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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« December 2010 | Main | February 2011 »

January 31, 2011

Hedging Your Bets

by Merry

Movie_still

Click here to download a movie from the Elowitz
lab showing different behaviors within a clonal
population of Bacillus subtilis in relatively
homogeneous conditions. Here, the cells express a
green fluorescent protein when growing normally,
but turn on a red fluorescent protein when
differentiating into a transient competent state.
Some others differentiate into resilient spores
(white objects). Source.

Bacteria that are born genetically equal aren't necessarily the same. The same genome, residing in cells side-by-side in the same medium in the same flask, does not guarantee the same phenotype. One example that comes to mind is the persisters in E. coli populations—the small number of cells that spontaneously stop growing. If the population is hit by a β-lactam antibiotic, those cells escape death. Similarly, under lab conditions that trigger genetic competence in B. subtilis, only a small fraction of the cells make the switch to competence.

B. subtilis cells growing in a rich growth medium offer yet another example. Here genetically identical cells comprise two distinct types. Most are flagellated and actively swimming about as individuals, while a minority have no flagella and form long chains. The game is different in cells in the stationary phase where virtually all of the cells are found in long chains, bound together by an abundant matrix. Losick, Kolter, and colleagues have been working with this system for some years (for earlier papers, click here and here) seeking to determine how such bimodal cell populations are established and maintained in growing cultures.

Others have approached this question from a theoretical point of view asking what sort of a regulatory "circuit" would it take to produce robust bistability. In other words, how might a cell, using a simple system employing but a few regulatory genes, be able to operate in either of two distinct states. In 2000, Gardner et al. started with a model for a bistable network (Figure 1) and then attempted to create such a circuit in E. coli. (A simple system this may be, but conveying it in words is not so simple. I suggest you wrap your mind around the diagrams first.)

Continue reading "Hedging Your Bets" »

January 27, 2011

My Geological Ignorance

by Elio

Snarvegbilde_from-page-geobio

A rock is being eaten away by chemo-
synthetic bacteria. Source.

Some years ago, I was standing on an overlook of the badlands in the Anza-Borrego California desert, explaining to a friend that the layers of red rocks in front of us were derived from the Grand Canyon, somewhat proud that I could exercise some of my extraordinarily limited knowledge of geology. It turned out that it was pure nonsense, the rocks being from a totally different era. Such is my ignorance of the planet on which I am a passenger.

But I expect that I’m not alone, that others also can lay claim to geological illiteracy. It was not always this way. Until the early 20th century, biologists were expected to know something about geology, and many knew a great deal. This has fallen by the wayside and rare is the biologist who can name the era when copious oxygen appeared in the atmosphere, when Pangea started to break up, when flowering plants began to diversify, or when dinosaurs dominated. This is not good. With the recent flourishing of microbial ecology and evolution, geomicrobiology has become a field of importance for all those interested in what makes the Earth tick. Many examples, including readily appreciated ones, attest to the pervasive role of microbes in this planet’s metabolism, from the White Cliffs of Dover to New Mexico’s Carlsbad Caverns. My way of atoning for my sins is to subscribe to the table of contents of the journal Geobiology. In the current issue, I found a paper with the curious title: Twelve Testable Hypotheses on the Geobiology of Weathering. It has 27 authors from all over the United States plus a lone one from Great Britain.

Continue reading "My Geological Ignorance" »

January 24, 2011

Some Like it Hot

by S. Marvin Friedman

Sulfolobus_solfataricus

Red coloration on rocks near Naples, Italy, produced by the
hyperthermophile Sulfolobus solfataricus. Source.

How can thermophilic bacteria not only survive, but actually proliferate, at elevated temperatures that would be lethal to all other forms of life? After extensive research during the past five decades, this question has been answered in a general way, but the molecular basis for this unusual capability has not been clearly resolved. Thermophiles [I use this term to include both thermophiles (optimal growth temperatures of 50-70 °C) and hyperthermophiles (optimal growth temperatures >80 °C)] synthesize intrinsically thermostable cellular components and/or extrinsic stabilizing factors (chaperonins and polyamines, for example).

Most proteins isolated from thermophiles are thermostable and the mechanisms underlying this property have been extensively studied. These investigations have their roots in the pioneering work on the heat stability of hemoglobin and ferredoxin carried out by Perutz in 1975. Some of the strategies reported to bring about protein thermostability include higher levels of charged amino acids on the protein surface that promote ionic interactions, amino acid preferences, hydrophobic cores, aliphatic side chains, disulfide bridges, and solute accumulation. It is obvious from these studies that a universal mechanism to achieve protein thermostability does not exist. The complexity of this problem is highlighted by differences that appear to be in play for multimeric proteins versus single polypeptide chains, for soluble proteins versus membrane proteins, and for proteins from thermophiles versus proteins from hyperthermophiles.

Continue reading "Some Like it Hot" »

January 20, 2011

We’ve Figured It Out!

by Elio

Sleeping_student

Source.

It’s been over 50 years since I began teaching graduate students, but only in the last few  do I think that we have it figured out. Here in San Diego, a consortium of research institutions has gotten together to provide a somewhat novel microbiology course for beginning graduate students. Here is what we do. For each of our biweekly 1.5 hour lectures we bring in a guest lecturer whose job it is to explain, in 40 minutes or less, why his or her field is the finest in all of biology This is followed by a discussion of a paper that has been read by the whole class. Now, I don’t pretend that this is totally original, but it is at variance with my previous experience of having one or two professors teach such a course by themselves.

Continue reading "We’ve Figured It Out!" »

January 16, 2011

Energetics of the Eukaryotic Edge

by Franklin M. Harold

Namnlös

Typical prokaryotic (a) and eukaryotic (b) cells. Source.

The most conspicuous feature in the landscape of cell evolution is the tremendous rift that separates eukaryotes from prokaryotes. This is not apparent at the level of ribosomal RNA sequences, or of molecular biology in general, but leaps to the eye of anyone intrigued by form, function and evolutionary potential. Prokaryotes have been biochemically most inventive, and found access to all the practicable energy sources our planet has to offer. It’s a good rule of thumb that, if a chemical reaction yields sufficient energy to support life, a prokaryote exists that exploits it. But when judged by their morphology and organization, prokaryotes seem to have advanced little beyond their fossil ancestors of 2 to 3 billion years ago. Some, it is true, have attained structural and behavioral complexity beyond the norm: cyanobacteria and planctomycetes with their internal membranes come to mind, and so do myxobacteria with their elaborate fruiting bodies and wolf-pack hunting habit. Still, these pale by comparison with even the plainest of eukaryotic protists, whose cells are typically a thousand times larger and stuffed with functional machinery. It is almost seems as though the prokaryotes made repeated starts up the ladder of complexity, but always fell short. By contrast eukaryotes, despite their meager metabolic repertoire, burst whatever constraints hampered prokaryotes to experiment with the opportunities afforded by greater cell size and more elaborate organization. Just what is it that made the eukaryotic mode of life so much more “evolvable” than the prokaryotic one?

Continue reading "Energetics of the Eukaryotic Edge" »

January 13, 2011

Talmudic Question #70

Do you think that all bacteria are lysogens?

January 10, 2011

Endless Forms Most Viral

This article first appeared as a Perspective in PLoS Genetics on November 18, 2010.

by Welkin E. Johnson

Possible_fig2

Assemblage of the middle Cambrian sponge Choia carteri seen
in the field at Walcott Quarry, Burgess Shale. Source.

Perhaps more than any other biological discipline, the study of animal viruses is confined to the present. Virions are simply not the stuff of which robust fossils are made. Phylogenetic analysis can help by revealing deep relationships between extant viral lineages, yet such reconstructions lack detail (telling us nothing about transitional or extinct viral forms, the movement of viruses between species, or the timing of major events in viral evolution), and molecular clock estimates are notoriously imprecise when applied to viruses [1]. Until recently, ancient endogenous retroviruses (ERVs) were the closest thing to a fossil record available to scientists with a proclivity for combining virology and natural history. Happily, a trio of recent studies appearing in PLoS Genetics [2], PLoS Biology [3], and PLoS Pathogens [4] reveal an unexpected wealth of non-retroviral virus sequences embedded in the genome sequence databases, a virtual equivalent of the Burgess Shale, ripe for excavation by eager paleovirologists.

Continue reading "Endless Forms Most Viral" »

January 06, 2011

A New Game for a New Year

Mono-lake-ii

Mono Lake. Source.

by Elio

Let's come up with ways to tell definitively whether or not the nucleic acids in the Mono Lake bug GFAJ-1  have substituted a sugar-arsenate backbone for the usual sugar-phosphate one, and if so, to what extent. We suspect that everyone will have a different notion. Please share yours by posting a comment.

January 03, 2011

Precious Metals

by Elio

Life should be like the precious metals, weigh much in little bulk 

                                    Seneca (Roman philosopher, mid-1st century AD)

Sweater_crop

One size might not fit all. Source.

Now that news of the arsenic-eating bacteria has saturated cyberspace, the airwaves, and even old-fashioned newsprint, we step back to raise a larger question: Why have so few elements from the periodic table made it into living things? You seldom hear about anything past the first few rows in the table. Turns out this is a gross oversight. Many more elements, previously unsuspected, are to be found in a large number of metalloproteins. So, move over, arsenic and make room for other elements.

Sup_fig

Source.

Until recently, the topic of metal ion cofactors and metalloproteins has been something of a biochemical stepchild. For sure, some researchers have avidly pursed it. However, in most cases, the presence of metal was revealed serendipitously after the protein was purified. But what if one set out to cast a wide net for metalloproteins? The authors of a recent paper did just that by examining the proteins of the archaeon Pyrococcus furiosus (a super-hyperthermophile that the authors call “a prototypical microbe,” an interesting point of view that we salute). They found several hundred such proteins containing an unexpected assortment of metals. Analysis of two additional organisms, Escherichia coli and Sulfolobus solfataricus, revealed the species-specific assimilation of yet more unexpected metals—cadmium, arsenic(!), uranium, and nickel in E. coli, and both tin and antimony in S. solfataricus.

Continue reading "Precious Metals" »

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  • We welcome readers to answer queries and comment on our musings. To leave a comment or view others, remarks, click the "Comments" link in red following each blog post. We also occasionally publish guest blog posts from microbiologists, students, and others with a relevant story to share. If you are interested in authoring an article, please email us at elios179 at gmail dot com.

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