Wednesday, September 29, 2010

Evidence that plants contributed to the rise in Oxygen levels that drove aquatic organisms to land

Scientists have predicted that the rise in oxygen levels in the atmosphere prompted aquatic life to move outside of the Ocean, where organisms were constantly fighting for Oxygen. A paper published by Dahl, et. Al. on September 28, 2010 (yesterday) provided the first evidence of this. Unfortunately, I could not find this paper yet, but I found a summary at Wired Science. The people involved in this study tested prehistoric seafloor samples (dating from 1.7 billion years ago to 400 million years ago) found all around the world. They were testing for molybdenum, a mineral found in soil and carried by erosion. In the Ocean, it takes particles about one million years to stop circulating and finally rest on the ocean floor. The lighter isotopes of molybdenum, in oxygenated water, sinks into the seabed. This means that deposits left behind are a stratified record of Earth's oxygen composition. The levels of oxygen in the water are believed to also reflect the levels of oxygen in the atmosphere.The main author of the paper, Tais Dahl, says that oxygen is a more detailed record that what can be read in carbon. Because of indeterminate data in carbon dating, there are two competing theories about Earth's early oxygen levels. Each theory accepts that oxygen levels first spiked about 550 million years ago along with the first mobile, symmetrical life forms. The traditional model states that oxygen levels steadily continued to rise, reaching levels like our modern levels, before organisms diversified again (approximately 400 million years ago). This model supports that it only took about another 50 million years before aquatic organisms came to land. The second model hold that oxygen levels stayed at a steady rate between 550 million years to 500 million years ago. This is when prehistoric plants evolved and diversified. This is when oxygen levels spiked, allowing fish to evolve into more predatory forms. This second model is supported by tests of molybdenum. Plants (release oxygen both while they live and decompose) are the key difference in the two hypotheses. According to Dahl, “The low oxygen level early in animal history limited evolution for fish. After this second oxygenation event, we begin to see large, predatory fish up to 30 feet long. When land animals walked out of water in the first place, it was to escape predation. It’s oxygen that drove the evolution of large predators in the ocean. It’s plants that caused oxygen to rise. In principle, you could connect this all.”

Here is the citing from the recently published paper.
“Devonian rise in atmospheric oxygen correlated to the radiations of terrestrial plants and large predatory fish.” By Tais W. Dahl, Emma U. Hammarlund, Ariel D. Anbare, David P. G. Bond, Benjamin C. Gill, Gwyneth W. Gordon, Andrew H. Knoll, Arne T. Nielsen, Niels H. Schovsbo, and Donald E. Canfield. Proceedings of the National Academy of Sciences, Vol. 107 No. 39, September 28, 2010.
Summary of paper found at Wired Science by Brandon Keim.
To learn more read Nature News
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Sunday, September 26, 2010

Community Vertebrates Rap

Didn't want you to miss this final scene from the season opener of Community.  Very funny, and it is great to see a little taxonomy in prime time comedy.  But can you catch the errors?  I'll give two bonus points to any scientific error posted in the comments.  First come first served.

Saturday, September 25, 2010

Evolution of tetrapod limbs

Partial deletions of HOX genes were done on mutant mice to understand the control they have on Sonic Hedgehog (Shh) expression.  It was already understood that Shh determined the anterior-to-posterior polarity of tetrapod limbs.  But this study (by Tarchini, Duboule, and Kmita,  published in Nature) showed that deleting a certain range of HOX genes inhibited Shh expression, which kept limbs from properly forming or sometimes from even forming at all.  

Figure 3: Skeletons in the presence or absence of Shh signaling.

Shh transcription was absent altogether when all Hoxa and Hoxd8 through Hoxd13 genes were deleted.  Interestingly, Shh transcription still did not take place even though Hoxd1, Hoxd3, and Hoxd4 were present, suggesting those genes are unable to trigger Shh transcription.  Adding both Hoxd8 and Hoxd9 did not cause Shh transcription.  Deleting Hoxd10 and Hoxd13 led to upregulation of Hoxd9, but that did not lead to Shh expression.  Addition of Hoxd13 alone induced the formation of both digits and a remnant of forearm.  Hoxd10 function induced a clear yet truncated forearm followed by a series of rays (see Figure 3a above).

Figure 1: Control of Shh expression by Hoxa and Hoxd genes.

This study reinforced that in order for tetrapod limbs to form correctly, the correct HOX genes must be activated (by Shh) in the correct order.  Tarchini, Duboule, and Kmita suggest that tetrapod limbs evolved along with the recruitment of the Hox mechanism implemented in the developing body axis.

Citation: Nature 443, 985-988 (26 October 2006); Received 14 July 2006; Accepted 15 September 2006

Sunday, September 12, 2010

How do hagfish make that slime?

This past week we saw a video of a hagfish instantly making large amounts of slime:

Black protein thread bundles
and small granular mucin vesicles

It turns out that a recently published paper in the Journal of Experimental Biology by scientists from Canada and Washington State examined how this slime is produced.  The researchers already knew from prior work that the slime glands of the hagfish contain two cell types: one that produces threads of protein filaments and another that makes vesicles containing the glycoprotein mucin (the same protein family secreted by your nasal passages).  When a hagfish is threatened, muscles contract to squeeze these two types of cells from the slime glands.  The cells rupture and their contents are extruded from the fish, producing a milky, not quite slimy exudate (see image to right).  But upon contact with seawater, the protein filaments uncoil and the mucin vesicles rupture, and the thick, clear slime is made.

The authors of the paper wanted to test the hypothesis that contact with seawater leads to the inward diffusion of ions and increasing osmotic pressure in the mucin vesicles, causing them to swell and burst.  Hagfish are isotonic with seawater, meaning that they do not reduce their internal solute concentrations compared to seawater as most vertebrates do.  Hagfish, like sharks, maintain high concentrations of organic osmolytes to match the osmolarity of seawater.  One of these osmolytes in particular, TMAO, is found at high levels in the fluid containing the exuded mucin vesicles.  The authors in this JEB paper wanted to characterize the components of this hagfish pre-slime fluid, and determine whether its organic osmolytes, such as TMAO, protect the mucin vesicles from osmotic pressure so that they do not rupture within the slime glands.

As often occurs in science, this was a sensible hypothesis that did not turn out to be correct.  While TMAO provided some protection against vesicle rupture, it was not complete, suggesting that some yet unknown mechanism is used to prevent pre-mature slime formation inside the hagfish slime glands.

Paper reference:  doi: 10.1242/jeb.038992