Difference between revisions of "20.109(F08): Mod 3 Day 2 Phage nanowires"
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==Introduction== | ==Introduction== | ||
− | The metal iridium has an interesting history as much for the things it | + | The metal iridium has an interesting history as much for the things it hasn t done as for the things it has. As one of the most corrosion-resistant metals known, it was forged with platinum into the bar that stood for years as the meter standard. In addition, iridium is one of the most brittle materials known, making it a suitable hardening agent for that platinum meter bar but also making pure iridium nearly impossible to machine. Finally, iridium is awfully hard to get unless you catch space dust. It is thought to be concentrated in the earth s molten core but is only rarely found in the earth s crust. Interestingly, there is a 30-fold enriched for iridium in the layer of clay that marks the end of the planet s Cretaceous period. This enrichment led the father and son team of Luis and Walter Alvarez to suggest in the 1970s that the dinosaurs died when a giant asteroid struck the earth, releasing an iridium-dense cloud that blocked the sunlight before settling over time. The enrichment of iridium in this clay layer could also be explained by a massive volcanic eruption (or series of them) that released iridium from the molten core. When Jurassic Park opens for real, perhaps there will be a way to find out from the dinosaurs themselves how the iridium came to rest in this clay layer. |
[[Image:Boundary.jpg|thumb|left|200 px| The iridium-rich clay layer at the boundary between Cretaceous and Tertiary rocks. Courtesy of Canadian Museum of Nature, Ottawa)]] | [[Image:Boundary.jpg|thumb|left|200 px| The iridium-rich clay layer at the boundary between Cretaceous and Tertiary rocks. Courtesy of Canadian Museum of Nature, Ottawa)]] | ||
− | The name iridium is derived from the latin word for rainbow, iris, and | + | The name iridium is derived from the latin word for rainbow, iris, and it s the colorful properties of this uncorrosive, unmachinable, dinosaur killing metal that s relevant for our work in this module. Iridium, when oxidized to IrO2, has a d-orbital conductance band [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TFM-4F973HJ-1&_user=10&_coverDate=06%2F27%2F2005&_alid=640919082&_rdoc=1&_fmt=summary&_orig=search&_cdi=5230&_sort=d&_docanchor=&view=c&_ct=12&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=679dd5d931cf3666623925298bfb42ea] rather than the usual s or p-orbital band that is associated with other oxides, such as indium tin oxide (ITO). The populated d-orbital makes this chemical species electrochromic, that is it will change color from purple to colorless when charge is applied. The particular usefulness of IrO2 over other inorganic electrochromic oxides is its switch speed, which is on the order of 10 msec for sputtered IrO2. And while faster switch speeds and greater contrast may be needed for future applications such as electronic paper [http://en.wikipedia.org/wiki/Electronic_paper], nature has given a good starting substrate to optimize. |
− | [[Image:Snowflake1 1.jpg|thumb|right| | + | [[Image:Snowflake1 1.jpg|thumb|right|100px| image from The Snowflake by Kenneth G. Libbrecht]] |
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− | One optimization strategy is to organize the IrO2 into crystals. Such a nanoscale highly ordered structure could improve the natural switch speed. Growing crystals in the lab requires as much art as it does skill. This is because odds are very low that two molecules might collide with the precise energy needed to nucleate the crystal formation and only select conditions enable crystals to grow from that newly formed nucleus. Think of that on the next snowy day. | + | One optimization strategy is to organize the IrO2 into crystals. Such a nanoscale highly ordered structure could improve the natural switch speed. Growing crystals in the lab requires as much art as it does skill. This is because odds are very low that two molecules might collide with the precise energy needed to nucleate the crystal formation and only select conditions enable crystals to grow from that newly formed nucleus. Think of that on the next snowy day. In this lab, we'll use M13 as a template to order the iridium colloidal particles that you're synthesizing. The ordered and polyvalent p8 coat protein provides ~900 nm of real estate for ordered iridium binding to occur. You will have the opportunity to visualize the phage-IrOx crystals by TEM during a lab period later in this module. |
==Protocols== | ==Protocols== | ||
− | ===Part 1: | + | ===Part 1: Complete the IrOx synthesis=== |
− | + | In these final steps of the synthesis you will remove the unreacted citrate using an ion exchange resin and then oxidize the iridium particles with H<sub>2</sub>O<sub>2</sub>. | |
− | + | # Stir your solution from last time with 2.8 grams of ion-exchange resin ("Amberlite" monobed MB-1) for 30 minutes at room temperature. | |
− | + | # Use a vacuum filtration unit to remove the resin. | |
− | + | # Dilute the filtered volume to 50 ml with deionized water. | |
− | + | # Return the filtered volume to your 120 ml amber bottle and add 1.4 ml of 6% H<sub>2</sub>O<sub>2</sub> (do not accidentally use the 30% stock). | |
− | # | + | # Stir for one more hour at room temperature. |
− | # | + | # These will rest until next time at room temperature in the dark in the amber bottles to allow for complete decomposition of the hydrogen peroxide. |
− | # | + | ===Part 2: Dilute the 3-12 phage stock=== |
− | # | + | Count the number of plaques on your phage titering plates from last time. Calculate the concentration of phage in your undiluted purified phage sample. Be sure to take into account each dilution when you try this calculation. Express the concentration as PFU/ul and determine the volume of phage needed for 2x10^13 PFU. You will need to know this volume for Mod3 Day 5. |
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− | ===Part 3: Research proposal=== | + | ===Part 3: Research proposal/Collaborative Science and Art Project=== |
− | 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 | + | ====For those interested in the 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 | * your interest in the topic | ||
* the availability of good background information | * the availability of good background information | ||
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* if your proposal could be carried out in a reasonable amount of time and with non-infinite resources | * 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 | + | 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: | A few ground rules that are 20.109 specific: | ||
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*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. | *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, | + | 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 [http://openwetware.org/wiki/Yeast_rebuild | |