Doug Briant

It appears that Nanopore sequencing is about to become commercially available (see the Nature review here). In this technology, a small protein pore is embedded in an electricaly resistant membrane. Current, which can only travel through the pore, is then applied and measured. As particles pass through the pore, they temporarily block the current, and this can be measured. Different bases give a different disruption profile. DNA can either be threaded through as a single strand, or it can be chewed up at the entrance to the pore, with individual nucleotides passing through the nanopore one at a time. It is very fast and cheap, but currently there is about a 4% error rate, which is a limitation. In terms of equipment  costs, the machine is very cheap. The MinION system will in fact be self contained in a USB key (shown above) that is estimated to cost around $1000, although it looks like large multiplex options will soon become available. It is very interesting technology. Oxford Nanopore Technologies has a good website (www.nanoporetech.com) describing the techology.

So, it looks as if a Russian scientific team has finally managed to drill into Lake Vostok in Antarctica. Here are two articles, one from Nature (here) and another from the BBC (here). According to the BBC, the project has taken about 20 years from start to finish! Lake Vostok is a very  large lake (think Great Lake sized) located almost 4kms below the ice surface. It has effectively been sealed off by ice for millions of years (estimated about 14 million), although the BBC points out that it is possible there has been water infiltration over time. In microbiological terms, it is possible that there are many interesting and unique organisms growing in this environment. This would make it ripe for a metagenomic analysis. In a metagenomic analysis, a sample of water from Lake Vostok would be recovered. This sample would then be analyzed using one or several next generation sequencing techniques which do not require successfully culturing the microbes (remeber, most microbes are not culturable, especially those from harsh environments). One marker may be to look at 16S rRNA sequences.  This then gives insight into the diversity of life in the lake. There is a great review on marine metagenomics by Gilbert and Dupont, 2011, found here.  The biggest problem seems to be sample recovery. This is because kerosene is used as an antifreeze during the drilling process, and it rapidly contaminates any samples. Also, it may be difficult to pull a Pleisosaurus up through the drill hole. Sorry, I am being wildly inaccurate with dates here. By 14 million years ago, all the Pleisosaurs would have relocated to Loch Ness and Lake Okanagan.

One of the ways in which scientific journals are compared is by their “impact factor”. How are these factors calculated? It is actually pretty simple. Let’s say I publish an article based on microbe X in a peer reviewed journal. Other labs working on microbe X may cite my work when they publish their findings, if my work has directly impacted their research. My article on microbe X now has one citation. The average number of citations for articles in a particular journal denote it’s impact factor. So, if a journal has an impact factor of 10, each article gets cited, on average, 10 times. Presumably that means that the work published here is of higher quaility or more interest than articles published in a journal with an impact factor of 5. Of course, the pitfalls here are obvious. Not all research will be of interest to all labs, and a disproportionate amount of weight is given to journals that publish reviews along with research articles, as reviews are cited more often. A study release this week in Science (impact factor 31.36) (link to article HERE) focuses on another huge problem with this system. Some journals basically force authors to cite other previously published work from the same journal to boost the impact factor. These citations are added without actually having contributed any useful information to the current study. While the article focuses on economics, business, sociology and psychology, the problem is likely endemic to all journals. As an added bonus, in the supplemental tables they list the most coercive journals!

Please cite this article often and randomly. My impact factor is at risk of fading into oblivion.

Today’s story was passed along to me by one of your classmates. In the article (abstract found here), a group of scientists was studying the feasibility of using non-thermal plasma to kill bacteria in a wound. Currently, almost all wound-associated antimicrobials are chemical agents. These may have limited ability to kill bacteria that is naturally resistant, or that lives in a biofilm (as most bacteria do). In their research, they discovered that treatment with non-thermal plasma reduced the number of colony forming units in both a rat model and biofilm. While the study is very preliminary, it may eventually lead to a novel form of treatment for infected wounds.

As we struggle through the remains of today’s blizzard, it’s a good time to ask, “do microbes make snow”? Apparently it is possible that they do. In this news item from 2008 by David Biello from Scientific American, he discusses how ski resorts use microbes when they are making artificial snow. The article also outlines other evidence supporting a role for microbes in manufacturing that which is falling all around us today.

Victoria’s very own Times Colonist had two articles today about DNA sequencing (article 1, article 2). Both of them relate to “personalized medicine”. The concept of personalized medicine is that a patient would have all or part of their genome sequenced. Using this information, it would then be possible to tailor treatments so they are more specific and effective for the patient. This not only leads to greater chances of successfully managing illness, but it also avoids the expense of undergoing treatments that will not be effective. The two sequencing techniques described in the second article, concerning the $1000 genome, are Illumina and Ion Torrent (Life Technologies).

Here is an interesting article that demonstrates a link between the diversity of the bacteria found on somebody’s skin with their likelihood to attract the mosquitos that serve as vectors for malaria. The diversity was determined by comparing 16SrRNA sequences, determined by pyrosequencing (which, of course, was not a technique we covered in the last lecture). It turns out that a high abundance, and low diversity of bacteria is more attractive to the mosquitos. In a similar, but more disgusting, study, it was revealed that the mosquitos are also attracted to “smelly feet“.

Click here for a quick explanation of pyrosequencing.