Author Archives: Adair

About Adair

I am a Senior Lecturer in the Department of Biology. My research interests are in genomics and microbiology, especially S. aureus and bacteriophage. I am convinced that the best way to teach science is to do science and my current work includes transforming our introductory labs to Classroom Undergraduate Research Experiences in Biology (CURES in BIO).

Adipose fins


Some researchers are looking at another morphological structure of modern day fish to investigate fish evolution.

“Adipose fins are small, fleshy and usually not as elaborately structured as other fins. Although some 6,000 species of fish—including trout, catfish, and salmon—have them, relatively few researchers have studied these structures in the last half-century.”

They plan to explore early changes that may be linked to the transition to tetrapods.  The beauty of cience is there is always another question!


Genome Analysis


I saw this headline today-
February 20, 2014, 10:30 AM EST.
Supercomputer Analyzes 240 Full Genomes in Two Days


It will probably take us several weeks with all of your brains put together to analyze 1 very small genome. The technology is changing fast.  Sequencing is getting faster and cheaper, but what about the time and expense of analyzing?  Data doesn’t mean much if it is just sitting on the desktop.

Your generation will be analyzing and utilizing genome sequences more and more for diagnostics.  Computers will be doing the analysis.  Who will decide what to do with the results? What do you think?




More Bioengineering in the News

I really enjoyed your presentations last week.  All of the topics demonstrated to me that we have only just begun to understand how cells work and communicate, but knowing what we know allows so many good things to occur.

Imagine being the scientists that spend their life designing and testing a prosthetic hand and then learning that the individual trying it out can actually feel with it!  This is the latest of several breakthroughs in this area.

The future looks bright to me!



Phage Introns and the mobilome

The SEA Phage members that isolated cluster J Phages all got together and published a paper in PLoS.

This is a great paper to read slowly over this semester as you learn more about phage genomes.

I think it is so interesting how they discovered 2 introns using the alignment tools and then confirmed their hypothesis by isolating and analyzing the predicted proteins.

They described a “luxuriant mobilome”….Maybe we will see something similar?

Vaccine for Staph?

I think most of you know that I am interested in Staphylococcus aureus, particularly alternatives to treating this disease with antibiotics.  This week I read a news report that describes a hopeful vaccine.

The research was published in the Journal of Infectious Disease.  I wonder what type of biotech is required to make this vaccine?



Bridges Across the Periplasmic Moat

Have you ever read Small Things Considered?  It is the Microbe Blog put out by American Society for Microbiology.  A recent blog describes how phages infect bacteria.  It seems that some icosahedral phages “grow” a tail after absorption.  These describe Gram negative bacteriophage, but Gram positive bacteria have a thicker peptidoglycan cell wall.  I wonder if any cryo EM has been taken on Mycobacteriophage adsorbing and infecting?



Grainy agar hypothesis #2

It is possible that the reason for our grainy agar (and lack of plaques) is not due to the concentration or age of our saturated culture, but instead the temperature of the incubator that the top agar plates were grown in.  Can you design an experiment to test this hypothesis?



Some of you were testing the hypothesis that your filtered samples were contaminated with bacteria so you refiltered the samples and respotted on Arthrobacter.
What were your results? Did you have phage? contamination? both? neither?

Please post a reply here and we will be able to see the sum of the experiment.