July 26 RNA Extraction

Today, I came into lab to work on RNA extraction with Sam. Sam had begun with the thawed homogenized RNA by the time I had entered. I pipetted the rest of the RNA into the column set up and then worked to finish the RNA extraction by following the protocol in the box. It went by smoothly. Due to the limited time we had, Sam took the lead in forming the cDNA. He guided me in understanding how cDNA is formed, and tomorrow, he will go in deeper description of how he did this process.

This is an image of the lining up of the tubes within the centrifuge
This is an image of the centrifuged tubes before DNAse was placed.

July 25th

Today begun with a lab meeting where we delved deep into Chapter 7 of Fresh Banana Leaves, and ended the meeting talking about the different projects we are all working on.

I am going to keep working on writing up procedures into my notebook and continue looking up articles that cover the same topic I am learning about.

July 20th

Today I begun the day by finishing Chapter 7 of Fresh Banana Leaves. I also worked on putting my notes into my notebook.

July 19th Tube Labeling

Today, I came into lab to work on setting up the vials for RNA extraction. I begun by adding another sheet to my spreadsheet of the mussel measurements (length, height, width), along with any data taken from previous days. The sheet would have the mussel ID, the tissue type, tube label, the date (including month, day and year), and treatment of the mussels. I am going to put together the spreadsheet into Google. This took about 10-20 minutes to complete. After this, Sam showed me how to label the tubes being used, and from there, I pipetted 500 microliters of RNAzol and 1 millimeter of 100% Ethanol into the tubes. I labeled the tubes for the gill sample of Mussels 1-10 and Mussels 16-25. I have also worked on the spreadsheets a little more this evening as I moved them from Excel into Google.

Next Tuesday, I will be coming in to do the RNA extraction of the samples.

This is an image of the setup I used in labeling and pipetting the tubes.

July 18th Lab Meeting

This morning I attended this Monday’s lab meeting, where we shared the progress in our work so far. I am planning to write up the lab procedures we did last week, and tomorrow, I am going to start the RNA extraction process.

July Summary

I took the first week of July off – headed back to Ohio for Pop’s funeral – but now it’s back to daily notebook posts! Goal is to do the following: Incorporate edits on proposal (ASAP) Finish first draft of paper (ASAP) Clean survey data to prepare for modeling (by end of month) Monday, June 11th Spent the day examining Chelsea’s edits to my proposal! There’s a lot of varying degrees of difficulty. Focused on the easy ones for today. I tend to not have the easiest time incorporating edits (I get stressed out and avoid them), so this might take longer than it should. Still, trying to push myself to get em back quick! Tuesday, June 12th Another day of proposal editing! Got to a fairly good place – hopefully should have them all finished by tomorrow. Need to rewrite a paragraph or two, and then should be set…

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July 11th Labeling Mussels

Today began with a lab meeting. We dived into Chapter 6 of Fresh Banana Leaves where the author focused on Ecofeminism in Indigenous culture, and finished the meeting by recapping what we are all working on individually. This afternoon, I went into the lab to finish labeling the mussels that I had not finished doing earlier on Thursday. The water the mussels were housed in is dirty so we will remove the mussels into a clean water tank tomorrow. I labeled 19 mussels to result in 30 mussels labeled in total, and I found that 1 mussel died. In total, 30 labeled, 16 unlabeled, and 1 dead. I poured in 8 ml of the mussel food into the tank, and I cleaned up by putting the materials away.

This is an image of the mussels I was labeling and the recording of the mussel’s measurements.

July 13th Tissue Sampling

Today, I came in person to work on sampling the mussels for RNA extraction. Matt came in early and helped me sample the mussels. We sampled the gills, mantle and feet of the mussels of both the controlled group and group of mussels that we manipulated. We then put the samples into the super-freezer and logged them into the spreadsheet that catalogs the different species. After sampling, I worked in removing the gonads and somatic tissues of the unlabeled groups of mussels that were exposed to heat. I measured the length, height and width of the mussels and then labeled the weighing tools for the different types of tissues. After removing these, I placed them into the weighing tools and Matt put them into the oven where they will be dried out and examined next week if possible.

The main plan for next week will be working on RNA extraction of the tissues sampled.

This photo, taken by Professor Roberts, of me is showing me removing the different tissues of the mussels.

July 12th RNA Extraction

This day, I came in to learn how to do RNA extraction with Sam. We begun by touring the lab, working through the safety handbook to get familiar with the layout of the space. From there, Sam taught me how to setup and sample the mussel – the set up of bleach to clean the tools during usage, how to use the pipette, etc. I learned about the use of RNAzol, ethanol, and the role of the centrifuge in this process. Though a bit overwhelming with all the new information being thrusted to me, this was an interesting and fun experience. I also worked with Matt to check on the mussels. We removed any smaller mussels and substituted them with larger mussels that we could observe. We also checked on the labeling, replacing them with sticky paper labels and any that we could not legibly read we replaced or gave them a new number. We put them all in a row from 1-30 to find any missing or illegible hand-painted labels. Matt also showed me how to set up the system the mussels would be residing in.

The next day would be focused on sampling the tissues from the mussels we would work on.

July 8th Mussel System Setup

Procedure

This day, I came in to get the mussels set up the in the system they will be staying in. The mussels were placed into a small white bucket. After laying down the absorption mat onto the table, I begun to take one mussel out of bucket at a time to remove the barnacles off the backs of mussels by using an oyster shucker. I separated the barnacles and other debris removed onto one side of the absorption pad and placed the cleaned barnacles onto another side. In addition to that, I cut off any of the thin stringy fibers that mussels grow from within by using scissors. After this, the cleaned off mussels were then rinsed off under cold water and brushed to remove any lingering debris. I then moved them into a different pile into a rinsed out clean white bucket. From there, the area was cleaned by rinsing off any pieces left in the sink, wiping down the countertop and the absorption pad was thrown away.

A new absorption pad was laid out to begin labeling and recording the measurements of the mussels. Nail polish and white-out were used to label the side of the mussel, and a caliber, though tricky to use at first, was used to measure the length (side to side/east to west), width (front to back) and height (up and down). It took some time to partially complete this. I got through 11 mussels, but in the coming week I will be finishing it on Monday. The mussels labeled went into a shellfish net, placed into the water and the white string of the net was held on the side of tank. The same occurred with the unlabeled mussels, resulting in two separated groups of the mussels. Matt poured in about 6 ml of food into the tank on the right to feed the mussels. I then cleaned up by placing the materials used (oyster shucker, paper towel, absorption pads, nail polishes) on a table in a lab to access them on Monday.

Images

This is an image of the original set up of the mussels before I began shucking off the barnacles.
This is an image of the system that we placed the mussels in. The tank on the right housed the mussels (both unlabeled and labeled) while the one on the left will be used to control the temperature (manipulated).
This image displays the work done after removing debris off the mussel and the separation of the two groups.
This is an image of the mussels before they had been cleaned.