LMU BioDB 2013 - User contributions [en]

Stephen Louie Deliverables

2013-12-15T17:38:33Z

Slouie: /* Assessment of Project */

==Statement of Work==

==Assessment of Project==
:In terms of individual roles, every group member was fairly competent when completing his or her own tasks. However, things did not work out as smoothly when the project had to come together. While each group member had an idea of what the other roles were responsible for, the specific procedures and details were only known by the people who were assigned to the task. This made it slightly difficult in coordinating overall efforts. If this project were to be repeated, it would be more ideal if the roles were less program specific and team members shared more duties. This is not to say that there was an inordinate distribution of work, but that the work flow may have been better if everyone worked at the same pace.
:In terms of quality,a lot of the results were actually skewed due to oversights. This oversight led to a highly exaggerated error report which was only caught after the presentation. These corrections are reflected in the final report. As of organization, the wiki page is somewhat cluttered. This is simply due to the massive amount of content that is related to the project. The wiki is still navigable. All of the project content is present, just difficult to find. This has been a common issue with the group where all members will have their respective content, but will have a difficult time in linking the content together. The project was partially completed. With the NaCl dataset, a successful gene database was produced. For the sucrose dataset, there were several issues with the data itself which caused a delay for several days. Thus, the gene database that was exported was done at last minute and contained an exceptional amount of errors.

==Reflection of Process==
I learned a lot about wiki interface that I did not know about before. I also have had a small taste of coding from the Gene ID project. I learned that about the importance of communication between team members. In terms of technical skills, I have become slightly more proficient with computer interface. Interms of what I will be doing a year from now, I am sure that the wiki skill I learned will come in handy.

Team Name

2013-12-13T23:56:30Z

Slouie: Added link

Species: ''Sinorhizobium Meliloti'' (Strain 1021)
==Group Project==
[[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]]
==Project Deliverables==
[[Team Name Deliverables]]
==Personnel==
===Stephen Louie===
Project Manager, Quality Assurance
:slouie4 at lion.lmu.edu
:1 LMU Drive MSB 5194
:Los Angeles, CA 90045
:[[Stephen Louie Project Notebook|Stephen Louie Project Notebook]]

===Lauren Magee===
GenMAPP Expert
:lmagee1 at lion.lmu.edu
:1 LMU Drive MSB-5258,
:Los Angeles, CA 90045
===Mitchell Petredis===
Coding Supervisor
:mpetredi at lion dot lmu dot edu
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659

===Miles Malefyt===
GenMAPP Coordinator
:milesm@malefyt.com
:mmalefyt@lion.lmu.edu
:8416 Campion drive
:Westchester, CA 90045
cell: 831-236-5402

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 10:31, 31 October 2013 (PDT)

==Micro Array paper==

[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype Osmotic upshift elicited by salt and sucrose]]
*[[http://jb.asm.org/content/188/21/7617 HTML version]]
*[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]]
*[[Media:A-MEXP-230.adf.txt]]
*[[Media:E-MEXP-785.eSet.r]]-unable to download, because the file is too big
*[[Media:E-MEXP-785.processed.1.zip]]
*[[Media:E-MEXP-785.raw.2.zip]]
*[[Media:E-MEXP-785.idf.txt]]
*[[Media:E-MEXP-785.raw.1.zip]]-unable to download, because the file is too big
*[[Media:E-MEXP-785.sdrf.txt]]
*Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]]
*[[Media:Compiled Ratios and Logs.xls]]
*[[Media:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.txt]]
*[[Media:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.xls]]
*[[Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.txt]]
*[[Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.EX.txt]]
*[[Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.gex]]
*[[Media:ColorSets.mapp]]
*[[Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.gmf]]
*[[Media:700S1-3-t15-Decreased-Criterion0-GO.txt]]
*[[Media:700S1-3-t15-Increased-Criterion0-GO.txt]]
Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti ''Journal of Bacteriology'' 188:7617-7625

==Genome Paper==

[http://search.proquest.com/docview/213572450?accountid=7418 The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668–672.]

Galibert, F., Finan, T.M., Long, S., Puhler, A., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti ''Science'' 293:668-672

[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

==Model Organism Database==
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01

==Compiled raw Data==
[[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Compiled processed data==
[[Media:Complete_processed_Data.xls|Processed Data]]

==Data ready for GenMAPP==
[[Media:Complete_processed_Data_MPM.xls|XLS Version]]

[[Media:Complete_processed_Data_MPM.txt|TXT version, USE THIS]]

==Important Files==

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]

Computer on which export was run: Keck Lab Computer, back computer (furthest from the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import:19.17 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the [http://beta.geneontology.org/page/download-ontology GO Download page] has been unzipped): from 11/4/2013
* Time taken to import: 17.81 minutes
* Time taken to process: 15.54 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.goa]]
* GOA version (News on [http://www.ebi.ac.uk/GOA/ this page] records past releases; current information can be found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): from 11/7/2013
* Time taken to import: 0.21 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
* Time taken to export .gdb: Started at 2pm on 11-7-2013, finished at 9:47pm
* Upload your file and link to it here.

Note:

replace geneID with ~ when you find MOD link

==Important Files 2==

Info based on export done on 11/21/2013

Taxon ID: 266834

Version of GenMAPP Builder: [[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 7.34 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the [http://beta.geneontology.org/page/download-ontology GO Download page] has been unzipped): from 11/4/2013
* Time taken to import: 6.31 minutes
* Time taken to process: 4.60 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.goa]]
* GOA version (News on [http://www.ebi.ac.uk/GOA/ this page] records past releases; current information can be found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
* Time taken to export .gdb: Started at 10:18 AM on 11/21/2013; ended at 1:34 PM

==Important Files 3==

'''From Week 14, December 3-5, 2013'''

NOTE: Forgot that I cannot import data into the same database. I will continue to do an export based on what I have, and will do another import/export cycle on another computer using the same version of gmbuilder that I used here.

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: SmelilotiGenMAPP_Builder_2.0b73.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.27 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the [http://beta.geneontology.org/page/download-ontology GO Download page] has been unzipped): from 11/4/2013
* Time taken to import: 6.07 minutes
* Time taken to process: 12.42 minutes
**NOTE: gmbuilder told me that the GO OBO-XML file was already processed in the database, and wanted to know if I wanted to process the information again. I chose yes.

GOA filename:[[Media:R meliloti.goa|R meliloti.goa]]
* GOA version (News on [http://www.ebi.ac.uk/GOA/ this page] records past releases; current information can be found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb: started around 10am
* Upload your file and link to it here.

==Important Files 4==

'''From Week 14, December 3-5, 2013'''

NOTE: Here is the other import/export, using a new database on a different Keck Lab computer

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: SmelilotiGenMAPP_Builder_2.0b73.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: S meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.25 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the [http://beta.geneontology.org/page/download-ontology GO Download page] has been unzipped): from 11/4/2013
* Time taken to import: 6.21 minutes
* Time taken to process: 4.50 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.goa]]
* GOA version (News on [http://www.ebi.ac.uk/GOA/ this page] records past releases; current information can be found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_mpetredi_2013123-2.gdb]]
* Time taken to export .gdb: Started at 10:28am. Finished at 1:36pm

* Upload your file and link to it here.

GEX File
*[[Media:2013125-Complete_processed_Data_MPM.gex]]

==Wiki Navigation==
[[Template:Team Name]]
{{Team Name}}
*[[Teamname Week 13 Status Report]]
*[[Laurmagee: Week 13]]
*[[Teamname Week 15 Status Report]]
*[[Laurmagee: Week 15]]
*[[Electronic notebook: sinorhizobium meliloti|Miles Malefyt electronic notebook]]

Stephen Louie Deliverables

2013-12-13T23:22:34Z

Slouie: added content

==Statement of Work==

==Assessment of Project==

==Reflection of Process==
I learned a lot about wiki interface that I did not know about before. I also have had a small taste of coding from the Gene ID project. I learned that about the importance of communication between team members. In terms of technical skills, I have become slightly more proficient with computer interface. Interms of what I will be doing a year from now, I am sure that the wiki skill I learned will come in handy.

Team Name Deliverables

2013-12-13T23:16:07Z

Slouie: /* Individual */ added individual deliverables

=Group=
:GenMAPP Gene Database:[[Media:Sinorhizobium_meliloti_1021_mpetredi_2013123-2.gdb]]
:ReadMe file: [[Media:ReadMe-SM.pdf|ReadME_S.meliloti]]
:Gene Database Schema diagram: [[Media:S.Meliloti_schema_20131205.pdf|S.meliloti_schema_20131205.pdf]]
:Gene Database Testing Report: [[Media:Match Test Sheet1.pdf]]
:Processed and analyzed DNA microarray dataset:[[Media:Complete_processed_Data_MPM.xls|300mm NaCl XLS Version]]
:GenMAPP Expression Dataset file: [[Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.txt]]
:Filtered MAPPFinder Results: .7 M files:
*[[Media:700s1-3-t15-Decreased-Criterion-GO.xls]]
*[[Media:700s1-3-t15-Increased-Criterion-GO.xls]]

*[[Media:MAPPFinder_results_T15-Criterion_Increased-GO.txt|Increased expression at T15]]

*[[Media:MAPPFinder_results_T15-Criterion_Decreased-GO.txt|Decreased expression at T15]]

*[[Media:MAPPFinder_t60-Criterion_Increased-GO.txt|Increased expression at t60]]

*[[Media:MAPPFinder_t60-Criterion_Decreasaed-GO.txt|Decreased expression at t60]]
:Sample MAPP file of a relevant biological pathway for your species:[[Media:regulation of transcription, DNA-dependent]]
:Group Report:
:PowerPoint presentation:

=Individual=

*[[Miles Malefyt deliverables]]
*[[https://xmlpipedb.cs.lmu.edu/biodb/fall2013/index.php/Individual_Assessment_and_Reflection Mitchell Petredis deliverables]]
*[[Stephen Louie Deliverables]]

Team Name Deliverables

2013-12-12T03:22:23Z

Slouie: /* Group */ Added S. meliloti ReadMe

=Group=
:GenMAPP Gene Database:
:ReadMe file: [[Media:ReadMe-SM.pdf|ReadME_S.meliloti]]
:Gene Database Schema diagram: [[Media:S.Meliloti_schema_20131205.pdf|S.meliloti_schema_20131205.pdf]]
:Gene Database Testing Report: [[Media:Match Test Sheet1.pdf]]
:Processed and analyzed DNA microarray dataset:
:GenMAPP Expression Dataset file:
:Filtered MAPPFinder Results:
:Sample MAPP file of a relevant biological pathway for your species:
:Group Report:
:PowerPoint presentation:

=Individual=

File:ReadMe-SM.pdf

2013-12-12T03:17:49Z

Slouie: ReadME

ReadME

Team Name Deliverables

2013-12-12T00:25:31Z

Slouie: /* Group */ added gene database testing report

=Group=
:GenMAPP Gene Database:
:ReadMe file:
:Gene Database Schema diagram: [[Media:S.Meliloti_schema_20131205.pdf|S.Meliloti_schema_20131205.pdf]]
:Gene Database Testing Report: [[Media:Match Test Sheet1.pdf]]
:Processed and analyzed DNA microarray dataset:
:GenMAPP Expression Dataset file:
:Filtered MAPPFinder Results:
:Sample MAPP file of a relevant biological pathway for your species:
:Group Report:
:PowerPoint presentation:

=Individual=

File:Match Test Sheet1.pdf

2013-12-12T00:20:40Z

Slouie:

Team Name Deliverables

2013-12-12T00:14:21Z

Slouie: /* Group */ Added Gene database schema diagram

=Group=
Gene Database Schema diagram:[[Media:S.Meliloti_schema_20131205.pdf|S.Meliloti_schema_20131205.pdf]]

=Individual=

File:S.Meliloti schema 20131205.pdf

2013-12-12T00:11:42Z

Slouie: scheme for README

scheme for README

Team Name Deliverables

2013-12-11T23:37:53Z

Slouie: Started on deliverables page

=Group=

=Individual=

Template:Team Name

2013-12-11T23:35:16Z

Slouie: created page for deliverables

*[[User:Slouie|Stephen Louie]]
*[[User:Mpetredi|Mitchell Petredis]]
*[[User:Laurmagee|Lauren Magee]]
*[[User:mmalefyt|Miles Malefyt]]
*[[Gene Database Project]]
*[[Gene Database Project Report Guidelines]]
*[[Project Manager]]
*[[Coder]]
*[[Quality Assurance]]
*[[GenMAPP User]]
*[[Team Name Week 12 | Teamname Week 12 Status Report]]
*[[Laurmagee: Week 12]]
*[[http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01 Sinorhizobium meliloti 1021 Genome Page]]
*[[Team Name Deliverables]]

Team Name

2013-12-11T23:34:14Z

Slouie: /* Wiki Navigation */ added template link

Species: ''Sinorhizobium Meliloti'' (Strain 1021)
==Group Project==
[[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]]

==Personnel==
===Stephen Louie===
Project Manager, Quality Assurance
:slouie4 at lion.lmu.edu
:1 LMU Drive MSB 5194
:Los Angeles, CA 90045
:[[Stephen Louie Project Notebook|Stephen Louie Project Notebook]]

===Lauren Magee===
GenMAPP Expert
:lmagee1 at lion.lmu.edu
:1 LMU Drive MSB-5258,
:Los Angeles, CA 90045
===Mitchell Petredis===
Coding Supervisor
:mrpetredis at gmail dot com
:mpetredi at lion dot lmu dot edu
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659
===Miles Malefyt===
GenMAPP Coordinator
:milesm@malefyt.com
:mmalefyt@lion.lmu.edu
:8416 Campion drive
:Westchester, CA 90045
cell: 831-236-5402

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 10:31, 31 October 2013 (PDT)

==Micro Array paper==

[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype Osmotic upshift elicited by salt and sucrose]]
*[[http://jb.asm.org/content/188/21/7617 HTML version]]
*[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]]
*[[Media:A-MEXP-230.adf.txt]]
*[[Media:E-MEXP-785.eSet.r]]
*[[Media:E-MEXP-785.processed.1.zip]]
*[[Media:E-MEXP-785.raw.2.zip]]
*[[Media:E-MEXP-785.idf.txt]]
*[[Media:E-MEXP-785.raw.1.zip]]
*[[Media:E-MEXP-785.sdrf.txt]]
*Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]]
*[[File:Compiled Ratios and Logs.xls]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.txt]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.xls]]

Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti ''Journal of Bacteriology'' 188:7617-7625

==Genome Paper==

[http://search.proquest.com/docview/213572450?accountid=7418 The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668–672.]

Galibert, F., Finan, T.M., Long, S., Puhler, A., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti ''Science'' 293:668-672

[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

==Model Organism Database==
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01

==Compiled raw Data==
[[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Compiled processed data==
[[Media:Complete_processed_Data.xls|Processed Data]]

==Data ready for GenMAPP==
[[Media:Complete_processed_Data_MPM.xls|XLS Version]]

[[Media:Complete_processed_Data_MPM.txt|TXT version, USE THIS]]

==Important Files==

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]

Computer on which export was run: Keck Lab Computer, back computer (furthest from the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import:19.17 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the [http://beta.geneontology.org/page/download-ontology GO Download page] has been unzipped): from 11/4/2013
* Time taken to import: 17.81 minutes
* Time taken to process: 15.54 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.goa]]
* GOA version (News on [http://www.ebi.ac.uk/GOA/ this page] records past releases; current information can be found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): from 11/7/2013
* Time taken to import: 0.21 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
* Time taken to export .gdb: Started at 2pm on 11-7-2013, finished at 9:47pm
* Upload your file and link to it here.

Note:

replace geneID with ~ when you find MOD link

==Important Files 2==

Info based on export done on 11/21/2013

Taxon ID: 266834

Version of GenMAPP Builder: [[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 7.34 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the [http://beta.geneontology.org/page/download-ontology GO Download page] has been unzipped): from 11/4/2013
* Time taken to import: 6.31 minutes
* Time taken to process: 4.60 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.goa]]
* GOA version (News on [http://www.ebi.ac.uk/GOA/ this page] records past releases; current information can be found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
* Time taken to export .gdb: Started at 10:18 AM on 11/21/2013; ended at 1:34 PM

==Important Files 3==

'''From Week 14, December 3-5, 2013'''

NOTE: Forgot that I cannot import data into the same database. I will continue to do an export based on what I have, and will do another import/export cycle on another computer using the same version of gmbuilder that I used here.

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: SmelilotiGenMAPP_Builder_2.0b73.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.27 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the [http://beta.geneontology.org/page/download-ontology GO Download page] has been unzipped): from 11/4/2013
* Time taken to import: 6.07 minutes
* Time taken to process: 12.42 minutes
**NOTE: gmbuilder told me that the GO OBO-XML file was already processed in the database, and wanted to know if I wanted to process the information again. I chose yes.

GOA filename:[[Media:R meliloti.goa|R meliloti.goa]]
* GOA version (News on [http://www.ebi.ac.uk/GOA/ this page] records past releases; current information can be found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb: started around 10am
* Upload your file and link to it here.

==Important Files 4==

'''From Week 14, December 3-5, 2013'''

NOTE: Here is the other import/export, using a new database on a different Keck Lab computer

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: SmelilotiGenMAPP_Builder_2.0b73.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: S meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.25 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the [http://beta.geneontology.org/page/download-ontology GO Download page] has been unzipped): from 11/4/2013
* Time taken to import: 6.21 minutes
* Time taken to process: 4.50 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.goa]]
* GOA version (News on [http://www.ebi.ac.uk/GOA/ this page] records past releases; current information can be found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_mpetredi_2013123-2.gdb]]
* Time taken to export .gdb: Started at 10:28am. Finished at 1:36pm

* Upload your file and link to it here.

GEX File
*[[Media:2013125-Complete_processed_Data_MPM.gex]]

==Wiki Navigation==
[[Template:Team Name]]
{{Team Name}}
*[[Teamname Week 13 Status Report]]
*[[Laurmagee: Week 13]]
*[[Teamname Week 15 Status Report]]
*[[Laurmagee: Week 15]]
*[[Electronic notebook: sinorhizobium meliloti|Miles Malefyt electronic notebook]]

Stephen Louie Project Notebook

2013-11-26T18:55:28Z

Slouie: Added entry to project notebook

==Week 12==
===11/12/2013===
*Gave presentation for Genome paper to class
===11/14/2013===
*Conducted meeting with guilds. No meeting was conducted for Quality Assurance
*Sat in on GenMAPP builder guild meeting for absent teammate
*Downloaded and extracted data source files with Mitchell
**UniProt XML
***Followed directions provided [[Running GenMAPP Builder|Here]]
**GOA
***'''Note:Current directions were not working. Follow these instructions for your respective species'''
***From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
***Was given an error message. Changed url from "ftp" to "http" at beginning.
***Was entered, was taken to Index of/pub/database/GO/goa
***Clicked on "proteomes" folder
***Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.
**GO OBO-XML
***Followed directions provided [[Running GenMAPP Builder|Here]]
*Created new database in PostgreSQL
**Followed directions provided [[Running GenMAPP Builder|Here]]
*Imported data into PostgreSQL
**Followed directions provided [[Running GenMAPP Builder|Here]]
**UniProt XML took 19.17 minutes
**GO OBO-XML took 17.81 minutes to import and to 15.54 minutes process
**GOA file took less than a minute
*Exported Gene Database
**Followed directions provided [[Running GenMAPP Builder|Here]]
**Export took ~8 hours
==Week13==
===11/19/2013===
*Conducted side by side comparison of GeneIDs for gdb. and microarray data
**For the gdb. file, used MS Access
***Under tab "Orderedlocusnames" GeneIDs appeared as RB####.
**Downloaded microarray data from wiki page. (Used Mitchell's draft version of the .3M NaCL results)
***Opened the file in Excel in a tab.delimited format. GeneIDs appeared as SM.#####

===11/21/2013===
*Ran a preliminary sanity check
**Used GenMAPP to analyze microarray data to see if there was a discrepancy in the gene IDs between the microarray data and the GenMAPP database.
***Followed instructions provided [[http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols here]]
***After the first run, the conversion yielded over 20,000 errors with no matches
[[Image:ExpressionDatasetManagerscreencap.PNG]]
*When observing the microarray data, the Gene IDs used an uncapitalized letter as the third character space in the ID. To see whether this was the cause of the discrepancy, one of the samples was changed to have a third capitalized letter in the ID
**After the second run, there was no change in the amount of errors or matches from the modification to the Gene ID in the microarray data
*In viewing the gdb. data in Microsoft Access, it was realized that the orderedlocusnames utilizes R.#### as the ID (Rhizobium Meliloti was the former name of the species).
**Instead of using SM, R will be used instead to see whether that will make any substantial difference.
==Week 14==
===11/26/2013===
*Opened XML file in XML editor.
**Located GeneID under the "ORF" tag
**Format of GeneID is SM.######
*Note:Tag Gene ID in XML file is irrelevant. The tag is for a external link
==External Links==

:[[User:Slouie|User Page]]
:[[Team Name|Team Page]]

[[Category: Journal Entry]]
[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

Stephen Louie Project Notebook

2013-11-22T07:53:31Z

Slouie: /* 11/19/2013 */ added more info to entry

==Week 12==
===11/12/2013===
*Gave presentation for Genome paper to class
===11/14/2013===
*Conducted meeting with guilds. No meeting was conducted for Quality Assurance
*Sat in on GenMAPP builder guild meeting for absent teammate
*Downloaded and extracted data source files with Mitchell
**UniProt XML
***Followed directions provided [[Running GenMAPP Builder|Here]]
**GOA
***'''Note:Current directions were not working. Follow these instructions for your respective species'''
***From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
***Was given an error message. Changed url from "ftp" to "http" at beginning.
***Was entered, was taken to Index of/pub/database/GO/goa
***Clicked on "proteomes" folder
***Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.
**GO OBO-XML
***Followed directions provided [[Running GenMAPP Builder|Here]]
*Created new database in PostgreSQL
**Followed directions provided [[Running GenMAPP Builder|Here]]
*Imported data into PostgreSQL
**Followed directions provided [[Running GenMAPP Builder|Here]]
**UniProt XML took 19.17 minutes
**GO OBO-XML took 17.81 minutes to import and to 15.54 minutes process
**GOA file took less than a minute
*Exported Gene Database
**Followed directions provided [[Running GenMAPP Builder|Here]]
**Export took ~8 hours
==Week13==
===11/19/2013===
*Conducted side by side comparison of GeneIDs for gdb. and microarray data
**For the gdb. file, used MS Access
***Under tab "Orderedlocusnames" GeneIDs appeared as RB####.
**Downloaded microarray data from wiki page. (Used Mitchell's draft version of the .3M NaCL results)
***Opened the file in Excel in a tab.delimited format. GeneIDs appeared as SM.#####

===11/21/2013===
*Ran a preliminary sanity check
**Used GenMAPP to analyze microarray data to see if there was a discrepancy in the gene IDs between the microarray data and the GenMAPP database.
***Followed instructions provided [[http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols here]]
***After the first run, the conversion yielded over 20,000 errors with no matches
[[Image:ExpressionDatasetManagerscreencap.PNG]]
*When observing the microarray data, the Gene IDs used an uncapitalized letter as the third character space in the ID. To see whether this was the cause of the discrepancy, one of the samples was changed to have a third capitalized letter in the ID
**After the second run, there was no change in the amount of errors or matches from the modification to the Gene ID in the microarray data
*In viewing the gdb. data in Microsoft Access, it was realized that the orderedlocusnames utilizes R.#### as the ID (Rhizobium Meliloti was the former name of the species).
**Instead of using SM, R will be used instead to see whether that will make any substantial difference.

==External Links==

:[[User:Slouie|User Page]]
:[[Team Name|Team Page]]

[[Category: Journal Entry]]
[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

Stephen Louie Project Notebook

2013-11-22T07:49:41Z

Slouie: /* 11/21/2013 */ added image for visual reference

==Week 12==
===11/12/2013===
*Gave presentation for Genome paper to class
===11/14/2013===
*Conducted meeting with guilds. No meeting was conducted for Quality Assurance
*Sat in on GenMAPP builder guild meeting for absent teammate
*Downloaded and extracted data source files with Mitchell
**UniProt XML
***Followed directions provided [[Running GenMAPP Builder|Here]]
**GOA
***'''Note:Current directions were not working. Follow these instructions for your respective species'''
***From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
***Was given an error message. Changed url from "ftp" to "http" at beginning.
***Was entered, was taken to Index of/pub/database/GO/goa
***Clicked on "proteomes" folder
***Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.
**GO OBO-XML
***Followed directions provided [[Running GenMAPP Builder|Here]]
*Created new database in PostgreSQL
**Followed directions provided [[Running GenMAPP Builder|Here]]
*Imported data into PostgreSQL
**Followed directions provided [[Running GenMAPP Builder|Here]]
**UniProt XML took 19.17 minutes
**GO OBO-XML took 17.81 minutes to import and to 15.54 minutes process
**GOA file took less than a minute
*Exported Gene Database
**Followed directions provided [[Running GenMAPP Builder|Here]]
**Export took ~8 hours
==Week13==
===11/19/2013===
*Conducted side by side comparison of GeneIDs for gdb. and microarray data
*For the gdb. file, used MS Access
===11/21/2013===
*Ran a preliminary sanity check
**Used GenMAPP to analyze microarray data to see if there was a discrepancy in the gene IDs between the microarray data and the GenMAPP database.
***Followed instructions provided [[http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols here]]
***After the first run, the conversion yielded over 20,000 errors with no matches
[[Image:ExpressionDatasetManagerscreencap.PNG]]
*When observing the microarray data, the Gene IDs used an uncapitalized letter as the third character space in the ID. To see whether this was the cause of the discrepancy, one of the samples was changed to have a third capitalized letter in the ID
**After the second run, there was no change in the amount of errors or matches from the modification to the Gene ID in the microarray data
*In viewing the gdb. data in Microsoft Access, it was realized that the orderedlocusnames utilizes R.#### as the ID (Rhizobium Meliloti was the former name of the species).
**Instead of using SM, R will be used instead to see whether that will make any substantial difference.

==External Links==

:[[User:Slouie|User Page]]
:[[Team Name|Team Page]]

[[Category: Journal Entry]]
[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

Stephen Louie Project Notebook

2013-11-22T07:48:17Z

Slouie: /* Week13 */ added info to entry

==Week 12==
===11/12/2013===
*Gave presentation for Genome paper to class
===11/14/2013===
*Conducted meeting with guilds. No meeting was conducted for Quality Assurance
*Sat in on GenMAPP builder guild meeting for absent teammate
*Downloaded and extracted data source files with Mitchell
**UniProt XML
***Followed directions provided [[Running GenMAPP Builder|Here]]
**GOA
***'''Note:Current directions were not working. Follow these instructions for your respective species'''
***From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
***Was given an error message. Changed url from "ftp" to "http" at beginning.
***Was entered, was taken to Index of/pub/database/GO/goa
***Clicked on "proteomes" folder
***Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.
**GO OBO-XML
***Followed directions provided [[Running GenMAPP Builder|Here]]
*Created new database in PostgreSQL
**Followed directions provided [[Running GenMAPP Builder|Here]]
*Imported data into PostgreSQL
**Followed directions provided [[Running GenMAPP Builder|Here]]
**UniProt XML took 19.17 minutes
**GO OBO-XML took 17.81 minutes to import and to 15.54 minutes process
**GOA file took less than a minute
*Exported Gene Database
**Followed directions provided [[Running GenMAPP Builder|Here]]
**Export took ~8 hours
==Week13==
===11/19/2013===
*Conducted side by side comparison of GeneIDs for gdb. and microarray data
*For the gdb. file, used MS Access
===11/21/2013===
*Ran a preliminary sanity check
**Used GenMAPP to analyze microarray data to see if there was a discrepancy in the gene IDs between the microarray data and the GenMAPP database.
***Followed instructions provided [[http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols here]]
***After the first run, the conversion yielded over 20,000 errors with no matches
***When observing the microarray data, the Gene IDs used an uncapitalized letter as the third character space in the ID. To see whether this was the cause of the discrepancy, one of the samples was changed to have a third capitalized letter in the ID
**After the second run, there was no change in the amount of errors or matches from the modification to the Gene ID in the microarray data
*In viewing the gdb. data in Microsoft Access, it was realized that the orderedlocusnames utilizes R.#### as the ID (Rhizobium Meliloti was the former name of the species).
**Instead of using SM, R will be used instead to see whether that will make any substantial difference.

==External Links==

:[[User:Slouie|User Page]]
:[[Team Name|Team Page]]

[[Category: Journal Entry]]
[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

File:ExpressionDatasetManagerscreencap.PNG

2013-11-22T07:47:53Z

Slouie:

Teamname Week 13 Status Report

2013-11-22T07:31:15Z

Slouie: /* Stephen Louie */ added more to entry

=='''[[Team Name]]'''==

=='''[[user:mmalefyt|Miles Malefyt]]'''==
#What were the week’s key accomplishments?
This weeks key accomplishments were compiling the raw data from many individual data sources and then calculating where or not the gene was shown to be repressed or induced. Then the fold change ratios, the STdev, and averages were calculated in a new processed data folder. The process I used was based off of the Vibrio Cholera exercise we did earlier in the semester.
#What are next week’s target accomplishments?
The next weeks key accomplishments are finishing up the processed data files and then moving on to working on the gen mapp portion of the project. Mostly the GenMapp part because I am going in tomorrow (friday) to finish up processing the data.
#What team strengths were seen this week?
The team strengths that were shown this week was our ability to understand each of our roles in the project and communicate between each other on any questions we had with our roles. The group has shown a good work ethic in getting done what they need to get done.
#What team weaknesses were seen this week?
I didnt exactly see many weaknesses this week since we were all working on our respective portions of the project. In the future as all of our roles converge I think we need to work on our communication which will be integral to getting the work done.
[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 17:25, 21 November 2013 (PST)

=='''[[user:laurmagee|Lauren Magee]]''': Reflection Questions==
#What were the week’s key accomplishments?
#*I was able to finalize a spreadsheet with the Gene IDs and corresponding log((Cy5 Signal- Cy5 background)/(Cy3 Signal- Cy3 background)) for every replicate (1-3) in the following file: [[File:Full Raw Data.xls]]. I was also able to clean up the data, so it was ready for the protocol used to prepare the [[http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae| Vibrio cholerae]] data in [[Week 8]] for GenMapp analysis.
#What are next week’s target accomplishments?
#*Next week, I will hopefully be able to finish the protocol mentioned above and have a data file ready for GenMapp.
#What team strengths were seen this week?
#*We were more geared toward independent work this week, so all of our tasks were done on our own time. I think my teammates and I worked well in dividing our duties and taking responsibility for its completion. If one person fails to include their part, then the project is halted to a certain degree. Therefore, it is very important we all stay on top of our personal assignments and hold each other accountable.
#What team weaknesses were seen this week?
#*I don't think we had any blatant weakness this week, but in the future I think we could all work on our communication with one another. Since we were all doing our own assignments this week, I think we lost track of each other and what was getting done outside of our own role.
[[User:Laurmagee|Laurmagee]] ([[User talk:Laurmagee|talk]]) 12:31, 21 November 2013 (PST)

=='''[[user:slouie|Stephen Louie]]'''==
*On the GenMAPP user side, a raw data collection of the microarray data was completed. Specifically, the data concerned the transcriptional responses of S. Meliloti when exposed to either 0.3 M NaCl or 0.7 M Sucrose. A new export of the GenMAPP database for S. Meliloti based on an update made available from GenMAPP Builder. With these two things, I ran a preliminary sanity check using Match and MS Access. Based on the results. There was 0 ID correlation between the gdb. and the microarray data.
*For next week, it is integral that I identify the discrepancy between the IDs used in the microarray data and gdb. file. From what I can tell, the main difference is that the gdb. uses the old name of S. Meliloti (Rhizobium Meliloti) and uses the gene ID RB####. This is the most apparent of the differences, but does not mean that this is the sole cause for the difference.
*The team primarily focused on their individual guild assignments as opposed to working together on one task. In light of this, I was particularly impressed as to how my teammates were able to finish their tasks and make their data available for the other members in an expedient and organized manner.
*This was more of a fault on my part then my team. There was only limited communication being facilitated between team members during this week's work sessions. This was not particularly harmful as we all had an implicit understanding of each others' progress. Next week, this will definitely be critical as we move further into the export stages.
[[User:Slouie|Slouie]] ([[User talk:Slouie|talk]]) 23:31, 21 November 2013 (PST)

[[Category:Journal Entry]]

Teamname Week 13 Status Report

2013-11-22T07:25:57Z

Slouie: /* Stephen Louie */ added more to entry

=='''[[Team Name]]'''==

=='''[[user:mmalefyt|Miles Malefyt]]'''==
#What were the week’s key accomplishments?
This weeks key accomplishments were compiling the raw data from many individual data sources and then calculating where or not the gene was shown to be repressed or induced. Then the fold change ratios, the STdev, and averages were calculated in a new processed data folder. The process I used was based off of the Vibrio Cholera exercise we did earlier in the semester.
#What are next week’s target accomplishments?
The next weeks key accomplishments are finishing up the processed data files and then moving on to working on the gen mapp portion of the project. Mostly the GenMapp part because I am going in tomorrow (friday) to finish up processing the data.
#What team strengths were seen this week?
The team strengths that were shown this week was our ability to understand each of our roles in the project and communicate between each other on any questions we had with our roles. The group has shown a good work ethic in getting done what they need to get done.
#What team weaknesses were seen this week?
I didnt exactly see many weaknesses this week since we were all working on our respective portions of the project. In the future as all of our roles converge I think we need to work on our communication which will be integral to getting the work done.
[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 17:25, 21 November 2013 (PST)

=='''[[user:laurmagee|Lauren Magee]]''': Reflection Questions==
#What were the week’s key accomplishments?
#*I was able to finalize a spreadsheet with the Gene IDs and corresponding log((Cy5 Signal- Cy5 background)/(Cy3 Signal- Cy3 background)) for every replicate (1-3) in the following file: [[File:Full Raw Data.xls]]. I was also able to clean up the data, so it was ready for the protocol used to prepare the [[http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae| Vibrio cholerae]] data in [[Week 8]] for GenMapp analysis.
#What are next week’s target accomplishments?
#*Next week, I will hopefully be able to finish the protocol mentioned above and have a data file ready for GenMapp.
#What team strengths were seen this week?
#*We were more geared toward independent work this week, so all of our tasks were done on our own time. I think my teammates and I worked well in dividing our duties and taking responsibility for its completion. If one person fails to include their part, then the project is halted to a certain degree. Therefore, it is very important we all stay on top of our personal assignments and hold each other accountable.
#What team weaknesses were seen this week?
#*I don't think we had any blatant weakness this week, but in the future I think we could all work on our communication with one another. Since we were all doing our own assignments this week, I think we lost track of each other and what was getting done outside of our own role.
[[User:Laurmagee|Laurmagee]] ([[User talk:Laurmagee|talk]]) 12:31, 21 November 2013 (PST)

=='''[[user:slouie|Stephen Louie]]'''==
*On the GenMAPP user side, a raw data collection of the microarray data was completed. Specifically, the data concerned the transcriptional responses of S. Meliloti when exposed to either 0.3 M NaCl or 0.7 M Sucrose. A new export of the GenMAPP database for S. Meliloti based on an update made available from GenMAPP Builder. With these two things, I ran a preliminary sanity check using Match and MS Access. Based on the results. There was 0 ID correlation between the gdb. and the microarray data.
*For next week, it is integral that I identify the discrepancy between the IDs used in the microarray data and gdb. file. From what I can tell, the main difference is that the gdb. uses the old name of S. Meliloti (Rhizobium Meliloti) and uses the gene ID RB####. This is the most apparent of the differences, but does not mean that this is the sole cause for the difference.
*The team primarily focused on their individual guild assignments as opposed to working together on one task. In light of this, I was particularly impressed as to how my teammates were able to finish their tasks and make their data available for the other members in an expedient and organized manner.
*This was more of a fault on my part then anybody elses'. There was

[[Category:Journal Entry]]

Teamname Week 13 Status Report

2013-11-22T07:21:42Z

Slouie: /* Stephen Louie */ added more to entry

Teamname Week 13 Status Report

2013-11-22T07:16:22Z

Slouie: /* Stephen Louie */ added more to entry

Teamname Week 13 Status Report

2013-11-22T07:06:18Z

Slouie: Added entry to progress report

=='''[[Team Name]]'''==

=='''[[user:mmalefyt|Miles Malefyt]]'''==
#What were the week’s key accomplishments?
This weeks key accomplishments were compiling the raw data from many individual data sources and then calculating where or not the gene was shown to be repressed or induced. Then the fold change ratios, the STdev, and averages were calculated in a new processed data folder. The process I used was based off of the Vibrio Cholera exercise we did earlier in the semester.
#What are next week’s target accomplishments?
The next weeks key accomplishments are finishing up the processed data files and then moving on to working on the gen mapp portion of the project. Mostly the GenMapp part because I am going in tomorrow (friday) to finish up processing the data.
#What team strengths were seen this week?
The team strengths that were shown this week was our ability to understand each of our roles in the project and communicate between each other on any questions we had with our roles. The group has shown a good work ethic in getting done what they need to get done.
#What team weaknesses were seen this week?
I didnt exactly see many weaknesses this week since we were all working on our respective portions of the project. In the future as all of our roles converge I think we need to work on our communication which will be integral to getting the work done.
[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 17:25, 21 November 2013 (PST)

=='''[[user:laurmagee|Lauren Magee]]''': Reflection Questions==
#What were the week’s key accomplishments?
#*I was able to finalize a spreadsheet with the Gene IDs and corresponding log((Cy5 Signal- Cy5 background)/(Cy3 Signal- Cy3 background)) for every replicate (1-3) in the following file: [[File:Full Raw Data.xls]]. I was also able to clean up the data, so it was ready for the protocol used to prepare the [[http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae| Vibrio cholerae]] data in [[Week 8]] for GenMapp analysis.
#What are next week’s target accomplishments?
#*Next week, I will hopefully be able to finish the protocol mentioned above and have a data file ready for GenMapp.
#What team strengths were seen this week?
#*We were more geared toward independent work this week, so all of our tasks were done on our own time. I think my teammates and I worked well in dividing our duties and taking responsibility for its completion. If one person fails to include their part, then the project is halted to a certain degree. Therefore, it is very important we all stay on top of our personal assignments and hold each other accountable.
#What team weaknesses were seen this week?
#*I don't think we had any blatant weakness this week, but in the future I think we could all work on our communication with one another. Since we were all doing our own assignments this week, I think we lost track of each other and what was getting done outside of our own role.
[[User:Laurmagee|Laurmagee]] ([[User talk:Laurmagee|talk]]) 12:31, 21 November 2013 (PST)

=='''[[user:slouie|Stephen Louie]]'''==
#On the GenMAPP user side, a raw data collection of the microarray data was completed. Specifically, the data concerned the transcriptional responses of S. Meliloti when exposed to either 0.3 M NaCl or 0.7 M Sucrose.

[[Category:Journal Entry]]

Stephen Louie Project Notebook

2013-11-21T19:11:19Z

Slouie: /* 11/21/2013 */ added more to entry

==Week 12==
===11/12/2013===
*Gave presentation for Genome paper to class
===11/14/2013===
*Conducted meeting with guilds. No meeting was conducted for Quality Assurance
*Sat in on GenMAPP builder guild meeting for absent teammate
*Downloaded and extracted data source files with Mitchell
**UniProt XML
***Followed directions provided [[Running GenMAPP Builder|Here]]
**GOA
***'''Note:Current directions were not working. Follow these instructions for your respective species'''
***From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
***Was given an error message. Changed url from "ftp" to "http" at beginning.
***Was entered, was taken to Index of/pub/database/GO/goa
***Clicked on "proteomes" folder
***Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.
**GO OBO-XML
***Followed directions provided [[Running GenMAPP Builder|Here]]
*Created new database in PostgreSQL
**Followed directions provided [[Running GenMAPP Builder|Here]]
*Imported data into PostgreSQL
**Followed directions provided [[Running GenMAPP Builder|Here]]
**UniProt XML took 19.17 minutes
**GO OBO-XML took 17.81 minutes to import and to 15.54 minutes process
**GOA file took less than a minute
*Exported Gene Database
**Followed directions provided [[Running GenMAPP Builder|Here]]
**Export took ~8 hours
==Week13==
===11/19/2013===
===11/21/2013===
*Used GenMAPP to analyze microarray data to see if there was a discrepancy in the gene IDs between the microarray data and the GenMAPP database.
**Followed instructions provided [[http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols here]]
**After the first run, the conversion yielded over 20,000 errors with no matches
**When observing the microarray data, the Gene IDs used an uncapitalized letter as the third character space in the ID. To see whether this was the cause of the discrepancy, one of the samples was changed to have a third capitalized letter in the ID
**After the second run, there was no change in the amount of errors or matches from the modification to the Gene ID in the microarray data
*In viewing the gdb. data in Microsoft Access, it was realized that the orderedlocusnames utilizes R.#### as the ID (Rhizobium Meliloti was the former name of the species).
**Instead of using SM, R will be used instead to see whether that will make any substantial difference.

==External Links==

:[[User:Slouie|User Page]]
:[[Team Name|Team Page]]

[[Category: Journal Entry]]
[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

Stephen Louie Project Notebook

2013-11-21T18:58:54Z

Slouie: Added entry to project notebook

==Week 12==
===11/12/2013===
*Gave presentation for Genome paper to class
===11/14/2013===
*Conducted meeting with guilds. No meeting was conducted for Quality Assurance
*Sat in on GenMAPP builder guild meeting for absent teammate
*Downloaded and extracted data source files with Mitchell
**UniProt XML
***Followed directions provided [[Running GenMAPP Builder|Here]]
**GOA
***'''Note:Current directions were not working. Follow these instructions for your respective species'''
***From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
***Was given an error message. Changed url from "ftp" to "http" at beginning.
***Was entered, was taken to Index of/pub/database/GO/goa
***Clicked on "proteomes" folder
***Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.
**GO OBO-XML
***Followed directions provided [[Running GenMAPP Builder|Here]]
*Created new database in PostgreSQL
**Followed directions provided [[Running GenMAPP Builder|Here]]
*Imported data into PostgreSQL
**Followed directions provided [[Running GenMAPP Builder|Here]]
**UniProt XML took 19.17 minutes
**GO OBO-XML took 17.81 minutes to import and to 15.54 minutes process
**GOA file took less than a minute
*Exported Gene Database
**Followed directions provided [[Running GenMAPP Builder|Here]]
**Export took ~8 hours
==Week13==
===11/19/2013===
===11/21/2013===
*Used GenMAPP to analyze microarray data to see if there was a discrepancy in the gene IDs between the microarray data and the GenMAPP database.
**Followed instructions provided [[http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols here]]
**After the first run, the conversion yielded over 20,000 errors with no matches
**When observing the microarray data, the Gene IDs used an uncapitalized letter as the third character space in the ID. To see whether this was the cause of the discrepancy, one of the samples was changed to have a third capitalized letter in the ID
**After the second run, there was a substantial decrease in the amount of errors and a dramatic increase in the amount of processed data that was compatible.
==External Links==

:[[User:Slouie|User Page]]
:[[Team Name|Team Page]]

[[Category: Journal Entry]]
[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

Stephen Louie Project Notebook

2013-11-15T06:56:32Z

Slouie: /* 11/14/2013 */ added more to entry

Template:Team Name

2013-11-15T06:42:05Z

Slouie: added MOD link to templates

Stephen Louie Project Notebook

2013-11-15T06:38:08Z

Slouie: /* 11/14/2013 */ added instructions

Stephen Louie Project Notebook

2013-11-15T05:10:39Z

Slouie: Added links

==Week 12==
===11/12/2013===
*Gave presentation for Genome paper to class
===11/14/2013===
*Conducted meeting with guilds. No meeting was conducted for Quality Assurance
*Sat in on GenMAPP builder guild meeting for absent teammate

==External Links==

:[[User:Slouie|User Page]]
:[[Team Name|Team Page]]

[[Category: Journal Entry]]
[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

Stephen Louie Project Notebook

2013-11-15T05:05:05Z

Slouie: Added categories

==Week 12==
===11/12/2013===
*Gave presentation for Genome paper to class
===11/14/2013===
*Conducted meeting with guilds. No meeting was conducted for Quality Assurance
*Sat in on GenMAPP builder guild meeting for absent teammate

[[Category: Journal Entry]]
[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

Stephen Louie Project Notebook

2013-11-15T05:02:15Z

Slouie: added entry to project notebook

Stephen Louie Project Notebook

2013-11-15T04:57:01Z

Slouie: Created Project Notebook

==Week 12==
===11/12/2013===
*Gave presentation for Genome paper to class

Template:Slouie

2013-11-15T04:53:05Z

Slouie: Added link to template

* [[Main Page]]
* [[User:Slouie|My User Page]]
* [[Team Name|Team Page]]
*[[Stephen Louie Project Notebook]]
* [[Week 1]]
* [[Class_Journal_Week_1#Stephen Louie|Class Journal 1]]
* [[Week 2]]
* [[Class_Journal_Week_2#Stephen Louie|Class Journal 2]]
* [[Stephen Louie Week 2]]
* [[Week 3]]
* [[Class_Journal_Week_3#Stephen Louie|Class Journal 3]]
* [[Stephen Louie Week 3]]
* [[Week 4]]
* [[Class_Journal_Week_4#Stephen Louie|Class Journal 4]]
* [[Stephen Louie Week 4]]
* [[Week 5]]
* [[Class_Journal_Week_5#Alina, Stephen|Class Journal 5]]
* [[Stephen Louie Week 5]]
* [[Week 6]]
* [[Class_Journal_Week_6#Stephen Louie|Class Journal 6]]
* [[Stephen Louie Week 6]]
* [[Week 7]]
* [[Class_Journal_Week_7#Stephen Louie|Class Journal 7]]
* [[Stephen Louie Week 7]]
* [[Week 8]]
* [[Class_Journal_Week_8#Stephen Louie|Class Journal 8]]
* [[Stephen Louie Week 8]]
* [[Week 9]]
* [[Class_Journal_Week_9#Stephen Louie|Class Journal 9]]
* [[Stephen Louie Week 9]]
* [[Week 10]]
* [[Class_Journal_Week_10#Stephen Louie|Class Journal 10]]
* [[Stephen Louie Week 10]]
* [[Week 11]]
* [[Class_Journal_Week_11#Stephen Louie|Class Journal 11]]
* [[Stephen Louie Week 11]]
* [[Week 12]]
* [[Class_Journal_Week_12#Stephen Louie|Class Journal 12]]
* [[Stephen Louie Week 12]]

Team Name

2013-11-15T04:52:42Z

Slouie: /* Stephen Louie */ changed link for project notebook

Team Name Week 12

2013-11-15T04:49:14Z

Slouie: /* Stephen Louie */ added signature

=='''[[Team Name]]'''==

=='''[[user:slouie|Stephen Louie]]'''==
For this week, the group primarily focused on creating a presentation for the literature. This presentation was turned in successfully and went over well. All import/export cycles were completed successfully. Next week's target accomplishments will be to download the GO terms form the gene ontology database. The team demonstrated an impressive ability to coordinate work and information flow in a short amount of time. A potential team weakness was the team's misinterpretation of the group presentation guidelines by studying the microarray paper before realizing that the presentation was only based on the genome paper.

[[User:Slouie|Slouie]] ([[User talk:Slouie|talk]]) 20:49, 14 November 2013 (PST)

=='''[[user:laurmagee|Lauren Magee]]''': Reflection Questions==
# What were the week’s key accomplishments?
#*
# What are next week’s target accomplishments?
#*
# What team strengths were seen this week?
#*
# What team weaknesses were seen this week?
#*
[[User:Laurmagee|Laurmagee]] ([[User talk:Laurmagee|talk]]) 12:32, 13 November 2013 (PST)
[[Category:Journal Entry]]

Team Name Week 12

2013-11-14T18:21:40Z

Slouie: added individual reflection to the team status report

=='''[[Team Name]]'''==

=='''[[user:slouie|Stephen Louie]]'''==
For this week, the group primarily focused on creating a presentation for the literature. This presentation was turned in successfully and went over well. All import/export cycles were completed successfully. Next week's target accomplishments will be to download the GO terms form the gene ontology database. The team demonstrated an impressive ability to coordinate work and information flow in a short amount of time. A potential team weakness was the team's misinterpretation of the group presentation guidelines by studying the microarray paper before realizing that the presentation was only based on the genome paper.

=='''[[user:laurmagee|Lauren Magee]]''': Reflection Questions==
# What were the week’s key accomplishments?
#*
# What are next week’s target accomplishments?
#*
# What team strengths were seen this week?
#*
# What team weaknesses were seen this week?
#*
[[User:Laurmagee|Laurmagee]] ([[User talk:Laurmagee|talk]]) 12:32, 13 November 2013 (PST)
[[Category:Journal Entry]]

Team Name Week 12

2013-11-14T17:50:08Z

Slouie: Added entry into team journal

=='''[[Team Name]]'''==

=='''[[user:slouie|Stephen Louie]]'''==

=='''[[user:laurmagee|Lauren Magee]]''': Reflection Questions==
# What were the week’s key accomplishments?
#*
# What are next week’s target accomplishments?
#*
# What team strengths were seen this week?
#*
# What team weaknesses were seen this week?
#*
[[User:Laurmagee|Laurmagee]] ([[User talk:Laurmagee|talk]]) 12:32, 13 November 2013 (PST)
[[Category:Journal Entry]]

Team Name

2013-11-14T17:47:33Z

Slouie: Added Stephen Louie Project Notebook

Template:Team Name

2013-11-14T17:44:07Z

Slouie: added links to template

Team Name

2013-11-14T17:41:31Z

Slouie: Deleted stray links from Wiki Navigation

Team Name

2013-11-14T17:38:52Z

Slouie: Edited link for Teamname Week 12 Status Report

Stephen Louie Week 11

2013-11-13T07:35:19Z

Slouie: Added group presentation to individual wiki page

==Note==

Apologies for the late terms and database. Accidentally created an outline and presentation for the Microarray paper.

==Terms==
*'''Induce''':to cause (something) to happen or exist
**Source:[[http://www.merriam-webster.com/dictionary/induce?show=0&t=1384324303 Merriam-Webster]]
*'''Replicon''':a linear or circular section of DNA or RNA which replicates sequentially as a unit
**Source:[[http://www.merriam-webster.com/dictionary/replicon Merriam-Webster]]
*'''Plasmid''':an extrachromosomal ring of DNA especially of bacteria that replicates autonomously
**Source:[[http://www.merriam-webster.com/dictionary/plasmid Merriam-Webster]]
*'''Mb''':mega base pairs = 1,000,000 bp
**Source:[[http://en.wikipedia.org/wiki/Megabase#Length_measurements Wikipedia]]
*'''α-probacterium''':a class of Proteobacteria. Proteobacteria are a major group (phylum) of bacteria.
**Source:[[http://en.wikipedia.org/wiki/Proteobacteria Wikipedia]]
*'''Paralogy''':shared ancestry caused by a gene duplication event in the genome.
**Source:[[http://en.wikipedia.org/wiki/Homology_(biology)#Paralogy Wikipedia]]
*'''Biosynthesis''':the production of a chemical compound by a living organism
**Source:[[http://www.merriam-webster.com/dictionary/biosynthesis?show=0&t=1384325587 Merriam-Webster]]
*'''Orthologs''':genes in different species that originated by vertical descent from a single gene of the last common ancestor.
**Source:[[http://en.wikipedia.org/wiki/Homology_(biology)#Orthology Wikipedia]]
*'''Endosymbionts''':any organism that lives within the body or cells of another organism, i.e. forming an endosymbiosis.
**Source: [[http://en.wikipedia.org/wiki/Endosymbiont Wikipedia]]
*'''Orphan genes''':a gene that has limited phylogenetic distribution. This also means that these genes lack detectable homology to organisms outside such phylogenetic distribution.
**Source: [[http://en.wikipedia.org/wiki/Orphan_gene Wikipedia]]

==Outline==
The Composite Genome of the Legume Symbiont Sinorhizobium meliloti
*Plant growth is reliant on the availability of usable nitrogen.
**Most nitrogen can only be found in soil or fertilizer.
* Rhizobia: aerobic gram-negative soil bacteria
** When plants are deprived of nitrogen, rhizobia are capable of establishing nitrogen-fixing symbiosis.
** Rhizobia infect roots to form root nodules. The bacteria then undergo nitrogen-fixation within the cell cytoplasm.
** Rhizobia and plant exchange signals during this process. The rhizobia continue to provide nitrogen to plant in exchange for plant carbon compounds
** Evolution in legumes has shown the ability to obtain nitrogen from rhizobia while growing in poor soils.
* Sinorhizobium meliloti: the rhizobia symbiont to alfalfa
** As an α-probacterium it is closely related to bacterial plant and animal pathogens
** Some topics of interest include: how microbe stimulates nodule formation, how it manages to invade plant without triggering immune system defenses, how and why microbe fixes nitrogen for the host as opposed to itself, and how bacterium maintains itself within the soil environment.
** Extensive genetic, biochemical, and metabolic research have already been done on it making it an ideal subject for genomic investigation.
** Sinorhizobium meliloti strain 1021 has been fully sequenced.
* The Sinorhizobium meliloti genome consists of three replicons
** One large replicon of 3.65 Mb and two smaller replicons pSymA (1.35 Mb) and pSymB (1.68 Mb).
** Genome is not highly repeated (A limited number of genes seem to be recently duplicated)
** 42% (2589) of Sinorhizobium meliloti genes belong to 548 paralogous families ranging from 2-134 genes per family.
** High paralogy levels indicate that genome size had very little limitation during its evolution. This means that the bacterium was able to gain new adaptive functions for living in the soil and plant-symbiosis.
** Insertion sequence and phage sequences compose 202% of genome with overall abundance on pSymA, particularly near symbiotic genes. This enforces the idea that symbiotic regions are subject to DNA rearrangements.
* The unusual size of pSymA and pSymB makes them difficult to determine whether they are plasmids or chromosomes.
** pSymA was shown to contain putative conjugate transfer genes traACDG and a putative oriT sequence found on other Rhizobial plasmids.
** Essential genes are found to be present on pSymB, showing it to be more chromosome-like.
* Genes encoding for transport systems compose the largest (12%) class of genes in the Sinorhizobium meliloti genome.
** Most of these (17.4%) are found on pSymB. Thus, pSymB is shown to be important for transporting small molecules.
* Regulatory genes make up 8.7% of the Sinorhizobium meliloti genome. The LysR family is prevalent on pSymA.
** Each replicon has a distinct regulatory gene profile.
** Sinorhizobium meliloti ecodes the most nucleotide cyclases of any bacterial genome
* It is not well known how rhizobia connect to plant hair.
** Surface polysaccharides (especially exopolysaccharides) are crucial for plant infection by suppressing the immune system of the plant.
** 12% of pSymB genes have been predicted to be involved with polysaccharide biosynthesis.
** Two new loci were found on the chromosome and nine on pSymB.
* Nodulation genes are found on pSymA
** Two well preserved duplications of nod genes in the genome were found. nodM is suggested to be recently duplicated from glmS.
** Sequence analysis hints that the origins of Sinorhizobium meliloti nod genes are either resident gene duplication or horizontal gene transfer mediated by import of pSymA from an unknown bacterium.
* Nitrogen metabolism is a major feature encoded by the Sinorhizobium meliloti genome, especially in pSymA.
** Only 9 nif genes were found in the genome. Most if not all of these genes were found on pSymA.
** pSymA also carries glutamate dehydrogenase, a subset of genes that are required for denitrification and nitrate transport.
* High levels of energy are necessary for Sinorhizobium meliloti to maintain nitrogen-fixation while in a low oxygen environment in the nodule.
** Both pSymA and the chromosome have been shown to carry a large NADH-ubiquinone dehydrogenase gene cluster that may enhance energy metabolism in symbiosis.
* Genome of Sinorhizobium meliloti was compared to the genome of M. loti
** 35% of M.loti genes had no ortholog in S. meliloti
** Megaplasmid genes in S. meliloti were spread out in the M. loti
** Aside from nitrogen-fixing and nodule forming genes, M. loti has no orthologs in S. meliloti
* Determination of S. meliloti 1021 shows that it has a composite structure consisting of three unique replicons of different architecture and service features.
** This is consistent with the hypothesis that both megaplasmids were inherited from an ancestor with a single chromosome.
** Acquirement of pSymB has increased the metabolic capacity considerably.
** Acquirement of pSymA also led to ability to nodulate, colonize low-oxygen environment of nodules, and metabolize nitrogen compounds under various chemical forms.
** Complete genome sequence allows for opportunities to study the rhizobium-legume symbiosis and the nitrogen-fixation mechanisms of these bacteria.

==Molecular Organism Database==
Database [[http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01 Sinorhizobium meliloti 1021 Genome Page]]

#The website provides information on the genome sequence attributes, organism taxonomy, and DNA molecule numerical data. Due to lack of funding, the database is curated on a ad hoc basis.
#J. Craig Venter Institute maintains the database
#The website is currently without direct funding. It is being partially funded by a Microbial Sequence Center (MSC) grant from the National Institute of Allergy and Infectious Diseases (NIAID)
#All information is publicly available
#There is no schedule of updates. The database was last updated 2 years ago
#Links are provided to the GenBank FTP, JCVI FTP, Sequencing Center Genome Page, NCBI Genome Page, and the Publication page
#The information can be downloaded in the tab delimited or MySQL format.
#The site is well-organized. There is a tutorial section. The sample query makes sense as long as you have an idea what the name of your organism is
#The format (regular expression) of the main type of gene ID for Sinorhizobium meliloti is simply "Sinorhizobium meliloti 1021"

==Genome Presentation==

[[File:Sinorhizobium Meliloti.pdf]]

==Template==
{{Team Name}}

Stephen Louie Week 11

2013-11-13T07:31:40Z

Slouie: Added information on database

Stephen Louie Week 11

2013-11-13T07:06:24Z

Slouie: Added Database link

==Note==

Apologies for the late terms and database. Accidentally created an outline and presentation for the Microarray paper.

==Terms==
*'''Induce''':to cause (something) to happen or exist
**Source:[[http://www.merriam-webster.com/dictionary/induce?show=0&t=1384324303 Merriam-Webster]]
*'''Replicon''':a linear or circular section of DNA or RNA which replicates sequentially as a unit
**Source:[[http://www.merriam-webster.com/dictionary/replicon Merriam-Webster]]
*'''Plasmid''':an extrachromosomal ring of DNA especially of bacteria that replicates autonomously
**Source:[[http://www.merriam-webster.com/dictionary/plasmid Merriam-Webster]]
*'''Mb''':mega base pairs = 1,000,000 bp
**Source:[[http://en.wikipedia.org/wiki/Megabase#Length_measurements Wikipedia]]
*'''α-probacterium''':a class of Proteobacteria. Proteobacteria are a major group (phylum) of bacteria.
**Source:[[http://en.wikipedia.org/wiki/Proteobacteria Wikipedia]]
*'''Paralogy''':shared ancestry caused by a gene duplication event in the genome.
**Source:[[http://en.wikipedia.org/wiki/Homology_(biology)#Paralogy Wikipedia]]
*'''Biosynthesis''':the production of a chemical compound by a living organism
**Source:[[http://www.merriam-webster.com/dictionary/biosynthesis?show=0&t=1384325587 Merriam-Webster]]
*'''Orthologs''':genes in different species that originated by vertical descent from a single gene of the last common ancestor.
**Source:[[http://en.wikipedia.org/wiki/Homology_(biology)#Orthology Wikipedia]]
*'''Endosymbionts''':any organism that lives within the body or cells of another organism, i.e. forming an endosymbiosis.
**Source: [[http://en.wikipedia.org/wiki/Endosymbiont Wikipedia]]
*'''Orphan genes''':a gene that has limited phylogenetic distribution. This also means that these genes lack detectable homology to organisms outside such phylogenetic distribution.
**Source: [[http://en.wikipedia.org/wiki/Orphan_gene Wikipedia]]

==Outline==
The Composite Genome of the Legume Symbiont Sinorhizobium meliloti
*Plant growth is reliant on the availability of usable nitrogen.
**Most nitrogen can only be found in soil or fertilizer.
* Rhizobia: aerobic gram-negative soil bacteria
** When plants are deprived of nitrogen, rhizobia are capable of establishing nitrogen-fixing symbiosis.
** Rhizobia infect roots to form root nodules. The bacteria then undergo nitrogen-fixation within the cell cytoplasm.
** Rhizobia and plant exchange signals during this process. The rhizobia continue to provide nitrogen to plant in exchange for plant carbon compounds
** Evolution in legumes has shown the ability to obtain nitrogen from rhizobia while growing in poor soils.
* Sinorhizobium meliloti: the rhizobia symbiont to alfalfa
** As an α-probacterium it is closely related to bacterial plant and animal pathogens
** Some topics of interest include: how microbe stimulates nodule formation, how it manages to invade plant without triggering immune system defenses, how and why microbe fixes nitrogen for the host as opposed to itself, and how bacterium maintains itself within the soil environment.
** Extensive genetic, biochemical, and metabolic research have already been done on it making it an ideal subject for genomic investigation.
** Sinorhizobium meliloti strain 1021 has been fully sequenced.
* The Sinorhizobium meliloti genome consists of three replicons
** One large replicon of 3.65 Mb and two smaller replicons pSymA (1.35 Mb) and pSymB (1.68 Mb).
** Genome is not highly repeated (A limited number of genes seem to be recently duplicated)
** 42% (2589) of Sinorhizobium meliloti genes belong to 548 paralogous families ranging from 2-134 genes per family.
** High paralogy levels indicate that genome size had very little limitation during its evolution. This means that the bacterium was able to gain new adaptive functions for living in the soil and plant-symbiosis.
** Insertion sequence and phage sequences compose 202% of genome with overall abundance on pSymA, particularly near symbiotic genes. This enforces the idea that symbiotic regions are subject to DNA rearrangements.
* The unusual size of pSymA and pSymB makes them difficult to determine whether they are plasmids or chromosomes.
** pSymA was shown to contain putative conjugate transfer genes traACDG and a putative oriT sequence found on other Rhizobial plasmids.
** Essential genes are found to be present on pSymB, showing it to be more chromosome-like.
* Genes encoding for transport systems compose the largest (12%) class of genes in the Sinorhizobium meliloti genome.
** Most of these (17.4%) are found on pSymB. Thus, pSymB is shown to be important for transporting small molecules.
* Regulatory genes make up 8.7% of the Sinorhizobium meliloti genome. The LysR family is prevalent on pSymA.
** Each replicon has a distinct regulatory gene profile.
** Sinorhizobium meliloti ecodes the most nucleotide cyclases of any bacterial genome
* It is not well known how rhizobia connect to plant hair.
** Surface polysaccharides (especially exopolysaccharides) are crucial for plant infection by suppressing the immune system of the plant.
** 12% of pSymB genes have been predicted to be involved with polysaccharide biosynthesis.
** Two new loci were found on the chromosome and nine on pSymB.
* Nodulation genes are found on pSymA
** Two well preserved duplications of nod genes in the genome were found. nodM is suggested to be recently duplicated from glmS.
** Sequence analysis hints that the origins of Sinorhizobium meliloti nod genes are either resident gene duplication or horizontal gene transfer mediated by import of pSymA from an unknown bacterium.
* Nitrogen metabolism is a major feature encoded by the Sinorhizobium meliloti genome, especially in pSymA.
** Only 9 nif genes were found in the genome. Most if not all of these genes were found on pSymA.
** pSymA also carries glutamate dehydrogenase, a subset of genes that are required for denitrification and nitrate transport.
* High levels of energy are necessary for Sinorhizobium meliloti to maintain nitrogen-fixation while in a low oxygen environment in the nodule.
** Both pSymA and the chromosome have been shown to carry a large NADH-ubiquinone dehydrogenase gene cluster that may enhance energy metabolism in symbiosis.
* Genome of Sinorhizobium meliloti was compared to the genome of M. loti
** 35% of M.loti genes had no ortholog in S. meliloti
** Megaplasmid genes in S. meliloti were spread out in the M. loti
** Aside from nitrogen-fixing and nodule forming genes, M. loti has no orthologs in S. meliloti
* Determination of S. meliloti 1021 shows that it has a composite structure consisting of three unique replicons of different architecture and service features.
** This is consistent with the hypothesis that both megaplasmids were inherited from an ancestor with a single chromosome.
** Acquirement of pSymB has increased the metabolic capacity considerably.
** Acquirement of pSymA also led to ability to nodulate, colonize low-oxygen environment of nodules, and metabolize nitrogen compounds under various chemical forms.
** Complete genome sequence allows for opportunities to study the rhizobium-legume symbiosis and the nitrogen-fixation mechanisms of these bacteria.

==Molecular Organism Database==
Database [[http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01 Sinorhizobium meliloti 1021 Genome Page]]

#
#J. Craig Venter Institute maintains the database
#No information given in terms of funding
#All information is publicly availible
#The database was last updated 2 years ago
#
#
#
#The site is well-organized. There is a tutorial section.
#

==Template==
{{Team Name}}

Stephen Louie Week 11

2013-11-13T07:02:58Z

Slouie: Changed template from page link to direct links

==Note==

Apologies for the late terms and database. Accidentally created an outline and presentation for the Microarray paper.

==Terms==
*'''Induce''':to cause (something) to happen or exist
**Source:[[http://www.merriam-webster.com/dictionary/induce?show=0&t=1384324303 Merriam-Webster]]
*'''Replicon''':a linear or circular section of DNA or RNA which replicates sequentially as a unit
**Source:[[http://www.merriam-webster.com/dictionary/replicon Merriam-Webster]]
*'''Plasmid''':an extrachromosomal ring of DNA especially of bacteria that replicates autonomously
**Source:[[http://www.merriam-webster.com/dictionary/plasmid Merriam-Webster]]
*'''Mb''':mega base pairs = 1,000,000 bp
**Source:[[http://en.wikipedia.org/wiki/Megabase#Length_measurements Wikipedia]]
*'''α-probacterium''':a class of Proteobacteria. Proteobacteria are a major group (phylum) of bacteria.
**Source:[[http://en.wikipedia.org/wiki/Proteobacteria Wikipedia]]
*'''Paralogy''':shared ancestry caused by a gene duplication event in the genome.
**Source:[[http://en.wikipedia.org/wiki/Homology_(biology)#Paralogy Wikipedia]]
*'''Biosynthesis''':the production of a chemical compound by a living organism
**Source:[[http://www.merriam-webster.com/dictionary/biosynthesis?show=0&t=1384325587 Merriam-Webster]]
*'''Orthologs''':genes in different species that originated by vertical descent from a single gene of the last common ancestor.
**Source:[[http://en.wikipedia.org/wiki/Homology_(biology)#Orthology Wikipedia]]
*'''Endosymbionts''':any organism that lives within the body or cells of another organism, i.e. forming an endosymbiosis.
**Source: [[http://en.wikipedia.org/wiki/Endosymbiont Wikipedia]]
*'''Orphan genes''':a gene that has limited phylogenetic distribution. This also means that these genes lack detectable homology to organisms outside such phylogenetic distribution.
**Source: [[http://en.wikipedia.org/wiki/Orphan_gene Wikipedia]]

==Outline==
The Composite Genome of the Legume Symbiont Sinorhizobium meliloti
*Plant growth is reliant on the availability of usable nitrogen.
**Most nitrogen can only be found in soil or fertilizer.
* Rhizobia: aerobic gram-negative soil bacteria
** When plants are deprived of nitrogen, rhizobia are capable of establishing nitrogen-fixing symbiosis.
** Rhizobia infect roots to form root nodules. The bacteria then undergo nitrogen-fixation within the cell cytoplasm.
** Rhizobia and plant exchange signals during this process. The rhizobia continue to provide nitrogen to plant in exchange for plant carbon compounds
** Evolution in legumes has shown the ability to obtain nitrogen from rhizobia while growing in poor soils.
* Sinorhizobium meliloti: the rhizobia symbiont to alfalfa
** As an α-probacterium it is closely related to bacterial plant and animal pathogens
** Some topics of interest include: how microbe stimulates nodule formation, how it manages to invade plant without triggering immune system defenses, how and why microbe fixes nitrogen for the host as opposed to itself, and how bacterium maintains itself within the soil environment.
** Extensive genetic, biochemical, and metabolic research have already been done on it making it an ideal subject for genomic investigation.
** Sinorhizobium meliloti strain 1021 has been fully sequenced.
* The Sinorhizobium meliloti genome consists of three replicons
** One large replicon of 3.65 Mb and two smaller replicons pSymA (1.35 Mb) and pSymB (1.68 Mb).
** Genome is not highly repeated (A limited number of genes seem to be recently duplicated)
** 42% (2589) of Sinorhizobium meliloti genes belong to 548 paralogous families ranging from 2-134 genes per family.
** High paralogy levels indicate that genome size had very little limitation during its evolution. This means that the bacterium was able to gain new adaptive functions for living in the soil and plant-symbiosis.
** Insertion sequence and phage sequences compose 202% of genome with overall abundance on pSymA, particularly near symbiotic genes. This enforces the idea that symbiotic regions are subject to DNA rearrangements.
* The unusual size of pSymA and pSymB makes them difficult to determine whether they are plasmids or chromosomes.
** pSymA was shown to contain putative conjugate transfer genes traACDG and a putative oriT sequence found on other Rhizobial plasmids.
** Essential genes are found to be present on pSymB, showing it to be more chromosome-like.
* Genes encoding for transport systems compose the largest (12%) class of genes in the Sinorhizobium meliloti genome.
** Most of these (17.4%) are found on pSymB. Thus, pSymB is shown to be important for transporting small molecules.
* Regulatory genes make up 8.7% of the Sinorhizobium meliloti genome. The LysR family is prevalent on pSymA.
** Each replicon has a distinct regulatory gene profile.
** Sinorhizobium meliloti ecodes the most nucleotide cyclases of any bacterial genome
* It is not well known how rhizobia connect to plant hair.
** Surface polysaccharides (especially exopolysaccharides) are crucial for plant infection by suppressing the immune system of the plant.
** 12% of pSymB genes have been predicted to be involved with polysaccharide biosynthesis.
** Two new loci were found on the chromosome and nine on pSymB.
* Nodulation genes are found on pSymA
** Two well preserved duplications of nod genes in the genome were found. nodM is suggested to be recently duplicated from glmS.
** Sequence analysis hints that the origins of Sinorhizobium meliloti nod genes are either resident gene duplication or horizontal gene transfer mediated by import of pSymA from an unknown bacterium.
* Nitrogen metabolism is a major feature encoded by the Sinorhizobium meliloti genome, especially in pSymA.
** Only 9 nif genes were found in the genome. Most if not all of these genes were found on pSymA.
** pSymA also carries glutamate dehydrogenase, a subset of genes that are required for denitrification and nitrate transport.
* High levels of energy are necessary for Sinorhizobium meliloti to maintain nitrogen-fixation while in a low oxygen environment in the nodule.
** Both pSymA and the chromosome have been shown to carry a large NADH-ubiquinone dehydrogenase gene cluster that may enhance energy metabolism in symbiosis.
* Genome of Sinorhizobium meliloti was compared to the genome of M. loti
** 35% of M.loti genes had no ortholog in S. meliloti
** Megaplasmid genes in S. meliloti were spread out in the M. loti
** Aside from nitrogen-fixing and nodule forming genes, M. loti has no orthologs in S. meliloti
* Determination of S. meliloti 1021 shows that it has a composite structure consisting of three unique replicons of different architecture and service features.
** This is consistent with the hypothesis that both megaplasmids were inherited from an ancestor with a single chromosome.
** Acquirement of pSymB has increased the metabolic capacity considerably.
** Acquirement of pSymA also led to ability to nodulate, colonize low-oxygen environment of nodules, and metabolize nitrogen compounds under various chemical forms.
** Complete genome sequence allows for opportunities to study the rhizobium-legume symbiosis and the nitrogen-fixation mechanisms of these bacteria.

==Molecular Organism Database==
#
#J. Craig Venter Institute maintains the database
#No information given in terms of funding
#All information is publicly availible
#The database was last updated 2 years ago
#
#
#
#The site is well-organized. There is a tutorial section.
#

==Template==
{{Team Name}}

Stephen Louie Week 11

2013-11-13T06:59:23Z

Slouie: Added notice

==Note==

Apologies for the late terms and database. Accidentally created an outline and presentation for the Microarray paper.

==Terms==
*'''Induce''':to cause (something) to happen or exist
**Source:[[http://www.merriam-webster.com/dictionary/induce?show=0&t=1384324303 Merriam-Webster]]
*'''Replicon''':a linear or circular section of DNA or RNA which replicates sequentially as a unit
**Source:[[http://www.merriam-webster.com/dictionary/replicon Merriam-Webster]]
*'''Plasmid''':an extrachromosomal ring of DNA especially of bacteria that replicates autonomously
**Source:[[http://www.merriam-webster.com/dictionary/plasmid Merriam-Webster]]
*'''Mb''':mega base pairs = 1,000,000 bp
**Source:[[http://en.wikipedia.org/wiki/Megabase#Length_measurements Wikipedia]]
*'''α-probacterium''':a class of Proteobacteria. Proteobacteria are a major group (phylum) of bacteria.
**Source:[[http://en.wikipedia.org/wiki/Proteobacteria Wikipedia]]
*'''Paralogy''':shared ancestry caused by a gene duplication event in the genome.
**Source:[[http://en.wikipedia.org/wiki/Homology_(biology)#Paralogy Wikipedia]]
*'''Biosynthesis''':the production of a chemical compound by a living organism
**Source:[[http://www.merriam-webster.com/dictionary/biosynthesis?show=0&t=1384325587 Merriam-Webster]]
*'''Orthologs''':genes in different species that originated by vertical descent from a single gene of the last common ancestor.
**Source:[[http://en.wikipedia.org/wiki/Homology_(biology)#Orthology Wikipedia]]
*'''Endosymbionts''':any organism that lives within the body or cells of another organism, i.e. forming an endosymbiosis.
**Source: [[http://en.wikipedia.org/wiki/Endosymbiont Wikipedia]]
*'''Orphan genes''':a gene that has limited phylogenetic distribution. This also means that these genes lack detectable homology to organisms outside such phylogenetic distribution.
**Source: [[http://en.wikipedia.org/wiki/Orphan_gene Wikipedia]]

==Outline==
The Composite Genome of the Legume Symbiont Sinorhizobium meliloti
*Plant growth is reliant on the availability of usable nitrogen.
**Most nitrogen can only be found in soil or fertilizer.
* Rhizobia: aerobic gram-negative soil bacteria
** When plants are deprived of nitrogen, rhizobia are capable of establishing nitrogen-fixing symbiosis.
** Rhizobia infect roots to form root nodules. The bacteria then undergo nitrogen-fixation within the cell cytoplasm.
** Rhizobia and plant exchange signals during this process. The rhizobia continue to provide nitrogen to plant in exchange for plant carbon compounds
** Evolution in legumes has shown the ability to obtain nitrogen from rhizobia while growing in poor soils.
* Sinorhizobium meliloti: the rhizobia symbiont to alfalfa
** As an α-probacterium it is closely related to bacterial plant and animal pathogens
** Some topics of interest include: how microbe stimulates nodule formation, how it manages to invade plant without triggering immune system defenses, how and why microbe fixes nitrogen for the host as opposed to itself, and how bacterium maintains itself within the soil environment.
** Extensive genetic, biochemical, and metabolic research have already been done on it making it an ideal subject for genomic investigation.
** Sinorhizobium meliloti strain 1021 has been fully sequenced.
* The Sinorhizobium meliloti genome consists of three replicons
** One large replicon of 3.65 Mb and two smaller replicons pSymA (1.35 Mb) and pSymB (1.68 Mb).
** Genome is not highly repeated (A limited number of genes seem to be recently duplicated)
** 42% (2589) of Sinorhizobium meliloti genes belong to 548 paralogous families ranging from 2-134 genes per family.
** High paralogy levels indicate that genome size had very little limitation during its evolution. This means that the bacterium was able to gain new adaptive functions for living in the soil and plant-symbiosis.
** Insertion sequence and phage sequences compose 202% of genome with overall abundance on pSymA, particularly near symbiotic genes. This enforces the idea that symbiotic regions are subject to DNA rearrangements.
* The unusual size of pSymA and pSymB makes them difficult to determine whether they are plasmids or chromosomes.
** pSymA was shown to contain putative conjugate transfer genes traACDG and a putative oriT sequence found on other Rhizobial plasmids.
** Essential genes are found to be present on pSymB, showing it to be more chromosome-like.
* Genes encoding for transport systems compose the largest (12%) class of genes in the Sinorhizobium meliloti genome.
** Most of these (17.4%) are found on pSymB. Thus, pSymB is shown to be important for transporting small molecules.
* Regulatory genes make up 8.7% of the Sinorhizobium meliloti genome. The LysR family is prevalent on pSymA.
** Each replicon has a distinct regulatory gene profile.
** Sinorhizobium meliloti ecodes the most nucleotide cyclases of any bacterial genome
* It is not well known how rhizobia connect to plant hair.
** Surface polysaccharides (especially exopolysaccharides) are crucial for plant infection by suppressing the immune system of the plant.
** 12% of pSymB genes have been predicted to be involved with polysaccharide biosynthesis.
** Two new loci were found on the chromosome and nine on pSymB.
* Nodulation genes are found on pSymA
** Two well preserved duplications of nod genes in the genome were found. nodM is suggested to be recently duplicated from glmS.
** Sequence analysis hints that the origins of Sinorhizobium meliloti nod genes are either resident gene duplication or horizontal gene transfer mediated by import of pSymA from an unknown bacterium.
* Nitrogen metabolism is a major feature encoded by the Sinorhizobium meliloti genome, especially in pSymA.
** Only 9 nif genes were found in the genome. Most if not all of these genes were found on pSymA.
** pSymA also carries glutamate dehydrogenase, a subset of genes that are required for denitrification and nitrate transport.
* High levels of energy are necessary for Sinorhizobium meliloti to maintain nitrogen-fixation while in a low oxygen environment in the nodule.
** Both pSymA and the chromosome have been shown to carry a large NADH-ubiquinone dehydrogenase gene cluster that may enhance energy metabolism in symbiosis.
* Genome of Sinorhizobium meliloti was compared to the genome of M. loti
** 35% of M.loti genes had no ortholog in S. meliloti
** Megaplasmid genes in S. meliloti were spread out in the M. loti
** Aside from nitrogen-fixing and nodule forming genes, M. loti has no orthologs in S. meliloti
* Determination of S. meliloti 1021 shows that it has a composite structure consisting of three unique replicons of different architecture and service features.
** This is consistent with the hypothesis that both megaplasmids were inherited from an ancestor with a single chromosome.
** Acquirement of pSymB has increased the metabolic capacity considerably.
** Acquirement of pSymA also led to ability to nodulate, colonize low-oxygen environment of nodules, and metabolize nitrogen compounds under various chemical forms.
** Complete genome sequence allows for opportunities to study the rhizobium-legume symbiosis and the nitrogen-fixation mechanisms of these bacteria.

==Molecular Organism Database==
#
#J. Craig Venter Institute maintains the database
#No information given in terms of funding
#All information is publicly availible
#The database was last updated 2 years ago
#
#
#
#The site is well-organized. There is a tutorial section.
#

==Template==
[[Template:Team Name]]

Stephen Louie Week 11

2013-11-13T06:57:45Z

Slouie: Added more term definitions

==Terms==
*'''Induce''':to cause (something) to happen or exist
**Source:[[http://www.merriam-webster.com/dictionary/induce?show=0&t=1384324303 Merriam-Webster]]
*'''Replicon''':a linear or circular section of DNA or RNA which replicates sequentially as a unit
**Source:[[http://www.merriam-webster.com/dictionary/replicon Merriam-Webster]]
*'''Plasmid''':an extrachromosomal ring of DNA especially of bacteria that replicates autonomously
**Source:[[http://www.merriam-webster.com/dictionary/plasmid Merriam-Webster]]
*'''Mb''':mega base pairs = 1,000,000 bp
**Source:[[http://en.wikipedia.org/wiki/Megabase#Length_measurements Wikipedia]]
*'''α-probacterium''':a class of Proteobacteria. Proteobacteria are a major group (phylum) of bacteria.
**Source:[[http://en.wikipedia.org/wiki/Proteobacteria Wikipedia]]
*'''Paralogy''':shared ancestry caused by a gene duplication event in the genome.
**Source:[[http://en.wikipedia.org/wiki/Homology_(biology)#Paralogy Wikipedia]]
*'''Biosynthesis''':the production of a chemical compound by a living organism
**Source:[[http://www.merriam-webster.com/dictionary/biosynthesis?show=0&t=1384325587 Merriam-Webster]]
*'''Orthologs''':genes in different species that originated by vertical descent from a single gene of the last common ancestor.
**Source:[[http://en.wikipedia.org/wiki/Homology_(biology)#Orthology Wikipedia]]
*'''Endosymbionts''':any organism that lives within the body or cells of another organism, i.e. forming an endosymbiosis.
**Source: [[http://en.wikipedia.org/wiki/Endosymbiont Wikipedia]]
*'''Orphan genes''':a gene that has limited phylogenetic distribution. This also means that these genes lack detectable homology to organisms outside such phylogenetic distribution.
**Source: [[http://en.wikipedia.org/wiki/Orphan_gene Wikipedia]]

==Outline==
The Composite Genome of the Legume Symbiont Sinorhizobium meliloti
*Plant growth is reliant on the availability of usable nitrogen.
**Most nitrogen can only be found in soil or fertilizer.
* Rhizobia: aerobic gram-negative soil bacteria
** When plants are deprived of nitrogen, rhizobia are capable of establishing nitrogen-fixing symbiosis.
** Rhizobia infect roots to form root nodules. The bacteria then undergo nitrogen-fixation within the cell cytoplasm.
** Rhizobia and plant exchange signals during this process. The rhizobia continue to provide nitrogen to plant in exchange for plant carbon compounds
** Evolution in legumes has shown the ability to obtain nitrogen from rhizobia while growing in poor soils.
* Sinorhizobium meliloti: the rhizobia symbiont to alfalfa
** As an α-probacterium it is closely related to bacterial plant and animal pathogens
** Some topics of interest include: how microbe stimulates nodule formation, how it manages to invade plant without triggering immune system defenses, how and why microbe fixes nitrogen for the host as opposed to itself, and how bacterium maintains itself within the soil environment.
** Extensive genetic, biochemical, and metabolic research have already been done on it making it an ideal subject for genomic investigation.
** Sinorhizobium meliloti strain 1021 has been fully sequenced.
* The Sinorhizobium meliloti genome consists of three replicons
** One large replicon of 3.65 Mb and two smaller replicons pSymA (1.35 Mb) and pSymB (1.68 Mb).
** Genome is not highly repeated (A limited number of genes seem to be recently duplicated)
** 42% (2589) of Sinorhizobium meliloti genes belong to 548 paralogous families ranging from 2-134 genes per family.
** High paralogy levels indicate that genome size had very little limitation during its evolution. This means that the bacterium was able to gain new adaptive functions for living in the soil and plant-symbiosis.
** Insertion sequence and phage sequences compose 202% of genome with overall abundance on pSymA, particularly near symbiotic genes. This enforces the idea that symbiotic regions are subject to DNA rearrangements.
* The unusual size of pSymA and pSymB makes them difficult to determine whether they are plasmids or chromosomes.
** pSymA was shown to contain putative conjugate transfer genes traACDG and a putative oriT sequence found on other Rhizobial plasmids.
** Essential genes are found to be present on pSymB, showing it to be more chromosome-like.
* Genes encoding for transport systems compose the largest (12%) class of genes in the Sinorhizobium meliloti genome.
** Most of these (17.4%) are found on pSymB. Thus, pSymB is shown to be important for transporting small molecules.
* Regulatory genes make up 8.7% of the Sinorhizobium meliloti genome. The LysR family is prevalent on pSymA.
** Each replicon has a distinct regulatory gene profile.
** Sinorhizobium meliloti ecodes the most nucleotide cyclases of any bacterial genome
* It is not well known how rhizobia connect to plant hair.
** Surface polysaccharides (especially exopolysaccharides) are crucial for plant infection by suppressing the immune system of the plant.
** 12% of pSymB genes have been predicted to be involved with polysaccharide biosynthesis.
** Two new loci were found on the chromosome and nine on pSymB.
* Nodulation genes are found on pSymA
** Two well preserved duplications of nod genes in the genome were found. nodM is suggested to be recently duplicated from glmS.
** Sequence analysis hints that the origins of Sinorhizobium meliloti nod genes are either resident gene duplication or horizontal gene transfer mediated by import of pSymA from an unknown bacterium.
* Nitrogen metabolism is a major feature encoded by the Sinorhizobium meliloti genome, especially in pSymA.
** Only 9 nif genes were found in the genome. Most if not all of these genes were found on pSymA.
** pSymA also carries glutamate dehydrogenase, a subset of genes that are required for denitrification and nitrate transport.
* High levels of energy are necessary for Sinorhizobium meliloti to maintain nitrogen-fixation while in a low oxygen environment in the nodule.
** Both pSymA and the chromosome have been shown to carry a large NADH-ubiquinone dehydrogenase gene cluster that may enhance energy metabolism in symbiosis.
* Genome of Sinorhizobium meliloti was compared to the genome of M. loti
** 35% of M.loti genes had no ortholog in S. meliloti
** Megaplasmid genes in S. meliloti were spread out in the M. loti
** Aside from nitrogen-fixing and nodule forming genes, M. loti has no orthologs in S. meliloti
* Determination of S. meliloti 1021 shows that it has a composite structure consisting of three unique replicons of different architecture and service features.
** This is consistent with the hypothesis that both megaplasmids were inherited from an ancestor with a single chromosome.
** Acquirement of pSymB has increased the metabolic capacity considerably.
** Acquirement of pSymA also led to ability to nodulate, colonize low-oxygen environment of nodules, and metabolize nitrogen compounds under various chemical forms.
** Complete genome sequence allows for opportunities to study the rhizobium-legume symbiosis and the nitrogen-fixation mechanisms of these bacteria.

==Molecular Organism Database==
#
#J. Craig Venter Institute maintains the database
#No information given in terms of funding
#All information is publicly availible
#The database was last updated 2 years ago
#
#
#
#The site is well-organized. There is a tutorial section.
#

==Template==
[[Template:Team Name]]

Stephen Louie Week 11

2013-11-13T06:53:31Z

Slouie: Added more term definitions

==Terms==
*'''Induce''':to cause (something) to happen or exist
**Source:[[http://www.merriam-webster.com/dictionary/induce?show=0&t=1384324303 Merriam-Webster]]
*'''Replicon''':a linear or circular section of DNA or RNA which replicates sequentially as a unit
**Source:[[http://www.merriam-webster.com/dictionary/replicon Merriam-Webster]]
*'''Plasmid''':an extrachromosomal ring of DNA especially of bacteria that replicates autonomously
**Source:[[http://www.merriam-webster.com/dictionary/plasmid Merriam-Webster]]
*'''Mb''':mega base pairs = 1,000,000 bp
**Source:[[http://en.wikipedia.org/wiki/Megabase#Length_measurements Wikipedia]]
*'''α-probacterium''':a class of Proteobacteria. Proteobacteria are a major group (phylum) of bacteria.
**Source:[[http://en.wikipedia.org/wiki/Proteobacteria Wikipedia]]
*'''Paralogy''':shared ancestry caused by a gene duplication event in the genome.
**Source:[[http://en.wikipedia.org/wiki/Homology_(biology)#Paralogy Wikipedia]]
*'''Biosynthesis''':the production of a chemical compound by a living organism
**Source:[[http://www.merriam-webster.com/dictionary/biosynthesis?show=0&t=1384325587 Merriam-Webster]]
*'''Orthologs'''
*'''Endosymbionts'''
*'''Orphan genes'''

==Outline==
The Composite Genome of the Legume Symbiont Sinorhizobium meliloti
*Plant growth is reliant on the availability of usable nitrogen.
**Most nitrogen can only be found in soil or fertilizer.
* Rhizobia: aerobic gram-negative soil bacteria
** When plants are deprived of nitrogen, rhizobia are capable of establishing nitrogen-fixing symbiosis.
** Rhizobia infect roots to form root nodules. The bacteria then undergo nitrogen-fixation within the cell cytoplasm.
** Rhizobia and plant exchange signals during this process. The rhizobia continue to provide nitrogen to plant in exchange for plant carbon compounds
** Evolution in legumes has shown the ability to obtain nitrogen from rhizobia while growing in poor soils.
* Sinorhizobium meliloti: the rhizobia symbiont to alfalfa
** As an α-probacterium it is closely related to bacterial plant and animal pathogens
** Some topics of interest include: how microbe stimulates nodule formation, how it manages to invade plant without triggering immune system defenses, how and why microbe fixes nitrogen for the host as opposed to itself, and how bacterium maintains itself within the soil environment.
** Extensive genetic, biochemical, and metabolic research have already been done on it making it an ideal subject for genomic investigation.
** Sinorhizobium meliloti strain 1021 has been fully sequenced.
* The Sinorhizobium meliloti genome consists of three replicons
** One large replicon of 3.65 Mb and two smaller replicons pSymA (1.35 Mb) and pSymB (1.68 Mb).
** Genome is not highly repeated (A limited number of genes seem to be recently duplicated)
** 42% (2589) of Sinorhizobium meliloti genes belong to 548 paralogous families ranging from 2-134 genes per family.
** High paralogy levels indicate that genome size had very little limitation during its evolution. This means that the bacterium was able to gain new adaptive functions for living in the soil and plant-symbiosis.
** Insertion sequence and phage sequences compose 202% of genome with overall abundance on pSymA, particularly near symbiotic genes. This enforces the idea that symbiotic regions are subject to DNA rearrangements.
* The unusual size of pSymA and pSymB makes them difficult to determine whether they are plasmids or chromosomes.
** pSymA was shown to contain putative conjugate transfer genes traACDG and a putative oriT sequence found on other Rhizobial plasmids.
** Essential genes are found to be present on pSymB, showing it to be more chromosome-like.
* Genes encoding for transport systems compose the largest (12%) class of genes in the Sinorhizobium meliloti genome.
** Most of these (17.4%) are found on pSymB. Thus, pSymB is shown to be important for transporting small molecules.
* Regulatory genes make up 8.7% of the Sinorhizobium meliloti genome. The LysR family is prevalent on pSymA.
** Each replicon has a distinct regulatory gene profile.
** Sinorhizobium meliloti ecodes the most nucleotide cyclases of any bacterial genome
* It is not well known how rhizobia connect to plant hair.
** Surface polysaccharides (especially exopolysaccharides) are crucial for plant infection by suppressing the immune system of the plant.
** 12% of pSymB genes have been predicted to be involved with polysaccharide biosynthesis.
** Two new loci were found on the chromosome and nine on pSymB.
* Nodulation genes are found on pSymA
** Two well preserved duplications of nod genes in the genome were found. nodM is suggested to be recently duplicated from glmS.
** Sequence analysis hints that the origins of Sinorhizobium meliloti nod genes are either resident gene duplication or horizontal gene transfer mediated by import of pSymA from an unknown bacterium.
* Nitrogen metabolism is a major feature encoded by the Sinorhizobium meliloti genome, especially in pSymA.
** Only 9 nif genes were found in the genome. Most if not all of these genes were found on pSymA.
** pSymA also carries glutamate dehydrogenase, a subset of genes that are required for denitrification and nitrate transport.
* High levels of energy are necessary for Sinorhizobium meliloti to maintain nitrogen-fixation while in a low oxygen environment in the nodule.
** Both pSymA and the chromosome have been shown to carry a large NADH-ubiquinone dehydrogenase gene cluster that may enhance energy metabolism in symbiosis.
* Genome of Sinorhizobium meliloti was compared to the genome of M. loti
** 35% of M.loti genes had no ortholog in S. meliloti
** Megaplasmid genes in S. meliloti were spread out in the M. loti
** Aside from nitrogen-fixing and nodule forming genes, M. loti has no orthologs in S. meliloti
* Determination of S. meliloti 1021 shows that it has a composite structure consisting of three unique replicons of different architecture and service features.
** This is consistent with the hypothesis that both megaplasmids were inherited from an ancestor with a single chromosome.
** Acquirement of pSymB has increased the metabolic capacity considerably.
** Acquirement of pSymA also led to ability to nodulate, colonize low-oxygen environment of nodules, and metabolize nitrogen compounds under various chemical forms.
** Complete genome sequence allows for opportunities to study the rhizobium-legume symbiosis and the nitrogen-fixation mechanisms of these bacteria.

==Molecular Organism Database==
#
#J. Craig Venter Institute maintains the database
#No information given in terms of funding
#All information is publicly availible
#The database was last updated 2 years ago
#
#
#
#The site is well-organized. There is a tutorial section.
#

==Template==
[[Template:Team Name]]

Stephen Louie Week 11

2013-11-13T06:46:17Z

Slouie: Added more term definitions

==Terms==
*'''Induce''':to cause (something) to happen or exist
**Source:[[http://www.merriam-webster.com/dictionary/induce?show=0&t=1384324303 Merriam-Webster]]
*'''Replicon''':a linear or circular section of DNA or RNA which replicates sequentially as a unit
**Source:[[http://www.merriam-webster.com/dictionary/replicon Merriam-Webster]]
*'''Plasmid''':an extrachromosomal ring of DNA especially of bacteria that replicates autonomously
**Source:[[http://www.merriam-webster.com/dictionary/plasmid Merriam-Webster]]
*'''Mb''':mega base pairs = 1,000,000 bp
**Source:[[http://en.wikipedia.org/wiki/Megabase#Length_measurements Wikipedia]]
*'''α-probacterium''':a class of Proteobacteria. Proteobacteria are a major group (phylum) of bacteria.
**Source:[[http://en.wikipedia.org/wiki/Proteobacteria Wikipedia]]
*'''Paralogy'''
*'''Biosynthesis'''
*'''Orthologs'''
*'''Endosymbionts'''
*'''Orphan genes'''

==Outline==
The Composite Genome of the Legume Symbiont Sinorhizobium meliloti
*Plant growth is reliant on the availability of usable nitrogen.
**Most nitrogen can only be found in soil or fertilizer.
* Rhizobia: aerobic gram-negative soil bacteria
** When plants are deprived of nitrogen, rhizobia are capable of establishing nitrogen-fixing symbiosis.
** Rhizobia infect roots to form root nodules. The bacteria then undergo nitrogen-fixation within the cell cytoplasm.
** Rhizobia and plant exchange signals during this process. The rhizobia continue to provide nitrogen to plant in exchange for plant carbon compounds
** Evolution in legumes has shown the ability to obtain nitrogen from rhizobia while growing in poor soils.
* Sinorhizobium meliloti: the rhizobia symbiont to alfalfa
** As an α-probacterium it is closely related to bacterial plant and animal pathogens
** Some topics of interest include: how microbe stimulates nodule formation, how it manages to invade plant without triggering immune system defenses, how and why microbe fixes nitrogen for the host as opposed to itself, and how bacterium maintains itself within the soil environment.
** Extensive genetic, biochemical, and metabolic research have already been done on it making it an ideal subject for genomic investigation.
** Sinorhizobium meliloti strain 1021 has been fully sequenced.
* The Sinorhizobium meliloti genome consists of three replicons
** One large replicon of 3.65 Mb and two smaller replicons pSymA (1.35 Mb) and pSymB (1.68 Mb).
** Genome is not highly repeated (A limited number of genes seem to be recently duplicated)
** 42% (2589) of Sinorhizobium meliloti genes belong to 548 paralogous families ranging from 2-134 genes per family.
** High paralogy levels indicate that genome size had very little limitation during its evolution. This means that the bacterium was able to gain new adaptive functions for living in the soil and plant-symbiosis.
** Insertion sequence and phage sequences compose 202% of genome with overall abundance on pSymA, particularly near symbiotic genes. This enforces the idea that symbiotic regions are subject to DNA rearrangements.
* The unusual size of pSymA and pSymB makes them difficult to determine whether they are plasmids or chromosomes.
** pSymA was shown to contain putative conjugate transfer genes traACDG and a putative oriT sequence found on other Rhizobial plasmids.
** Essential genes are found to be present on pSymB, showing it to be more chromosome-like.
* Genes encoding for transport systems compose the largest (12%) class of genes in the Sinorhizobium meliloti genome.
** Most of these (17.4%) are found on pSymB. Thus, pSymB is shown to be important for transporting small molecules.
* Regulatory genes make up 8.7% of the Sinorhizobium meliloti genome. The LysR family is prevalent on pSymA.
** Each replicon has a distinct regulatory gene profile.
** Sinorhizobium meliloti ecodes the most nucleotide cyclases of any bacterial genome
* It is not well known how rhizobia connect to plant hair.
** Surface polysaccharides (especially exopolysaccharides) are crucial for plant infection by suppressing the immune system of the plant.
** 12% of pSymB genes have been predicted to be involved with polysaccharide biosynthesis.
** Two new loci were found on the chromosome and nine on pSymB.
* Nodulation genes are found on pSymA
** Two well preserved duplications of nod genes in the genome were found. nodM is suggested to be recently duplicated from glmS.
** Sequence analysis hints that the origins of Sinorhizobium meliloti nod genes are either resident gene duplication or horizontal gene transfer mediated by import of pSymA from an unknown bacterium.
* Nitrogen metabolism is a major feature encoded by the Sinorhizobium meliloti genome, especially in pSymA.
** Only 9 nif genes were found in the genome. Most if not all of these genes were found on pSymA.
** pSymA also carries glutamate dehydrogenase, a subset of genes that are required for denitrification and nitrate transport.
* High levels of energy are necessary for Sinorhizobium meliloti to maintain nitrogen-fixation while in a low oxygen environment in the nodule.
** Both pSymA and the chromosome have been shown to carry a large NADH-ubiquinone dehydrogenase gene cluster that may enhance energy metabolism in symbiosis.
* Genome of Sinorhizobium meliloti was compared to the genome of M. loti
** 35% of M.loti genes had no ortholog in S. meliloti
** Megaplasmid genes in S. meliloti were spread out in the M. loti
** Aside from nitrogen-fixing and nodule forming genes, M. loti has no orthologs in S. meliloti
* Determination of S. meliloti 1021 shows that it has a composite structure consisting of three unique replicons of different architecture and service features.
** This is consistent with the hypothesis that both megaplasmids were inherited from an ancestor with a single chromosome.
** Acquirement of pSymB has increased the metabolic capacity considerably.
** Acquirement of pSymA also led to ability to nodulate, colonize low-oxygen environment of nodules, and metabolize nitrogen compounds under various chemical forms.
** Complete genome sequence allows for opportunities to study the rhizobium-legume symbiosis and the nitrogen-fixation mechanisms of these bacteria.

==Molecular Organism Database==
#
#J. Craig Venter Institute maintains the database
#No information given in terms of funding
#All information is publicly availible
#The database was last updated 2 years ago
#
#
#
#The site is well-organized. There is a tutorial section.
#

==Template==
[[Template:Team Name]]

Stephen Louie Week 11

2013-11-13T06:37:21Z

Slouie: Added term definitions

==Terms==
*'''Induce''':to cause (something) to happen or exist
**Source:[[http://www.merriam-webster.com/dictionary/induce?show=0&t=1384324303 Merriam-Webster]]
*'''Replicon''':a linear or circular section of DNA or RNA which replicates sequentially as a unit
**Source:[[http://www.merriam-webster.com/dictionary/replicon Merriam-Webster]]
*'''Megaplasmid'''
*'''Mb'''
*'''α-probacterium'''
*'''Paralogy'''
*'''Biosynthesis'''
*'''Orthologs'''
*'''Endosymbionts'''
*'''Orphan genes'''

==Outline==
The Composite Genome of the Legume Symbiont Sinorhizobium meliloti
*Plant growth is reliant on the availability of usable nitrogen.
**Most nitrogen can only be found in soil or fertilizer.
* Rhizobia: aerobic gram-negative soil bacteria
** When plants are deprived of nitrogen, rhizobia are capable of establishing nitrogen-fixing symbiosis.
** Rhizobia infect roots to form root nodules. The bacteria then undergo nitrogen-fixation within the cell cytoplasm.
** Rhizobia and plant exchange signals during this process. The rhizobia continue to provide nitrogen to plant in exchange for plant carbon compounds
** Evolution in legumes has shown the ability to obtain nitrogen from rhizobia while growing in poor soils.
* Sinorhizobium meliloti: the rhizobia symbiont to alfalfa
** As an α-probacterium it is closely related to bacterial plant and animal pathogens
** Some topics of interest include: how microbe stimulates nodule formation, how it manages to invade plant without triggering immune system defenses, how and why microbe fixes nitrogen for the host as opposed to itself, and how bacterium maintains itself within the soil environment.
** Extensive genetic, biochemical, and metabolic research have already been done on it making it an ideal subject for genomic investigation.
** Sinorhizobium meliloti strain 1021 has been fully sequenced.
* The Sinorhizobium meliloti genome consists of three replicons
** One large replicon of 3.65 Mb and two smaller replicons pSymA (1.35 Mb) and pSymB (1.68 Mb).
** Genome is not highly repeated (A limited number of genes seem to be recently duplicated)
** 42% (2589) of Sinorhizobium meliloti genes belong to 548 paralogous families ranging from 2-134 genes per family.
** High paralogy levels indicate that genome size had very little limitation during its evolution. This means that the bacterium was able to gain new adaptive functions for living in the soil and plant-symbiosis.
** Insertion sequence and phage sequences compose 202% of genome with overall abundance on pSymA, particularly near symbiotic genes. This enforces the idea that symbiotic regions are subject to DNA rearrangements.
* The unusual size of pSymA and pSymB makes them difficult to determine whether they are plasmids or chromosomes.
** pSymA was shown to contain putative conjugate transfer genes traACDG and a putative oriT sequence found on other Rhizobial plasmids.
** Essential genes are found to be present on pSymB, showing it to be more chromosome-like.
* Genes encoding for transport systems compose the largest (12%) class of genes in the Sinorhizobium meliloti genome.
** Most of these (17.4%) are found on pSymB. Thus, pSymB is shown to be important for transporting small molecules.
* Regulatory genes make up 8.7% of the Sinorhizobium meliloti genome. The LysR family is prevalent on pSymA.
** Each replicon has a distinct regulatory gene profile.
** Sinorhizobium meliloti ecodes the most nucleotide cyclases of any bacterial genome
* It is not well known how rhizobia connect to plant hair.
** Surface polysaccharides (especially exopolysaccharides) are crucial for plant infection by suppressing the immune system of the plant.
** 12% of pSymB genes have been predicted to be involved with polysaccharide biosynthesis.
** Two new loci were found on the chromosome and nine on pSymB.
* Nodulation genes are found on pSymA
** Two well preserved duplications of nod genes in the genome were found. nodM is suggested to be recently duplicated from glmS.
** Sequence analysis hints that the origins of Sinorhizobium meliloti nod genes are either resident gene duplication or horizontal gene transfer mediated by import of pSymA from an unknown bacterium.
* Nitrogen metabolism is a major feature encoded by the Sinorhizobium meliloti genome, especially in pSymA.
** Only 9 nif genes were found in the genome. Most if not all of these genes were found on pSymA.
** pSymA also carries glutamate dehydrogenase, a subset of genes that are required for denitrification and nitrate transport.
* High levels of energy are necessary for Sinorhizobium meliloti to maintain nitrogen-fixation while in a low oxygen environment in the nodule.
** Both pSymA and the chromosome have been shown to carry a large NADH-ubiquinone dehydrogenase gene cluster that may enhance energy metabolism in symbiosis.
* Genome of Sinorhizobium meliloti was compared to the genome of M. loti
** 35% of M.loti genes had no ortholog in S. meliloti
** Megaplasmid genes in S. meliloti were spread out in the M. loti
** Aside from nitrogen-fixing and nodule forming genes, M. loti has no orthologs in S. meliloti
* Determination of S. meliloti 1021 shows that it has a composite structure consisting of three unique replicons of different architecture and service features.
** This is consistent with the hypothesis that both megaplasmids were inherited from an ancestor with a single chromosome.
** Acquirement of pSymB has increased the metabolic capacity considerably.
** Acquirement of pSymA also led to ability to nodulate, colonize low-oxygen environment of nodules, and metabolize nitrogen compounds under various chemical forms.
** Complete genome sequence allows for opportunities to study the rhizobium-legume symbiosis and the nitrogen-fixation mechanisms of these bacteria.

==Molecular Organism Database==
#
#J. Craig Venter Institute maintains the database
#No information given in terms of funding
#All information is publicly availible
#The database was last updated 2 years ago
#
#
#
#The site is well-organized. There is a tutorial section.
#

==Template==
[[Template:Team Name]]

Stephen Louie Week 11

2013-11-13T06:19:58Z

Slouie: added more terms

==Terms==
*Induce
*Replicon
*Megaplasmid
*Mb
*α-probacterium
*Paralogy
*Biosynthesis
*Orthologs
*Endosymbionts
*Orphan genes

==Outline==
The Composite Genome of the Legume Symbiont Sinorhizobium meliloti
*Plant growth is reliant on the availability of usable nitrogen.
**Most nitrogen can only be found in soil or fertilizer.
* Rhizobia: aerobic gram-negative soil bacteria
** When plants are deprived of nitrogen, rhizobia are capable of establishing nitrogen-fixing symbiosis.
** Rhizobia infect roots to form root nodules. The bacteria then undergo nitrogen-fixation within the cell cytoplasm.
** Rhizobia and plant exchange signals during this process. The rhizobia continue to provide nitrogen to plant in exchange for plant carbon compounds
** Evolution in legumes has shown the ability to obtain nitrogen from rhizobia while growing in poor soils.
* Sinorhizobium meliloti: the rhizobia symbiont to alfalfa
** As an α-probacterium it is closely related to bacterial plant and animal pathogens
** Some topics of interest include: how microbe stimulates nodule formation, how it manages to invade plant without triggering immune system defenses, how and why microbe fixes nitrogen for the host as opposed to itself, and how bacterium maintains itself within the soil environment.
** Extensive genetic, biochemical, and metabolic research have already been done on it making it an ideal subject for genomic investigation.
** Sinorhizobium meliloti strain 1021 has been fully sequenced.
* The Sinorhizobium meliloti genome consists of three replicons
** One large replicon of 3.65 Mb and two smaller replicons pSymA (1.35 Mb) and pSymB (1.68 Mb).
** Genome is not highly repeated (A limited number of genes seem to be recently duplicated)
** 42% (2589) of Sinorhizobium meliloti genes belong to 548 paralogous families ranging from 2-134 genes per family.
** High paralogy levels indicate that genome size had very little limitation during its evolution. This means that the bacterium was able to gain new adaptive functions for living in the soil and plant-symbiosis.
** Insertion sequence and phage sequences compose 202% of genome with overall abundance on pSymA, particularly near symbiotic genes. This enforces the idea that symbiotic regions are subject to DNA rearrangements.
* The unusual size of pSymA and pSymB makes them difficult to determine whether they are plasmids or chromosomes.
** pSymA was shown to contain putative conjugate transfer genes traACDG and a putative oriT sequence found on other Rhizobial plasmids.
** Essential genes are found to be present on pSymB, showing it to be more chromosome-like.
* Genes encoding for transport systems compose the largest (12%) class of genes in the Sinorhizobium meliloti genome.
** Most of these (17.4%) are found on pSymB. Thus, pSymB is shown to be important for transporting small molecules.
* Regulatory genes make up 8.7% of the Sinorhizobium meliloti genome. The LysR family is prevalent on pSymA.
** Each replicon has a distinct regulatory gene profile.
** Sinorhizobium meliloti ecodes the most nucleotide cyclases of any bacterial genome
* It is not well known how rhizobia connect to plant hair.
** Surface polysaccharides (especially exopolysaccharides) are crucial for plant infection by suppressing the immune system of the plant.
** 12% of pSymB genes have been predicted to be involved with polysaccharide biosynthesis.
** Two new loci were found on the chromosome and nine on pSymB.
* Nodulation genes are found on pSymA
** Two well preserved duplications of nod genes in the genome were found. nodM is suggested to be recently duplicated from glmS.
** Sequence analysis hints that the origins of Sinorhizobium meliloti nod genes are either resident gene duplication or horizontal gene transfer mediated by import of pSymA from an unknown bacterium.
* Nitrogen metabolism is a major feature encoded by the Sinorhizobium meliloti genome, especially in pSymA.
** Only 9 nif genes were found in the genome. Most if not all of these genes were found on pSymA.
** pSymA also carries glutamate dehydrogenase, a subset of genes that are required for denitrification and nitrate transport.
* High levels of energy are necessary for Sinorhizobium meliloti to maintain nitrogen-fixation while in a low oxygen environment in the nodule.
** Both pSymA and the chromosome have been shown to carry a large NADH-ubiquinone dehydrogenase gene cluster that may enhance energy metabolism in symbiosis.
* Genome of Sinorhizobium meliloti was compared to the genome of M. loti
** 35% of M.loti genes had no ortholog in S. meliloti
** Megaplasmid genes in S. meliloti were spread out in the M. loti
** Aside from nitrogen-fixing and nodule forming genes, M. loti has no orthologs in S. meliloti
* Determination of S. meliloti 1021 shows that it has a composite structure consisting of three unique replicons of different architecture and service features.
** This is consistent with the hypothesis that both megaplasmids were inherited from an ancestor with a single chromosome.
** Acquirement of pSymB has increased the metabolic capacity considerably.
** Acquirement of pSymA also led to ability to nodulate, colonize low-oxygen environment of nodules, and metabolize nitrogen compounds under various chemical forms.
** Complete genome sequence allows for opportunities to study the rhizobium-legume symbiosis and the nitrogen-fixation mechanisms of these bacteria.

==Molecular Organism Database==
#
#J. Craig Venter Institute maintains the database
#No information given in terms of funding
#All information is publicly availible
#The database was last updated 2 years ago
#
#
#
#The site is well-organized. There is a tutorial section.
#

==Template==
[[Template:Team Name]]