Posts Tagged ‘barnacles’

“Blood clots, I thought we were dealing with barnacles?!”

Saturday, October 24th, 2009

Hello All. 

On the surface, human beings and barnacles don't really seem to have much in common. Sure, we share a kingdom with them, but they're crustaceans and we're homo sapiens. We've evolved to possess the beautiful gift and curse of consciousness and barnacles, well, they've really perfected the art of sticking to things. 

The unexpected biological link between humans and barnacles becomes illuminated by answering a simple question of fluid properties. What fluids, besides barnacle cement, have the capacity to coagulate within a seawater composition? The list is short: blood and semen. Why is this significant to barnacle research? Human blood and barnacle cement don't seem to be related phenotypically (Brian's word), or aesthetically (my word), but genotypically, they are more similar than either of us imagined. 

When we suffer an injury resulting in an open wound, whether a cut by knife or a simple knee scrape, we as a humans rely on Human Factor XIII to form a cross-linked meshwork of fibrin to coagulate the blood seeping from the wound. Human Factor XIII is an important element in the stablization of the meshwork of fibrin, which are agrigation of thrombin, the initial coagulate protein. Human Factor XIII increases the stability of the previously existing fibrin-thrombin matrix, connecting thrombin monomers to fibrin monomers across polymer chains, as the picture below illustrates.

Human Factor XIII stabilizing a protein chain (source: Wikipedia)

Human Factor XIII stabilizing a protein chain (source: Wikipedia)

 HFXIII is that thin blue line connecting the blue dots from one polymer chain (one of the linear chains running horizontally), to the little red dot situated diagonally below the big blue in a polymer chain running parallel to the one above it. The sequence of the coagulate proteins (i.e. the thrombin, fibrin polymer chains) allows for cross-linking to occur on a diagonal plane, creating a meshwork that reinforces the bonds existing vertically between the polymer chains. 

Basically, HFXIII weaves the parallel polymer chains into a kind of protective biochemical fabric. And tada! human blood clots.

A hot new article in Science Daily, Super Sticky Barnacle Glue Cures Like Clots, suggests that the amino acid sequence making up the cross-linking protein, Human Factor XIII, is remarkably similar, and in some regions, identical, to the adhesive proteins present in barnacle cement. Fascinating stuff! For Rittschof, Dickinson, and Wahl, the researchers conducting the study, this means that barnacle adhesion could potentially be classified as a form of "wound healing." 

The biological connection between the parasite plaguing our poor Scarlet and our own bodies really hit Brian and myself pretty hard. We began to re-evaluate the way we had been approaching barnacle-fouling possibilities. Our entire focus on anti-fouling prior had revolved around aggressive chemical compositions of surface coatings. Our main question had been: How could we alter the chemical composition of the surface of the glider? But Human Factor XIII introduced the delicacy of chemical composition into our discussion. If one of the most important factors of barnacle adhesion also exists in a similar biochemical system in our own bodies, chemical composition seems like a delicate thing to be toying with. The biological consequences are now prevalent in our minds...

That said, here's our list for possible chemical bio-fouling techniques as of the moment. They don't look promising:

- urea

- monochloroacetic acid

-  polydimethylsiloxane

- trypsin-like serine protease inhibitor

Each of these possibilities is unsustainable for their own reasons. Obviously, we cannot coat the glider in urea and send it off into the ocean. Monochloroacetic acid is another liquid substance, and a halocarbon, which tends to be insoluable in water, but is also toxic. Polydimethylsiloxane used to be applied to boat bottom in oil form, but is also highly toxic to the marine environment. And a trypsin-like serine protease inhibitor would prevent the polymerization of fibrin into the first matrix of the diagram above, but couldn't possible be crafted into a material that could be coated on the glider to serve as a bio-fouling agent. So, chemically, we are at a standstill.

But, altering the topography of the surface of the glider itself, not the chemical composition of the coating necessarily, could be a viable bio-fouling option. 

Development and Testing of Hierarchically Wrinkled Coatings for Marine Anti-Fouling

This study suggests that altering the topographical surface of a vessel (or vehicle) could be an effective way to prevent bio-fouling up to eighteen months. But, Brian and myself are uncertain as to whether or not this topographical manipulation would actually be something that could be applied to a glider, given the potential drag and piloting issues that could result from a topographically hierarchical surface.

Scott, Oscar, Josh, anyone?? We went on a feverish search for our mentors to ask them about the possible benefits/drawbacks to an option like this, but everyone had mysteriously vanished... very Nancy Drew mystery novel.

 

Until next time,

Amanda and Brian

 

[thanks to Kunal for sending me the Science Daily article!]

Us: 1, Barnacles: 0!

Monday, October 19th, 2009

Hello All.

Tonight marks the hurtle over a gigantic milestone in gooseneck barnacle research. From the basement of Mabel Smith Douglass Library, Brian and I finally conquered the barnacle JPEGS, capturing their size in a pixel-to-pixel ratio using the the ruler tool in the Photoshop program. We measured the theoretical, tangential diameter of the glider at the point closest to the sample barnacle, and then measured either the height or the width of the sample barnacle itself. Pretty simple.

The tricky part for us was figuring out how to successfully convert pixel measurements into millimeters. Luckily, there are conversion tools floating around the web, waiting to be found by a pair of eager researchers like Brian and myself. We fished for a bit, and decided to go with a .org site (...based on the mythical legitimacy of the .org genre of websites). The website we chose can be found here. Just put in your pixel measurements, and voila: mm, cm, km, whatever.

By using a proportions formula, that we hope we've set up correctly (...remember, we're biologists, not mathematicians!), we scaled 2 barnacles and a large cluster situated near the front segment of the glider, on the "R" side of the vehicle.

Here is an example of the formula we used (all measurements in millimeters):

Theoretical Glider Diameter/Actual Glider Diameter = Actual Barnacle Height/Theoretical Barnacle Height

"Theoretical" values represent the pixel measurements taken from the JPEG converted to millimeters. The value in bold was the one we were searching for.

We were surprised by the accuracy of the conversion. Our first test subject, Barnacle 1, measured a height - from first visible point of peduncle (stalk) to tip of cirri (featherlike feeding apparatus) - of 43.14 mm after conversion.

lepas anatifera

Lepas anatifera

Our barnacle books have told us that a full grown Lepas anatifera can clock in at around 40 mm! So, Barnacle 1 can be assumed to be a full grown parasite, secreting disulfide fluids with adult-sized vigilance and malice.

The cluster, comprised of 15 visible barnacles, measured 90.58 mm from top to bottom, slightly off-kilter, but helpful. The cluster takes up approximately a little less than half of the glider's diameter (212. 725 mm).

Our third specimen, Barnacle 2, was the sample from which we measured the average height and width of the capitula (flowerhead, or plated body) of the barnacles. The height of B2 was just shy of 30 mm (28.22 mm), and the width was 24.11 mm. The measurements for B2 are interesting because this barnacle rests on (or rather sinisterly cements itself to) the frontmost ring of the vehicle, the width of which is only 15 mm across in actual measurement. So, the capitula of Barnacle 2 is actually both wider and taller than the ring it rests on. The height of B2's capitula (28.22 mm) compared with the total height Barnacle 1, is about half of B1's entire length from tip of stalk to tip of cirri. Just interesting.

The specific measurements themselves, of course, are of vital importance. But, the main point we're trying to make here is: most of barnacles on the glider are full-grown, which means that they were probably residing on the glider itself for around 2 weeks before the photos were taken in the Azores. They also fit within size range suggested for a full-grown barnacle of the Lepas species.

Thanks, Sage, for showing us how to use the Photoshop ruler tool!

Goodevening everyone,

Amanda and Brian

Pesky barnacles evade our attempt to scale them!

Sunday, October 11th, 2009

Friday, the biology student research group got together in the COOL Room for a meeting. The prospective outcome of the meeting was to have been the successful scaling of the JPEG provided to us by Tina, showing both the growth on the tail and around the sealing rings of RU27. We were excited. Finally, something tangible to say about these disasterous parasites: their size. Knowing the approximate size of the Lepas species would allow us to go ahead and narrow down our species list, speculate growth rate, and send sample measurements to barnacle experts. 

Unfortunately, the images we were provided with show Scarlet on an angle! The team sat around the long table in the lab pondering this unexpected conundrum. What on earth were we to do? The tail on the image is larger than the tail on the gliders itself, and the depth of perspective of the glider in the image is not proportional! The ring closest to the tail is a different size from the ring closest to the nose in the image, making scaling of the glider very difficult. Very quickly, the group realized that understanding barnacle size was a trickier business than first anticipated. We are, uh, 'biologists,' not mathematicians, and so, accounting for this angle would be a difficult task indeed. The consensus that we came to (after seeking advice from Chip in the glider lab) was that it would be much easier to try to procure another image from the original footage; one that illustrates the glider from a direct profile (where the rings are all proportional to one another), rather than attempting a complicated equation.

A glitch in our plans, certainly. But the meeting was not entirely a failure. After doing a bit of light reading in the books we checked out from the library last week, we stumbled upon a key factor in barnacle physiology, the specific characteristic that promotes adhesion to surfaces like Scarlet: the cement gland. This gland secretes a protein compound that bonds with the substrate, in our case the surface of RU27 in particular, forming disulfide bonds.

disulfide bond

Once formed, these stable bonds are not easily broken and are insoluble in water. Very convenient for a barnacle catching a ride on a whale, or a turtle, or an AUV, but a dangerous reality for Scarlet. As Scott has been posting in recent days, Scarlet's vertical velocity is declining rapidly, steadily, however graceful.

More on Cement Gland

Our current task, aside from accurately scaling a more suitable JPEG, is to find surface materials that inhibit disulfide bonding. But scaling is the priority. The quicker we can size these crustaceans, the quicker we can compare growth rate to vertical velocity. I guess we better get moving...

 

Side note: We are also trying to checkout the bibliography you've provided for us this weekend, Antonios. Thank you.

 

Cheers, everyone.

 

Amanda [...Brian, Gina, and Montana]