GcatWiki - User contributions [en]

Cleaning Plate Replication Pads

2014-07-07T19:53:54Z

Mquaney: Created page with "'''For first time and reuse''' 1. Rinse thoroughly with warm tap water. Detergent may be used. Do not use bleach. 2. Air dry completely and brush to raise the fibers. 3. ..."

'''For first time and reuse'''

1. Rinse thoroughly with warm tap water. Detergent may be used. Do not use bleach.

2. Air dry completely and brush to raise the fibers.

3. Lay flat and wrap in foil.

4. Autoclave on DRY cycle for 15 minutes at 121 degrees Celsius to sterilize.

MWSU protocols

2014-07-07T19:51:46Z

Mquaney:

'''Purification of DNA'''

[[Isolation of Genomic DNA from Bacteria]]

'''PCR'''

[[iPCR]]

[[Standard PCR]]

[[Resuspending Oligos]]

[[Davidson_Missouri_W/colony_PCR | Colony PCR]]

[[Template Preparation for RT-qPCR]]

[[New Chaperone PCR]]

[[LongAmp PCR]]

'''Recombinant DNA Production'''

[[Zymo Research Plasmid Minipreps]]

[[Golden Gate Assembly Protocol for BsmB1]]

[[Pouring an Agarose Gel]]

[[BioBrick Digestions for Fragment and Vector Preparation]]

[[Fragment Purification]]

[[Gibson Assembly]]

[[Direct Synthesis with Overlapping Oligos]]

[[Annealing Oligos for Cloning]]

[[Ethanol Precipitation of Vector DNA]]

[[Reducing Background from Double Digested Vector]]

[[File: PClone_Procedure_for_GCAT_SB_Workshop_2014_new_version.pptx]]

'''Ligation and Transformation'''

[[BioBrick Ligations]]

[[Ligation and Transformation]]

[[Electroporation Transformation]]

[[SOC Protocol for Transformations]]

'''Screening Clones'''

[[Diagnostic RP Digestion for Checking Insert Size]]

[[DNA Sequencing at Iowa State University]]

[[What to do with a new clone]]

'''Measuring Phenotypes'''

[[Measuring Fluorescence in Bacteria]]

[[Camera Settings for Taking Pictures of Plates]]

'''DNA and E coli'''

[[GCAT Library of Quality Parts]]

[[MWSU Freezer Parts]]

'''Working With Bacteria'''

[[Bacterial Media]]

[[Washing Beads]]

[[Cleaning Plate Replication Pads]]

MWSU protocols

2014-07-07T19:51:19Z

Mquaney:

MWSU protocols

2014-07-07T19:49:34Z

Mquaney:

MWSU protocols

2014-07-07T19:49:18Z

Mquaney:

MWSU protocols

2014-07-07T19:48:22Z

Mquaney:

Camera Settings for Taking Pictures of Plates

2014-07-03T19:33:23Z

Mquaney: Created page with "'''Camera Settings''' Shutter Speed = 1 second Aperture = 3.5 seconds ISO = 400 or 800 MF = press down for lower Timer = 10 seconds Use 3-sided box with a front flap for..."

'''Camera Settings'''

Shutter Speed = 1 second

Aperture = 3.5 seconds

ISO = 400 or 800

MF = press down for lower

Timer = 10 seconds

Use 3-sided box with a front flap for letting in light.

MWSU protocols

2014-07-03T19:30:44Z

Mquaney:

'''Purification of DNA'''

[[Isolation of Genomic DNA from Bacteria]]

'''PCR'''

[[iPCR]]

[[Standard PCR]]

[[Resuspending Oligos]]

[[Davidson_Missouri_W/colony_PCR | Colony PCR]]

[[Template Preparation for RT-qPCR]]

[[New Chaperone PCR]]

[[LongAmp PCR]]

'''Recombinant DNA Production'''

[[Zymo Research Plasmid Minipreps]]

[[Golden Gate Assembly Protocol for BsmB1]]

[[Pouring an Agarose Gel]]

[[BioBrick Digestions for Fragment and Vector Preparation]]

[[Fragment Purification]]

[[Gibson Assembly]]

[[Direct Synthesis with Overlapping Oligos]]

[[Annealing Oligos for Cloning]]

[[Ethanol Precipitation of Vector DNA]]

[[Reducing Background from Double Digested Vector]]

[[File: PClone_Procedure_for_GCAT_SB_Workshop_2014_new_version.pptx]]

'''Ligation and Transformation'''

[[BioBrick Ligations]]

[[Ligation and Transformation]]

[[Electroporation Transformation]]

[[Bacterial Media]]

[[Washing Beads]]

[[SOC Protocol for Transformations]]

'''Screening Clones'''

[[Diagnostic RP Digestion for Checking Insert Size]]

[[DNA Sequencing at Iowa State University]]

[[What to do with a new clone]]

'''Measuring Phenotypes'''

[[Measuring Fluorescence in Bacteria]]

[[Camera Settings for Taking Pictures of Plates]]

'''DNA and E coli'''

[[GCAT Library of Quality Parts]]

[[MWSU Freezer Parts]]

SOC Protocol for Transformations

2014-07-03T19:18:50Z

Mquaney:

'''Transformation Protocol'''

1. Combine GGA (Golden Gate Assembly) products then redistribute 10 uL of GGA product into PCR tubes.

2. Add GGA product to 50 uL (whole tube) of competent cells.

3. Place tube in ice box for 5 minutes.

4. Meanwhile, put media plate faced down in the bottom shelf of the incubator.

5. Take tube out of ice box after 5 minutes and add 4 volumes of SOC broth (240 mL to 60 mL of cells, 300 mL total) to a 1.5 mL tube, add competent cells in the SOC 1.5 mL tube.

6. Incubate the tubes in a foam rack (sideways in a beaker) in the shaker for 1 hour.

7. After 1 hour, take tubes and spin in centrifuge for 1 minute.

8. Pipette off 250 uL of supernatent and discard.

9. Mix pellet and approximately 50 uL of remaining supernatent.

10. Plate whole (approx. 50 uL) tube on LB + Amp plate.

(if transforming cells in broth, stop after step 6, place all 300 uL of SOC broth and GGA product into the aliquotted tube (8 mL for single, 16 mL for double)

SOC Protocol for Transformations

2014-07-03T19:18:31Z

Mquaney: Created page with "''''''Transformation Protocol''' 1. Combine GGA (Golden Gate Assembly) products then redistribute 10 uL of GGA product into PCR tubes. 2. Add GGA product to 50 uL (whole tub..."

''''''Transformation Protocol'''

1. Combine GGA (Golden Gate Assembly) products then redistribute 10 uL of GGA product into PCR tubes.

2. Add GGA product to 50 uL (whole tube) of competent cells.

3. Place tube in ice box for 5 minutes.

4. Meanwhile, put media plate faced down in the bottom shelf of the incubator.

5. Take tube out of ice box after 5 minutes and add 4 volumes of SOC broth (240 mL to 60 mL of cells, 300 mL total) to a 1.5 mL tube, add competent cells in the SOC 1.5 mL tube.

6. Incubate the tubes in a foam rack (sideways in a beaker) in the shaker for 1 hour.

7. After 1 hour, take tubes and spin in centrifuge for 1 minute.

8. Pipette off 250 uL of supernatent and discard.

9. Mix pellet and approximately 50 uL of remaining supernatent.

10. Plate whole (approx. 50 uL) tube on LB + Amp plate.

(if transforming cells in broth, stop after step 6, place all 300 uL of SOC broth and GGA product into the aliquotted tube (8 mL for single, 16 mL for double)

MWSU protocols

2014-07-03T18:50:50Z

Mquaney:

'''Purification of DNA'''

[[Isolation of Genomic DNA from Bacteria]]

'''PCR'''

[[iPCR]]

[[Standard PCR]]

[[Resuspending Oligos]]

[[Davidson_Missouri_W/colony_PCR | Colony PCR]]

[[Template Preparation for RT-qPCR]]

[[New Chaperone PCR]]

[[LongAmp PCR]]

'''Recombinant DNA Production'''

[[Zymo Research Plasmid Minipreps]]

[[Golden Gate Assembly Protocol for BsmB1]]

[[Pouring an Agarose Gel]]

[[BioBrick Digestions for Fragment and Vector Preparation]]

[[Fragment Purification]]

[[Gibson Assembly]]

[[Direct Synthesis with Overlapping Oligos]]

[[Annealing Oligos for Cloning]]

[[Ethanol Precipitation of Vector DNA]]

[[Reducing Background from Double Digested Vector]]

[[File: PClone_Procedure_for_GCAT_SB_Workshop_2014_new_version.pptx]]

'''Ligation and Transformation'''

[[BioBrick Ligations]]

[[Ligation and Transformation]]

[[Electroporation Transformation]]

[[Bacterial Media]]

[[Washing Beads]]

[[SOC Protocol for Transformations]]

'''Screening Clones'''

[[Diagnostic RP Digestion for Checking Insert Size]]

[[DNA Sequencing at Iowa State University]]

[[What to do with a new clone]]

'''Measuring Phenotypes'''

[[Measuring Fluorescence in Bacteria]]

'''DNA and E coli'''

[[GCAT Library of Quality Parts]]

[[MWSU Freezer Parts]]

Bacterial Media

2014-07-03T18:49:32Z

Mquaney:

'''Missouri Western Synthetic Biology Protocols
Bacterial Media Prep'''

'''LB Broth'''

5 g Yeast Extract

10 g Tryptone

5 g NaCl

QSV 1 liter

'''LB Plates''' (makes about 35 plates)

5 g Yeast Extract

10 g Tryptone

5 g NaCl

15 g BactoAgar

QSV 1 liter

'''SOC Broth'''

2 g Bacto Tryptone

0.5 g Bacto Yeast Extract

0.2 mL 5M NaCl

0.25 mL 1M KCl

1 mL 1M MgCl2

1 mL 1M MgSO4

2 mL 1M Dextrose (Glucose)

90 mL of dH2O

Mix, then fill up to 100 mL with dH2O

'''Plate Codes'''

#Black line only LB none
#Black line, Red line LB Amp
#Black line, Blue line LB Tet
#Black line, Green line LB Kan
#Black line, Cyan line LB Chlor

'''Ampicillin'''
Stock – 50 mg/ml

Weigh out 2.5 g Ampicillin, sodium salt (Sigma A0166)
Dissolve in 25 ml dH20
Add 25 ml Ethanol

Working concentration 50 ug/ml (1 ml stock solution per liter)

'''Tetracycline'''
Stock – 5 mg/ml

Weigh out 0.25 g Tetracycline HCl (Sigma T7660)

Dissolve in 50 ml 70% Ethanol

Mix/vortex vigorously

Filter sterilize

Make 4 ml aliquot in foil covered 15 ml tubes

Working concentration 20 ug/ml (4 ml stock solution per liter)

Light Sensitive! Keep plates in darkness

'''Kanamycin'''
Stock – 10 mg/ml

Weigh out 0.5 g Kanamycin sulfate (Sigma K1377)
Dissolve in 50 ml dH20

Working concentration 20 ug/ml (2 ml stock solution per liter)

'''Chloramphenicol'''
Stock – 35 mg/ml

Weigh out 1.75 g Chloramphenicol (Sigma C0378)
Add 50 ml 100% Ethanol
Mix/vortex vigorously

Working concentration 35 ug/ml (1 ml stock solution per liter)

'''L-Arabinose'''
Stock – 250 mg/ml

Weigh out 2.5 g L-Arabinose
Add 10 ml dH2O
Mix/vortex vigorously

Working concentration 0.5 mg/ml (2 ml stock solution per liter)

Bacterial Media

2014-07-03T18:48:22Z

Mquaney:

'''Missouri Western Synthetic Biology Protocols
Bacterial Media Prep'''

'''LB Broth'''

5 g Yeast Extract
10 g Tryptone
5 g NaCl

QSV 1 liter

'''LB Plates''' (makes about 35 plates)

5 g Yeast Extract
10 g Tryptone
5 g NaCl
15 g BactoAgar

QSV 1 liter

'''SOC Broth'''

2 g Bacto Tryptone
0.5 g Bacto Yeast Extract
0.2 mL 5M NaCl
0.25 mL 1M KCl
1 mL 1M MgCl2
1 mL 1M MgSO4
2 mL 1M Dextrose (Glucose)
90 mL of dH2O

Mix, then fill up to 100 mL with dH2O

'''Plate Codes'''

#Black line only LB none
#Black line, Red line LB Amp
#Black line, Blue line LB Tet
#Black line, Green line LB Kan
#Black line, Cyan line LB Chlor

'''Ampicillin'''
Stock – 50 mg/ml

Weigh out 2.5 g Ampicillin, sodium salt (Sigma A0166)
Dissolve in 25 ml dH20
Add 25 ml Ethanol

Working concentration 50 ug/ml (1 ml stock solution per liter)

'''Tetracycline'''
Stock – 5 mg/ml

Weigh out 0.25 g Tetracycline HCl (Sigma T7660)

Dissolve in 50 ml 70% Ethanol

Mix/vortex vigorously

Filter sterilize

Make 4 ml aliquot in foil covered 15 ml tubes

Working concentration 20 ug/ml (4 ml stock solution per liter)

Light Sensitive! Keep plates in darkness

'''Kanamycin'''
Stock – 10 mg/ml

Weigh out 0.5 g Kanamycin sulfate (Sigma K1377)
Dissolve in 50 ml dH20

Working concentration 20 ug/ml (2 ml stock solution per liter)

'''Chloramphenicol'''
Stock – 35 mg/ml

Weigh out 1.75 g Chloramphenicol (Sigma C0378)
Add 50 ml 100% Ethanol
Mix/vortex vigorously

Working concentration 35 ug/ml (1 ml stock solution per liter)

'''L-Arabinose'''
Stock – 250 mg/ml

Weigh out 2.5 g L-Arabinose
Add 10 ml dH2O
Mix/vortex vigorously

Working concentration 0.5 mg/ml (2 ml stock solution per liter)

File:High-Resolution Molecular Discrimination by RNA.pdf

2014-06-27T20:56:46Z

Mquaney:

References

2014-06-27T20:56:26Z

Mquaney:

Applications of Genetically-Encoded Biosensors for the
Construction and Control of Biosynthetic Pathways [[File:Josh K. Michener.pdf]]

Synthetic RNA switches as a tool for temporal and spatial
control over gene expression [[File:Andrew L. Chang.pdf]]

Molecular Chaperones in the Cytosol: from Nascent Chain to Folded Protein [[File:F. Ulrich Hartl.pdf]]

Soluable expression of recombinant proteins in the cytoplasm of E.coli [[File:Hans Peter Sørensen.pdf]]

Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis [[File:Vierstra.pdf]]

Riboswitches, methods for their use, and compositions for use with riboswitches [[File:US.pdf]] (If wanted I can email. The file is too large)

Theophylline-dependent riboswitch as a novel genetic tool for strict regulation of protein expression in cyanobacterium Synechococcus elongatus PCC 7942 [[File:Tozawa.pdf]]

Caffeine Riboswitch (possibly biosensor) [[File:Caffeine Riboswitch Paper.pdf]]

Emerging Applications of Riboswitches in Chemical Biology [[File:Emerging Applications of Riboswitches in Chemical Biology.pdf]]

Metabolic engineering of a reduced-genome strain of Escherichia coli
for L-threonine production [[File:Streamlining E. Coli Genome.pdf]]

SELEX (systematic evolution of ligands by exponential enrichment) to Identify Protein-Binding Sites on RNA [[File:SELEX to Identify Protein-Binding Sites on RNA.pdf]]

Philosophy of Biology References [[File:Philosophy_of_Biology_references_programmed_evolution.docx]]

High-Resolution Molecular Discrimination by RNA (how to make aptamer sequences) [[File:High-Resolution Molecular Discrimination by RNA.pdf]]

References

2014-06-27T20:55:48Z

Mquaney:

Applications of Genetically-Encoded Biosensors for the
Construction and Control of Biosynthetic Pathways [[File:Josh K. Michener.pdf]]

Synthetic RNA switches as a tool for temporal and spatial
control over gene expression [[File:Andrew L. Chang.pdf]]

Molecular Chaperones in the Cytosol: from Nascent Chain to Folded Protein [[File:F. Ulrich Hartl.pdf]]

Soluable expression of recombinant proteins in the cytoplasm of E.coli [[File:Hans Peter Sørensen.pdf]]

Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis [[File:Vierstra.pdf]]

Riboswitches, methods for their use, and compositions for use with riboswitches [[File:US.pdf]] (If wanted I can email. The file is too large)

Theophylline-dependent riboswitch as a novel genetic tool for strict regulation of protein expression in cyanobacterium Synechococcus elongatus PCC 7942 [[File:Tozawa.pdf]]

Caffeine Riboswitch (possibly biosensor) [[File:Caffeine Riboswitch Paper.pdf]]

Emerging Applications of Riboswitches in Chemical Biology [[File:Emerging Applications of Riboswitches in Chemical Biology.pdf]]

Metabolic engineering of a reduced-genome strain of Escherichia coli
for L-threonine production [[File:Streamlining E. Coli Genome.pdf]]

SELEX (systematic evolution of ligands by exponential enrichment) to Identify Protein-Binding Sites on RNA [[File:SELEX to Identify Protein-Binding Sites on RNA.pdf]]

Philosophy of Biology References [[File:Philosophy_of_Biology_references_programmed_evolution.docx]]

High-Resolution Molecular Discrimination by RNA (how to make aptamer sequences) [[High-Resolution Molecular Discrimination by RNA.pdf]]

File:SELEX to Identify Protein-Binding Sites on RNA.pdf

2014-06-23T21:07:14Z

Mquaney:

References

2014-06-23T21:07:01Z

Mquaney:

References

2014-06-23T21:06:28Z

Mquaney:

Applications of Genetically-Encoded Biosensors for the
Construction and Control of Biosynthetic Pathways [[File:Josh K. Michener.pdf]]

Synthetic RNA switches as a tool for temporal and spatial
control over gene expression [[File:Andrew L. Chang.pdf]]

Molecular Chaperones in the Cytosol: from Nascent Chain to Folded Protein [[File:F. Ulrich Hartl.pdf]]

Soluable expression of recombinant proteins in the cytoplasm of E.coli [[File:Hans Peter Sørensen.pdf]]

Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis [[File:Vierstra.pdf]]

Riboswitches, methods for their use, and compositions for use with riboswitches [[File:US.pdf]] (If wanted I can email. The file is too large)

Theophylline-dependent riboswitch as a novel genetic tool for strict regulation of protein expression in cyanobacterium Synechococcus elongatus PCC 7942 [[File:Tozawa.pdf]]

Caffeine Riboswitch (possibly biosensor) [[File:Caffeine Riboswitch Paper.pdf]]

Emerging Applications of Riboswitches in Chemical Biology [[File:Emerging Applications of Riboswitches in Chemical Biology.pdf]]

Metabolic engineering of a reduced-genome strain of Escherichia coli
for L-threonine production [[File:Streamlining E. Coli Genome.pdf]]

SELEX (systematic evolution of ligands by exponential enrichment) to Identify Protein-Binding Sites on RNA [[SELEX to Identify Protein-Binding Sites on RNA.pdf]]

File:Emerging Applications of Riboswitches in Chemical Biology.pdf

2014-06-23T16:25:07Z

Mquaney:

References

2014-06-23T16:24:10Z

Mquaney:

References

2014-06-23T16:23:52Z

Mquaney:

File:Caffeine Riboswitch Paper.pdf

2014-06-20T21:08:16Z

Mquaney:

References

2014-06-20T21:07:54Z

Mquaney:

Washing Beads

2014-06-17T14:27:00Z

Mquaney:

'''Protocol for washing the plating beads used for bacterial distribution'''

'''Step 1'''

Place used beads in a large beaker (depending on amount of beads) and soak for 30 minutes in dishwashing soap and hot water, stirring occasionally.

'''Step 2'''

Rinse beads after 30 minutes in a sieve (or strainer) with cold water.

'''Step 3'''

Dry beaker, then take beads from sieve and place in the beaker with 95% EtOH. Soak 30 minutes, stirring occasionally.

'''Step 4'''

Place in sieve for 5 minutes.

'''Step 5'''

Let dry by placing in a warm autoclave for 1 hour (WARNING: DO NOT RUN AUTOCLAVE)

'''Step 6'''

Place dry beads in bottles or smaller beakers with a funnel, then autoclave with the caps loosened (if using beakers, just place aluminum foil over the top).

Washing Beads

2014-06-17T14:26:16Z

Mquaney: Created page with "'''Protocol for washing the plating beads used for bacterial distribution''' '''Step 1''' Place used beads in a large beaker (depending on amount of beads) and soak for 30 m..."

'''Protocol for washing the plating beads used for bacterial distribution'''

'''Step 1'''

Place used beads in a large beaker (depending on amount of beads) and soak for 30 minutes in dishwashing soap and hot water.

'''Step 2'''

Rinse beads after 30 minutes in a sieve (or strainer) with cold water.

'''Step 3'''

Dry beaker, then take beads from sieve and place in the beaker with 95% EtOH. Soak 30 minutes.

'''Step 4'''

Place in sieve for 5 minutes.

'''Step 5'''

Let dry by placing in a warm autoclave for 1 hour (WARNING: DO NOT RUN AUTOCLAVE)

'''Step 6'''

Place dry beads in bottles or smaller beakers with a funnel, then autoclave with the caps loosened (if using beakers, just place aluminum foil over the top).

MWSU protocols

2014-06-17T14:17:40Z

Mquaney:

'''Purification of DNA'''
[[Isolation of Genomic DNA from Bacteria]]

'''PCR'''

[[iPCR]]

[[Standard PCR]]

[[Resuspending Oligos]]

[[Davidson_Missouri_W/colony_PCR | Colony PCR]]

[[Template Preparation for RT-qPCR]]

[[New Chaperone PCR]]

'''Recombinant DNA Production'''

[[Zymo Research Plasmid Minipreps]]

[[Golden Gate Assembly Protocol for BsmB1]]

[[Pouring an Agarose Gel]]

[[BioBrick Digestions for Fragment and Vector Preparation]]

[[Fragment Purification]]

[[Gibson Assembly]]

[[Direct Synthesis with Overlapping Oligos]]

[[Annealing Oligos for Cloning]]

[[Ethanol Precipitation of Vector DNA]]

[[Reducing Background from Double Digested Vector]]

[[File: PClone_Procedure_for_GCAT_SB_Workshop_2014_new_version.pptx]]

'''Ligation and Transformation'''

[[BioBrick Ligations]]

[[Ligation and Transformation]]

[[Electroporation Transformation]]

[[Bacterial Media]]

[[Washing Beads]]

'''Screening Clones'''

[[Diagnostic RP Digestion for Checking Insert Size]]

[[DNA Sequencing at Iowa State University]]

[[What to do with a new clone]]

'''Measuring Phenotypes'''

[[Measuring Fluorescence in Bacteria]]

'''DNA and E coli'''

[[GCAT Library of Quality Parts]]

[[MWSU Freezer Parts]]

File:Broth Growth Experiment Reports Revised.docx

2014-06-12T17:03:44Z

Mquaney: uploaded a new version of "File:Broth Growth Experiment Reports Revised.docx"

File:Broth Growth Experiment Reports Revised.docx

2014-06-12T16:49:37Z

Mquaney:

Summer 2014 SynBio Project (Davidson and MWSU)

2014-06-12T16:49:09Z

Mquaney:

=== Presentations during MWSU visit to Davidson ===

Central Dogma presentation [[File:Central_dogma.pptx]]

PCR presentation [[File:PCR.pptx]]

Cloning presentation [[File:Cloning.pptx]]

Riboswitch presentation [[File:Riboswitch_function.pptx]]

Agent based modeling presentation [[File:AgentBased_Modeling.pptx]]

Competition presentation [[File:Competition_Modeling.xlsx]]

Programmed evolution presentation [[File:Programmed_Evolution.pdf]]

Caffeine results [[File:Caffeine_Disk.pptx]]

Ammeline presentation [[File:Ammeline.pptx]]

Repressilator modeling exercises [[File:repressilator_modeling.docx]]

Repressilator modeling Excel file [[File:Repressilator_model.xls]]

Repressilator modeling Netlogo file [[File:Repressilator_mod.nlogo.zip]]

=== Biology Files ===

Chaperone plasmid DNA sequences [[File:Chaperone_plasmid_DNA_sequences.docx]]

Origin PCR Gels 5-26-14[[File:5-26-14 Orig PCR Elecpho Gel Pic.doc]]

Chaperone PCR and Repeat Origin PCR 5-27-14[[File:5-27-14_Chap_PCR_and_Repeat_Ori_PCR.doc]]

Chaperone PCR of original clones 5-27-14[[File:5-27-14_chaperone_pcr_clones_1-24.doc]]

Origin PCR of original clones 5-27-14[[File:5-27-14 Ori PCR 1-24.doc ]]

New Chap PCR clones 1-5[[File:5-28-14_New_Chap_PCR_1-5.doc ]]

Combinations Labeling System [[File:Labeling.xlsx]]

ThyA Fitness Module [[File:ThyA fitness module.docx]]

Alternative Riboswitches[[File:Alternative Riboswitches.docx]]

Origin PCR Pictures 6-5-14 [[File:6-5-14 Origin PCR.docx]]

Chaperone PCR PA 6-5-14 [[File:6-5-14 Chaperone PCR.docx]]

Broth Growth Experiments [[File:Broth Growth Experiment Reports Revised.docx]]
===Sub-pages on various topics===

'''
[[MATH]]
'''

[[Catherine Doyle Thesis Materials]]

[[Repeating 20 Clone Experiments]]

[[Extending theophylline application]]

[[Melamine iteration]]

[[Ramping up Programmed Evolution]]

[[Rational Design of Riboswitches: papers to read]]

[[ThyA Fitness Module]]

[[Caffeine Disk Replication Data]]

File:Broth Growth Experiment Reports.docx

2014-06-12T16:45:27Z

Mquaney: uploaded a new version of "File:Broth Growth Experiment Reports.docx"

File:Broth Growth Experiment Reports.docx

2014-06-12T16:44:09Z

Mquaney: uploaded a new version of "File:Broth Growth Experiment Reports.docx"

File:Alternative Riboswitches.docx

2014-06-12T16:04:44Z

Mquaney: uploaded a new version of "File:Alternative Riboswitches.docx"

File:Broth Growth Experiment Reports.docx

2014-06-11T21:45:52Z

Mquaney:

Summer 2014 SynBio Project (Davidson and MWSU)

2014-06-11T21:45:23Z

Mquaney:

=== Presentations during MWSU visit to Davidson ===

Central Dogma presentation [[File:Central_dogma.pptx]]

PCR presentation [[File:PCR.pptx]]

Cloning presentation [[File:Cloning.pptx]]

Riboswitch presentation [[File:Riboswitch_function.pptx]]

Agent based modeling presentation [[File:AgentBased_Modeling.pptx]]

Competition presentation [[File:Competition_Modeling.xlsx]]

Programmed evolution presentation [[File:Programmed_Evolution.pdf]]

Caffeine results [[File:Caffeine_Disk.pptx]]

Ammeline presentation [[File:Ammeline.pptx]]

Repressilator modeling exercises [[File:repressilator_modeling.docx]]

Repressilator modeling Excel file [[File:Repressilator_model.xls]]

Repressilator modeling Netlogo file [[File:Repressilator_mod.nlogo.zip]]

=== Biology Files ===

Chaperone plasmid DNA sequences [[File:Chaperone_plasmid_DNA_sequences.docx]]

Origin PCR Gels 5-26-14[[File:5-26-14 Orig PCR Elecpho Gel Pic.doc]]

Chaperone PCR and Repeat Origin PCR 5-27-14[[File:5-27-14_Chap_PCR_and_Repeat_Ori_PCR.doc]]

Chaperone PCR of original clones 5-27-14[[File:5-27-14_chaperone_pcr_clones_1-24.doc]]

Origin PCR of original clones 5-27-14[[File:5-27-14 Ori PCR 1-24.doc ]]

New Chap PCR clones 1-5[[File:5-28-14_New_Chap_PCR_1-5.doc ]]

Combinations Labeling System [[File:Labeling.xlsx]]

ThyA Fitness Module [[File:ThyA fitness module.docx]]

Alternative Riboswitches[[File:Alternative Riboswitches.docx]]

Origin PCR Pictures 6-5-14 [[File:6-5-14 Origin PCR.docx]]

Chaperone PCR PA 6-5-14 [[File:6-5-14 Chaperone PCR.docx]]

Broth Growth Experiments [[File:Broth Growth Experiment Reports.docx]]
===Sub-pages on various topics===

'''
[[MATH]]
'''

[[Catherine Doyle Thesis Materials]]

[[Repeating 20 Clone Experiments]]

[[Extending theophylline application]]

[[Melamine iteration]]

[[Ramping up Programmed Evolution]]

[[Rational Design of Riboswitches: papers to read]]

[[ThyA Fitness Module]]

[[Caffeine Disk Replication Data]]

File:Broth Growth Experiment Reports.doc

2014-06-11T21:44:54Z

Mquaney:

Summer 2014 SynBio Project (Davidson and MWSU)

2014-06-11T21:44:25Z

Mquaney:

=== Presentations during MWSU visit to Davidson ===

Central Dogma presentation [[File:Central_dogma.pptx]]

PCR presentation [[File:PCR.pptx]]

Cloning presentation [[File:Cloning.pptx]]

Riboswitch presentation [[File:Riboswitch_function.pptx]]

Agent based modeling presentation [[File:AgentBased_Modeling.pptx]]

Competition presentation [[File:Competition_Modeling.xlsx]]

Programmed evolution presentation [[File:Programmed_Evolution.pdf]]

Caffeine results [[File:Caffeine_Disk.pptx]]

Ammeline presentation [[File:Ammeline.pptx]]

Repressilator modeling exercises [[File:repressilator_modeling.docx]]

Repressilator modeling Excel file [[File:Repressilator_model.xls]]

Repressilator modeling Netlogo file [[File:Repressilator_mod.nlogo.zip]]

=== Biology Files ===

Chaperone plasmid DNA sequences [[File:Chaperone_plasmid_DNA_sequences.docx]]

Origin PCR Gels 5-26-14[[File:5-26-14 Orig PCR Elecpho Gel Pic.doc]]

Chaperone PCR and Repeat Origin PCR 5-27-14[[File:5-27-14_Chap_PCR_and_Repeat_Ori_PCR.doc]]

Chaperone PCR of original clones 5-27-14[[File:5-27-14_chaperone_pcr_clones_1-24.doc]]

Origin PCR of original clones 5-27-14[[File:5-27-14 Ori PCR 1-24.doc ]]

New Chap PCR clones 1-5[[File:5-28-14_New_Chap_PCR_1-5.doc ]]

Combinations Labeling System [[File:Labeling.xlsx]]

ThyA Fitness Module [[File:ThyA fitness module.docx]]

Alternative Riboswitches[[File:Alternative Riboswitches.docx]]

Origin PCR Pictures 6-5-14 [[File:6-5-14 Origin PCR.docx]]

Chaperone PCR PA 6-5-14 [[File:6-5-14 Chaperone PCR.docx]]

Broth Growth Experiments [[File:Broth Growth Experiment Reports.doc]]
===Sub-pages on various topics===

'''
[[MATH]]
'''

[[Catherine Doyle Thesis Materials]]

[[Repeating 20 Clone Experiments]]

[[Extending theophylline application]]

[[Melamine iteration]]

[[Ramping up Programmed Evolution]]

[[Rational Design of Riboswitches: papers to read]]

[[ThyA Fitness Module]]

[[Caffeine Disk Replication Data]]

File:6-5-14 Chaperone PCR.docx

2014-06-09T16:46:08Z

Mquaney:

Summer 2014 SynBio Project (Davidson and MWSU)

2014-06-09T16:45:03Z

Mquaney:

=== Presentations during MWSU visit to Davidson ===

Central Dogma presentation [[File:Central_dogma.pptx]]

PCR presentation [[File:PCR.pptx]]

Cloning presentation [[File:Cloning.pptx]]

Riboswitch presentation [[File:Riboswitch_function.pptx]]

Agent based modeling presentation [[File:AgentBased_Modeling.pptx]]

Competition presentation [[File:Competition_Modeling.xlsx]]

Programmed evolution presentation [[File:Programmed_Evolution.pdf]]

Caffeine results [[File:Caffeine_Disk.pptx]]

Ammeline presentation [[File:Ammeline.pptx]]

Repressilator modeling exercises [[File:repressilator_modeling.docx]]

Repressilator modeling Excel file [[File:Repressilator_model.xls]]

Repressilator modeling Netlogo file [[File:Repressilator_mod.nlogo.zip]]

=== Biology Files ===

Chaperone plasmid DNA sequences [[File:Chaperone_plasmid_DNA_sequences.docx]]

Origin PCR Gels 5-26-14[[File:5-26-14 Orig PCR Elecpho Gel Pic.doc]]

Chaperone PCR and Repeat Origin PCR 5-27-14[[File:5-27-14_Chap_PCR_and_Repeat_Ori_PCR.doc]]

Chaperone PCR of original clones 5-27-14[[File:5-27-14_chaperone_pcr_clones_1-24.doc]]

Origin PCR of original clones 5-27-14[[File:5-27-14 Ori PCR 1-24.doc ]]

New Chap PCR clones 1-5[[File:5-28-14_New_Chap_PCR_1-5.doc ]]

Combinations Labeling System [[File:Labeling.xlsx]]

ThyA Fitness Module [[File:ThyA fitness module.docx]]

Alternative Riboswitches[[File:Alternative Riboswitches.docx]]

Origin PCR Pictures 6-5-14 [[File:6-5-14 Origin PCR.docx]]

Chaperone PCR PA 6-5-14 [[File:6-5-14 Chaperone PCR.docx]]
===Sub-pages on various topics===

'''
[[MATH]]
'''

[[Catherine Doyle Thesis Materials]]

[[Repeating 20 Clone Experiments]]

[[Extending theophylline application]]

[[Melamine iteration]]

[[Ramping up Programmed Evolution]]

[[Rational Design of Riboswitches: papers to read]]

[[ThyA Fitness Module]]

File:6-5-14 Chaperone PCR PA.docx

2014-06-09T16:42:11Z

Mquaney: uploaded a new version of "File:6-5-14 Chaperone PCR PA.docx"

File:6-5-14 Chaperone PCR PA.docx

2014-06-09T16:40:29Z

Mquaney: uploaded a new version of "File:6-5-14 Chaperone PCR PA.docx"

File:6-5-14 Chaperone PCR PA.docx

2014-06-09T16:38:20Z

Mquaney: uploaded a new version of "File:6-5-14 Chaperone PCR PA.docx"

File:6-5-14 Chaperone PCR PA.docx

2014-06-09T16:35:27Z

Mquaney:

Summer 2014 SynBio Project (Davidson and MWSU)

2014-06-09T16:34:46Z

Mquaney:

=== Presentations during MWSU visit to Davidson ===

Central Dogma presentation [[File:Central_dogma.pptx]]

PCR presentation [[File:PCR.pptx]]

Cloning presentation [[File:Cloning.pptx]]

Riboswitch presentation [[File:Riboswitch_function.pptx]]

Agent based modeling presentation [[File:AgentBased_Modeling.pptx]]

Competition presentation [[File:Competition_Modeling.xlsx]]

Programmed evolution presentation [[File:Programmed_Evolution.pdf]]

Caffeine results [[File:Caffeine_Disk.pptx]]

Ammeline presentation [[File:Ammeline.pptx]]

Repressilator modeling exercises [[File:repressilator_modeling.docx]]

Repressilator modeling Excel file [[File:Repressilator_model.xls]]

Repressilator modeling Netlogo file [[File:Repressilator_mod.nlogo.zip]]

=== Biology Files ===

Chaperone plasmid DNA sequences [[File:Chaperone_plasmid_DNA_sequences.docx]]

Origin PCR Gels 5-26-14[[File:5-26-14 Orig PCR Elecpho Gel Pic.doc]]

Chaperone PCR and Repeat Origin PCR 5-27-14[[File:5-27-14_Chap_PCR_and_Repeat_Ori_PCR.doc]]

Chaperone PCR of original clones 5-27-14[[File:5-27-14_chaperone_pcr_clones_1-24.doc]]

Origin PCR of original clones 5-27-14[[File:5-27-14 Ori PCR 1-24.doc ]]

New Chap PCR clones 1-5[[File:5-28-14_New_Chap_PCR_1-5.doc ]]

Combinations Labeling System [[File:Labeling.xlsx]]

ThyA Fitness Module [[File:ThyA fitness module.docx]]

Alternative Riboswitches[[File:Alternative Riboswitches.docx]]

Origin PCR Pictures 6-5-14 [[File:6-5-14 Origin PCR.docx]]

Chaperone PCR PA 6-5-14 [[File:6-5-14 Chaperone PCR PA.docx]]
===Sub-pages on various topics===

'''
[[MATH]]
'''

[[Catherine Doyle Thesis Materials]]

[[Repeating 20 Clone Experiments]]

[[Extending theophylline application]]

[[Melamine iteration]]

[[Ramping up Programmed Evolution]]

[[Rational Design of Riboswitches: papers to read]]

[[ThyA Fitness Module]]

File:6-5-14 Origin PCR.docx

2014-06-09T14:23:18Z

Mquaney: uploaded a new version of "File:6-5-14 Origin PCR.docx"

File:6-5-14 Origin PCR.docx

2014-06-09T14:21:31Z

Mquaney: uploaded a new version of "File:6-5-14 Origin PCR.docx"

File:6-5-14 Origin PCR.docx

2014-06-09T14:07:53Z

Mquaney: uploaded a new version of "File:6-5-14 Origin PCR.docx"

File:6-5-14 Origin PCR.docx

2014-06-09T14:05:25Z

Mquaney:

Summer 2014 SynBio Project (Davidson and MWSU)

2014-06-09T14:03:08Z

Mquaney:

=== Presentations during MWSU visit to Davidson ===

Central Dogma presentation [[File:Central_dogma.pptx]]

PCR presentation [[File:PCR.pptx]]

Cloning presentation [[File:Cloning.pptx]]

Riboswitch presentation [[File:Riboswitch_function.pptx]]

Agent based modeling presentation [[File:AgentBased_Modeling.pptx]]

Competition presentation [[File:Competition_Modeling.xlsx]]

Programmed evolution presentation [[File:Programmed_Evolution.pdf]]

Caffeine results [[File:Caffeine_Disk.pptx]]

Ammeline presentation [[File:Ammeline.pptx]]

Repressilator modeling exercises [[File:repressilator_modeling.docx]]

Repressilator modeling Excel file [[File:Repressilator_model.xls]]

Repressilator modeling Netlogo file [[File:Repressilator_mod.nlogo.zip]]

=== Biology Files ===

Chaperone plasmid DNA sequences [[File:Chaperone_plasmid_DNA_sequences.docx]]

Origin PCR Gels 5-26-14[[File:5-26-14 Orig PCR Elecpho Gel Pic.doc]]

Chaperone PCR and Repeat Origin PCR 5-27-14[[File:5-27-14_Chap_PCR_and_Repeat_Ori_PCR.doc]]

Chaperone PCR of original clones 5-27-14[[File:5-27-14_chaperone_pcr_clones_1-24.doc]]

Origin PCR of original clones 5-27-14[[File:5-27-14 Ori PCR 1-24.doc ]]

New Chap PCR clones 1-5[[File:5-28-14_New_Chap_PCR_1-5.doc ]]

Combinations Labeling System [[File:Labeling.xlsx]]

ThyA Fitness Module [[File:ThyA fitness module.docx]]

Alternative Riboswitches[[File:Alternative Riboswitches.docx]]

Origin PCR Pictures 6-5-14 [[File:6-5-14 Origin PCR.docx]]

===Sub-pages on various topics===

'''
[[MATH]]
'''

[[Catherine Doyle Thesis Materials]]

[[Repeating 20 Clone Experiments]]

[[Extending theophylline application]]

[[Melamine iteration]]

[[Ramping up Programmed Evolution]]

[[Rational Design of Riboswitches: papers to read]]

[[ThyA Fitness Module]]

File:Alternative Riboswitches.docx

2014-06-04T16:36:53Z

Mquaney: