Posts Tagged ‘cell’

Sizes in Biology

In animation, cell, Cool stuff, DNA, molecular biology on June 30, 2010 at 6:09 pm

Dear colleagues,

An excellent tool is available to get a feeling about molecular sizes in Biology.

The tool is available here and was developped by “Learn Genetics” program from the University of Utah.

You can have a short movie on it below, but please check the original one from here!!!


Why Molecular Biology?

In animation, cell on February 19, 2009 at 3:14 pm

At the very end you might ask why is the life in a molecular biology lab so interesting?

We discussed about water, pipettes and we will go on with several topics, but at the very end there is a wonderful, miraculous world. Each cell in our body and each cell in any living organism works based on the same principles. Information is stored, processed and replicated in cells.

If we could have an insight into these processes we could better understand what is life. Yes, I think this is still a question! What is life? How can you explain the abundance seen on every cubic centimetre of the surface of this planet?

Instead of giving a flat answer, let us look to the best animation I have ever seen about THE INNER LIFE OF THE CELL!

Here it is:

Water in the Lab

In Lab equipment, Water on February 1, 2009 at 5:50 pm


Before we make the first experiment we have to discuss about some trivialities that might be different in the lab than in the outside world.

For example: water. Everyone knows what water is and I don’t want to recapitulate again the basics. You can have a real good overview here.

We use water for plenty of applications in the lab. Some of them are not specific to the lab world. Here are some examples:


Of course we use water for various lab specific purposes. The most important of these purposes is to prepare various solutions. In order to control as much as possible how our solutions will work we need a realy pure water. Tap water although is considered as pure drink water contains plenty of soluble components like: ions, colloids particles and so on. This water can not be used to prepare solutions. We use it to wash dishes but even after dish washing all dishes has to be rinsed with ion exchanged water. Ion exchaged water replaced distilled water in the last decades and stands for water that contains almost no ions at all. Distilation was used earlier to evaporate and … water and by this procedure you can get rid of the soluble salts from the water. The procedure was simmilar to the destilation of alcohool in distileries like this. The ion exchange resins are able to bind the ions from the water and produce a water that has the same qualities as distilled water has.

But how do you know if a water is pure?

It was told that you shoud use your senses: like smell it, view it, taste it. A clean water should be clear, tasteless and should not smell. But this is not enough. The easiest way to measure the presence of ions in water is by measuring its electrical conductivity. Soluble ions in the water will allow electricity to pass through the water. A really pure water is having very low conductivity.

In our lab we have a special tap for central ion exchanged water:


So don’t worget, after washing lab dishes, please rinse everything at least twice with the ion exchanged water from this tap!

Can we use this water for solutions?

In some cases we could. Nevertheless due to the fact that we process sensitive biological samples like DNA and proteins we do not use this water for solutions in a molecular biology lab!

In order to prepare water for solutions we use so called “MilliQ” water. We introduce the ion exchanged water into an apparatus which is filtrating it through a replaceble cartridge. This filtrated water is free from colloids, proteins, ions and is suitable to be used in regular molecular biology solutions. Of course not for all applications! We will discuss this later. Here is the instrument that is producing the “Milli Q” water:


You will find the water for solutions right in in a plastic carboy (also called demijohn) like this:


You can use this water for preparing buffers for gel electrophoresis, western blot and so on.

By sterilizing it, you can make sterile solutions for cell culture applications. Nevertheless I would stronglly recommend that you should filtrate these solutions through a 0.2 micrometer filter. Majority of infecting agents (from bacterial origin) are larger than 0.2 micrometers so a sterilizes and/or filtered solution should be OK for cell culture applications.

There are some special applications that need special waters.

Two of them are RNA applications and cell culture applications for immune studies.

1. RNA applications.

While DNA can be protected quite easilly by adding EDTA as a chelating agent to the solutions (by this you get rid of the soluble Mg and other ions and you block the activity of DN-ases) RNA can not be protected like this. RN-ases are everywhere and are destroing the free RNA. That means that we have to use a special water that has no active RN-ases. Earlier we used so called DEPC treated water. Now we we use so called “Nuclease free water”. Earlier we were buying it in small 25ml bottles like this:


Now we buy it in larger quantities and alliquot it. We use this water as NFW (Nuclease Free Water):


As a rule: USE ALLWAYS YOUR OWN NFW!!! Mark it with your name, and put a date when you oppened the tube.

2. The second type applications when we need an even purer water are the immunologic studies. In these cases we need a water thet is free of LPS (bacterial lipopolysaccharides, or endotoxins). The water we use for these applications is called “Embryo water” although we do not use it for embryological manipulations, it is LPS free. It is very important to alloquote it only in endotoxin free tubes, like cell freezing sterile vials.

Here is our LPS free water:


So these are the water types in our lab. We will discuss about the price of our water types later!