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'''What's hot?  What's not?'''


Paste in ".ezp1.harvard.edu" between "journal.com" and "/articleID" to access full text.<br>
'''Who's responsible for keeping track of which journal?'''  Find out [[Paulsson:Journal responsibilities | here]].


Go [http://dx.doi.org.ezp1.harvard.edu/ here] to get the article using its DOI (Digital Object Identifier)<br>
To access journals through HMS, insert '''.ezp-prod1.hul.harvard.edu''' between domain (e.g. ".com", ".org") and remainder of URL
 
Who's responsible for keeping track of which journal?  Find out [[Paulsson:Journal responsibilities | here]].


[[Paulsson:Journal watch archive | Archive of previous entries]]
[[Paulsson:Journal watch archive | Archive of previous entries]]


==List of Journals==
==Journal Club papers==
 
===Past===
===Biophysical Journal===
Tanaguchi et al., Science, 2010 [http://www.ncbi.nlm.nih.gov/pubmed/20671182 pubmed]
 
 
===Cell===
*A Common Mechanism of Cellular Death Induced by Bactericidal Antibiotics
Michael A. Kohanski1, 2, 5, 6, Daniel J. Dwyer1, 3, 6, Boris Hayete1, 4, Carolyn A. Lawrence1, 2 and James J. Collins<br>
 
Antibiotic mode-of-action classification is based upon drug-target interaction and whether the resultant inhibition of cellular function is lethal to bacteria. Here we show that the three major classes of bactericidal antibiotics, regardless of drug-target interaction, stimulate the production of highly deleterious hydroxyl radicals in Gram-negative and Gram-positive bacteria, which ultimately contribute to cell death. We also show, in contrast, that bacteriostatic drugs do not produce hydroxyl radicals. We demonstrate that the mechanism of hydroxyl radical formation induced by bactericidal antibiotics is the end product of an oxidative damage cellular death pathway involving the tricarboxylic acid cycle, a transient depletion of NADH, destabilization of iron-sulfur clusters, and stimulation of the Fenton reaction. Our results suggest that all three major classes of bactericidal drugs can be potentiated by targeting bacterial systems that remediate hydroxyl radical damage, including proteins involved in triggering the DNA damage response, e.g., RecA.
[http://www.sciencedirect.com.ezp1.harvard.edu/science?_ob=MImg&_imagekey=B6WSN-4PKPNW8-B-H&_cdi=7051&_user=209690&_orig=browse&_coverDate=09%2F07%2F2007&_sk=998699994&view=c&wchp=dGLbVlb-zSkzV&md5=ff5c51b1cecce5f0ed08b45dba21b7a1&ie=/sdarticle.pdf]
 
===EMBO===
*Structural analysis of the ParR/parC plasmid partition complex
Jakob Møller-Jensen1, 4, Simon Ringgaard2, Christopher P Mercogliano1, Kenn Gerdes3 and Jan Löwe1<br>
The EMBO Journal (2007) 26, 4413–4422, doi:10.1038/sj.emboj.7601864<br>
 
Accurate DNA partition at cell division is vital to all living organisms. In bacteria, this process can involve partition loci, which are found on both chromosomes and plasmids. The initial step in Escherichia coli plasmid R1 partition involves the formation of a partition complex between the DNA-binding protein ParR and its cognate centromere site parC on the DNA. The partition complex is recognized by a second partition protein, the actin-like ATPase ParM, which forms filaments required for the active bidirectional movement of DNA replicates. Here, we present the 2.8 Å crystal structure of ParR from E. coli plasmid pB171. ParR forms a tight dimer resembling a large family of dimeric ribbon–helix–helix (RHH)2 site-specific DNA-binding proteins. Crystallographic and electron microscopic data further indicate that ParR dimers assemble into a helix structure with DNA-binding sites facing outward. Genetic and biochemical experiments support a structural arrangement in which the centromere-like parC DNA is wrapped around a ParR protein scaffold. This structure holds implications for how ParM polymerization drives active DNA transport during plasmid partition.
[http://www.nature.com.ezp1.harvard.edu/emboj/journal/v26/n20/pdf/7601864a.pdf]
 
===Genetics===
 
 
===Journal of Bacteriology===
*Lon Protease Degrades Transfer-Messenger RNA-Tagged Proteins
Jennifer S. Choy,1,2 Latt Latt Aung,1 and A. Wali Karzai<br>
 
Bacterial trans translation is activated when translating ribosomes are unable to elongate or terminate properly. Small protein B (SmpB) and transfer-messenger RNA (tmRNA) are the two known factors required for and dedicated to trans translation. tmRNA, encoded by the ssrA gene, is a bifunctional molecule that acts both as a tRNA and as an mRNA during trans translation. The functions of tmRNA ensure that stalled ribosomes are rescued, the causative defective mRNAs are degraded, and the incomplete polypeptides are marked for targeted proteolysis. We present in vivo and in vitro evidence that demonstrates a direct role for the Lon ATP-dependent protease in the degradation of tmRNA-tagged proteins. In an endogenous protein tagging assay, lon mutants accumulated excessive levels of tmRNA-tagged proteins. In a reporter protein tagging assay with {lambda}-CI-N, the protein product of a nonstop mRNA construct designed to activate trans translation, lon mutant cells efficiently tagged the reporter protein, but the tagged protein exhibited increased stability. Similarly, a green fluorescent protein (GFP) construct containing a hard-coded C-terminal tmRNA tag (GFP-SsrA) exhibited increased stability in lon mutant cells. Most significantly, highly purified Lon preferentially degraded the tmRNA-tagged forms of proteins compared to the untagged forms. Based on these results, we conclude that Lon protease participates directly in the degradation of tmRNA-tagged proteins.
[http://jb.asm.org.ezp1.harvard.edu/cgi/reprint/189/18/6564]
 
===Journal of Chemical Physcis===
 
 
===Journal of Molecular Biology===
 
 
===Journal of Physical Chemistry-A===
 
 
===Journal of Physical Chemistry-B===
 
 
===Journal of Physical Chemistry-C===
 
 
===Journal of Physical Chemistry-D===
 
 
===Journal of Physical Chemistry-E===
 
 
===Journal of Statistical Physics===
 
 
===Journal of Theoretical Biology===
 
 
===Lab on a Chip===
 
 
===Molecular Microbiology===
*Plasmid partition and incompatibility – the focus shifts (REVIEW)
Jean-Yves Bouet, Kurt Nordström, David Lane<br>
 
The mitotic apparatus that a plasmid uses to ensure its stable inheritance responds to the appearance of an additional copy of the plasmid's centromere by segregating it from the pre-existing copies: if the new copy arises by replication of the plasmid the result is partition, if it arrives on a different plasmid the result is incompatibility. Incompatibility thus serves as a probe of the partition mechanism. Coupling of distinct plasmids via their shared centromeres to form mixed pairs has been the favoured explanation for centromere-based incompatibility, because it supports a long-standing assumption that pairing of plasmid replicas is a prerequisite for their partition into daughter cells. Recent results from molecular genetic and fluorescence microscopy studies challenge this mixed pairing model. Partition incompatibility is seen to result from various processes, including titration, randomized positioning and a form of mixed pairing that is based on co-activation of the same partition event rather than direct contact between partition complexes. The perspectives thus opened onto the partition mechanism confirm the continuing utility of incompatibility as an approach to understanding bacterial mitosis. The results considered are compatible with the view that direct pairing of plasmids is not essential to plasmid partition.
[http://www.blackwell-synergy.com.ezp1.harvard.edu/doi/pdf/10.1111/j.1365-2958.2007.05882.x]
 
===Molecular Systems Biology===
 
 
===Nature===
 
 
===Nature Biotechnology===
 
 
===Nature Genetics===
 
 
===Nature Methods===
 
*PCR's next frontier
Tech Feature
Vol. 4 No. 10 October 2007 p869
 
*Keeping tabs on fluorescent tags
Tech Feature
Vol. 4 No. 9 September 2007 p755
 
*High-throughput cloning and expression in recalcitrant bacteria
 
Eric R Geertsma & Bert Poolman
 
We developed a generic method for high-throughput cloning
in bacteria that are less amenable to conventional DNA
manipulations. The method involves ligation-independent
cloning in an intermediary Escherichia coli vector, which is
rapidly converted via vector-backbone exchange (VBEx) into
an organism-specific plasmid ready for high-efficiency
transformation. We demonstrated VBEx proof of principle for
Lactococcus lactis, but the method can be adapted to all
organisms for which plasmids are available.
 
Vol. 4 No. 9 September 2007
 
===Plasmid===


===next?===
A.  '''Stoichiometry and architecture of active DNA replication machinery in Escherichia coli''' [http://www.ncbi.nlm.nih.gov/pubmed/20413500 pubmed] <br>
B. '''Functional microdomains in bacterial membranes''' [http://www.ncbi.nlm.nih.gov/pubmed/20713508 pubmed]<br>
C. '''Interdependence of behavioural variability and response to small stimuli in bacteria''' [http://www.ncbi.nlm.nih.gov/pubmed/21076396 pubmed]<br>
D. '''A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus''' [http://www.sciencemag.org/content/early/2010/12/01/science.1197258]<br>


===PLOS===
Vote for:<br>
*Recombination Speeds Adaptation by Reducing Competition between Beneficial Mutations in Populations of Escherichia coli.  
A. Shay, Burak, Dann, Dirk<br>
B. <br>
C. Mariana, Rishi, Raul, Nate, Andy<br>
D. Ylaine<br>


Cooper TF
==Journal Review Summaries (first page of every article we discussed, text-searchable pdfs)==


PLoS Biol 5(9): e225 [http://dx.doi.org/10.1371/journal.pbio.0050225]
[http://openwetware.org/images/8/83/081023_jr_summary.pdf October 23, 2008]
*Quantitative Characteristics of Gene Regulation by Small RNA.


Levine E, Zhang Z, Kuhlman T, Hwa T
[http://openwetware.org/images/5/51/081120_jr_summary.pdf November 20, 2008]


PLoS Biol 5(9): e229 [http://dx.doi.org/10.1371/journal.pbio.0050229]
[http://openwetware.org/images/0/02/081217_jr_summary.pdf December 17, 2008]


===PLOS Computational Biology===
[http://openwetware.org/images/c/cf/090122_jr_summary.pdf January 22, 2009]


[http://openwetware.org/images/c/c5/090225_jr_summary.pdf February 25, 2009]


===PNAS===
[http://openwetware.org/images/0/07/090423_jr_summary.pdf April 23, 2009]


[http://openwetware.org/images/1/17/090603_journal_review.pdf June 3, 2009]


===PRLandE===
[http://openwetware.org/images/3/32/090729_jr_summary.pdf July 29, 2009]


[http://openwetware.org/images/3/34/090909_jr_summary.pdf September 9, 2009]


===Quarterly Reviews of Biophysics===
[http://openwetware.org/images/a/ad/091110_jr_summary.pdf November 10, 2009]


==Journal Review with CiteULike==
===Getting Started===
1.  Go to [http://www.citeulike.org/ CiteULike]<BR>
2.  Create an account (username, password, email)<br>
3.  Email Per your username and he'll send you an invitation to join the group 'paulsson journal review'.<br>  Everyone in the 'paulsson journal review' group has administrative access, so anyone already in the group can also send an invitation to join the group<br>
*Highly recommended:<br>
4.  Add the 'post to citeulike' [http://www.citeulike.org/bookmarklets.adp bookmarklet] to your browser's toolbar.  I'd recommend the Advanced bookmarklet with no pop-up.<br>
5.  Install the [http://userscripts.org/scripts/show/56486 CiteULike Enhancement Toolkit] - among other things, it gets rid of the ads!<br>
6.  Install the [http://lib.harvard.edu/tools/libx.html LibX] toolbar to simplify getting full access to articles through Harvard.


===Science===


There is plenty of advice on how to use CiteULike on their [http://www.citeulike.org/howto HowTo] page.  Here's a little primer to get you going...


===Systems Biology===
===Searching, posting, tagging, and sorting===
1.  Search in PubMed for an article you want to contribute to 'paulsson journal review' (fyi: there are many other ways to browse and link articles to CiteULike).<br>
2.  Click the 'Post to CiteULike' button in your browser's toolbar and you will be redirected to a CiteULike posting page:
*Tags:  '''please enter 'new' if you will present this article at the next Journal Review session'''
*Post to:  select the 'paulsson journal review' library
*Priority:  choose how important do you think this article is to read
*Privacy:  don't check this box! The 'paulsson journal review' group is already private.
*Notes:  if you've read the article and have something to say about it...
*Post:  before posting, select the box to return to the original article page (this preference should be remembered for future posts)<br>
3.  Tags are useful, too many tags are not.  There is a search engine, so think of tags as folders rather than just search terms.  If you were going to file a single printed article in your drawer, which folder would you put it in (Tag#1).  If you had a few more copies of that printed article, which folders would you place these extra copies in (Tags#2-n).<br>
4.  Sorting: 
*  Use the tags.
*  Use the Enhancement Toolkit sort button in your library (for some reason the sort button doesn't show up in the group library!?!).  Have a look at what it does to the URL when you use the sort tool in your library and just modify the URL yourself.  For example, append </order/pubdate,desc,last> to the library URL and the citations will be organized by publication date in descending order, and articles without publication date metadata will be placed at the bottom of the list.  Replace 'pubdate' with other logical terms, eg. postdate, author, year...

Latest revision as of 15:33, 19 August 2013

Home        Group Meeting        Protocols        Inventory        Journal Watch        Top 100        Links        Facts of Life       


Who's responsible for keeping track of which journal? Find out here.

To access journals through HMS, insert .ezp-prod1.hul.harvard.edu between domain (e.g. ".com", ".org") and remainder of URL

Archive of previous entries

Journal Club papers

Past

Tanaguchi et al., Science, 2010 pubmed

next?

A. Stoichiometry and architecture of active DNA replication machinery in Escherichia coli pubmed
B. Functional microdomains in bacterial membranes pubmed
C. Interdependence of behavioural variability and response to small stimuli in bacteria pubmed
D. A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus [1]

Vote for:
A. Shay, Burak, Dann, Dirk
B.
C. Mariana, Rishi, Raul, Nate, Andy
D. Ylaine

Journal Review Summaries (first page of every article we discussed, text-searchable pdfs)

October 23, 2008

November 20, 2008

December 17, 2008

January 22, 2009

February 25, 2009

April 23, 2009

June 3, 2009

July 29, 2009

September 9, 2009

November 10, 2009

Journal Review with CiteULike

Getting Started

1. Go to CiteULike
2. Create an account (username, password, email)
3. Email Per your username and he'll send you an invitation to join the group 'paulsson journal review'.
Everyone in the 'paulsson journal review' group has administrative access, so anyone already in the group can also send an invitation to join the group

  • Highly recommended:

4. Add the 'post to citeulike' bookmarklet to your browser's toolbar. I'd recommend the Advanced bookmarklet with no pop-up.
5. Install the CiteULike Enhancement Toolkit - among other things, it gets rid of the ads!
6. Install the LibX toolbar to simplify getting full access to articles through Harvard.


There is plenty of advice on how to use CiteULike on their HowTo page. Here's a little primer to get you going...

Searching, posting, tagging, and sorting

1. Search in PubMed for an article you want to contribute to 'paulsson journal review' (fyi: there are many other ways to browse and link articles to CiteULike).
2. Click the 'Post to CiteULike' button in your browser's toolbar and you will be redirected to a CiteULike posting page:

  • Tags: please enter 'new' if you will present this article at the next Journal Review session
  • Post to: select the 'paulsson journal review' library
  • Priority: choose how important do you think this article is to read
  • Privacy: don't check this box! The 'paulsson journal review' group is already private.
  • Notes: if you've read the article and have something to say about it...
  • Post: before posting, select the box to return to the original article page (this preference should be remembered for future posts)

3. Tags are useful, too many tags are not. There is a search engine, so think of tags as folders rather than just search terms. If you were going to file a single printed article in your drawer, which folder would you put it in (Tag#1). If you had a few more copies of that printed article, which folders would you place these extra copies in (Tags#2-n).
4. Sorting:

  • Use the tags.
  • Use the Enhancement Toolkit sort button in your library (for some reason the sort button doesn't show up in the group library!?!). Have a look at what it does to the URL when you use the sort tool in your library and just modify the URL yourself. For example, append </order/pubdate,desc,last> to the library URL and the citations will be organized by publication date in descending order, and articles without publication date metadata will be placed at the bottom of the list. Replace 'pubdate' with other logical terms, eg. postdate, author, year...
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