tag:blogger.com,1999:blog-10781944.post2019448745760936706..comments2024-03-28T00:36:36.460-07:00Comments on The Tree of Life: Cracking the microbial code: Pam Ronald @pcronald and her story behind recent papersJonathan Eisenhttp://www.blogger.com/profile/07953790938128734305noreply@blogger.comBlogger36125tag:blogger.com,1999:blog-10781944.post-14733058080978571952013-09-11T08:48:43.587-07:002013-09-11T08:48:43.587-07:00Ivan Oransky has an update hereIvan Oransky has an update <a href="http://retractionwatch.wordpress.com/2013/09/11/doing-the-right-thing-researchers-retract-quorum-sensing-paper-after-public-process/" rel="nofollow"> here </a>Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-15969131667645603062012-02-04T13:52:49.622-08:002012-02-04T13:52:49.622-08:00Uranotaenia -- the key is to measure the impact of...Uranotaenia -- the key is to measure the impact of papers not journals --- impact factor is a very coarse metric -- it has some value as do many metrics --- but it does not directly tell you anything about a specific paper ---Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-9571662748361997612012-02-04T12:40:56.713-08:002012-02-04T12:40:56.713-08:00I really enjoyed this post and the final comment t...I really enjoyed this post and the final comment that "ultimately it may not matter where the results are published; if it has legs, it will stand." is precisely the topic I recently had a heated discussion over with another postdoc in the lab. She maintained that impact factor was critically important and when I pointed out that POne has a great impact factor she told me that people don't think POne is a good journal because of its high acceptance rate. My argument was that if impact factor is a true measure of how much that body of work is contributing to the advancement of science then POne articles must be relevant and important because they are getting read and cited.uranotaeniahttps://www.blogger.com/profile/08022085650089887822noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-46593621095609241762012-01-14T03:24:32.180-08:002012-01-14T03:24:32.180-08:00Oops, I haven't seen the additional replys fur...Oops, I haven't seen the additional replys further down in this thread. Sorry for the duplication.suicytehttps://www.blogger.com/profile/12600193381378314838noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-8849071190593213672012-01-14T03:23:21.212-08:002012-01-14T03:23:21.212-08:00Pamela, some porins (OmpA, FhuA) are larger becaus...Pamela, some porins (OmpA, FhuA) are larger because they have additional (folded) periplasmic domains. The size of the membrane-spanning beta barrel is about the same, and Ax21 clearly belongs to the OmpA-fold.<br />The big question for me is whether the OmpA fold always means that the protein is embedded in the outer membrane (which should go along with a hydrophobic covering at the outside) or if some of them can exist outside of membranes.<br />Your experiments suggest the latter, which is very interesing. It might also offer an explanation how a secreted 20KDa protein can have access to the inner membrane.suicytehttps://www.blogger.com/profile/12600193381378314838noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-89886829411732141172012-01-13T20:47:06.820-08:002012-01-13T20:47:06.820-08:00Sorry.. I accidently erased my comments... I am no...Sorry.. I accidently erased my comments... I am not familiar with blogs...<br /><br /><br />Brook.. Yes. it is true. Gram negative outer membrane proteins can be 'secreted' in outer membrane vesicles (OMV). However, there is an example that the secretion of porin is not related with OMV. In the case of Oms28 porin, its secretion is not associated with outer membrane blebs..<br /><br />Now we are doing some experiments for the structure of Ax21 and its detail analysis. I hope we can solve a big puzzle in the near future..Sang-Wook Hanhttps://www.blogger.com/profile/02406501816587876836noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-91769348899631658632012-01-13T20:35:44.912-08:002012-01-13T20:35:44.912-08:00This comment has been removed by the author.Sang-Wook Hanhttps://www.blogger.com/profile/02406501816587876836noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-3278276183862147952012-01-13T20:33:44.338-08:002012-01-13T20:33:44.338-08:00Sang Wook Han, the lead author (but not a blogger-...Sang Wook Han, the lead author (but not a blogger- he is too busy doing science) has a comment:<br /><br />Nowadays, it is recognized that OmpA can make two different size channels. One is 8-beta strands and the other is 16 beta strands. OmpA is around 350aa. 1-20 is signal peptide, 20~190 is 8 beta strand and 190 ~ 350 is c-term domain ( http://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=3NB3 ). But, C-term domain can also form 8 beta strands and OmpA forms total 16 beta strands porin. (FEMS microbiology letters, 2007. A molecular Swiss army knife: OmpA structure, function and expression<br />Stephen G.J. Smith1,2, Vivienne Mahon1, Matthew A. Lambert1 & Robert P. Fagan Please see figure 2). <br /><br />Although the N-terminal domain of OmpA shows a similar structure with the predicted structure of Ax21, I doubt that the function of OmpA is similar to that of Ax21. After crystallization, we will know the details.Pamela Ronaldhttps://www.blogger.com/profile/08905736049638342587noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-67184027280623147982012-01-13T20:31:10.531-08:002012-01-13T20:31:10.531-08:00This comment has been removed by the author.Sang-Wook Hanhttps://www.blogger.com/profile/02406501816587876836noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-73378924028410020412012-01-13T20:06:27.701-08:002012-01-13T20:06:27.701-08:00Kay, sorry I mistyped. Ax21 is smaller than a typi...Kay, sorry I mistyped. Ax21 is smaller than a typical porin (Not larger). For example, OmpA-like porins, are 30~35kda and the FhuA porin is 78.9 kDa. The mature Ax21 is around 20kDa.<br /><br />We agree it would be useful to look at the side chains sticking out of the barrel. In our I-TASSER results, Ax21 has 8 beta-barrels (OmpA-like porins also have 8). We can look more closely at the amino acid sequence. Once we get the structure, we will know more.Pamela Ronaldhttps://www.blogger.com/profile/08905736049638342587noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-21152325758035834982012-01-13T18:09:36.543-08:002012-01-13T18:09:36.543-08:00It is my understanding that Gram negative outer me...It is my understanding that Gram negative outer membrane proteins can be 'secreted' in outer membrane vesicles that bleb off from the cells under certain stress conditions. Beta-barrel porins may be the main protein components of these vesicles, as has been seen with OprF in Pseudomonas aeruginosa.brook chttps://www.blogger.com/profile/08729270150708182352noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-59183737188919946312012-01-13T16:30:22.009-08:002012-01-13T16:30:22.009-08:00Dear Pamela,
thanks for the response! What you sa...Dear Pamela, <br />thanks for the response! What you say is very interesting, I had no idea that porins could be secreted. That of course changes everything - I had naively assumed that a porin would be stuck within the outer membrane, which would make for a poor QS factor.<br /><br />I am well aware of the pitfalls of structural prediction (I am in the business myself) but with Xa21 I am quite sure that it is a beta barrel. It would be interesting to have a look at the side chains sticking out of the barrel - in a typical OM protein you would expect mostly hydrophobics, while for a secreted factor you would expect residues that feel comfortable in water. <br /><br />Why do you think that AX21 is too big for a porin? Have a look at the stucture pdb:3NB3, chain A (OmpA), which is a perfect structual template for AX21. The barrel domain has the same length as Ax21 (sans leader).<br /><br />I acknowledge that this might be hard to reconcile with your experiments, but I am optimistic that in the end things will make perfect sense. Good luck with your experiments !suicytehttps://www.blogger.com/profile/12600193381378314838noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-46888985165506811752012-01-13T13:18:13.355-08:002012-01-13T13:18:13.355-08:00I completely agree with that statement Irene but w...I completely agree with that statement Irene but with a caveat - there is still work that needs to be done to get everyone to focus solely the quality of the science and not the name of the journal where something is published ...Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-89693790683263815602012-01-13T13:04:29.393-08:002012-01-13T13:04:29.393-08:00As a junior faculty member, dealing with the publi...As a junior faculty member, dealing with the publication process, I really liked reading: "ultimately it may not matter where the results are published; if it has legs, it will stand."Irene Newtonhttps://www.blogger.com/profile/17527839249947537641noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-52191287257034228992012-01-13T11:26:21.219-08:002012-01-13T11:26:21.219-08:00Kay, thanks for your interesting observations and ...Kay, thanks for your interesting observations and questions.<br /><br />Yes, we also observed that Ax21 models as a porin, which is quite interesting because it may be that Ax21 can directly insert into the cell without assistance of additional import proteins. <br /><br />However, structural predictions are often not accurate. Furthermore Ax21 is much larger that typical porins, so if it is a porin, it would be quite unusual (although there is at least one example of a secreted porin (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC523065/ ). We are now carrying out detailed genetic/structural studies to address these questions. <br /><br />A couple years ago we published the DNA sequence of Ax21, which you may not have been able to access if it is behind a paywall (see Lee et al., Science 2009; http://www.ncbi.nlm.nih.gov/gene/6304108; protein sequence pasted below). It is a small protein (PXO_3968) with a predicted N terminal leader. <br /><br />In this new open access Plos one paper, we show the Ax21 protein sequence that we derived from LC-MS/MS data (Figure S2). <br /><br />In 2009, we showed that a 17 aa sulfated peptide derived from the protein is sufficient to activate XA21-mediated immunity. In this paper we show that this small peptide is not sufficient to induce QS. We also showed that the RaxABC type 1 system is required for secretion and for Ax21 activity (Lee et al., 2009; Goes da silva, 2004).<br /><br />In the first version of the paper, the reviewers asked for additional experiments to prove that Ax21 acts extracellularly. <br /><br />In the second version, we provide several additional lines of evidence to address this question. We showed that show that the mature, processed Ax21 (lacking the N-terminal leader) is present outside the cell. We show that bacterial mutants lacking Ax21 (which no longer carry out QS) can be complemented with exogenous addition of mature recombinant Ax21 lacking the N-terminal leader. This work convinced the reviewers that Ax21 acts extracellularly. It is difficult to envision a different interpretation of these results and the reviewers did not question this. Instead one reviewer asked, how does Ax21 get back into the cell to bind the RaxH receptor? This is what we are working on now.<br /><br />By the way, XA21 is a receptor kinase. Please see Science 1995.<br /><br /><br /><br />The axY22 peptide that triggers XA21-mediated immunity is AENLSYNFVEGDYVRTP<br /><br /><br />The signal peptide is MLALGLLAALPFAASA. <br /><br />The signal peptide with mature protein (space in between):<br /><br />MLALGLLAALPFAASA AENLSYNFVEGDYVRTPTDGRDADGWGVKASYAVAPNFHVFGEYSKQNADDNKNLFKNTNSDFQQWGVGVGFNHEIATSTDFVARVAYRRLDLDSPNINFDGYSVEAGLRNAFGEHFEVYALAGYEDYSKKRGIDAGNDFYGRLGAQVKLNQNWGINGDIRMDGDGNKEWSVGPRFSWPamela Ronaldhttps://www.blogger.com/profile/08905736049638342587noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-63761378600119946832012-01-13T08:06:42.208-08:002012-01-13T08:06:42.208-08:00Kay
It appears your comment was flagged as SPAM -...Kay<br /><br />It appears your comment was flagged as SPAM - not sure why. I have released it though I see now you have also reposted it and the second time it was not flagged as SPAM ... fun with BLOGGER I guess ...Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-56738508649900484222012-01-13T07:42:42.893-08:002012-01-13T07:42:42.893-08:00Here we go, take #3:
This is clearly an interesti...Here we go, take #3:<br /><br />This is clearly an interesting research topic and an impressive piece of work. I am not a plant or bacteria person, but I am interested in PAMPs and bioinformatics and thus read (most of) the papers linked here - and some more papers linked therein. Nevertheless, I was quite disappointed that I was not able to actually find out what exactly constitutes the ax21 entity. This is not because I hit a paywall, most of the papers where in OA journals or those that I subscribe to.<br /><br />At several places, the ax21 entity (which actually binds to the XA21 receptor) is referred to as 'a secreted sulfated peptide', but I was not able to find the sequence in the manuscript or the figures.<br /><br />What I did find is a protein called ax21 (http://www.uniprot.org/uniprot/G0CLY5) which I suspect is the precursor of the active entity. The Ax21 protein has a leader-sequence which is mentioned in the papers, and an artificial peptide derived from the N-terminus of the mature protein seems to phenocopy the Xa21 activation. However, I don't see any mentioning what the physiological XA21 activator is supposed to be.<br /><br />The Ax21 protein is a fairly typical member of the porin-type outer membrane protein family and thus can probably be ruled out as the secrted factor. This would leave a peptie derived from the Ax21 by some post-insertion maturation event. I am not a particular porin expert, but it appeas that the sequence of the artificial peptide forms a membrane-spanning strand of the beta-barrel and thus would not be expected to be the secreted agent (or leave behind a properly folded barrel for the remainder of the protein)<br /><br />I wonder why this question has not been adddressed and has not been asked for by the reviewers. Or is it mentioned somewhere and I have missed it?suicytehttps://www.blogger.com/profile/12600193381378314838noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-16780873881499582872012-01-13T07:40:15.569-08:002012-01-13T07:40:15.569-08:00This will probably be my 2nd version, which has mi...This will probably be my 2nd version, which has miraculously disappeared after being visible for a few hours. I can also re-post it (after the first fiasko, I have made a backup copy of the 2nd version).<br /><br />BTW, my name is Kay, it is just my Google account that goes by the name 'suicyte', which used to be my old blog back when I had time for those things....suicytehttps://www.blogger.com/profile/12600193381378314838noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-67358157638409370202012-01-13T07:36:12.941-08:002012-01-13T07:36:12.941-08:00I don't want to be a pain in the neck, but wha...I don't want to be a pain in the neck, but what happened to my second attempt of commenting? It used to be online for a few hours and now it has disappeared again ?suicytehttps://www.blogger.com/profile/12600193381378314838noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-59979899555031706322012-01-13T07:34:08.249-08:002012-01-13T07:34:08.249-08:00Suicyte - I note - I have some of the text from at...Suicyte - I note - I have some of the text from at least one of your longer comments - should I post?Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-15968142374277292532012-01-13T07:08:22.242-08:002012-01-13T07:08:22.242-08:00uggh - this may be related to my attempt to use Go...uggh - this may be related to my attempt to use Google's new commenting feature ... will try to fixJonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-86072915904829701192012-01-13T05:04:10.928-08:002012-01-13T05:04:10.928-08:00Ok, I'll write a shorter version of my origina...Ok, I'll write a shorter version of my original comment. I don't expect anybody to read it anyway...<br /><br />This is clearly an interesting research topic and an impressive piece of work. I am not a plant or bacteria person, but I am interested in PAMPs and bioinformatics and thus read (most of) the papers linked here - and some more papers linked therein. Nevertheless, I was quite disappointed that I was not able to actually find out what exactly constitutes the ax21 entity. This is not because I hit a paywall, most of the papers where in OA journals or those that I subscribe to.<br /><br />At several places, the ax21 entity (which actually binds to the XA21 receptor) is referred to as 'a secreted sulfated peptide', but I was not able to find the sequence in the manuscript or the figures.<br /><br />What I did find is a protein called ax21 (http://www.uniprot.org/uniprot/G0CLY5) which I suspect is the precursor of the active entity. The Ax21 protein has a leader-sequence which is mentioned in the papers, and an artificial peptide derived from the N-terminus of the mature protein seems to phenocopy the Xa21 activation. However, I don't see any mentioning what the physiological XA21 activator is supposed to be.<br /><br />The Ax21 protein is a fairly typical member of the porin-type outer membrane protein family and thus can probably be ruled out as the secrted factor. This would leave a peptie derived from the Ax21 by some post-insertion maturation event. I am not a particular porin expert, but it appeas that the sequence of the artificial peptide forms a membrane-spanning strand of the beta-barrel and thus would not be expected to be the secreted agent (or leave behind a properly folded barrel for the remainder of the protein)<br /><br />I wonder why this question has not been adddressed and has not been asked for by the reviewers. Or is it mentioned somewhere and I have missed it?suicytehttps://www.blogger.com/profile/12600193381378314838noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-78175608725544627402012-01-13T04:24:02.446-08:002012-01-13T04:24:02.446-08:00I just posted a longish comment addressing some sc...I just posted a longish comment addressing some scientific questions raised in this interesting post, but whenever I press 'publish' or 'preview', the only thing blogspot does is to delete my comment - I had taken me more than an hour to write it :-(<br />This was on my linux box running firefox 9. The only way I can post here is to move down the hall to a computer running M$-Windows, which is hardly the way things should be...suicytehttps://www.blogger.com/profile/12600193381378314838noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-82633718870769056262012-01-11T19:35:29.912-08:002012-01-11T19:35:29.912-08:00mrr - I actually am fine with people posting ANY r...mrr - I actually am fine with people posting ANY reviews as it seems that there would be no obvious reason not to ---Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-49312846338372222752012-01-11T13:28:43.877-08:002012-01-11T13:28:43.877-08:00like others, I am a bit puzzled by the use of &quo...like others, I am a bit puzzled by the use of "confidentiality" as an issue preventing the publication of peer reviews by the author of the peer-reviewed manuscript. Confidentiality, I'd think, is about avoiding certain consequences that the publication of a text or claim would have on the author or source of that claim or text. But if the identity of the peer reviewer is and remains unknown to both the author of the reviewed manuscript and to the readers s/he may share those reviews with, what's the confidentiality problem? I'd have assumed that in peer contexts "confidentiality" referred to the identity of the referee, not the content of his/her report.Anonymousnoreply@blogger.com