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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September 28, 2009

Talmudic Question #53A

In recent years, the use of radioactive isotopes has diminished considerably in microbiological research. What has been lost in the process?

Commentary by Elio

Radioactive Symbol

Source.

This is a nostalgia trip. Molecular microbiologists of my generation relied on the use of radioactive isotopes for much of their research. Those days, the size of a department’s research effort could be measured by the number of scintillation counters it had at its disposal. Radioactivity was a convenient way of detecting and quantitating very small amounts of cell constituents. This has now been superseded by fluorescence and other non-radioactive methods. However, there are some things that radioactive isotopes do best. Thus, they are still in use. Here are two such uses.

  1. Determining which molecules are made anew. Adding radioactive precursors of macromolecules to a growing culture will result in selective labeling of the newly synthesized molecules. If the labeled compound is added for a short time ("pulse labeling"), the radioactivity is found in the portion of the molecule most recently made. Among many other things, such methods were used to elucidate the direction of synthesis of proteins (from N- to C-terminus) and of nucleic acids (5'- to 3'-terminus). Moreover, with this strategy you could estimate the speed with which such macromolecules are synthesized.
  2. Measuring the stability of a molecule. Adding a labeled precursor for some period of time, then replacing it with its non-radioactive counterpart (“pulse-chase”) lets us measure the stability of synthesized molecules. If the molecules are stable, they will retain the radioactive label; if unstable, the label will be lost. This method enabled us to determine the half-life of high-turnover molecules such as mRNA and certain regulatory proteins.

These days, when I mention radioactive isotopes, the response I get tends to focus on the dangers of working with them. Well, in the past we were not only careful but also aware of what constitutes danger. Mostly, we worked under safe conditions. Or so we thought. And I'm still around, many millicuries of P32 later.

The Three Stages of My Experience in Discovering the Mode of Action of Penicillin

Once penicillin came into common use, it became imperative to figure out how it works. This knowledge might be expected to lead to the development of better antibiotics or a more effective use of their therapeutic power. In actuality, the research effort directed to understanding the mode of action of penicillin led to major insights into basic biological phenomena. We are delighted to be able to share this personal perspective by one who made many of the key discoveries in this field.

Ted_2005


by Ted Park,
aka James T. Park


Ted Park is Professor Emeritus, Department of Molecular Biology and Microbiology, Tufts University.

Act 1: Precursors of an unknown, and presumably essential, metabolic process accumulate in penicillin-treated Staphylococcus aureus cells.

The scene opens in 1943. I was a graduate student in fermentation biochemistry at the University of Wisconsin in Madison. As this was at the height of World War II, most research projects were war-related. My first assignment was no different: to identify mutants of Aerobacter aerogenes that produced improved yields of 2,3-butylene glycol (2,3-butanediol), a potential candidate for conversion to synthetic rubber. It was not a terribly exciting project.

My fortune changed when a new assignment came to the lab. Penicillin had recently been shown to be a miracle drug. Production had started in England by growing the mold, Penicillium notatum, as mycelial mats on the surface of media in individual bottles—hardly an efficient method for mass production. The new project was to produce penicillin by growing the mold in submerged culture in large vats, and I was able to sign on to the team. My job was to develop a turbidometric assay for penicillin. It was easy enough to produce a beautiful standard curve of final turbidity versus penicillin concentration using Staphylococcus aureus 209P. However, the fermentation broths varied in their effects—because, as we learned much later, they contained multiple penicillins with different fatty acid side chains with different potencies. Somewhere along the way I managed to pick up an S. aureus 209P infection in my eye. It was treated successfully with a mercury salt cream, penicillin not yet being available for the general public.

Continue reading "The Three Stages of My Experience in Discovering the Mode of Action of Penicillin" »

September 21, 2009

Good Guys, Bad Guys

by Merry Youle

Hits_mark

The Good Guy. Aphidius wasps are commonly used for
for biocontrol of aphids. Here, a female wasp hits
her mark. Source.

Because it prefers to dine on some of our valued crop plants, the pea aphid (Acyrthosiphon pisum) is considered a major pest—thus a Bad Guy from our perspective. Pea aphids are not without their enemies. Enemy number one is a parasitoid wasp, Aphidius ervi. As parasitoid wasps are wont to do, females provide for their offspring by depositing their eggs in the haemocoel of another insect, in this case a pea aphid. The wasp larva feeds and develops there for about a week, eventually killing the host. When the host viscera have been consumed, the larva causes the aphid’s cuticle to harden and dry. Soon, an adult wasp emerges from the aphid "mummy." Agriculturally speaking, parasitoid wasps are Good Guys, important partners in our integrated pest management strategies. You can buy wasp eggs for your fields by the hundreds or thousands online.

Early on it was noticed that aphid (A. pisum) clones vary greatly in their resistance to the wasps. In some, the development of the wasp larva is arrested and the host survives. Because the pea aphid was known to harbor Buchnera aphidicola as a primary endosymbiont and also as many as five other bacteria as secondary endosymbionts, it was suspected that this variation in resistance might be due to which endosymbionts are on board. (What makes a symbiont a primary rather than a secondary symbiont? That depends on who you ask. Some distinguish based on the evolutionary age of the symbiosis, others mention the obligate nature of the relationship for both partners.)

Continue reading "Good Guys, Bad Guys" »

September 17, 2009

Fine Reading: The Good-Enough Clockus of Prochlorococcus

by Elio

Hourglass.large

Source.

The very first post on this blog (It Don't Mean a Thing If It Ain't Got That Swing) was about the circadian rhythm of cyanobacteria. They turn their photosynthetic apparatus on and off to match the daily course of light and dark. This is a true clock-driven circadian rhythm because it manifests whether or not the light is on or off, thus is not just a response to a stimulus.

What fascinated us then and continues to bedazzle us now is that this rhythm has an understandable biochemical basis.

Continue reading "Fine Reading: The Good-Enough Clockus of Prochlorococcus" »

September 14, 2009

Exciting Resolution

by Jennifer Gutierrez

Fluorescence microscopy of bacteria has long been a challenge due to the size of the organisms and the diffraction limit of visible-light microscopy. Although much valuable data has been collected by refining optical systems, automating microscopy setups, and using deconvolution algorithms, localization of single molecules inside cells has rarely been possible. With the advent of PALM and STORM microscopy, however, single-molecule resolution inside live cells has the potential to become routine!

In principle, a point of light, as emitted by a single fluorescent molecule, should define its location. However, if there are several close light emitters, the optical microscope cannot resolve them and sees them as one. This is due to diffraction of light and the fact that microscopes can only 'see' a portion of the radiated light through the lens. (To learn more about this point spread function, click here.) Several methods have been developed to get around this problem, generating a whole alphabet soup of abbreviations: SIM, SSIM, STED, and others. The two that may gain great acceptance are PALM (PhotoActivation Localization Microscopy) and STORM (STochastic Optical Reconstruction Microscopy).

These super-resolution, light microscopy techniques can provide information below the limit of resolution determined by the Rayleigh criterion (about 200 nanometers in near-ultraviolet light). Both systems achieve this resolution by sequentially and randomly turning on and off a small number of fluorescent molecules. This way, two adjacent molecules are unlikely to turn on at the same time. The molecules used must be capable of photoswitching, meaning that after being activated by light of one wavelength, they can then be excited by a different wavelength and their resulting fluorescence detected. Also, excitation must irreversibly photobleach them so that they can be activated/excited only once. By hitting a sample with a very small dose of activation light, only a small number of fluorophores will become activated. The sample is imaged by hitting it with excitation light, which also bleaches the activated/excited fluorophores. This process is then repeated many times until all the fluorescent molecules have been imaged and bleached.

F&GH

PALM visualization of a main component of the E coli chemotaxis network. A photoactivatable fluorescent protein fusion was constructed for Tar, the high-abundance aspartate receptor. PALM images show numerous solitary Tar receptors (F), small clusters consisting of tens or hundreds of receptors (G), and large clusters with thousands of receptors (H) that can also be observed by conventional fluorescence microscopy. (mEos is the monomeric form of the photoactivatable fluorescent protein Eos.) Source.

Continue reading "Exciting Resolution" »

September 11, 2009

Mycodiesel

This is the fourth (and final) post for this year's Week of the Fungi on STC, a sporadic undertaking. This annual festival is our way to hail the start of the fall mushroom collecting season in parts of our home territory (the northern hemisphere).

G. roseum micro_c

Colorized environmental SEM photo
of Gliocladium roseum. Source.

by Elio

Huge amounts of money and effort are going into making automotive fuels using biological processes, but a fully satisfactory answer is not yet at hand. Well, fungi may come to the rescue. Strobel et al. found that a fungus called Gliocladium roseum actually makes a complex mixture of volatile hydrocarbons and derivatives that resemble those found in diesel fuels. Not only that, this fungus decomposes cellulose without needing any help. It sounds just right, but before you talk to your broker about your Exxon Mobile stock, read on.

Continue reading "Mycodiesel" »

September 10, 2009

Fungal Stars in the Forest Dark

This is the third post for this year's Week of the Fungi on STC, a sporadic undertaking. This annual festival is our way to hail the start of the fall mushroom collecting season in parts of our home territory (the northern hemisphere).

Japanese lumin-fugnus

Mycena lux-coeli, a Japanese fungus
photographed by its own light. Source.

by Elio

Fungi, along with selected bacteria and invertebrates, are included in the list of bioluminescent organisms. These fungi are pretty unique because, unlike the other light-emitting organisms, fungi don't walk, swim, or fly. Thus, the usual explanations for bioluminescence (e.g., attraction, repulsion, communication) do not seem to apply. Dispersing spores is a central preoccupation among mushrooms, so one can guess that the light may facilitate visits by animals that could help in this process. Plus, as Dennis Desjardin writes in a news item from the NSF, some may well glow to attract the predators of insects that eat the mushrooms...befriend the enemy of your enemy!

Continue reading "Fungal Stars in the Forest Dark " »

September 08, 2009

A Thing of Beauty

This is the second post for this year's Week of the Fungi on STC, a sporadic undertaking. This annual festival is our way to hail the start of the fall mushroom collecting season in parts of our home territory (the northern hemisphere).

New_1

The entombed springtail with numerous
conidiophores. Source.

by Elio

A thing of beauty is a joy for ever:
Its loveliness increases; it will never
Pass into nothingness

      from Endymoin, by John Keats (1878)

New_2

Close-up of the conidiophores. Bar = 50 μm.
Source.

We can attest to these truths through a lone piece of amber. Between 50 and 35 million years ago, a springtail (Collembola) got stuck in some resin, probably from a conifer. Before it could free itself, more resin dripped on it, eventually entombing it completely. In time, the resin became amber, but before that happened, a fungus grew on the insect's cadaver, sprouting numerous spore-bearing structures (conidiophores). Fortunately, this piece of amber found its way to two paleomycologists, Heinrich Dörfelt and Alexander Schmidt, who readily identified the fungus as a member of the genus Aspergillus.

Continue reading "A Thing of Beauty" »

September 07, 2009

Myco-kleptomaniacs

This is the second annual Week of the Fungi on STC, a sporadic undertaking. It is our way to hail the start of the fall mushroom collecting season in parts of our home territory (the northern hemisphere).

Mycan

SEM micrograph of adult southern pine beetle. The
arrow indicates the location of a mycangium. Source.

by Elio

Anyone who has gone out hunting for wild mushrooms and came back with a nearly empty basket has been tempted to "borrow" specimens from someone more lucky. This cardinal sin now has a name: mycoklepty.

Stealing fungi is not limited to humans. Beetles do it too.

Continue reading "Myco-kleptomaniacs" »

September 03, 2009

Fine Reading: The Biocentric View of the Microbial World

by Elio

Anthropocentric:
      1. considering human beings as the most significant entity of the universe.
      2. interpreting or regarding the world in terms of human values and experiences.

Ramy_Bioquest

How does anthropocentrism apply to microbiologists? In a current commentary in the new journal Gut Pathogens, Ramy Aziz reminds us that it shows up all over the place. Take the very term microbe, meaning small living thing. "Small," says who? Not the microbes. To them, other microbes would be of "normal" size and we humans Rabelaisian gargantuas. This wouldn't much matter if it stopped there, with our choice of words alone. Aziz points out that anthropocentrism in microbiology can have serious consequences. For instance, "pathogens" have been considered to be special group of microbes, separate from the rest. Nothing could be farther from the truth, and nothing could be more objectionable than to consider the human body to be anything but another habitat.

In recent years, it has been increasingly realized that pathogenic microbiology is merely another branch of microbial ecology. However, a gentle reminder in Aziz’ well-turned words is welcomed. A truly integrated view of the microbial world, or of the biological world in general, cannot be anthropocentric but can only be, as Aziz says, biocentric.

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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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