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


The Preliminary Exam

While you will probably take a small smattering of courses that have more traditional midterm and final exams, these are not really that critical to your success in graduate school. Rather than caring about your grades in them, the goal is to actually master the materials in relation to your research.

Instead, graduate school typically has three major milestones:

1. Qualifying Exam (aka Quals)
2. Preliminary Exam (aka Prelims)
3. Final Defense

There are a lot of variations on the qualifying and preliminary exams, even within a university. Taking a separate qualifying exam appears to be rare based on other graduate students I have spoken with both within the University of Illinois and from other schools. However, whether or not your program has separate Quals will change the goals and expectations of the Prelim exam.

Continue reading


Stickleback fish

A mostly blue fish with a bright red throat. Meet your typical stickleback dad. My research is based on understanding how genes contribute to his behavior.

You can tell this is a male ready to become a dad because of his blue color and the red-orange color under his throat. Its only during the summer breeding season that he will look like this. Not all males will color up this brightly as it depends on a number of factors including the amount of light and the surrounding environment (gravel color). This particular male has improvised a nest out of small pebbles in his tank that you can see to the right of the plant. Normally, stickleback fish use algae and sand to build nests, but he wasn’t given any.

Continue reading


Diversity in academia

I have ADHD and dyslexia. It has taken me years to be comfortable openly talking about this. I think the most surprising thing to me was that the greatest obstacle was myself. Not only the ‘diversity community’ but the academic community as a whole have been very welcoming. Below are my thoughts and experiences but I realize that many have not been so fortunate as myself.

I think its important to talk openly about this. First, it helps us accept ourselves - both our strengths and weakness. Secondly, there are a lot of opportunities for those brave enough to identify themselves, especially those with non-apparent disabilities.

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