Team:MichiganState/Notebook/Bioinformatics
Judging
Awards
Human Practices
Lab Notebook
May
Week 1
05/03 - 05/09
Sunday
- Brainstormed diferent methods to approach a bioinformatics project
- Established meeting schedule
Monday
- Creation of GitHub repository
- Discussed objectives for bioinformatic project
Tuesday
- Discussed possible start points for a bioinformatics project
- Possible start points include looking at related species, improving native enzymes, and codon optimization
Thursday
- Began discussing different detoxification strategies in different microorganisms
- Selected Jacob as the Bioinformatics representative for general meetings
Friday
- Revised strategies to find a candidate enzyme by keeping a broader scope with target organisms
- Suggestion from Dr. Hamberger to refrain from de novo protein design due to time constraints
- Discussed the enzyme classes of cytochrome p450s, carboxylesterases, and ABC transporters
Week 2
05/10 - 05/16
Monday
- Took a closer look at the 2015 project of University of British Columbia
- Debriefed on the current degradation pathway readings
Thursday
- Continued discussion on cytochrome p450s and it's integration requirements for S. alvi
- Introduced a sequestration approach to minimize bee imidacloprid exposure
- Discussed potenital byproducts of each degradation pathway and their toxicity to different organisms
- Discussed usage of RCSB to search for structural homologs
- Reviewed concept of gene stacking and its potential usage in the overall project
Friday
- Continued disucssion on potential Phase I metabolism solutions
- Planned out the following week's research:
- Nathaniel: Bee physiology, Honey residues, Methylene bridge breaking
- Jacob: Imidacloprid sequestration feasibility, Glutathione S-transferases
- Madeline: Nitro-reduction pathway with aldehyde oxidases
Saturday
- Discussed different bioinformatic tools from iGEM opening weekend
- Finalized list of potential Phase I enzymes
Week 3
05/17 - 05/23
Tuesday
- Introduced SELEX aptamers as a possible sequestration molecule instead of proteins
- Began work on feasibility calculations for sequestration method
- Met with Dr. Quinn and discussed foreign protein response, solubilization of enzymes, and IMG-JGI as a potenital source
Thursday
- Met with Dr. Hamberger and discussed more requirements for cytochrome p450s in the context of S. alvi
- Reviewed background information of Phase II enzymes in the context of plant and bacterial systems
- Carboxylesterase findings show problems with optimum pH and unclear applications for imidacloprid
- Met with Dr. Krishnan and reviewed current protein modeling projects.
Friday
- Inital feasibility calcaultions for sequestration model calculated with poor outlook
- Continued discussion of Phase II enzymes
Week 4
05/24 - 5/30
Thursday
- Debated the positives and negatives of Phase I detoxification pathways
Friday
- Refined discussion of Phase I to hydroxylation or nitro-reduction pathway
June
Week 5
05/31 - 06/06
Sunday
- Discussed the plausibility of an artifical selection experiment over genetic engineering
Monday
- Reviewed protein catalog detailing various potential enzymes to implement
Tuesday
- Recieved guidance about a combination of transcriptomics and metabolomics to understand biodegradation of imidacloprid
- Decided to pursue nitro-reduction pathway due to issues with cytochrome p450 integration
Thursday
- Discussed performance of various biodegrading microbes
- Synthesized questions for Dr. Hamberger
Friday
- Clarified individual team goals with the gene engineering team
- Updated on the status of Rosetta modeling
Week 6
06/07 - 06/13
Monday
- Reviewed guidance from Dr. Hamberger
- Discussed usage of Rosetta alternatives such as Swiss Model, Phyre2, and PyRosetta
- Formal conclusion that Pseudomonas putida KT2440 would be microbe of choice for pathway cracking
Tuesday
- Clarified project process with mentors
- Started order process for P. putida KT2440
Thursday
- Began research on metabolites and analytical methods for imidacloprid
- Contacted Dr. Pappan from the MSU BMB department to gain access to remote workstations
- Began work with PyRosetta and troubleshooting with Windows
Friday
- Continued troubleshooting PyRosetta
- Clarified P. putida KT2440 information regarding publication results
Week 6
06/14 - 06/20
Monday
- Gained access to remote BMB workstations
- Continued independent PyRosetta training
Tuesday
- Meeting with Dr. Quinn to discuss the foundations of metabolomics studies
- Introducted to GNPS database and the logistics of a metabolomics experiment
Thursday
- Continued work with Pyrosetta and troubleshooting remote installation of Pyrosetta to BMB workstations
Friday
- Reviewed relevant safety form information for the bioinformatics team
Week 8
06/21 - 06/27
Monday
- Drafted an application for the MSU HPCC network
- Started compliling LC-MS/MS method papers
Tuesday
- Submission of MSU HPCC application by Dr. Hamberger
Thursday
- Partial installation of PyRosetta on to BMB workstations. Dependent libraries still needed to be installed
- Followed-up on the MSU HPCC application
Friday
- Met with Garret Miller where he clarified the workflow of the MSU HPCC and pointed towards I-TASSER for homology modeling
- Gained access to the MSU HPCC
Week 9
06/28 - 07/04
Monday
- Abandoned resolving dependency issues with BMB workstations and Pyrosetta. Inquired about workstation upgrade with Dr. Pappan
- Began discussion of transcriptomics
- Developed starting framework for a guide to installation of modeling software for future iGEM teams
Tuesday
- Switched to the P. putida strain EM371, a derivative of KT2440 with a prophage gene set removed
- Began reinstallation of Pyrosetta on updated BMB workstations
Thursday
- Successfully installed I-TASSER
- Explored more of LC-MS/MS protocols and methods
July
Week 10
07/05 - 07/11
Monday
- Discussed overview of transcriptomics study
Thursday
- Discussed RNA-Seq preparation and cost of running an experiment
- Discussed issues with modeling with Garret Miller
Friday
- Began iGEM Check-in form for the metabolomics study
- Continued research on transcriptomics
Week 11
07/12 - 07/18
Monday
- Finished iGEM Check-in form
- Refined protocol details
Tuesday
- Clarified sample preparation for metabolomics experiment
Thursday
- Began work on manipulating GNPS datasets
- Discussed different programs and workflows installed in the MSU HPCC for transcriptomics
Friday
- Explored GNPS and RNA-Seq applications
Week 12
07/19 - 07/25
Monday
- Finalized metabolomics protocol
- Modeled the Mdgst protein structure
Thursday
- Recieved a quote on RNA-Seq from MSU RTSF
Friday
- First metabolomics study processed successfully
- Discussion of different RNA-Seq conditions
Week 13
07/26 - 08/01
Monday
- Continued learning about RNA-Seq and other outreach projections
Tuesday
- Inquired about the cost of RNA-Seq through MSu RTSF with mentors
- Recieved initial data from the metabolomics experiment
Wednesday
- Began analyzing experimental data from the metabolomics experiment
- Initialized usage of NAP and MS2LDA to parse out additional data
Thursday
- Continued analyzing of first metabolomics experimental data
- Discussed more RNA-Seq workflow
- Discussed wiki information
Friday
- Began to infer certain identities of spectra clusters in the metabolomics data
- Attempted to use feature-based netowrking over classical molecular networking
August
Week 14
08/02 - 08/08
Monday
- Refined and re-analyzed classical molecular netowrking data from first metabolomics experiment
Thursday
- Consolidated both feature-based and classical molecular netowrking results
- Prepared Revive and Restore Grant presentation slides
Friday
- Began installation process of Sparta on MSU HPCC accounts
Week 15
08/09 - 08/15
Monday
- Finalized result analysis for first metabolomics experiment
Tuesday
- Clarified timeline for the upcoming fall semester
- Discussed experimental conditions for P. putida EM371
Wednesday
- Met with Dr. TerAvest to discuss the current data and its analysis
- Inquired about a general vs. specific response in terms of imidacloprid exposure
- Discussed the potential of using RT-qPCR to determine upregulation of specific genes
Thursday
- Discussed logistics of RT-qPCR
- Paused Sparta installation due to time constraints
Friday
- Met with gene engineering to discuss research in general oxidative stressors for microorganisms
Week 16
08/16 - 08/22
Monday
- Discussed with gene engineering team the outcome of stressor research