Cheung Lab, Day 9


UMass College of Natural Sciences Research Greenhouse

Today started out by visiting the growth room on the 12th floor and selecting plants to collect seeds from.  We were collecting the T0 seeds from both arabidopsis wildtype and the feronia line.  The seed collection process uses newspaper and shaking the seed pods to release the seeds onto the newspaper.  Then you use a sifter, which allows the seeds through but keeps most of the debris from passing through.  In this way, you are able to get as many seeds as possible while minimizing the debris.


Collected seeds in eppendorf tubes
One of the most important aspects of seed collection is the potential for contamination.  You must clean up your work bench, because if seeds from a previous line enter your tube for the new line, it can be catastrophic for results, and can cause a lot of confusion in regards to results.
After we collected seeds, Norice came into lab, and we started running a gel.  We used 15 microliters instead of 10, because we were having some slight issues seeing the results earlier in the week.  We left the gel running, and analyzed other gels.  We were able to tell which of the genes were homozygous and which of the genes were heterozygous.  I haven’t read a gel in years, so this was a great review for me.IMG_20130717_130343

Gel print-outs; can you tell which plants are homozygous vs heterozygous?

We then spent time in the greenhouse in the afternoon, collecting pollen from the tobacco plants.  The process was very straightfoward- remove the tobacco flowers with the most pollen on their anthers and lay them in a tray.  I worked collecting the wildtype pollen (wildtype means “normal”) and Norice collected the pollen from the transgenic plants.  We went back to the lab with these flowers, and started to empty the pollen into eppendorf tubes.


Tobacco in research greenhouse


Collected tobacco, ready for pollen extraction in the lab.

We then tried to analyze our gel, but there were no bands on the gel.  Something had gone wrong in the PCR process, and we were not sure what it was.  It ended up being time for me to leave, so I’m not sure what could have gone wrong in our PCR.


Good example of a selection plate- the green plants are the transformed ones that survived the screening process due to antibiotic resistance.  The medium on these plates has antibiotics, which kills the other plants, which are more yellow in this picture.

UMass Nanotechnology Institute, Day 2


Our atomic force microscope protoype

The second day of the UMass Nanotechnology Institute started off with Mort Sternheim talking about why size matters.  I currently teach the importance of why size matters when it has to deal with cell size.  When we are talking about very small items, they have a larger surface area:volume ratio.  I usually teach this lab using phenopthalein agar and sodium hydroxide.  Mort provided 3 other activities (which were cheap and awesome) to teach the concept of surface area:volume , using a deck of cards, wood blocks, and a crushed versus whole alka-seltzer tablet in bromo-thymol blue.

The next activity was to about Atomic Force Microscopes.  Atomic Force Microscopes use Van der Waals forces to interact with whatever medium you are studying.  More about Atomic Force Microscopes can be found in this powerpoint.  We then tried to build an atomic force microscope model using common classroom materials.  More of the handouts, including teacher’s guides can be found in this repository.

The third activity of the day was by (newly tenured) associate professor Dr. Jenny Ross.  Dr. Ross talked about her work with microtubules and biology.  She talked specifically about how motor proteins interact with microtubules.  It was interesting to hear about this current research, unfortunately, it’s not in the public domain (yet), so I cannot post the materials.

The fourth activity of the day focused on sunscreen and how (mostly) everyone uses too little sunscreen, which is leading to an increased risk of skin cancer..  We ended up completing a series of activities about what types of materials block ultraviolet light.  It was interesting to test different materials using UV beads.IMG_20130709_152215

Testing UV Beads

Finally, we heard from Dr. Mark Tuominen about the iCons program at UMass Amherst.  Had this program existed when I was an undergraduate, I would have loved to be a part of this program.  The iCons program is a concentration, and focuses on team collaboration- a skill that all scientists today must have.  We are no longer in the days of one person being intelligent and solving a problem.  We need groups of people to solve problems.  I’ll be posting more about this on my personal blog.  For more information about the UMass iCons program, check out the website here.

Alice Cheung’s Lab, Day 1


A lab bench with containers and seeds, Ethanol and Bleach Wash in Background.

Today, I started my first day of working for my first day in Dr. Alice Cheung’s Pollen Laboratory at the University of Massachusetts Amherst.  We started the day meeting with Dr. Cheung to discuss the schedule for the summer.  The schedule is very dynamic because I am attending (or already have attended) STEM Digital Institute at UMass Amherst, STEM Nanotechnology Institute at UMass Amherst, and the NWABR Bioethics Course, amongst my hours in working in Dr. Cheung’s lab.

We started the day learning how to do Arabidopsis screening with a T1 generation stock.  What this means is that the seeds that we are screening had an gene introduced by agrobacteria.  We use a medium with antibiotics in petri dishes, which helps us screen for the offspring that we’re looking for.  The antibiotics affect (thus killing) the normal (called wildtype) seeds, while allowing the gene that we inserted (in this case RK11p:Gus) to survive, because we added antibiotic resistance in addition to the RK11p:Gus gene.  We wash the seeds before we put them on the medium in ethanol (twice) and a 50% bleach solution with detergent (once).  We then use a laminar flow bench to maintain a sterile environment, while rinsing the seeds with double-distilled water (4 times).


We use this contraption to shake the seeds during the rinses.

To standardize germination, the seeds are stored at 4 degrees celsius for 2 days- making the seeds believe it is winter.  Then, when they are transferred to the growth chamber (at 22 degrees Celsius), a more uniform sprouting occurs.

We prepared a number of RK11p:Gus plates, which we will be transferring to the growth chamber on Wednesday.


Laminar Flow Bench for a sterile environment.


Eric Johnson in front of a growth chamber in the basement of Lederle Graduate Research Tower.