Team:Johns Hopkins/Protocols

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{{JHU}}
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== Protocols ==
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[[Media:JHU_0708_Jaime-protocols.pdf|PCR Protocols from Jaime]]<br>
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[[Media:JHU_0708_IGEM_Ligation_and_Transformation.pdf|Ligation/Cloning and Transformation]]<br>
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[[Media:JHU_0708_Colony_Screening_PCR.pdf|Moodle Colony Screening PCR]]<br>
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[[Media:JHU_0708_Plasmid_Miniprep_Protocol.pdf|Plasmid Miniprep]] <br>
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[[Media:CMBD.pdf|Checking Minipreps to Prepare for Sequencing]] <br>
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[[Media:SSS.pdf|Sequence Sample Submission]] <br>
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[[Media:JHU_Glycerol_Stocks.pdf|Making Glycerol Stocks]]<br>
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[[Media:JHU_Moving_Insert_to_iGEM_Vector.pdf| Moving Insert to iGEM Vector]]<br>
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== Papers ==
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=== Important Papers ===
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<a href="http://www.jbioleng.org/content/2/1/5">Reshma P Shetty, Drew Endy, and Thomas F Knight Jr; <i>Engineering BioBrick vectors from BioBrick parts</i></a><br>
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[[Media:JHU_0708_paper_Aregularoryheirarchy.pdf| Herskowitz I. <i> A regulatory hierarchy for cell specialization in yeast. </i> (REVIEW.) Nature. 342:749-757 (1989)<br>]] 
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[[Media:JHU_0708_paper_MolecularMechanismofcell-typedeterminationinbuddingyeast.pdf|Johnson AD. <i> Molecular mechanisms of cell-type determination in budding yeast. </i>(REVIEW.) Current Opinion in Gen. & Dev. 5:552-558 (1995)<br>]]
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[[Media:JHU_0708_paper_The_N-end_Rule_Pathway_as_a_Nitric_Oxide_Sensor_Controlling_the_Levels_of_Multiple_Regulators.pdf| Hu R-G <I>et al.</I> <I>The N-end rule pathway as a nitric oxide sensor controlling the levels of multiple regulators.</I> Nature. 437:981-986 (2005)<br>]] 
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[[Media:JHU_0708_paper_TheN-endRule.pdf|Varshavsky A. <I>The N-end Rule pathway of protein degradation. (REVIEW.)</I> Genes to Cells. 2:13-28 (1997)<br>]]
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[[Media:JHU_0708_paper_Optimizedcassettes.pdf| Sheff MA & Thorn KS. <I>Optimized cassettes for fluorescent protein tagging in</I> Saccharomyces cerevisiae. Yeast. 21:661-670 (2004)<br>]]
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[[Media:JHU_0708_paper_Awalk.pdf| Bardwell L. <I>A walk-through of the yeast mating pheromone response pathway. (REVIEW.)</I> Peptides. 25:1465-1476 (2004)<br>]] 
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</div>
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<div id="book"><h2>Welcome to Johns Hopkins iGEM</h2>
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=== Yeast Vector Papers ===
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[[Media:JHU_0708_paper_Development_of_a_hybrid_cloning_vector_and_isolation_of_the_can1_gene.pdf|Broach JR. <I>Transformation in yeast: development of a hybrid cloning vector and isolation of the </I>CAN1<I> gene.</I> Gene. 8(1):121-133 (1979)<br>]]
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The International Genetically Engineered Machines Competition (iGEM) is an annual intercollegiate challenge that seeks to answer the question: "Can simple biological systems be built from standard, interchangeable parts and operated in living cells? Or is biology simply too complicated to be engineered in this way?" The newly-formed iGEM team at Johns Hopkins is composed of mostly undergraduate students with diverse majors ranging from Materials Science Engineering to Biology. While the team has graduate and faculty input, it is almost totally undergraduate run. The iGEM teams work over the summer at their, respective university, and then attend the iGEM Jamboree in November to present their work. We plan to create novel genetic parts that could be added to the existing iGEM registry of biological parts. The MIT iGEM Registry of Parts is the databank of biological standards to which iGEM teams from 2003 and onward have contributed. Currently, the databank only has 16 yeast "biobricks". These biobricks are reporters, tags, plasmids and other useful interchangeable genetic parts, that could one day revolutionize genetic and synthetic biology. By the end of our project, we will have most likely doubled the amount of yeast biobricks in the registry.
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[[Media:JHU_0708_paper_Manipulating_Yeast_Genome_Using_Plasmid_Vectors.pdf|Stearns, T. <I>Manipulating yeast genome using plasmid vectors. (REVIEW.)</I> Methods in enzymology. 185:280-297 (1990)<br>]]
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  [[Media:JHU_0708_IGEM_Ligation_and_Transformation.pdf|Ligation and Transformation Protocol]]
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[[Media:JHU_0708_paper_Shuttle_Vectors_with_Multiple_Unique_Restriction_Sites.pdf| Hill JE <I>et al.</I> <I>Yeast/</I>E. coli<I> Shuttle Vectors with Multiple Unique Restriction Sites.</I> Yeast. 2:163-167 (1986)<br>]]
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  [[Media:JHU_0708_Plasmid_Miniprep_Protocol.pdf|Plasmid Miniprep Protocol]]
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[[Media:JHU_0708_paper_System_of_Shuttle_Vectors_and_Yeast_Host_Strains_Designed_for_Efficient.pdf|Sikorski RS. <I>A System of Shuttle Vectors and Yeast Host Strains Designed for Efficient Manipulation of DNA in </I>Saccharomyces cerevisiae. Genetics. 122:19-27 (1989)<br>]]
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[[Media:JHU_0708_paper_Yeast_vectors_for_the_controlled_expression_of_heterologous_proteins.pdf| Mumberg D <I>et al. Yeast vectors for the controlled expression of heterologous proteins in different genetic backgrounds.</I> Gene. 156:119-122 (1995)<br>]]
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=== Other ===
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[[Media:JHU_0708_paper_TransfofYeast.pdf|JHU_0708_paper_TransfofYeast.pdf]]<br>
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[[Media:JHU_0708_paper_Three-prongedgenomicanalysis.pdf|JHU_0708_paper_Three-prongedgenomicanalysis.pdf]]<br>
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[[Media:JHU_0708_paper_SCPD_a_promoter_database_of_the_yeast.pdf|JHU_0708_paper_SCPD_a_promoter_database_of_the_yeast.pdf]]<br>
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[[Media:JHU_0708_paper_Human_Left-Handed_Z-DNA_-_Schwartz_-_Science.pdf|JHU_0708_paper_Human_Left-Handed_Z-DNA_-_Schwartz_-_Science.pdf]]<br>
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[[Media:JHU_0708_paper_GlobalTranscriptionRegulators.pdf|JHU_0708_paper_GlobalTranscriptionRegulators.pdf]]<br>
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[[Media:JHU_0708_paper_ForeignGeneExpression.pdf|JHU_0708_paper_ForeignGeneExpression.pdf]]<br>
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[[Media:JHU_0708_paper_DNAbendingnegativeregulatoryproteins.pdf|JHU_0708_paper_DNAbendingnegativeregulatoryproteins.pdf]]<br>
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[[Media:JHU_0708_paper_BentDNA.pdf|JHU_0708_paper_BentDNA.pdf]]<br>
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[[Media:JHU_0708_paper_Aregularoryheirarchy.pdf|JHU_0708_paper_Aregularoryheirarchy.pdf]]<br>
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Latest revision as of 22:59, 27 October 2008

Contents

Protocols

PCR Protocols from Jaime
Ligation/Cloning and Transformation
Moodle Colony Screening PCR
Plasmid Miniprep
Checking Minipreps to Prepare for Sequencing
Sequence Sample Submission
Making Glycerol Stocks
Moving Insert to iGEM Vector

Papers

Important Papers

Reshma P Shetty, Drew Endy, and Thomas F Knight Jr; Engineering BioBrick vectors from BioBrick parts

Herskowitz I. A regulatory hierarchy for cell specialization in yeast. (REVIEW.) Nature. 342:749-757 (1989)

Johnson AD. Molecular mechanisms of cell-type determination in budding yeast. (REVIEW.) Current Opinion in Gen. & Dev. 5:552-558 (1995)

Hu R-G et al. The N-end rule pathway as a nitric oxide sensor controlling the levels of multiple regulators. Nature. 437:981-986 (2005)

Varshavsky A. The N-end Rule pathway of protein degradation. (REVIEW.) Genes to Cells. 2:13-28 (1997)

Sheff MA & Thorn KS. Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae. Yeast. 21:661-670 (2004)

Bardwell L. A walk-through of the yeast mating pheromone response pathway. (REVIEW.) Peptides. 25:1465-1476 (2004)

Yeast Vector Papers

Broach JR. Transformation in yeast: development of a hybrid cloning vector and isolation of the CAN1 gene. Gene. 8(1):121-133 (1979)

Stearns, T. Manipulating yeast genome using plasmid vectors. (REVIEW.) Methods in enzymology. 185:280-297 (1990)

Hill JE et al. Yeast/E. coli Shuttle Vectors with Multiple Unique Restriction Sites. Yeast. 2:163-167 (1986)

Sikorski RS. A System of Shuttle Vectors and Yeast Host Strains Designed for Efficient Manipulation of DNA in Saccharomyces cerevisiae. Genetics. 122:19-27 (1989)

Mumberg D et al. Yeast vectors for the controlled expression of heterologous proteins in different genetic backgrounds. Gene. 156:119-122 (1995)

Other

JHU_0708_paper_TransfofYeast.pdf
JHU_0708_paper_Three-prongedgenomicanalysis.pdf
JHU_0708_paper_SCPD_a_promoter_database_of_the_yeast.pdf
JHU_0708_paper_Human_Left-Handed_Z-DNA_-_Schwartz_-_Science.pdf
JHU_0708_paper_GlobalTranscriptionRegulators.pdf
JHU_0708_paper_ForeignGeneExpression.pdf
JHU_0708_paper_DNAbendingnegativeregulatoryproteins.pdf
JHU_0708_paper_BentDNA.pdf
JHU_0708_paper_Aregularoryheirarchy.pdf

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