Difference between revisions of "Streptococcus pneumoniae"

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(→‎Additional Microarray Papers: article 2 ajvree)
(→‎Individual Assessment and Reflection: Alina's assessment link)
 
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==Reference Paper==
+
==Group Deliverables==
−
:[http://jb.asm.org/content/183/19/5709.full link]
+
[[tATK Final Group Deliverables]]
 +
 
 +
[[Media:TeamATK.pdf|Team Journal Club Presentation]]
 +
 
 +
* GenMAPP Gene Database: [[Media:Streptococcus_pneumoniae_TIGR4_20131125.gdb]] --known good
 +
* ReadMe file (PDF): [[Media:ReadMe_Streptococcus_pneumoniae_TIGR4_20131125.pdf|ReadMe_Streptococcus_pneumoniae_TIGR4_20131125.pdf]]
 +
*Gene Database Schema: [[Media:Streptococcus_schema_20131210.pdf|Streptococcus_schema_20131210.pdf]]
 +
* Gene Database Testing Report (print from wiki to ''.pdf'' file): [[Media:Streptococcus pneumoniae TIGR4 20131125 GeneTestingReport.pdf|PDF Gene Testing Report]]; [[Streptococcus_pneumoniae_TIGR4_20131125_GeneTestingReport|Gene Testing Report Wiki Page]]
 +
* Processed and analyzed DNA microarray dataset (''.xls''): [[Media:20131125_teamATK_KM_CompiledRawData.xls|20131125_teamATK_KM_CompiledRawData.xls]]
 +
* GenMAPP Expression Dataset file (''.gex''): [[Media:20131212_teamATK_KM_compiledrawdata_GMAPP.gex|20131212_teamATK_KM_compiledrawdata_GMAPP.gex]]
 +
* Filtered MAPPFinder Results (''.xls''): [[Media:20131210_tATK_filteredresults.xls|20131210_tATK_filteredresults.xls]]
 +
* Sample MAPP file of a relevant biological pathway for your species (''.mapp''): [[Media:20131211_tATK_sugar_transmembrane_transporter_activity.mapp|20131211_tATK_sugar_transmembrane_transporter_activity.mapp]]
 +
[[Media:MAPP.JPG|tATK jpeg MAPP]]
 +
* [[Gene Database Project Report Guidelines#Group Report | Group Report]] (''.doc'' or ''.pdf''):
 +
 
 +
* PowerPoint presentation (''.ppt'', given on Thursday, December 12): [[Media:TeamATK_finalpresentation.pdf|tATK presentation]]
 +
 
 +
==Papers==
 +
===Genome Paper===
 +
Title: Genome of the Bacterium Streptococcus pneumoniae Strain R6
 +
:By Hoskins et al. (2001)
 +
:Web [http://jb.asm.org/content/183/19/5709.full link]
 
:[[Media: R6_Reference_Genome_Paper.pdf|PDF]]
 
:[[Media: R6_Reference_Genome_Paper.pdf|PDF]]
  
−
==Additional Microarray Papers==
+
:Reference: Hoskins, J., Alborn, W.E. Jr., Arnold, J., Blaszczak, L.C., Burgett, S., Bradley, S., DeHoff, S.T., Estrem, L.F., Fu, D.J.,  Fuller, W., Geringer, C., Gilmour, R., Glass, J.S., Khoja1, H., Kraft, A.R., Lagace, R.E., LeBlanc, D.J., Lee, L.N., Lefkowitz, E.J., Lu, J., Matsushima, P., McAhren, S.M., McHenney, M., McLeaster, K., Mundy, C.W., Nicas, T.I., Norris, F.H., O'Gara1, M.J., Peery, R.B., Robertson, G.T., Rockey, P., Sun, P.M., Winkler, M.E., Yang, Y., Young-Bellido, M., Zhao, G., Zook, C.A., Baltz, R.H., Jaskunas, S.R., Rosteck Jr., P.R., Skatrud, P.L., and Glass, J.I. (2001) Genome of the bacterium Streptococcus pneumoniae strain R6. Journal of Bacteriology 183(19): 5709-5717. doi: 10.1128/JB.183.19.5709-5717.2001
−
# Author name and year
+
−
#* PDF and link
+
−
#* Full citation
+
  
−
# Mukesh Kumar Yadav et al., 2012
+
<!-- ===1: Identification of Genes That Contribute to the Pathogenesis of Invasive Pneumococcal Disease by In Vivo Transcriptomic Analysis===
−
#* [[Media:Geneexpressionarticle1.pdf|PDF]][http://onlinelibrary.wiley.com/doi/10.1111/j.1348-0421.2012.00483.x/abstract|link] Data: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL15071]
+
Ogunniyi et al. 2012
−
#* Yadav, M. K., Kwon, S. K., Cho, C. G., Park, S.-W., Chae, S.-W. and Song, J.-J. (2012), Gene expression profile of early in vitro biofilms of Streptococcus pneumoniae. Microbiology and Immunology, 56: 621–629.
+
:Web Link: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0028738]
 +
:PDF: [[Media:Article1.pdf|Ogunniyi et al. 2012]]
 +
:Data at: [http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=305&action=view&l=a]
 +
:Experiment Performed: This paper compared the gene expression between pneumococci in virulent and non-virulent strains that had grown in the nasopharynx, lungs, and blood of mice.
 +
:Replicates: There were 3 biological replicates in this data set.
  
−
#Ng, WL, Kazmierczak, KM Robertson, GT, et al., 2003
 
−
#*Link to PDF (had trouble downloading it to computer): [http://jb.asm.org/content/185/1/359.full.pdf+html]  Data: [http://www.streppneumoniae.com/microarray_data.htm]
 
−
#*Ng, WL, Kazmierczak, KM Robertson, GT, et al., 2003. ''Transcriptional regulation and signature patterns revealed by microarray analyses of Streptococcus pneumoniae R6 challenged with sublethal concentrations of translation inhibitors.'' Journal of Bacteriology. Volume 185, Issue 1, Pages 359-370.
 
  
−
==Team==
+
:Reference: Ogunniyi, AD, Mahdi, LK, Trappetti, C, Verhoeven, N, Mermans, D, Van der Hoek, MB, et al. (2012). Identification of genes that contribute to the pathogenesis of invasive pneumococcal disease by in vivo transcriptomic analysis. Infection and Immunity, 80(9): 3268-3278.
−
'''Team Leader: [[User:Ajvree|Alina]]'''
+
:Found by [[User:Taur.vil|Tauras]]
 +
 
 +
===2: Gene expression profile of early in vitro biofilms of Streptococcus pneumoniae===
 +
Yadav et al. 2012
 +
:Web Link: [http://onlinelibrary.wiley.com/doi/10.1111/j.1348-0421.2012.00483.x/abstract]
 +
:PDF: [[Media:Geneexpressionarticle1.pdf|PDF]]
 +
:Data at: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL15071]
 +
:Experiment Performed: Differential gene expression profile of Streptococcus pneumoniae early biofilm cells and planktonic cells
 +
:Replicates: 21 biological microarray replicates were used.
 +
---Put in by Tauras: Please very experiment and replicates---
 +
 
 +
 
 +
:Reference: Yadav, MK, Kwon, SK, Cho, CG, Park, SW, Chae, SW, & Song, JJ (2012). Gene expression profile of early in vitro biofilms of Streptococcus pneumoniae. Microbiology and Immunology, 56: 621–629. doi: 10.1111/j.1348-0421.2012.00483.x
 +
:Found by [[User:Ajvree|Alina]]
 +
 
 +
===3: Global transcription profiling and virulence potential of Streptococcus pneumoniae after serial passage===
 +
Pandya et al. 2009
 +
:Web Link: [http://www.sciencedirect.com/science/article/pii/S037811190900184X]
 +
:PDF: Not available (under copyright). May be downloaded directly from the link above.
 +
:Data at: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12607]
 +
:Experiment Performed: In this experiment, they compared transcription profiles as virulent ''Streptococcus pneumoniae'' crossed from the nasopharynx into the blood. The control was transcription in the nasopharynx, the experimental condition transcription in the blood.
 +
:Replicates: For this paper there are 2 biological replicates and 4 spot replicates
 +
 
 +
 
 +
:Reference: Pandya, U, Sinha, M, Luxon, BA, Watson, DA, & Niesel, DW (2009). Global transcription profiling and virulence potential of ''Streptococcus pneumoniae'' after serial passage. Gene, 443(1): 22-31.
 +
:Found by [[User:Taur.vil|Tauras]]
 +
 
 +
===4. Transcriptional regulation and signature patterns revealed by microarray analyses of Streptococcus pneumoniae R6 challenged with sublethal concentrations of translation inhibitors===
 +
Kazmierczak et al. 2003
 +
:Web Link: [http://jb.asm.org/content/185/1/359.full.pdf+html]
 +
:PDF: had trouble downloading it to computer, link is available at: [http://jb.asm.org/content/185/1/359.full.pdf+html]
 +
:Data at: [http://www.streppneumoniae.com/microarray_data.htm]
 +
:Experiment Performed: Cell cultures were exposed to 4 different translation inhibitors to determine the effect on the transcript activity. The control used was a 1% DMSO culture that contained no antibiotics.
 +
:Replicates: 3 replicates done, along with Northern blot analysis.
 +
 
 +
 
 +
:Reference: Ng, WL, Kazmierczak, KM, Robertson, GT, Gilmour, R, & Winkler, ME (2003). Transcriptional regulation and signature patterns revealed by microarray analyses of Streptococcus pneumoniae R6 challenged with sublethal concentrations of translation inhibitors. Journal of bacteriology, 185(1): 359-370.
 +
*Note: Ng is actually the authors last name. I thought it was a mistake too. [[User:Taur.vil|Taur.vil]] ([[User talk:Taur.vil|talk]]) 20:44, 31 October 2013 (PDT)
 +
:Found by [[User:Ajvree|Alina]]
 +
 
 +
===5. A Transcription Factor Contributes to Pathogenesis and Virulence in Streptococcus pneumoniae===
 +
 
 +
Mahdi et. al. 2013
 +
:Web Link: [http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=9357a1f5-2154-46a1-be7d-1d692b28473e%40sessionmgr115&vid=2&hid=102 Transcription Factor paper]
 +
:PDF: [[Media:A_Transcription_Factor_Contributes_to_Pathogenesis_and_Virulence_in_Streptococcus_pneumoniae.pdf]]
 +
:Data at: [http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=288&action=view&l=a 1] and [http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=305&action=view&l=a 2]
 +
:Experiments Performed: Effect of transcription factors on tissue-specific gene expression
 +
:Replicates: 3 biological replicates, 1 technical for link 1; 3 biological replicates, 0 technical for link 2
 +
 
 +
 
 +
:Reference: : Mahdi LK, Ebrahimie E, Adelson DL, Paton JC, Ogunniyi AD (2013) A Transcription Factor Contributes to Pathogenesis and Virulence in Streptococcus pneumoniae. PLoS ONE 8(8): e70862. doi:10.1371/journal.pone.0070862
 +
:Found by [[User:Kmeilak|Kevin]] -->
 +
 
 +
===Microarray Paper===
 +
Sanchez et. al. 2011
 +
:Streptococcus pneumoniae in Biofilms Are Unable to Cause Invasive Disease Due to Altered Virulence Determinant Production
 +
:Web Link: [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26976/?query=Streptococcus+pneumoniae Biofilm paper]
 +
:PDF: [[Media:Biofilms_paper.pdf]]
 +
:Data at: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26976 GEO link] and [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26976/?query=streptococcus+pneumoniae Array Express link]
 +
:Experiments Performed: Examined genes related to biofilm formation of Streptococcus pneumoniae
 +
:Replicates: 3 biological replicates, 3+ technical replicates
 +
 
 +
:Reference: Sanchez, C.J., Kumar, N., Lizcano, A., Shivshankar, P., Dunning Hotopp, J.C., Jorgensen, J.H., Tettelin, H., and Orihuela, C.J. (2011) Streptococcus pneumoniae in Biofilms Are Unable to Cause Invasive Disease Due to Altered Virulence Determinant Production. PLoS ONE 6(12): e28738. doi:10.1371/journal.pone.0028738
 +
:Found by [[User:Kmeilak|Kevin]]
 +
 
 +
==Downloaded Files==
 +
 
 +
Uniprot XML File:<br>
 +
R6: [[Media:20131105_UniProtXML_tATK_R6_AJV.xml|XML]]<br>
 +
TIGR4: [[Media:20131107_UniProtXML_tATK_TIGR4_AJV.xml|XML]]<br>
 +
G54: [[Media:20131107_UniProtXML_tATK_G54_AJV.xml|XML]]<br>
 +
 
 +
GOA:<br>
 +
TIGR4: [[Media:20131107_UniProtXML_tATK_TIG4_AJV.goa|GOA]]<br>
 +
R6: [[Media:20131107_UniProtXML_tATK_R6_AJV.goa|GOA]]<br>
 +
G54: [[Media:20131107_UniProtXML_tATK_G54_AJV.goa|GOA]]<br>
 +
 
 +
GO-OBO File: [[Media:20131107_GO-OBO_tATK_KM.gz|GO-OBO zip]]
 +
 
 +
*Raw Data
 +
 
 +
#[[Media:20131106_ArrayExpressADF_tATK_KM.adf.txt|Associated Data Files]]
 +
#[[Media:20131106_ArrayExpressarraydesign_tATK_KM.txt|Array Design]]
 +
#[[Media:20131106_ArrayExpressrawdata_tATK_KM.zip|Raw Data]]
 +
#[[Media:20131106_ArrayExpressprocesseddata_tATK_KM.zip|Processed Data]]
 +
#[[Media:20131106_ArrayExpresssdrf_tATK_KM.txt|Sample and Data Relationship]]
 +
 
 +
*Data Explanation Files
 +
 
 +
#[[Media:20131118_tavrawdata_teamATK_KM.txt.txt]]
 +
#[[Media:20131118_dataexplanation_teamATK_KM.pdf.pdf]]
 +
 
 +
==Import-Export Cycle One==
 +
:[[tATK Export One: TIGR4 Testing Report]]
 +
:[[tATK Export One: R6 Testing Report]]
 +
:[[tATK Export One: G54 Testing Report]]
 +
 
 +
 
 +
Files
 +
:G54: [[Media:20131113 G45export tATK TPV.gdb]]
 +
:R6: [[Media:20131113 R6export tATK TPV.gdb]]
 +
:TIGR4: [[Media:20131107_GenMAPPExport_tATK_TIGR4_TPV.gdb]]
 +
 
 +
Cycle procedure terminated due to inconsistent/unclear file versions and updated files available.
 +
:[[User:Taur.vil|Taur.vil]] ([[User talk:Taur.vil|talk]]) 21:36, 18 November 2013 (PST)
 +
 
 +
==Import-Export Cycle 2==
 +
:[[tATK E2: TIGR4 Testing Report]]
 +
 
 +
===Files Used===
 +
[[Media:20131118_OBOXML_tATK_TPV.gz|Compressed obo-xml file]]
 +
 
 +
TIGR4
 +
*XML: [[Media:20131118_UniProtXML_tATK_TIGR4_TPV.xml]]
 +
*Goa: [[Media:20131118_GOA_tATK_TIGR4_TPV.goa]]
 +
 
 +
===Files Exported===
 +
TIGR4
 +
*Export: [[Media:20131118_E2_tATK_TIGR4.gdb]]
 +
 
 +
==Import-Export Cycle 3==
 +
:[[tATK E3: TIGR4 Testing Report]]
 +
 
 +
===Files Used===
 +
[[Media:20131120_OBOXML_tATK_TPV.gz|Compressed obo-xml file]]
 +
 
 +
TIGR4
 +
*XML: [[Media:20131118_UniProtXML_tATK_TIGR4_TPV.xml]]
 +
*Goa: [[Media:20131118_GOA_tATK_TIGR4_TPV.goa]]
 +
 
 +
===Files Exported===
 +
TIGR4
 +
* [[Media:20131120_E3_tATK_TIGR4.gdb]]
 +
 
 +
 
 +
==Import-Export Cycle 4==
 +
:[[tATK E4: TIGR4 Testing Report]]
 +
 
 +
===Files Used===
 +
[[Media:20131120_OBOXML_tATK_TPV.gz|Compressed obo-xml file]]
 +
:gmbuilder: dist_Experimental20131121 (created in class 21Nov2013)
 +
 
 +
TIGR4
 +
*XML: [[Media:20131118_UniProtXML_tATK_TIGR4_TPV.xml]]
 +
*Goa: [[Media:20131118_GOA_tATK_TIGR4_TPV.goa]]
 +
 
 +
===Files Exported===
 +
TIGR4
 +
* [[Media:20131125_E4_tATK_TIGR4.gdb]]
 +
 
 +
==Compiled Raw Data==
 +
 
 +
*[[Media:20131119_teamATK_KM_compiledrawdata.xls]]
 +
 
 +
*[[Media:20131203_tATK_genenotfounderrors.xls]]
 +
 
 +
===MAPPFinder Data===
 +
 
 +
====4 hr====
 +
 
 +
*[[Media:20131205_teamATK_KM_compiledrawdata_4hr_GMAPP.gex]]
 +
 
 +
====12 hr====
 +
*[[Media:TATK_MAPPFinder_results-Criterion1-GO.txt]]
 +
 
 +
*[[Media:TATK_MAPPFinder_results-Criterion0-GO.txt]]
 +
 
 +
*[[Media:20131119_teamATK_KM_compiledrawdata_GMAPP.gex]]
 +
 
 +
====24 hr====
 +
 
 +
*[[Media:20131119_teamATK_KM_compiledrawdata_24hr_GMAPP.gex]]
 +
 
 +
====48 hr====
 +
 
 +
*[[Media:20131119_teamATK_KM_compiledrawdata_48hr_GMAPP.gex]]
 +
 
 +
==Team ATK==
 +
'''Team Leader: [[User:Taur.vil|Tauras]]'''
  
 
*Coder: [[User:Taur.vil|Tauras]]
 
*Coder: [[User:Taur.vil|Tauras]]
Line 23: Line 220:
 
*GenMAPP User: [[User:Kmeilak|Kevin Meilak]]
 
*GenMAPP User: [[User:Kmeilak|Kevin Meilak]]
  
 +
==Progress Report Links==
 +
 +
*[[tATK Week 12 Status Report]]
 +
*[[tATK Week 13 Status Report]]
 +
*[[tATK Week 15 Status Report]]
 +
 +
==Individual Assessment and Reflection==
 +
 +
*[[Kevin's Assessment and Reflection]]
 +
*[[Alina's Assessment and Reflection]]
  
 +
==Template==
 +
{{Team ATK}}
  
  
 +
[[Template: Team ATK]]
 
[[Category: Streptococcus pneumoniae]]
 
[[Category: Streptococcus pneumoniae]]
−
[[Category: Group Project]]
+
[[Category: Group Projects]]
 +
[[Category: Team ATK]]

Latest revision as of 18:50, 13 December 2013

Contents

[edit] Group Deliverables

tATK Final Group Deliverables

Team Journal Club Presentation

tATK jpeg MAPP

[edit] Papers

[edit] Genome Paper

Title: Genome of the Bacterium Streptococcus pneumoniae Strain R6

By Hoskins et al. (2001)
Web link
PDF
Reference: Hoskins, J., Alborn, W.E. Jr., Arnold, J., Blaszczak, L.C., Burgett, S., Bradley, S., DeHoff, S.T., Estrem, L.F., Fu, D.J., Fuller, W., Geringer, C., Gilmour, R., Glass, J.S., Khoja1, H., Kraft, A.R., Lagace, R.E., LeBlanc, D.J., Lee, L.N., Lefkowitz, E.J., Lu, J., Matsushima, P., McAhren, S.M., McHenney, M., McLeaster, K., Mundy, C.W., Nicas, T.I., Norris, F.H., O'Gara1, M.J., Peery, R.B., Robertson, G.T., Rockey, P., Sun, P.M., Winkler, M.E., Yang, Y., Young-Bellido, M., Zhao, G., Zook, C.A., Baltz, R.H., Jaskunas, S.R., Rosteck Jr., P.R., Skatrud, P.L., and Glass, J.I. (2001) Genome of the bacterium Streptococcus pneumoniae strain R6. Journal of Bacteriology 183(19): 5709-5717. doi: 10.1128/JB.183.19.5709-5717.2001


[edit] Microarray Paper

Sanchez et. al. 2011

Streptococcus pneumoniae in Biofilms Are Unable to Cause Invasive Disease Due to Altered Virulence Determinant Production
Web Link: Biofilm paper
PDF: Media:Biofilms_paper.pdf
Data at: GEO link and Array Express link
Experiments Performed: Examined genes related to biofilm formation of Streptococcus pneumoniae
Replicates: 3 biological replicates, 3+ technical replicates
Reference: Sanchez, C.J., Kumar, N., Lizcano, A., Shivshankar, P., Dunning Hotopp, J.C., Jorgensen, J.H., Tettelin, H., and Orihuela, C.J. (2011) Streptococcus pneumoniae in Biofilms Are Unable to Cause Invasive Disease Due to Altered Virulence Determinant Production. PLoS ONE 6(12): e28738. doi:10.1371/journal.pone.0028738
Found by Kevin

[edit] Downloaded Files

Uniprot XML File:
R6: XML
TIGR4: XML
G54: XML

GOA:
TIGR4: GOA
R6: GOA
G54: GOA

GO-OBO File: GO-OBO zip

  • Raw Data
  1. Associated Data Files
  2. Array Design
  3. Raw Data
  4. Processed Data
  5. Sample and Data Relationship
  • Data Explanation Files
  1. Media:20131118_tavrawdata_teamATK_KM.txt.txt
  2. Media:20131118_dataexplanation_teamATK_KM.pdf.pdf

[edit] Import-Export Cycle One

tATK Export One: TIGR4 Testing Report
tATK Export One: R6 Testing Report
tATK Export One: G54 Testing Report


Files

G54: Media:20131113 G45export tATK TPV.gdb
R6: Media:20131113 R6export tATK TPV.gdb
TIGR4: Media:20131107_GenMAPPExport_tATK_TIGR4_TPV.gdb

Cycle procedure terminated due to inconsistent/unclear file versions and updated files available.

Taur.vil (talk) 21:36, 18 November 2013 (PST)

[edit] Import-Export Cycle 2

tATK E2: TIGR4 Testing Report

[edit] Files Used

Compressed obo-xml file

TIGR4

[edit] Files Exported

TIGR4

[edit] Import-Export Cycle 3

tATK E3: TIGR4 Testing Report

[edit] Files Used

Compressed obo-xml file

TIGR4

[edit] Files Exported

TIGR4


[edit] Import-Export Cycle 4

tATK E4: TIGR4 Testing Report

[edit] Files Used

Compressed obo-xml file

gmbuilder: dist_Experimental20131121 (created in class 21Nov2013)

TIGR4

[edit] Files Exported

TIGR4

[edit] Compiled Raw Data

[edit] MAPPFinder Data

[edit] 4 hr

[edit] 12 hr

[edit] 24 hr

[edit] 48 hr

[edit] Team ATK

Team Leader: Tauras

[edit] Progress Report Links

[edit] Individual Assessment and Reflection

[edit] Template

Alina's User Page Kevin's User Page Tauras's User Page
Biological Databases Class Page Gene Database Project Gene Database Project Report Guidelines

Streptococcus pneumoniae

Import Export Cycle 1: tATK Export One: TIGR4 Testing Report
Import Export Cycle 2: tATK E2: TIGR4 Testing Report
Import Export Cycle 3: tATK E3: TIGR4 Testing Report
Import Export Cycle 4: tATK E4: TIGR4 Testing Report
Data Information
Project Roles: Project Manager Coder GenMAPP User Quality Assurance
Retrieved from "https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Streptococcus_pneumoniae&oldid=7058"
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