From 2007.igem.org

Revision as of 23:16, 29 May 2007 (view source) Dbellin (Talk | contribs) (→Our Project Plan) ← Older edit		Latest revision as of 22:29, 20 October 2007 (view source) Linger (Talk | contribs) (→Plays of the Week)
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-	== About Us ==	+	[[Image:BU_banner.JPG|center]]
-	Welcome to the wiki for Boston University's iGEM 2007 team!	+
-	Our team consists of David Shi, Rahul Ahuja, Christian Ling, and Danny Bellin, all soon-to-be juniors majoring in Biomedical Engineering at Boston University.
		+	== About Us ==
-	We are advised by [http://www.bu.edu/dbin/bme/faculty/?prof=tgardner Dr. Timothy Gardner], Assistant Professor of Biomedical Engineering, as well as Frank Juhn and Stephen Schneider, students in the [http://www.gardnerlab.bu.edu Gardner Laboratory], where we work.  We are grateful to our advisors for their time and support!	+	Welcome to the wiki for Boston University's iGEM 2007 team!
-		+	[[Image:BU_bubio.jpg|right]]
-		+
-	We are also grateful to Pfizer for their generous support of our team.	+
-		+
-	== Our Project Plan ==	+
-		+
-	Our project is aimed at increasing current production from Shewanella Oneidensis by directed evolution of global transcription factors.	+
-		+
-	Our plan so far:	+
-		+
-	# Mutate global transcription factors	+
-	## Design primers for amplification	+
-	## Perform error-prone PCR	+
-	# Transform mutated genes into E. coli	+
-	## Choose plasmids	+
-	## Restriction enzyme digestion	+
-	## Ligation	+
-	## Transformation into E. coli	+
-	# Conjugate E. coli with Shewanella	+
-	# Screen/select Shewanella strains for increased current production due to mutations.  Potential methods:	+
-	## A...ose beads and fluorocytometer	+
-	## Metallo-Antibiotics	+
-	## (DB's random idea):  Could we take advantage of spectrophotometry?  Perhaps we could split our collection of mutants into different groups, measure their absorbances with spectrophotometry, and assume that the sample with the lowest absorbance contains mutants producing more electricity and therefore growing slower.  We could then split this sample into different groups and repeat.  While there might be some inefficient strains in the successful broth samples, on the whole, the broth might be a good one for use in a fuel cell.  Problem:  Low absorbance could be due to mutants losing viability.  Potential Solution:  Let initial sample grow for a while so all mutants unable to grow will die off, all mutants able to grow will thrive, and then perform the screen.	+
-		+
-	== Week's (Ambitious) Goals ==	+
-		+
-	Wednesday 5/30	+
-	# Get all protocols	+
-	#  Identify materials/prepare order	+
-	#  Design Primers	+
-	#  Learn about budget/POs	+
-		+
-	Thursday 5/31	+
-	# Do primer order	+
-	# Start conjugation practice	+
-	# Confirm restriction enzymes, ligases	+
-	# Order confirmed/needed materials	+
-	# Team Revew Meeting	+
-	Friday 6/1	+	Our team consists of [[Boston_University/DS | David Shi]], [[Boston_University/RA | Rahul Ahuja]], [[Boston_University/CL | Christian Ling]], and [[Boston_University/DB | Danny Bellin]],
-	# Evaluate/continue conjugation, practice electroporation for E. coli	+	all soon-to-be juniors majoring in Biomedical Engineering at Boston University.
-	# Meeting with Tim:  Budgets/protocols, Pfizer/fundraising, iGEM registration, beads	+
		+	We are advised by [http://www.bu.edu/dbin/bme/faculty/?prof=tgardner Dr. Timothy Gardner], Assistant Professor of Biomedical Engineering, as well as [[Boston_University/FJ | Frank Juhn]], [[Boston_University/KL | Kevin Litcofsky]], and [[Boston_University/SS | Stephen Schneider]], students in the [http://gardnerlab.bu.edu/ Gardner Laboratory], where we work.  We are grateful to our advisors for their time and support!
		+	We are also grateful to [http://www.pfizer.com Pfizer], the [http://www.bu.edu/eng Boston University College of Engineering], and the [http://www.bu.edu/eng/bme Boston University Department of Biomedical Engineering], for their generous support of our team.
-	== Materials We Need ==	+	== Our Project==
-	Primers:  Need to Buy	+	The goal of our project is to use [[Directed_Evolution | directed evolution]] to increase the current output of the electrogenic bacteria [[Shewanella_oneidensis | Shewanella oneidensis]] (affectionately referred to as Shewie in the Gardner Lab). As the name suggests, directed evolution consists of two main steps: intentionally mutating DNA and then selecting for the expression of desired traits.
-	Error-Prone PCR:  Need to Buy	+	In the case of S. oneidensis, certain [[GTRs_in_S_oneidensis | global transcription regulators]] in its genome have been identified as being related to the metabolic processes of the bacteria. These global transcription regulators will be mutated via [[Error_prone_PCR | error-prone PCR]] and transformed into S. oneidensis in hopes of altering current output.
-	Plasmids:  Need to Buy?	+	Bacteria that express greater electrogenic capability will then be selected via [[Boston_University/Fluorescence-Activated_Cell_Sorting | flow cytometry]] or other viable selection methods.
-	Restriction Enzymes:  Need to Buy?	+	This process of directed evolution can be repeated with previously selected S. oneidensis in order to increase the level of
-	Ligases:  Need to Buy?	+	electrogenesis even further.
-	== Short-Term Status ==
-	Lab Orientation: Completed
-	Design of Primers: Not Completed	+	{| align="center" style="color:white;" border="1"
		+	|-
		+	| bgcolor="#990000" color="white" height="30pt" align="center" | '''Our Team'''
		+	| bgcolor="#990000" color="white" align="center" | '''Project Design'''
		+	| bgcolor="#990000" color="white" align="center" | '''Project Results'''
		+	| bgcolor="#990000" color="white" align="center" | '''Miscellany'''
		+	|- style="color:#990000;"
		+	| align="left" width="375pt" |
		+	:'''Undergraduate Students'''
		+	::[[Boston_University/RA | Rahul Ahuja]] • [[Boston_University/DB | Daniel Bellin]]
		+	::[[Boston_University/CL | Christian Ling]] • [[Boston_University/DS | David Shi]]
		+	:'''Graduate Advisors'''
		+	::[[Boston_University/Frank Juhn | Frank Juhn]] • [[Boston_University/Kevin Litcofsky | Kevin Litcofsky]]
		+	::[[Boston_University/Stephen Schneider | Stephen Schneider]]
		+	:'''Principal Advisor'''
		+	::[http://www.bu.edu/dbin/bme/faculty/?prof=tgardner Dr. Timothy Gardner]
		+	| align="left" width="350pt"|
		+	:'''[[Boston_University/Why_Shewie | Why ''S. oneidensis''?]] '''
		+	:'''Directed Evolution'''
		+	::1. [[Boston_University/Plasmid Selection and Design | Plasmid Selection and Design]]
		+	::2. [[Boston_University/Mutation of GTFs | Mutation of GTFs]]
		+	::3. Transformation of GTFs into Shewie
		+	::::[[Boston_University/TOPO Cloning | TOPO Cloning]] • [[Boston_University/Conjugation | Conjugation]] [[Boston_University/Zymo | Zymo]]
		+	::4. Selection Methods
		+	::::[[Boston_University/Microencapsulation | Microencapsulation ]]
		+	::::[[Boston_University/Redox-sensitive fluorescent dye | Redox-sensitive fluorescent dye]]
		+	::::[[Boston_University/Fluorescence-Activated Cell Sorting | Fluorescence-Activated Cell Sorting]]
		+	| align="left" width="250pt" |
		+	:'''[[Boston_University/Zymo Transformation Results | Zymo Transformation]]'''
		+	:'''[[Boston_University/Electroporation Results | Electroporation]]'''
		+	:'''[[Boston_University/Bacterial Conjugation Results | Bacterial Conjugation]]'''
		+	:'''[[Boston_University/Plasmid Customization | Plasmid Customization]]'''
		+	:'''[[Boston_University/TOPO Cloning Results | TOPO Cloning]]'''
		+	:'''[[Boston_University/TOPO Transformation Results | TOPO Transformation]]'''
		+	:'''[[Hi-Scores and Other Greatness]]'''
		+	| align="left" width="250" |
		+	:'''[[Boston_University/Project Progress | Project Progress]]'''
		+	:'''[[Boston_University/Protocols | Protocols]]
		+	:'''[[Boston_University/Lab Photos | Lab Photos]]
		+	<!--:'''[[Boston_University/Team Photos | Team Photos]]-->
		+	:'''[[Boston_University/BU Photos | BU Photos]]
		+	:'''[[Boston_University/Image Dump | Image Dump (56k stay away!)]]
		+	|-
		+	|}
-	Ordering of Primers:  Not Completed
-	Gathering of Protocols: Not Completed	+	<!--
		+	[[Image:shewie.jpg]]
		+	[[Image:shewie2.jpg]]
		+	[[Image:pjq200.jpg]]
		+	[[Image:conjugation.jpg]]
		+	[[Image:fluorescent1.jpg]]
		+	[[Image:fluorescent2.jpg]]
		+	[[Image:fluorescent3.jpg]]
		+	[[Image:fluorescent4.jpg]]
		+	[[Image:facs.jpg]]
		+	[[Image:topo.jpg]]
		+	[[Image:topo2.jpg]]
		+	[[Image:bulogo.jpg]]
		+	[[Image:gardnerlogo.jpg]]
		+	[[Image:bu_collegeofengineering.jpg]]
		+	[[Image:gardner_logo.jpg]]
		+	[[Image:bubio.jpg]]
		+	!-->
-	Ordering of Error-Prone PCR Materials: Not completed	+	==Supported By==
		+	{| align="center" style="color:white;"
		+	|-
		+	| width="150pt" | [[Image:BU_pfizer.gif]]
		+	| width="325pt" | [[Image:bu_collegeofengineering.gif]]
		+	|[[Image:Bu_Gardner_logo_small.jpg]]
		+	|-
		+	|}

---

Latest revision as of 22:29, 20 October 2007

About Us

Welcome to the wiki for Boston University's iGEM 2007 team!

Our team consists of David Shi, Rahul Ahuja, Christian Ling, and Danny Bellin, all soon-to-be juniors majoring in Biomedical Engineering at Boston University.

We are advised by [http://www.bu.edu/dbin/bme/faculty/?prof=tgardner Dr. Timothy Gardner], Assistant Professor of Biomedical Engineering, as well as Frank Juhn, Kevin Litcofsky, and Stephen Schneider, students in the [http://gardnerlab.bu.edu/ Gardner Laboratory], where we work. We are grateful to our advisors for their time and support!

We are also grateful to [http://www.pfizer.com Pfizer], the [http://www.bu.edu/eng Boston University College of Engineering], and the [http://www.bu.edu/eng/bme Boston University Department of Biomedical Engineering], for their generous support of our team.

Our Project

The goal of our project is to use directed evolution to increase the current output of the electrogenic bacteria Shewanella oneidensis (affectionately referred to as Shewie in the Gardner Lab). As the name suggests, directed evolution consists of two main steps: intentionally mutating DNA and then selecting for the expression of desired traits.

In the case of S. oneidensis, certain global transcription regulators in its genome have been identified as being related to the metabolic processes of the bacteria. These global transcription regulators will be mutated via error-prone PCR and transformed into S. oneidensis in hopes of altering current output.

Bacteria that express greater electrogenic capability will then be selected via flow cytometry or other viable selection methods.

This process of directed evolution can be repeated with previously selected S. oneidensis in order to increase the level of

electrogenesis even further.

Our Team	Project Design	Project Results	Miscellany
Undergraduate Students Rahul Ahuja • Daniel Bellin Christian Ling • David Shi Graduate Advisors Frank Juhn • Kevin Litcofsky Stephen Schneider Principal Advisor [http://www.bu.edu/dbin/bme/faculty/?prof=tgardner Dr. Timothy Gardner]	Why S. oneidensis? Directed Evolution 1. Plasmid Selection and Design 2. Mutation of GTFs 3. Transformation of GTFs into Shewie TOPO Cloning • Conjugation Zymo 4. Selection Methods Microencapsulation Redox-sensitive fluorescent dye Fluorescence-Activated Cell Sorting	Zymo Transformation Electroporation Bacterial Conjugation Plasmid Customization TOPO Cloning TOPO Transformation Hi-Scores and Other Greatness	Project Progress Protocols Lab Photos BU Photos Image Dump (56k stay away!)

Supported By