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Molecular Biology Summer Notebook
5/27/21 Transformation Results of KCNJ3, KCNJ9, and OPRM1 in pGHE
5/26/21 Transformation Results
5/25/21 Transformation Results
6/02/21 Inoculation
6/07/21 Gel Electrophoresis
6/07/21 Streaking
6/09/21 Streaking
6/10/21 Gel Electrophoresis
6/11/21 Midiprep
6/14/21 Gel Electrophoresis
6/11/21 Sequencing
6/17/21 Nanodrop
6/17/21 Streaking
6/17/21 Gel Electrophoreses
6/16/21 Sequencing Results
7/12/21 Transformation
7/13/21 Transformation
7/14/21 Sequencing
7/15/21 Transformation
7/20/21 Maxiprep
Oocyte Imaging Notebook
IBRS posters
Shelby's Project
mRNA VS Modified mRNA
COVID-19 Project
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Images (COVID-19)
Side Chain Interactions
SARS-CoV-2 RBD h-ACE2 Complex
SARS-CoV vs SARS-CoV-2
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COVID-19 Project Methodology
COVID-19 Literature Review
Designed Decoy
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COVID-19 Progress
Using Modeller (COVID-19)
Using CHARMM-GUI Solution Builder
Running MD Simulations (COVID-19)
Using VMD (COVID-19)
Using Tool.py
Generating RMSF data
Using NAMD Energy (COVID-19)
Installing GROMACS to Bridges-2
Simulation Data
Total RMSD Data
RMSD Data by Residue
Absolute Interaction Energy Data
Interaction Energy Comparison Data
Interaction Energy
COVID-19 Plasmids
mRuby DNA
SARS-CoV-2-S-RBD-sfGFP
hACE2_pcDNA3.1
MD simulation files about COVID-19
Spring 21 COVID Notebook
Byeonguk, John, Truett, Sophia and Andrew's Project
Epitope Tag Project
CFTR_pGHE FLAG Tag
CFTR_FLAG_pGHE Notebook
Transformation of CFTR_FLAG_pGHE
Redo Transformation of CFTR_FLAG_pGHE
Maxiprepped CFTR_FLAG
Purified with a Miniprep CFTR
OPRM1_pGHE FLAG Tag
OPRM1_FLAG_pGHE Notebook
Transformation of OPRM1_FLAG_pGHE
Redo transformation of OPRM1_FLAG_pGHE
Maxiprep of OPRM1_FLAG_pGHE
Purified with a Miniprep OPRM1
LM45 Cell Notebook
L102C_FLAG_pcDNA3
PCR of L102C to wt FLAG pcDNA3
Linearize L102C_FLAG_pcDNA3
Dpn1 Digestion of wtCFTR_FLAG_pcDNA3
L102C_FLAG_pcDNA3 Sequencing Results
Circularization of wtCFTR_FLAG_pcDNA3
Transcription of L102C_FLAG_pcDNA3
Transformation of L102C_CFR_FLAG_pcDNA3.1
Redo transformation of L102C_CFTR_FLAG_pcDNA3.1
Maxiprep of L102C_CFTR_FLAG_pcDNA3
Purified with a Miniprep L102C
wtCFTR_FLAG_pcDNA3
PCR Mutagenesis of wtCFTR_FLAG_pcDNA3
Circularization of wtCFTR_FLAG_pcDNA3
Transformation of wtCFTR_FLAG_pcDNA3
Single Colony Inoculation of wtCFTR_FLAG_pcDNA3
Maxiprep of wtCFTR_FLAG_pcDNA3
Opioid Project
Class A Activation Mechanism
Ballesteros-Weinstein Numbering
Drug Addiction
Homology Models
Inactive Model based on 4DKL
4DKL Paper
KCNJ9
Subcloning of KCNJ9 into pGHE
KCNJ9_FLAG_pcDNA3
Transformation of KNCJ9_FLAG_pcDNA3.1
Maxiprep of KCNJ9_FLAG_pcDNA3.1
Maxiprep of KCNJ9_FLAG_pcDNA3.1 (2)
Literature Review
Mutagenesis
Pain Management
Running MD Simulations (Opioid)
6DDF-Fentanyl
Benchmarking (Opioid)
SnapGene Files
Subcloning
Unfinished Subcloning Projects
ARRB2 Subcloning Project
GRK2 Subcloning Project
KCNJ9 Subcloning Project
Finished Subcloning Projects
OPRM1_pGHE
KCNJ3_pGHE
Dose Response Protocol
KCNJ5 Subproject
Making LB Plates
Transformation
Single Colony Inoculation
Maxi Prep
Resuspension
Gel Electrophoresis
Sequencing
Linearization
RNA Synthesis
RNA Expression Test
KCNJ6 Subproject
Making LB + AMP plates
Resuspending
Transformation
re transformation
single colony inoculation
MaxiPrep
Making a Gel
Running a Gel
running a gel round 2
Designing Primer
Resuspending Primers
Linearization
Running a gel
Transcription
CFTR Project
CFTR Background Information
CFTR True Open
CFTR WT
R334C and A107C
PCR Mutagenesis R334C
Circularization of R334C
Transformation of R334C
Single Colony Inoculation R334C (Miniprep)
Miniprep R334C
Single Colony Inoculation R334C (Midiprep)
Midiprep R334C
Sequencing 6.29
Y109C and T1121C
I121C and T1122C
E116C and R104C
Making More E116C/R104C
E116C/R104C/E1371Q
Other Mutations
E116C and R334C
E116C and S108C
R334C and R104C
L218C and I332C
L218C and L100C
Bottleneck Project
Bottleneck Experiments
Relative Permeability Analysis
GlyH-101 Analysis
MD Simulations
GlyH-101 Project
Molecular Modeling (CFTR)
Calculate distance of residue pairs
MD Simulation (CFTR)
CHARMM-GUI (CFTR)
DESMOND (CFTR)
Equilibration (CFTR)
Gromacs (CFTR)
XSEDE ACCOUNT
Benchmarking (CFTR)
Mock Modeling Trial
RMSD Analysis (CFTR)
Modeling Training (CFTR)
Simulated Annealing
Modeller (CFTR)
Alignment File Creation (CFTR)
PSC Bridges
SA Simulation
Molecular Modeling Videos (CFTR)
CFTR Partial OPEN PROJECT
CFTR Project Mutant Summary
CFTR Modeller
Abnormal aromatic list
CLC-1
Box 16
Cell Culture Project
New Students
Background
Transfection Notebook
CRISPR
CRISPR vs Base Editing vs Prime Editing
Cell Culture
Deep Freezing Cells
Observing Cells Under Fluorescence
Passaging Cells
Sterile Technique
Thawing Frozen Cells
Transfection
Cell Culture Materials
Literature Review
CRISPR 3.0 plasmid
Designing the plasmids
COVID and Cell Culture
Magnetic Project
HIFI Subcloning
TAAR1 Project
Zinc Project
OPRM1_pGHE Subcloning
KCNJ3_pGHE Subcloning
KCNJ9_pGHE Subcloning
Mutants
I290C
b2AR HiFi Subcloning
b2AR pGHE Plasmid Map
Mutagenesis Protocol Overview
Background Information
A renaissance in trace amines inspired by a novel GPCR family
Diversity and Modularity of G protein-coupled receptor structures
Inserting b2AA9 into pGHE
Insights into the Structure and Pharmacology of the hTAAR1
Pharmacological Characterization of Membrane-Expressed hTAAR1...
TAAR1 Expression Booster Strategies
TAAR1 Expression Trial March 12-17, 2017
Expression patterns
Old to do lists
TAAR 1 model clustering
TAAR1 Project Mutant Summary
FDA Drug Approvals
TAAR1_pGHE
Amplification of TAAR1_pGHE
Human Galpha-s Expression
Pertussis Toxin Expression
Zinc Project
Zack and Dzenana
Protocols
Cell Culture Protocol
Chemicals
Solution Recipes
Electrophysiology
Protocol Videos
Setting up an experiment
KCl Salt Bridge
Clean up
Analyzing electrophysiology data
Good vs. Bad Data
Priority Experiments
Priority experiments for R104C, L102C
Priority experiments for R104C, L102C, G103C
ES and ET concentration for each mutant
Experiment Protocol Graphs
Electrophysiology Solution Recipes
Functions of Common Electrophysiology Solutions
Electrophysiology Tips & Troubleshooting
Pulling pipettes
P-97 Pipette Puller
RNA Injection Protocol
Breaking/Polishing Injection Micropipettes
(Old) Injecting Protocol
Oocyte Health
AB + AF 1xMBSH Recipe
Molecular Biology
PCR with Q5 Master Mix
Site-Directed Mutagenesis with PCR
Dpn1 Explained
HiFi Subcloning Protocol
Blunt Ended PCR Subcloning
Circularization of Linear DNA
Transformation
Single Colony Inoculation
TENS Prep and Ethanol Precipitation
Maxiprep FAQ
Streaking and Isolating Bacterial Colonies
Primers
Nucleic Acid Quality Control
Sequencing
Sequencing Instructions
Making LB Agar Plates
NanoDrop Instructions
Interpreting NanoDrop Results
DNA Linearization
RNA Synthesis
DNA Sequence Alignment/Mutant Verification
Plasmid Maps
M.B Solutions
Molecular Modeling
Modeller
Bridges-2 On Demand
New Student Training
How to use Shotcut
How to edit the Lab Wiki
How to Make a Lab Wiki Page
Hazardous Waste Training
Pipette Training
Protein Locking Readings
Understanding Protein Structure
Modeling sACE2 and decoy receptors
Xenopus laevis
Housekeeping Instructions
Using the Small Autoclave
Using the Large Autoclave
Refilling DI Water
Ordering Supplies
Using the pH Meter
Hazardous Waste Deposit
Replacing Pippette Tips
Norimatsu Lab
Cell Culture Materials
Table For Cell Culture Materials
Cell Culture Materials Table Page 2
(Page 3) Table For Cell Culture Materials
(Page 4) Table For Cell Culture Materials
(Page 1) Table for Cell Culture DNA
(Page 2) Table for Cell Culture DNA
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