Second Semester Update

The start to the second semester saw slow progression. With new experiments being held in the lab, we now have to share part of the lab table, as well as some of the equipment. Near the end of first semester we were having trouble with the table set up and had to change it to re-align the blue laser. We spent the first week of this semester cleaning up the lab and finishing what we had started with the table set up.

Next we had to adjust to the move of the biology lab from main building over to the renovated Olmsted hall. Although it is nice to be in the new labs, this took so time to adjust to because the supplies need for the worms was all over the place. We also had to gain card access to the building to access the lab on the weekends.

After we spent approximately the first two weeks finishing the lab set up we had to harvest a new culture of worms. Since Elias and I have different schedules this semester, and the fact that he is devoted more time to the worms this semester, we decided to harvest two plates of worms. This works better because we can now run data on worms three days a week, depending on the life cycle of the worms as they are on a four day life cycle. We run data on the fourth day of the cycle to keep consistence throughout all the trails.

Next it was on to starting to run data. We realized that last semester we were having problems with too much ambient light coming into the lab space from the outside windows. To fix this we repositioned the curtain in the lab to better block out the light. This helps get a better reading on the true thrashing frequency of the worm because there is less disturbance from outside light.

This semester, with added practice and a better set up we have become much more efficient with our time in the lab. We have been running a lot of data on the worms twice a week. However at times, it is still frustrating that we don’t get as much done in the lab each week as we may like. Since I am only spending 4 hours a week in the lab, the whole semester is equivalent to the amount of time spent in the lab over one week during the summer. It is difficult to get a lot done in some of the sessions because some of the time is spent harvesting the worms, and readjusting the table alignment if it was disturbed.

We have also developed a solid procedure to analyze the data using MatLab.  We have a code that we insert the data from the Picoscope into MatLab and it analyzes the frequency.  This frequency is equivalent to the thrashing frequency of the C. elegans. We have begun to gather a large amount of analyzed data, and are working to hopefully get enough data to better the consistency of our results.

Weeks 8 & 9

Two very successful weeks in the lab.

We have continued running data on the worms with the blue laser.  We changed the scale on the x axis of the picoscope software to collect data in intervals of 10 seconds per frame instead of 1 second per frame. This is the match the data from over the summer.  Sadly, we found out that we have been collecting data with the intensity of the laser at too high of a value.  Mostly we had been using the laser at a power of about 5mW.  Over the summer they ran data with the laser at a power of around 1.5mW.  In order to add to the data from over the summer, we must have the same power.  Therefore all the trials we ran with 5mW, will not be useful for this data analysis.  Hopefully we can find a use for those data sets.

We had to realign the laser some because it happened to somehow be out of alignment.  Later in week nine we realized that the picoscope was reading a very low value for the power of the laser. We think it was due to the fact that Brian turned all the photo diodes off one day.

This brings us to the end of the semester.  After a bit of a slow start, in order to get accumulated with the lab, I think we had a very successful semester.  We came to a realization that we cannot get that much work done in the lab during the semester due to the sheer lack of time.  Over the summer, approximately 40 hours a week are spent working in the lab, while we only spent 3.5 hours a week in the lab this semester.  I look forward to continuing research next semester, and hopefully starting some data analysis to find out what our data is really telling us!

Weeks 5-7

I have been extremely busy as of lately, and apologize for not posting earlier.

Week 5 was shortened due to fall break. Therefore we only were able to work in the lab one day. We finished the setup and alignment for the blue laser that day. Below is a picture of the blue laser final set up. It is very similar to the previous table set up, however we got rid of the beam splitter.

Week 6 saw a slight set back in the lab.  Over break, due to miscommunication between Brian and Elias, our worm stock was never harvested.  We came back from break to an empty incubator.  All our previous stocks had been discarded! We began a new stock, but had to wait until later in the week to collect any data on the worms.

Week 7 was a very productive week in the lab.  Eli and I developed a good system to collect data with using the blue laser.  Wearing the safety goggles makes it more difficult to view the worm and also the laser beam itself.  One of us starts the PicoScope software, and then quickly walks over and helps the other find the worm and get the diode positioned so the diffraction pattern can be seen.

Below is a picture of what the PicoScope data looks like when we collect it.  The sinusoidal peaks are the data we are trying to achieve.  As the worm moves around in the laser light it changes the diffraction pattern that turns out on the screen as peaks in the graph. We can then use those peaks to analyze to motion of the worms. The flatline sections (none pictured below) in the data are when the worm is not being illuminated by the laser and therefore creates change in the diffraction pattern.


New Blue Laser Setup
New Blue Laser Setup


Example of data collected
Example of data collected


Week 4

Another successful week in the lab.

Early in the week we ran data on the worms with the red laser. With a more efficient procedure, a little more experience under our belts, and an extra set of hands in the lab, we were able to run data and collect data on seven worms in one lab session.

Later in the week we attempting to collect data with the blue laser. However we ran into trouble with the table setup. When we originally set up the table, we used a beam splitter to send both lasers to one slider holder. Using a beam splitter caused the power of the blue laser to be reduced greatly.  When we went to use the blue laser to analyze the worms, we could not even see the beam inside the cuvette due to the lack of power and the safety goggles.  The laser is too strong to be viewed with the naked eye, and the safety goggles that must be worm make it extremely difficult to view the weak beam.

We began to fix the table set up so that each laser has its own slide holder, and there will be no use of a beam splitter anymore.  The new setup is almost finished, we just have to finish aligning the lasers.

Week 3

Exciting things happened this week in the VAOL lab.  For the first time this semester we were able to collect data on the worms.

In the beginning of the week we spent time practicing transferring the worms from the cup they are grown in, into a cuvette filled with distilled water.  This is more challenging than one would expect because the worms are microscopic and the process must be down under a microscope, using a tiny pick to lift the worms up and transfer them to the cuvette.  We also practiced finding the worm once it was in the cuvette and getting the laser to pass through them to create a diffraction pattern.  Once the worm is found in the cuvette with the naked eye it is pretty easy to keep the laser on it as it swims around.

Later in the week, we actually collected data using the pico scope software on the computer.  The pico scope evaluates the change in diffraction pattern observed by the photo diode as the laser passes through the worms.  It then shows the results in voltage.  We ran trials on four worms total, getting data for each one using only the red laser.  The plan is to continue running data on more worms with both the blue and red lasers, after which we will combine all the data for analysis.

Things are finally starting to come together in the lab after what seemed like a lot of grunt work putting the lab together after the move.

Week 2

This week saw a lot of progress for the lab.

We were able to finish the table set up.  It is pictured below. To the left you can see the blue laser. This laser is sent through a pin hole to a mirror that reflects the beam to the right at a beam splitter.  The beam splitter sends part of the beam towards the slide holder, and another part to the black shield at the right.

On the right is the Helium Neon laser (red laser).  The red laser is aligned to also go through the beam splitter and to the slide holder.

This set up allows us to easily switch between the lasers without having to adjust the set up.  A slide will be placed on the slide holder, and as the beam passes through the object on the slide, a diffraction pattern will then be read by a photo diode detector.

This week I also learned how to grow and maintain the C. elegans population we will be using for analysis.  This process involves using a microscope to transfer a few mature C. elegans to a new tray with food from a pre-existing non-mutated population.  These mature worms will then reproduce and give rise to a new population.  The C. elegans are on a four day maturation cycle meaning that it takes four days for then to mature to adult stage.  Therefore we have to repeat this process four days prior to when we want to use the worms in the lab in order to ensure they are at the correct cycle for analysis.

If all goes well, next week we may be able to start collecting actual data!

Final Table Set Up
Final Table Set Up

Week 1

Hi everyone! I would first like to introduce myself. I am Trey Cimorelli, a sophomore here at Vassar College. I will be a lab intern this semester in VAOL working mostly on the C. elegans project, and I’m extremely excited. 

As this is my first time working in a research lab, the first week was my opportunity to learn the ropes.  I have some experience in lab through intro physics and chemistry classes my freshman year, and also some from high school. However the VAOL lab is completely different from anything I have worked with in the past.

We spent last week (unofficial week one) setting up the lab after the move to the new, absolutely beautiful, Sanders Physics building.  Many boxes of different instruments and equipment had to be unpacked and needed homes in the lab.  After the bulk of the boxes were removed and the lab was semi-organized, the lab table was ready for set up.

Before we began to set up the table, I first had to watch a laser safety video in order to learn how to safely and properly use the lasers we will be dealing with.  The lasers we use are for the most part very safe, however for the blue laser we must wear safety goggles.  I also had to learn how to handle and clean the optics. This process involves using a piece of lens paper, folding it multiple times with forceps, and then wetting it with a few drops of methanol or acetone and wiping in one direction across the optic piece. Proper cleaning and handing of the optics is necessary to obtain a clear image.

After that we were able to start the table set up.  This is a very tedious and time consuming process and we have only just begun to mount the lasers and some of the other pieces (pin hole, mirrors, etc) onto the lab table.

Next we will have to finish mounting the rest of the necessary optics and align the set up.  I also have to learn how to handle and grow the worms, and will be continuing to further my knowledge on the equipment and basis of the C. elegans experiment.

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