Paleogenetics Lab, General Genetic Labs

AWI - Alfred Wegener Institute

last updated: July 19, 2023

About the Laboratory

Paleogenetics Lab, General Genetic Labs

AWI - Alfred Wegener Institute

@ Geosciences / Polar Terrestrial Environmental Systems

This Laboratory is part of:

Networks: Geo.X

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Visit us on our website in DE / EN

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Description

The palaeogenetics lab is a part of the larger molecular genetic facility specialized to analyse ancient sedimentary DNA and is placed in a separate building apart from the modern and recent environmental lab and Post-PCR areas. In the palaeogenetics lab we analyse ancient DNA from sediment cores (lakes or marine archives) or permafrost deposits.
We apply DNA metabarcoding and metagenomics (shotgun and hybridisation capture) to investigate spatial and temporal biodiversity with the aim of identifying the taxonomic and functional composition of assemblages on population, community or ecosystem-level and their changes in Arctic (terrestrial and marine) ecosystems.

Instruments

DNA/RNA Extraction Kit
A fluorometer is an instrument that measures the amount of fluorescent radiation produced by a sample exposed to monochromatic radiation. Additional information available at "http://gcmd.gsfc.nasa.gov/cgi-bin/createsensorsupweb" [Summary provided by NOAA] (Source: Global Change Master Directory (GCMD). 2023. GCMD Keywords, Version 16.3 [...] )
Fluorometer
Fluorimeter
Homogenizer
PCR Cycler
Thermal Cycler, Thermal PCR Cycler
Clean Room Facility
PCR Workstation

Analytical Methods

Method used for determining the order of bases in long DNA using sequencing of DNA broken up randomly into numerous small segments. (Source: IUPAC; https://doi.org/10.1515/iupac.90.0262)
Shotgun Method
Shot Gun Sequencing
A fluorometer is an instrument that measures the amount of fluorescent radiation produced by a sample exposed to monochromatic radiation. Additional information available at "http://gcmd.gsfc.nasa.gov/cgi-bin/createsensorsupweb" [Summary provided by NOAA]
A fluorometer is an instrument that measures the amount of fluorescent radiation produced by a sample exposed to monochromatic radiation. Additional information available at "http://gcmd.gsfc.nasa.gov/cgi-bin/createsensorsupweb" [Summary provided by NOAA] (Source: NASA; UUID: e904c3c7-0111-4d09-bb01-2b7bea9b4d3f) Own comment: For Bioanalytics a fluorometer is used to measure quantity and quality of DNA. (Source: Global Change Master Directory (GCMD). 2023. GCMD Keywords, Version 16.3 [...] )
Fluorometry
Fluorescence Spectroscopy, Fluorimetry
DNA Isolation
DNA/RNA Isolation, Homogenization
Assay with specifically designed single-stranded DNA probe with a defined (known) nucleotide sequence usually immobilized on a surface (in such a case, the nucleic acid probe is called the capture probe). Note: The probe is used as a recognition element to test for the nucleotide sequence within the target DNA in the sample solution. If target DNA contains a sequence complementary to the probe, a hybrid dsDNA is formed. (Source: IUPAC; https://doi.org/10.1515/iupac.90.0262)
Hybridization Assay
DNA Hybridization Capture
Method for determining nucleotide sequence of DNA based on incorporating chain-terminating dideoxynucleotides. Note: The method is named after Frederick Sanger (1918–2013, awarded the Nobel Prize in 1958 and 1980). (Source: IUPAC; https://doi.org/10.1515/iupac.90.0262)
Sanger Sequencing
Chain Termination Sequencing
DNA Extraction
Next generation sequencing methods require a DNA library preparation prior to processing. (Own definition)
DNA Library Preparation
Determination of nucleotide sequence (the DNA primary structure). (Source: IUPAC; https://doi.org/10.1515/iupac.90.0262)
DNA Sequencing
Nuclear or mitochondrial DNA released into the environment as bodily secretions, hair, or similar materials other than whole individuals. Used to detect organisms that are not observed directly. (Source: USGS; https://apps.usgs.gov/thesaurus/term-simple.php?thcode=2&code=2055)
Environmental DNA
Metagenomics
Determination of nucleotide sequence (the DNA primary structure). Note: Next-generation sequencing refers to non-Sanger-based high-throughput DNA sequencing technologies where millions of DNA strands can be sequenced in parallel. (Source: IUPAC; https://doi.org/10.1515/iupac.90.0262)
NGS - Next Generation Sequencing
Massive Parallel Sequencing, Second Generation Sequencing
Laboratory technique for rapid amplification and pre-determination of regions of double-stranded DNA using DNA polymerase. (Source: IUPAC; https://doi.org/10.1515/iupac.90.0262)
PCR - Polymerase Chain Reaction
DNA Amplification, DNA Enrichment
Polymerase chain reaction to quantify target nucleotide sequences of interest. (Source: IUPAC; https://doi.org/10.1515/iupac.90.0262)
qPCR - Quantitative Polymerase Chain Reaction
DNA Amplification, DNA Enrichment, Quantitative PCR

Laboratory Keywords

In addition to the instruments and analytical methods listed above, these keywords help to describe the work done in the laboratory. This may include the type of samples, standard materials, specific preparative or analytical methods and specific instrument characteristics.

Ancient DNA
Cloning and Preparation for Sanger Sequencing
Metabarcoding
Microsatellites (SNP Analyses)
Preparation for Amplicon and Shot Gun Next-Generation Sequencing

Disciplines

Geoscience > Paleogeosciences > Paleogeoscience
Paleogeoscience
Interdisciplinary > Biology/Ecosystems Science > Biology
Biology
Interdisciplinary > Biology/Ecosystems Science > Ecosystem Science
Ecosystem Science

The Research Network for Geosciences in Berlin and Potsdam

Paleogenetics Lab, General Genetic Labs

AWI - Alfred Wegener Institute

About the Laboratory

Paleogenetics Lab, General Genetic Labs

Access

Description

Instruments

Analytical Methods

Laboratory Keywords

Disciplines

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