20.109(F11): Mod 3 Day 2 Phage nanowires

Phage nanowires

Introduction

Today in lab you will react your SWNT:phage with titanium isopropoxide, then wash the nanowires several times, first with ethanol, then with water. You will have time during these steps to work on the research proposal idea you've got started with your lab partner.

Protocols

Part 1: React SWNTs:phage with Ti(I-pro)4

Today's lab has some safety hazards and you must work extremely carefully. Lab coats, gloves and goggles are a must when you're at the chemical hood. The reaction of the SWNT:phage with the titanium will take place in the hood at supercooled temperatures (a NaCl/ice bath at ~ -20°C). One the titanium has been deposited on the surface of the phage, the solution is less hazardous, though you should still treat the materials with care since no reactions run to completion.

1. Retrieve your dialyzed samples.
2. Carefully transfer the contents of the dialysis bag to a 50 ml falcon tube. This is best done by carefully holding the dialysis bag vertically while you remove one of the alligator clips, cover the open end of the tubing with the falcon tube, then invert the tubing and the falcon tube so the SWNT:phage solution can be collected.
3. Chill your SWNT:phage on ice on your bench until you are ready to react it with the titanium.
4. Prepare a supercooled ice bath by mixing 1 g NaCl + 3 g ice in an evaporation dish and allow the mixture to cool to -20°C. Place the dish in the fume hood on a stir plate.
5. Place a beaker in the ice bath with 7 ml 100% EtOH and a stirbar. Pre-cool the EtOH at least 5 minutes.
6. Add 50 ul Ti(I-pro)4 to the supercooled EtOH. Stir at least 5 minutes.
7. Add 3 ml of your SWNT:phage solution to the EtOH:titanium and stir vigorously for 10-15 minutes.

Part 2: Wash

1. Transfer the reaction to a 50 ml falcon tube. Remove 200 ul of this solution to an eppendorf tube to store for next time at the TEM. Spin the remaining volume in the clinical centrifuge at room temperature, 3000 rpm 10 minutes. At the end of this spin you should see dark material collected at the bottom of the tube. These are your nanowires!!
2. Decant the supernatant into a chemical waste bottle in the chemical hood. Resuspend the nanowires in 20 ml 100% EtOH. Spin as before.
3. Decant the supernatant into a chemical waste bottle in the chemical hood. Resuspend the nanowires in 20 ml dH₂O. Spin as before.
4. Repeat the wash with water.

Part 3: Research proposal

Writing a research proposal requires that you identify an interesting topic, spend lots of time learning about it, and then design some clever experiments to advance the field. It also requires that you articulate your ideas so any reader is convinced of your expertise, your creativity and the significance of your findings, should you have the opportunity to carry out the experiments you’ve proposed. To begin you must identify your research question. This may be the hardest part and the most fun. Fortunately you started by finding a handful of topics to share with your lab partner. Today you should discuss and evaluate the topics you’ve gathered. Consider them based on:

• your interest in the topic
• the availability of good background information
• your likelihood of successfully advancing current understanding
• the possibility of advancing foundational technologies or finding practical applications
• if your proposal could be carried out in a reasonable amount of time and with non-infinite resources

It might be that not one of the topics you’ve identified is really suitable, in which case you should find some new ideas. It’s also possible that through discussion with your lab partner, you’ve found something new to consider. Both of these outcomes are fine but by the end of today’s lab you should have settled on a general topic or two so you can begin the next step in your proposal writing, namely background reading and critical thinking about the topic.

A few ground rules that are 20.109 specific:

• you should not propose any research question that has been the subject of your UROP or research experience outside of 20.109. This proposal must be original.
• you should keep in mind that this proposal will be presented to the class, so try to limit your scope to an idea that can be convincingly presented in a ten minute oral presentation.

Once you and your partner have decided on a suitable research problem, it’s time to become an expert on the topic. This will mean searching the literature, talking with people, generating some ideas and critically evaluating them. To keep track of your efforts, you should start a wiki catalog on your OpenWetWare user page. How you format the page is up to you but check out the “yeast rebuild” or the “T7.2” wiki pages on OpenWetWare for examples of research ideas in process. As part of your “for next time assignment” you will have to print out your wiki page specifying your topic, your research goal and at least five helpful references that you’ve read and summarized.

DONE!

For next time

Define your research proposal or exhibit ideas by making a wiki page to collect your thoughts and resources (you can do this on one page with your partner or split the effort and each turn in an individual page). Please start your wiki page name with "20.109(F11): your names and/or topic here"
Keep in mind that your presentation to the class will need:

• a brief project overview
• sufficient background information for everyone to understand your proposal
• a statement of the research problem and goals
• project details and methods
• predicted outcomes if everything goes according to plan and if nothing does
• needed resources to complete the work

You can organize your wiki page along these lines or however you feel is most helpful. Print your user page(s) for next time, making sure it defines your topic, your idea and some references you've collected and summarized.

Reagents list

• 100% EtOH
• Ti(I-pro)4 [Media:Ti(I-pro) MSDS.pdf| msds]