Research update: Isochrysis galbana

from dtplankton.com

  

  Meet the brown algae that we are using in our experiment! We were concerned that the pigment given by chloroplasts in standard green algae would not be picked up by the PIV laser. Preliminary tests this afternoon show that the Isochrysis galbana (I. galbana) may be used in place of the 10 micron glass spheres! This algae is about 10 microns also. The low reflectivity of the algae meant that we had to open up the f-stop and increase the laser power to be able to accurately track these guys. One factor that we have noticed is that Instant Ocean doesn't completely dissolve in water but has a higher rate of reflectivity than the algae. So, we are working on making sure that any overexposure from the salt does not affect the study. 

  However, this made me curious as to why we obtained this particular set of algae versus the standard green algae. Come to find out that the accessory brown pigment is from an organic compound called fucoxanthin. Fucoxanthin is under heavy investigation based on a few other preliminary studies that point to this compound as a possible substance for human use in aiding with weight loss, as an anticancer agent, and an anti-inflammatory agent. These are only preliminary studies, so don't go running out looking to buy up the market on I. galbana. 

  Another factor, and one that is more prevalent to our experiment, is that these little guys are high in lipids and help sustain the diet of our oyster larvae (veligers). Why does this matter? It matters because we want to keep the veligers alive during the experiment and it would be optimal to recreate the veligers environment as much as possible. 

  One of the major issues in the scientific process is developing a plan of study for the experiment that not only gives optimal measurements but can also more closely replicate the natural environment of the living creatures involved. Experiments must be repeatable. Hence why we have a lab notebook to keep track of changes in the experimental set up. We try to keep this information in multiple places, if possible. Good science is repetitive science. 

  Remember when the first studies were released at the possibility of Higgs-Boson being proven? There was a mistake in some of the calculations. You can be sure that anyone who researches Higgs-Boson particles was reading that paper intently and trying to make sure that it was accurate, precise, and truthful to the best of our knowledge and instrumentation. This is what we aim for in the scientific community. Breakthroughs are nice but solid science must win out at the end of the day. 

Research: Optimize, optimize, optimize

  I have been showing you pics of our experimental setup and some of the details about it. One thing I have not talked about is how we determine aspects of the system that are working or are not working. We have been optimizing the system for the past week in order to get the best results.
  The kind of movement we expect in a beaker with a stir bar is a vortex. In the pictures below, you will see vector field lines determined by the analysis of the data from Insight 4G. The flood maps are what you would expect from a vortex structure. The speed of the magnetic stir bar is approximately about 60 revolutions per minute.

U Bar graph in pixels

V bar graph in pixels

Vorticity in pixels

U root mean square

V root mean square

  Root mean square is a statistical measure of the magnitude. It is the square root of the average speed, squared. For the moment, I just wanted to show you what we have been up to for the past few days. One of the things we realized is that when we analyze an area, it needs to be the same for all the experimental runs that day. If you notice, the center of the vortex is not centered. Therefore we should make sure that the vortex is in the center of our post-processing window which will make a lot of analysis code run smoother. We also need to convert our graphs to a meaningful unit. Pixels don't mean much to the scientific world and it is not a conversion anyone wants to do in their head so we will convert the pixels to centimeters per second.

  There are a few things we have noticed from the data and from observations while running the experiment. The first is that the magnetic stir bar gets weighed down easily by the electrical tape. I have been changing the tape on the stir bar at the beginning of the day. Convergence tells us how accurate and precise our statistical data set is over the course of the experiment. However, the experiment was run again when I was not there and we had poor convergence from that one versus the experiments I ran earlier that day.

70 revolutions per minute from the morning, good convergence

70 revolutions per minute from the afternoon, poor convergence

  One of the things that might be happening is that the covered stir bar is sitting in the water between runs. Water has some very cool properties but these properties may also affect the setup. The solution is to take the stir bar out of water between extended breaks, dry it off, and check it before putting it back in the water. We will also have to check the motion of the stir bar in between the individual runs to make sure that it is not "jumping" due to friction issues, such as the tape loosening up in the corners giving the bar a jagged circular motion. 

  We have also noted that we have had to wait longer than three minutes between increasing and decreasing the speeds. Therefore we are waiting five minutes. The majority of the graphs are showing that the system reaches convergence by 150 to 200 frames by doing this which is what we want.

  During the analysis of the convergence graphs from yesterday, we noticed that the green line was a consistent outlier. We tracked down the position of the point and realized it was close to the center of the vortex, which should have an average speed of zero, and realized that the vector readings for this point might have larger errors if it is averaging the data around a zero point. The good thing is that we can go back into the code, pick another pixel point close by that will give us x and y readings and not just x readings. 

  I am going to be a picky bugger in the morning so we can do our last set of data collection for freshwater now that we know what we are looking for that might be problematic in the system before the other team runs their 18 experiment runs in the afternoon. We should be testing the saltwater setup by Friday. We get algae next week! And remember the picture that included the big tank next to the beaker from yesterday's post? We will be putting everything in there the following week!

Research Setup and Pictures

  This particular post is not going to be very wordy post but I wanted to give you an idea of the experimental setup. 

Our setup of the beaker on the magnetic stir plate. The large tank is for another project on turbidity. 

Closer inspection of setup. Yes, that is a third leg in order to keep the shelf perfectly flat. 

View of the setup from the CCD camera. The laser produces a "sheet" of 3 mm that is horizontal to the ground.

The ND:YAG laser with lenses. The lens closest to the laser is the one that creates the "sheet" and the other lens helps the signal maintain focus. I will replace description with technical names of the lenses soon.

A different angle of the setup. 

Research Update: Sketchy Plastic and Funky Tanks

  Hey, everyone! I was hoping to get some more news to you before this past weekend but it has been a bit of a whirlwind. Our time frame for the experiment is excruciatingly tight for the rest of June. As it turns out, the algae and the veligers will be ready for testing! And, of course, as usual, we're not quite ready for them but we will have to push forward. Which will mean that we will be crossing our fingers and hope we are doing it right during the experimental runs. We will not know the full results until the analysis in July. It'll be like receiving an inappropriate Christmas present every day and trying to explain what it means. Now do you see what I mean by not everything running smoothly?

What's a veliger? A fancy term for oyster larvae.

Source: pbs.org

Parts of the larvae. Source: uas.alaska.edu

Oyster life cycle. Source: el.erdc.usace.army.mil

  I will be taking a lot of pictures tomorrow of our set up(s) which should give you folks at home a better idea as to what we are doing. Until then, let me share a few experiences with you.
  Yes, we were able to test the equipment last week and we are continuing to modify the setup. The calibration target I built works pretty well but I am improving the design. We have completed two data sets, after processing and running the analysis to check for convergence (convergence is a technique in which the Matlab code picks five random points and like a needle going through 300 pictures, tells us how well our data corresponds in the system), we had decided to run two more sets of data with improvements that I had suggested. First, give more time between the three speeds for the turbidity pattern to be well established and instead of beginning the stir plate at speed 1 (about 60 rpm) to begin with Speed 3 (about 100 rpms) and work backwards. After that, we should be ready to switch from freshwater data collection to saltwater data collection on Wednesday.
  But this is not the only thing we are doing, we have been gathering materials to create our own laboratory ocean and keep the algae and veligers until testing time. What this has incorporated is buying an inexpensive garbage can from which we can mix freshwater and a measured portion of something called Instant Ocean which is used in hobbyist's saltwater tanks (I had to call PetSmart this past Saturday to hold a massive bucket of the stuff for us. The advisor on the project said that it was a good thing that I did because they were all out by this morning).
  We had to fill the garbage can with water this past Friday to let it out-gas over the weekend so that it would reduce the amount of toxin exposure. Unfortunately, someone from another lab emptied it because they thought it was going to burst. So, it is near full again and sitting outside for the night to out-gas. My advisor did mention that the plastic garbage can being so inexpensive might make it look sketchy when it is full of water. We will dump out the water and wipe and down in the morning. I have also drilled a hole through the trash can lid so that we can stick a couple of air stones in it to help keep the dissolved oxygen content at a respectable level.
  We also acquired a 55 gallon saltwater tank someone was going to throw out. It needs a massive clean up but it has a filter and we are going to check it as soon as we can remove all the gunk off of it. One thing is for sure, there is no shortage of work to do this week.

Concept Review: Water Cycle

  Another name for the water cycle is the hydrologic cycle. I am sure that you can guess that the Greek root, hydr-, means water. Most of the terms you should remember from grade school. 

  A few new ones for the general public might be sublimation, which is the transition of a substance from the solid phase directly to the gas phase. Desublimation would be the opposite, the gas phase transitioning directly to the solid phase. Normally when substances transition phases, they pass through an intermediate liquid phase. Therefore, sublimation and desublimation would only occur in extreme cases of high temperature or pressure gradients. Gradient is the difference between final and initial conditions over time. Remember when you had to learn about slopes of lines in high school geometry? If you remember, you may have talked about how "steep" the slope of the line is. The temperature or pressure profile of a substance sublimation or desublimation would have a steep slope. 

  Another new term for you may be evapotranspiration. You might be able to guess that two processes are involved in this, evaporation and transpiration. However, evapotranspiration takes into account the sum of evaporation across vegetation in habitats as well as transpiration which is the loss of water from plants. 

  My mom taught middle school science for 20 years. An assignment she would give her students for homework was to write a journal entry of a day in the life of a water drop going through the water cycle. I truly think that assignments like this are what help students remember science facts without a lot of worksheets or memorization. If you are a teacher or homeschooler, you may want to try this assignment in your classroom! 

Summer Research: Stardate 6/3/2014

   You should know that summer research is an undergraduate practice in which the student is submersed in one narrowly focused project. Before coming down for the summer, our physics department has a practice of engaging the student in a half unit class that prepares the student for the main course. For the past month, I have been working on readings and learning Matlab. Our group witnessed the group working with turbulence struggling with the programming they needed to read files and perform an analysis of their results from yesterday's data collection. We observed the process of data collection and rendering the images.

  The images are collected using a PIV system which consists of a laser and camera which is attached to the computer. Granted, this description is quite oversimplified and I will explain a little more about the system towards the weekend. PIV, for now, is another way of talking about particle velocimetry which uses seed particles to track the movement of the flow of the fluid in a test area. The image below is from the US Department of Transportation's Hydraulics Engineering Department and is similar, with a few modifications. 

  These modifications entail using a stir plate, a magnetic stir bar, and a beaker of water in place of the culvert set up above. 

   The next two images are what the seed particles look like in a flow of water and the next image is the vector field obtained from the images. This is to give you an example of what I will be seeing. These images are from the University of Wisconsin's Engineering Department. 

The Scientific Process

Step 1: Ask a question that needs to be answered

  The first question we have, based on the readings, is can we use Particle Velocimetry techniques to study the behavior of oyster larvae when they experience turbulence? Will our system work with a green laser compared to an IR laser?

Step 2: Design the experiment

  Wait... what?!?! I thought you were supposed to form a hypothesis? In this case, we have to test to see if we can build a workable solution that allows us to answer the question. We have also had several issues to consider. The first, and most important issue, was to move as little of the equipment as possible. We did not want to move the massive tank of water from the turbulence experiment or the laser. So my partner and I built a shelf today that can hold our set up. The only thing we will have to move is the CCD camera between the two experiments. Which means that we will have to calibrate the camera before every day we collect data. 

  The idea is to obtain data about the system and the type of turbulence it produces before tossing in the larvae. It's our control, our base reading. We have taken extra parts and piece and built a shelf to hold the equipment. Tomorrow we set it up to see if we need to make adjustments. We're hoping that we can begin testing it by Thursday and Friday. 

Tomorrow is training day! We have a training on power tools and hand tools, training on using lasers, and hazardous communication training. Phew! I won't bore you with that training!

Introduction

  Hey everyone!

   I have decided to add another blog to the list. Much like education, science is near and dear to my heart, specifically the ocean and atmospheric sciences. Many of my readers may be familiar with my Google+ page  and my Facebook page. It is on these pages that I post links to current research abstracts and some fun things about weather and oceans.
   Science blogs are not always the most popular blogs but I hope I can enlighten what the research I read means to you. You don't need to be a rocket scientist to enjoy this blog just an interest in the process of science. I follow many people who make weather predictions. I don't want to do that here. I would rather talk about the bigger picture, overall implications, and the impacts that these climate patterns involving weather and ocean systems can have on our society.
   Before I talk about some really big things, such as El Nino or hurricanes. I will attempt to give you a basic overview of the scientific concepts involved. I am looking forward to the opportunity to discuss these things with you! If at any point you have any questions, please ask! There is a good chance that someone else has the same question!
   I will also be writing, on occasion, the research projects that I am or have worked on. I began at Virginia Western Community College as a Math major and switched to Chemistry when I began Roanoke College. Until I took a Physics class, then I knew I was in love and much better prepared for the material this time around. Therefore, I will talk about Atmospheric Chemistry and Physics, Fluid Dynamics (tough stuff but I am going to give it a try!), Climatology, Atmosphere-Ocean Interactions, Physical Oceanography, and how all these topics can influence biological factors.
   Currently, I am in Myrtle beach area for the summer working on an interdisciplinary project involving oyster larvae and turbulence. In these particular posts, I will talk about the scientific process and what goes on behind the scenes of these studies. The only spoiler that I can give you is that they do not always work as they are planned!