Notebook
Week 1 (March 19-25)
- Consulted with our advisor, Frank, to advise researchers and scientists
- Reached out to scientists at Mt Sinai Hospital, Jason Fuller and Russell Hanson
- Met with Jason Fuller and Russell Hanson, scientists at Genetics Department at Mt Sinai Hospital
- Scheduled weekly meetings for the rest of the year
Week 2 (March 26-Apr 1)
- Brainstormed for a potential topic (Sickle Cell Anemia, Cystic Fibrosis, Huntington’s Disease); decided on HD, proposed by Yeji Cho
- Determined project leaders of the project
- Divided into subsections (website, design, fundraising, social media, computational) and assigned roles, such as other team leads
Week 3 (Apr 2-8)
- Determined possible method to target the disease
- Outlined the abstract for the project
Week 4 (Apr 9-15)
- Took headshots of members and team pictures to put on website
- Administered Drug Tests for medical clearance
- HIPAA (Health Insurance Portability and Accountability Act) Training
- Fire Drill Practice
Week 5 (Apr 16-22)
- Decided to use WordPress as website template
- Happily received our lab coats and Mount Sinai IDs
Week 6 (Apr 23-29)
- Submitted payment for iGEM group registration
- Signed consent forms
Week 7 (Apr 30-May 6)
- Designed graphic of brain and neuron for website
Week 8 (May 7-13)
- Brainstormed for a team name and designed logo; decided on HD Resolution
Week 9 (May 14-20)
- Designed T-shirts, hats, and sweaters
- Brainstormed for companies/sponsors to partner with us
- Received iGEM parts kit
Week 10 (May 21-27)
- Organized home page of website
- Created sponsorship/partnership letters for possible companies
Week 11 (May 28-Jun 3)
- Julia, Erik and Stacy organized a table at Peace Angels Benefit Concert at Steinway and Sons Concert Hall in May 28, 2017
- Mailed out consent forms
- Scheduled wetlab training dates for the summer
Week 12 (Jun 4-10)
- Early Training: lab safety, project overview, practiced lab techniques such as pipetting, centrifugation, PCR, etc.
Week 13 (Jun 11-17)
- Organized team page of website
- Contacted over 50 private and public companies in pharmaceutical and biotech industries, non-profit organizations for sponsorship and support.
Week 14 (Jun 18-24)
- Created Twitter account
- Christi and Marianne completed safety form 1, 2, 3
Week 15 (Jun 25-Jul 1)
- Jason, Justin, Jeewhan, Marianne met up to analyze the data collection
Week 16 (Jul 2-8)
- Computational Lab Weeks:
- First weeks we talked about how to get an application called mFold
- mFold helps to create a simulation of the RNA bonds fusing instead having to actual do it experimentally
Week 17 (Jul 9-15)
- Computational Lab Weeks (continued):
- Looked for Huntington’s mRNA in particular in NCBI
- NM numbers, other prefixes gave types of mRNA
- HW: Find huntington’s-related sequences in NCBI database (assumed at least 5-10 sequences)
Week 18 (Jul 16-22)
- Christi, Rachel, Esther, and Marianne organized a fundraising and information table at Dominico-American Society of Queens in Flushing Town Hall in Flushing, Queens NY in July 22 2017
- Created Facebook account
- Created GoFundMe page
Week 19 (Jul 23-29)
- Received over 100 likes on Facebook page thanks to our Social Media and Outreach team.
- Computational Data:
- We used data we received from [ncbi.com] and used it to compare with the wild type and the infected types.
- HW Results: Found 2 accession numbers- NM_002111.8 (mRNA) and NP_002102.4 (protein); however, only one was mRNA and none were disease form
- We then collected the data in our shared folder
- Looked through other databases for other mutants; found:
- Study with “20 Huntington’s Disease and 49 neurologically normal control samples from post-mortem human subjects”
- http://trace.ddbj.nig.ac.jp/DRASearch/study?acc=SRP051844
- Results for HTT on DNA Data Bank of Japan (includes above):
- http://trace.ddbj.nig.ac.jp/DRASearch/query?keyword=htt&show=20&fq_rep_name=Homo%20sapiens
- HW: Run wild-type mRNA on mfold (Create a text document with the NM_00211.8 RNA and run mFold on it http://unafold.rna.albany.edu/?q=mfold)
- We then collected the data in our shared folder
Week 20 (Jul 30-Aug 5)
- Ordered materials (E. coli, etc)
- Computational Data:
- HW Results: Nobody able to run mfold successfully locally or on web
- Changed programs to ViennaRNA:
HW: Re-calculate sequences with artificially added CAG repeats (added 42 and 60 repeats)
Week 21 (Aug 6-12)
- Wrote letters to respective schools to ask for partnerships
- Manually analyzed results of ViennaRNA calculations for chaperone/guideRNA hairpin targets.
- Determined that this process was less reproducible than desired, and it worried the most viable hairpin loop might be buried in the the tertiary structure
- Decided to change approach: Use RNAi tools to calculate the toe-hold footing (areas in RNA that can be used to initiate strand displacement and/or break apart mRNA secondary structures).
- Spent remainder of the day testing the following tools:
- We used to addgene.com to find plasmids that had less than 26Q repeats.
- We used a genome to protein sequence converter called [] in order to compare the wild type plasmid and the infected.
- At first we thought we had a good candidate with 20Q that was very similar, however, didn’t work because the sequence didn’t completely match up with the wild type.
- Therefore kept looking and decided to use pEGFP-Q23 https://www.addgene.org/40261/
Week 22 (Aug 13-19)
- Created Instagram account
- Grew cell subcultures of E. Coli for future testing
- Familiarized ourselves with autoclaving and basic sterilizing processes
- Learned how to store E. coli for future experiments
- HDSA agreed to be sponsor
Week 23 (Aug 20-26)
- Learned about transfection and tested cells for competency
- Updated team Wiki’s page on the iGem website
- Reached out to our respective high schools for sponsorship
- Hereditary Disease Foundation/Huntington’s Disease Foundation agreed to be sponsor
Week 24 (Aug 27-Sept 2)
- Jessica, Erin, Catherine, and Yunsu helped organize a presentation table at Dominico-American Society of Queens Benefit Concert at National Opera America Center in New York NY on August 30 2017
- Reached out to Cerebral Palsy Alliance Research Foundation about partnering and sponsorship and discussed creating a joint campaign CPARF’s Steptember campaign to promote 10,000 steps a day goal
- Registered team members and created a team roster
