Team:UANL Mty-Mexico/Workshop CIDEB

iGEM-UANL team conducted a training workshop to enlist the team CIDEB-UANL Mexico to the iGEM competition for its participation in iGEM HSD 2013. They did fabulous! They came 2nd runner up in the competition just like the last year

The topics that were included in the workshop were about molecular biology related with the nucleic acids function and the proteins involved in the “Central dogma”. About the laboratory, different techniques of molecular biology in the laboratory that are used in the genetic engineering and the synthetic biology, were taught to the students and a Practices Handbook was given to them elaborated by the instructors of the workshop.

1: DNA

Topics: -DNA as the information storage molecule in all living things. -Organization of DNA within cells. -Molecular structure of DNA -DNA structure model. Activity: Puzzle board game to learn how DNA is copied.

2: Genes

Topics: -Genes as functional units of DNA -Organization and parts of a genes -How do the genes work? -Central dogma of molecular biology.  Activity: Puzzle with multiple options to explain gene function through the central Dogma. -Use of common examples.

3: Proteins

Topics: -Proteins as carriers of most biological processes -Types of proteins -Examples of  common proteins -The genetic code  Activity: Build a protein from DNA code (translation), Protein models.

4: Genetic Engineering

Topics: -Recombinant DNA technology -Restriction enzymes, ligase and vectors -Examples.  Activity: Build a recombinant DNA molecule with colored cables  and transform a cell.

5: Synthetic Biology

Topics: -Universality, modularity and abstraction of bioparts -Synbio as the application of engineering concepts to biology -Advancements in DNA synthesis and sequencing technologies. Activity:  Construct a genetic circuit on a board and estimate time and costs to build it.

6: Biobricks

Topics: -BioBricks as standard DNA parts - Parts of a BioBrick - Types of BioBricks. -Biobrick assembly -The Registry of Standard Biological Parts Activity: Put compatible bricks together.

7: Biological machine

Topics: -Imagine the possibilities -Addressing high impact problems through biomachines. -Metabolic load -Advantages of biomachines over robots. Activity: "Labyrinth of metabolism" so that the visitor knows that "parts" must be manipulated to make a organism perform certain function.

8: Applications of SynBio

Topics: -Impact of SynBio in a wide variety of areas - Examples of issues solved through SynBio (How do these projects work?)  Activity: The visitor must correlate a specific genetic circuit to its application area.

9: iGEM

Topics: iGEM as the biggest synthetic biology competition, rules, motivation, scope. - iGEM UANL 2011 and 2012 -CIDEB-UANL 2012  Activity: -Explain our 2011 project -Exhibition of the light-machine used in our project -Explain CIDEB's 2012 project

10: Ethics and Biosafety

Topics: -Ethics definition -Human quality of life -Good and ugly -Impact awareness -Acceptance of SynBio -Potential problems -Precautions taken to prevent them -Biosafety levels Activity: Dress with biosafety equipment  (lab coat, glasses, gloves…) as fast as possible!

Description Back to top

Objectives

• To prepare the high school students from the CIDEB that are interested in participate in iGEM in the High School Division (HSD) of mentioned workshop in its version 2013 with introductory topics to molecular biology, engineering, nucleic acids manipulation, biology with data processing and synthetic biology.

• To present to the interested students in an easy, clear and precise panorama about the principal laboratory techniques that are used in synthetic biology in order to make them develop the ability to work in the laboratory.

• To aid the students with the doubts that can be presented during the workshop in order to increase their interest in molecular and synthetic biology.

Activities

During the Training workshop week, some activities took place:

1. In the semester July - December 2012, during 8 Saturdays some theory classes were given to the students with an approximate duration of 2 hours.

2. The laboratory workshop was given during the first week of December. Before starting work with the laboratory practice, an explanation was given.

3. The participants were divided in groups and there was designed a instructor for each group to help them with some doubts they can have so they were able to perform the practice by themselves.

The TOPICS in the Training Workshop Theory Class were the following:

Day 1 – 29 September

- What is DNA?

- DNA Properties

- DNA Structure

Day 2 – 6 October

- Genomics

- Structural composition of a gene

- Gene Function

Day 3 – 13 October

- Proteins

- Function of proteins

- Types of Proteins

Day 4 – 20 October

- Genetics Egineering

- Characterization through restriction enzymes

Day 5 – 27 October

- Synthetic Biology

- Assembly using Building Standards

Day 6 – 3 November

- BioBricks™ in the Parts Registry

- A detailed view to the BioBricks™

Day 7 – 10 November

- Biology Systems

- Metabolic Engineering

Day 8 – 24 November

- Checking of the iGEM projects

- Project requirements:

• Development of ideas

• Parts construction

• Human Practices

• Poster

• Wiki

• Presentation

Then, we continued with the practice section of the workshop as the following:

Day 1 – 10 December

• Practice 1: Manipulation of DNA plates lyophilized of BioBrick™

• Practice 2: Preparation and transformation of calcium competent bacteria

Day 2 – 11 December

• Practice 3: Inoculation and cultivation

• Practice 4: Miniprep

• Practice 5: Quantification by spectrophotometry

Day 2 – 12 December

• Practice 6: Characterization through restriction enzymes

Day 4 – 13 December

• Practice 7: BioBricks™ Assembly

• Practice 8: Ligation

Practices Handbook Back to top

As part of the activities of the training workshop that was performed by the iGEM-UANL team to prepare the CIDEB high school students interested in participate in the iGEM HSD a practices handbook was made to the students. The handbook was made with the objective to present to the CIDEB participant students an easy, clear and precise panorama about the principle laboratory techniques that are used in the synthetic biology, useful and needed tools for the development of projects in the iGEM HSD competition. In mentioned handbook a series of laboratory practices was included in order to teach the students topics since the use of the Parts Registry of the MIT and the manipulation of plates with BioBricks™, also the manipulation and assembly of them. Each procedure described in the handbook was made during the training workshop. Support material such as some simple bioinformatics tools was used in order to perform mentioned procedures.

The realization of the handbook had the principal purpose of introduce the CIDEB students in the basic, practice and experimental knowledge of the synthetic biology in order to prepare them to the iGEM HSD competition. Inside of the handbook was included a little section where the participants were able to write the obtained results in each practice and themselves could interpret them using the information studied in the workshop, as well as a section of questions that allowed us as instructors to know their weakness and explain the doubts later. We could observe that the use of the handbook with protocols and the experimental practice suring the training workshop were very useful to the participants, because they could develop the ability of working in the molecular biology and genetic engineering and they learn to take important notes to a efficient work in the laboratory. Notes that showed that they were understanding the calculus of the enzymes in cuts and ligations, the gels results, fragments size expected, notes about the bioinfomatics programs, Internet data or books that helped to the participants to obtain a critical mind with their experiments and achieve to formulate their own conclusions.