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Molecular facilities

A wide range of DNA techniques and data analysis.

Our lab facilities


Ancient DNA lab
Ion Torrent lab
Barcoding sampling lab
Barcoding molecular lab
Post lab

Ancient DNA lab

In this laboratory, DNA extractions on very old specimens such as mammoths and museum material, are performed under ultra clean conditions.

1. PCR-cabinet. Provides an ultra-clean working space during PCR setup minimizing the risk of contamination. A powerful UV light is used to sterilize the interior before use.
2. UV cross linker. Sterilizes all lab ware before use.
3. Extraction cabinet. Provides an ultra-clean space to work in during DNA extraction. A powerful UV light is used to sterilize the interior before use.

Ion Torrent lab

In this laboratory, large amounts of DNA reads from e.g. environmental samples or genomes, are produced cost and time effective by means of next generation sequencing.

1. One Touch 2. Attaches one DNA fragment to a particle. This fragment will be multiplied on the particle.
2. Enricher. Purifies only the particles with DNA attached to them out of the mix coming from the One Touch 2.
3. Ion Torrent. Sequencer which can simultaneously read the DNA-sequence of 1,000,000 fragments. Each fragment is attached to a particle and each particle is in its own well on a chip.
4. Argon tank. Provides pressure for the operation of different Ion Torrent machines.
5. Server. Processes all data from the Ion Torrent.

6. Bioanalyzer. Determines the length and concentration of DNA-fragments by means of a chip.
7. Qubit fluorometer. Quantitates DNA, RNA, and protein concentration with fluorescence.
8. QIAxcel. Determines the length and concentration of DNA-fragments.

9. Thermocycler. Amplifies the signal of particular DNA-fragments by means of a chain reaction.
10. Real-time thermocycler. Amplifies the signal of particular DNA-fragments by means of a chain reaction. During the reaction the amount of DNA is measured with fluorescence.
11. SpeedVac. Removes solvents from DNA-solutions for long term storage.

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Barcoding sampling lab

In this part of the DNA barcoding lab, specimens are photographed, sub-sampled and prepared for high-throughput DNA extraction.

1. SLR setup. To photograph samples larger than 3 cm.
2. Carl Zeiss Discovery V20 stereo microscope for stacking photography. To photograph samples smaller than 3 cm. By merging several photographs of one sample, at different focal planes, a single final photograph is created in which the entire sample is in focus.
3. Carl Zeiss Discovery V12 stereo microscope for stacking photography. To photograph samples smaller than 3 cm.

4. Carl Zeiss Discovery V8 stereo microscope. Enlarges up to 60x to aid with subsampling small samples.
5. Hot bead sterilizers. Sterilizes forceps in 20 seconds, without damaging them, by using glass beads heated to 250°C.
6. Fume hood. Extracts hazardous vapors of e.g. alcohol or formalin.
7. Cabinet. For temporary storage of samples.

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Barcoding molecular lab

In this part of the DNA barcoding lab, DNA is extracted and prepared for PCR.

1. Vortex. For mixing the contents of plates or tubes.
2. Shaking heat block. Heats the contents of plates while shaking them, thus dissolving tissue.
3. Scales. For very accurately weighing chemicals.
4. Centrifuge. Can spin plates at 3700 rpm to move all liquid to the bottom of the wells.
5. Scanner. Reads the matrix-codes on the bottom of tubes with DNA-extracts.

6. Xiril pipetting station. Automatically fills plates, creates dilutions, reaction mixes and can join samples from several plates to a single plate using 8 automatic pipettes.
7. Fume hood. Extracts hazardous vapors of e.g. chloroform.
8. Heat block. Heats tubes accurately to the desired temperature.

9. Kingfisher extraction robot. Extracts DNA from dissolved tissue using magnetic beads. These beads are covered with a coating to which the DNA is attached.
10. SELMA pipetting station. Can pipette an entire plate at once with 96 pipettes.

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Post lab

In this laboratory, the size and amount of DNA in PCR products is analyzed.

1. E-gel. Separates DNA-fragments of different lengths by running them on an agarose-gel with an electric current. Additionally ethidium bromide is attached to the DNA.
2. Gel imager. Visualizes DNA-fragments in an agarose-gel with uv-light. Ethidium bromide, attached to the DNA, is illuminated by uv-light.

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For more information about our Molecular facilities, please contact Arjen Speksnijder, Head of Laboratories

arjen.speksnijder@naturalis.nl