Fossils demonstrate beyond any doubt that Mesozoic dinosaurs laid eggs, as of course do all dinosaurs today. But back during the 1960s, 70s and 80s - back when Robert Bakker and his idea about dinosaur biology were regularly featured in magazines and other popular sources - the scientific community was (sarcasm alert) delighted and enthralled by Bakker's proposal of sauropod viviparity.
Yes, mostly forgotten today is the idea that sauropod mothers were once suggested to give birth to a single, live, proportionally large baby, and to then engage in protracted parental care. Read the rest of this post... | Read the comments on this post...... Read more »
About 250 million years ago in what is today the vast backwater of north central Siberia, the Earth coughed forth an unimaginable quantity of lava over 1 million years. The liquid rock was a low-viscosity, thin stuff (for lava), so instead of forming a field of towering volcanoes it oozed out into endless plains. Covering [...]... Read more »
Meyer, K., Yu, M., Jost, A., Kelley, B., & Payne, J. (2011) δ13C evidence that high primary productivity delayed recovery from end-Permian mass extinction. Earth and Planetary Science Letters, 302(3-4), 378-384. DOI: 10.1016/j.epsl.2010.12.033
To say that paleontologists can’t make heads or tails of the Tully Monster would be untrue. The claw-tipped proboscis on the front end and the arrow-shaped rear fins at the posterior end can be easily identified in complete specimens. Beyond that, though, this 300 million year old invertebrate remains one of the most vexing fossil [...]... Read more »
Richardson, E. (1966) Wormlike Fossil from the Pennsylvanian of Illinois. Science, 151(3706), 75-76. DOI: 10.1126/science.151.3706.75-a
Chen, J., Huang, D., & Bottjer, D. (2005) An Early Cambrian problematic fossil: Vetustovermis and its possible affinities. Proceedings of the Royal Society B: Biological Sciences, 272(1576), 2003-2007. DOI: 10.1098/rspb.2005.3159
Ralph Gordon Johnson, Eugene S. Richardson. (1969) The Morphology and Affinities of Tullimonstrum. Fieldiana: Geology, 12(8), 119-149. info:/
by lucy6660 in the Node
To accompany our paper “Long-term live imaging provides new insight into stem cell regulation and germline-soma coordination in the Drosophila ovary” I have been asked by staff at the Node to discuss the path we took when developing a successful imaging protocol. Germline follicle formation in the Drosophila ovary is a very dynamic process – [...]... Read more »
Morris, L., & Spradling, A. (2011) Long-term live imaging provides new insight into stem cell regulation and germline-soma coordination in the Drosophila ovary. Development, 138(11), 2207-2215. DOI: 10.1242/dev.065508
Some of my favorite proteins ride on the ends of microtubules. I don’t usually like to anthropomorphize proteins, but I always think of Dr. Strangelove hopping on the growing end of a microtubule (and I didn’t even like that movie!). Today’s image is from a paper that adds a satisfying piece to the mitotic spindle puzzle.... Read more »
Dunsch, A., Linnane, E., Barr, F., & Gruneberg, U. (2011) The astrin-kinastrin/SKAP complex localizes to microtubule plus ends and facilitates chromosome alignment. originally published in The Journal of Cell Biology, 192(6), 959-968. DOI: 10.1083/jcb.201008023
Many species of bacteria make decisions about which genes to express based, in part, on how dense their populations are. The most famous example of this phenomenon, called “quorum sensing”, is seen in the bioluminescent bacterium Vibrio fischeri, which turns on its light-producing genes only when its population reaches a certain level. This bacterium has [...]... Read more »
Our friends at Bioversity have meta-done it again. After a milestone contribution a few years ago on the patterns of landrace diversity in farmers’ fields, now arrives a monumental review of the kinds of things that can be done to keep it there. It comes as part of a special issue of Critical Reviews in [...]... Read more »
Jarvis, D., Hodgkin, T., Sthapit, B., Fadda, C., & Lopez-Noriega, I. (2011) An Heuristic Framework for Identifying Multiple Ways of Supporting the Conservation and Use of Traditional Crop Varieties within the Agricultural Production System. Critical Reviews in Plant Sciences, 30(1), 125-176. DOI: 10.1080/07352689.2011.554358
A world without light is quite an alien place. There are many examples of fish that live in completely dark caves. Remarkably, if you compare these fish to their relatives that live in rivers or in the ocean, the cavefish often undergo a similar set of changes. Their eyes do not fully develop, they lose skin pigmentation, and their jaws and teeth tend to develop in particular ways. But what about changes in behavior? In the absence of any daylight, how do their sleep patterns evolve?... Read more »
Duboué ER, Keene AC, & Borowsky RL. (2011) Evolutionary convergence on sleep loss in cavefish populations. Current biology : CB, 21(8), 671-6. PMID: 21474315
The Xia lab group members at Washington University in St. Louis are modern day alchemists, daily converting very small cubes of silver into hollow, porous boxes of gold, termed gold nanocages. Beyond conquering the age-old quest to turn base metals into precious gold, these scientists are going a step further, using gold nanocages as 'magic bullets' in the war against cancer.... Read more »
Xia Y, Li W, Cobley CM, Chen J, Xia X, Zhang Q, Yang M, Cho EC, & Brown PK. (2011) Gold Nanocages: From Synthesis to Theranostic Applications. Accounts of chemical research. PMID: 21528889
Cobley, C., Au, L., Chen, J., & Xia, Y. (2010) Targeting gold nanocages to cancer cells for photothermal destruction and drug delivery. Expert Opinion on Drug Delivery, 7(5), 577-587. DOI: 10.1517/17425240903571614
Chen J, Glaus C, Laforest R, Zhang Q, Yang M, Gidding M, Welch MJ, & Xia Y. (2010) Gold nanocages as photothermal transducers for cancer treatment. Small (Weinheim an der Bergstrasse, Germany), 6(7), 811-7. PMID: 20225187
Lionfish are one of my favorite animals (I study them, after all). They're stunningly beautiful. Of course, they're also a devastating invasive species. Though they've only been in the Atlantic Ocean for some 15 years or so, they've taken over reefs, eating everything in their path. They've been found to reduce the recruitment of native fish by 79% on average, and are occurring in densities 8 times higher than in their native range. To say they're bad is an understatement. The damage is so severe that they were listed as one of the top 15 threats to global biodiversity in 2010.
There's little hope that the reefs will adjust to their newest members on their own. Lionfish are armed with an array of venomous spines, and aren't known to have natural predators even in their native range. They spawn year round, producing millions of eggs each time. Estimates place the founding population in the Atlantic below 10 individuals; now, you can find that many on a single head of coral in the Bahamas. Though they've been invasive for less than two decades, the lionfish are already having ecosystem-level effects. The local reefs simply don't have time to figure things out for themselves.
So it's up to us to combat this invasion. Already, areas with high infestation rates like the Bahamas have launched a full-on assault. The goal: kill them. Every one of them. Period. So-called 'lionfish derbies' can round up thousands in an afternoon, and local communities have begun trying to eat the lionfish out of their reefs by promoting them as a delicacy. But the big question is, is such a plan going to work? Read the rest of this post... | Read the comments on this post...
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Barbour, A., Allen, M., Frazer, T., & Sherman, K. (2011) Evaluating the Potential Efficacy of Invasive Lionfish (Pterois volitans) Removals. PLoS ONE, 6(5). DOI: 10.1371/journal.pone.0019666
by Florence Janody in the Node
Genetic screens in flies brought me by chance to have a look at one of the basic apparatus of the cell: the actin cytoskeleton. At that time, I remembered my cell biology courses at University and since the actin cytoskeleton was not one of the hot spot, I though it was just a machinery required [...]... Read more »
Fernandez, B., Gaspar, P., Bras-Pereira, C., Jezowska, B., Rebelo, S., & Janody, F. (2011) Actin-Capping Protein and the Hippo pathway regulate F-actin and tissue growth in Drosophila. Development. DOI: 10.1242/dev.063545
Sansores-Garcia, L., Bossuyt, W., Wada, K., Yonemura, S., Tao, C., Sasaki, H., & Halder, G. (2011) Modulating F-actin organization induces organ growth by affecting the Hippo pathway. The EMBO Journal. DOI: 10.1038/emboj.2011.157
How X and Y chromosomes affect neurodevelopment... Read more »
Wijchers PJ, & Festenstein RJ. (2011) Epigenetic regulation of autosomal gene expression by sex chromosomes. Trends in genetics : TIG, 27(4), 132-40. PMID: 21334089
This is my first post for a while, since I've been pretty busy - first I was writing a grant proposal for some research money, then I was on holiday in Bavaria and Austria, after which I was busy finishing off a manuscript on evolution of starvation response enzymes. As of yesterday, the manuscript is with my boss, so time to catch up with the world.I noticed an interesting upcoming PNAS paper: Measuring the evolutionary rate of protein–protein interaction. This tackles a subject close to my heart - functional evolution of proteins. The authors tackle measuring the rate at which functional changes happen, with function in this case measured by gain and loss of PPIs (protein-protein interactions).They start by comparing yeast S. cerevisiae, which has abundant PPI data with another yeast Kluyveromyces waltii. These two diverged ∼150 MYA, and they are sort of special relatives since a whole genome duplication occurred in the lineage to S. cerevisiae before the divergence of K. waltii. This worried me that this could affect the rate of PPI change, due to the sudden influx of homologues in the S. cerevisiae lineage inflating the PPI count. However, the problem of duplicates was surmounted by only considering one to one orthologs (ie proteins related by vertical descent and not gene duplication (which would be paralogues)). In all, 43 proteins passed the yeast 2 hybrid test for PPIs, and all of these were found to be conserved in both yeasts. From this, they estimated that the 95% confidence interval of the total rate of PPI evolution is between 0 and 4.6 × 10−10 per PPI per yearThey then went on to consider animals. Using PPI data from nemtodes, they found two of five confirmed S. cerevisiae PPIs are conserved in C. elegans. These two species diverged ~1,300 MYA, so the 95% confidence interval is 1.6 × 10<sup>−10</sup> to 2.0 × 10−9. Using transcription factor PPI data from humans and mice, which diverged 90 MYA, they found that six of six mouse PPIs are conserved in humans. From this, they estimate the 95% confidence interval is 0 to 5.5 × 10−9. Using all the dataset together, they arrive at the final value for the rate of PPI change: (2.6 ± 1.6) × 10−10 per PPI per year.It's great to have a value for the rate of this sort of rare evolutionary change, and the authors are certainly very rigorous is eliminating the possibility of false positives and false positives. However, I'm left wondering whether after all this filtering, they're left with enough data to be really sure of their estimates. I count 54 PPIs in total, of which only 3 are lost, and that's in one lineage. Is that really enough data to go on? Well, I'm certainly not a statistician, so I can only assume that this was checked out thoroughly by folks much more informed on this kind of thing than I am.An interesting future route would be to compare protein substitution and PPI rates between lineages. I'm wondering whether organisms with high amino acids substituion rates (like nematodes and other parasites) have a PPI rate that's (relatively) just as high, or whether this is dampened by compensatory mutations in binding interfaces. It'd also be interesting to compare the eukaryotic PPI rate to the bacterial one.Qian W, He X, Chan E, Xu H, & Zhang J (2011). Measuring the evolutionary rate of protein-protein interaction. Proceedings of the National Academy of Sciences of the United States of America PMID: 21555556... Read more »
Qian W, He X, Chan E, Xu H, & Zhang J. (2011) Measuring the evolutionary rate of protein-protein interaction. Proceedings of the National Academy of Sciences of the United States of America. PMID: 21555556
Researcher David Hughes has expanded research on a parasitic fungus and its carpenter ant host. As explained in an excerpt from a previous EcoTone post: Scientists have found that the parasitic fungus Ophiocordyceps unilateralis has possibly been invading carpenter ants (Camponotus) for 48 million years. The parasite not only infects the ant, but it manipulates [...]
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Hughes, D., Andersen, S., Hywel-Jones, N., Himaman, W., Billen, J., & Boomsma, J. (2011) Behavioral mechanisms and morphological symptoms of zombie ants dying from fungal infection. BMC Ecology, 11(1), 13. DOI: 10.1186/1472-6785-11-13
Where do giant pandas come from? Of course, the proximal answer involves a male and female panda – and maybe some panda porn, if life in captivity dampens the mood – but I’m not talking about that. What I’m wondering about is the evolutionary origin of these bamboo-eating bears.
Until recently, there was little to be [...]... Read more »
Dong, W. (2008) Virtual cranial endocast of the oldest giant panda (Ailuropoda microta) reveals great similarity to that of its extant relative. Naturwissenschaften, 95(11), 1079-1083. DOI: 10.1007/s00114-008-0419-3
Figueirido, B., Palmqvist, P., Pérez-Claros, J., & Dong, W. (2010) Cranial shape transformation in the evolution of the giant panda (Ailuropoda melanoleuca). Naturwissenschaften, 98(2), 107-116. DOI: 10.1007/s00114-010-0748-x
Jin, C., Ciochon, R., Dong, W., Hunt, R., Liu, J., Jaeger, M., & Zhu, Q. (2007) The first skull of the earliest giant panda. Proceedings of the National Academy of Sciences, 104(26), 10932-10937. DOI: 10.1073/pnas.0704198104
Salesa, M. (2006) Evidence of a false thumb in a fossil carnivore clarifies the evolution of pandas. Proceedings of the National Academy of Sciences, 103(2), 379-382. DOI: 10.1073/pnas.0504899102
Integrating large data sets for queries within–and across–various collections is one of the arenas that has lately been pretty active in bioinformatics. As more and more “big data” projects yield huge numbers of data points and data types, this is only becoming more necessary. I love to browse data, but there are times when a large-scale customized query is what you’ll want to make some broader discoveries.
Right now there are a number of resources and interfaces that I turn to for structured and customized queries of data collections. The UCSC Table Browser, BioMart, Galaxy–these are the ones I have my hands on almost continuously. But there is another warehouse and interface system that we’re seeing more and more: InterMine.
My first real encounter with InterMine was for the modENCODE data. There’s some really terrific data flowing out of that project now (I talked a bit about that recently here), and the interface and storage system they are using is InterMine.
FlyMine was the initial impetus for the “Mine” system. Some years back FlyMine was created as a warehouse and query system for the increasing amounts of fly data that was coming from various projects. The goal was to have a system powerful enough for bioinformatics + super users, but also a friendly yet powerful interface for bench biologists to use.
The initial paper described the basic components: a user interface with 3 primary components: a Quick Search that’s great for browsing; a Template library that lets users access some pre-defined standard or likely query types that they can tweak for their needs; and a fully customizable Query Builder for the most advanced access. Since this paper development has continued, and there are other new and cool features present as well.
Another big goal of the FlyMine effort was to be able to deal with lists. One of the most common questions we still get in workshops is: “I have a list of _____. What’s the best way to deal with that?” FlyMine–and the InterMines in general–help people to query and manage their explorations with lists of stuff.
The MyMine feature of the InterMines is also a nice component. You can create a login and store things you want to have repeated access to: queries, lists, etc.
There are other people using InterMine for their systems too–a recent paper on TargetMine, for “Gene Prioritization and Target Discovery” is available, and might appear as an upcoming tip! Jennifer did a tip on YeastMine from SGD once as well.
But what triggered me to do this tip is that a letter came from the RGD mailing list last week that said this:
Effective Friday, May 20th, 2011 the MCW BioMart tool will be retired by RGD and the MCW Proteomics Center. For mining rat data, we have found that the RatMIne tool is easier to use, more flexible and incorporates more types of data than BioMart. In addition, RatMine includes analysis tools not found in BioMart, giving RatMine users a single, intuitive interface for both obtaining and analyzing data.
So they are moving fully to InterMine and retiring the Rat BioMart, exclusively using RatMine at their installation. So this tip of the week will explore InterMine, RatMine, and some other Mines. That’s a lot of ground to cover–but it’s probably worth your time to know about InterMine as it becomes more broadly available. It’s also important to understand how to query with the Mines if you want to bring the data to Galaxy for further analysis. If you visit Galaxy you’ll see that their “Get Data” section lets you access Mine tools–but you still need to know how to do the basic queries at the host site first.
Although this tip will touch on RatMine, the focus is the more general InterMine suite. RGD also said this in their notice:
For an overview of RatMine and how to use it, go to the RGD tutorial video, “An Introduction to the RatMine Database”, at http://rgd.mcw.edu/wg/home/rgd_rat_community_videos/an-introduction-to-the-ratmine-database2. Alternatively, follow the “self-guided tour” of RatMine by clicking the “Take a tour” link at the top of any RatMine page.
To try out RatMine for yourself, go to http://ratmine.mcw.edu/ and get started with simplified data mining and analysis.
So if you want to have more specific information about using RatMine, be sure to check out their introduction.
Lyne, R., Smith, R., Rutherford, K., Wakeling, M., Varley, A., Guillier, F., Janssens, H., Ji, W., Mclaren, P., North, P., Rana, D., Riley, T., Sullivan, J., Watkins, X., Woodbridge, M., Lilley, K., Russell, S., Ashburner, M., Mizuguchi, K., & Micklem, G. (2007). FlyMine: an integrated database for Drosophila and Anopheles genomics Genome Biology, 8 (7) DOI: 10.1186/gb-2007-8-7-r129
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Lyne, R., Smith, R., Rutherford, K., Wakeling, M., Varley, A., Guillier, F., Janssens, H., Ji, W., Mclaren, P., North, P.... (2007) FlyMine: an integrated database for Drosophila and Anopheles genomics. Genome Biology, 8(7). DOI: 10.1186/gb-2007-8-7-r129
Memory erasing is a hot topic in Hollywood. From the 1997 sci-fi flick Men in Black to the 2004 romantic comedy Eternal Sunshine of a Spotless Mind, characters are constantly trying to erase painful or dangerous memories from their minds. While neuroscientists are currently aiming their memory-erasing efforts at clinical conditions such as post traumatic [...]... Read more »
Wang, H., Feng, R., Wang, L., Li, F., Cao, X., & Tsien, J. (2008) CaMKII Activation State Underlies Synaptic Labile Phase of LTP and Short-Term Memory Formation. Current Biology, 18(20), 1546-1554. DOI: 10.1016/j.cub.2008.08.064
Cai D, Pearce K, Chen S, & Glanzman DL. (2011) Protein kinase m maintains long-term sensitization and long-term facilitation in aplysia. The Journal of neuroscience : the official journal of the Society for Neuroscience, 31(17), 6421-31. PMID: 21525283
Shema, R., Sacktor, T., & Dudai, Y. (2007) Rapid Erasure of Long-Term Memory Associations in the Cortex by an Inhibitor of PKM . Science, 317(5840), 951-953. DOI: 10.1126/science.1144334
A very well-written review of an orally-active drug for multiple sclerosis has just appeared in the April 25th issue of the Journal of Natural Products, a publication of ACS in conjunction with the American Society of Pharmacognosy. The review, Fingolimod (FTY720): A Recently Approved Multiple Sclerosis Drug Based on a Fungal Secondary Metabolite, is co-authored [...]... Read more »
Strader, C., Pearce, C., & Oberlies, N. (2011) Fingolimod (FTY720): A Recently Approved Multiple Sclerosis Drug Based on a Fungal Secondary Metabolite. Journal of Natural Products, 74(4), 900-907. DOI: 10.1021/np2000528
Each year, the British Society for Developmental Biology awards the Beddington Medal for the best PhD thesis in developmental biology. At the 2011 BSDB meeting, this award went to Carlos Carmona-Fontaine, who completed his PhD in Roberto Mayor’s lab at UCL. Now a postdoc at Sloan-Kettering Institute in New York, Carlos returned to the UK [...]... Read more »
Carmona-Fontaine, C., Matthews, H., Kuriyama, S., Moreno, M., Dunn, G., Parsons, M., Stern, C., & Mayor, R. (2008) Contact inhibition of locomotion in vivo controls neural crest directional migration. Nature, 456(7224), 957-961. DOI: 10.1038/nature07441
Bazazi, S., Buhl, J., Hale, J., Anstey, M., Sword, G., Simpson, S., & Couzin, I. (2008) Collective Motion and Cannibalism in Locust Migratory Bands. Current Biology, 18(10), 735-739. DOI: 10.1016/j.cub.2008.04.035
Dr. Ranjan Perera examines how long, non-coding RNAs affect melanoma.... Read more »
Khaitan D, Dinger ME, Mazar J, Crawford J, Smith MA, Mattick JS, & Perera RJ. (2011) The melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates apoptosis and invasion. Cancer Research. info:/10.1158/0008-5472.CAN-10-4460
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