Equipment and Services
AIMS Lab Equipment for Organismal Analysis
AIMS is developing and will maintain a Polar Microbial Culture Collection that is used to perform a complete phenotypic and genomic characterization, including growth kinetics across environmental conditions (i.e. temperature, pH, salinity) as well as nutritional and energy requirements. AIMS already maintains 216 isolates. Details on these organisms will be coming soon.
Microbiology Suite
Microbiology suite was renovated in 2020 with support from Alaska INBRE. This room contains a laminar flow hood, two UV hoods, NanoPure water, and a gassing station.
Incubators
The AIMS lab maintains five incubators with a temperature range of 4-75掳C, two shaking incubators with a temperature range of 4-65掳C, and a CO2 incubator.
Anaerobic Chamber
The Core also provides equipment and expertise needed to grow microbes requiring anaerobic conditions including a Bactron anaerobic chamber with internal incubator. The Bactron anaerobic chamber allows for culturing microbes in oxygen depleted environments. The chamber also contains an incubator to maintain optimal growth temperatures (between room temperature to 55掳C) while under anoxic conditions.
Eppendorf Bioreactor
The Eppendorf DAS-Box 8 is a unique mini bioreactor system for microbial and cell culture as well as stem cell applications. It can run up to eight parallel incubations in working volumes of 60-250 mL. All critical process parameters can be precisely controlled with the DASware software suite. Gasses can be controlled for both aerobic and anaerobic incubations. Users must be trained by AIMS personnel before use.
BioTeck Cytation 5
The Cytation is a cell imaging multimode plate reader. This combines automated microscopy and conventional microplate detection in a configurable platform. The microscopy module offers up to 60x magnification in fluorescence, brightfield, high contrast brightfield, color brightfield, and phase contrast. The multimode detection modules include filter and monochromator-based fluorescence detection, luminescence, and UV-Vis absorbance detection. The additional Take3 plate allows for simultaneously reading DNA concentrations from 2uL of sample for up to 16 samples.
AIMS Core Equipment for Molecular Analysis
Molecular Analysis is needed to understand microbial life especially when pure cultures are not available. The AIMS Core provides specialized nucleic acid extractions, library prep and sequencing services specific for the microbiome including genome, transcriptome, metagenomic, metatranscriptomic, and amplicon sequencing of the 16S, 18S, and ITS (fungal and plant) rRNA gene sequencing. Below is the key equipment available for molecular analyses.
Illumina MiSeq
The AIMS Core maintains an Illumina MiSeq that can produce up to 200 million DNA sequences at a length of 600bp (300bp paired end) that are high quality (95% >Q30). This level of sequencing is sufficient for sequencing of microbial genomes and transcriptomes of isolates, and amplicon sequencing. Protocols are currently in place for 16S, 18S, and ITS regions. Contact us for additional amplicon targets.
Molecular Clean Room
All DNA extraction activities occur in the Molecular Clean Room to ensure contamination free sample preparation.
Covaris Ultrasonicator
This is a high precision sonicator for shearing DNA at user defined lengths.
Oxford NanoPore MinION
The MinION is a portable devise that sequences DNA bases on electrical changes caused by nucleotides that pass through a port. This can produce very long DNA reads.
Thermocyclers
Thermocyclers include ABI Veriti 96 well Fast PCR, and three ABI SimpliAmp. All are capable of running 96 samples.
Agilent TapeStation
An automated electrophoresis tool for DNA and RNA sample quality control. This provides an analysis of size, concentration, and integrity.
Blue Pippin
Automated size selection using gel cassettes. Fragment sizes can range from 90bp-50kb.
MP Biomedicals FastPrep
The FastPrep is a bead beater that is capable of lysing complex materials. Adapter are available for 2mL, 15mL, or 50mL tubes.
PCR Hood
A PCR hood equipped with UV light sterilization is a available for all pre-PCR needs.
AIMS Core Equipment for Bioinformatics
Bioinformatic analyses are often needed to understand the large and complex datasets created in microbiome research. The AIMS lab also supports bioinformatic analyses.
Bioinformatic Server
The AIMS Lab maintains two bioinformatic servers. The Beowulf cluster is a teaching server that provides a GUI interface for navigating a linux server. Key bioinformatic programs are installed and training modules are provided through BIOL A455 and A655 Experiential Learning: Bioinformatics. The Beowulf Cluster is a 64-core parallel-compute cluster supporting up to 128 parallel execution threads. The Beowulf cluster has 512Gb of RAM and sixteen 1 Tb SATA drives.
The AIMS Core also supports a research server. This cluster is a 64-core parallel-compute cluster supporting up to 128 parallel execution threads with 1,024Gb of RAM and sixteen 2.4Tb SATA drives. Contact the AIMS core for training and login permissions for either server.
Contact
A laboratory manager is on hand to provide training on equipment, perform sample analysis, and to support bioinformatic analysis. Contact us at uaa_aims_core@alaska.edu