State of the art research infrastructure

The Agilent 2100 Bioanalyzer is used during library preparation for next generation sequencing with the Illumina MiSeq. It makes use of microfluidics to determine DNA quality and fragment length distribution. In principle it is an advanced form of gel electrophoresis.

The digital PCR (dPCR) system is a quantitative method to measure specific DNA or RNA amounts. dPCR is a simple and reproducible method that does not rely on a calibration curve for sample target quantification. While PCR carries out one reaction per single sample, dPCR carries out the same single reaction, however, the sample is separated into many partitions and the reaction is carried out in each partition individually. This separation allows a more reliable collection and sensitive measurement of nucleic acid amounts. This method has been demonstrated as useful for studying variations in gene sequences and clonal amplification of samples for next-generation sequencing. 

The digital sonifier has 3 parts: converter, disruptor, and probe. This apparatus is ideal for cell disruption, nanoparticles, chip assay, emulsification, homogenization, cell lysing, processing DNA and proteins, acceleration of reactions, leaching and extraction, and fine mixing degassing. The sonifier takes advantage of multiple modes of operation, including continuous, pulsed, timed, and temperature end-point.

The thermocycler is also known as the PCR machine, or DNA amplifier. It is most commonly used to amplify segments of DNA via the polymerase chain reaction (PCR). The cycler raises and lowers the temperature of the heating block in discrete, preprogrammed steps. This apparatus can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion. 

The Illumina MiSeq is a benchtop next generation DNA sequencer. The most used application in the EBG group is 16S/18S rRNA amplicon sequencing, which provides information on who is there in biological samples. Sediment, soil, reactor and culture samples are typically extracted using Qiagen DNA extraction kits but in specific cases the phenol/chloroform method is also used. After extraction, amplicons are generated by PCR using primers targeting Bacteria, Eukarya, and/or Archaea. DNA libraries for sequencing are created in a second PCR reaction. The Miseq generates clusters of DNA strands using solid phase PCR bridge amplification. DNA is then sequenced using fluorescence scanning and the data is compiled and sent to our in-house server. Data produced by the Miseq instrument is usually processed using the in-house online platform MetaAmp, which performs quality filtering, clusters reads into operational taxonomic units, or creates amplicon sequence variants, taxonomic classification, and analyzes alpha and beta diversity. 

MetaAmp

The bead ruptor is a powerful tool specifically designed for grinding, lysing, and homogenization of biological samples prior to molecular extraction. Using sample tubes pre-filled with lysing beads, the bead ruptor vigorously and uniformly shakes the tubes providing an efficient, consistent, high-yield, and quality homogenization in as little as 40 seconds.

This is a different DNA sequencing technology which compliments Illumina sequencing. It provides a smaller number of very long sequence reads which improve DNA assembly in complex biological samples. It consists of ‘flongle’ and ‘minION’ flow cells as well as a dedicated GPU based server for data collection and flow cell conditioning. Nanopore sequencing works by passing DNA through nanopores, while recording the voltage over those pores, a signal that responds differently to the four DNA bases. 

The Qubit by Invitrogen is a bench top instrument used for quantification of DNA, RNA, and protein. The Qubit fluorometer uses fluorescent dyes to determine the concentration of either nucleic acids or proteins in your sample. New illumination and detection technologies allow you to use as little as one microliter of still and still attain high levels of accuracy, even with dilute samples.

The PikoReal Real-Time (RT) PCR system is a gene quantification and genotyping machine in 24- and 96-well block formats. Using the system’s software, it is applicable to absolute quantification, relative quantification, melt curve analysis, high resolution melt analysis, and allelic discrimination. It is more sensitive than microarrays in detecting small changes in expression.

The transilluminator is located in our molecular biology lab to view DNA (or RNA) that has been separated by electrophoresis through an agarose gel. After the gel is stained with a fluorescent dye which binds to nucleic acids, the gel is exposed to UVB light source that causes the DNA-dye to fluoresce and become visible. This is used whenever the researcher needs to view their sample, such as sizing a PCR product.

The bioreactors are the core equipment of the Energy Bio-Engineering group. The extensive bioreactor facilities allow us to investigate many different bioprocesses in parallel and create dynamic processes with advanced process control. Typically, when developing a new bioprocess we would start with a vision of what the full scale process will ultimately look like and down scale that process into a laboratory bioreactor. Bioreactors can contain suspended bacteria, biofilms, aggregates, whatever is most suitable. We develop bioprocesses for environmental or energy applications and make use of microbial communities instead of pure cultures. The unique aspect of our group is that we combine the bioreactor engineering with metagenomic characterization of bioprocesses and make use of these molecular data for optimization, troubleshooting and to create IP. While the ez-Control accurately controls pH, temperature, dissolved oxygen, foam/level and agitation in bioreactors and fermenters. The color touch screen interface guides the user through the intuitive operation.

The 5977A MSD is a single quadrupole mass spectrometer combined with a custom assembled heated direct injection port. This instrument is used for continuous monitoring of gasses such as oxygen and methane in gas streams.

This is a valved gas chromatograph mainly used to quantify inert gasses (e.g. oxygen, nitrogen, carbon dioxide, hydrogen, nitrous oxide) and volatile hydrocarbons (e.g. methane, ethane) in gaseous samples. It is equipped with flame ionization detector (FID), electron capture detector (ECD), and thermal conductivity detector (TCD).

Ion chromatography is a form of liquid chromatography, measuring concentrations of ionic species by separating them based on their interaction with a resin. Sample solutions are passed through a pressurized chromatograph column where ions are absorbed by column constituents. As an extraction liquid, known as eluent, runs through the column, the absorbed ions begin separating from the column. This ion chromatography system fitted with an anion column can measure concentrations of major anions, such as fluoride, chloride, nitrate, nitrite, and sulfate. Concentrations of organic acids can also be measured using cation chromatography.

The high-performance liquid chromatography (HPLC) is a chromatographic technique used to separate a mixture of compounds. The main purpose is to identify, quantify and purify the individual components of the mixture. In small amounts, the sample mixture is sent into a stream of mobile phase flowing through a column. The times at which a specific analyte emerges from the column is the retention time, and is considered as one of the identifying characteristics of a given analyte. 

The highly-sensitive fluorescence detector is ideal for analysis of carbohydrates, glycans, and polyaromatic hydrocarbons (PAHs). A number of small molecules (ex. acids) can be analyzed using metal chelation. Our fluorescence detector is connected with the Thermo Scientific Dionex UltiMate 3000 UHPLC system. 

The liquid scintillation counter (LSC) provides high performance for laboratories detecting and measuring ionization radiation by using the excitation effect of incident radiation on a scintillation material. Scintillation is an emission of light produced in a transparent material by the passage of a particle, whether it is an electron, an ion, or a high-energy photon. The basic principle of operation involves the radiation reacting with a scintillator, which produces a series of light flashes of varying intensity, and the intensity of the flashes is proportional to the energy of the radiation.

The radioisotope lab is equipped with the apparatus and equipment needed for performing distillation procedures with radiolabeled 35S sulfate for determining the rate of sulfate reduction in soils and sediments. The cold chromium distillation process yields higher radiotracer detection levels while reducing the amount of background radioactivity.

The microscope is used to visualize bacteria and protists in bioprocess samples. It is equipped with bright field, differential interference contrast microscopy (DIC), fluorescence and several filtersets and a sensitive digital camera. It can also be combined with labeled molecular probes for fluorescence in situ hybridization (FISH and/or CARD-FISH).

The ultrasonic bath is a common technique for ultrasonic extraction procedures and high-quality cleaning. This equipment uses high-frequency, high-intensity sound waves in a liquid to facilitate or enhance the movement of particles from surfaces submerged in an ultrasonically activated liquid. 

Our vinyl anaerobic chamber eliminates oxygen to 0-5 parts per million (ppm) using a hydrogen gas mix reacting with a palladium catalyst to remove oxygen by forming a water molecule. A vacuum airlock is used to reduce oxygen levels prior to transfer of samples and tools in and out of the glove box. 

The PIPETMAX is an automated pipetting machine for efficient processing of high-throughput biological assays. It helps improve the accuracy, reproducibility, and consistency during sample processing.

Freeze drying is a water removal process by sublimation of ice from frozen material at reduced pressure and requires storage in an inert atmosphere either under vacuum or at atmospheric pressure in an inert gas. The freeze dryer is an important piece of equipment in sample preparation and for the preservation and storage of biological samples, including proteins, plasma, viruses, and cell lines. The nondestructive nature of this process has been demonstrated by the retention of viability in freeze dried viruses and microorganisms.

The microcalorimeter consists of a highly precise thermostat that maintains the stable temperatures within a 1 microkelvin range. Continuous bioprocesses can be operated within the thermostat and heat production can be measured with extremely high sensitivity and accuracy.

Our specially designed one-of-a-kind temperature gradient blocks generate a gradient which can be used to determine the maximum, optimum, and minimum temperatures of growth for microorganisms. By establishing a gradient, multiple microcosms or reaction mixtures held in wells on the gradient block can be simultaneously run at temperatures that differ only slightly, thereby permitting an optimum temperature for your experiment. The gradient block temperatures can be set to as low as -25°C to a maximum of 120°C. There are 47 lateral wells for 47 individual temperature points and 6 vertical wells per temperature point to create accurate replicates. 

The muffle furnace is widely used in laboratories with means to create a high-temperature up to 1200°C. It is ideal for ashing most types of organic and inorganic samples. The furnace is an oven type instrument that achieves its high-temperature on the basis of the insulating material which is fitted inside the chamber. The insulation acts as a muffle and stops the heat from escaping. It is mainly used to determine volatile organic solids and ash contents of biological samples. 

The speed-vac is used to concentrate small-volume samples. Under vacuum (very low pressure), the vapor-liquid equilibrium of the solvent is shifted towards the gas phase, while the sample (DNA, peptide, etc.) remains primarily in the solid phase. Using a vacuum solvent can be easily removed with very little stress on the solute, leaving a dry, solid sample (plus salts that were present in the solvent buffer, etc.). Speed vac concentration systems use a technique that combines centrifugal force, vacuum, and applied heat to eliminate sample bumping and foaming.

The ultracentrifuge is used for density gradients such as percol (to separate individual cells) or cesium chloride (to separate labeled DNA in stable isotope probing applications). It is also used to separate viral particles to characterize the virome with next generation sequencing. Spinning up to 100,000 rpm, the ultracentrifuge delivers the speed and performance required for these high performance applications.