Questions about Greg's section
In an effort to be a bit more organized...
If you have any questions regarding Greg Doheny's section (chromatin, transcription in eukaryotes, contig assembly, bioinformatics, pedigrees, transposable elements, techniques), please post them in this post's comments section.
(Thanks to the person who suggested this!)
posted by pam39 @ 10:33 AM
17 Comments:
Can someone please exlain the whole p-element business. what's the basic idea and is there an easy way to actually understand the concepts without going out of ur mind?
P elements are specific to drosophila (which also has other transposable elements).
What i think is a pretty simple and clear explanation can be found at:
http://en.wikipedia.org/wiki/P_element
For DNase, in the notes it said that it can help determine the easily "accessible" DNA. What does this mean? and what's the use of this information? Also, what are DNase hypersensitive sites? I'm just unsure and the notes didn't really say much.
Thanks
Hi
Does anyone know how to construct a physical map? what patterns are we supposed to look for in our table?
Hi guys...i need help!!! I'm really not understanding the whole transposable elements idea, if u have Ac then the gene will jusmp out and you will get spots? But if you have Ds then there is no jumping and therefore no spots? Is this right? And so, the Ds element would be analogous to the P element in fruit flies? If someone couls kindle clear this up for me it would be greatly appriciated :)
THNX
is anyone even checking the blog???
If you have C/c(ds) and functional Ac present, technically you should get spotted, right? Because in some cells, no insertion will happen in the big C, while in other cells, the functional Ac can insert itself as well as mobilize the ds to move into the big C. So that is both yellow and purple = spotted. But when I asked Greg, he said that the ds isn't likely to move into a different chromosome, so the answer is purple.
So, on the exam, what do we write? The technical answer, or the probability answer?
I thought that if you have a Ds and a functional Ac, then the Ds does jump out returning the corn to wild type, but if you have a Ds only, u will get yellow. But just to get one thing clear, Ac means it is functional and Ac+ is not functional? So, Ac can jump in and out regarless of any activator present or not and therefore you will get spots, but the thing is that Ac jumping in is not likely, i think that's what the text said. SO basically with the corn q...i think if u have a C/c-Ds; Ac/Ac+ crossed with c/c; Ac/Ac, then you would get all purple with a slight chance of a spotted...can you see how the functional Ac will take the Ds out restoring the c back to wildtype C? If you had C/c; Ac+/Ac+ crossed with c/c; Ac/Ac, then you are most likely to get yellows because the Ac will jump into C making it into c. I hope that helps, but looking at P elements is much harder. Has anyone seen the practice final on the course site? It looks really bad!!!
I'm going through problem set #12 and I've gotten stuck on question 14, part B, regarding the concentration of Not I required to digest the fly DNA. Anyone have any ideas?
For the corn question, I think that regardless of the fact if you have C/c+ds; Ac/Ac you will get purple. If you have c-ds/c, Ac/Ac+ you will get purple spots. (as long as you have an Ac element present you will get some of the domianant characteristic)
Problem set 12:
A) did you figure it was 4^8 fragment pieces?
B)How do we know how large of a fragment can the plasmid hold? So, I think that when you figure that out, you can firgure out how much it Not1 to use based on the fragment sixe it cuts found in A.
Nice work with the transposable elements stuff!!
Just to share a "trick": if you have one C, then the kernels will be purple, always. If you have an Ac element around, and it jumps, the chances of it landing inside the C gene are really quite slim (you can mention this if you want, but don't lose any sleep over it).
You get spots when the c is caused by the fact that there's a transposon inside the C gene, AND you have no completely wt C, AND you have the Ac element somewhere in the genome.
Cheers!
Pam
For the Not I problem, that's correct, since it's an 8-cutter, it cuts on average once every 4^8 bps (I think it's about 65kb or something). You want your fragments to be 400kb long (it says in the question that that's the maximum size for the insert in that vector).
NOW:
- if you use 1 umol of NotI for 1 mg of DNA you get complete digestion (i.e. one cut every 65kb)
- we want one cut every 400 kb
--> 400kb/65kb=about 6 (I don't have a calculator)
--> we need about 6 times less Not I to get 400kb fragments than for 65kb fragments
----->1umol/6=about 0.16umol of NotI for every mg of DNA.
Makes sense?
Study well!
Pam
By the way,
the practice final is totally doable for you guys. Don't worry if there are things that you don't get (ask for help, but don't panic-it is actually a bit harder than the exam itself will be).
Pam
PS: there are office hours on Monday, 2-4pm!
for question 3 in the mock final, If the progeny has a repressor protein, but the mother doesnt, does the TE still move around?
Yea I'm also having trouble with the final posted on the 335 website. For number 3, what is the answer to a)?
Any help would be appreciated
i think that even though the mother TE does move around due to maternal effects. It doesn't matter if the porgeny has it or not because it won't be activated yet
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