From 2013.igem.org

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Parts

Notebook

Brainstorming

Dengue diagnosis tool
bla
3d printer human tissue machine

Day by Day

January 2013

Team was formed.
We decided to have meetings every Tuesday’s afternoon.
Introductory presentations: what is iGEM, what are Biobricks, computational science.

February and March 2013

We researched about previous projects developed for iGEM, to give us some direction.
Each team member had to bring ideas of a project. There were several presentations and discussion until we get to our project: cardiovascular diseases biomarkers.

April 2013

19th April: we presented our project to professors and students of Biochemistry and Immunology Department. It was very important to test our ability of putting our ideas on a screen and discussing them with people that were not part of the team. It was good to have a feedback.
At our meetings, we were always studying and discussing about cardiac diseases biomarkers, in order to improve our project.

May 2013

More improvements to our project.
Discussions about human practices.

June 2013

Final design of our project.
In late June, we received iGEM’s biobricks kit.

July 2013

We started our experiments. We had a lot of trouble, as the chloramphenicol that we were using was expired and didn’t work well (we took a long time to solve this problem...).
Biosafety Human Practices: a one-week course with Neuza Antunes about biosafety. By the end of the week, an interview was made to conclude the course (colocar link para o vídeo).
19th July - Human Practices at UFMG Escolas: it was a wonderful experience! Teaching synthetic biology to children and teenagers was very pleasant. We used our Brickard Game to make it more attractive (colocar links para o arquivo do jogo de cartas e para o vídeo). - Cloning of RCNA+YFP into PSB1A3.

August 2013

We finally started fluorimetric assays with the composite RCNA+YFP, using cobalt.
The oligonucleotide that we had sent to be synthesized (Promoter TorCAD) arrived.
Cloning of TorCAD into PSB1C3.
Primers arrived.
PCRs and digestions to confirm the constructs PSB1A3_RCNA+YFP and PSB1C3_TorCAD.
17th August: Jamboré at USP - Meeting of Brazilian iGEM teams.

September 2013

More fluorimetric assays.
Cloning of TorCAD+RFP into PSB1C3.
We sent our new biobricks to iGEM Headquarters.
The E. coli Dilemma video (colocar link).
21th September: an interview with our team was published in the biggest newspaper of Minas Gerais’ State, “Estado de Minas”.
27th September: WIKI FREEZE!!!!

October 2013

Regional Jamboree in Chile.

Protocols

1. Solid and liquid culture media 2xYT

For 1 liter of liquid medium:

- 16 g of triptone - 10 g of yeast extract - 5 g NaCl - Add ddH2O (di-deionized) to 1000 mL

For 1 liter of solid media

- Same compounds as liquid medium - 3.95 grams of agar to 250 mL of liquid medium

2. Chemically competent cell preparation 1. In 5 mL of 2xYT media inoculate a clone of Escherichia coli and let it grow overnight, 37°C, 180 rpm. 2. Inoculate 2 mL of E. coli culture in 200 mL of liquid culture medium in a recipient of 2 L. Grow it at 37°C, 250 rpm, until it reaches OD590 0.3 or 0.4. 3. Divide aliquots of 50 mL in 4 conical tubes and let it in ice from 5 to 10 minutes. 4. Centrifuge for 7 minutes, 4°C, 3000 rpm (~1600 x G). 5. Purge the supernatant and resuspend each pellet obtained in a recipient with 5 mL of cold solution of CaCl2. 6. Centrifuge the cells for 5 minutes, 4°C, 2500 rpm (~1333 x G). Repeat step 5 and let the cells in ice for 30 minutes. 7. Repeat step 6, but using 1 mL of cold solution of CaCl2 to resuspend the cells. Note: In this solution, cells can stay from 12 to 24 hours. 8. Divide the cells in aliquots of 100 uL and freeze it at -80°C.

CaCl2 100 mL 500 mL - 60mM CaCl2 0.882 g 4.4106 g - 15% glicerol 15 mL 75 mL - 10 mM PIPES 0.3785 g 1.8925 g

 - Sterilize (autoclave) and store it in a room temperature

Note: Do not use PIPES free acid

3.CoCl2 solution preparation (250 mM)

- Weight 0.3246 g of CoCl2 (1 M = 129,84 g). - Add 10 mL H2O to cobalt. Homogenize mixture. - Filter it using a 0.22 um strainer.

4. DNA digestion

A) Single reaction (10 uL) - DNA 125 ng - Buffer 10X* 1.0 uL - BSA 10x 1.0 uL - Enzyme* 0.25 uL - ddH2O (di-deionized) Complete to 10 uL

Enzymes and buffers used

Enzyme Restriction site Buffer EcoRI G↓AATC ECO SpeI A↓CTAGT Tango 1x XbaI T↓CTAGA Tango 1x PstI CTGCA↓G Orange

B) Cobalt promoter and reporter

DNA Buffer BSA 10x ddH2O Enzymes RCNA 5 uL 2 uL 2 uL 10 uL EcoRI + SpeI 0.5 uL YFP 3.2 uL 2 uL 2 uL 11.3 uL XbaI + PstI 0.5 uL + 1 uL Plasmid 10 uL 2 uL 2 uL 5 uL EcoRI + PstI 0.5 uL

C) TorCAD and Chloramphenicol plasmid resistance (PSB1C3)

DNA Buffer Orange 10x BSA 10x ddH2O Enzymes - PSB1C3 25 ng/uL 2 uL 2 uL 5 uL EcoRI + PstI 0.5 uL - TorCAD 10 ng/uL 2 uL 2 uL 5 uL EcoRI + PstI 0.5 uL

- 37°C for 4 hours

5. Ligation A) RCNA-YFP-PSB1A3

- Plasmid 2 uL - RCNA 2.5 uL - YFP 2.5 uL - Buffer 10x 1 uL - T4 DNA ligase 1 uL - ddH2O (di-deionized) 1 uL - Incubate it overnight at 4ºC

B) PSB1C3 and TorCAD (10uL) - Plasmid 2 uL - TorCAD 2.5 uL - Tampon 10x 1.0 uL - T4 DNA ligase 1 uL - ddH2O (di-deionized) 3.5 uL - Incubate it overnight at 4ºC

6. Transformation Protocol 1. Start thawing the chemically competent cells on ice. 2. Add 1 - 2 uL of DNA to the 2 mL tube. Pipet up and down a few time, gently. Make sure to keep the competent cells on ice. 3. Close the tubes and incubate the cells on ice for 30 minutes. 4. Add cells tubes by immersion in a preheated water bath at 42 °C for 60 seconds. 5. Incubate the cells on ice for 5 minutes. 6. Add 400 uL of 2xYT media (make sure that the broth does not contains antibiotics and is not contaminated) to each transformation. 7. Incubate the cells at 37°C for 1 hour while the tubes are rotating or shaking. Important: 2 hours recovery time helps in transformation efficiency, especially for plasmid backbones with antibiotic resistance other than ampicillin. 8. Label two petri dishes with 2xYT agar (AMP or CHL). Plate 20 uL and 200 uL of the transformation onto the dishes, and spread. This helps you ensure that you will be able pick out a single colony. 9. Incubate the plates at 37°C for 12-14 hours, making sure the agar side of the plate is up. If incubated for too long the antibiotics start break down and untransformed cells will begin to grow, because the resistance enzyme will be excreted by the bacteria inactivating the antibiotic outside of it. 10. Pick a single colony, make a glycerol stock, grow up a cell culture and miniprep.

7. Miniprep

- We used Promega and Invitrogen kits. We followed manufacturer’s indications .

8. PCR Protocol

Compound Volume Program Cilcles Repeat 1. ddH2O 8 uL - - - 2. Buffer IB 10x 1.5 uL - 10 min - 3. dNTP’s 2.5 mM 1.5 uL 94 °C 1 min 1x 4.. Primer VF2 10 uM 0.4 uL 94 °C 1 min 30x 5. Primer VR 10 uM 0.4 uL 50 °C 1.5 min 30x 6. Taq 5u / uL 0.2 72 °C 10 min 30x 7. DNA 3 uL 72 °C 10 min 1x 8. Final volume 15 uL 4° C - -

Note:  Using a thermocycling on steps 3 to 7

9. Fluorimetric assay for RCNA-YFP activation

1. Measure OD 600 of cultures to be assessed. 2. Dilute cultures to OD 600 = 0.02, in a volume of 3 mL. 3. Prepare a solution of CoCl2 1 mM, using 6 uL of 250 mM solution ( look protocol 3) and 1494 uL of 2xYT media. 4. Make other 6 solutions using the mixture on step (3). 50 uM -> 50 uL solution + 950 uL of media 2xYT 100 uM -> 100 uL solution + 900 uL of media 2xYT 150 uM -> 150 uL solution + 850 uL of media 2xYT 200 uM -> 200 uL solution + 800 uL of media 2xYT 250 uM -> 250 uL solution + 750 uL of media 2xYT 300 uM -> 300 uL solution + 700 uL of media 2xYT 5. Add 100 uL of the cultures from step (2) in each well completing 21 wells. Separating appropriately the cultures in triplicate, add to each column a different solution from step (4). 6. Add 100 uL of media 2xYT in another wells completing 21 wells, to discard the noise from media 7. Prepare the designed wells from step (5) adding 100 uL of cobalt solution from step (3) 8. Seal the plaque 9. Read fluorescence: 514 nm (excitation) and 527 nm (emission), every 15 minutes, for 16 hours.

Note: It is not recommended read absorbance using black plaque as it causes interference on reading, despite of it is better for fluorimetric assay. Instead of it, use transparent plaques.

Safety

Course

Before performing experiments, we were invited to know more about the lab routine and the procedures required to cope with organisms genetically modified and compounds usually required to perform experiments as well. Everyone interested in performing experiments during the competition was invited to a course to receive instructions and to learn more about the biosafety and its implications on lab working. The central idea of this course was discuss about what is biosafety, why this is important and what is its implications on lab working. Under this perspective we started reading several texts to increase our knowledge about this theme. Firstly, we started reading the book Manual de biossegurança reader the most important procedures for control, handling and discard of biological products, for avoiding experiment contamination and the vigent law (at least the main) related to manipulation of biological organisms in teaching and researching as well. It is a very detailed book, that helped us to get a notion about where we are inside this big area named biosafety. Beside this book, we have read some documents related to ethics, since we proposed a mechanism to detect biomarkers in a human serum in order to diagnose heart diseases. It is known that we cannot simply perform any sort of experiments using wild animals or even human to look for results that corroborates hypothesis of a work. But in many cases people do not know what is the correct behavior to use samples gotten from human being or from wildlife for research purposes. That is, until where we can go with research in a way that do not harm the species analysed in the experiment, mainly humans? Each country have its culture and people may have different interpretations of what actions can cause ethical problems a common point for everyone in ethics on researching? In Biology, a science that deals with life, it is very important define minimal limits which we shall obey to perform tests and other hypothesis validation and avoiding the rising of ethical reprobation by society. In short, the end do not justify the means. Many things can be done towards society, or for its bad as well, using the knowledge acquired inside university. Recently, some a group created a plant with ability to glow in dark people using a mechanism named crowdfunding. The intense interest of common people about this plant cause a general commotion in scientific mean about the consequences of spreading such modified organism unsupervised. It is not easy to predict the behaviour of such organisms into nature as well as its interactions between other organisms in environment. Since the genetical engineering grew as a big research field, many things emerged providing improvements to health (as the production of insulin), to nourishment (production of soy resistant to plagues) and energy (production of biofuels), for example, but all under restrict safety control. During the course, we talk about such events and we comprehended biosafety not just as a list of rules that must be followed. Beyond of all restrictions applied to ensure safety, biosafety should be understood as what do you do not want carry to your friends, relatives or all sort of people you know in order to keep them safe of any kind of risks. It is more related to avoid risks of being carried from lab to the environment than just hold them in a safe place. In the end we also concluded that we must have our critical sense always keen when dealing with science, mostly with life.

References [1] Manual de biossegurança/Biosafety manual, Hirata, Mario H., Hirata, Rosário D.C., Mancini Filho, Jorge, 2012 [2] Science and ethics, Iaccarino. M, Nature - EMBO reports vol. 14, September 2013, doi:10.1093/embo-reports/ kve191 [3] Glowing plant spark debate, Callaway, E, Nature 498, 2013 June 06, doi:10.1038/498015a [1] , a collection of texts written focused to teach the [2] . For this reason and many others, ethics is so debated in research. There must be [3] and they were sponsored by