Tuesday, July 29, 2014

Ebola strikes again

"Ebola virus virion" by CDC/Cynthia Goldsmith - Public Health Image Library, #10816

In alarming news, an outbreak of the Ebola virus that started in West Africa is now being called the worst in history. The three affected countries - Sierra Leone, Liberia and Guinea - are reporting over 670 deaths. Worse still, medical personnel now number among the victims. The health minister of Guinea said that the virus probably spread from local communities eating infected bats; bats serve as the animal host for the virus. People have also been advised to stay away from eating rats and monkeys.

The Ebola virus is highly infectious, with a mortality rate of upto 90 percent. Patients with Ebola often have severe internal and external hemorrhaging - they're basically bleeding to death. (If you want to know more, Ebola and its other deadly cousins, like the Lassa and Marburg viruses, are profiled in Richard Preston's The Hot Zone, a book I read and loved as an undergraduate. And when I say loved, I mean it scared the daylights out of me. No, really. I challenge you to read it and look a coughing man in the face without flinching).

Sunday, July 27, 2014

Can genomics save a struggling town?

 Like many manufacturing centres across the United States, the town of Kannapolis in North Carolina took a massive hit to its economy when the textile mill around which the town revolved downed its shutters. This article describes Kannapolis's unlikely re-invention as a centre for genomics research, thanks to an elderly billionaire named David Murdock, who is a fervent believer in longevity expansion through better nutrition (Here's a fun profile of Murdock in the New York Times that takes the term "health nut" to a whole new level).

The article raises a lot of interesting questions - can the biotech industry really revive a faded mill town? And more importantly, do the residents have a chance of profiting from any diagnostic tests or other inventions developed by using their biological materials? Right now the answers seem to be "Maybe" and "No". What is also not clear to me are the reasons why the residents of Kannapolis would make good candidates for recruitment into a biobank - what kind of population are they representative of? Nonetheless, it's interesting to think of this as a glimpse into a "brave new economy", where the residents are now literally the lifeblood of their town.

Saturday, July 26, 2014

A well-handled retraction

Recently, the Institute of Microbial Technology (IMTECH) made headlines for a rather unfortunate reason: data fraud. Three papers published by a research group at IMTECH in the journal PLoS ONE were retracted earlier this month for "fabrication of data", and now another four are being retracted as well. The first author on these studies (Dr. Fazlurrahman Khan) has reportedly resigned from the institution.

PLoS ONE, an open access journal, is considered both prestigious and rigorous; in a Science paper that used a fake article to expose abysmal peer review standards in open-access journals, PLoS ONE was commended for its "rigorous peer review" and for being "the only journal that called attention to the paper's potential ethical problems", eventually rejecting the fake study for lack of scientific quality. Even so, the review process for the first three papers had failed to catch any of the manipulated data; Willem van Schaik, editor of one of the papers, later told the blog Retraction Watch that three separate reviewers had edited the papers, making it harder to notice any glaring errors, and that "even with hindsight, I find it difficult to find which data have been fabricated."

 It was Dr. Khan's former post-doc boss at Georgia Tech who, noticing some similarities between the published data and the work that Dr. Khan had done during his postdoc, contacted the Director of IMTECH, Dr. Girish Sahni. Commendably, an inquiry committee was immediately set up to investigate the matter, and found that "there are no data available underlying this study and thus that the published results are fabricated". The Council of Scientific and Industrial Research (CSIR), with which IMTECH is affiliated, immediately requested a retraction of the three papers in question.

Sunday, July 20, 2014

One is a lonely number

I recently came across a very interesting feature article in the New Yorker, "One of a Kind", which describes the dizzying journey parents undertake when their child is identified as the only person known to be affected by a particular genetic condition. The article focuses on one family, the Mights, whose son Bertrand was born with a previously unknown double mutation in one gene, NGLY1, involved in the deglycosylation of proteins - the product of the gene is an enzyme that helps in protein recycling by removing sugar molecules linked to these proteins. It took the Mights several years to learn what exactly was wrong with their son, during which they shuttled from one specialist to the next, trying desperately to map their son's illness while worrying about the damage all the poking and prodding was doing to him.

The conclusion from all these tests was that Bertrand was a complete medical novelty - whatever he suffered from was a disease unknown to medical science at the time. Rather than giving up the battle, the Mights chose to enroll Bertrand in a study designed to test whether genetic sequencing could be used to identify unknown conditions. Genetic sequencing, as most of us are familiar with, is usually designed to test a specific gene for mutations that would explain a medical condition. This only works if you already know that a mutation in gene X causes disease Y. What do you do in a case like Bertrand's, where you have absolutely no idea where in the genome you should be looking?