Research+Page-+Marshall

Week 14:
Completed Protein Characterization, FPLC, and FPLC protein fraction concentration



Week 13:
Week of Thanksgiving

Week 12:
4 colonies found on plate A. 5 colonies found on plate B. Completed MasterPlate protocol. Completed Purification and Concentration. Nanodropped Elution Sample 1 and 2.



Week 11:
Fill out form to order 5 of my top ligands from cb-306-3d and hf9. Finished Ligation and Annealing. Checking for clones monday the 14th.

Week 10:
Finished Protein Expression Protocol with pellet weights of 2.51 and 2.57 grams. Ran Accepting Vector through Nanodrop

Week 9:
Sent 6 samples to the DNA core for sequencing. My sequencing results revealed that I have hollow clones without the insert I want in them. I have started the first run on all of the libraries I am supposed to virtually screen.



Week 8:
1st Virtual Screening job submitted today. I have 2 jobs submitted and am waiting on for results. I also nanodropped my miniprep product Colony 1 Colony 7 Colony 8 my concentrations were not high as I would like but I'm still going to send them to dna sequencing Colony 1,7, and 8 are also the only colonies to produce bacteria during the master plate protocol

Week 7
After 2 days of incubation colonies showed up on my plates. Moved from cloning version 3 to making a master plate and growing up the bacteria I found on my plate from cloning version 3. Also finished Virtual Refresher this week, and finished my research report.

Week 6:
Did cloning Version 3. After a night incubation only one colony has grown. I'm going to incubate longer and see what happens. Cloning Version 3 didn't work see images below: Made the Pymol Version of my active site:

Week 5:
Accepting Vector gel check proved that once again my accepting vector preparation failed. I found out it was due to the new enzyme requring incubation at 37 degrees and not 50 lanes from left to right: 1kb ladder, accepting vector (one faint line)

Redid Accepting Vector protocol and got the following results when I did the PCR clean up. It has two different tops of curves that show up which gives me hope that my accepting vector was successfully cut. But my gel check will confirm or deny this.

Week 4:
Nanodropped PCR^2 Results. Had Concentration of 159 ng/ul. Completed PyMol Refresher. Started Gold Refresher. Completed Preparation of Accepting Vector.

Week 3:
Gel Checked secondary PCR and had no contamination. Worked on PyMol Refresher which was uploaded to my student folder on google docs.

Week 2:
Did PyMol Lab 1 and 2. PCR^2 completed.

Week 1:
Analyzed DNA results from summer to discover that my cloning was unsuccessful. Primary and Secondary PCR completed

06/22/11 **PCR Gel 2: Red**

**PCR Gel 1**

Gel or PCR fail? - Dr .B

06/15/11 Target Discovery: Possible Targets:

Bubonic Plague caused by bacteria Yersinia Pestis EC 3.6.1.11 Structure of Exopolyphosphatase from Yersinia pestis 

African Sleeping Sickness caused by protozoan Trypanosoma brucei pdb number 3M4U EC 3.1.3.48 Enzyme is Protein-Tyrosine-Phosphatase 

6/7/11 Transformation Efficiency Results






The low number of colonies found could have resulted from using bacteria too long after they had thawed. 11/7/2011 mjf962 Marshall YopH 7575772 3-{5-[(4-methoxybenzoyl)amino]-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl}propanoic acid C19 H16 N2 O6 cb_306_3d 1 77.62 23.29 41.11 0 -2.2 368 2.21 5 2 6 3 AutoScale : 2 11/7/2011 mjf962 Marshall YopH RH00719SC sodium 1-acetylindoline-2-sulfonate " C10 H10 N Na O4 S" HF9PlatesPlates5_9 1 76.36 39.86 28.56 0 -2.77 263.24347 0.87 1 1 5 AutoScale: 2 11/7/2011 mjf962 Marshall YopH 5467784 2-(3,4-dimethoxyphenyl)succinic acid C12 H14 O6 cb_306_3d 2 76.03 26.36 37.06 0 -1.28 254 0.51 4 2 6 1 AutoScale: 2 <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: -25px; width: 1px;">11/7/2011 mjf962 Marshall YopH 7842136 {[1-(carboxymethyl)-1H-benzimidazol-2-yl]thio}acetic acid C11 H10 N2 O4 S cb_306_3d 3 74.45 28.71 34.12 0 -1.18 266 1.29 5 2 5 1 AutoScale: 2 <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: -25px; width: 1px;">11/7/2011 mjf962 Marshall YopH 7726180 1-{3-[2-(4-methyl-1-piperazinyl)ethoxy]phenyl}ethanone oxalate C15 H22 N2 O2. C2 H2 O4 cb_306_3d 4 74.06 30.7 36.03 0 -6.18 352 -2.16 1 2 8 3 AutoScale: 2