Description:

• The Institute of Molecular Systems Biology (IMSB) has granted us use of a shelf in one of the -80°C freezers within the institute’s freezer farm, located on the A-floor of the HPM building.

• Samples are stored in standard cardboard boxes and need clear labeling to indicate:
  • Potential hazards.
  • Owner identity.

Typical Uses:

• Properly frozen and stored at -80°C, bacteria, yeast cells, and mammalian cell lines can remain viable almost indefinitely.
• -80°C storage is also recommended for flash-frozen samples of purified proteins.

Description:

• Applying heat above 121°C for more than 20 minutes is a very effective sterilization method.
• Autoclaves use pressurized steam for sterilization, allowing efficient heat transfer and heating of water-based solutions beyond water’s boiling point.
• Note that pressurized steam and super-heated liquids can cause severe burns.
• A number of precautions are required to use an autoclave safely, and users must receive an introduction to safe use before operating it for the first time.

Typical Uses:

• Autoclaves are routinely used to sterilize both solid objects (e.g., glassware and plastic consumables) and aqueous solutions.
• This autoclave has specific features that make it especially effective for sterilizing large solution volumes and solids enclosed in bags.

Description:

• The lab has a small centrifuge suitable for 1.5 ml “Eppendorf” tubes.
• Larger centrifuges, for sample volumes ranging from a few milliliters to liters, are available through the institute’s shared equipment pool.

Typical Uses:

• Centrifuges are used to separate solids (such as cells and aggregated macromolecules) that are finely dispersed in solutions or growth media from the surrounding liquids.

Description:

• A chemical fume hood maintains a constant, gentle airflow from the room into its interior.
• The air is then filtered and expelled outside the building.
• Ventilated cabinets below the hood provide safe storage for volatile and highly flammable liquids (e.g., organic solvents) and corrosive liquids (e.g., concentrated acids).

Typical Uses:

• Facilitates safe handling of chemicals that may release harmful fumes or dust.
• Commonly used when weighing dry chemical powders for solutions or pouring acrylamide gels for electrophoresis

Gel electrophoresis is a technique used to separate and analyse biomacromolecules (such as DNA, RNA, and proteins) based on their size (and, in some cases, charge) within a porous gel matrix. Under an applied electric current in an aqueous solution, the negatively charged molecules migrate toward the positively charged electrode, where smaller fragments move faster and travel farther through the gel pores than larger ones. This allows for approximate sizing and identification of the molecules or fragments by comparison against a size standard or ladder.

Gel electrophoresis is widely used for applications such as verifying the presence or size of DNA fragments (e.g. colony PCR, restriction enzyme digests), isolating individual fragments from preparative gels, and analysing proteins (e.g. SDS‑PAGE).

Gels / samples are usually mixed with a visualising agent (e.g. DNA-intercalating agents such as GelRed dye). The gel imager (AlphaImager) allows for said visualisation of the gel using UV light, which causes various dyes to fluoresce. Images can be saved digitally.

Requires LSL staff instruction for first time use.

Description:

• The Zeiss AxioVert 35 is a high-quality, older model inverted microscope, designed with the objective below the sample stage to view samples from the bottom.
• It has four objectives with magnifications of 2.5x, 10x, 20x, and 32x.
• The microscope supports bright-field, phase-contrast, and GFP fluorescence modes (GFP fluorescence available only at 20x and 32x).
• An introduction is required before first-time use.

Typical Uses:

• In inverted microscopes, light passes from a light source positioned above the sample, through the sample, and into the objective below.
• This design works best with samples that are thin and transparent.
• Common applications include observing cells grown on the bottoms of cell-culture flasks and examining thin samples on microscope slides.

A laminar flow hood is a partially enclosed workbench which allows for work in a sterile environment. Air is drawn through a HEPA filter and is circulated in a unidirectional flow across the work surface, creating a separate environment which prevents the contamination of samples through airborne particles.

Please note that the current setup does not allow for the sterility required for sensitive tissue cultures (mammalian or plant cell cultures).

Usage instruction included in general lab introduction.

Description:

• Liquid chromatography systems, such as the Äkta Xpress, integrate valves, pumps, detectors, and fraction collectors with a computer control system to enable automation of liquid chromatography experiments.
• These systems can be equipped with a variety of chromatography columns to separate molecules based on a range of physical and chemical properties (e.g., size, charge, ligand affinity).

Typical Uses:

• In biochemistry and molecular biology, liquid chromatography is commonly used to isolate specific biological macromolecules, especially proteins, from complex cellular samples.
• It enables the study of the properties and biochemical activity of these macromolecules in isolation from other surrounding molecules within a cell.

Liquid nitrogen (with a temperature of circa -196°C) is used for the immediate freezing of samples (“snap freezing”), which is useful for cryopreservation purposes – samples/cells are less likely to be destroyed or killed via this immediacy compared to slower cooling processes.

Handling liquid nitrogen is dangerous and requires additional safety precautions to be met (use of a suitable container, full coverage of the user’s body and wearing an additional face visor and insulated gloves).

Requires LSL staff instruction and supervision for first time use.

Description:

• This plate reader is fully equipped for absorbance, fluorescence, and luminescence measurements of samples, capable of handling both cuvettes and multiwell plates.
• It features monochromator-based optics, allowing freely selectable wavelengths over the UV-to-NIR range.
• Equipped with an injector, thermal regulation, and agitator hardware, it can handle complex measurement protocols.
• Computer control enables the instrument to run complex mixing and measurement sequences.

Good to Know:

• Plate readers like this one are used to automate optical measurements on liquid samples.
• Typical applications include checking cell growth, measuring enzymatic activity, and determining the concentration of specific chemicals in samples.

Description:

• PCR machines perform precise heating and cooling cycles required for the Polymerase Chain Reaction (PCR).
• This reaction enables the selective and exponential amplification (copying) of specific DNA sequences, even in the presence of various other DNA sequences

Typical Uses:

• PCR is used extensively in molecular biology and genetic engineering experiments.
• Common applications include detecting specific DNA sequences in a sample (e.g., checking for genetic modifications in organisms or identifying specific microorganisms).
• PCR is also used to generate DNA samples for transfer into other organisms.

A pH electrode is used to measure the pH (acidity or alkalinity) of a given sample or media via hydrogen ions (H+), allowing for the manual adjustment using acids or bases (usually solutions of HCl or NaOH).

Calibration of the pH meter using standard solutions at different pH levels (e.g. pH 7.0, 4.0 and 10.0) is required and recommended before every use.

Requires LSL staff instruction for first time use.

Description:

• This is a high-precision balance for weighing moderate quantities (up to 200 grams) of samples with extremely high precision (± 0.01 mg).
• Other balances are available for larger quantities.

Typical Uses:

• The balance is typically used to weigh small quantities of dry chemicals for preparing solutions.
• Another use is measuring biomass from liquid cultures, where cells are captured through filtration, and the filters are then dried and weighed.

Description:

• Real-time PCR machines can perform the heating and cooling cycles that enable exponential DNA copying via Polymerase Chain Reactions (PCR).
• Unlike traditional PCR, in real-time PCR, the main interest lies in tracking the rate of the exponential DNA copying reaction, rather than the PCR products themselves.
• These machines are equipped with a multi-channel fluorescence detection system that measures the concentration of fluorescent molecules, which are released each time a DNA molecule is copied.

Typical Uses:

• Real-time PCR machines are employed in a wide range of experiments, with the two most popular uses being:
  • Determining an individual’s genotype at a specific location in their genome.
  • Measuring the concentration of a specific DNA or RNA sequence in a sample.

Description:
The lab houses two large-capacity shaking incubators, which can be temperature-adjusted from room temperature to 80°C and orbital shaking from 20 to 400 rpm (rotations per minute). They can hold different flask sizes, with fixtures to accommodate flask volumes between 50 mL to 5L, alongside racks for cell culture tubes.

Typical uses:

• The incubators are primarily used to grow aerobic bacteria and other microorganisms dispersed in liquid media at their optimal growth temperatures.
• Using dilute starter solutions or individual colonies from agar plates as inoculants allows for the dense growth of liquid cell cultures.
• By measuring the optical density of a sample (OD600), one can determine the number of cells present in the sample.
• Liquid cultures are e.g. used for the production and amplification of desired DNA plasmids or protein expression.
• Liquid cultures are useful for the long-term storage of an individual strain. This is done by cryopreservation, using glycerol as a cryoprotectant for storage at -80°C (hence the name “glycerol stocks”).

Description:

• The lab houses two large-capacity incubators that can be temperature-adjusted from room temperature to 100°C.

Typical Uses:

• The incubators are primarily used to grow bacteria and other microorganisms on agar plates at their optimal growth temperatures.
• Using dilute starter solutions allows individual cells to spread out on the agar plate, where each cell grows into a small colony visible to the naked eye.
• By counting the number of colonies, one can determine the number of individual cells initially present in the sample.

The Olympus SZ51 is a type of optical microscope which allows for the three-dimensional view of a specimen (rather than the 2D-view in compound light microscopes, which typically require sample preparation on glass slides).

Also known as a dissecting microscope, stereo microscopes aid in the study of larger multicellular organisms (e.g. plants, insects), and can be used for precise tissue dissection in these fields.

It has a set of 10x eyepieces, allowing for a magnification range of 8x to 40x, with moveable LED light sources.

Usage instruction included in General Lab Introduction.

The water bath and heat plate are used for the uniform heating of small samples (usually in 1.5-2 mL Eppendorf tubes) up to 100°C. They are used in standard molecular biology practices such as the genetic transformation of cells using the heat shock method, to maintain the correct temperature conditions for the enzymatic digestion of samples, or for the thermal denaturation of proteins.

Usage instruction included in general lab introduction.