Small Things Considered

The Age of Imaging

Image courtesy of BibliOdyssey

Not so long ago, it would have seemed implausible that biology would return to its origins as a visual science. Some would have considered this a regression to the days when biologists were pretty much confined to studying just what they could see, such as the shapes of organisms and their tissues. Back then, they focused on refining what Pliny had observed with his bare eyes, what Hooke and Leeuwenhoek saw under the microscope. The methodological lines of attack were dramatically redirected from the visual by the revolutionary discoveries of the second half of the last century. Biochemistry, genetics, molecular biology—none of them relied primarily on visualizing the structure of objects. For some time, doing morphology was suspect and, in some quarters, even using a microscope was equated with doing old-fashioned science.

How biology has (once again) changed!

Earliest Archaeology

3D representation of a phenyalanine tRNA.
Source: Department of Biosciences and
Nutrition, Karolinska Institute, Stockholm.

by Merry

It has been dazzling, the insights into the evolutionary history and relationships of organisms gained in recent years through phylogenetic approaches. As the mountain of sequence data continues to grow exponentially and increasingly clever methods of analysis are devised, we can't help but wonder how far back in evolutionary history we might be able to see . We'd surely like to know who came first (Bacteria? Archaea?) and where viruses fit in and how an RNA world led to the DNA world and…and… A recent paper gives us a glimpse into long long ago.

Talmudic Question #30

Many bacteria, e.g., E. coli and B. subtilis, regulate their gene expression via a large number of distinct devices that operate on almost all conceivable biochemical levels. Why so many?

Fine Reading: Mycobacteria Grow and Divide Like Other Bacteria — Only Differently

Tubercle bacilli, scanning
EM. Source: Zimek Systems

I've been trying to find a simile for mycobacteria, those outliers in the world of bacterial pathogens (and saprobes). Maybe they are to other bacteria like cacti are to other plants. They’re not exactly spiny but they sure are different. (Come up with your own simile, if you wish.) They’re acid fast, resistant to drying, slow growing, and—to round out the picture—cause diseases like TB and leprosy that, if not unique, are not your ordinary infections. But, just as cactuses are green and have leaves, so do mycobacteria share a common physiological repertoire with other bacteria.

A recent review by Hett and Rubin tells much of what is known about the differences and similarities between mycobacteria and the rest of the bacteria with regard to cell structure, cell division, and growth. Also discussed are the particular challenges faced by mycobacteria, such as entering and escaping from dormancy. The writing features a string of refreshingly Socratic questions. Where else would you find queries such as: Are mycobacteria gram positive or gram negative? and Why are mycobacteria rods? and Does resuscitation involve normal homeostatic processes? Twenty-one pages of text and 463 references later, you will have found the answers to these and many other questions central to the mycobacterial way of life.

BYOG: Bring Your Own Gene

by Merry

A 17th century illustration of the
Copernican model of a heliocentric
universe. Courtesy of Knowledge 2008

Of necessity, viruses rely on their host cells for both energy and molecular building blocks. Typically, lytic infection shuts down the synthesis of host proteins, and the cell's translation machinery is put to work in the service of viral replication. For marine cyanophage, this strategy runs into a troublesome wrinkle.

Let's first digress for a moment and look at the problem faced by all photosynthesizers, cyanobacteria included. Capturing sunlight for cellular work is a risky business. Both UV and visible light can damage the proteins that make up the core of the cell's photosystems. Too much sunlight, and photosynthesis doesn't just level off, it slows down—a phenomenon dubbed photoinhibition. Photoinhibition results when the cell's mechanisms for photosystem repair can't keep up with the damage caused by excess light energy. In cyanobacteria, photosystem II—which catalyzes the light-dependent production of oxygen from water—is particularly vulnerable. At its core sits a dimer of two related proteins, D1 and D2. To keep up with the light-induced damage, D1 turns over very rapidly, and D2 more slowly. De novo synthesis of D1 is required for sustained photosynthesis.

There is a Catch-22 here.

International Women's Day and the Discovery of Nystatin

Sixty years ago, the deliberate testing and analysis of soil samples netted two women—Elizabeth Hazen and Rachel Brown—the discovery of nystatin, the first useful antifungal antibiotic. Its producer, found residing in soil collected near a cow pasture, was a newly-identified member of the Streptomycetes, named Streptomyces noursei in honor of the owner of the pasture, a Mr. Nourse.

Their discovery is appropriately celebrated in a blog that focuses on the actinomycetes and that we are very fond of: Twisted Bacteria. In the author’s words: This post modestly celebrates March 8th, International Women's Day. The discovery of nystatin seems a good example of an important contribution of women scientists to microbiology, natural product chemistry, and medicine.

Women were well represented among the early discoverers of antibiotics, with cycloheximide and fosfomycin (and probably others) also to their credit. You can find additional links on the subject of women in microbiology in that celebratory post. We join the author, César Sánchez, in this salute.

Plentisillin and Penicillin: An Antibiotic Spoof and a Tragedy

by Ronald Bentley and Joan W. Bennett

The year 1946 was one in which it was possible for many of the world’s peoples to have a hopeful view for the future. The horrors of World War II were over and rebuilding was in progress. International travel resumed and, as fleets of airplanes were constructed, became somewhat easier than previously. A new world-wide organization, The United Nations, had been established and the General Assembly and Security Council held their first meetings in January of that year. In scientific disciplines, new technologies stemming from the war-time investigations of the release of atomic energy, were transforming research. The analytical work that would eventually lead to the double helix structure for DNA and the very extensive use of biotechnology was underway.

A culture of a penicillin-producing Penicillium
and the structure of penicillin G. Source:
Department of Pharmaceutical Sciences
Institute for Pharmaceutical Biology, Basel,
Switzerland

In medicine, a major development was the antibiotic revolution leading to the control of many, previously intractable, infectious diseases. Significant amounts of penicillin for civilian use became available in the USA in 1945 and the UK in 1946 (Bud, 2007). Indeed, penicillin can now be considered as a commodity chemical (Bentley and Bennett, 2008). An organization for the relief of war-devastated countries, The United Nations Relief and Rehabilitation Agency (UNRRA), had been established and, beginning in 1946, provided antibiotic expertise and even entire penicillin production plants to several nations (Bud, 2007). Slowly, antibiotic use became a world-wide phenomenon and the term, antibiotic, came into the common vocabulary.

Everybody Is Always Talking About The Weather… Revisited

Lenticular clouds above the Big Island.
Credit: astroday.net

A recent paper in Science adds evidence to the notion that ice nuclei, the particles that lead to the formation of rain and snow, are mainly of biological origin. In fact, lots of the ice nuclei contain bacteria that have wafted aloft. The researchers found that fresh snow in various parts of the world, including Antarctica, contains DNA in particles that are sensitive to both lysozyme and heat. We expect that metagenomics of such samples will follow.

Where do these bacteria that fly through the air with the greatest of ease come from?

All in the Family — Another Update

One of the most curious phenomena we have reported here is that of bacteria living inside the mitochondria of a tick. The name given to these bacteria is Midichloria mitochondrii (the genus name alluding to the midi-chlorians in Star Wars). This surprising finding was confined to a single species of hard ticks (Ixodidae). A new report tells us that seven other species of related ticks also display this intriguing endosymbiosis. PCR analysis and some electron microscopy nailed down the presence of the bacteria, all closely related to the original M. mitochondrii and members of the Rickettsiales—those masters of host cell penetration. So, the harboring of a bacterium by an ex-bacterium (the mitochondrion) may be more widespread than previously thought.

In a previous post, we discussed a research report that pointed out how similar the strategy used by these rickettsiae-like bacteria to invade mitochondria is to that of Bdellovibrio preying on free-living bacteria.

Fungal Cuckoo

A Common Cuckoo being raised by
a Reed Warbler. Source: Wikipedia

Cuckoo birds have an unsavory reputation for laying their eggs in somebody else’s nest. There the eggs are tended with care by duped surrogate parents. When hatched, the young cuckoos unceremoniously push their nestmates over the edge and, in a case of consummate avian chutzpah, open their maw to make their "hosts" feed them as if they were their own. By the time they are fledglings, the young cuckoos may be considerably larger than their foster parents.

Nu, you ask, why this feathery preamble? The reason is that this brood parasitism, as the phenomenon is called, has its counterpart in the fungal world.