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Molecular laboratory

Our state-of-the-art facilities provide a great opportunity for a wide variety of researches, with a special emphasis on molecular population genetics and evolutionary ecology. These laboratories are open to students, staff, as well as visiting scholars.

Lab Facilities

• DNA Extraction and Gel Electrophoresis
• Post-PCR Laboratory
• The Genome Sequencing Laboratory

Equipments

• 1x DNA extraction robot
• 4x PCR machines
• 1x Q-PCR machine
• 1x GelDoc Gel imaging system
• 1 x Spectrofluorometer to measure DNA concentration
• 2x automatic CEQ8000 Beckman Coulter 8-capillary genetic analyzers
• 1x ABI 3130XL 16-capillary genetic analyzer
  
  

Lab Pictures

The DNA Extraction and Pre-PCR Lab

Many molecular projects in Fish Ecology and Evolution begin with the extraction of DNA from fish. The department is equipped with a DNA Extraction Lab where genomic DNA is regularly extracted from ethanol preserved specimens. Various methods and equipments are used to carry out the process of DNA extraction, including homogenizers to break down tissues, as well as water baths, shakers, incubators, extraction robot and centrifuges that are used to isolate DNA from the samples.

Post-PCR Lab

Once DNA is extracted, researchers set up PCR (Polymerase Chain Reaction) for amplifying genomic regions of interest. Actual procedure of PCR depends on the type of molecular techniques being used. In our lab we mainly use three techniques, DNA sequencing, microsatellites and AFLPs (Amplified Fragment Length Polymorphisms).

The Post PCR Lab is equipped with thermocyclers (PCR machines). Because an optimal PCR condition varies among organisms, target sequences and techniques, researchers pay special attention to find the best condition such as temperature, reaction time and a number of reaction cycles.

To determine whether a particular set of temperatures and reaction time have produced the desired PCR products, our researchers carry out an electrophoresis analysis.

Gel electrophoresis is the process of placing the DNA in a gelatin-like slab and applying an electrical current to the gel. Because DNA has a negative electrical charge it is attracted by and moves towards the positive side of the gel. How far it moves depends on its size. The DNA is stained with a special dye to make it visible and then compared against a DNA standard. The Laboratory is equipped with many gel boxes to carry out multiple runs of gel electrophoresis and a video documentation system to permanently record the results.

The Genome Sequencing Laboratory

Before loading samples to an auto sequencer researchers prepare their samples in one of the three genome sequencing labs.

Once the researchers have a successful PCR result, they determine the exact order or sequence of the bases in their amplified DNA sample. This is accomplished by using an automatic genetic analyzer. Our lab is equipped with three genetic analyzers, including two CEQ8000 Beckman Coulter 8 capillary sequencers and an ABI 3130xl 16-capillary genetic analyzer. These on-site genetic analyzers are most suitable for low to mid-throughput genetic analyses. High-throughput analyses in our department are outsourced to the Genetic Diversity Centre (GDC), a core sequencing centre in ETH. We are one of the main founding groups of GDC since 2008.

In the case of DNA sequencing, a fluorescent dye is attached to each individual base of DNA so that each of the four bases (adenine [A], thymine [T], guanine [G], and cytosine [C]) has its own distinct color. Another electrophoresis is then carried out within the automatic sequencer. This time each base (or letter) is separated from the others as the DNA is pulled through the gel in a capillary. The sequencing machine then relays the matching “letter” to a computer where the sequence is constructed.

After the sequencing run is complete, our researchers analyze the data on one of the three computers dedicated to analysis. We have Power Mac and PC computers installed with necessary software and dedicated exclusively for analysis.