Category Archives: General

Deconstructing the Written Comprehensive Exam

We've all felt like this at some point leading up to comprehensive exams. Photo from Flickr user Jixar, used under CC license.
We’ve all felt like this at some point leading up to comprehensive exams. Photo from Flickr user Jixar, used under CC license.

This article appeared in its original form at Gradhacker.org on March 22, 2013.

The dreaded written comprehensive exam. Many graduate students will have to pass some form of comprehensive exam at some point in their program. This can often include putting together a multi-page grant-style project proposal. Putting one of these together for the first time can be a daunting process if you are unprepared. But have no fear, there are ways to make crafting a solid document far less painful and even somewhat enjoyable.

Now at this point I have to mention that this advice will be most relevant for students preparing an exam on their own projects in the style of an NIH grant. However, this basic approach can apply to putting together any large proposal for your project. Continue reading

Ask a Microbiologist #3: What’s in the almond milk?

Today’s installment of Ask a Microbiologist comes from a reader wondering what might be in that old almond milk in the fridge:

English: Raw Almond Milk
Raw Almond Milk (Photo credit: Wikipedia)

“I found an open container of almond milk in my fridge the other day and it was OLD – I’m talking it had been opened for at least a month at this point. I know that as soon as it’s opened, the pasteurized almond milk is immediately primed for bacterial breeding. I was just curious as to which pathogenic (entero) bacteria are most likely to colonize at this point; I’m curious because there were zero indications of growth (ie no swelling of the container and no abnormal smells, colors, or textures).”

-Wondering what’s in there

Well WWIT, I’m glad you asked this, as I was starting to wonder about my soy milk as well.

This is a very open ended question and three main ways to inoculate your drink that could potentially lead to different contaminating microbes, some of which could be pathogenic. Continue reading

Beyond Fever: Fungal infections and the benefits of body heat

Histopathologic features of aspergillosis incl...
Histopathologic features of aspergillosis including the presence of conidial heads PHIL 4335 lores (Photo credit: Wikipedia)

So far on this site I’ve tried to address microbiology topics from all areas of the field; from the standards in bacteriology and virology to some more exotic parasites and fungal infections. When you look at the range of infections that people can acquire you see many bacteria, viruses, and parasites. However, invasive fungal infections, especially those that occur in healthy immune-competent hosts, are exceedingly rare when you compare mammals to insects, plans, and amphibians. I never gave this much thought until coming across a group of papers that together indicate that something as fundamental as a warm body temperature could protect us from a variety of pathogenic fungi.

Read on to see how endothermy may be a protective mechanism against fungal disease. Continue reading

Our genome is not ours alone

Dendrogram of various classes of endogenous re...
Dendrogram of various classes of endogenous retroviruses (Photo credit: Wikipedia)

The last twenty years have been marked by a veritable explosion in sequencing technology. The Human Genome Project and it’s completion in 2003 was the crowning jewel of this burgeoning genomics revolution and played a major role in my early introduction to science. I distinctly remember being a sophomore in high school completely fascinated with the fact that we as a species have taken it upon ourselves to read the basic text that makes us all human. It still awes me that we are capable of this level of technology and that it just keeps getting better, smaller, and faster. Case in point: I am currently sitting 20 feet from an Illumina MySeq, an object the size of a 1990s-era desktop computer capable of delivering sequencing results in 24 hours. The amount of information to come from this branch of science is literally mind-boggling and only grows with each passing day.

Interesting observations have come out of this massive amount of genomic data relating to the  non-coding DNA in our genome. Less than 2% of the over 3 billion nucleotides in our genome are responsible for coding all of the protein that makes up a human being. This leaves a large question as to what exactly that other 98% of our genome is up to. Large parts (roughly 50%) are known as “junk DNA” with no accepted role, although new research is beginning to shed light on the functions of this DNA. The remainder of our genome is composed of long and short repeated sequences, transposons, retrotransposons and the topic of today’s article: endogenous retroviruses.

These elements are not human, they are fully viral in origin. This means that our genome is not just ours alone, we carry the DNA of many viruses that infected our ancestors in every cell in our own bodies.

Keep reading to find out what an endogenous retrovirus is, why exactly these viruses have invaded our own genetic code, and the implications of this discovery for the treatment of modern retroviruses such as HIV… Continue reading

Passion for Communication

microphone
microphone (Photo credit: TOM81115)

Today I’ve been thinking about all of the influences that have made me so passionate about scientific literacy and effective science communication. As a global society we are challenged daily with obstacles that can most effectively be solved using our modern scientific understanding of the world. Yet for a variety of reasons much of the general public is unaware of the startling leaps and bounds generated by the modern global scientific community, aware but misinformed by sloppy reporting, to downright distrustful of science and those involved.  While we could go into these various issues and their origins at length, I would rather take a moment and share some of the resources that have pushed me to share my love of science with the public in the hopes that I can spread my passion for scientific communication to others. Continue reading

Guest Post at Gradhacker

Hello readers! I have started contributing articles to the Gradhacker website in order to share some of the things I learned in my first year of graduate school. This month I’ve written an article for those of you about to start graduate programs and how to choose the best laboratory rotations for your personality and interests.

Head over to Gradhacker and check out my new piece: How to Find the Right Lab Rotation