositol 3-kinase C2alpha on neurosecretory vesicles.” Molecular biology of the cell 19, no. 12 (December 2008): 5593-603. PMC, PubMed, DOI.

(3) Maffucci, Tania, Anna Brancaccio, Enza Piccolo, Robert C Stein, and Marco Falasca. “Insulin induces phosphatidylinositol-3-phosphate formation through TC10 activation.” The EMBO journal 22, no. 16 (August 15, 2003): 4178-89. PubMed, DOI.

(4) Falasca, Marco, William E Hughes, Veronica Dominguez, Gianluca Sala, Florentia Fostira, Michelle Q Fang, Rosanna Cazzolli, Peter R Shepherd, David E James, and Tania Maffucci. “The role of phosphoinositide 3-kinase C2alpha in insulin signaling.” The Journal of biological chemistry 282, no. 38 (September 21, 2007): 28226-36. PubMed, ,DOI.... Read more »

Dominguez, V., Raimondi, C., Somanath, S., Bugliani, M., Loder, M., Edling, C., Divecha, N., da Silva-Xavier, G., Marselli, L., Persaud, S.... (2010) Class II Phosphoinositide 3-Kinase Regulates Exocytosis of Insulin Granules in Pancreatic   Cells. Journal of Biological Chemistry, 286(6), 4216-4225. DOI: 10.1074/jbc.M110.200295  

  • April 16, 2011
  • 09:45 AM
  • 733 views

What the EHEC is that diagram of ?

by db in Defectivebrain @ FOS

 The history of science is peppered with great moments where people have gone above and beyond the call of duty in order to present their work in an accessible way. Think Florence Nightingale, and how she drew attention to the abominable conditions in hospitals through the use of a simple chart.  Or perhaps Vesalius, and his intricate and detailed diagrams of the human anatomy. The following paper deserves it's place among the greats, as it too has taken the graphical representation of science to a whole new level.So what is this paper about?

The paper itself is about a bacterium known as Escherischia Coli, or E.coli for short. This species of bacterium lives in the digestive system of many animal species. Not all E.coli are the same, and there is a diverse set of different strains of this bacteria, including ones that can cause disease. The focus of this paper is on Enterohaemorraghic  E.coli serotype O157, or EHEC for short. EHEC causes bloody diarrhoea in humans, and hemolytic uremic syndrome. This is best known for regularly causing food outbreaks due to improperly cleaned meat.It causes these diseases due to the way it attaches to cells in the large intestine. It has a set of genes, known as the LEE (Locus of Enterocyte Effacement), which causes the expression of proteins that force an attachment to the microvilli of the intestine. This attachment causes the microvilli to be severely damaged, and leads to diarrhoea.Like many bacteria that cause disease in humans, EHEC does it because it doesn't necessarily belong in the human digestive tract. The LEE, which make it cause this disease in humans, are actually essential to its survival in it's natural host: the humble cow.The cow's digestive system is far more complex than the human one, containing a stomach with four compartments, and a variety of different commensal bacteria to aid with digestion. Here, the EHEC's specific niche within the cow is at the reticulo-anal junction. When it gets there, it can express it's attachment genes in this area without causing the cow the slightest bit of discomfort.In order to get there though, it has to run through the acidic compartments of the stomach. But this bacteria doesn't have any idea of when it's going to have to cope with stomach acids. Nor does it have any idea of when it reaches the recto-anal-junction. What it does to work these out is quite clever. The first compartment of the stomach the EHEC encounters is the rumen. This is home to lots of other bacteria, which help the cow break down the tough cellulose in grass.These bacteria are in constant communication with eachother, using bacterial pheromones. These compounds are called Acyl-Homoserine Lactones, or AHL's for short. The rumen is choc full of them. Whilst the EHEC doesn't produce any of these chemicals itself, it can sense their presence using a regulatory gene called sdiA.This regulatory gene tells the bacteria when it can express it's attachment proteins. If AHL's are present, they will filter into the EHEC, and when they bind the SdiA protein, it undergoes a transformation that allows it to do two things:1. It will  sit on the DNA encoding the LEE, preventing it being read. This stops the attachment proteins being made.2. It force other proteins to activate a gene called  gad,  which encodes acid resistance genes, and it will ensure that it is transcribed more. This will make the cell more resistant to acid.
So what do these two things mean? Well, the diagram of a cow pictured below will explain:
  In the rumen, where there is lots of AHL's present, the genes encoding the LEE are repressed, whilst the genes encoding gad are upregulated. This prevents the bacteria sticking to the wrong place of the stomach, where there is high competition, and also prepares it for the environments within the acidic stomachs,
However, as it travels though the digestive system of the cow, the amount of AHLs decrease, until you get to the recto-anal junction. Here there are no AHL's, and so the LEE genes can be expressed, allowing for the bacteria to attach to this area. 


So why do I think this diagram has a place in history?
... Read more »

  • April 16, 2011
  • 09:45 AM
  • 1,331 views

What the EHEC is that diagram of ?

by DefectiveBrayne in The Defective Brain

 The history of science is peppered with great moments where people have gone above and beyond the call of duty in order to present their work in an accessible way. Think Florence Nightingale, and how she drew attention to the abominable conditions in hospitals through the use of a simple chart.  Or perhaps Vesalius, and his intricate and detailed diagrams of the human anatomy. The following ... Read more »

  • April 16, 2011
  • 07:06 AM
  • 1,339 views

A list of enigmas: bamboo bats, frogs-head flyers, Rohu's bat and the false serotines (vesper bats part XVI)

by Darren Naish in Tetrapod Zoology



By now (if, that is, you've been following this thrilling, roller-coaster ride of a series) we've gotten through the better part of vesper bat phylogeny: we've climbed 'up' the vesper bat cladogram and are now within the youngest major section of the group. Recent phylogenetic studies have recognised a serotine clade (Eptesicini or Nycticeiini), a hypsugine clade (including Savi's bat and a load of relatives), and a clade that includes pipistrelles and noctules (Vespertilionini).



Seemingly fitting somewhere within these three clades - or, perhaps, close to them - are a list of oddballs that have either proved difficult to place, or haven't yet been incorporated into modern studies on account of being so poorly known and little studied. It's these species that we'll look at here: they include some of the weirdest vesper bats of them all. Species with adhesive pads on their thumbs and feet, and others with weird, flattened, frog-like heads and uniquely short wings. Read the rest of this post... | Read the comments on this post...... Read more »

  • April 16, 2011
  • 12:02 AM
  • 1,625 views

Citing versioned papers, robots and reviewers?

by Daniel Mietchen in Research Cycle Research

Established scholarly citation practices are tailored towards static documents. With the use of versioned documents spreading, citation formats have to follow suit. This requires to balance the need for proper identification of the source of a claim with the demands for cited information being up to date. Getting this right is particularly important in naturally versioned environments like wikis or GitHub. Continue reading →... Read more »

  • April 15, 2011
  • 02:21 PM
  • 1,558 views

The Allure of Gay Cavemen

by Eric Michael Johnson in The Primate Diaries

The latest stop in the #PDEx tour is being hosted by Neuron Culture at Wired:In 1993 the reputable German weekly Der Spiegel reported a rumor that Otzi, the 5,300-year-old frozen mummy discovered in the Otztal Alps two years earlier, contained evidence of the world's earliest known homosexual act. "In Otzi's Hintern," wrote the editors, referring to the Iceman's hinterland, "Spermien gefunden worden." (If you require a translation, chances are you didn't want to know anyway.) The rumor quickly spread on computer bulletin boards as the recently unveiled World Wide Web inaugurated a new age in the free flow of misinformation. The origin of the rumor, as Cecil Adams discovered, turns out to have been an April Fool's prank published in the Austrian gay magazine Lambda Nachrichten. The joke about our ancient uncle being penetrated deep in the Alps was then picked up by other periodicals, but with a straight face.Twenty years later it appears that little has changed. Last week Czech archaeologist Katerina Semradova spoke with the Iranian news service PressTV about their ongoing excavation of a burial in Prague that contained evidence suggesting a "third gender" identity. Dated to approximately 4,700 years ago, the archaeologists found what they said was a man from the Corded Ware culture who had been buried in a way that was highly uncharacteristic for the time. Typically, males from this Chalcolithic society were interred laying on their right side facing east while women were placed on their left side facing west. Accompanying the bodies would be gender specific grave goods that the deceased individual would presumably need in the afterlife (weapons or tools in the case of males and jewelry or domestic jugs for women)."We found one very specific grave of a man lying in the position of a woman, without gender specific grave goods, neither jewelry nor weapons," said Semradova. "[I]t could be a member of a so-called third gender, which were people either with different sexual orientation or transsexuals or just people who identified themselves differently from the rest of the society."Read the rest of the post here and stay tuned for the next entry in the Primate Diaries in Exile tour.Will Roscoe (2000). Changing Ones: Third and Fourth Genders in Native North America, Palgrave Macmillan.Joan Roughgarden (2004). Evolution's Rainbow: Diversity, Gender, and Sexuality in Nature and People, University of California Press.... Read more »

Will Roscoe. (2000) Changing Ones: Third and Fourth Genders in Native North America. Macmillan. info:/

  • April 15, 2011
  • 02:21 PM
  • 1,324 views

The Allure of Gay Cavemen

by Eric Michael Johnson in The Primate Diaries in Exile

The latest stop in the #PDEx tour is being hosted by Neuron Culture at Wired:In 1993 the reputable German weekly Der Spiegel reported a rumor that Otzi, the 5,300-year-old frozen mummy discovered in the Otztal Alps two years earlier, contained evidence of the world's earliest known homosexual act. "In Otzi's Hintern," wrote the editors, referring to the Iceman's hinterland, "Spermien gefunden worden." (If you require a translation, chances are you didn't want to know anyway.) The rumor quickly spread on computer bulletin boards as the recently unveiled World Wide Web inaugurated a new age in the free flow of misinformation. The origin of the rumor, as Cecil Adams discovered, turns out to have been an April Fool's prank published in the Austrian gay magazine Lambda Nachrichten. The joke about our ancient uncle being penetrated deep in the Alps was then picked up by other periodicals, but with a straight face.Twenty years later it appears that little has changed. Last week Czech archaeologist Katerina Semradova spoke with the Iranian news service PressTV about their ongoing excavation of a burial in Prague that contained evidence suggesting a "third gender" identity. Dated to approximately 4,700 years ago, the archaeologists found what they said was a man from the Corded Ware culture who had been buried in a way that was highly uncharacteristic for the time. Typically, males from this Chalcolithic society were interred laying on their right side facing east while women were placed on their left side facing west. Accompanying the bodies would be gender specific grave goods that the deceased individual would presumably need in the afterlife (weapons or tools in the case of males and jewelry or domestic jugs for women)."We found one very specific grave of a man lying in the position of a woman, without gender specific grave goods, neither jewelry nor weapons," said Semradova. "[I]t could be a member of a so-called third gender, which were people either with different sexual orientation or transsexuals or just people who identified themselves differently from the rest of the society."Read the rest of the post here and stay tuned for the next entry in the Primate Diaries in Exile tour.Will Roscoe (2000). Changing Ones: Third and Fourth Genders in Native North America, Palgrave Macmillan.Joan Roughgarden (2004). Evolution's Rainbow: Diversity, Gender, and Sexuality in Nature and People, University of California Press.... Read more »

Will Roscoe. (2000) Changing Ones: Third and Fourth Genders in Native North America. Macmillan. info:/

  • April 15, 2011
  • 12:43 PM
  • 1,115 views

Great, now I’m yawning too.

by helikonios in The view from Helicon

From the annals of adorable research: You know how yawning is contagious? That’s not just a human thing. Chimpanzees, several other primates, and possibly dogs can “catch” yawns from others of their own species. This strange effect might be a byproduct of empathy—not the complex empathy that involves understanding and sharing someone else’s suffering, but [...]... Read more »

  • April 15, 2011
  • 11:45 AM
  • 2,109 views

BIG Physics for small Science

by Paige Brown in From The Lab Bench

Metallic particles can be synthesized which are adequately small to be suspended in a liquid phase, where the particles exist on a size scale such that buoyancy in the medium and forces of gravity are balanced, and the particle solution, known as a colloid, is stable. In this state, these nanoparticles, named after their dimensions on the nanometer scale (1/billionth of a meter), will stay dispersed instead of precipitating out of solution. It might help to think of the similar way in which large sugar cubes might fall to the bottom of your iced tea, but smaller sugar crystals will disperse and dissolve if you warm up and stir that same drink of tea. However, there is more to very small metallic particles, or nanoparticles, than their small size and defiance of our macroscopic ideas of gravity. Indeed, there is more here than meets the eye. Ironically, it is due to interactions with the very medium by which we have vision at all - electromagnetic energy (light) - that nanoparticles derive some of their most unique and interesting properties. ... Read more »

Hutter, E., & Fendler, J. (2004) Exploitation of Localized Surface Plasmon Resonance. Advanced Materials, 16(19), 1685-1706. DOI: 10.1002/adma.200400271  

  • April 15, 2011
  • 11:43 AM
  • 1,586 views

Development of first selective inhibitor of LRRK2 mutation found in Parkinson’s disease is progress on road towards new therapy

by Pieter Droppert in Biotech Strategy Blog

This month is Parkinson’s awareness month.  Following on from my recent interview (that you can read here & here) with Dr Todd Sherer of The Michael J. Fox Foundation for Parkinson’s Research, I was interested to read about progress being … Continue reading →... Read more »

Deng, X., Dzamko, N., Prescott, A., Davies, P., Liu, Q., Yang, Q., Lee, J., Patricelli, M., Nomanbhoy, T., Alessi, D.... (2011) Characterization of a selective inhibitor of the Parkinson's disease kinase LRRK2. Nature Chemical Biology, 7(4), 203-205. DOI: 10.1038/nCHeMBIO.538  

  • April 15, 2011
  • 10:50 AM
  • 1,766 views

ENCODE Chromatin state data offers nice insights. Take this and run with it.

by Mary in OpenHelix

mmmmm….another “big data” paper illustrates a point I’ve been hammering on: there is terrific data coming out of these projects–but it’s not in the publications. So I’m going to talk about this paper in this post (1), but I’ll direct you to the database where the information is really available for your perusal–and to a tutorial that explains how to access it. Off we go….
The ENCODE project is one of the “big data” consortium-type efforts that is so common these days. ENCODE stands for ENCyclopedia Of DNA Elements, and it was begun to take us beyond the basic framework that the reference genome sequencing provided–to find out more about the control and structural organizational features encoded in the genome. I won’t go into the entire background here–you can find that at NHGRI and in the previous publications from the ENCODE team members. Some of you will recall that there was a pilot phase to explore the strategies and technologies that might be used to accomplish their goals, which was completed and published in 2007 (2). But that covered only 1% of the genome. After the success of the pilot phase, ENCODE was rolled out in a scale-up or production phase–which is now genome-wide.
The data from the production phase has been flowing into the UCSC Genome Browser since 2009 (3). New strategies for storing, displaying, and visualizing related data have been developed–so even if you aren’t specifically interested in the data types that ENCODE is providing–you may want to be aware of how this next-gen type of data is being managed and displayed effectively.
One of the data types that has now been published is about the chromatin state dynamics that were determined using ChIP-Seq technologies, various antibodies for immuno-precipitation, and a number of different cell lines. The researchers explored the various combinations of signals that could be derived from the binding of different histones, insulator and transcription machinery proteins to different DNA segments, and developed a way to characterize the resulting states as weak or strong promoters, enhancers, insulators, transcription regulators and more.
I won’t go into the details of the biological meaning more here–a nice take on that was offered yesterday by Joe at Genomes Unzipped in his post: How do variants outside genes influence disease risk? So go there for some insights into the larger meaning of this data. I wanted to focus on ways you can access and explore this data yourself, and to get you to go mine this for regions that you are interested in.
The paper lays out the strategy and shows the typical compelling examples that all big data papers offer. But this is a mere fraction of what’s available to you–rarely is your favorite gene/region/whatever going to be singled out and mentioned in these kinds of papers. And because of that, it won’t be curated by traditional editors/curators as has been done in the good (?) old days of one-gene-one-paper for you to find later in some repository. It just can’t happen that way anymore.
You need to look at at this kind of data in your favorite regions yourself. All of this data has been deposited in the UCSC Data Coordination Center (DCC). It’s all available for you to peruse in the UCSC Genome Browser.
Figure 1c in the paper gives you a color-coded way to evaluate the data that you might see in your regions of interest. Use that as a guide to consider what the data shows when you visualize it. Figure 4 illustrates a specific example of one specific putative strong enhancer with a Gata1 binding site. This should help you to recognize this kind of pattern in the display when you find it over at UCSC.
Now–finding the data at UCSC: the first thing I would encourage is to watch the tutorial that is freely available, sponsored by the UCSC DCC group. This provides an overview, a guide to recognizing ENCODE data, and ways to interact with the data. Then go over to UCSC Genome Browser and look for the appropriate tracks in the 2009 assembly (for some data) and a lot of ENCODE data on the 2006 assembly. Keep in mind: not all of the ENCODE data has been mapped to the 2009 assembly–so it’s wise to explore both. Find the Regulation track section, and look for ENCODE transcription-factor binding tracks, and Enhancer and Promoter tracks, and the super-track data collections as well–these bring several related data types together for visualization (ENCODE Regulation track on Mar 2006 is one example of a super-track). Some of the data may also be found on the Preview server.
Well, that should keep you busy for a while. Go and mine this stuff for regions that you are interested in. I know you want to put some of the leads from this data into your next grant application….   If you are going to publish the results of your mining be sure to review the ENCODE data use and release policy, and ensure it’s past the publication embargo window or meets the other criteria that might apply. But it’s all there for the lookin’ right now.
Quick links:
ENCODE background at NHGRI: http://www.genome.gov/10005107
ENCODE portal at UCSC: http://encodeproject.org
ENCODE tutorial at OpenHelix, freely available because it is sponsored by UCSC: http://openhelix.com/ENCODE
References:
(1) Ernst, J., Kheradpour, P., Mikkelsen, T., Shoresh, N., Ward, L., Epstein, C., Zhang, X., Wang, L., Issner, R., Coyne, M., Ku, M., Durham, T., Kellis, M., & Bernstein, B. (2011). Mapping and analysis of chromatin state dynamics in nine human cell types Nature DOI: 10.1038/nature09906
(2). ... Read more »

Ernst, J., Kheradpour, P., Mikkelsen, T., Shoresh, N., Ward, L., Epstein, C., Zhang, X., Wang, L., Issner, R., Coyne, M.... (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. DOI: 10.1038/nature09906  

Birney, E., Stamatoyannopoulos, J., Dutta, A., Guigó, R., Gingeras, T., Margulies, E., Weng, Z., Snyder, M., Dermitzakis, E., Stamatoyannopoulos, J.... (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447(7146), 799-816. DOI: 10.1038/nature05874  

Rosenbloom, K., Dreszer, T., Pheasant, M., Barber, G., Meyer, L., Pohl, A., Raney, B., Wang, T., Hinrichs, A., Zweig, A.... (2009) ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Research, 38(Database). DOI: 10.1093/nar/gkp961  

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