Difference between revisions of "20.109(F07): Journal article discussion"
From Course Wiki
(→Experimental techniques) |
MAXINE JONAS (Talk | contribs) m (19 revisions: Transfer 20.109(F07) to HostGator) |
||
(12 intermediate revisions by one user not shown) | |||
Line 1: | Line 1: | ||
{{Template:20.109(F07)}} | {{Template:20.109(F07)}} | ||
+ | Turn in your mid-semester class evaluation before the end of lab. The evaluation form can be [[Media:Macintosh HD-Users-nkuldell-Desktop-MidsemesterEval 20.109.doc| found here]]. Complete the questionnaire and then print it out <b>without including your name </b> to turn in before you leave. | ||
==Journal articles to be discussed== | ==Journal articles to be discussed== | ||
* [http://www.nature.com/doifinder/10.1038/448855a The news story] by Erika Check called "RNA interference: hitting the on switch" published in Nature 2007 vol. 448 pp. 855-8 | * [http://www.nature.com/doifinder/10.1038/448855a The news story] by Erika Check called "RNA interference: hitting the on switch" published in Nature 2007 vol. 448 pp. 855-8 | ||
* [http://www.pnas.org/cgi/content/abstract/103/46/17337 The original paper] by Long-Cheng Li et. al. "Small dsRNAs induce transcriptional activation in human cells" published in PNAS 2006 vol. 103 pp. 17337-42. | * [http://www.pnas.org/cgi/content/abstract/103/46/17337 The original paper] by Long-Cheng Li et. al. "Small dsRNAs induce transcriptional activation in human cells" published in PNAS 2006 vol. 103 pp. 17337-42. | ||
==Questions to guide your reading== | ==Questions to guide your reading== | ||
− | 1. Read [http://www.nature.com/doifinder/10.1038/448855a the news story] by Erika Check first, noting particularly the | + | Helpful information and guidelines for reading are presented here. <font color = purple> Questions you should try to answer are in purple</font color>. The answers will not be collected but most or all will be part of the class discussion of this paper. |
− | 2. Next skim the whole scientific article. <br> | + | ===1.=== |
+ | Read [http://www.nature.com/doifinder/10.1038/448855a the news story] by Erika Check first, noting particularly the reporter's description of the scientists motivation and path to RNA activation. You will <font color = purple> compare this description to how the scientific authors describe their path to RNAa in the introduction to the paper they wrote. Keep track of other reactions you have to the news story. Does it raise any questions for you? Is there anything surprising? Would you characterize the events as comedy or tragedy or neither? </font color><br> | ||
+ | ===2.=== | ||
+ | Next skim the whole scientific article. <br> | ||
This means read the abstract once. Read the first and last sentence of the introduction. Read the subdivision headings of the Results section. Look at all the figures and their legends. Read the first and last paragraph of the Discussion.<br> | This means read the abstract once. Read the first and last sentence of the introduction. Read the subdivision headings of the Results section. Look at all the figures and their legends. Read the first and last paragraph of the Discussion.<br> | ||
− | 3. Now it's time to really comb through the data. <br> | + | ===3.=== |
+ | Now it's time to really comb through the data. <br> | ||
We'll focus on the reported results, including the [http://www.pnas.org/cgi/content/full/0607015103/DC1 supplemental information.] To help you organize the material, a few links and tables are given here. | We'll focus on the reported results, including the [http://www.pnas.org/cgi/content/full/0607015103/DC1 supplemental information.] To help you organize the material, a few links and tables are given here. | ||
− | ====Experimental matrix==== | + | ====3A. Experimental matrix==== |
<center> | <center> | ||
{| border="1" | {| border="1" | ||
Line 16: | Line 21: | ||
! Cell types examined | ! Cell types examined | ||
|- | |- | ||
− | | dsRNA <br>Aza-C (demethylase) | + | | dsRNA <br>Aza-C (demethylase)<br> IFN-alpha2a (nonspecific inducer) |
| E-cadherin <br> p21<br> VEGF | | E-cadherin <br> p21<br> VEGF | ||
| PC3 and DU45 (human prostate cancer cell lines)<br> Hela (human cervical carcinoma)<br> MCF-7 (human breast cancer line)<br> HEK293 (embryonic kidney line)<br> LNCaP (human prostate cancer)<br>J82 and T24 (bladder cancer) | | PC3 and DU45 (human prostate cancer cell lines)<br> Hela (human cervical carcinoma)<br> MCF-7 (human breast cancer line)<br> HEK293 (embryonic kidney line)<br> LNCaP (human prostate cancer)<br>J82 and T24 (bladder cancer) | ||
|} | |} | ||
</center> | </center> | ||
− | ====Experimental techniques==== | + | |
− | < | + | ====3B: Experimental techniques==== |
+ | =====<i>Western analysis</i>===== | ||
+ | see [[20.109(F07): Western analysis| this link]] for refresher info.<br> | ||
Data can be presented like this | Data can be presented like this | ||
<center> | <center> | ||
[[Image:SampleWestern fig10B.png|thumb|left|300 px|sample western data, fig 10B]] | [[Image:SampleWestern fig10B.png|thumb|left|300 px|sample western data, fig 10B]] | ||
</center> | </center> | ||
− | <br> where the treatment variation is shown above the gel lanes, the intensity of the protein band is shown inside the boxes (a cutout of the whole blot to | + | <br> where the treatment variation is shown above the gel lanes, the intensity of the protein band is shown inside the boxes (a cutout of the whole blot to show just the relevant bands). GAPDH is a "housekeeping gene" whose level is rarely affected by experimental perturbations. <font color = purple> Why is it important to include data for this gene product? Thinking back to when you performed your Western analysis, did you included a similar control? </font color> |
− | < | + | |
− | Data can be presented like | + | =====<i>RT-PCR (also sometimes called q-PCR)</i>===== |
− | or | + | see[http://openwetware.org/wiki/BE.109:Systems_engineering/Measuring_DNA,_RNA,_protein | this link] for some description of RNA measurement techniques including RT-PCR. You might also want to learn a little about standard PCR if you're not already familiar with this technique. Most biology textbooks describe PCR or you could look at some animations of the process, for example [http://www.dnai.org/b/index.html here], just follow the links through |