Saturday, August 31, 2013

Phage Therapy: A Brief Primer on the History and Current Outlook

As I discussed in a previous post, bacteriophages can play crucial roles in promoting bacterial pathogenesis by acting as reservoirs for antibiotic resistance genes, and by promoting the transfer of those genes across bacterial populations.  Interestingly, while phages can promote bacterial pathogenesis, they can also be used in "phage therapy", meaning they are used as therapeutic agents to treat bacterial infections.  While this idea may sound like a novel approach for treating bacterial infections, the use of phages to treat bacterial infections is quite old.

Felix d'Herelle (seated) at a bacteriophage research center.
Picture Source: Reference [6]
Bacteriophages were first described by Frederick Twort in 1915 [1], and again independently discovered by Felix d'Herelle in 1917 [2].  Early on, scientists (especially d'Herelle) recognized the potential of phages as therapeutic agents against bacterial infections, and while the interest continued in Eastern Europe (where even today, phage therapy centers treat patients), it was largely abandoned in the Americas and Western Europe.  This abandonment occurred in light of Alexander Fleming's discovery of Penicillin and the promise of the new antibiotic drug type.  With the recent rise in the threat of antibiotic resistant bacteria, and the increasingly apparent limitations of antibiotics in certain infectious scenarios (i.e. antibiotics are often unable to penetrate bacterial biofilms), phage therapeutics have gained a renewed interest as important antibiotic alternatives.

Sunday, August 18, 2013

Graphing with R and Adobe Illustrator

R is a great resource for making graphs, but it is still limited in its ability to fine-tune and format figures.  Adobe Illustrator complements R by providing an incredible amount of tools for figure formatting and fine-tuning.  Using these programs together is a great way to make quality graphs, so I want to make some notes on using R graphs in Illustrator (CS6).
First the graphs need to be generated in R.  I have been using {ggplot2} to generate my graphs, although the R {graphics} package works too.  Once a graph is made in R, it needs to be saved as a pdf and opened in Illustrator.

Sunday, August 11, 2013

R Reference Sheet

Recently I have been spending a lot of time learning about the statistical environment R.  R is command line based and is worth learning because it is more powerful than programs like Excel, and ultimately it saves a lot of time (especially when you will have to perform repetitive tasks or if you will have to redo the analysis again with updated data).  I am still new at R, but I have been learning a lot and I want to share that with others who are learning.

First of all, you can download R by clicking the 'download, packages' CRAN link on the left of the homepage.  Just follow the directions.  In addition to using R, there is a nice program for writing R scripts called R Studio, which has more features in a nice GUI.  It kind of reminds me of the way SAS is set up, and it is worth a try for sure.