Week of 4/2/17

Today was my first day back in the lab in over a month! I was really eager to get back. Yi finished his thesis defense, which is awesome, but that also meant that e was really tired so we ended up just doing a few simple tasks in the lab today.

First, we prepared some cultures and began growing bacteria. I pipetted three milliliters of LB broth into a tube under a flame, and repeated this process five times. Then, Yi gave me six different samples of bacteria to pipette into the individual tubes. Again, we performed this process under the flame.

Once all of the bacteria had been loaded into the tubes with growth medium and labeled, we placed them in the fridge to grow. If we had wanted them to grow faster, we could have put them in an incubator shaker for two to three hours at thirty-seven degrees. When bacterial samples are shook, the agitation incorporates oxygen and evenly distributes nutrients to all the bacteria, helping promote faster growth.


An incubator shaker. https://megadepot.com/product/ika-works-3940100-ks-3000-ic-control-incubator-shaker

After leaving the bacteria in the fridge, Yi and I had no more work to do. We offered help to another graduate student working in the lab, and she asked us to prepare 250 milliliters of 3 M NaCl. It was quite simple to calculate how many grams of powdered NaCl to use, I have outlined my calculations below.

3 mol / L * (.250 L) = .75 mol NaCl wanted
.75 mol 8 (58.44 g / mol) = 43.83 grams of NaCl

I weighed 43.83 grams of NaCl and poured it into a liter flask. Then, I added enough distilled water to bring the total number of milliliters of solution to 250 mL, and then shook and swirled the flask vigorously until the solution was completely dissolved.

I was very happy to get back in the lab this week. Even the simplest tasks are really fun, and I appreciate them even more as the year winds down. Can't wait for next week!

Week of 3/26/17

Yi had his thesis defense today, so I didn't end up going to RPI. I can't wait to get back!

Week of 3/5/17

Yi had a meeting today so I couldn't get to RPI, but I eagerly anticipate our next session!

Week of 2/5/17

This week's meeting was great! Yi and I used the agar growth mediums we prepared a few weeks ago to plate the bacteria. We unwrapped the three petri dishes from their parafilm seals and set them aside. Next, we gathered the materials necessary for plating the bacteria- a sterile loop, Bunsen burner, and the bacteria culture.

Once we had all of our materials, it was time to plate the bacteria. We turned on the Bunsen burner and waved the loop quickly through the flame to ensure the surface was sterile. Making sure to keep all activity under the burner (again, to prevent contamination), we stuck the loop into the tube of bacteria and picked up a small quantity of bacteria. Then, we transferred the bacteria onto the agar plate using a criss-cross pattern, as shown below.




Bacteria on agar criss-cross pattern. http://teachersinstitute.yale.edu/curriculum/units/2010/3/10.03.01.x.html

Why were the bacteria plated in a criss-cross pattern? This is to ensure that the bacteria do not grow clumped and crowded with one another. This pattern not only ensures a more equal distribution of resources, but also makes it so that individual colonies can be observed as they grow, rather than a mass collection of colonies impossible to study.

It should also be noted that our bacteria culture included a small amount of antibiotic within its medium. The bacteria we were studying possessed resistance to the antibiotic, and thus were not affected by the drug. This again was a preventative measure against contamination- any bacteria that somehow enters the chamber will be killed by the antibiotic, ensuring that the only growing bacteria will be the desired strain of study.

By observing the growth patterns of our strain of bacteria, we can see the expansion of individual colonies. Although I have performed experiments like this before, it was great to be exposed to more lab techniques and practice scientific skills in a real laboratory setting. This meeting was great, and I cant wait for next week's internship meeting!

Week of 1/30/17

Time for the interview! After working in the lab and placing our bacteria in the growth medium that we prepared last week, Yi and I sat down for a few minutes so that I could ask him some questions. Enjoy!

Interviewer: Molly Smullen, Senior at Emma Willard (M)

Interviewee: Yi Zhang – graduate PhD candidate at RPI (Y)

M: Yi, can you provide a short summary of the work you do at CBIS?

Y: I study protein folding with NMR fluorescence and Saxs under high pressure.

M: What does studying proteins entail?

Y: To study protein folding, you need to break the balance of proteins in the unfolded versus folded states to understand what propels the protein into its folded state. Whatever parameter you use to break this balance is called a denaturant. Common denaturants are chemicals (such as urea), pressure, or temperature. In my lab, we use high pressure as our denaturant, because we believe it is a softer denaturant, and targets protein structure locally. Only the cavity, where proteins are not perfectly packed, is targeted.

M: What are some different techniques for studying proteins?

Y: You should always use a wide range of biophysical methods for studying proteins because they each reveal something different. For example, Sexs provides information about the overall conformation of the protein, and informs you of overall change in protein shape. Fluorescence is also used to study the general form of proteins. NMR provides more detailed information because its resolution is resolved to the atomic residue. Therefore, you are provided with sequence-based information.

M: How did you become interested in this sort of work?

Y: I have always been interested in biology, since high school, or even middle school. It was very natural to take on this research path, and proteins are a hot topic right now. Also, the techniques you use in protein studies are widely used, so you are trained for many different areas when you study proteins.

M: What implications does your research have in the scientific community/the world?

Y: It’s always good to study protein folding mechanisms because proteins are the major functional components of our bodies. Drug design is also becoming more target-based on protein structures, so this research could provide some insight and guidelines for future drug design.

M: What are your future plans?

Y: I am planning on going to law school and becoming a patent lawyer.

M: Why did you open your doors for an intern?

Y: I am a student, so I know what such an extracurricular activity means to a student who is eager to learn an explore that interest. It is my pleasure and honor to help introduce students to their passions. My father and grandfather were also teachers, so it is good for me to share my knowledge with others, especially younger students.

M: Is there anything you would like to add?

Y: Good luck. When you go to college, you should definitely study, but don’t only study. Do some extracurricular activities, and not just academic ones. Be social, develop interpersonal skills. College is a great time for you to explore and grow into an adult. Study, but don’t be a nerd. Grow into your own person, and have fun!

M: Thanks, Yi. I really appreciate it.

Y: You are welcome.

Great meeting this week, and Yi really provided some valuable knowledge and insight. I can't wait to get back in the lab next week!

Week of 1/23/17

Today was my first day at RPI of 2017! My internship is going swimmingly and I cannot wait to continue my work this semester.

This meeting was a preparation session. Yi and I are planning to grow some bacteria, but first had to prepare the growth medium in order for them to thrive. We mixed 50 grams of agar powder into 2 liters of deionized water and divided the dissolved mixture into two flasks. Additionally, we poured some of this solution into a smaller jar for a median solution. Finally, we added 2.5 grams of another agar powder into 60 milliliters of water.

Once our solutions were prepared with the correct ratio of powder to water, we brought all of the flasks and jars downstairs to the autoclave. An autoclave is a heated pressure chamber that is used to sterilize media to be used in industrial processes. In our case, we autoclaved the agar to sterilize and prepare it for the bacteria. I have included a diagram below that outlines how an autoclave actually works.



The mechanics of an autoclave. http://www.used-autoclave-s.com/autoclave-process/

After placing the agar in the autoclave and setting the timer for a fifteen minute cycle, Yi and I retreated to his office and waited for the temperature and pressure to rise within the chamber. Once this waiting period ended, we moved back down to the lower floor and removed our agar flasks from the chamber.

Following their extraction from the autoclave, the flasks and jars of agar needed to cool until they were comfortable enough to handle. We placed them in a bath of cold tap water and waited for about ten minutes until it was not painful to pick them up. Next, we gathered four small dishes and their lids to pour the agar into. After pouring a small sample of liquid agar into each dish and labeling each one, we wrapped the dishes with parafilm as a seal and set them upside down in the refrigerator. Placing them upside down ensures that the condensation that rests on the inside of the lid does not fall into the agar and corrupt the sample.

This internship meeting was so much fun. I cannot wait until next week, when we will place the bacteria in our growth medium!

Week of 12/5/16

This was my last internship meeting of 2016! Today was another hands-on day, so it was a lot of fun. Yi and I continued our use of the fluorescence spectrometer to determine the intensity (measured by absorbance) of folded versus unfolded proteins at various urea concentrations. To begin, I had to calculate the number of milliliters of buffer to add to the 1.1 grams of peptide.

9.7 milligrams of peptide - molecular weight = 2.9 kDa = 2900 grams per mole

9.7 * 10^-3 (1 mol / 2.9 * 10^3) = 3.34 * 10^-6 moles of protein

Final molarity should be 70 * 10^-6 M

(3.34 * 10^-6) / x = 70 * 10^-6 M

x = .048 L = 48 mL of buffer necessary

Following our calculations, we prepared our sample of protein and buffer, adding a predetermined concentrations of buffer and urea (of the sample prepared the previous week). The combined sample was pipetted into small cuvettes and placed into the large fluorescence spectrometer.

I should note that preparing the fluorescence spectrometer was no small task. Yi told me that the pressure had to be moderated very carefully, using a pump to add or remove water from the inside of the system. Traditionally, the user will turn a wheel using their hands to pump in more water, but two weeks before my visit, RPI had switched to a computer modulated pump system. Unfortunately, Yi was unfamiliar with the new computer system. We asked several other grad students in the lab for assistance, but no one could figure out why the system was malfunctioning!

Fluorescence spectrometer diagram. Image taken from: http://www.mpip-mainz.mpg.de/62430/Fluorescence_Correlation_Spectroscopy

Because of our computer troubles, we could not finish our experiment. Yi had to head to his chemistry seminar and I had to catch the shuttle back to Emma Willard. Although our experiment time was cut short, we had a lot of fun and I learned a lot about how fluorescence spectrometers work, and how delicate they are. I'm very excited for my first internship meeting of 2017!