Microfuge Tubes
Microcentrifuge tubes (also called Eppendorf tubes or "microfuge" tubes for short) are commonly used to hold and mix small amounts of liquid. They may or may not actually be used in a microcentrifuge. In this laboratory, one may assume that microfuge tubes are sterile and free of contaminants (such as protein, DNA, or RNA). In order to keep the tubes uncontaminated by materials from your skin, you should not remove a tube by reaching into the storage beaker. Rather, pour one (or a few) microfuge tubes into the foil lid of the beaker, pick up the one tube that you will use (being careful to only touch its outside), and return the rest of the tubes to the beaker.
Vortexer
A vortexer (or "Vortex Genie") is a device used to facilitate mixing. To use a vortexer in pulse mode (as we nearly always do), make sure that the switch is set to pulse and press the tube containing the solution to be mixed down on the rubber cup on the top of the machine. The cup will vibrate as long as it is depressed. The speed of the vortexer can be adjusted by rotating the knob on the front. Usually the best speed is the fastest speed that will not slop the liquid out of the top of a tube (if it is open).
When do you use a vortexer? A vortexer can be used to mix small amounts of liquids in a test tube or microcentrifuge tube. However, if the amounts are very small, the microcentrifuge tube may need to be spun in a microcentrifuge for a few seconds to collect the liquid in the bottom of the tube again. For very tiny amounts of liquid (fewer than about 20 µl) it is more effective to mix by sucking the liquid in and out of the micropipette tip several times. A vortexer is particularly useful in resuspending centrifuged bacterial pellets, which may be difficult to dislodge. Most bacteria (such as the Escherichia coli that we commonly use) are quite robust and are not harmed by the agitation. In contrast, larger cells that are more fragile may be ruptured by the agitation. A vortexer should never be used to mix solutions containing enzymes, because the forceful agitation can decrease the enzyme's activity. In the case of enzyme solutions, the "finger flick" method of mixing (or moving the liquid in and out of a micropipetter tip) is more appropriate.
Microcentrifuge
Although we will not be using a microcentrifuge ("microfuge") for this week's experiment, we will use it commonly later in the semester. The purpose of a microfuge is the opposite of a vortexer. We use a microfuge when we want to force a suspended material into a pellet in the bottom of a microfuge tube. Two materials that we commonly centrifuge are bacteria and precipitated DNA.
Because of the high speed at which the microfuge operates, it is critical that the centrifuge be "balanced" and that the lid be closed properly before turning it on. Each tube in the microfuge must have another tube directly opposite of it in the rotor. If other students are also centrifuging a similar amount of material as you, you can just balance your tube with somebody else's tube. However, if there are an odd number of tubes to be centrifuged, then you must put a "dummy" tube opposite the odd sample tube. If the tube contains a negligible amount of material (i.e. less than 20 microliters), then you can simply put a closed, empty tube opposite the odd tube. However, if the volume is significant (more than about 20 microliters), then you should place in the dummy tube a volume of water approximately equal to the volume of the sample in the odd tube. Our lab has a variety of centrifuges which have a variety of lids. In some cases, the rotor must be covered with a plastic cap before closing the lid. It is easy to tell when someone has not followed the guidelines listed here because a loud buzzing or whirring sound can be heard when the microfuge is turned on. An unbalanced centrifuge can "walk" (vibrate) its way off of the tabletop and crash to the floor. Give the cost of a microfuge (over a thousand dollars), we do not want this to happen
Although the microfuges can be set for a variety of speeds, we usually just turn them on at full speed. The timers on some of the microfuges are not very good, so for short spins of less than a minute, it is often easiest to just turn the microfuge on with the timer set for a long time, then turn the knob to off manually after timing the spin with a watch or digital timer. The exact length of the spin is usually not very critical.
Depending on the amount of suspended material, you may or may not be able to see the pellet in the bottom of the tube. Because the tube is held in the rotor at an angle, the pellet is not actually in the bottom of the tube. It is somewhat off to one side. (Note the image at the above.) By noticing the orientation of the hinge of the microfuge tube lid (i.e. toward the center or toward the side), you can predict the location of the pellet even if you can't see it. Usually, after pelleting a suspension, one wishes to remove the supernatant by either pouring or sucking it out with a micropipetter. By knowing the position of the pellet, one can take care not to dislodge the pellet with the tip of a micropipetter. Fortunately, bacteria are relatively "sticky" and so bacterial pellets rarely fall out of their tube. However, large DNA pellets can sometimes slide out and be lost with the supernatant, so more care is needed with them.
