Notebook Table of Contents

Leadership Policy	Budget	Letter to Admin	August-December
March	April	May	June

Leadership Policy

The Budget

Letter to Administration

AUGUST-DECEMBER

The founding of the St. Mark's School of Texas iGEM Team required overcoming many administrative and logistical hurdles from funding to lab space. Through garnering the support of the science department, we were fortunate enough to have a laboratory set aside for us

Fundamental Research: Go over http://parts.igem.org/Help:Learn, the folder "Learn" in Dropbox

Applied Research: Organize and store DNA Distribution kit materials, (time permitting) go over pipetting with Mr. Adame

Outreach: brainstorm ideas about getting more Marksmen interested in iGEM, plan to make a brochure, determine a date to display the posters Killian created around the campus Web Development: go over wiki design/layout, ask Mr. Rummel if you all are having trouble


October 2, 2013: Our first meeting will be on October 17th during the 10:30 period. We'll be introducing iGEM, an exciting synthetic biology and genetic engineering competition.

October 8, 2013: Hey everyone, before our meeting the 17th, I encourage you all to check out this video that provides a great introduction to iGEM. It talks about an astrobiology project done by Stanford and Brown students for this competition. To give you guys some perspective on what we could do, in the high school division last year, a winning team modified E. Coli bacteria to mass produce the hormone, oxytocin!

October 16, 2013: Hey guys, I'd just like to remind you all that our first meeting is tomorrow during the 10:30 period. Unless we have an assembly, we will be talking about iGEM and possible projects we'll be doing.

October 18, 2013: Here are the assignments. You can find team wikis at https://igem.org/Team_Wikis?year=2013&division=high_school. Remember that for now, our meetings will be every Thursday during the 10:30 period in Mr. Adame's room. For our next meeting, please come with information about your team's project. Be able to explain what, why, and how. This will help immensely when we start brainstorming ideas for our own iGEM project.

October 24, 2013: We had a very productive meeting today. Thanks for spending time thoroughly researching your assigned team. You all knew details of your projects very well! For our next meeting, continue looking into your assigned team and focus primarily on cost and parts. See what BioBricks or other resources they utilized to create their project. This next meeting will be the last one focused solely on what other teams have done in the past. We need to start generating ideas for our own project. You can see how one collegiate team that worked on converting CO into CO2 biologically came up with their idea here: https://2012.igem.org/Team:METU/Brainstorm

November 2, 2013: Hey guys, At our next meeting, we'll start brainstorming iGEM projects to pursue. I've seen some great ideas from the leadership applications we've received. Please continue exploring topics we could look into. Science magazines, journals, and blogs are great sources for inspiration. Even the news is a viable source. The World iGEM Collegiate Championship Jamboree is also live right now!! You can check out the live videos or the archives of specific teams. Listening to the presentations should give us some valuable insight.

November 6, 2013: Hey all, We have a meeting tomorrow at 10:30. Please bring some iGEM project ideas and if you'd like to apply for a leadership position, remember that the deadline is next Friday, November 15. If you have any questions, please let me know.

November 7, 2013: I think Gopal mentioned producing bacteria to create O2 to promote healing in bandages. Well Thomas Jefferson High School studied a similar project last year, check it out here: https://2013hs.igem.org/Team:Jefferson_VA_SciCOS/Project. Notice how they took a simple idea and expanded upon it. Here are some of the ideas we generated today. Mr. Adame also sent us a link to a great article on treating contaminated water. Check it out below! Remember, we don't have to come up with a completely original idea for our project. We can take a project someone else has worked on and modify it.

November 10, 2013: Hope you all had a great weekend! Go Lions! I'd just like to update you guys on the direction of our iGEM project. Aarohan, Jeffrey, Nikhil, and I thoroughly considered all of the great ideas you all proposed. This afternoon, we made a final decision; we are pursuing a project centered on probiotic production. After consulting with Dr. Sandeep Burma, we found that creating bacteria that would facilitate enzyme production and promote healing in certain populations would not only have useful applications, but also be practical for us accomplish with the resources we have available.

November 12, 2013; Hey guys, We'll be going over gene expression/regulation during Thursday's meeting. To help lay the groundwork, I have sent you all two PDFs from chapters of the AP Biology textbook on the basics of DNA, transcription, and translation (check your e-mail). I hope you all will scan them over. The two chapters go in depth on what you learned in first year biology. If you're thinking about competing in the USA Biology Olympiad in the spring, Campbell's Biology (the text used in AP Biology) is the official textbook and most questions come from material covered in the book.

November 17, 2013; Hey guys, Check out this TED talk if you have a chance. Here's a little intro from TED.com: "Once it's created, plastic (almost) never dies. While in 12th grade Miranda Wang and Jeanny Yao went in search of a new bacteria to biodegrade plastic -- specifically by breaking down phthalates, a harmful plasticizer. They found an answer surprisingly close to home."

November 20, 2013: If you're interested in iGEM, find some time to go over Unit 1: Biotechnology Techniques on http://www.nature.com/scitable/ebooks/intro-to-biotechnology-techniques-and-applications-16570330/contents. You must know these basic techniques before you can do anything biotechnology related. The tutorial covers restriction enzymes, PCR, and the cloning of expressed genes. If you have any questions, feel free to message me this Thanksgiving break.

December 4, 2013: Hey guys, Just a reminder that we are having a regular club meeting tomorrow. We have read through all your applications and have determined the remaining leadership positions for this year's Biology Club and iGEM team. We'll announce those and talk about the direction of our iGEM project.

December 11, 2013: Hey guys, We have an important meeting tomorrow. Financial support for our iGEM project is contingent upon your attendance at the next two meetings. But sadly, seniors have a conflict with the meeting time again. Fortunately, Raymond Guo has agreed to lead this meeting. Please try to get to the next two meetings promptly at 10:30.

December 18, 2013: Hey guys, We have a really important meeting tomorrow. Please be there promptly at 10:30. Be sure to give a warm welcome to our three incredible guests tomorrow.

December 19, 2013: The help and support we have received for our biotechnology initiative is truly incredible. Now with the school's financial backing, we will be able to pursue new frontiers of research and discovery through the iGEM competition. To finalize the details of our project, I've created a new Dropbox folder specifically for the iGEM Team. We will start reviewing literature on probiotics over winter break. If you're on the iGEM team, please be on the lookout for documents placed in the iGEM Dropbox folder along with e-mails regarding our project and your individual roles. So far, I have contracts of commitment from the following guys. You will receive an invitation to join the folder from the e-mail address below. If you'd like me to send the invitation to an alternate e-mail, please let me know.

December 21, 2013: I'm really excited to announce that we are now an official iGEM team. You can see our team page and our fellow competitors from around the world at https://igem.org/Team_List?year=2014&division=high_school. Our team name is SMTexas.


DEVELOPMENTAL PHASE


WEEK OF MARCH 17

General Meeting: Captain introduces details of iGEM to new members, reveals the project direction to all members, and introduces the creation/makeup of the Committees (30 min), divide the team into groups, have first group meetings, discuss having an additional Tuesday or Wednesday after school meeting

Fundamental Research: Go over http://parts.igem.org/Help:Learn, the folder "Learn" in Dropbox

Applied Research: Organize and store DNA Distribution kit materials, (time permitting) go over pipetting with Mr. Adame

Outreach: brainstorm ideas about getting more Marksmen interested in iGEM, plan to make a brochure, determine a date to display the posters Killian created around the campus Web Development: go over wiki design/layout, ask Mr. Rummel if you all are having trouble


March 19, 2014: Hey guys, Just like to remind you all that we will be officially unveiling our project direction tomorrow after school. Committee sign-ups will begin as well. I'd like to encourage you all to recruit your friends and peers. We need all the guys we can get, and this is the perfect time for them to join. Thanks, Halbert. Hey guys, There will be a meeting tomorrow in Mr. Adame's room for Bio Club at 10:30. We will be doing a biology trivia. Note that this is not the iGEM meeting. That will still happen after school. See you guys tomorrow!

March 22, 2014: Detecting cancer will be challenging, and we need all the help we can get. Please peruse the information in the packet I handed out last Thursday. Committee sign ups have begun. If you weren't able to make Thursday's meeting, please fill out this online form. https://docs.google.com/forms/d/19b9k1h3Tb8ORI5F0efW-5QO1xOht0JdmT9-zugtR7lU/viewform. Every member of the iGEM Team must be on a Committee. You can find the schedule for the next few weeks at bit.ly/smbiology. As a Committee member, you will be responsible for completing the weekly goals. I will send out e-mails regarding the leadership team and the responsibility of your chosen Committee in the next few days as you all sign up. Hope you guys have a nice weekend.

WEEK OF MARCH 24

General Meeting: Captain introduces Gene Designer (20 min)

Fundamental Research: Start designing in Gene Designer by looking at possible promoters & repressors, peruse: http://www.biotechniques.com/news/University-of-Cambridge-team-wins-iGEM-synthetic-biology-competition/biotechniques-180278.html & http://biospot10.blogspot.com/2011/07/igem-grand-prize-2009-biosensors-and.html

Applied Research: Work with the Fundamental Research group to develop a streamlined construct, go over best practices in the lab with Mr. Adame

Outreach: start posting posters, print out 300-400 copies of the brochure depending on cost, plan to distribute the brochures after Friday's Upper School Assembly (April 11)

Web Development: follow iGEM Wiki guidelines and create relevant content, make sure to work on the team page


March 24, 2014: We will begin meeting Wednesdays and Thursdays after school this week. If you haven't done so already, please sign up for a Committee. Not doing so would infringe the Contract of Commitment you signed in the fall last year. iGEM Committee Online Sign Up Form: https://docs.google.com/forms/d/19b9k1h3Tb8ORI5F0efW-5QO1xOht0JdmT9-zugtR7lU/viewform If you weren't able to make the meeting last week, be sure to peruse the packet I attached in the e-mail I sent you all. It covers the basics of synthetic biology. Try to understand the information and ask any questions you may have on Wednesday.

March 27, 2014: Looking at our competition, we are beginning to get behind some of the highly competitive teams, which mostly have University support. Just to let you all know, if we want to do well on the international stage, we will have to work extra hard over the course of these three months. Remember, we're representing both St. Mark's and the state of Texas. To this end, if you all have a chance, please download these two programs and watch the following tutorial video.

WEEK OF MARCH 31

General Meeting: presentation by the Fundamental Research Group on their findings & in-development construct

Fundamental Research: work with the Applied Research Group to start constructing the plasmid, continue research

Applied Research: find protocols for implementing the construct, identify problems and consult the Fundamental Research Group

Outreach: brainstorm ideas on promoting the biotechnology further, esp. ideas for getting additional funding, possibly think about hosting parents for a luncheon, e-mail Dr. Burma and any other professors at UTSW for lab tour/advice/guidance

Web Development: document progress and work with the Outreach Group

POSTPONED B/C of ISAS Mandatory Meeting: APRIL 2 Evaluation: Meeting with Mr. Adame, Mr. Rummel, and Committee Leaders

ISAS Commitments will be taken into consideration


CONSTRUCTION PHASE


WEEK OF APRIL 7

General Meeting: Captain speech on the leadership policy, Evaluation of Committees by Captain/Faculty Sponsors

Fundamental Research: Continue research; Finalize research on genes for the detection of VOC biomarkers

Applied Research: 3A Assembly; Work with the Fundamental Research Team on finding the DNA sequences, reinforce laboratory skills, calculate potential budget for future years

Outreach: Finalize Brochure; Posters around campus, print out 200 copies of the brochure and distribute to interested science instructors, begin development of a more formal packet of info for the administration

Web Development: Continue work on the wiki

April 7, 2014: We have lots to do for the Biotechnology Initiative. Making the goals this week is CRITICAL. Regular meetings Wednesday and Thursday.

Captain seeks new recruits for next year's iGEM Team; reveals ultimate vision of the Project to the Upper School; sends the Biotechnology Initiative brochure to underclassmen


WEEK OF APRIL 14

General Meeting: Committee Meetings

Fundamental Research: Finalize research on genes for the detection of VOC biomarkers

Applied Research: Work with the Fundamental Research Team on finding the DNA sequences, reinforce laboratory skills, calculate potential budget for future years

Outreach: Posters around campus, print out 200 copies of the brochure and distribute to interested science instructors, begin development of a more formal packet of info for the administration

Web Development: Assist Outreach, finalize at least half of the wiki

CANCELED UNTIL CONSTRUCT DEVELOPMENT IS COMPLETE: Plan for a UTSW visit April 18


WEEK OF APRIL 21

General Meeting: Brief presentation by Web Development on Thursday

Fundamental Research: Begin creating construct in Gene Designer if necessary, look for options for the purchase of these sequences from biotech companies, check iGEM Registry for existing BioBricks

Applied Research: Finalize budget, continue refining laboratory skills, assist the Fundamental Research Team

Outreach: Finalize packet for the admininstration, print 10 color copies

Web Development: Finalize wiki with detailed content & designs, brief presentation to the Team on how to add/modify content


WEEK OF APRIL 28

General Meeting: Presentation on established construct by the Fundamental Research Team

Fundamental Research: Order sequences, collaborate with the Applied Research Team to address possible issues during the actual creation of the construct

Applied Research: Collaborate with the Fundamental Research Team to identify room for error

Outreach: Design iGEM wearable gear (t-shirt, sweatshirt, and/or hat) and list cost in a document

Web Development: Address iGEM requirements, including Human Practices


WEEK OF MAY 5: AP EXAMINATIONS

General Meeting: Meeting Cancelled

Fundamental Research: N/A

Applied Research: N/A

Outreach: N/A

Web Development: N/A


WEEK OF MAY 12: AP EXAMINATIONS

General Meeting: Meeting Cancelled

Fundamental Research: N/A

Applied Research: N/A

Outreach: N/A

Web Development: N/A


May 16, 2014: We're planning to order iGEM Shirts regardless of whether we attend the Jamboree. If you would like one, please fill out this quick online form.

WEEK OF MAY 19

General Meeting:

Fundamental Research: Prepare to finalize gene constructs. Look for any last minute corrections and do any other research that will aid in later implementation.

Applied Research: continue working with 3A assembly. Work with basic research team and prepare to implement concepts and ideas of basic research team.

Outreach: continue working on human practices, including community outreach and global outreach; continue filming as well

Web Development: work extensively on the wiki; write more content; work with other committees to do so


WEEK OF MAY 26

General Meeting: Evaluate progress

Fundamental Research: continue piecing together constructs and preparing for implementation

Applied Research: prepare lab space and order necessary materials and do orientation for summer wet lab work and research.

Outreach: continue human practices as mentioned above; work with other committees as well

Web Development: work extensively on the wiki and work with other committees


MAY 30: REGULAR REGISTRATION FOR HIGH SCHOOL JAMBOREE CLOSES, JAMOREE ATTENDANCE FEES DUE


WEEK OF JUNE 2

General Meeting: Evaluate progress

Fundamental Research: Researched novel solutions to the genetic construct, found outstanding research paper, continued research on potential VOC biomarkers; Arrived after lunch, researched solutions to mechanism discrepancies, Aste gene; gene sequence, researched solutions to constructing genetic circuits, Applied--developed prototype genetic circuit system, assigned special duties, specified equipment available, purchased additional equipment and poster;

Applied Research: Do another 3A Assembly and analyze possibility of Gibson Assembly. Work with Fundamental Research to help identify genes. Made bacteria cultures, prepared more ampicillin and kanamycin solutions, found gene sequence for RFP; applied research: prepared more ampicillin and kanamycin bacteria cultures, miniprep; Did gel electrophoresis previous day's miniprep; all were successful. Worked with Basic Research to map and understand a potetnial mechanism for the expression of the aldb gene; Arrived after lunch, helped research potential genetic circuit solutions; developed prototype genetic circuit system, assigned special duties, specified equipment available, purchased additional equipment and poster

Outreach: Created a detailed production timeline for the first week, brainstormed and came up with a mind map for the film, help decide the wiki design layout;

Web Development: Worked extensively on the wiki, added interactive elements and modified existing layout significantly;


JUNE 8: TRACK SELECTION DUE, PROJECT ABSTRACTS DUE, TEAM ROSTERS DUE


WEEK OF JUNE 9

General Meeting: Evaluate progress

Fundamental Research: help applied research as well as other committees that require help

Applied Research: Finish and analyze 3A Assembly and finish work with Fundamental Research Committee. Also work with Outreach Committee on Poster.

Outreach: continue work with human practices

Web Development: continue work on wiki and work with other committees


WEEK OF JUNE 16

General Meeting: Evaluate progress

Fundamental Research: help other committees

Applied Research: Work with Outreach Team.

Outreach: work on human practices (extensively)

Web Development: work on wiki (extensively)


JUNE 20: WIKI FREEZE AT 11:59PM BOSTOM TIME (SEE: WIKI REQUIREMENTS AND SAFETY QUESTIONS)


WEEK OF JUNE 23

Practice presentation, polish poster, submit part to iGEM


JUNE 28: JAMBOREE!