Wednesday, December 26, 2012

Macroscopic fungi

In the lab I have only dealt with microscopic fungi, such as yeasts, but a couple of weeks ago I had the privilege to accompany a group of UC Davis students and staff on a mushroom hunting trip! This excursion was led by the very knowledgeable mycologist Dr. Mike Davis, author of the Field Guide to Mushrooms of Western North America, and Professor of Plant Pathology at UCD.

Fungi are curious organisms, neither animal nor plant, with unique chemical traits such as the presence of chitin in the wall of their cells. My beloved Brock Biology of Microorganims reminds me that there are three major groups of fungi: the molds (the type you don't want in your household); the yeasts, which we commonly use to ferment sugars; and finally the mushrooms, or macroscopic fungi.

Tuesday, December 18, 2012

Scientists keep an eye on a new SARS-like virus

Coronavirus. Electron microscope photo by Phil Murphy/CDC.
In 2003, a coronavirus named SARS (for Severe Acute Respiratory Syndrome) made nine hundreds victims, most of them in Asia. Usually coronaviruses are not dangerous - they cause a cold or stomach flu -, but this one killed one among ten infected human beings. Thanks to the prompt response of the sanitary authorities all over the world, SARS was relatively rapidly controlled.

This year, a SARS-like virus has appeared in Middle East, and scientists and health officers keep a very close eye on it, as Nature News reports. At present it remains unclear whether this new virus could become a real worldwide threat, but it killed five of the nine cases known so far. 
The first cases were reported this Summer in Saudi Arabia and in Qatar, but in November evidence showed that people had been infected by the new virus in Jordan already this Spring.

Tuesday, December 11, 2012

A Planet of Viruses by Carl Zimmer

Published by University of Chicago Press
This is popular science writing at its best: concise, edifying and not condescending. But I did not expect less from Carl Zimmer, a seasoned science writer and the author of many books (e.g. Microcosm, Soul Made Flesh, Evolution:Making Sense of Life), as well as a contributor to many high profiles newspapers and magazines (e. g. NYT, Time, Scientific American). On top of that he's a widely read blogger (The Loom).

You can tell that it is good when you would recommend the book to a non-scientist, and at the same time you find plenty in the book to enjoy for yourself.
A Planet of Viruses is a short book, so don’t expect an exhaustive treatise on viruses. But if the scope is narrow, it is due to clever choices that help keep the book focused.  For instance, Zimmer doesn’t discuss the molecular details so much. We won’t learn here about RNA vs. DNA viruses, single vs. double stranded, and so forth. Neither will we learn the elaborated tricks of viral replication or the taxonomy of viruses – but textbooks are just for that, aren’t they?

Tuesday, November 27, 2012

The comeback of whooping cough

October issue of Microbe, published by ASM.

I read a very interestingand somewhat alarmingarticle in the October issue of the journal Microbe (formerly ASM News). In this article, Merry Buckley explains that whooping cough (aka pertussis), a childhood disease that has strongly declined since the introduction of a vaccine in the 1940s, is now on the rise again. We even see epidemics! says Buckley.

In 2012, in the USA, the number of pertussis cases is expected to be the highest in fifty years, approaching 40,000. Other countries such as Australia and the Netherlands also have high incidence of the diseasein the Netherlands, 6,000 cases were reported in 2009, against only 30 cases in 1980. The causes of this comeback are not fully understood, but scientists have gathered many clues.

Whooping cough is caused by Bordetella pertussis, a Gram negative bacterium belonging to the group beta Proteobacteria. It infects the respiratory system, causing a characteristic ‘whoop’ sound in sick children. Teens and adults can also be infected, although the symptoms are milder than in small children. In the prevaccine era, pertussis was a terrible threat, killing on average 5,000 children a year during the 1920s and 30s in the USA alone. At this period, the epidemics peaked following a cyclic pattern of a couple of years.

Sunday, November 18, 2012

Naming Nature by Carol Kaesuk Yoon

Published by W. W. Norton & Company
For a book that aims at a large readership, Naming Nature (2009) dares to explore a topic that seems anything but sexy at first sight: taxonomy. But we know better and we won’t turn away from the book, since the act of naming and classifying organisms is of course a very exciting activity! (No, I’m not kidding.)

In her book, Carol Yoon recapitulates the history of the discipline and presents the main scientific actors who contributed to the advance of taxonomy. She thus tells us about important figures:  Linné (Carolus Linnaeus), who is considered the founder of modern taxonomy, and who notably popularized the use of the binomial nomenclature (Felis catus and Escherichia coli, to name two lovable examples); Charles Darwin, who needs no introduction, and who revolutionized taxonomy by showing that species were not immutable; Ernst Mayr,  one of the main architects of the modern synthesis of evolutionary theory; Linus Pauling, the Nobel laureate chemist who had the brilliant idea of classifying organisms by looking at the amino acid sequence of hemoglobin; and Carl Woese, microbiologists’ modern hero, who classified organisms by looking at their DNA sequence and turned the tree of life topsy-turvy. Nothing new to me here, but, after all, this book is not written for biologists.

On the other hand, I learned facts that I was ignorant of (and this seems to be an inexhaustible category of facts...). For instance, I learned that it was Julian Huxley (member of a family in which each member is either a literary or a scientific genius) who coined the term ‘systematics’ and proposed to use it in place of taxonomy.

Wednesday, November 07, 2012

Plant pathogen focus: black Sigatoka as a worldwide threat to banana

Banana trees affected by Sigatoka in Malawi. Photo courtesy of APS.
Since I work in the department of plant pathology at UCDand even though I am not a plant pathologist myself!I decided to start a series of posts on microbes that cause plant disease, focusing on stories that are of economic and societal importance.

A couple of weeks ago, one of my colleaguehim a true plant pathologist, managed to scare me by claiming during a talk that banana could disappear in the not-so-distant future! The culprit? The fungus Mycosphaerella fijiensis: This ascomycete causes a disease (black Sigatoka) that damages the leaves of banana trees and reduces photosynthesis. Moreover, the fungus triggers a premature ripening that spoils the fruit. Together these effects of black Sigatoka provoke the loss of 50% or more of the fruit production. 
[I learnt a lot about black Sigatoka in an online article by Randy Ploetz on the website of the American Phytopathological Society (APS). When no other source is explicit, the information in this post comes from the Ploetz article. In general, the APS website is a great starting point for everything related to plant pathology!]

Sunday, October 28, 2012

The science and art of David Goodsell

Portion of an E. coli cell. Image courtesy of David Goodsell.
At the University of Lausanne, when I was a biology student, our great professor Jacques Dubochet tried to instil in us some sense of the physics at play in the biological world. He would ask us questions such as: “So, how thick is the plasmic membrane?” or “How fast will a protein diffuse in the cell?”.  And we would be like: “Huhhh….” So I’m convinced my former professor must be a great fan of the work of David S. Goodsell.

David Goodsell is associate professor of molecular biology at the Scripps Research Institute in La Jolla, California. He is an expert in the structure of biomolecules, and he uses computer simulations to illustrate molecular organizations and interactions.  But what makes his work truly unique is the use of classic watercolor painting to represent cells and their compartments: anything from a bacterium to the Golgi apparatus of a eukaryotic cell, nerve synapses or even viral particles. At odds with the oversimplistic representations of cellular organization that many biologists enjoy, David Goodsell’s drawings offer a real sense of what the biophysical world is. And did I mention they were beautiful too? His websiteMolecular Art/Molecular Scienceis a great resource to learn more about his work.

Saturday, October 20, 2012

Has popular science writing become too wordy?

It’s probably a bit unfair to ask that question, but I can’t help it. These days, I feel like most of the recent science books I read dilute interesting information into too many pages. Well, it could be that the majority of readers prefer long books. It may be true, but it’s definitely not my case. [To be precise, what I mean by “recent” is what has been published in the past ten to fifteen years.] 

Thinking of what I read in the not-so-distant past, I find for instance: “The elegant universe” by Brian Greene (1999), 448 pages; “The stuff of thought” by Steven Pinker (2007), 499 pages; “A guinea pig’s history of biology” by Jim Endersby (2007), 499 pages. Don’t get me wrong, I’m not questioning here the quality of the books. Greene’s book is an informative introduction to string theory, Pinker’s is a clever journey into linguistics, and Endersby’s is a highly original work on the history of model organisms. I really enjoyed reading Endersby and Pinker; I didn’t enjoy Greene that much, but it might be the topic. But quality notwithstanding, could they have been shorter without losing of their substance? 

Thursday, October 04, 2012

The tree of life versus the rhizome of life

Tree by Haeckel (1866). Source wikimedia commons

The metaphor of the tree of lifewhich illustrates the common descent of all life on Earthwas popularized by Darwin in its Origin of species and later by his contemporary Haeckel, but apparently its roots can be traced back as early as the 18th century in the writings of various authors (Archibald,2009). On a different line, it also of course echoes the biblical tree of life mentioned in the Genesis.

However, about a decade ago, authors such as W. FordDoolittle (1999) have cast doubt on the tree as a valid representation of the history of living organisms. Since then, articles that question the tree of life have flourished1. And the debate is far from being settled.

A tree or a rhizome?

Based on the recent development of comparative genomics, the microbiologist Didier Raoult suggested in the journal the Lancet that Darwin’s tree of life should be replaced by a rhizome of life (Raoult, 2010). Raoult sees the rhizome – a complex net of interconnected roots – as a more faithful representation of the history of living organisms.

Saturday, September 22, 2012

The Logic of Chance by Eugene Koonin (continuation)

Published by FT Press

In the first part of this post, I insisted on living organisms (viruses, bacteria, eukaryotes) and their evolutionary history. 

Here I want to look at what Koonin writes about the mechanism of evolution.

What drives evolution?

One central idea in Koonin’s book, I think, is to propose an evolutionary outlook that is based on an analogy with the physical world. Central, for instance, is stochasticity, as a force shaping the genomic evolution. Equally important, in Koonin’s view, are the statistical principles that govern the interactions between all genes within a genome (he likens the collection of all genes in a genome to the ideal gas model in physics). Thus, genes are influenced by a number of statistical rules. On this line, even though it is apparently not possible to define “laws of genomics”, certain regularities can be identified, such as the proportion of different functional classes of genes within a given prokaryotic genome.

Koonin writes, p. 405:

“it is remarkable that the advances of genomics and systems biology, while revealing an extremely complex, multifaceted picture of evolution, at the same time allow us to derive powerful and simplifying generalizations. It is tempting to offer yet another version of the famous phrase: Nothing in evolutionand in population geneticsmakes sense except in light of statistical physics.”

Sunday, September 16, 2012

The Logic of Chance by Eugene Koonin

Published by FT Press
About fifteen years ago, a revolution started in the biological sciences, which goes by the name whole genome sequencing. I don’t have memories of the announcement of the first bacterial genome in 1995 (I was in high school and not really following biology news…), but at the time of the human genome project I was a biology student at the University and I remember very well when the paper describing the human genome came out in 2001 (we had to read it in class!).

Until recently, my feeling about whole genome sequencing was that it was a technical revolution, not a conceptual one. After all, I thought, the sequence information revolution already took place in the seventies, when Carl Woese pioneered the use of 16S ribosomal RNA to construct phylogeny. 

I revised this feeling, thanks in part to the excellent book of Eugene Koonin, The Logic of Chance (2011)subtitled the nature and origin of biological evolution—and published by Financial Times Press (yes, they do have a science catalog!).

Sunday, September 09, 2012

Something scientists should consider about nature

Here, for a change, I want to wander into philosophical territory. I should first admit that I am rather ignorant of it, since I never studied philosophy past the high school level. But my interest remained vivid and I read philosophical books regularly. More important, I believe that every scientist has to keep an eye – even if it is half-open – on philosophy. Isn’t science the daughter of philosophy? (After all, science used to be “natural philosophy”.) And ironically, aren’t I a doctor in philosophy (Ph.D.)?

One year ago I was talking about philosophy with a colleague in the lab (although I can’t remember how the discussion drifted to this topic!). At some point my colleague said that he couldn’t find any use in philosophy, and this baffled me. I mentioned the philosophy of science and Karl Popper as a counter example, but retrospectively I didn’t need to be so specific. Philosophy is important per se if it has practical applications for scientists it is a good thing but not its final goal. 

Nonetheless, I started thinking about examples of philosophical inquiries that have repercussions in the day-to-day life of scientists, and I realized there’s plenty. Here I would like to share one which I think is essential: the reflection on nature and natural phenomena.

Wednesday, August 29, 2012

Back from ISME 14

I just left Copenhagen, where the 14th International Symposium on Microbial Ecology took place from August 19 to 24. This was a busy meeting, with 2,200 attendees (a new record), hundreds of presentations and countless posters. ISME is the biggest meeting of microbial ecologists – a wide crowd that covers everything from molecular biologists to bioengineers, ecologists and evolutionary biologists.

This diversity is part of what makes ISME an interesting meeting. Not only the diversity of the participants’ background, but also the variety of topics: within the same day you can follow talks about forest soil, deep-sea vents, biogas plants or the human body.

Sunday, August 05, 2012

Francis Crick and Directed Panspermia

Francis Crick. Photo Marc Lieberman
Every biologist knows that Francis Crick is the co-discoverer of the structure of DNA. What is less known, probably, is the fact that Crick was a proponent of a theory that stands at the border of science, the theory of directed panspermia.

In 1973, Crick (together with chemist Leslie Orgel) published an article describing the theory, and in 1981 he dedicated a full book to directed panspermia, entitled Life itself

According to Crick, the idea of panspermia – which means “seeds everywhere” – was proposed by the physicist Arrhenius at the end of the 19th century. Arrhenius suggested that life on Earth originated from space, that our world was seeded by spores of micro-organisms traveling between planets. 

But because the radiations in space were thought to be too intense for the spores to survive, Crick and Orgel postulated a variant of the theory in which spores were transported by an interplanetary spaceship sent by an alien civilization!

Sunday, July 29, 2012

Indole teaches persistence to bacteria

Indole molecule (C8H7N). Source: wikimedia commons
When a bacterial infection is treated with antibiotics, bacteria that are in a so-called dormant, inactive state may escape death – this because antibiotics only kill growing bacteria. It becomes a serious problem when these sleeping beauties start to grow again, in particular when they do so after the period of antibiotic treatment has ended… Thus, an infection that was apparently cured could be followed by a secondary infection days or weeks later. This problematic phenomenon is called bacterial persistence, and it should not be confused with bacterial resistance, in which growing bacteria are immune to one or several antibiotics.

Now what about indole? (The molecule displayed on top of this post.) Actually indole is present in very common and important biomolecules, such as the amino acid tryptophan, the animal hormone serotonin and the plant growth hormone auxin. We have known for more than a century that E. coli produces indole in stationary phase (Lee, 2010), and it does so thanks to an enzyme called tryptophanase, which cleaves tryptophane into indole, pyruvate and ammonia. 

But E. coli is not the only bacterium capable of that: more than 85 species (both Gram-negative and Gram-positive) can synthesize indole (Lee, 2010).  For a long time the biological functions of indole were overlooked, but now we know that indole can act as an extracellular signal and can for instance increase antibiotic resistance and control biofilm formation in E. coli.

Sunday, July 15, 2012

Are all our modern health issues linked to our microbiome?

June issue of Scientific American
The human microbiome is definitely the sensation of this Summer 2012. [Kind of a Carly Rae Jepsen for science!]

In June alone, our microbial inhabitants were featured on the cover of Scientific American (watch their beautiful infographics), Nature, Science and Microbe

The Human Microbiome Project (HMP), a $170 million research consortium funded by the US National Institute of Health (NIH), just released two reports in Nature accompanied by fifteen publications in PLoS ONE. The consortium, strong of about 200 researchers, studied the diversity of microbes inhabiting the body (skin, mouth, nose, gut, urogenital tract) of 242 healthy people, using new sequencing technologies to catalog the microbes.

The bottom line? Microbial diversity is very high between healthy individuals. It is therefore impossible to define a typical ‘healthy’ microbiome. In a way, every individual develops his/her own personal set of microbes. The diversity, however, is not totally random and patterns are clearly present in various areas of the body.

Monday, July 09, 2012

Science publishes two reports that contradict the 'arsenic life' story

This is a short follow-up post about the bacteria from Mono lake (California) that allegedly incorporate arsenic instead of phosphorus in their DNA

The journal Science just published two papers on the topic. The first report is from Rosie Redfield's lab in Canada, the second from Julia Vorholt's lab in Switzerland. Together, they claim that the arsenic bacteria in fact must have some phosphate to grow, and that arsenic is not incorporated into DNAthus refuting the main conclusions of the original arsenic bacteria paper.

I only read the abstracts so far, but at first sight it seems to bury the arsenic story for good... It's not that often that we see researchers repeating someone's experiment to challenge it, so Redfield and Vorholt should be praised for the effort. 

Thursday, July 05, 2012

Kingdoms or domains?

I view taxonomy – the classification of organisms – at the same time as the most useless and the most useful science. Useless because we know that all life forms are related to one another, and therefore the categories that we create to separate them are arbitrary (with the exception of the distinction at the species level). Most useful, since naming and organizing things seem necessary if we are to claim any knowledge. And isn't it a true pleasure (I almost dare to write "bliss") to point at a plant, a mushroom or an animal (if the latter doesn't move too fast) and be able to name it? 

I learned my share of taxonomy as a student, but I also forgot quite a bunch… At least I remember that I got a good grade at my zoology exam (I had to talk about the subphylum Chelicerata!), based on a course by one of the best professors I ever had, Peter Vogel

Taxonomy, which is part of Systematics (the study of biological diversity), proposes a hierarchy from the most particular to the most general: Species, Genera, Families, Orders, Classes, Phyla… (In the classic evolutionary taxonomy, classification is mostly based on morphology, while modern molecular systematics compares the sequence of amino acids in proteins or of nucleotides in nucleic acids.) But, what about higher (more global) levels of classification? 

Saturday, June 30, 2012

Unwanted guests

Microbial contaminants (three species) on a plate
Microbiologists use Petri dishes, filled with a variety of agar media, to grow microbes. Even a small lab can produce hundreds of plates every week… And it is quite common to store in the fridge those of these plates that are not directly inoculated for a future use. Thus, when you open a microbiologist's fridge, you may find columns of Petri plates labeled with the medium and antibiotics they contain, waiting to be covered with a suspension of microbes.

Sometimes, when you store them for long periods, you can have the disagreeable surprise to find unwanted guests on your plates, that is, contaminant microbes!

Friday, June 22, 2012

Back from ASM General Meeting

I'm just back from the 112th general meeting of the American Society for Microbiology, which took place from June 16 to 19 in San Francisco. The general meeting is huge: thousands of microbiologists from all over the US and abroad, representing all fields of microbiology; hundreds of talks and more than 3,000 posters presented; about 200 biotech companies showing their products. 

That is something to see! It's great to feel part of this large community of microbiologists. We are one big family, even though we work on topics as varied as human health, environmental ecosystems, agriculture, food safety, biotechnology, etc.

Saturday, June 09, 2012

The endosymbiotic theory of Lynn Margulis

Published by Basic Books
Lynn Margulis passed away last November, sadly. She was renowned for the endosymbiotic theory of evolution, which is now part of biology textbooks. She had a wonderful insight: the mitochondria and chloroplasts that are found in eukaryotic cells were, in distant past, free-living bacteria. Thanks to at least two distinct endosymbiosis events, they were incorporated—and not digested—in the eukaryotic ancestor. They became responsible of key functions within the new association, namely respiration and photosynthesis. These symbionts persisted until at some point they were indistinguishable from their host, and all merged to become one new organism, a eukaryotic cell. 

Recently I found a copy of her book Symbiotic Planet (1998) in my usual second-hand bookshop in Davis. It is a short book in which Margulis deals with the scientific idea that has occupied her during most of her career: the serial endosymbiosis theory (or SET). The author sums up the book as follows (p.33):
In short, I believe that most evolutionary novelty arose, and still arises, directly from symbiosis.

Sunday, May 27, 2012

Filamentous bacteria under the microscope

Filamentous bacteria from soil, seen with phase contrast microscopy.
It's pretty easy to isolate soil bacteria: take a scoop of soil, mix it with some water, then plate the liquid on a Petri dish and incubate it overnight at 25-30 °C. Voilà. 

The isolated bacterial species will vary with the conditions (type of medium, temperature); here I found many filamentous bacteria on the plate. They look a little bit like filamentous fungi (since they also form a mycelium), but usually you can easily tell them apart (with a microscope) because of their smaller diameter. 

Saturday, May 19, 2012

The Human Zoo by Desmond Morris

Back in the days when I was a biology student in Lausanne I had a great time reading Desmond Morris' best seller The Naked Ape (1967), in which the British zoologist discusses what sort of curious social animals we are—and he does so with a lot of wit and humor.  

The Human Zoo (1969) is his follow-up book, thus when I found a copy of it in a second-hand bookshop I happily bought it (probably equally motivated by the lovely vintage yellow cover!). Newer editions are available, as you can see in the author's bibliography.

The Human Zoo still deals with the human animal, but this time the focus is on the social ties that we develop between each other and the sort of society in which we live. The underlying question is: How beings used to living in tribes of at most hundreds of individuals can cope with our modern society and its super-tribes of millions? The city, writes Morris, is not a concrete jungle, it is a human zoo. In the modern life and its crowded places, we tend to behave as animals in captivity.

Tuesday, May 08, 2012

Mother of vinegar

Mother of vinegar from a wine vinegar pot
I'm currently visiting my parents in Switzerland, in a lovely region located between the lake Léman (lake Geneva) and the mountains of Jura (see Nyon région tourisme). On that occasion my father gave me a tour of his vinegar pots, and even fished out the mother of vinegar from inside the pot so that I could take a picture. Have a look at this biofilm of acetic acid bacteria: it's a large and thick disc with the color of a liver!

As their name implies, these bacteria transform alcohol, for instance from wine, into acetic acid. From what I read during a quick overview of the literature, common acetic acid bacteria include species of the genera Acetobacter and Gluconobacter

Thursday, April 12, 2012

The invention of multicellularity

Multicellular yeast cluster. Photo courtesy of William Ratcliff.
In January, William Ratcliff and his colleagues from the University of Minnesota caused quite a stir with their study on the experimental evolution of multicellularity in yeast, published in PNAS. Many media covered the story, including the New York Times, Wired and Scientific American. Briefly, what they did was using artificial selection on unicellular yeast (the baker's yeast Saccharomyces cerevisiae) in order to create an obligate multicellular organism after many generations of selection. What is impressive is that it worked pretty well in all their different test cultures!

Multicellularity was invented several times during the history of life (Rokas, 2008), but since it happened a long time ago it is difficult to reconstruct the exact sequence of events. Experimentation on today's unicellular organisms, however, allows researchers to test mechanisms (and associated mutations) that could lead to a multicellular lifestyle. Of course, this cannot decide for good how the phenomenon occurred many millions years ago – which is not at all the author's claim – but this can prove that such mechanisms can occur, given that an appropriate selection pressure is present.

Monday, April 02, 2012

The publications of the American Academy of Microbiology

Published by AAM and ASM
Do you know your E. coli fact sheet well enough? If needed, you can set your record straight by having a look at one of the new publications of the American Academy of Microbiology: E. coli: Good, Bad & Deadly. This booklet is part of the FAQ series, a collection on important microbe-related topics written for a large public. 

To me, this series is a great resource to learn how to write for the layman: keep the writing engaging but do not cloud or sacrifice the facts. It contains such nice piece of writing as "E. coli is genetically promiscuous. It can exchange genes with other strains of E. coli and even other types of bacteria." The first sentence is funny and intriguing, whereas the second sentence explains briefly. The content of the whole booklet is substantial but not indigestible (about 6,000 words) and nicely illustrated.

Tuesday, March 27, 2012

Synthetic life and vitalism

Illustration courtesy of Harry Campbell
In 1966, Francis Crick—the co-discoverer of the structure of DNA—gave a series of lectures at the University of Washington in which he discussed vitalism and the nature of life (Crick, 1966). Vitalism is this old idea according to which some sort of special force is present in living organisms, and that this force cannot be explained in terms of physics and chemistry. Crick notes that a way to refute vitalism would be to create a living organism synthetically—in other words, make a cell from scratch. Crick's remark finds a striking echo in today's research in synthetic biology, particularly in the efforts of Craig Venter.

In 2010, Venter and his team from the J. Craig Venter Institute achieved a scientific tour de force: the synthesis of a whole bacterial genome (one circular chromosome) and its transplantation into a recipient cell (a mycoplasma). The resulting bacterium was able to grow and multiply thanks to its artificial chromosome. The results were announced during a press conference in May 2010 and published in Science two months later. The long-term goal of the JCVI is not to disprove vitalism, but to design and implant synthetic genomes that can perform specific tasks, such as to produce biofuels. The mycoplasma synthetic genome, which is only slightly different from the original, serves as a proof of concept, paving the way to more important genome (re-)engineering. 

Monday, March 19, 2012

Reporter bacteria to monitor arsenic concentration in groundwater

Vials containing bioreporter bacteria. Photo courtesy of UFZ.
It is not widely known, but analytical measurements with bacterial bioreporters can 
compete with commercially available detection kits, inasmuch as the bioreporters' efficiency (sensitivity, detection limit, etc.) is often comparable - if not better - than the chemical-based systems. So why are bioreporters not more widespread? Well, the leap from the laboratory to the field is a difficult one, which demands a tight collaboration between fundamental research and engineering. In addition, economical and policy challenges need to be overcome. Today, most developed bioreporters have never left the lab.

But this may change, and a recent study by Konrad Siegfried et al. published in Environmental Science & Technology is a remarkable demonstration of the usefulness of reporter bacteria in the field. [Among the authors of this paper are three scientists with whom I had the privilege to work: Antonis Chatzinotas and Hauke Harms from the UFZ in Leipzig and Jan Roelof van der Meer from the University of Lausanne (HH directed my master thesis and JRvdM directed my PhD thesis).]

In this study, the authors used a strain of E. coli that produces bioluminescence when it is exposed to arsenite and arsenate (oxidized forms of arsenic). Bacteria detect the poison thanks to a specific activator protein which binds arsenic and triggers the expression of specific genes. The result is the production of a set of proteins, including the bacterial luciferase, which makes the bacteria glow. 

Sunday, March 11, 2012

Jacques Monod and the origins of molecular biology

A beautiful model or theory may not be right; but an ugly one must be wrong. 
Jacques Monod 

 Published by ASM Press
After his work on bacterial growth, I'm now reading about Monod's later career and the discoveries that contributed to the creation of molecular biology. And for that purpose, I warmly recommend the revised edition of "Origins of molecular biology – A tribute to Jacques Monod", published at ASM Press. In this book, Agnes Ullmann and André Lwoff (two former collaborators of Monod) have compiled a collection of essays by colleagues and peers who recall their memories of the great scientist (among whom François Jacob, Francis Crick, Salvador Luria and many others). The book should be praised for providing a mosaic view that tells both the story of the science and the story of the man. And what a man! Bacterial growth kinetics, messenger RNA, enzymatic repression, lac operon, allosteric proteins… A Nobel prize received in 1965 (together with André Lwoff and François Jacob) rewarded their «discoveries concerning the genetic regulation of enzyme and virus synthesis». But, although the book portrays Jacques Monod as an extraordinary man and a great scientist, this is no hagiography, and the darker sides of his personality are evoked as well. 

Thursday, March 01, 2012

The mechanics of bacterial cluster formation on plant leaf surfaces as revealed by bioreporter technology

Green and red fluorescent bacteria on the surface of a leaf
Our new publication is out there as an early view in Environmental Microbiology, and I shamelessly take this opportunity to write about it here!

Here's the story. The plant foliage is colonized by a crowd of microbes (with bacteria on the front line—up to 108 bacteria per gram of leaf has been reported!). Some of them can be pathogenic, hence a threat, but most of them are harmless or even favorable inhabitants of the plant ecosystem.

Bacteria form large clusters (aggregates) of cells on the surface of leaves, but the mechanism of formation of such structures is not very well understood. What we want to know is how these bacteria grow and colonize this specific environment at the microscale, that is, at their own scale.

First, bacteria have to land on the leaf. Wind, rain, insects can all contribute to bring microbial visitors onto the leaf surface (what we call the phyllosphere), usually few cells at a time. Once on the leaf, these immigrants will grow at the expense of the plant sugars available on the leaf and, if the conditions are favorable, rapidly multiply to form clusters of up to thousands of cells. Do these clusters result from the random aggregation of cells or do they result from the reproduction of a single bacterium? The two mechanisms—that we call aggregative and replicative—are fundamentally different but not necessarily mutually exclusive. 

Thanks to fluorescence microscopy it is possible to visualize glowing bacteria on the surface of a leaf. One difficulty, however, is that we cannot follow the same microarea of leaf overtime… We are limited to a snapshot view, and so it's impossible to decide whether a given cluster was formed through aggregative or replicative behavior. For this reason we developed techniques that would enable us to deduce a posteriori what was the mechanism of formation. 

Monday, February 20, 2012

The role of textbooks in biology

"Hey, this is textbook knowledge, you should know that!"

This is what I would be told, if I were to ask a stupid question about microbiology in the laboratory. (And for the record, I believe that such things as "stupid questions" do in fact exist.) 

"Textbook knowledge" is often used to define the core knowledge that a biologist (or any scientist, as far as I can tell) should possess as a result of her education. When I was an undergraduate biology student, we used to talk about "the Campbell" and "the Alberts" to refer to our textbooks of general biology and molecular biology, respectively, and today I talk of "the Brock" to mention a reference textbook in microbiology. Textbooks are not only useful to students; personally, I often find relevant information in them, although most of my readings are scientific papers. 

A textbook should provide you with the background knowledge sufficient to operate in the current state of your discipline. (Although, of course, some will be more general or conversely will be more specific than others, depending on their goals.) 

The University of Chicago Press (Image source)
The reason I want to write about textbooks here is a consequence of my reading of "The structure of scientific revolutions" (1962), the landmark book by science philosopher Thomas Kuhn. Together with Popper, Kuhn is among the most famous philosophers of science: he coined the term "paradigm shift", which is not only a fascinating concept, but also a very catchy idea. Scientists like to use it often and in many different contexts. (Probably too often in my opinion, since paradigm shifts do not take place that frequentlyif they take place at all.) 

Kuhn's book is an excellent read because it is rather concise (my edition is about 200 pages, with a 30 pages postscript) and almost devoid of jargon, which makes it very engaging. My only regret was maybe that I felt I already knew too much of it, since Kuhn's ideas have been widely explained and discussed. For instance, I remember reading a very good recapitulation of Kuhn's theses in a French translation of Alan Chalmers' book "What is that thing called science?". Nonetheless, a lot of fascinating details were still to be found.

Sunday, February 12, 2012

Jacques Monod and the study of bacterial growth

Among the great scientists of the 20th century, Jacques Monod holds a prominent place. Together with François Jacob and André Lwoff he contributed to the creation of molecular biology through his study of genetic regulation, in particular the lac operon in E. coli. Before this achievement, which was awarded a Nobel prize in 1965, Monod helped define the nature of bacterial growth in a variety of experiments that took place during his doctorate. He published it in 1942, exactly seventy years ago, under the title "Recherches sur la croissance des cultures bactériennes" (a second edition, the one I read, was published in 1958).

In his experiments, Monod followed the growth of liquid bacterial cultures in flasks at controlled conditions of temperature and oxygenation. The turbidity of the culture, which was used as a surrogate value for bacterial biomass, was measured with a nephelometer (in laboratories, today, a spectrophotometer is usually employed, but the principle is the same). Bacteria were grown in complex (brain broth) or defined media with variable sources of carbohydrates. Monod used Bacillus subtilis and Escherichia coli (that he calls B. coliBacterium coli I suppose, which is the ancient taxonomy). 

Most notably, Monod showed that bacterial growth is limited by the amount of nutrients, but that the yield is independent of the concentration of these nutrients. The growth rate, however, is dependent of the nutrients' concentration and rapidly reaches a limit. What is more, this maximal growth rate can vary a lot with different carbon sources and temperatures. Today, we still talk about 'Monod kinetics' when we describe the growth of bacterial cultures.

Sunday, February 05, 2012

What news from the ‘arsenic life’ front?

Mono Lake, CA, photo by NASA
This story has already become sort of a case study. In December 2010, NASA held a press conference about its astrobiology research program and the discovery of a bacterium from Mono Lake (CA) allegedly capable of substituting phosphorus by arsenic in its DNA. The research was published in ScienceExpress and attracted a lot of attention from the media - mostly as a consequence of the ‘hype’ factor brought by NASA, which went as far as saying that “The definition of life has just expanded”. All life on Earth shares the same DNA, whose backbone is made of sugar and phosphate. If any organism could replace phosphate by arsenate, that indeed would be very surprising and exciting.

Sunday, January 29, 2012

The controversy over H5N1 research

Ferret, photo by Mika Hiltunen
Since last November, the scientific community has been shaken by what the journal Science has called "a media storm" on H5N1 research. I don't really have an a priori opinion about the potential risks of this research – I am not a virologist, after all – but this is a fascinating controversy which is of importance for microbiologists in general. Science provides us with a special page archiving the news and commentaries related to these events

It all started with experiments on H5N1 avian influenza virus that were meant to study what mutations can increase its transmissibility in ferrets (commonly used as a model animal for influenza research). Two virologists in different countries – Ron Fouchier in the Netherlands and Yoshihiro Kawaoka in the USA/Japan – have managed to create H5N1 strains that are transmissible between ferrets (and thus, potentially, between human beings) and want to publish their independent results in Science (Fouchier) and Nature (Kawaoka). The question that these researchers are willing to answer is: can H5N1 cause a human pandemia, and if yes, what mutations would allow it to do so? Fouchier argues, for instance, that knowing the mutations will allow the researchers to look for them in the field, thus being proactive against the virus spread.

Saturday, January 21, 2012

Bacteria, Archaea, bacteria, or prokaryotes?

In this blog, I use the term ‘bacteria’ (with a lower case), as a generic term equivalent to prokaryotes (that is, Bacteria and Archaea). In this I follow the example of the Brock Biology of Microorganisms, a reference textbook in microbiology (and a wonderful read, by the way).
If you are not familiar with these denominations, here is a brief recap:

Thursday, January 19, 2012

How many bacteria out there?

At first sight, it seems a very difficult question to answer. How can we possibly estimate such a number? Well, William Whitman, David Coleman and William Wiebe - all from the University of Georgia, USA - have provided us with a very exciting proposition in a 1998 article published in the Proceedings of the National Academy of Sciences of the USA.

And the astonishing number is: ~5 x 1030 bacteria!


Our own 7,000,000,000 suddenly seem less impressive.
Whitman and his colleagues noted that the actual total number of bacterial cells had never been assessed, ‘because an estimation of the number of prokaryotes would seem to require endless cataloging of numerous habitats’. It certainly seemed to me that way, but they ended up with a convincing estimation after looking for representative habitats in both aqueous and terrestrial environments. What is striking is that many habitats that show very high densities of bacteria, such as, say, animals’ gut (up to 1011 per g of human colon), account for a negligible fraction of the total. The main crowd is apparently to be found in subsurface sediments and terrestrial subsurface (probably >95%). Hence, what is directly accessible to us (plants, animals, soil, oceans, lakes, etc.) represents a mere 5% of the total bacterial environment. Talking about the tip of the iceberg…