Journal Club

Interested in a B&G Journal club?

  • Yes

    Votes: 8 100.0%

  • No

    Votes: 0 0.0%

  • Don't know

    Votes: 0 0.0%

  • Some other opinion

    Votes: 0 0.0%
  • Total voters
    8
  • Poll closed .
S.A.M.

S.A.M.

uniquely dreadful
Valued Senior Member
INDEX OF JOURNAL CLUB ARTICLES:


1. Strong Inference -Platt

2. HIF-independent regulation of VEGF and angiogenesis by the transcriptional coactivator PGC-1alpha - Arany et al

3. Zinc transporters and cancer growth

4. Diversity and evolutionary history of plastids and their hosts

HOT TO READ/WRITE A RESEARCH ARTICLE:
http://www.sciforums.com/showthread.php?t=79053


Is anyone interested in a Biology and Genetics journal club?

The OP could post a thread with the words "Journal Club"+topic in it. A link to a relevant article would be present in the first post and members could read the article and discuss the methods, results, conclusions and critique the same.

It would be useful if the OP presented their critique of the article in the first post, which would give a good take off point for the discussion to start.

If sufficient people are interested in reading an article and discussing it, I'll start the first one, as a trial. I like the Platt paper as a starting point.

The poll will be open for 7 days

I think it might be a good idea to keep this sticky as an index for the Journal club threads.
 
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I hope it leads to discussion. :O

Is this the place to discuss your link or are you making a new thread later?
 
Be nice to get at least a few more people, I was hoping the paper would be interesting enough to stimulate discussion. :)
 
S.A.M. said:
Is anyone interested in a Biology and Genetics journal club?

The OP could post a thread with the words "Journal Club"+topic in it. A link to a relevant article would be present in the first thread and members could read the article and discuss the methods, results, conclusions and critique the same.

It would be useful if the OP presented their critique of the article in the first post, which would give a good take off point for the discussion to start.

If sufficient people are interested in reading an article and discussing it, I'll start the first one, as a trial. I like the Platt paper as a starting point.

The poll will be open for 7 days
Click to expand...

Interesting idea, I like it, but don't know if I'm interested in Biology articles. I really like biology! Really, really, but I'm not competent enough in it. I'll see if I can make similar threads in other sciences, if I find the time. Which I don't have at all lately... :(
But I'll keep it in mind.
 
If I am to participate significantly the papers discussed need to be much more detailed in facts I can learn, not broad generalities, such as "methodology."

For example, I found the following very interesting:

"Peregrine-pharmaceuticals...is developing a monoclonal antibody bavituximab, which targets phosphatidylserine molecules [PS] presented on the outer side of cancer blood vessel cells. PS is only a side-effect, a characteristic of cancerous tissues from which cancer does not benefit. In normal, healthy vascular cells, PS is tightly segregated to the internal side of the cell. This segregation appears to be impaired in many kinds of tumor blood vessels, where PS becomes present on the external side of the cells. This phenomenon was observed in lung, breast, prostate and pancreatic cancer, among others. Monoclonal antibodies that are injected into the blood stream can recognize only targets that are presented on the external side of cells, healthy cells that have PS exclusively on their inner side will be unaffected, while cancer blood vessels would be targeted by the antibody exclusively. ..."

I.e. unlike VEGF drugs (such as very succesful Avastin now being sold) that only arrest the growth of solid tumors (by inhibiting new blood supply) this approach may kill the exisiting tumor. ("chemical surgery" to selectively remove it.) I have learned of at least a dozen other clever ideas for developing "magic bullets" for cancer and other diseases. One for viral infections "works" by keeping the newly made viral particles inside an infected cells "folded up" - to exit thru the cell wall and infect other cells, most viral particles need to "unfold" and become more linear, or spear like. I.e.they are trapped in the jail of the cell they were born in, greatly reducing their rate of infection and adding the body's defenses get the upper hand to eliminate them. Also many great idea for heart and arterial problems are now in the labs. Humans are about to enter an exciting new age of medicine and not only because of the new understanding of DNA etc.

Summary: If I am to actively particiapte, the papers will need to be about exploitable facts which can help in major medical problem areas. (I love to learn in any scientific area, but it can also be useful economically to recognize some things before everyone dose.) Do not take the above as a recommendation to invest in PPHM - they will may never get their developmental drug, bavituximab, to market. (Most early stage drugs fail to be profitable even if they do get thru the FDA.)
 
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S.A.M. said:
You can put up any paper you want to discuss Billy
Click to expand...
When I worked (for money) I avoided the 5PM leaving traffic by spending an hour of two reading journals in our rather good technical library. (It had a few excelent non-technical publications including the then quarterly Foreign Affairs, but now I rarely read in the library. Instead I read the claims of many different companies. I also have four or five biologic/ drug news services Emails everyday - ocassionally they do mention some University discoveries and I may suggest one of them, if article is available one the net.

My hope (for my benefit) from the "journal club" is that some more university (not corporate research) based significant developments of some underderstanding will be brought to my attention by others (certainly CharonZ, spidermonkey, and you must still be reading some good biological journals.)


BTW I had forgotten the "punch line" of the joke I PMed you. Shorter, and more subtile version is:

Slam,BAM; Sorry SAM.
 
Billy T said:
When I worked (for money) I avoided the 5PM leaving traffic by spending an hour of two reading journals in our rather good technical library. (It had a few excelent non-technical publications including the then quarterly Foreign Affairs, but now I rarely read in the library. Instead I read the claims of many different companies. I also have four or five biologic/ drug news services Emails everyday - ocassionally they do mention some University discoveries and I may suggest one of them, if article is available one the net.

My hope (for my benefit) from the "journal club" is that some more university (not corporate research) based significant developments of some underderstanding will be brought to my attention by others (certainly CharonZ, spidermonkey, and you must still be reading some good biological journals.)


BTW I had forgotten the "punch line" of the joke I PMed you. Shorter, and more subtile version is:

Slam,BAM; Sorry SAM.
Click to expand...

If you write down some of the compounds you are interested in learning about, (like VEGF) I can find some current articles.
 
SAM:
Perhaps, in effort not to immediately kill (or make it a "still birth") this journal club idea, a more general topic (but less "philosophical" and quite technical) would be a good idea.

For exmaple, I have only a physicist's guess at "sense" & "Anti-sense" compounds and their role in biological processes. I have long wondered, without making any effort to find out, if they are just what physicist and chemists call "optical isomers" - for example "dextros sugar" rotates a polarized light beam to the right.

Not sure, but I think Pasture, while paid by some French wine company, carefull segregated some "tarter crystals" of one sense from old wine and redisolved them and then let them recrystalze again during evaporation to discover that "sense" is preserved at the mocular level. etc.

Summary: Some review of how "sense" is important in biology might be good, and if man made (both senses equally) "levos surgar" is both sweet and non-fatting, you may already know a lot about all this.
 
Billy T said:
For exmaple, I have only a physicist's guess at "sense" & "Anti-sense" compounds and their role in biological processes. I have long wondered, without making any effort to find out, if they are just what physicist and chemists call "optical isomers" - for example "dextros sugar" rotates a polarized light beam to the right.

Not sure, but I think Pasture, while paid by some French wine company, carefull segregated some "tarter crystals" of one sense from old wine and redisolved them and then let them recrystalze again during evaporation to discover that "sense" is preserved at the mocular level. etc.
Click to expand...

I'm fairly certain the term is not meant to be enantiomers. A "sense" compound/strand is the mRNA which gets translated. Antisense is the DNA that was the template and complementary bases of the mRNA. There are also antisense small mRNAs that bind to a mRNA and prevent translation.

About the Pasteur thing, iirc he was supposedly able to segregate the enantiomers by luck, leading to his famous quote "Luck favors the prepared mind", or something like that : o
 
I see no reason why we cannot read some good technical papers as well.
 
Sorry to say this, but I am not sure whether this makes much sense (at least to me). I assume that even if enough people are interested, one would need quite some time to explain technicalities or have to dumb it down to the level of a newspaper report (which I personally wouldn't like to do).
Also the topics of general interest might be a bit limiting. I might for instance put forth a review of certain sigma factors and their control of virulence factors (which I actually can't because it is not a free access paper) , but I am not sure who else might find it interesting. I'd assume that it will have a similar outcome as RL paper discussion seminars (with hardly anyone responding on their own volition).
I assume the usual Q&A threads might be better suited, simply because in that case at least one person (the questioner) might have some interest on the subject at hand.
 
Billy T said:
SAM:
Perhaps, in effort not to immediately kill (or make it a "still birth") this journal club idea, a more general topic (but less "philosophical" and quite technical) would be a good idea.

For exmaple, I have only a physicist's guess at "sense" & "Anti-sense" compounds and their role in biological processes. I have long wondered, without making any effort to find out, if they are just what physicist and chemists call "optical isomers" - for example "dextros sugar" rotates a polarized light beam to the right.
Click to expand...

There is a thread about it: http://sciforums.com/showthread.php?t=73660

It seems to have a lot of use with working with DNA, like for use as a "probe" by seeing if it is complimentary to some DNA.
 
I'd like feedback on the articles here: too easy, too hard, more perspective/protocol/review, less molecular.

I'm going to put together an FAQ/article on

-How to read a research paper
-How to critique a research paper

Maybe this weekend or the next.
 
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I don't think too easy or too hard should be a concern, as long as it is interesting, though I'd personally prefer non-introductory material. If things are too hard for non-bio oriented people we can resolve it in discussion :O

The first article was on the easy side, but I personally found it interesting enough to more than make up for it. I still keep it in mind when thinking of experiments. I probably heard the all of the ideas mentioned in the article before, but the article helped permanently emphasize the importance. I'll edit this post on the difficulty of the second article after I read it (which I'm about to do).

I think protocol would be interesting to see more of. I'm neutral on the others, and unsure what type of article would have more perspective.

Unasked for feedback: Should ban everyone in the poll who voted in favor of the journal club and did not participate. -_-

edit:
took me a while to read the latest article, so from that aspect it was "hard" (I had to look up 5 words, at least, in the first paragraph :p). How long did it take others to read?!

I stick with what I said before though, difficulty shouldn't be a deciding factor, so more of those, or articles with greater difficulty, are OK imo.
 
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Thanks, I like to read science papers on perspective as well as procedure, basically how to think and then act and then review.

Since the Platt paper was perspective, I have used a technical paper this time. I'll try to find one that highlights the importance of protocol in problem solving for the next one.

Too bad we can't upload documents here, I have some great papers we could use. :)
 
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