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  • April 6, 2010
  • 09:35 AM

Fossil Fragments are Table Scraps of an Enormous Alligator

by Brian Switek in Dinosaur Tracking

I love B-grade monster movies, and one of my all time favorites is the 1980 creature feature Alligator. As its title suggests, the film’s protagonist is a 40-foot-long alligator, literally pumped up on steroids from consuming the bodies of medical research lab animals which had been dumped in the sewers under Chicago, and it spends [...]... Read more »

Héctor E. RIVERA-SYLVA, Eberhard FREY, José Rubén GUZMÁN-GUTIÉRREZ. (2009) Evidence of predation on the vertebra of a hadrosaurid dinosaur from the Upper Cretaceous (Campanian) of Coahuila, Mexico. Notebooks on Geology, 1-6. info:/

  • April 6, 2010
  • 08:00 AM

Speculation Surrounding Sporulation in the Mycobacteria

by Tim Sampson in The Times Microbial

by TimThe Mycobacteria are quite the unique genus; not quite Gram-positive due to their waxy mycolic acids on their outer surface, but certainly not Gram-negative as they do not have an outer lipid bilayer. (Although, there are some interesting micrographs showing a structural feature that does look a lot like a typical Gram-negative outer membrane on the surface of Mycobacteria.) Much slower growing than the average bacteria studied in the lab and not so easily manipulated genetically (though s........ Read more »

Ghosh, J., Larsson, P., Singh, B., Pettersson, B., Islam, N., Sarkar, S., Dasgupta, S., & Kirsebom, L. (2009) Sporulation in mycobacteria. Proceedings of the National Academy of Sciences, 106(26), 10781-10786. DOI: 10.1073/pnas.0904104106  

Traag, B., Driks, A., Stragier, P., Bitter, W., Broussard, G., Hatfull, G., Chu, F., Adams, K., Ramakrishnan, L., & Losick, R. (2009) Do mycobacteria produce endospores?. Proceedings of the National Academy of Sciences, 107(2), 878-881. DOI: 10.1073/pnas.0911299107  

  • April 6, 2010
  • 06:47 AM

The Top Down Effect of Turbidity Within Marine Ecosystems

by Daniel Bassett in Chew the Fat

Most studies on turbidity investigate freshwater ecosystems and few studies have focused on the impacts of turbidity on marine ecosystems. Eianne et al. (1999) showed that invertebrate planktivores (jellyfish) replaced planktivorous fish within Norwegian turbid fiords. This was likely to be because increased turbidity levels reduced the possibility of foraging in visually oriented fish, while tactile feeding in jellyfish allowed them to continue to feed under light-limited conditions.... Read more »

Eiane, K., Aksnes, D.L., Bagoien, E., & Kaartvedt, S. (1999) Fish or jellies - a question of visibility?. Limnology and Oceangraphy, 44(5), 1352-1357. info:/

  • April 6, 2010
  • 05:02 AM

More on Branch Lengths and Species

by Bob O'Hara in Deep Thoughts and Silliness

On Monday I wrote about one of those frustrating papers that asks an interesting question, but the more you look at it, the less sure you are of the results. In this case they might be right, but I...... Read more »

  • April 6, 2010
  • 05:00 AM

Canadian prairie wetlands undergoing widespread degradation

by Rob Goldstein in Conservation Maven

... Read more »

Bartzen, B., Dufour, K., Clark, R., & Caswell, F. (2010) Trends in agricultural impact and recovery of wetlands in prairie Canada. Ecological Applications, 20(2), 525-538. DOI: 10.1890/08-1650.1  

  • April 6, 2010
  • 02:34 AM

RNA Journal Club 3/18/10

by YPAA in You'd Prefer An Argonaute

Mammalian cell penetration, siRNA transfection, and DNA transfection by supercharged proteins
Brian R. McNaughton, James J. Cronican, David B. Thompson and David R. Liu
PNAS 106 (15): 6111-6116, 14 April 2009.
doi: 10.1073/pnas.0807883106
This week’s shrewd summary/analysis–impressively his third contribution to this blog–by David Weinberg:
In their 2009 PNAS paper, David Liu and colleagues demonstrate that a green fluorescent protein [...]... Read more »

McNaughton BR, Cronican JJ, Thompson DB, & Liu DR. (2009) Mammalian cell penetration, siRNA transfection, and DNA transfection by supercharged proteins. Proceedings of the National Academy of Sciences of the United States of America, 106(15), 6111-6. PMID: 19307578  

  • April 6, 2010
  • 12:21 AM

Now starring in movies: human genes

by aimee in misc.ience

I do so love it when people make accessibly, entertaining, highly educational science stuff.
In the latest of such moves, researchers from EMBL and the Mitocheck Consortium (both in Europe) have built up a library of movies showing what happens to a human cell when a particular gene is switched off.  One at a time.
This is [...]

[Click on the hyperlinked headline for more of the goodness]... Read more »

Neumann, B., Walter, T., Hériché, J., Bulkescher, J., Erfle, H., Conrad, C., Rogers, P., Poser, I., Held, M., Liebel, U.... (2010) Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature, 464(7289), 721-727. DOI: 10.1038/nature08869  

  • April 5, 2010
  • 06:24 PM

Changes in DNA and Aging

by Reason in Fight Aging!

Do changes in nuclear DNA significantly affect the course of aging? A good question, one that is still open and energetically debated in the scientific community. How about epigenetic changes, mechanisms that alter the process of producing proteins from genetic blueprints without changing the genes themselves, such as those involving DNA methylation? Insofar as degenerative aging is concerned, are epigenetic changes cause, consequence of other, more fundamental changes, or a mix of both? Also go........ Read more »

Murgatroyd C, Wu Y, Bockmühl Y, & Spengler D. (2010) The Janus face of DNA methylation in aging. Aging, 2(2), 107-10. PMID: 20354272  

  • April 5, 2010
  • 03:26 PM

Watershed land use and nutrients

by JL in Analyze Everything

The widespread problems associated with cultural eutrophication are well-known.  Essentially, humans dump a lot of biotically important elements into water, and the resulting algal and bacterial dynamics render those waters pretty unfavorable for native species and desirable species (i.e., you get a lot of fish kills and stinky water).

A big source of those nutrients is agriculture.  Row-crop ... Read more »

Arbuckle, K.E., & Downing, J.A. (2001) The influence of watershed land use on lake N: P in a predominantly agricultural landscape. Limnology and Oceanography, 46(4), 970-975. info:/

  • April 5, 2010
  • 02:47 PM

ResearchBlogCast: Bloggers dissect a paper on parenting in poison arrow frogs

by Dave Munger in News

We’re trying something new this week. Each week, in addition to all the great written blogs you can find on, we’re posting a podcast about science.
Each week, Research Bloggers Kevin Zelnio, Razib Khan, and I will choose a journal article to discuss in podcast form. We’ll make sure it’s an article that we or [...]... Read more »

  • April 5, 2010
  • 01:00 PM

A Most Lively Virus

by Merry Youle in Small Things Considered

Morphologically speaking, the viruses of mesophilic and moderately thermophilic bacteria and archaea are a dull bunch. Of 5,100 surveyed, 97% are ho-hum head-and-tail phages—icosahedral heads with helical tails. The remainder were tailless icosahedra or filaments, except for two spindle-shaped oddballs. If you'd like more structural excitement, best to go virus hunting in geothermally-heated aquatic environments above 80 ºC—the hot springs, mud holes, and deep-sea hydrothermal vents—and b........ Read more »

Häring M, Vestergaard G, Rachel R, Chen L, Garrett RA, & Prangishvili D. (2005) Virology: independent virus development outside a host. Nature, 436(7054), 1101-2. PMID: 16121167  

  • April 5, 2010
  • 10:45 AM

Use of Multiple Proteases for Improved Protein Digestion

by gkobs in Promega Connections

One of the approaches to identify proteins by mass spectrometry includes the separation of proteins by gel electrophoresis or liquid chromatography. Subsequently the proteins are cleaved with sequence-specific endoproteases. Following digestion the generated peptides are investigated by determination of molecular masses or specific sequence. For protein identification the experimentally obtained masses/sequences are compared with theoretical [...]... Read more »

  • April 5, 2010
  • 10:41 AM

The Social Brain and the Human Condition

by Robert Deyes in Promega Connections

The plans had been made, details finalized and all expenses paid. I was to travel to the south coast of England to complete my training for the British Sub-Aqua Club Sports Diver certificate. I boarded a train from London’s Waterloo station down to the quiet seaside resort of Bournemouth where I was received [...]... Read more »

Cole SW, Hawkley LC, Arevalo JM, Sung CY, Rose RM, & Cacioppo JT. (2007) Social regulation of gene expression in human leukocytes. Genome biology, 8(9). PMID: 17854483  

Panksepp J. (2003) Neuroscience. Feeling the pain of social loss. Science (New York, N.Y.), 302(5643), 237-9. PMID: 14551424  

Eisenberger NI, Lieberman MD, & Williams KD. (2003) Does rejection hurt? An FMRI study of social exclusion. Science (New York, N.Y.), 302(5643), 290-2. PMID: 14551436  

Lieberman MD, & Eisenberger NI. (2009) Neuroscience. Pains and pleasures of social life. Science (New York, N.Y.), 323(5916), 890-1. PMID: 19213907  

  • April 5, 2010
  • 10:09 AM

Matryoshka dolls in biology, the connection between flowers, stem cells and fat and more, in my Picks of the Week from RB

by Alejandro Montenegro-Montero in MolBio Research Highlights

Another week has gone by and some very interesting molbio blog posts have been aggregated to Every week [see my opening post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.Note that I'm ... Read more »

Craddock, N., Hurles, M., Cardin, N., Pearson, R., Plagnol, V., Robson, S., Vukcevic, D., Barnes, C., Conrad, D., Giannoulatou, E.... (2010) Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature, 464(7289), 713-720. DOI: 10.1038/nature08979  

Cleveland, L., & Grimstone, A. (1964) The Fine Structure of the Flagellate Mixotricha paradoxa and Its Associated Micro-Organisms. Proceedings of the Royal Society of London. Series B, Biological Sciences (1934-1990), 159(977), 668-686. DOI: 10.1098/rspb.1964.0025  

Koretke KK, Lupas AN, Warren PV, Rosenberg M, & Brown JR. (2000) Evolution of two-component signal transduction. Molecular biology and evolution, 17(12), 1956-70. PMID: 11110912  

Zhang, Q., Raoof, M., Chen, Y., Sumi, Y., Sursal, T., Junger, W., Brohi, K., Itagaki, K., & Hauser, C. (2010) Circulating mitochondrial DAMPs cause inflammatory responses to injury. Nature, 464(7285), 104-107. DOI: 10.1038/nature08780  

Kilian, K., Bugarija, B., Lahn, B., & Mrksich, M. (2010) Geometric cues for directing the differentiation of mesenchymal stem cells. Proceedings of the National Academy of Sciences, 107(11), 4872-4877. DOI: 10.1073/pnas.0903269107  

  • April 5, 2010
  • 08:00 AM

Forecasting the impact of climate change on fisheries

by Rob Goldstein in Conservation Maven

... Read more »

  • April 5, 2010
  • 06:49 AM

The many lives of an inverted genomic region

by Razib Khan in Gene Expression

About five years ago Kari Stefansson published an interesting paper, A common inversion under selection in Europeans. The basic thrust of the results was that a particular genomic region in Europeans exhibited a pattern of variation whereby there was one variant which was inverted in relation to the modal type. They labelled them “H2″ and [...]... Read more »

Donnelly, M., Paschou, P., Grigorenko, E., Gurwitz, D., Mehdi, S., Kajuna, S., Barta, C., Kungulilo, S., Karoma, N., & Lu, R. (2010) The Distribution and Most Recent Common Ancestor of the 17q21 Inversion in Humans. The American Journal of Human Genetics, 86(2), 161-171. DOI: 10.1016/j.ajhg.2010.01.007  

  • April 5, 2010
  • 03:30 AM

Monday Pets: The Gambler

by Jason Goldman in The Thoughtful Animal

So I’m in Las Vegas, gambling capital of the world. And I was reminded of the Kenny Rogers song, The Gambler. And of this video of Kenny Rogers singing The Gambler with the muppets. Because the muppets make everything better.

Figure 1: Isn’t the whole guy dying and turning into a ghost thing a little much [...]... Read more »

van den Bos R, Lasthuis W, den Heijer E, van der Harst J, & Spruijt B. (2006) Toward a rodent model of the Iowa gambling task. Behavior research methods, 38(3), 470-8. PMID: 17186757  

  • April 4, 2010
  • 07:28 PM

Crunching The Data on Human Brain Evolution

by Luke Jostins in Genetic Inference

Lee, S., & Wolpoff, M. (2003). The pattern of evolution in Pleistocene human brain size Paleobiology, 29 (2), 186-196 DOI: 10.1666/0094-8373(2003)0292.0.CO;2

There has been a bit of debate around the biology blogoverse recently about the evolution of human brain size. It started off as an “idle speculation” type argument, but then took a satisfying swerve into [...]... Read more »

  • April 3, 2010
  • 06:21 AM

fusing biology and computer science?

by Greg Fish in weird things

When two of the leading experts in genomics published their thoughts about the future of genetics in Nature’s retrospective on the Human Genome Project, one of them didn’t devote significant parts of his editorial to a simple laundry list of goals and challenges in his field. Instead, J. Craig Venter called on a seemingly unlikely [...]... Read more »

Venter, J. (2010) Multiple personal genomes await. Nature, 464(7289), 676-677. DOI: 10.1038/464676a  

  • April 2, 2010
  • 08:15 PM

Six Hours Per Day

by Reason in Fight Aging!

An article from the Duke University media outlet reminds us of the bigger historical picture of human life expectancy: continual incremental improvement ever since the Industrial Revolution. It's also a good example of how to write a decent popular science press piece, one that adds context to the research it references, rather than dumbing it down or papering it over. From the perspective of the reliability theory of aging and longevity, the historical increase in life expectancy has occurred b........ Read more »

Vaupel, J. (2010) Biodemography of human ageing. Nature, 464(7288), 536-542. DOI: 10.1038/nature08984  

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