Team:Johns Hopkins/Notebook

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Latest revision as of 04:50, 30 October 2008

Groups

iGEM Groups 1.0
iGEM Groups 2.01
iGEM Groups 2.02

Important reminders and notes

[Make general comments here, so they don't get lost in peoples e-mail boxes]

July 11: Primers for group 1 were delivered yesterday.
July 11: Lab meeting at 7:30PM in the lab to go over miniprep protocol.
July 15: Lab meeting at 6:30PM with Jessica. Have status reports ready.
Bring labtop if you can.
July 17: Restriction Digest/Sequencing Preparation (with James) 6:00PM.
July 21: 6:00PM or 6:30PM Lab meeting with Jessica. Have status reports ready.
July 29: 7:00PM Lab Meeting. Meet in Conference Room across from lab. Have Status Reports ready
Aug. 05: 7:00PM Lab Meeting. Meet in Conference Room across from lab. Have Status Reports ready.
Aug. 12: 7:00PM Lab Meeting. Have Status Reports Ready.
Journal Club Topic: Fluorescent Proteins; James and Ingrid.
Aug. 19: 7:00PM Lab Meeting. Have Status Reports Ready.
Journal Club Topic: Yeast Mating Pathway/MAP Kinase Pathway ; Jasper and Tejas
Aug. 26: 7:00PM Lab Meeting. Have Status Reports Ready!
Journal Club Topic: S. cerevisiae Promoters; Allison and Nate

EVERY TUESDAY 7 PM LAB MEETING! Mudd 120

September: Do well in classes. Do what you can for the team when you can.

October: Do well on midterms. Good Luck!!

Oct. 28, 2008: 7:00 PM Lab Meeting,
REALLY IMPORTANT LAB MEETING. SHOW UP. BRING SUMMARIES.
FINAL DAY BEFORE WIKI FREEZES.

Nov. 4, 2008: 7:00 PM Lab Meeting,
REALLY IMPORTANT LAB MEETING. SHOW UP.
LAST LAB MEETING. PRESENTATION PRACTICE AND PREP FOR TRAVEL

Journal Club

8/12/08:Fluorescent Proteins- Ingrid and James
Fluorescent Protein Powerpoint
Paper: Green Fluorescent Protein as a Marker for Gene Expression

8/19/08: Yeast Mating Pathway/MAP Kinase Pathway- Jasper and Tejas
MAP Kinase Powerpoint , Paper: Map Kinase Scaffold

8/26/08: Yeast Promoters- Allison and Nate
Gene structure powerpoint
Paper:
Genomic Footprinting of the Promoter Regions of STE2 and STE3 genes in the Yeast Saccharomyces cerevisiae
Additional Reading:
Interspecies variation reveals a conserved repressor of alpha-specific genes in Saccharomyces yeast
A genomic code for nucleosome positioning

09/02/08: Mating Type Regulation -Brian and Jonathan
Papers:
Herskowitz- A Regularory Hierarchy for Cell Specialization in Yeast

09/09/08: Yeast as a model organism- Ambhi and Raghav
Yeast as a model organism (ppt presentation)
Papers:
Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis
The original Yeast two hybrid paper

Data

To upload data, go here, click on upload data, and provide the necessary information and results.

How to submit data:

1. log-in as you once had to from the www.jhu.edu/iGEM website "login"

User: ****** etc...
Pass: ***** etc...

2. click on UPLOAD DATA from the 'x-files page'
3. add data etc.... and click submit: This generates a webpage and the URL to it is linked in the page you are directed to after you press submit. Copy that URL and past it into the wiki or into the web-browser url box to see what it looks like.
\* If you find that the picture you are uploading is not showing up e-mail Tejas.

Alternatively, you can also just upload files directly to the iGEM wiki. Either way is fine.

Status Reports

The status reports of each group below were continuously updated as we worked on the biobricks.
Click on the name of each group to find past status reports throughout the sex detector project.

To learn more about each biobrick, please refer to the Biobrick page.

GROUP 1: Fluorescent Proteins

Summary for Fluorescent Proteins Group

 Venus YFP (BBa_K110021) was able to be constructed and sequence verified(with one possible
 mutation), however due to being unable to RE digest the insert out of the biobrick
 vector, possibly due to contamination,  the part was not sumbittied to the registry... yet.
 We will submit it after it is verified, after the competition.
 
 To see info about this biobrick check out oru patrs:
 http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2008&group=Johns_Hopkins

GROUP 2: MATa Specific-promoters

Summary for MATa Specific Promoters Group

 We were able to produce sequence-verified clones of BBa_K110008 and BBa_K110016:
 http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2008&group=Johns_Hopkins .

GROUP 3: Short Two-Way Stops

 We were able to produce a truncated two-way terminator (thus a one way) 
 from the STE2 gene - BBa_K110012. Please see Link for information:
 http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2008&group=Johns_Hopkins

GROUP 4: Long Two-Way Stops & MAT(alpha) Specific Promoters

Summary for Long Two-Way Stops & MAT(alpha) Specific Promoters Group

 We were able to produce BBa_K110005 and BBa_K110006 (alpha Promoters) in iGEM vectors.
 Also BBa_K110003 was able to be produced and sequence verified. Check out these parts here
 http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2008&group=Johns_Hopkins

GROUP 5: MATa Specific Promoters II

Summary for MATa Specific Promoters II Group

 Part Description: Ste2 Promoter Reverse
 Summary here: We were able to grow colonies with sequence verified Ste2 promoters. 
   The promoter is currently located in a glycerol stock in pGEM vector. One attempt to 
   transfer to the iGEM vector has been made, unsuccessfully. This was due to a mistake 
   in protocol however, so final transfer to the iGEM vector should still be straightforward. 
   Progress on this bio-brick has been paused in order to focus on MFA1, which is more 
   applicable to our project design because this Ste2 designed for the wrong direction.
 
 Part no.: BBa_K110015
 Part Description: MFA1 Promoter Forward
 Summary here: We have been unable to get successful, sequence verified clones with 
   our MFA1 promoter thus far. We currently have a few samples of DNA ready to be tested 
   by restriction enzyme digest, and then, hopefully, sequencing.

For more information about the parts go to: 
http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2008&group=Johns_Hopkins

GROUP 6: Vectors

Summary for Vectors Group

 Date: July 31, 2008
 Status report by: Tejas
 Part no.: BBa_K1100XX -> BBa_K1100YY
 Part Description: Vectors for concatenating and executing BioBricks
 
 The vectors to be used were delivered to us in STABS from MIT. They are pSB4A5 (amp), pSB4C5
 (cam), pSB3K5 (kan), and pSB4K5 (kan). The vectors come pre-inserted with the ccdB gene,
 preventing growth in all E. coli strains except DB3.1. Total amount of DNA extracted from mini
 -prep is estimated between 5 to 20 ug per vector. Restriction digests confirmed the extracted
 DNA was vectors.(Digestion of all four vectors).
 Vectors were transformed into JM109, BB#2198 (DB3.1), and BB#5777 (DB3.1). All gave expected
 results. 1 ug of each vector was digested for future use. Gel of digestion shows DNA is correct.
 (Vectors ready for insertions)

GROUP 7: Microscopy/Yeast

Summary for Microscopy/Yeast Group

 Date: Oct 27, 2008
 Status report by: Tejas
 Part no.: no Biobrick part
 Part Description: Yeast vector pRS414 to be temporarily used.
 
 The yeast vector pRS414 will be temporarily used until it can be adjusted to meet registry 
 standards. pRS414 contains one EcoRI site and one PstI site, both directly adjacent to each 
 other. This may make digest a little less efficient. Procedure involves first digesting with 
 Pst1 for one hour, then digesting with EcoRI overnight (sequentially, not simultaneously), as 
 EcoRI can tolerate low overhangs better than PstI, according to the NEB catalog. The following 
 is a gel run on an E/P simultaneous digest of pRS414.
 Lane one is log 2 ladder. Lane 2 is uncut pRS414 (supercoiled so runs fater). Lane 3 is cut 
 vector. It may have only one cut, with half at EcoRI and half at PstI, depending on efficiency of 
 the second cut occuring after the first.

 pRS414 digest

GROUP 8: Assembly Progress

Summary of Biobrick Assemblies:

 Planned Schedule for Further Work:

 October 31st- Successful transformants from either set of ligations (of Promoter + Fluorescent 
 Protein) and transformations will be grown up for Miniprep. 

 November 1st- These pieces will be miniprepped and digested.  Digested fragments will be ligated 
 together with the terminator in the middle, into a pRS414 yeast/bacterial shuttle vector.  
 Non-digested fragments of a promoter + fluorescent protein will also individually be transformed 
 into yeast, with hopes that they will fluoresce.

 November 3rd- Full construct insert will be transformed into yeast, pending identity verification.

 November 6th- Pretty Yeast! (Hopefully).

@@ Line 1: / Line 1: @@
-<html>
+{{JHU}}
-<head>
+== Groups ==
-	<style>
+[[Media:JHU_0708_IGEMgroups.pdf|iGEM Groups 1.0]]<br>
-		#globalWrapper {
+[[Media:JHU_iGEM_groups2.01.pdf|iGEM Groups 2.01]]<br>
-			 margin: 0px;
+[[Media:JHU_iGEM_groups2.02.pdf|iGEM Groups 2.02]]<br>
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-		div#header a {
-			bottom: 0px;
-			margin: 65px 0 0 0;
-		}
-                /*div#header a#Biobrick{margin-right:20px;}*/
-		/* leftcol nav */
+== Important reminders and notes ==
-		#Home { background-image: url(https://static.igem.org/mediawiki/2008/b/bd/JHU_0708_HomeB.gif); }
+  [Make general comments here, so they don't get lost in peoples e-mail boxes]
-		#Home:hover { background-image: url(https://static.igem.org/mediawiki/2008/0/06/JHU_0708_HomeH.gif); }
-		#People { background-image: url(https://static.igem.org/mediawiki/2008/1/1b/JHU_0708_PeopleB.gif); }
+  July 11: Primers for group 1 were delivered yesterday.
-		#People:hover { background-image: url(https://static.igem.org/mediawiki/2008/8/87/JHU_0708_PeopleH.gif); }
+  July 11: Lab meeting at 7:30PM in the lab to go over miniprep protocol.
-		#Money { background-image: url(https://static.igem.org/mediawiki/2008/6/6b/JHU_0708_MoneyB.gif); }
+  July 15: Lab meeting at 6:30PM with Jessica. Have status reports ready.
-		#Money:hover { background-image: url(https://static.igem.org/mediawiki/2008/1/16/JHU_0708_MoneyH.gif); }
+           Bring labtop if you can.
+  July 17: Restriction Digest/Sequencing Preparation (with James) 6:00PM.
+  July 21: 6:00PM or 6:30PM Lab meeting with Jessica. Have status reports ready.
+  July 29: 7:00PM Lab Meeting. Meet in Conference Room across from lab. Have Status Reports ready
+  Aug. 05: 7:00PM Lab Meeting. Meet in Conference Room across from lab. Have Status Reports ready.
+  Aug. 12: 7:00PM Lab Meeting. Have Status Reports Ready.
+                Journal Club Topic: Fluorescent Proteins; James and Ingrid.
+  Aug. 19: 7:00PM Lab Meeting. Have Status Reports Ready.
+                Journal Club Topic: Yeast Mating Pathway/MAP Kinase Pathway ; Jasper and Tejas
+  Aug. 26: 7:00PM Lab Meeting. Have Status Reports Ready!
+                Journal Club Topic: ''S. cerevisiae'' Promoters; Allison and Nate
+  EVERY TUESDAY 7 PM LAB MEETING! Mudd 120
+  September: Do well in classes. Do what you can for the team when you can.
+  October: Do well on midterms. Good Luck!!
+  Oct. 28, 2008: 7:00 PM Lab Meeting,
+                <b>REALLY IMPORTANT LAB MEETING. SHOW UP. BRING SUMMARIES.
+                FINAL DAY BEFORE WIKI FREEZES.</b>
+  Nov. 4, 2008: 7:00 PM Lab Meeting,
+                <b>REALLY IMPORTANT LAB MEETING. SHOW UP.
+                LAST LAB MEETING. PRESENTATION PRACTICE AND PREP FOR TRAVEL</b>
-		/* header nav */
+== Journal Club ==
-		#Research { background-image: url(https://static.igem.org/mediawiki/2008/0/04/JHU_0708_ResearchB.gif); }
+<html>
-		#Research:hover { background-image: url(https://static.igem.org/mediawiki/2008/2/20/JHU_0708_ResearchH.gif); }
+/12/08:<b>Fluorescent Proteins</b>- Ingrid and James<br>
-		#Notebook { background: url(https://static.igem.org/mediawiki/2008/4/47/JHU_0708_NotebookB.gif); }
+</html>
-		#Notebook:hover { background: url(https://static.igem.org/mediawiki/2008/1/11/JHU_0708_NotebookH.gif) }
+[[Media:JHU_Fluorescent_Protein_Journal_Club.ppt| Fluorescent Protein Powerpoint]] <br> Paper: [[Media:Green_Fluorescent_Protein_as_a_Marker_for_Gene_Expression.pdf|Green Fluorescent Protein as a Marker for Gene Expression]]<br>
-		#Biobrick { background: url(https://static.igem.org/mediawiki/2008/0/05/JHU_0708_BiobrickB.gif);}
+<html><br>
-		#Biobrick:hover { background: url(https://static.igem.org/mediawiki/2008/8/8c/JHU_0708_BiobrickH.gif); }
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-		#Protocols:hover { background: url(https://static.igem.org/mediawiki/2008/a/a3/JHU_0708_ProtocolH.gif); }
-		#book {
+/19/08: <b>Yeast Mating Pathway/MAP Kinase Pathway-</b> Jasper and Tejas<br>
-			float: top;
+</html>
-			background: #FFFF99;
+[[Media:MAPK_Pathway.ppt | MAP Kinase Powerpoint]] , Paper: [[Media:MapK_Scaffold_SynBio_Paper.pdf | Map Kinase Scaffold]]<br>
-			width: 750px;
+<html><br>
-			/*height: 85%;*/
-			border: 10px solid #FFFF99;
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-	</style>
-</head>
-<body>
+/26/08: <b>Yeast Promoters</b>- Allison and Nate<br>
-	<div id="header">
+</html>
-           <div id="divholder">
+[[Media:Gene_sturucture_powerpoint.ppt| Gene structure powerpoint]]<br>
-                <div id="name"><font class=ir></font></div>
+Paper:<br>[[Media:Genomic_Footprinting_of_the_Promoter_Regions_of_STE2_and_STE3_genes_in_the_Yeast_Saccharomyces_cerevisiae.pdf| Genomic Footprinting of the Promoter Regions of STE2 and STE3 genes in the Yeast Saccharomyces cerevisiae]]<br>
-		<a href="https://2008.igem.org/Team:Johns_Hopkins/Biobricks" id="Biobrick"></a>
+Additional Reading: <br>[[Media:JHU_0808_Interspeciesvariation.pdf‎|Interspecies variation reveals a conserved repressor of alpha-specific genes in Saccharomyces yeast]]<br>
-		<a href="https://2008.igem.org/Team:Johns_Hopkins/Protocols" id="Protocols"></a>
+[[Media:JHU_0808_Agenomiccode.pdf|A genomic code for nucleosome positioning]]
-                <a href="https://2008.igem.org/Team:Johns_Hopkins/Research" id="Research"></a>
+<html><br>
-                <a href="https://2008.igem.org/Team:Johns_Hopkins/Notebook" id="Notebook"></a>
+<br>
-           </div>
-	</div>
-	<div id="leftcol">
+/02/08: <b> Mating Type Regulation </b>-Brian and Jonathan <br>
-		<a href="https://2008.igem.org/Team:Johns_Hopkins" id="Home"></a>
+Papers:  <br></html>
-		<a href="https://2008.igem.org/Team:Johns_Hopkins/Team" id="People"></a>
+[[Media:JHU_0708_paper_Aregularoryheirarchy.pdf|Herskowitz- A Regularory Hierarchy for Cell Specialization in Yeast]]<br>
-		<a href="Donations" id="Money"></a>
+<html>
-	</div>
+<br>
+/09/08: <b>Yeast as a model organism</b>- Ambhi and Raghav<br>
+</html>
+[[Media:Model organism.ppt| Yeast as a model organism (ppt presentation)]]<br>
+Papers:<br>
+[[Media:Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis.pdf| Functional characterization of the ''S. cerevisiae'' genome by gene deletion and parallel analysis ]]<br>
+[[Media:A novel genetic system to study protein protein interactions.pdf‎|The original Yeast two hybrid paper]]<br>
+<html><br>
-	<div id="book"><h1>Notebook</h1>
-			<font class=ir>
 </html>
-== Files ==
-[[Media:JHU_0708_IGEMgroups.pdf|iGEM Groups V1.0]]<br>
-[[Media:JHU_iGEM_groups2.01.pdf|iGEM Groups V2.01]]
-== Important reminders and notes ==
+== Data ==
-  [Can make general comments here, so they don't get lost in peoples e-mail boxes]<br>
-  July-11:
+To upload data, go <b>[http://www.jhu.edu/iGEM/X_files/Read2.html here]</b>, click on <b>[http://www.jhu.edu/iGEM/X_files/Read2.html upload data]</b>, and provide the necessary information and results.
-  Primers for group 1 were delivered yesterday<br>
-  July 11:
+<b><h5>How to submit data:</h5></b>
-  Lab meeting at 7:30PM in the lab to go over miniprep protocol<br>
+. log-in as you once had to from the www.jhu.edu/iGEM website "login"
-  Tuesday July 15:
+*User: ****** etc...
-  Lab meeting at 6:30PM with Jessica. Have status reports ready.<br>
+*Pass: ***** etc...<br>
+. click on UPLOAD DATA from the 'x-files page'<br>
+. add data etc.... and click submit: This generates a webpage and the URL to it is linked in the page you are directed to after you press submit. Copy that URL and past it into the wiki or into the web-browser url box to see what it looks like.<br>
+\* If you find that the picture you are uploading is not showing up e-mail Tejas.
+Alternatively, you can also just upload files directly to the iGEM wiki. Either way is fine.
 == Status Reports ==
-=== GROUP 1: Fluorescent Proteins ===
-  status report by: Ingrid (work done by James)
+The status reports of each group below were continuously updated as we worked on the biobricks.<br>
-  Part no.: BBa_K110017
+<b>Click on the name of each group to find past status reports throughout the sex detector project.</b>
-  Part Description: yESapphire RtL
-   Part Location (in build a genome lab): In James and Jasper's PCR product Box,
+To learn more about each biobrick, please refer to the [[Team:Johns_Hopkins/Biobricks|Biobrick]] page.
-   Stainless Steel 4 degree
-   PCR successful?; Yes
-   Cloning of PCR product successful: Y/N
-   Sequencing of cloned PCR product successful: Not done
+=== [[Team:Johns Hopkins/Notebook/GROUP 1: Fluorescent Proteins | GROUP 1: Fluorescent Proteins]] ===
-   Joining of validated part to adjacent part(s) status: Not done
-   Problems to be solved: The PCR of this part yielded a very large product
+	<b>Summary for Fluorescent Proteins Group</b>
-   Current status of this part:
+   Venus YFP (BBa_K110021) was able to be constructed and sequence verified(with one possible
+  mutation), however due to being unable to RE digest the insert out of the biobrick
+   vector, possibly due to contamination,  the part was not sumbittied to the registry... yet.
+   We will submit it after it is verified, after the competition.
+   To see info about this biobrick check out oru patrs:
+   http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2008&group=Johns_Hopkins
+=== [[Team:Johns Hopkins/Notebook/GROUP 2: MATa Specific-promoters | GROUP 2: MATa Specific-promoters]] ===
+<b>Summary for MATa Specific Promoters Group</b>
+   We were able to produce sequence-verified clones of BBa_K110008 and BBa_K110016:
+   http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2008&group=Johns_Hopkins .
+=== [[Team:Johns Hopkins/Notebook/GROUP 3: Short two way stops | GROUP 3: Short Two-Way Stops]] ===
-   status report by: Ingrid (work done by James)
+   We were able to produce a truncated two-way terminator (thus a one way)
-   Part no.: BBa_K110010
+   from the STE2 gene - BBa_K110012. Please see Link for information:
-   Part Description: yESapphire LtR
+   http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2008&group=Johns_Hopkins
-  Part Location (in build a genome lab): In James and Jasper's PCR product Box,
-  Stainless Steel 4 degree
-  PCR successful?; Yes
-  Cloning of PCR product successful: Not done
-  Sequencing of cloned PCR product successful: No
-  Joining of validated part to adjacent part(s) status: Not done
-  Problems to be solved: The PCR of this part yielded a very large product
-  Current status of this part:
-=== GROUP 2: MATa Specific-promoters ===
+=== [[Team:Johns Hopkins/Notebook/GROUP 4: Long Two-way Stops & Mat(alpha) specific promoters | GROUP 4: Long Two-Way Stops & MAT(alpha) Specific Promoters]] ===
-  Status report by Allison and Nate
+<b>Summary for Long Two-Way Stops & MAT(alpha) Specific Promoters Group</b>
-  Part no.: BBa_K110008
-  Part Description: MFA1 (L+R)
-  Part Location: in a labeled box, second shelf from the top, -20
-  degrees C refrigerator next to front door
-  Date: 7/10/08
-  PCR successful? Yes
-  Cloning of PCR product successful: in progress
-  Sequencing of cloned PCR product successful: not done
-  Joining of validated part to adjacent part(s) status: not done
-  Problems to be solved: to be determined
-  Current status of this part: PCR was being troubleshooted, appeared to
-  have good results with regular PCR protocol (not touchdown) in which
-  there was a constant annealing temperature of 55 degrees C - see gel
-   Status report by Allison and Nate
+   We were able to produce BBa_K110005 and BBa_K110006 (alpha Promoters) in iGEM vectors.
-  Part no.: BBa_K110016
+   Also BBa_K110003 was able to be produced and sequence verified. Check out these parts here
-  Part Description: Ste2 (R+L)
+   http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2008&group=Johns_Hopkins
-  Part Location: in a labeled box, second shelf from the top, -20
-   degrees C refrigerator next to front door
-   Date: 7/10/08
-  PCR successful? Yes
-  Cloning of PCR product successful: in progress
-  Sequencing of cloned PCR product successful: not done
-  Joining of validated part to adjacent part(s) status: not done
-  Problems to be solved: to be determined
-  Current status of this part: Both PCR protocols (touchdown and second
-  PCR with constant annealing temperature) produced product of the
-  correct size. BBa_K110016 was used as a control in the second PCR with
-  BBa_K110008.
-=== GROUP 3: Short two way stops ===
+=== [[Team:Johns Hopkins/Notebook/GROUP 5: MATa Specific Promoters II | GROUP 5: MATa Specific Promoters II]] ===
-  Date: 7/11/08
+<b>Summary for MATa Specific Promoters II Group</b>
-  status report by: James
+   Part Description: Ste2 Promoter Reverse
-   Part no.: BBa_K110011
+   Summary here: We were able to grow colonies with sequence verified Ste2 promoters.
-   Part Description: Between-bud 27-W FRS2-C LtR
+    The promoter is currently located in a glycerol stock in pGEM vector. One attempt to
-  Part Location (in build a genome lab): In James and Jasper's PCR product Box,
+    transfer to the iGEM vector has been made, unsuccessfully. This was due to a mistake
-   Stainless Steel 4 degree
+    in protocol however, so final transfer to the iGEM vector should still be straightforward.
-  PCR successful?; Yes
+    Progress on this bio-brick has been paused in order to focus on MFA1, which is more
-  Cloning of PCR product successful: Yes (will come soon; I can put it
+    applicable to our project design because this Ste2 designed for the wrong direction.
-   in the wiki to make it easier for you)
-   Sequencing of cloned PCR product successful: No
+   Part no.: BBa_K110015
-   Joining of validated part to adjacent part(s) status: Not done
+   Part Description: MFA1 Promoter Forward
-   Problems to be solved:
+   Summary here: We have been unable to get successful, sequence verified clones with
-   Current status of this part:  Miniprep of Overnight
+    our MFA1 promoter thus far. We currently have a few samples of DNA ready to be tested
-   cultures will be completed today
+    by restriction enzyme digest, and then, hopefully, sequencing.
-  status report by: James
+ For more information about the parts go to:
-  Part no.: BBa_K110012
+ http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2008&group=Johns_Hopkins
-  Part Description: Between STE2-W and BST1-C LtR
-  Part Location (in build a genome lab): In James and Jasper's PCR product Box,
-   Stainless Steel 4 degree
-  PCR successful?; Yes
-  Cloning of PCR product successful: Yes (will come soon; I can put it in the
-   wiki to make it easier for you)
-  Sequencing of cloned PCR product successful: No
-  Joining of validated part to adjacent part(s) status: Not done
-  Problems to be solved:
-  Current status of this part:  Miniprep of Overnight cultures will be completed today
-  status report by: James
+=== [[Team:Johns Hopkins/Notebook/GROUP 6: Vectors | GROUP 6: Vectors]] ===
-  Part no.: BBa_K110013
-  Part Description: Between-SWP82-W and EMP47-C LtR
-  Part Location (in build a genome lab): In James and Jasper's PCR product Box,
-   Stainless Steel 4 degree
-  PCR successful?; No
-  Cloning of PCR product successful: No (will come soon; I can put it in the wiki
-   to make it easier for you)
-  Sequencing of cloned PCR product successful: No
-  Joining of validated part to adjacent part(s) status: Not done
-  Problems to be solved: The PCR of this part yielded a very large product
-  Current status of this part:
-=== GROUP 4: Long Two-way Stops & Mat(alpha) specific promotors ===
+<b>Summary for Vectors Group</b>
-  [Jaime- Please split]
-   Date: 7/10/08
+   Date: July 31, 2008
-   Status report by: Jaime Liu
+   Status report by: Tejas
-   Part no.: BBa_K110001, BBa_K110003, BBa_K110005, BBa_K110006
+   Part no.: BBa_K1100XX -> BBa_K1100YY
-   Part Description:
+   Part Description: Vectors for concatenating and executing BioBricks
-  BBa_K110001 - Between-bud 27-W FRS2-C + 200bp into each gene LtR
-  BBa_K110003 - Between-SWP82-W and EMP47-C +200 into each gene LtR
+   The vectors to be used were delivered to us in STABS from MIT. They are pSB4A5 (amp), pSB4C5
-   BBa_K110005 - MFalpha2 LtR
+   (cam), pSB3K5 (kan), and pSB4K5 (kan). The vectors come pre-inserted with the ccdB gene,
-   BBa_K110006 - MFalpha1 LtR
+   preventing growth in all E. coli strains except DB3.1. Total amount of DNA extracted from mini
-  Part Location (in build a genome lab): In 4C fridge #2
+  -prep is estimated between 5 to 20 ug per vector. Restriction digests confirmed the extracted
-   PCR successful?; Y/N (link such as this)- Yes
+   DNA was vectors.<b>([http://www.jhu.edu/iGEM/Group6:Vectors/2008-7-24.Vectors%20(CAM,AMP,KAN3,KAN4)%20after%20Digest.Tejas.html Digestion of all four vectors])</b>.
-  BBa_K110001, BBa_K110003:
+   Vectors were transformed into JM109, BB#2198 (DB3.1), and BB#5777 (DB3.1). All gave expected
-   http://baderlab.bme.jhu.edu:8888/moodle18/mod/data/view.php?d=4&rid=1462
+   results. 1 ug of each vector was digested for future use. Gel of digestion shows DNA is correct.
-   http://baderlab.bme.jhu.edu:8888/moodle18/mod/data/view.php?d=4&rid=1463
+  <b>([http://www.jhu.edu/iGEM/Group6:Vectors/2008-8-12.Digest%20of%20vectors,%20ready%20for%20distribution.Tejas.html Vectors ready for insertions])</b>
-   BBa_K110005, BBa_K110006:
-   http://baderlab.bme.jhu.edu:8888/moodle18/mod/data/view.php?d=4&rid=1470
-  Cloning of PCR product successful: Y/N  Yes
-  Sequencing of cloned PCR product successful: Y/N  No
-  Joining of validated part to adjacent part(s) status:  Not Done
-  Problems to be solved: Not really a problem, but need do a mini-Prep and sequence
-  Current status of this part: All cloned and inoculated into 1.5 mL LB for mini-prep.
-=== GROUP 5: MATa Specific Promoters II ===
+=== [[Team:Johns Hopkins/Notebook/GROUP 7: Microscopy/Yeast | GROUP 7: Microscopy/Yeast]] ===
-  Date: 7/11/08
+<b>Summary for Microscopy/Yeast Group</b>
-  status report by Rick Carrick
-  Part no.: BBa_K110015,
-  Part Description: MFA1
-  Part Location (in build a genome lab):
-  PCR successful?; Y (on moodle somewhere)
-  Cloning of PCR product successful: Y
-  Sequencing of cloned PCR product successful:N
-  Joining of validated part to adjacent part(s) status: Not done
-  Problems to be solved: None so far
-  Current status of this part: This parts must be restriction enzyme digested and sequenced next.
-   Date: 7/11/08
+   Date: Oct 27, 2008
-   status report by Rick Carrick
+   Status report by: Tejas
-   Part no.: BBa_K110009
+   Part no.: no Biobrick part
-   Part Description: Ste2
+   Part Description: Yeast vector pRS414 to be temporarily used.
-   Part Location (in build a genome lab):
-   PCR successful?; Y (on moodle somewhere)
+  The yeast vector pRS414 will be temporarily used until it can be adjusted to meet registry
-   Cloning of PCR product successful: Y
+  standards. pRS414 contains one EcoRI site and one PstI site, both directly adjacent to each
-   Sequencing of cloned PCR product successful:N
+  other. This may make digest a little less efficient. Procedure involves first digesting with
-   Joining of validated part to adjacent part(s) status: Not done
+   Pst1 for one hour, then digesting with EcoRI overnight (sequentially, not simultaneously), as
-   Problems to be solved: None so far
+   EcoRI can tolerate low overhangs better than PstI, according to the NEB catalog. The following
-   Current status of this part: This part must be restriction enzyme digested and sequenced next
+   is a gel run on an E/P simultaneous digest of pRS414.
+   Lane one is log 2 ladder. Lane 2 is uncut pRS414 (supercoiled so runs fater). Lane 3 is cut
+   vector. It may have only one cut, with half at EcoRI and half at PstI, depending on efficiency of
+   the second cut occuring after the first.<br>
+  [[Media: PRS414.tif|pRS414 digest]]
-=== GROUP 6: Vectors ===
+=== [[Team:Johns Hopkins/Notebook/GROUP 8: Assembly Progress | GROUP 8: Assembly Progress]] ===
+<b>Summary of Biobrick Assemblies:</b>
-   Status report by ____
+   Planned Schedule for Further Work:<br>
-   Vector transformed into bacteria strain DB3.1 Y/N
+   October 31st- Successful transformants from either set of ligations (of Promoter + Fluorescent
-   Permanent culture made in the Boeke lab for future reference Y/N
+   Protein) and transformations will be grown up for Miniprep. <br>
-   Selectable marker for this vector
+   November 1st- These pieces will be miniprepped and digested.  Digested fragments will be ligated
-  Medium made and tested Y/N  (link)
+   together with the terminator in the middle, into a pRS414 yeast/bacterial shuttle vector.
-   DNA preps made Y/N
+   Non-digested fragments of a promoter + fluorescent protein will also individually be transformed
-   DNA preps tested by RE digest  - (link)
+   into yeast, with hopes that they will fluoresce.<br>
-   DNA preps tested by transformation into DB3.1 and DH5alpha (or JM109) – put data as
+   November 3rd- Full construct insert will be transformed into yeast, pending identity verification.<br>
-    Table on moodle.
+   November 6th- Pretty Yeast! (Hopefully). <br>
-  Sample format/data follows:<br>
-   Amount transformed		cfu/micGm in DB3.1		cfu/micGm in JM109
-.1 ng					5 * 10e7			<2 * 10e2<br>
-  Preparative digests ready for use are located – where?
-=== GROUP 7 ===
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