Open Field Tests

A line drawing of two mice walking similar paths, but one is curvy because that mouse is woozy. Understanding or measuring how animals think is difficult when they can’t talk to you. You can’t ask ‘what are you feeling?‘ much less, ‘why do you feel that way?‘, but it is still important to understand. For instance, we study drugs to all kinds of psychological issues (depression, alzheimer’s, Parkinson’s disease, etc) in rodents like mice and rats. Therefore, biologists have developed behavioral tests that inform us about what the animal is thinking or feeling.

The open field test measures general activity level and exploration behaviors. This lets us get a feel for how the animal behaves normally and is frequently used as a control in an experiment. In addition, numerous factors can influence how much an animal moves so by controlling what changes between tests, we can begin to understand how what we are testing influences the animal’s thinking.

Continue reading

In situs

In situ hybridization (ISH) is a technique that allow you to visualize a gene’s location. The location is typically determined at the level of the cell or tissue region. However, chromosome painting is also a form of in situ and has a better resolution. In general, if a scientist is talking about ‘in situs’ or WISH, they are referring to the form that shows where a gene is being expressed.

In situ hybridization is like a Google search, where the probe is our search term.

At the most basic level, ISH simply attaches a labeled probe of DNA or RNA (nucleic acids) to other DNA or RNA. You can think of in situs as the Google search of biology. In Google, you can search a variety of media (websites, videos, or images) based off whatever you put in the search box. Using in situs we can search the various forms of nucleic acids based off the probe whose sequence is known.

Thus, many different techniques with a variety of goals fall under the broad category of ISH. This can lead to a lot of confusion even within the field of biology. At a conference dinner I was discussing my work on developing FISH for sticklebacks and at least one PhD at the table thought I was talking about chromosome painting for most of the conversation until what I was saying stopped making any sense. So if you find this confusing, you are in good company.

Continue reading

PCR - Photocopying Genes

PCR is a common technique used to amplify specific regions of DNA. Put more simply, its a process that allows us to create copies of a piece of DNA. There are two main properties of PCR that we take advantage of - amplification (getting many copies) and isolation (of a single region).

If you understand the basic idea of photocopying, then you can understand PCR.

A short stretch of DNA that goes through 2 cycles of amplification ending up with 4 copies. I should note that the role of PCR has changed over time and I will mostly be focusing on the current use. Additionally, there are several variants based off the standard PCR, including rt/qPCR, but those will be covered in a different post.

Why do a PCR?

Typically PCR is just a step to let us do something else with a gene or region of DNA. It is the first step in gene cloning or for things like gene editing. It can also be used ‘genotype’ an individual for a gene, i.e. figure out which specific copy of a gene someone has.

Continue reading

Gene Cloning: vectors, plasmids, ligations, and transformation - oh my!

The goal of gene cloning is to get a single copy of the gene from an animal and into an archive. The rest is just the individual steps necessary to do this. Cloning genes allows us to easily and consistently retrieve the exact same copy and to share it between labs or even organisms.

Step Description Biology Jargon
1     Get a copy of the gene from the animal PCR
2     Put the gene in an archival format Ligation into a plasmid
3     Make backup copies or archive it Bacterial transformation
4     Confirm that the copies match the original    Sequence the insert
5     Retrieve a copy to use Miniprep

What is a vector and what how is it used?

A vector is a small, self contained piece of DNA that can be added to an organism, typically bacteria. It is how we archive the gene we are cloning.

Continue reading