Journal Club

Anything that doesn't fit anywhere else below.

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Re: Journal Club

#61  Postby natselrox » Jul 24, 2010 8:55 am

May I propose this article as the next one? It would be an interesting read and could potentially lead to discussions on vision and other fascinating discoveries in opthalmology (one of the subjects in my ongoing semester :D ). Optogenetics is also a fascinating new discipline!

Most importantly, I need someone to mail the whole article to me! :shifty:

The Abstract wrote:Retinitis pigmentosa refers to a diverse group of hereditary diseases that lead to incurable blindness, affecting two million people worldwide. As a common pathology, rod photoreceptors die early, whereas light-insensitive, morphologically altered cone photoreceptors persist longer. It is unknown if these cones are accessible for therapeutic intervention. Here, we show that expression of archaebacterial halorhodopsin in light-insensitive cones can substitute for the native phototransduction cascade and restore light sensitivity in mouse models of retinitis pigmentosa. Resensitized photoreceptors activate all retinal cone pathways, drive sophisticated retinal circuit functions (including directional selectivity), activate cortical circuits, and mediate visually guided behaviors. Using human ex vivo retinas, we show that halorhodopsin can reactivate light-insensitive human photoreceptors. Finally, we identified blind patients with persisting, light-insensitive cones for potential halorhodopsin-based therapy.


Genetic Reactivation of Cone Photoreceptors Restores Visual Responses in Retinitis Pigmentosa
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Re: Journal Club

#62  Postby GenesForLife » Jul 24, 2010 9:15 am

I thought the club was restricted to openly accessible articles?
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Re: Journal Club

#63  Postby natselrox » Jul 24, 2010 9:18 am

GenesForLife wrote:I thought the club was restricted to openly accessible articles?


Oops! :oops:

Natselrox-fail. What's new in that? :coffee:
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Re: Journal Club

#64  Postby GenesForLife » Jul 24, 2010 9:25 am

I propose this one http://www.plosbiology.org/article/info ... io.1000422

During the initial stages of carcinogenesis, transformation events occur in a single cell within an epithelial monolayer. However, it remains unknown what happens at the interface between normal and transformed epithelial cells during this process. In Drosophila, it has been recently shown that normal and transformed cells compete with each other for survival in an epithelial tissue; however the molecular mechanisms whereby “loser cells” undergo apoptosis are not clearly understood. Lgl (lethal giant larvae) is a tumor suppressor protein and plays a crucial role in oncogenesis in flies and mammals. Here we have examined the involvement of Lgl in cell competition and shown that a novel Lgl-binding protein is involved in Lgl-mediated cell competition. Using biochemical immunoprecipitation methods, we first identified Mahjong as a novel binding partner of Lgl in both flies and mammals. In Drosophila, Mahjong is an essential gene, but zygotic mahjong mutants (mahj−/−) do not have obvious patterning defects during embryonic or larval development. However, mahj−/− cells undergo apoptosis when surrounded by wild-type cells in the wing disc epithelium. Importantly, comparable phenomena also occur in Mahjong-knockdown mammalian cells; Mahjong-knockdown Madin-Darby canine kidney epithelial cells undergo apoptosis, only when surrounded by non-transformed cells. Similarly, apoptosis of lgl−/− cells is induced when they are surrounded by wild-type cells in Drosophila wing discs. Phosphorylation of the c-Jun N-terminal kinase (JNK) is increased in mahj−/− or lgl−/− mutant cells, and expression of Puckered (Puc), an inhibitor of the JNK pathway, suppresses apoptosis of these mutant cells surrounded by wild-type cells, suggesting that the JNK pathway is involved in mahj- or lgl-mediated cell competition. Finally, we have shown that overexpression of Mahj in lgl−/− cells strongly suppresses JNK activation and blocks apoptosis of lgl−/− cells in the wild-type wing disc epithelium. These data indicate that Mahjong interacts with Lgl biochemically and genetically and that Mahjong and Lgl function in the same pathway to regulate cellular competitiveness. As far as we are aware, this is the first report that cell competition can occur in a mammalian cell culture system.
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Re: Journal Club

#65  Postby natselrox » Jul 24, 2010 9:34 am

Anything and everything works for me! :thumbup:
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Re: Journal Club

#66  Postby Mr.Samsa » Jul 24, 2010 11:39 am

natselrox wrote:May I propose this article as the next one? It would be an interesting read and could potentially lead to discussions on vision and other fascinating discoveries in opthalmology (one of the subjects in my ongoing semester :D ). Optogenetics is also a fascinating new discipline!

Most importantly, I need someone to mail the whole article to me! :shifty:

The Abstract wrote:Retinitis pigmentosa refers to a diverse group of hereditary diseases that lead to incurable blindness, affecting two million people worldwide. As a common pathology, rod photoreceptors die early, whereas light-insensitive, morphologically altered cone photoreceptors persist longer. It is unknown if these cones are accessible for therapeutic intervention. Here, we show that expression of archaebacterial halorhodopsin in light-insensitive cones can substitute for the native phototransduction cascade and restore light sensitivity in mouse models of retinitis pigmentosa. Resensitized photoreceptors activate all retinal cone pathways, drive sophisticated retinal circuit functions (including directional selectivity), activate cortical circuits, and mediate visually guided behaviors. Using human ex vivo retinas, we show that halorhodopsin can reactivate light-insensitive human photoreceptors. Finally, we identified blind patients with persisting, light-insensitive cones for potential halorhodopsin-based therapy.


Genetic Reactivation of Cone Photoreceptors Restores Visual Responses in Retinitis Pigmentosa


I don't mind which article comes up next, but Natselrox, this article is open access: http://www.hal.inserm.fr/docs/00/49/67/ ... mall-2.pdf
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Re: Journal Club

#67  Postby natselrox » Jul 24, 2010 11:42 am

Mr.Samsa wrote:I don't mind which article comes up next, but Natselrox, this article is open access: http://www.hal.inserm.fr/docs/00/49/67/ ... mall-2.pdf



Like I said, you're a ROCKSTAR!!!!

Thanks! :hugs: :smile: :smile: :smile:
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Re: Journal Club

#68  Postby Mr.Samsa » Jul 24, 2010 11:52 am

natselrox wrote:
Mr.Samsa wrote:I don't mind which article comes up next, but Natselrox, this article is open access: http://www.hal.inserm.fr/docs/00/49/67/ ... mall-2.pdf



Like I said, you're a ROCKSTAR!!!!

Thanks! :hugs: :smile: :smile: :smile:


Naw, it's just that my google-fu is strong.. :dopey:

EDIT: I'm not sure how you're currently searching for your articles, but if you use Google scholar and click the part where it tells you how many versions of the article they have available, then usually you'll find at least one free copy online. Google scholar is brilliant for that.
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Re: Journal Club

#69  Postby MedGen » Jul 25, 2010 2:25 pm

We've got two articles here to discuss. Does anyone have any particular preference for either? (I'm happy to read and discuss either of them).
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Re: Journal Club

#70  Postby twistor59 » Jul 25, 2010 4:35 pm

Either, but any "discussion" from me will be limited to asking questions !
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Re: Journal Club

#71  Postby GenesForLife » Jul 26, 2010 5:36 pm

Well, screw those two

http://www.plosone.org/article/info%3Ad ... ne.0010995

Disrupting Circadian Homeostasis of Sympathetic Signaling Promotes Tumor Development in Mice

Background
Cell proliferation in all rapidly renewing mammalian tissues follows a circadian rhythm that is often disrupted in advanced-stage tumors. Epidemiologic studies have revealed a clear link between disruption of circadian rhythms and cancer development in humans. Mice lacking the circadian genes Period1 and 2 (Per) or Cryptochrome1 and 2 (Cry) are deficient in cell cycle regulation and Per2 mutant mice are cancer-prone. However, it remains unclear how circadian rhythm in cell proliferation is generated in vivo and why disruption of circadian rhythm may lead to tumorigenesis.

Methodology/Principal Findings


Mice lacking Per1 and 2, Cry1 and 2, or one copy of Bmal1, all show increased spontaneous and radiation-induced tumor development. The neoplastic growth of Per-mutant somatic cells is not controlled cell-autonomously but is dependent upon extracellular mitogenic signals. Among the circadian output pathways, the rhythmic sympathetic signaling plays a key role in the central-peripheral timing mechanism that simultaneously activates the cell cycle clock via AP1-controlled Myc induction and p53 via peripheral clock-controlled ATM activation. Jet-lag promptly desynchronizes the central clock-SNS-peripheral clock axis, abolishes the peripheral clock-dependent ATM activation, and activates myc oncogenic potential, leading to tumor development in the same organ systems in wild-type and circadian gene-mutant mice.

Conclusions/Significance

Tumor suppression in vivo is a clock-controlled physiological function. The central circadian clock paces extracellular mitogenic signals that drive peripheral clock-controlled expression of key cell cycle and tumor suppressor genes to generate a circadian rhythm in cell proliferation. Frequent disruption of circadian rhythm is an important tumor promoting factor.
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Re: Journal Club

#72  Postby natselrox » Jul 26, 2010 5:38 pm

Uh oh! There go my irregular sleeping patterns. :waah:
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Re: Journal Club

#73  Postby Mr.Samsa » Aug 05, 2010 3:57 am

For those paying attention, Natselrox has started up threads here:

Circadian homeostasis and tumorigenesis

Retinitis Pigmentosa

:cheers:
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Re: Journal Club

#74  Postby rEvolutionist » Oct 13, 2010 12:12 am

:popcorn:

*Although, if the articles are too technically specific in a field I'm not familiar with, then I might not be so interested. I haven't read all the preceding pages yet, so don't know if this has been suggested, but would it be a good idea to limit the articles to ones of a more general nature, so as not to disenfranchise those who don't know the specifics?
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Re: Journal Club

#75  Postby Mr.Samsa » Oct 13, 2010 12:25 am

rEvolutionist wrote::popcorn:

*Although, if the articles are too technically specific in a field I'm not familiar with, then I might not be so interested. I haven't read all the preceding pages yet, so don't know if this has been suggested, but would it be a good idea to limit the articles to ones of a more general nature, so as not to disenfranchise those who don't know the specifics?


That's what I thought too.. The articles that have been presented looked interesting, but even with a science background I had little understanding of what language they were speaking. The journal club has been a bit quiet lately, but if you can think of a good article then present it and hopefully we can get it started again! :cheers:
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Re: Journal Club

#76  Postby rEvolutionist » Oct 13, 2010 12:31 am

Oh, yeah. I just saw the date of the post previous to mine. :oops:

I'll ask our library what the copyright issues are with some of the journals. I know that it is legal to copy up to about 10% of a bound book (so that includes a bound journal of multiple volumes/issues), and that in some cases it is ok to use that for educational purposes. I suspect you are right that we couldn't post a whole article from Nature or Science, but I'll ask anyway, and see what answer I get. We might be able to get away with posting the Abstract/Introduction and Conclusions perhaps? :dunno:
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Re: Journal Club

#77  Postby Mr.Samsa » Oct 13, 2010 1:25 am

rEvolutionist wrote:Oh, yeah. I just saw the date of the post previous to mine. :oops:

I'll ask our library what the copyright issues are with some of the journals. I know that it is legal to copy up to about 10% of a bound book (so that includes a bound journal of multiple volumes/issues), and that in some cases it is ok to use that for educational purposes. I suspect you are right that we couldn't post a whole article from Nature or Science, but I'll ask anyway, and see what answer I get. We might be able to get away with posting the Abstract/Introduction and Conclusions perhaps? :dunno:


Well if you do a Google Scholar search for the article then a lot of the time it's been reproduced somewhere for free. This obviously doesn't apply for every single article, but for a lot of the more popular articles it seems to be the case.
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Re: Journal Club

#78  Postby Darwinsbulldog » Oct 13, 2010 3:56 am

rEvolutionist wrote:Oh, yeah. I just saw the date of the post previous to mine. :oops:

I'll ask our library what the copyright issues are with some of the journals. I know that it is legal to copy up to about 10% of a bound book (so that includes a bound journal of multiple volumes/issues), and that in some cases it is ok to use that for educational purposes. I suspect you are right that we couldn't post a whole article from Nature or Science, but I'll ask anyway, and see what answer I get. We might be able to get away with posting the Abstract/Introduction and Conclusions perhaps? :dunno:

Anyone can quote a citation and abstract like this:-

Wilkinson, G. S. (1988). "Reciprocal altruism in bats and other mammals." Ethology and Sociobiology 9(2-4): 85-100.
In this paper five conditions are specified which must be met before reciprocal altruism, rather than kin selection, should be invoked. Four purported mammalian examples-- social grooming in coati, cluster position in roosting pallid bats, information exchange among greater spear-nosed bats, and blood regurgitation among vampire bats--are examined to determine if reciprocal altruism is necessary to plausibly explain each situation. Results from a computer simulation which apportions the relative selective advantage of vampire bat food sharing to kin selection and reciprocal altruism are then presented. The results demonstrate that the increase in individual survivorship due to reciprocal food sharing events in this species provides a greater increase in inclusive fitness than can be attributed to aiding relatives. This analysis suggests that reciprocal altruism can be selectively more important than kin selection when altruistic behaviors in a relatively large social group occur frequently and provide a major fitness benefit to the recipient even when that recipient is related to the donor.

Beyond that, most jurisdictions would allow photocopying posting or quoting around 10% of the article. I think the main concern is that you don't distribute the article, particularly for money. fair use for personal education or whatever is OK. But if you distributed a paper in class without getting permission first that would be a plain breach of copyright.
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Re: Journal Club

#79  Postby GenesForLife » Oct 13, 2010 6:48 am

This is the US Copyright Act's provisions on fair use...

Notwithstanding the provisions of sections 17 U.S.C. § 106 and 17 U.S.C. § 106A, the fair use of a copyrighted work, including such use by reproduction in copies or phonorecords or by any other means specified by that section, for purposes such as criticism, comment, news reporting, teaching (including multiple copies for classroom use), scholarship, or research, is not an infringement of copyright. In determining whether the use made of a work in any particular case is a fair use the factors to be considered shall include:

1. the purpose and character of the use, including whether such use is of a commercial nature or is for nonprofit educational purposes;
2. the nature of the copyrighted work;
3. the amount and substantiality of the portion used in relation to the copyrighted work as a whole; and
4. the effect of the use upon the potential market for or value of the copyrighted work.

The fact that a work is unpublished shall not itself bar a finding of fair use if such finding is made upon consideration of all the above factors.[1]


I would argue that research papers communicate news, that they would in the setting of the journal club motivate criticism, discussion and scholarship, which is actually more than sufficient (if Wikipedia is right about the Fair Use Provisions) to enable posting a copy on here as long as the copyright of the research paper was obtained in the US of A.

But the trouble I'm foreseeing is that most journals may have had their copyrights granted elsewhere, which would mean that
the laws of the countries in which they were registered would take precedence.
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Re: Journal Club

#80  Postby Mr.Samsa » Oct 13, 2010 6:51 am

I imagine that the problem is this bit:

3. the amount and substantiality of the portion used in relation to the copyrighted work as a whole; and


This is why you can't copy and paste an entire news article and post it on a forum. So it would be illegal to distribute a full version of a copyrighted article (which is any that has been published), but it's fair use to reproduce sections of it for educational purposes.
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