In the lab we used many devices to perform our experiments. Followed is a short description of each equipment.
The MiniSpin Centrifuge (figure 1A) is a powerful centrifuge that can accelerate up to twelve 1.5/2.0 ml Eppendorf Tubes to a maximum speed of 13,400 rpm (rcf: 12,100 x g). Balance is very important for this equipment. We used this centrifuge for several experiments, such as PCR Purification, Miniprepping, Gel Extraction and preparing samples for FACS.
The Tabletop Centrifuge (figure 1B) can be used to centrifuge culture tubes. For this centrifuge, balance is also very important, just as with the MiniSpin Centrifuge. We used this centrifuge for several experiments, such as miniprepping.
MJ Mini Thermal Cycler
The compact, 48-well MJ Mini thermal cycler (figure 2) is a powerful thermal cycler that has been used to perform all kinds of PCR reactions, such as digestion and ligation. 0.2 ml PCR tubes can be used. Its thermal range is 0-99°C. This thermal cycler also offers a thermal gradient technology, so that you can optimize reactions for maximum efficiency and accurate quantification with a gradient range of 35-99°C.
This equipment allows high-resolution scans of for example monochromatic fluorescence gels and Western Blots. We used it to make scans of all of our agarose gels and SDS PAGE gels.
NanoDrop 1000 Spectrophotometer
The Thermo Scientific NanoDrop 100 Spectrophotometer measures 2 μl samples with high accuracy and reproducibility. It also has the capability to measure highly concentrated samples without dilution (50X higher concentration than the samples measured by a standard cuvette spectrophotometer). The NanoDrop software has several modes. We always selected the Nucleic Acid option, because we only measured the concentration of DNA samples. Before you can measure the concentration of your samples, you have to place a 2 μl MiliQ sample on the NanoDrop to perform a blank measurement. After this the pedestal needs to be cleaned before you can place your first sample. Cleaning after every sample is very important to prevent contamination and accurate measurement.
The Gallenkamp Environmental Shaker Model has been used for small culturing and protein expression. It can speed up to 400 rpm in combination with a wide 32 mm orbit. We used a shake incubator with standard settings of 37°C and 250 rpm. In our lab there is also a shake incubator for which you can determine the settings on your own. We used this one for protein expression.
Cary Eclipse Fluorescence Spectrophotometer
This fluorescence spectrophotometer uses a Xenon flash lamp for superior sensitivity, high signal-to-noise, and fast kinetics. It measures the emission of light from samples in four modes (fluorescence, phosphorescence, chemi/bioluminescence, and time resolved phosphorescence). Using Xenon lamp technology, it captures a data point every 12.5 ms and scans at 24,000 nm/min without peak shifts. The Cary Eclipse is the only spectrophotometer with room light immunity. A cuvette is needed to be able to measure.
Tecan Infinite F500 Plate Reader
The Infinite F500 is Tecan’s most sensitive filter-based multimode microplate reader. It is capable of reading 6 to 384-well plates, including standard, half-area and low volume 384-well plates. This plate reader is ideal for a broad range of applications, in particular ratiometric assays. It has been used for fluorescence- and luminescence-based assays. Its high speed allows complete reading of a 1,536-well plate in under 30 seconds. The wavelength range for fluorescence varies for excitation from 230 to 900 nm and for emission from 280 to 900 nm. This plate reader gives the intensity value at a specific excitation and emission. This excitation and emission value can be chosen with a specific filter.
Tecan Safire 2 Plate Reader
The Safire 2 is also a plate reader from Tecan that offers a range of high-speed detection techniques. It can be used to measure fluorescence, luminescence, and absorbance. It eliminates the need for cumbersome filter changes and allows for pinpoint precision, accuracy, and sensitivity. This plate reader gives the intensity value for a broad range of wavelengths. This gives you a spectrum of intensity values as a result.
This incubator has two separate parts. The 37°C incubator has been used to dry agar plates before plating and to grow the bacteria on the plates. The 50°C incubator has been used for gel extraction. It maintains optimal temperature, humidity and other conditions such as the carbon dioxide (CO2) and oxygen content of the atmosphere inside.
The water bath has been used during transformation. It is set at 42°C, which is the temperature at which the bacteria need to be heat shocked.
The thermomixer conveniently offers simultaneous mixing and temperature control. It has a mixing speed from 300 to 1,500 rpm and a temperature accuracy of 20°C to about 45°C. In our project it has been used to incubate bacteria such as NovaBlue and NEB-5α.
The autoclave has been used to autoclave LB medium, LB agar, 2YT, MiliQ, Eppendorf tubes, PCR tubes and sequencing tubes. We have two different autoclaves present in our lab.
Eppendorf BioPhotometer (OD 600)
The BioPhotometer from Eppendorf is used for rapid, simple and convenient measurement of the most common methods in research labs in the fields of molecular biology and biochemistry. Standard rectangular cuvettes made of glass or plastic that transmit light at every measuring wavelength may be inserted into the cuvette shaft. We used the OD600 mode to measure the OD, which is an indication for the absorption at a wavelength of 600 nm and consequently for the amount of bacterial cells that are present.
BD FACSAria III
A Fluorescence-Activated Cell Sorter (FACS) is a specialized flow cytometer. The FACS can provide information about cell size, complexity and fluorescence. The relative cell complexity is measured using size scatter (SSC). The relative cell size is measured using forward scatter (FSC). The fluorescence can be measured using a wide range of filters. These cell characteristics can be combined to sort cells.