Sunday, April 19, 2015

Principles of Microbial Diversity, by James Brown

Published by ASM Press
A new textbook on microbial diversity has just been published by ASM Press. Principles of Microbial Diversity is a relatively thin textbook (392 pages) that is intended for undergraduate students who need to follow a course on microbial diversity, hence filling a gap in the available teaching material. His author is James W. Brown, a professor at North Carolina State University.

The book is pleasant to read and richly illustrated by hundreds of micrographs. But what is quite original, and to me very justified, is the author's perspective, which is, in James Brown's own words in the preface, "phylogenetic and organismal, from the Carl Woese school".  I applaud that! Woese, as I discussed in a previous post, revolutionized biology by showing that we had until then totally ignored a whole distinct domain of life, the Archaea. This discovery was made through the careful analysis of the sequence of 16S rRNA gene (not an easy feat in the days of Woese's work). Because of this pedagogical and scientifical choice, Brown's book dedicates lots of pages to introduce phylogenetic concepts. Notably, he gives a didactic and useful explanation of how to construct a phylogenetic tree (Chapter 3). Brown explains his focus as follows (p. 351):
"In this book, the vantage point from which all of microbial diversity is viewed is the phylogenetic perspective. Other perspectives are possible and are very useful. Medical microbiology views the microbial world from the perspective of its influence on microbe-human interactions and human health. Environmental microbiology views the microbial world from the perspective of biogeochemical processes and ecosystems. […] However, the organizing principle of biology is evolutionary theory. The phylogenetic perspective is the view of biological diversity as the outcome of evolutionary history. This perspective is not exclusive of any other perspective on microbiology, but instead enriches these other perspectives."
Brown's textbook contribution is very welcome, and should find a place in each university's library.

Example of book photo. The eukaryote Arcella. Source: Wikimedia Commons


References:

Tuesday, February 24, 2015

Mining soil for new antibiotics

Methicillin-resistant Staph aureus. Photo NIAID
The beginning of 2015 brought (potentially) good news for medicine: the discovery of a new antibiotic - teixobactin - isolated from soil bacteria. This result was published in Nature on January 22. (Unfortunately the whole text is not visible without payment or subscription.) Many newspapers and news outlets covered the story in early January, for instance the Guardian, and the New York Times. Teixobactin is a small peptide that acts as an inhibitor of cell wall synthesis in Gram-positive bacteria, which means it can kill pathogens like drug-resistant Staphylococcus aureus (often referred to as MRSA, or methicillin-resistant S. aureus).

The issue at stake here is, of course, the increasing prevalence of antibiotic-resistant bacteria worldwide, a situation well summarized in an article at Swissinfo.ch. We have thus seen a dramatic increase in resistant strains of, for instance, S. aureus, Escherichia coli and Klebsiella pneumoniae. Who or what is to blame? Most probably the overuse of antibiotics, not only in humans but also in animals. It is frightening to know that some pathogenic strains can survive our entire arsenal of antibiotics, while new potent drugs are extremely hard to find. Some simple solutions have helped mitigate the problem, notably more effective and systematic hand disinfection by hopital personnel, but this will not prevent all cases of infection. New antimicrobials are clearly needed, but where to find them?

Monday, January 26, 2015

The Logic of Life, by François Jacob


The Logic of Life (La logique du vivant) opens with the following quote by the French philosopher and Enlightenment figure Denis Diderot:
"Do you see this egg? It's with it that we overturn all theological schools and all temples on Earth".
[All translations in this post are mine.]
The choice of a 18th century thinker for the epigraph prefigures a lot of this book, which was published by the late Nobel laureate François Jacob in 1970. The booksubtitled "a history of heredity"thus proves to be of great erudition and cites the original work of, among many names, Paré, Montaigne, Paracelse, Descartes, Galilée, Harvey, Réaumur, Buffon, Redi, Leibniz, D'Holbach, La Mettrie, Lamarck, Linné, Geoffroy Saint-Hilaire... and I haven't even mentioned the 20th century references yet! Excusez du peu!

This story of heredity truly is a huge endeavor, spanning about four centuries of philosophical and scientific attempts to understand what kind of stuff we're made of. Articulated in long chapters that correspond to conceptual milestones ("visible structure", "organization", "time", "gene", "molecule", and "integron"), the book follows the chronological development of our biological knowledge (which was part of "natural philosophy") with plenty of referenced sources and with a quality of writing that is hardly matched today.

Sunday, August 31, 2014

The debate over influenza research is still on



H5N1 virion. Photo Cynthia Goldsmith/Jackie Katz

Two years ago, a controversy emerged about the research on influenza virus H5N1, and the potential risk associated with it. This controversy followed the publication of two research articles in Science and Nature, and I wrote about it in January 2012 in this blog post. Briefly, scientists have used so-called “gain-of-functions” experiments, in which strains of influenza viruses are selected for new traits such as higher transmissibility between ferrets (the preferred animal model in these studies). The objections that were raised by some critics of this research were of two kinds: first, the information available in these papers could be used by terrorists in order to produce bioweapons; second, modified influenza viruses could escape the lab by accident and create a pandemic. The first objection led to a very rare decision in scientific publishing, namely the redaction of the articles to remove potentially sensitive data. The important public concern also led the authors of these studies to promulgate a moratorium on this type of work. After this temporary stop, the experiments started again with additional biosafety measures. 

The debate, however, is far from over. The reason for this? Well, the recent publications of several studies dealing with influenza virus, most notably a paper by Y. Kawaoka (the author of the 2012 Nature publication) on avian influenza viruses related to the 1918 “Spanish flu” virus. This research triggered a heated response from several scientists, which was loudly echoed in the mainstream press (see for instance in the Guardian and in the Independent). In that particular case, it seems that the scientific community is truly divided on the matter. An example of this dissent was the publication of a statement of concern by a group of scientists known as the Cambridge Working Group, which in essence asked for a better assessment of the risks of virus research via the organization of a conference that would deal with all present issues. Such a meeting could resemble the famous Asilomar conference of 1975, where the risks associated with recombinant DNA were debated. Other virologists, however, have fought back these reactions of distrust and have created another group, Scientists for Science, which aims at promoting the benefits of this research, and highlight the fact that serious safety regulations are already in place for virus research. 

Sunday, August 03, 2014

Microbe Hunters by Paul de Kruif



Microbe Hunters’, as I have often been told, is a classic reading in microbiology—one of those books that can inspire the beginning of a career. In this book, written in 1926, American microbiologist and author Paul de Kruif proposes to acquaint us with the great pioneers of microbiology, from Leeuwenhoek to Ehrlich, via Pasteur, Koch, Roux and several more. 

I gave it a try, and I must confess that at first I was a bit taken aback by the quite unusual style of the author: extremely enthusiastic, overly lyric, made to immerge us in the life of the protagonists with a plethora of details that may or may not be true.  I can’t remember reading anything quite approaching the surprising and unusual tone of Microbe Hunters. Here’s an example describing Spallanzani’s early experiments (p. 34):

“What’s this?” [Spallanzani] cried. Here and there in the gray field of his lens he made out an animalcule playing and sporting about—these weren’t large microbes, like some he had seen—but they were living little animals just the same.
“Why, they look like little fishes, tiny as ants,” he muttered—and then something dawned on him— “These flasks were sealed- nothing could get into them from the outside, yet here are little beings that have stood a heat of boiling water for several minutes!”
[…] It was a great day for Spallanzani, and though he did not know it, a great day for the world.

But as I was reading further I grew accustomed to this prose, and, to my own surprise, I started to enjoy it! It is indeed difficult not to share de Kruif’s enthusiasm for these great men of the past and, even though I would take the author’s factual accuracy with more than a grain of salt, the book really makes you want to learn more about the personal life of these pioneers.

Sunday, February 23, 2014

Oceans, bacteria, and the quest for new drugs



A marine sponge of the genus Theonella. Photo by Nick Hobgood.
We rely on natural products in medicine: the vast majority of pharmaceutical drugs are thus of plant or microbial origin. (The purely synthetic drugs, which have no counterparts in the environment, are the exception rather than the rule.) To name potent examples of natural products, take antibiotics (discovered in fungi and bacteria), the anti-malaria drug artemisinin (isolated from sweet wormwood) or simply aspirin (salicylic acid is present in willow bark). Many people, I think, forget about this, as they oppose a so-called ‘natural’ medicine to a ‘chemical’ medicine (the pills you get from your doctor). 

It is not easy to find new active compounds, however, and much more difficult to test them and turn them into a real medicine. The situation doesn’t look that good, notably because of the high increase of antibiotic-resistant strains of bacteria, and the paucity of new drugs available. A natural environment that has long been recognized as a promising source of new chemicals is the largest on Earth—oceans—, and many researchers are mining the sea in search of new organisms and their specific biochemical abilities. For instance, the research project PharmaSea, funded by the European Union, was launched in 2013 with the goal of discovering new microbial organisms that could be the source of useful chemicals for medicine or industry. This team of academics and industry researchers plan to explore the deep bottom of the sea, looking for environments that are poorly known and potentially harbor interesting organisms. Here’s an excerpt from the project website:

Marine organisms that live more than 6,000 meters below the sea level are considered to be an interesting source of novel bioactive compounds as they survive under extreme conditions. "Trenches are separated from each other and represent islands of diversity. They are not connected to each other and life has evolved differently in each one", explains Marcel Jaspars [PharmaSea project leader]. “

PharmaSea is an ambitious project, and it may not be easy at all to get many new products out of it, but the goal has to be praised, as we surely are in need of new biochemicals, particularly new antibiotics.

Sunday, January 26, 2014

Communicating science: TED talks



Is it even necessary to introduce TED talks?...  I guess everyone has seen at least one of these 18-minute-ish presentations on topics that deal with (broadly speaking) Technology, Entertainment or Design. These “ideas worth spreading” (as they are advertised), are presented during the TED Conference, an event occurring every year on the US West Coast since 1990. It is thanks to the development of the internet and video streaming, however, that TED talks have accessed global fame. The first talks were uploaded in 2006, and in 2012 the total views passed 1-billion! (According to TED.com, there are now more than 1,600 talks available!) With as famous speakers as Al Gore, Bill Gates or Bono, TED talks have become an unprecedented cultural phenomenon. 

Today TED conferences are organized not only in the US, but also in Canada, in South America, in Europe and in Asia. More than this, TED has become a label, since all over the world are organized so-called TEDx events, conferences that share the TED format but are organized by independent local committees. 

Given the format and the varied audience, TED talks are not meant to treat a topic exhaustively and should be accessible to the layman. This is not necessarily an easy job for scientists, still you can find almost four hundreds science talks on the TED website! It seems thus that science fares pretty well in the TED universe…