Team:Lubbock TTU/Notebook



Start of iGEM!
The TTU Raider Research Team began member recruitment and team selection for the 2016 iGEM competition. Members began discussions on synthetic biology literature and identified a potential project to pursue. Full time and part time researchers were identified. Start of fundraising.
iGEM Bootcamp - Day 1
On the first day of iGEM Bootcamp, team members were given commitment forms, discussed individual schedules, and were assigned teaching roles for the following day. Members began to design a fundraising brochure, created a timeline of our goals, sent out thank you letters to sponsors, and brainstormed ideas for fundraising, human practices, and future discussions with actors and regulators. Members who were assigned a teaching role began to work on their powerpoint presentations.
iGEM Bootcamp - Day 2
On the second day of iGEM Bootcamp, an "Introduction to Biology" presentation was given by iGEM members Ellen Wilson and Cody Fell; DNA structure, DNA replication, information flow (central dogma), the genetic code, mutations, proteins, transcriptional control, translational control, RNA regulation, Bio-engineering, and more were reviewed to accommodate members studying other STEM fields.

An "Introduction to Model Organisms and Microbial Interactions" presentation was given by members Zachary Nguyen and Alejandra Duran; history strains, growth and maintenance, plasmids, transformations, and etc were covered.

Following lunch, an "Introduction to Synthetic Biology and iGEM" presentation was given by members Holden Fried and Brandon Palomo; history, DNA parts and assembly, circuits, standard registry, BioBrick design, methods, and technology were covered.

The last presentation of the day, "Research and Basic Lab Review", was given by members Marilyn Mathew and Gregory Knox, which covered how to search and read a scientific paper, keep a notebook, and stay organized; assignments, required safety training, BLAST and Ape, and other programs algorithms and programs we covered.

Wrap up discussions completed the second day of iGEM training.
iGEM Bootcamp - Day 3
On the final day of iGEM Bootcamp, team members Aric Denton, Gregory Knox, and Marilyn Mathew led an "Introduction to Lab Techniques" for the other members. Restriction digest-ligation, cloning and PCR, primer design, and flow cytometry were discussed. Members received a hands-on lesson over mini prepping, inoculation, transformation recap, gel electrophoresis, how to pour plates, and DNA assembly methods.
ULabs Outreach
The Lubbock_TTU team met up at ULabs Makerspace for the "Fun Day of Science" outreach event to teach young students about synthetic biology. Several experiments were conducted.

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Week One
Wet Lab team obtained access badges to the Department of Cell Physiology and Molecular Biophysics. Members identified sequences for PDGF-BB and other cytokines and began to learn how to clone in the lab. Protocols associated with construction of the genetic design were identified and discussed with an instructor.

Dry Lab team finished refining sponsorship packet and assigned members departments and companies to contact. Members began engineering a scaffold design: literature sources and components to make or buy for scaffold were discussed. Design of bioreactor began: literature sources and components to make or buy for bioreactor designs also discussed.
Dry Lab Meeting
Dry Lab team met to discuss design of scaffold and bioreactor. Members brainstormed materials needed for "Hackerspace" outreach and possible themes for Lubbock_TTU wiki page.

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Wiki Development Begins
The Lubbock_TTU wiki page begins to undergo changes.

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Meeting with Dr. Sutton
The team met with, Faculty Member, Dr. Sutton to discuss project progress and to ask wet lab questions. Members met at the TTU Innovation Hub afterwards to take headshots for Lubbock_TTU wiki page.

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Dry Lab Meeting
Dry Lab team met to discuss necessary changes to Bioreactor schematic. A parts list was created for the bioreactor. View meeting notes.

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Team Meeting
Short general meeting for all members to discuss progress from both Wet Lab and Dry Lab teams. Tasks were assigned to various team members. View meeting notes.
Wiki Update #1
New wiki theme implemented into Home and Team pages. Notebook page updated with more streamlined design. Team member portfolio design updated to include Fancybox caption feature. Sponsors section updated to include MR DNA. Notebook content updated.
Wiki Update #2
New wiki theme implemented into Description, Notebook, and Safety pages. Demonstrate page removed due to redundancy to Results page. "Scroll to Top" feature added to all pages. Anchor tag feature implemented into Notebook and Safety pages. Content added to Description and Safety pages. Notebook content updated.
Team Meeting
General meeting for all members to discuss progress from both Wet Lab and Dry Lab teams and individual assignments. The team began brainstorming ideas for a promotional video.

Wet Lab status: Designed and ordered aprotinin and PDGF biobricks. Designed basic construct for fusion proteins. Basic constructs KIL, DSB(A), and DSB(C) are complete. All wet lab members are up-to-date with basic lab procedures such as transformations and overnights/cryos. View meeting notes.

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Wiki Update #3
New wiki theme implemented into Attribution and Parts pages. Braining storming section removed from Description page due to redundancy to Project Start section on Attribution page. Notebook content updated. Basic Parts, Composite Parts, and Part Collection pages removed to create a single Parts page. Content added to Attribution and Parts pages. Anchor tag feature implemented into Parts page.
Wiki Update #4
Home page and Notebook content updated. "Under construction" pop up window added to home page.
PDGF gBlocks Arrive
Wet Lab team met with Dean Linquist and received $7500 in support from the college of arts and sciences. The Lubbock_TTU iGEM team officially launches our GoFundMe page!
Primers for gBlocks are Designed
Wet Lab team made Tet and Kan LB plates for transformations and identified plasmid backbones and promoters for transformation and cloning (* BBa_10500, pSB4k5 and pSB3T5).
Plasmids and Promoters Transformed
Wet Lab team identified another more desirable promoter, BBa_K206000 and BBa_K914003, and identified sequence for DsbC signal peptide.
Transformations and Overnights
Wet Lab team transformed K206000 and K914003. Overnights of 10500, pSB4K5 and 3T5 are grown.



Wet Lab Meeting
Wet Lab team made overnights of selected K206000 and K914003 colonies and plated lawns of 10500, pSB4K5 and 3T5.
Enzymes and Aprotinin gBlocks Arrive
Wet Lab team plated lawns of K206000 abd K914003 and made Cryos of 10500, pSB4K5 and pSB3T5.
Student Leader, Brandon Palomo, met with University of Texas iGEM team. The Lubbock_TTU team received EIN numbers from the IRS and met with mentor Xavier on Skype. Wet Lab team picked up thermocyclers from MR. DNA Labs and delivered them to ULabs. Overnights for midiprep of promoters and backbones are made.
DsbC and Kil protein BioBricks
Team members Cody Fell, Ellen Wilson, and Zachary Nguyen designed DsbC and Kil protein biobricks. Promoters andbackbones are midiprepped. ULabs lesson plan is created by Cody Fell and Marilyn Mathew.
Quick Update
Wet Lab team amplifies gBlocks with PCR. A survey for Synthetic Biology Outreach is made.
Microbial Fuel Cell Prototype Created
A script for ULabs lesson plan is created. The Lubbock_TTU iGEM team met with Frenship ISD and Boy Scout Representatives to schedule classes. Team members Cody Fell and Kennady Abbott meet up to plan cloning protocols.
Group meeting to discuss the state of the project.



Team Meeting
The Lubbock_TTU team held a team meeting to discuss goals for Wet Lab and Dry Lab. Dry Lab's goal for the week is completing the Bioreactor. Necessary changes to the wiki page were covered.
Growth curves of PDGF and aprotinin transformed bacteria were performed to evaluate transformation efficiency.



We ran PCR's of our gblocks and tried to clone them into the submission vectors, but it failed.
We ran and tested the bioreactor and cloned our gblocks into the submission vectors.