Tuesday, May 6, 2014

URSP Student Andrei Cesin Conducts a Preliminary Test for Correlation Between H. pylori Presence and IPF

Originally, we set out to test if the bacteria Heliobacter pylori was the definitive causative agent within stomach reflux (known to have a correlation to a disease known as IPF). In a nut shell, we planned to test for the presence of H. pylori using PCR in the tissue of various samples, then check patient history to see which individuals had a history of stomach reflux, and if there was a statistically-valid correlation. However, upon looking into the literature, I realized a great opportunity for uncovering a wider strategic awareness within this possibly-causative relationship: I would instead look into the mechanisms of IPF pathogenesis, then once I identified the critical mechanistic factors, examine the literature on H. pylori to see if that bacteria’s mechanism of infection involved similar factors (and presto, there might be a causative bridge between IPF and the bug, which would be the basis for a future experiment of specific design).

It is because my project is purely literature based, it directly relates to (I think) the most important graduate skill set of all: extracting the deepest value of scientific literature. It’s the basis of the old scientific adage: “A couple months in the laboratory can frequently save a couple of hours in the library.” – Westheimer. In graduate school, you will have to be able to read and understand the scientific literature (for the candidate’s own success and survival). This teaches the language and organization of how ideas are expressed. Beyond that, it also teaches (or at least gives hints) on how scientists think (as in how they develop their questions). Lastly, being familiar with the literature enriches the reader with a sense of how the logic of an experiment’s parameters/logical premises (an experiment’s design) forms the basis for a set of results that have a definite and compelling logical conclusion (say for example, regarding the nature of a relationship; A causes B, and not the other way around). As the scientist articulates in her language (which you become familiar with, with practice) the model that guides their thinking, you will also experience how that model gets updated in light of the experiment’s logically-compelling and valid results.

On a weekly basis, I dive into the underlying literature of reviews to get to the nuances that have been omitted by editors. Without those important nuances, some of these reviews read like a poorly translated foreign-language novel. This week, I discovered that the mechanism that involves inducing IPF via killing Alveolar cells can be done without inducing the inflammatory mechanism. This doesn’t mean that IPF pathogenesis is inflammation dependent, only that it doesn’t necessarily involve the triggering of the inflammatory response (which makes a competing, inflammation-based theory less likely).