GcatWiki - User contributions [en]

File:Ammeline Riboswitch Sequences.docx

2014-05-22T14:47:24Z

Gchester:

Melamine iteration

2014-05-22T14:47:10Z

Gchester:

The point of our research is to help prove the concept of Programmed Evolution. We will try to do this by creating a system in ''E. coli'' that uses melamine deaminase to create ammeline. The presence of ammeline will be shown by using a riboswitch that will turn on a biosensor module and a fitness module. Our first goal is to create a riboswitch system that works well to show the presence of ammeline and then to work to build a system that efficiently produces ammeline from melamine.

'''Goals For Summer'''

1) create an effective riboswitch system
*retest riboswitches with biosensors
*find best riboswitches, test them with the thyA fitness module (insert thyA riboswitch into mutant thyA- cells)
*use mathematical models to create new riboswitches
2) create an efficient melamine deanimase
*place melamine deaminase gene in the correct location in plasmid (MWSU)
*put both the gene and the riboswitch into the plasmid
*vary the promoter, RBS, and compy number to get efficient ammeline production

[[MWSU]]

[[Davidson]]

Eckdahl's riboswitches [[File:Ammeline_Riboswitch_Sequences.docx]]

[https://www.idtdna.com/Unafold/Home/Index Online UNAcode interface]
*note - change to RNA before using

[[MATH for melamine]]

MATH for melamine

2014-05-22T14:44:36Z

Gchester: Created page with "Thursday, May 22nd: *get results from ammeline experiment, take best riboswitch and optimize it using the UNAcode interface *learn what sequences we can change"

Thursday, May 22nd:
*get results from ammeline experiment, take best riboswitch and optimize it using the UNAcode interface
*learn what sequences we can change

Melamine iteration

2014-05-22T14:42:18Z

Gchester:

The point of our research is to help prove the concept of Programmed Evolution. We will try to do this by creating a system in ''E. coli'' that uses melamine deaminase to create ammeline. The presence of ammeline will be shown by using a riboswitch that will turn on a biosensor module and a fitness module. Our first goal is to create a riboswitch system that works well to show the presence of ammeline and then to work to build a system that efficiently produces ammeline from melamine.

'''Goals For Summer'''

1) create an effective riboswitch system
*retest riboswitches with biosensors
*find best riboswitches, test them with the thyA fitness module (insert thyA riboswitch into mutant thyA- cells)
*use mathematical models to create new riboswitches
2) create an efficient melamine deanimase
*place melamine deaminase gene in the correct location in plasmid (MWSU)
*put both the gene and the riboswitch into the plasmid
*vary the promoter, RBS, and compy number to get efficient ammeline production

[[MWSU]]

[[Davidson]]

[https://www.idtdna.com/Unafold/Home/Index Online UNAcode interface]
*note - change to RNA before using

[[MATH for melamine]]

Melamine iteration

2014-05-22T14:41:13Z

Gchester:

The point of our research is to help prove the concept of Programmed Evolution. We will try to do this by creating a system in ''E. coli'' that uses melamine deaminase to create ammeline. The presence of ammeline will be shown by using a riboswitch that will turn on a biosensor module and a fitness module. Our first goal is to create a riboswitch system that works well to show the presence of ammeline and then to work to build a system that efficiently produces ammeline from melamine.

'''Goals For Summer'''

1) create an effective riboswitch system
*retest riboswitches with biosensors
*find best riboswitches, test them with the thyA fitness module (insert thyA riboswitch into mutant thyA- cells)
*use mathematical models to create new riboswitches
2) create an efficient melamine deanimase
*place melamine deaminase gene in the correct location in plasmid (MWSU)
*put both the gene and the riboswitch into the plasmid
*vary the promoter, RBS, and compy number to get efficient ammeline production

[[MWSU]]

[[Davidson]]

[https://www.idtdna.com/Unafold/Home/Index Online UNAcode interface]
*note - change to RNA before using

Melamine iteration

2014-05-22T14:40:56Z

Gchester:

The point of our research is to help prove the concept of Programmed Evolution. We will try to do this by creating a system in ''E. coli'' that uses melamine deaminase to create ammeline. The presence of ammeline will be shown by using a riboswitch that will turn on a biosensor module and a fitness module. Our first goal is to create a riboswitch system that works well to show the presence of ammeline and then to work to build a system that efficiently produces ammeline from melamine.

'''Goals For Summer'''

1) create an effective riboswitch system
*retest riboswitches with biosensors
*find best riboswitches, test them with the thyA fitness module (insert thyA riboswitch into mutant thyA- cells)
*use mathematical models to create new riboswitches
2) create an efficient melamine deanimase
*place melamine deaminase gene in the correct location in plasmid (MWSU)
*put both the gene and the riboswitch into the plasmid
*vary the promoter, RBS, and compy number to get efficient ammeline production

[[MWSU]]

[[Davidson]]

[https://www.idtdna.com/Unafold/Home/Index Online UNAcode interface]
*note* change to RNA before using

Melamine iteration

2014-05-22T14:39:51Z

Gchester:

The point of our research is to help prove the concept of Programmed Evolution. We will try to do this by creating a system in ''E. coli'' that uses melamine deaminase to create ammeline. The presence of ammeline will be shown by using a riboswitch that will turn on a biosensor module and a fitness module. Our first goal is to create a riboswitch system that works well to show the presence of ammeline and then to work to build a system that efficiently produces ammeline from melamine.

'''Goals For Summer'''

1) create an effective riboswitch system
*retest riboswitches with biosensors
*find best riboswitches, test them with the thyA fitness module (insert thyA riboswitch into mutant thyA- cells)
*use mathematical models to create new riboswitches
2) create an efficient melamine deanimase
*place melamine deaminase gene in the correct location in plasmid (MWSU)
*put both the gene and the riboswitch into the plasmid
*vary the promoter, RBS, and compy number to get efficient ammeline production

[[MWSU]]

[[Davidson]]

[https://www.idtdna.com/Unafold/Home/Index Online UNAcode interface]

MATH

2014-05-21T18:20:24Z

Gchester: Created page with "Nava: "NAVA is a tool for visualising and analysing annotated secondary structures of large single-stranded RNA or DNA sequences (such as full-length virus genomes). The purpo..."

Nava:
"NAVA is a tool for visualising and analysing annotated secondary structures of large single-stranded RNA or DNA sequences (such as full-length virus genomes). The purpose of this tool is to assist investigators in evaluating the biological relevance of RNA or DNA secondary structures within particular sequences."
[https://sites.google.com/site/cbiomichael/software Nava Link]

StatAlign:
"StatAlign is an extendable software package for Bayesian analysis of Protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable measurement of the accuracy of the results.
This approach eliminates common artifacts that traditional methods suffer from, at the cost of increased computational time. These artifacts include the dependency of the constructed phylogeny on a single (probably suboptimal) alignment and bias towards the guide tree upon which the alignment relies.
The models behind the analysis permit the comparison of evolutionarily distant sequences: the TKF92 insertion-deletion model can be coupled to an arbitrary substitution model. A broad range of models for nucleotide and amino acid data is included in the package and the plug-in management system ensures that new models can be easily added."
[http://statalign.github.io/index.html StatAlign link]

UNAFold:
"UNAFold is a comprehensive software package for nucleic acid folding and hybridization prediction."

Summer 2014 SynBio Project (Davidson and MWSU)

2014-05-21T18:08:31Z

Gchester:

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]]

'''
[[MATH]]
'''

[[Catherine Doyle Thesis Materials]]

[[Repeating 20 Clone Experiments]]

[[Extending theophylline application]]

[[Melamine iteration]]

[[Ramping up Programmed Evolution]]

File:Doyle Python.zip

2014-05-21T17:29:58Z

Gchester: Gchester uploaded a new version of "File:Doyle Python.zip"

Mathematics

2013-06-26T15:01:29Z

Gchester:

Nucleotide Sequence Alignment website (EMBOSS Water): [http://bit.ly/10LvziF EMBOSS Water]

[http://modelingcommons.org/browse/one_model/3772 netlogo model]

-micah

Tm Calc for Oligos: [http://bit.ly/13fT96P BioMath Oligos Temp Calc]

Sachii's graphs:

[[File:Tet.xlsx]]

[[File:Graph 2.xlsx]]

[[File:Graph3.xlsx]]

Calculators:

Frequency of desirable results during transformation [https://dl.dropboxusercontent.com/u/16663498/Frequency%20calculator.xlsm excel file]

Population dominating time [https://dl.dropboxusercontent.com/u/16663498/Ecoli%20dominating%20time.xlsx excel file] (work in progress)

Transformation distribution experimental calculator [https://dl.dropboxusercontent.com/u/16663498/Frequency%20calculator.xlsm excel file]

PCN calculator [[File:PCN calculator.xlsx]]

File:PCN calculator.xlsx

2013-06-26T14:57:41Z

Gchester: PCN calculator

PCN calculator