User:MartinLubell/sandbox

Quick Links for our sandboxes, main 81H page, etc.

 * RNA Silencing
 * User:Ppelletier/sandbox
 * Education_Program:Johns_Hopkins_University/Molecular_Biology,_Section_81_(2013_Q1)
 * USEP/Courses/JHU_MolBio_Ogg_2013/Group_81H
 * I am not able to create a direct link to the talk page of Group_81H, but use link above, then click "Talk".

Comments from MartinLubell about Immunolabeling Wikipedia article
I think that overall your article was very informative. I definitely learnt a lot about "immunolabeling"! It's very cool that you were able to get permission from Dr. Thomas Caceci to use his images using the "immunolabeling" technique. I can't wait to see them.

Following are a few small edits:
 * Issues with singular and plurals: use "piped links" to solve problem.

Antigens are organic molecules, proteins, capable of binding to antibodies. Linking antigen-specific antibodies with a means of detection, known as a tag, provides a way to observe the location of the antigens to which the antibodies bind. If the immunolabeling process is meant to reveal information about a cell or its substructures, the process is called immunocytochemistry. Immunolabeling of larger structures, such as biological tissues, is called immunohistochemistry.

There are two complex steps in the manufacture of antibodies for immunolabeling. The first is the production of antibodies that bind specifically to the antigen of interest and the second is the fusion of the tag to the said antibodies. Since it is impractical to fuse a tag to every conceivable antigen-specific antibody, most immunolabeling processes use an indirect method of detection. This indirect method employs a primary antibody that is antigen-specific and a secondary antibody fused to a tag that specifically binds the primary antibody. This indirect approach permits mass production of secondary antibodies that can be bought off the shelf.[1]


 * 3rd paragraph: Add enzyme link
 * 4th paragraph: question to myself: if the gold is so dense that it is impenetrable, why is there radiation from it? Wouldn't it be more of a black spot?
 * Very good 5th paragraph!
 * 8th paragraph: extra space at end of: "... haptenylated primary antibodies can be used ,"
 * 9th paragraph: missing some links for "tag" & "antibodies"
 * 10th paragraph: For references, should there be a space before the number or not? (I'm not sure.)

RNA Silencing Mechanisms
The most basic mechanistic flow for RNA Silencing is as follows:

1: RNA with inverted repeats hairpin/panhandle constructs --> 2: dsRNA --> 3: miRNAs/siRNAs --> 4: RISC --> 5: Destruction of target mRNA

1: It has been discovered that the best precursor to good RNA silencing is to have single stranded antisense RNA with inverted repeats, which in turn build small hairpin RNA and panhandle constructs. The hairpin or panhandle constructs exist so that the RNA can remain independent and not anneal with other RNA strands.

2: These small hairpin RNAs and/or panhandles then get transported from the nucleus to the cytosol through the nuclear export receptor called exportin-5, and then get transformed into a dsRNA, a double stranded RNA, which, like DNA, is a double stranded series of nucleotides. If a dsRNA were only built with a single strand, there would be a higher chance for it to anneal to other "good" mRNAs. As a double strand, it can be kept on call for when it is needed.

3: The dsRNA then gets cut up by a Dicer into small (21-28 nt = nucleotides long) strands of miRNAs (microRNAs) or siRNAs (short interfering RNAs.) A Dicer is an endoribonuclease RNase, which is a complex of a protein mixed with strand(s) of RNA.

4: Lastly, the double stranded miRNAs/siRNAs separate into single strands; the antisense RNA strand of the two will combine with another endoribonuclease enzyme complex called RISC (RNA-induced silencing complex) and will guide the RISC to break up the "perfectly complementary" target mRNA or viral genomic RNA so that it can be destroyed.

5: It means that based on a short sequence specific area, a corresponding mRNA will be cut. To make sure, it will be cut in many other places as well. (If the mechanism only worked with a long stretch, then there would be higher chance that it would not have time to match to its complementary long mRNA.) (Question: why aren't many different "good" mRNAs cut at the same time?) It has also been shown that the repeated-associated short interference RNAs (rasiRNA) have a role in guiding chromatin modification. [2, p. 364]

Biological Functions
RNA silencing is the mechanism that our cells (and cells from all kingdom (biology)) use to fight RNA viruses and transposons (which originate from our own cells as well as from other vehicles.) [2]

From what we have learnt from RNA silencing mechanisms, "artificial introduction of long dsRNAs or siRNAs has been adopted as a tool to inactivate gene expression, both in cultured cells and in living organisms. [2]

The same way that RNA silencing regulates downstream target mRNAs, RNA silencing itself is regulated. For example, silencing signals get spread between cells by a group of enzymes called RdRPs (RNA-dependent RNA polymerases) or RDRs.[2]

Preliminary outline for our RNA Silencing article

 * Explain the differences between the related Wikipedia articles: RNAi, RNA Silencing, etc.
 * Maybe regroup different articles under one-mixed-title article? (Be bold!)
 * If not under one mixed title, maybe use layout of RNAi article:
 * Definition
 * Summary
 * Molecular mechanisms
 * Key players
 * Mechanistic description
 * Biological functions
 * Processes affected
 * Manifestations
 * In-depth
 * Recent discoveries
 * Laboratory techniques
 * Medical implications
 * Technological applications
 * History and Discovery
 * Evolution
 * Open ended questions

Unit 7 Wiki homework: initial work on our article on RNA silencing

 * 1) Identified key points that should be in the Wikipedia article for this topic.


 * 1) Picked my sandbox in which to work since it does not matter which one we choose.
 * 2) We have to make sure we explain the differences between the related Wikipedia articles: RNAi, RNA Silencing, even DNA silencing (in our textbook, but not a Wikipedia article), etc.
 * 3) Start with a definition of "RNA silencing" move on to a basic summary which underscores its significance in the genetic molecular machinery, state the biological impact (if any), summary of lab techniques used, provide a history of how it was discovered and how studies have progressed, leave an open ended discussion at the end about questions left unanswered by the most recent articles on the subject.
 * 4) Do we point to the other articles, or do we somehow eliminate some and regroup them under one mixed title? Initial thought is to point where possible to form hyperlinks/connections between concepts.
 * 5) Moved (I only copied, but maybe we have to delete in group page?) the list of references found in Unit 5/6? from our group page to the working sandbox page.
 * 6) An accessible article, discussing the topic as a general concept.
 * 7) One regarding a specific RNA silencing mechanism described.
 * 8) One with a clinical/therapeutic focus to apply the concepts.
 * 9) Authors are also now conceiving of RNA silencing as a mechanism for cellular protection against viruses, transposons, as well as disposing of aberrant or nonfunctional mRNAs.
 * 10) An interesting article about RNAi that related to HW#5:
 * 11) Two articles cited in the existing RNA silencing Wikipedia article.
 * 12) Good background article to set up the definition in context
 * 13) Discussion of potential impact on Alzheimer's disease (i.e., bio-medical impact)
 * 14) Article on RNAi Cell-Based Microscopic Screening
 * 15) Found more high-quality references, and added them to a list.
 * 16) Found some Wikipedia Commons images that you can use that show up on the right side of the page. ( I added the image link on the first line of our section.)
 * 17) Prepared a preliminary outline for the article, and wrote that in a new section of the working sandbox page.
 * 18) Added ideas for how we would like to improve the article to the [] talk page of the article. This will open communication between our group and other wiki editors who are interested in improving the article.

Two very complicated articles that we had to decipher for our HW #5
The first one was about the PRDM9 recombination-motif recognition protein that initiates DNA breakage and then a rearrangement.

The second one was about how one could look at patterns of linkage disequilibrium (or chromatin structure) instead of DNA sequence recognition to look for hotspots for recombination frequencies.

Two articles relating to our group project
Here is a great article that relates to one of our chosen Wikipedia articles and to our homework as well. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329497/

Unfortunately I was not able to comment on the "Structure and function of helix-loop-helix" article because I was not able to download it even though I've successfully found others through the Johns Hopkins Library System. I could have actually taken out the hard copy. I'll have to spend some more time searching for it later.

The 5 pillars of Wikipedia

 * 1) It is an online information sharing system.
 * 2) Be neutral and objective. Don't use it to promote yourself or your beliefs or politics.
 * 3) It is free, and your labor is donated.
 * 4) Be civil.
 * 5) No rigid rules, but still be cool.

Still having trouble really understanding the linking number concept!
The text in Box 7-2 of p. 166 of our textbook uses the term overall linking number versus just linking number, and that's pretty confusing. Also, why do they say "change in linking number" and not "change in the linking number?