Archive for the ‘Atlantic Crossing Seminar’ Category

“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

Heading to the mountains!

Thursday, September 3rd, 2009

mid-atlantic_ridgeRU27 is about the cross one of Earth’s largest features, the Mid-Atlantic Ridge. While we pass over this amazing feature, we hope we don’t actually encounter it. The Mid-Atlantic Ridge is well below the crush depth. The Mid-Atlantic Ridge is a spreading tectonic plate boundary in the sea floor located along the floor of the Atlantic Ocean. This system is the longest mountain range in the world. It separates the Eurasian and North American Plates in the North Atlantic, and the African Plate from the South American Plate in the South Atlantic. The Mid-Atlantic Ridge runs from 333 km south of the North Pole to Bouvet Island offshore South Africa. The Mid-Atlantic Ridge is about 10,000 km long and connects a series of oceanic ridges. RU27 this labor day weekend will fly over a deep valleys that run along the axis of the ridge. This ridge is the actual boundary between adjacent tectonic plates.

images
The ridge was first suggested to exist by Matthew Maury in 1850. He was a giant, who was nicknamed the Pathfinder of the Seas and the Farther of modern Oceanography. Wow, like when in Wayne’s world when they encounter Alice Cooper, “We are not worthy!!!”. The Pathfinder of the Sea was made famous by books, the most important being the Physical Geography of the Sea. This is considered the first published work of oceanography. This grand intuition was confirmed by the greatest oceanographic cruise of all time the HMS Challenger. The scientists onboard found this massive undersea mountain chain (hoping to deploy a transatlantic cable). Later future giants of oceanography Marie Tharp, Maurice Ewing, and Bruce Heezen discovered the large valleys, mountains, and cliffs. These are the large features, which tonight RU27 is heading to. This weekend the we should be passing over the Mid-Atlantic Ridge. So as the weekend grills stoke up  and cold brew is pulled from the Coleman cooler, toast Ru27 out in the North Atlantic.

News from Svalbard

Friday, March 20th, 2009

Hey guys

Sorry for the delay getting these posts up, we know how anxious you all are to hear how we are doing up here in the far north

. Starting with the trip over, all flights went smoothly and we ended up in Longyearbyen on Svalbard Sunday afternoon where we were instantly taken aback by the allure of the surrounding snow covered mountains. However we were surprised to see a thermometer actually read -20° C. Longyearbyen is a small mining town actually founded by an American who’s last name was longyear (byen is Norwegian for city). The town is pretty small only having about 40 km of roads and is set up with a main street running through the middle of the town with most housing just a short distance away.

After entering the airport, we saw Mark(professor at Cal Poly) and Geir(professor at NTNU/UNIS) waiting for us with their NORUS sign where the rest of our company also gathered. The group ranges from the Rutgers undergrads to graduating seniors mastersand post doc students from Cal Poly and NTNU and the accompanying professors. Later that day Geir and Mark took us on a tour of a near by mountain where we saw a greater view of the surrounding area along with fish and seal drying racks, sled dog kennels, giant satellite dishes, the Northern Lights Observatory, and Santa’s house! Unfortunately we were all a bit under-dressed so we weren’t too keen about leaving the van for long periods of time. Starting that night we had the first of many meals from the Kroa restaurant where we have had a variety of local dishes including grilled and raw whale, stockfish, fish cakes, venison, and reindeer. On Monday we had our safety training session for snowmobiling, but we were all disappointed to find out there wasn’t enough time to go to the shooting range where we were supposed to learn to defend ourselves from possible polar bear attacks. Afterwards Geir gave us a tour of the UNIS(University Center in Svalbard) building and we got settled into our conference room where we were given a quick overview of what we would be doing over the course of the week. Tuesday we met back in the NORUS room and each of the professors, Mark(Cal Poly), Geir(NTNU/UNIS), Chris(Cal Poly), Jorgen(UNIS), and Oscar(Rutgers) through teleconference gave talks on their backgrounds and what work they are currently doing. Wednesday, the professors let the students take charge of the conversation and we came up with what was posted on our blog from the 18th. On Thursday we went snowmobiling (or as the locals call it, snow scootering) to Barentsburg, which is a small Russian settlement west of Longyearbyen. Over the past couple days there had been some wind and precipitation so the trails had a covering of loose snow. This lead to all of the American students tipping the snowmobiles, but luckily no one got hurt. Overall however it was an amazing journey riding over the glaciers and through valleys to our destination. Barentsburg is a small Russian mining town that had some success while the Soviet Union was still in one piece, but since then they have gone pretty far down hill and many of the buildings are now worn down and abandoned. But upon arrival we went to a restaurant where they were waiting for us with a nice hot meal of soup, chicken, and wafers. The ride back was a completely different experience from the ride there because the sun had set behind the mountains by the time we left the settlement, so we traveled by twilight and the headlights of the snow scooters. After returning back to town we sat down to a fancy dinner of scallops, reindeer, spiced ice cream and a variety of wines after which we all sleepily returned to our rooms. Finally today we had a quick session reviewing what we have covered this week and then gave our blessings to part of our group, as they had to leave. Tomorrow we plan on taking a quick trip to the Svalbard museum and after lunch going on a hike to the ice caves and exploring so we will give you an update on that later.

Hope everyone else is well!

Pictures from Svalbard

Friday, March 20th, 2009

Here are pictures form the island! Included are the tour around the island, and the snowscooter trip to barentsburg!

1) Neilsen with frosty

2) the NORUS group at dinner

3)Dinner!

4)The three of us in front of the 'watch for polar bears' sign

5)The mountains

6)Dani and I off the plane in Svalbard

7) View from the hotel in Tromso

SVALBARD UPDATE! :D

Wednesday, March 18th, 2009

Greetings from the coolest place on Earth--literally!

Besides the beautiful scenery here, the NORUS workshop has been very productive.  The purpose of NORUS is to establish an international partnership between Norway and U.S. students and to study the effects of climate change on biological interactions.  We have had a lot of professors educating us about the Arctic so that by 2011 we can address biology and climate interactions in the Arctic and eventually publish our findings.

After collaboration, we have plenty of ideas and objectives for the next workshop in the Fall of 2009 in San Luis.  We decided we wanted to focus on biology-ice interactions and how organisms are affected by ice melt-off, so to obtain our goal we want to measure nutrients, algae blooms, attenuation and currents.  We are taking this project one step at a time, but for now the procedure to implement this problem is as follows:

1. The area of research in the Arctic needs modelling.

2. Send a glider/REMUS to test fluorometry, productivity and bathymetry of ice edge

3. Send out the glider twice: Spring 2010 and spring 2011

4. Those focusing on biology need to figure out which sensors they need so that Rutgers and Cal Poly can check to see if we could supply instruments.

Also in NORUS we discussed what Rutgers can do to help Norway advance technologically.  The Norway part of the group LOVES the idea of putting a glider into Norway and have it travel to Svalbard!  Therefore Rutgers and Cal Poly must identify the sensors we have and do not have for the gliders/ AUVs and then notify the Norwegians; this will then determine the amount of research we can do in the future.  As for RU, we were discussing how effective CODAR would be in Norway along with the glider.

For more info about NORUS, go to http://norus-svalbard.blogspot.com/

In other news, everybody gets along so well here!  There are 15 people involved, 10 of them as students.  We laugh, drink, and are very merry :).  Not to mention that you can't go wrong with the scenery here!

That's all for now!

OBIS update-Dani

Tuesday, March 3rd, 2009

This morning I have compiled a list of larger organisms that the glider could run into (Kaycee compiled one of smaller organisms).  OBIS wasn't cooperating when searching for sharks, so this list contains mainly whales and dolphins for now.

Most whales are popular along the coast; this map includes the humpback, sperm, and  north atlantic beaked whale (the purple is the humpback and sperm, and the green is the beaked): whales1There are a TON of dolphin species, the main two species being the Bottle-nosed Dolphin (it also appears in the puerto rico and virgin islands area, which is something to consider), and the Long-finned Pilot Whale:

pilot_bottlenosed

OBIS progress

Tuesday, March 3rd, 2009

Here are the species I've mapped so far that the glider can run into.  Dani is mapping most of the larger organisms that could crash into the glider, and I'm mapping the smaller ones that could slow the glider down.

Comb Jelly: (5 species total)

obis_comb-jelly

Salps: (12 species total)

obis_salps

Jellyfish (Scyphozoan and Box Jellys): (10 scyphozoan species, 1 box jelly species)

obis_jelly

Squid: (this data set is not finished, its only half done so as of now there are 38 species on this map)

obis_squid1

This is a first post

Wednesday, February 11th, 2009

This is a test please delete