Moselio Schaechter

  • The purpose of this blog is to share my appreciation for the width and depth of the microbial activities on this planet. I will emphasize the unusual and the unexpected phenomena for which I have a special fascination... (more)

    For the memoirs of my first 21 years of life, click here.

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March 28, 2011

Geobacter: Microbial Superhero

by Suzanne Winter


Iron-breathing microbes, Geobacter. © Derek Lovley
Kelly Nevin & Ben Barnhart, University of Massa-
chusetts. Source.

If the power of Superman resided solely in his supernatural abilities, then Bruce Wayne’s Batman would never have been able to compete on his level. But when the other factors that superheroes depend upon are accounted for—sidekicks, spandex, sarcasm—both Superman and Batman can claim success in the world of do-goodery and hunky haircuts. In other words, the strength and effectiveness of an individual’s power often depends entirely on the creative use of raw materials.

This reality is mirrored in the microbial realm: organisms compete to occupy and dominate specific niches through adaptation and natural selection, and it’s the ones that play by an entirely different set of rules that may have the possibility to change the world.

Notably, species that have evolved innovative and, subjectively, weird methods of living have long intrigued scientists with their survival abilities and preferences. Consider the fascination with the extremophiles in the hot springs at Yellowstone National Park that led to the isolation of Taq DNA polymerase from Thermus aquaticus, surely one of the most important enzymes in the molecular biology lab. And while many microbes follow the well-studied route of using oxygen as a final electron receptor, researchers are increasingly looking at Geobacter species that use iron oxides as the final electron receptor in order to uncover the secrets enigmas of environmental restoration, energy harvesting, and the creation of the world.

Continue reading "Geobacter: Microbial Superhero" »

March 24, 2011

About the Events in Japan

by Elio

This blog celebrates the Small Things and, by implication, those who relish their study. Thus, I think now of our colleagues who worked or have trained in Japan. One way to express our solidarity is to mention the names of scientists who exemplify the great achievements of Japanese microbiology, earlier on and now. I compiled this arbitrary list in haste and apologize for its obvious incompleteness.

Teruhiko Beppu: symbiotic bacteria
Akira Endo: statins
Yukinori Hirota: bacterial genetics
Koki Horikoshi: deep sea bacteria extremophiles
Masayori Inouye: cellular adaptation to stresses
Shigetane Ishiwata: Bacillus thuringiensis
Akira Kaji: protein synthesis
Shibasaburo Kitasato: bubonic plague
Hiroshi Nikaido: bacterial cell walls
Hideyo Noguchi: syphilis, yellow fever
Riichi Sakazaki: bacterial taxonomy
Kiyoshi Shiga: shigellosis
Noboru Sueoka: bacterial cell cycle
Gazuko Tamura: mevalonic acid as growth factor
Susumu Tonegawa: immunology (Nobel prize)
Shigezo Udaka: amino acid producers
Hamao Umezawa: kanamycin
Tsutomu Watanabe: antibiotic resistance
Takashi Yura: heat shock sigma and proteins

March 21, 2011

A Viral Pyramid Scheme

by Merry Youle

Lower gesyer basin mud pot

A mudpot in the Lower Geyser Basin, Yellowstone
National Park, USA. Source.

In order to release their newly assembled virions, most viruses lyse the cells that have fed and housed them. This lysis is not a haphazard affair. Some phages, for example, employ a holin-endolysin system to rupture their host's cell membrane and digest the cell wall at a precisely controlled time. (For our earlier posts about this, click here and here.) Others instead interfere with cell wall synthesis—the same strategy that we use with our β-lactam antibiotics. Now yet another completely different scheme has been discovered in a virus that infects an acidophilic hyperthermophilic Crenarchaeon.


Figure 1. A typical S. islandicus cell
is an irregularly-shaped coccus.
Bar = 200 nm. Source.

We have come to expect novelty in the bizarre zoo of crenarchaeal viruses; witness the Acidianus two-tailed virus that "grows" its two long tails after leaving the host cell. Still we weren't prepared to find a novel lysis strategy among them. The ones that infect the extremophilic Crenarchaeota weren't even thought to be lytic. Instead, it appeared that they resided long-term within their host in a carrier state, continuously secreting virions from the host cell without killing it (but also without integrating their genome into the host chromosome as do the temperate phages such as λ). This benign strategy was, we thought, how the wily virus protected itself from rapid degradation by extreme environments. Not necessarily so.

Continue reading "A Viral Pyramid Scheme" »

March 17, 2011

Fine Reading: Cell Biology of Bacteria

by Elio


Clusters of chemoreceptors of Escherichia coli. The largest
clusters are at the poles. The image shows Tar receptors
visualized by super-high resolution fluorescence microscopy
(PALM). Bar = 1µm. Source.

The publication of an exciting book, Cell Biology of Bacteria, sent me into a reflective frame of mind. You see, I am among the few left from the beginning of the modern era of Bacterial Cell Biology. When I was a graduate student, in the early 1950s, “Bacterial Cytology,” as it was then called, was a subject rife with contentions and contradictions. Soon, however, new studies led to the serious affirmation of the now banal fact that bacteria have recognizable and definable body parts. The curtain was lifted. The nucleoid, the cell membrane, the cell wall, all became respectable entities, amenable to serious study. Just ahead lay the discovery or adapting of advanced techniques. On one hand, suitable cell fractionation methods were developed, on the other hand, microscopic techniques, notably fluorescence microscopy, came of age.

Today, Cell Biology occupies center stage in studies of bacterial physiology and genetics. In my mind, so pervasive is this influence that I was prompted to call ours the Age of Imaging. Now for the book. It is edited by Lucy Shapiro and Rich Losick, both of whom entered this field later in their work, both after having made stellar discoveries in developmental microbiology (in Caulobacter crescentus and Bacillus subtilis, respectively). I’m not about to write a book review, so I will just to say that this 250+ page book covers a wide variety of topics written by major investigators. As you would expect, the book has some stunning images. Pictures here are worth many a kiloword each. One of these merits reproducing here, given that it opens a window into a great future. It shows the distribution of chemoreceptors in Escherichia coli, visualized at a nearly incredible degree of resolution using a novel technique for localizing fluorescence called PALM (for Photoactivated localization microscopy). (Click here for Jennifer Gutierrez's earlier post about this methodology: Exciting Resolution.) Stay tuned for more of such marvels. This is just the beginning.

March 14, 2011

Targeting an Achilles' Heel of Plasmodium

by S. Marvin Friedman


SEM of female Anopheles mosquito. Source.

Plasmodium falciparum accounts for 85% of all cases of malaria, and thus is the most deadly of the many species in this genus. About 250 million people are infected annually, of which about one million die. Of these deaths, 90% occur south of the Sahara desert in Africa, and most of the victims are children under the age of five. Malaria also occurs in southern Asia, Central and South America, the Caribbean, and the Middle East. Plasmodium, an apicomplexan protozoan, is also famous for its complex life cycle, some stages of which take place while within females of certain species of Anopheles mosquitoes, others while resident in the liver and red blood cells of humans who were bitten by these mosquitoes. The huge health problem of malaria is exacerbated by the alarming ability of this protozoan to rapidly develop resistance to chemotherapeutic agents. Thus, new antimalarials are desperately needed to bring this deadly disease under control.

In order to identify new drug targets, Istvan and coworkers analyzed P. falciparum mutants resistant to two commonly used antimalarials: thioisoleucine (an analog of isoleucine) and mupirocin (an antibacterial agent used clinically to treat MRSA infections). These two drugs kill blood stage parasites at micromolar and mid-nanomolar concentrations, respectively. For both drugs, increasing the isoleucine concentration in the medium increases the IC50 values (i.e., reduces killing efficiency), suggesting a competitive interaction between isoleucine and both drugs. The kinetics of killing are dissimilar for these two compounds, indicating that they inhibit different isoleucine utilization targets. These results are not surprising since, upon entering red blood cells (“ring stage”), the parasites degrade hemoglobin to obtain a supply of amino acids necessary for replication. Such scavenging is essential because the parasites lack most amino acid biosynthetic pathways. But isoleucine is the only amino acid absent from adult human hemoglobin, hence is the only one that must be obtained from other, less convenient sources.

Continue reading "Targeting an Achilles' Heel of Plasmodium" »

March 10, 2011

Talmudic Exobiology Redux


We recently asked this Talmudic Question as our TQ #71:

As NASA’s hotshot exobiologist, you are asked to design an Earth satellite system in which some organism(s) can live actively (i.e.. no spores) for millennia. How would you go about it? Specify an orbit of your choice.

Ami Bachar replied:

I would take a clean coca cola bottle, fill it half with soil and half with sea water, and make sure it stays liquid for the next 1000 years. "Everything is everywhere and the environment selects" (Martinus Beijerinck) + "life is what happens to you while you're busy making other plans" (John Lennon). If it is well closed and nothing escape from the bottle than there should be enough of everything needed to sustain life for much longer than a millennia.

To which I (Elio) replied: The simplicity of your proposal wins out over all the complex schemes that I had dreamt up. Good for you!

It turns out that I jumped the gun. It's not so simple, as fellow blogger Russell Neches insightfully pointed out.

by Russell Neches

Feeling a bit giddy with sleep deprivation (and the first successful run on our lab's new sequencing machine), I decided to take a crack at Talmudic Question #71:

As NASA's hotshot exobiologist, you are asked to design an Earth satellite system in which some organism(s) can live actively (i.e., no spores) for millennia. How would you go about it? Specify an orbit of your choice.

Ami Bachar gamely suggested entrusting a cargo of seawater and dirt to a Coca Cola bottle, and lobbing it into orbit. I liked this idea so much that I couldn't resist embroidering it.

Continue reading "Talmudic Exobiology Redux" »

March 07, 2011

Gut Microbes and the Infant Brain: A Surprising Symbiosis

by Micah Manary

The ancient genes versus environment argument (i.e., nature versus nurture) about the development of the infant human brain has taken a swerve in a direction few thought possible. A recent paper by investigators from Sweden and Singapore reports on studies using a mouse model to demonstrate that the presence of the gut microbiota significantly influences the developing brain, influencing developmental pathways that affect both motor control and anxiety-related behaviors. The implications for human development are certainly not yet realized, but could be profound. Our anxiety, motor control, and even cognitive pathways are implicated in this paper. Microbes may indeed be subtly changing our brain early on—and for what purposes we cannot yet say. The article would imply that this interaction is beneficial to us, and thus indirectly to our microbiota, but the mere fact that microorganisms can shape our minds brings up many more questions about how humans develop their identity.

Continue reading "Gut Microbes and the Infant Brain: A Surprising Symbiosis" »

March 03, 2011

Talmudic Question #72

Suppose a marine bacterium evolved the perfect phage defense, one that no phage could overcome. A thousand years hence, what changes would you expect to see in the marine microbial community?

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