methionine
Posts: 75
Joined: Sat Nov 11, 2006 11:48 am
Occupation: Student

Reading Scientific Papers

Postby methionine » Wed Aug 29, 2007 1:35 pm

Hi all,

I'm working on another research project. Naturally, a large part of starting another research project is a lot of reading. The topic I'm reading about is pretty new to me and the papers seem to be much more difficult to understand than any other paper I have ever read. I know this is partially due to the fact that my "foundation" in my topic (genes... splicing) isn't complete, but I really feel like I should be able to handle it somehow.
Does anybody have any recommendations on how I could digest a research paper? My personal method goes something like this: Read the abstract, read the introduction. I go through those with two different colors of highlighters-- for example, pink will indicate a word I am not familliar with, while yellow will simply indicate an important fact (explanation on how something works, the effect of .. whatever, etc). I go along until I finish the introduction, then jump to the discussion section and do the same. I do this because I want to know how the paper "changed" anything/ "discovered" anything new; why the paper is important. Then after I'm done highlighting that, I will generally skim over the materials and procedures section, noting any "new" procedure I don't know about, just to keep in mind how that particular assay is generally used. Sometimes I will highlight other sources that the paper had referred to in order to get a better idea of where the researchers are coming from.
After that, I transcribe/paraphrase the important highlighted stuff into my notebook and annotate accordingly... I look up and define all the new words I don't get, and try to piece it together.

While I suppose that this is a pretty thorough way of reading a paper, I still feel like I don't get some of it. It also gets frustrating when there are just waaay too many new words to go look up. Piecing together all the new information is also difficult for me-- defining is much easier, but connections need to be made.

Does anybody have any suggestions? I have at least ten papers to go through, and I really don't want to only understand 30% of what I read. Thank you so much for your help!

-M
People do not see the world as it is, they see it as they are.

MelissaB
Moderator
Posts: 1055
Joined: Mon Oct 16, 2006 11:47 am

Postby MelissaB » Wed Aug 29, 2007 1:50 pm

Well, first of all I'd love it if the students at my university read papers with half the thoroughness that you do.

One thing I might suggest is to go from the oldest papers to the newest papers. Oftentimes ideas are more thoroughly explained when they're first introduced whereas they're just mentioned in newer papers with the understanding that everyone will have read that first paper. Likewise, if you see a citation listed for a concept you don't understand, you may try to look up that paper and see if it's explained better there.

Another unfortunate recommendation is just to re-read the paper. Sometimes you just miss an important point or connection the first time around.

Have you read information in textbooks or online about your new topic? Oftentimes that's a good way to get some of the basic building blocks that will help you understand more complicated papers. Another place (also online) you might try is the personal websites of the researchers whose articles you're reading. Sometimes they will have a summary of their current research on their webpage (though it's often out of date), and they're usually a bit more careful about not using jargon (or at least not using so MUCH jargon) than they are in a paper aimed at their peers.

I hope this helps!

methionine
Posts: 75
Joined: Sat Nov 11, 2006 11:48 am
Occupation: Student

Postby methionine » Wed Aug 29, 2007 2:07 pm

Thanks for your suggestions!

About reading about things in textbooks... The research I'm doing is too "recent" to really be in any textbooks yet.

...Okay now, back to reading...
People do not see the world as it is, they see it as they are.

tdaly
Former Expert
Posts: 1415
Joined: Sat Nov 08, 2003 11:27 pm
Occupation: Planetary Scientist

Postby tdaly » Wed Aug 29, 2007 4:47 pm

Methionine,

As someone who's been in your shoes, I can't emphasize enough how crucial it is to read texts in your field of study. I know that what you are studying probably isn't discussed in the texts, but it is a good place to get general information and become familiar with the terminology and style of the discipline. Even the books are not specificallly about your topic, a good general background is a must to understand what you are doing, why you are doing it, and why it matters. It also prepares you for answers judges questions, which are liable to involve topics beyond the strict definition of your project.
All the best,
Terik

methionine
Posts: 75
Joined: Sat Nov 11, 2006 11:48 am
Occupation: Student

Postby methionine » Wed Aug 29, 2007 7:02 pm

Thanks. Yes, I have been pretty devoted to this area... I've taken several courses on genetics and genomics, and also have been reading material about the general field for over a year now (I guess that seems like a short time to you, but that is the majority of my "research career"). I guess the problem here is that now that I'm switching from yeast cells to mammalian cells, there are some new things that I really have never heard about before, and that's what really is causing the frustration here.

thanks :)
People do not see the world as it is, they see it as they are.

methionine
Posts: 75
Joined: Sat Nov 11, 2006 11:48 am
Occupation: Student

Postby methionine » Fri Aug 31, 2007 6:28 pm

Oh yes, and I have one more question... if any of you know...
What are "variable" C and N termini (in a protein)? I had previously thought that the C terminal simply was the carboxyl group at one end of a protein and the N terminal was the NH2... but what exactly does "variable" mean here? I never knew that COOH groups and NH2 s could actually.. change...... ? I have searched it, but I keep getting lots of other scientific papers that don't really answer my question. If any of you know what this means, it would be helpful. Thanks so much!
People do not see the world as it is, they see it as they are.

MelissaB
Moderator
Posts: 1055
Joined: Mon Oct 16, 2006 11:47 am

Postby MelissaB » Fri Aug 31, 2007 7:46 pm

No idea, but off the top of my head...is there a different protein at the two ends? Or does it sound like something different? It's been a while since I took genetics.

Louise
Former Expert
Posts: 921
Joined: Mon Jan 16, 2006 2:17 pm

Postby Louise » Sat Sep 01, 2007 6:58 am

methionine wrote:Oh yes, and I have one more question... if any of you know...
What are "variable" C and N termini (in a protein)? I had previously thought that the C terminal simply was the carboxyl group at one end of a protein and the N terminal was the NH2... but what exactly does "variable" mean here? I never knew that COOH groups and NH2 s could actually.. change...... ? I have searched it, but I keep getting lots of other scientific papers that don't really answer my question. If any of you know what this means, it would be helpful. Thanks so much!


I think all they are saying is the variable end changes. So, for example, a protein might have the c-terminus conserved (all the residues at that end the same (from context you should be able to figure out
the same as what)) and the n-terminus variable, meaning the residues there are different (than the other proteins in the class). Does this make sense in the papers you are reading?

Your understanding of C and N terminus is correct.

Lise Byrd
Former Expert
Posts: 95
Joined: Sun Sep 18, 2005 10:00 pm

Postby Lise Byrd » Sat Sep 01, 2007 8:20 am

Methionine,

I think that when they talk about the C- or N-terminus being variable, they're talking about the functional groups attached to the carboxyl or amine groups, not the carboxyl or amine groups themselves.

In terms of reading scientific papers, I find it useful to scribble notes in the margins summarizing what I just read in a sentence or two. This focuses my reading and also means that, later on, I can go back through the paper and pull out relevant information without re-reading the entire thing. You may already be doing this; you mentioned that you transcribe notes into a notebook.

Going through the diagrams thoroughly can also help you understand the topics presented in the paper, particularly for the results and discussion sections. If you haven't learned how to interpret results of gel electrophoresis or Northern or Western analyses, for example, I suggest you sit down with your teacher or mentor and go through a few step-by-step. While it is time-consuming to dissect diagrams in this way, they are extremely useful because they enable you to see what is happening, as opposed to just reading about it.

I applaud you for taking so much care over the papers. They are not easy to read; sometimes the only solution is to read the same sentences or paragraph over and over (doing it on different days sometimes helps). However, gaining such a thorough understanding of their subject can be very rewarding.

Sonia

methionine
Posts: 75
Joined: Sat Nov 11, 2006 11:48 am
Occupation: Student

Postby methionine » Tue Sep 11, 2007 7:58 pm

Hi,
thanks for all your helpful replies.
I've read each paper over several times, and now I think I get them much better. The part that is most confusing is the part on the prodecures, because I am not at all familiar with some of them (immunoblotting, cross-linking, siRNAs, etc). Do you guys know of any resources where I could learn about what these procedures really are and how they work? Textbooks, websites, anything? I can always ask my mentor as well, but I don't want to bog him down with questions that I should be finding answers to on my own, unless I REALLY can't find the answer.

Thanks!!
-M
People do not see the world as it is, they see it as they are.

Louise
Former Expert
Posts: 921
Joined: Mon Jan 16, 2006 2:17 pm

Postby Louise » Wed Sep 12, 2007 6:14 am

methionine wrote:Hi,
thanks for all your helpful replies.
I've read each paper over several times, and now I think I get them much better. The part that is most confusing is the part on the prodecures, because I am not at all familiar with some of them (immunoblotting, cross-linking, siRNAs, etc). Do you guys know of any resources where I could learn about what these procedures really are and how they work? Textbooks, websites, anything? I can always ask my mentor as well, but I don't want to bog him down with questions that I should be finding answers to on my own, unless I REALLY can't find the answer.

Thanks!!
-M


I assume your mentor has other students (like graduate students). I'd ask them what resources are really good. Also, many companies that sell the supplies for the techiques or instruments will have good tutorials on the basic science.


Louise

Lise Byrd
Former Expert
Posts: 95
Joined: Sun Sep 18, 2005 10:00 pm

Postby Lise Byrd » Sat Sep 15, 2007 6:08 pm

Methionine,

Here are a couple of websites that I found:

http://www.bio.davidson.edu/COURSES/gen ... nblot.html
(Immunoblotting is another name for Western blotting. The page also has a link to a clear explanation of SDS-PAGE.)

http://www.chemicon.com/resource/ANT101/a2B.asp
(Detailed procedure and clear graphic of the blotting step of Western blotting.)

http://a32.lehman.cuny.edu/molbio_cours ... otocol.htm
(The page focuses on Southern blotting, but the basic procedure is the same as for Western blotting; Southern just uses DNA instead of protein. There is a good set of graphics at the bottom that may help you understand how the procedure works.)

Cross-linking is part of the blotting technique (Western/ Southern/ Northern). After the molecules in question have been transferred to the membrane, they are cross-linked to the membrane, I think usually with UV light. This way you don't lose your molecules (because they're attached to the membrane!). Cross-linking also means you can use the same membrane multiple times--the probes or antibodies are simply washed off.

For other procedures, you can try searching [procedure name]+"procedure" or [procedure name]+"protocol". Also, you should feel free to ask your mentor about the specific procedures--that is what he's there for!

Post if you have more questions,
Sonia

Lise Byrd
Former Expert
Posts: 95
Joined: Sun Sep 18, 2005 10:00 pm

Postby Lise Byrd » Sat Sep 15, 2007 6:35 pm

Methionine,

You had also mentioned siRNAs in your last post. I have a link to an article that defines siRNAs, miRNAs, dsRNAs, and snoRNAs in its Glossary. (The subject matter of the paper is probably not what you're studying, so you won't need to worry about the rest of it.)

I don't know whether you will be able to access the article from your home computer, but you should be able to access it using the computer in your mentor's lab.

http://www.sciencedirect.com/science?_o ... d&ref=full

Here's the citation, just in case you can't access the paper directly from the link:
Lavorgna, G., Dahary, D., Lehner, B., Sorek, R., Sanderson, C.M., and Casari, G. (2004). In search of antisense. Trends in Biochemical Sciences 29, 88-93.

Sonia


Return to “Life, Earth, and Social Sciences”