by Welkin Johnson Do the seven strategies in the Baltimore scheme of viral replication represent all possible ways of being a virus? Have other strategies fallen by the evolutionary wayside? Read more →
First, some musings about life and death, two matters that don't seem to occupy the same space in our brain. We tend to celebrate the former and resent the latter, and we often see the world through this perspective. Only on reflection do we realize how wrong this is, especially with regard to biology. The cycle of life depends fundamentally on living things dying. But this is not always the prevailing way we approach biological questions. Think of how long it took for the concept of apoptosis (in itself an old realization) to take hold. In microbiology, most of the early modern studies on bacterial physiology dealt with growth and seldom with how bacteria deal with adverse conditions, such as starvation, and death. But all this is changing, as we realize that organisms have evolved to cope as much with danger as with good times. And their coping is often due to a collaborative effort, which is why the adaptation to hard times is a primary concern of the emergent science of Microbial Sociology.
Among the big-time adjustments in our views of the microbial world has been the recognition in the last few decades that bacteria do not particularly behave as individuals. That was the preferred way of thinking about them, not the least because it made life simpler. Remember that modern biology (the post-World War II variety) was greatly influenced by physicists, who brought along a predilection for simple units as model systems (e.g., a single atom, ergo a single T4 coliphage particle or one E. coli cell). As is now obvious, this is an incomplete way of thinking because bacteria interact in important and diverse ways with members of their same or other species. So intricate are these interactions that bacteria are beginning to vie for sophistication in communication with the social insects. Remember, both speak a chemical language. Read more →
The Fukushima nuclear power plant in better days. Source. by Elio Reports in the media of the nuclear plant disasters in Japan often cite the amount of radioactivity released in units called millisieverts. Not knowing what a millisievert is, I resorted to Wikipedia for the needed clarification. We reproduce some... Read more →
by Merry Youle
Phage predation on bacteria is intense, but bacteria are not defenseless sitting ducks. They make use of a repertoire of diverse strategies to stay even with even the wiliest of phages. First line defenses are those that block phage entry at the door. Often these involve modifying a surface component that is used by the phages as a recognition, attachment, or entry site. Such changes typically carry fitness costs, by impacting essential transporters for example; as a result, phage sensitive strains often outcompete the phage-resistant mutants when there are no phages around. Also, when resistance is gained by modifying the bacterium's surface LPS or O-antigen, acquiring resistance to one phage can mean the loss of resistance to another.
CRISPRs, on the other hand, are a second line phage defense, one that swings into action after the phage has successfully attached and injected its genome into the cell. Although it may be risky letting the wolf in the door, a successful CRISPR defense offers several advantages. For one, the bacterium may get a nucleotide lunch; for another, CRISPRs can defend against plasmids, too. And as we'll see, this system allows for resistance to multiple phages without apparent fitness costs. So far CRISPRs have been found in approximately 40% of the sequenced bacterial genomes, but that number may be an underestimate as many of the sequenced strains, having been maintained in phage-free culture for a long time, may have lost their CRISPRs. Read more →
by Elio A Schistosoma mansoni pair, with the thin female located in the male's so-called gynaecophorical canal. Source. There are embraces and there are embraces. Some may last for a lifetime, as was thought to be the case with some schistosomes (though it turns out that a few pairs do... Read more →
by Spencer Diamond and Britt Flaherty Cyanobacteria, present as stromato- lites, oxygenate the atmosphere of earth in this artist's representation. Source. With such famous bacteria as Escherichia coli and Bacillus subtilis hogging the stage, it can be hard for bugs like cyanobacteria to enter the limelight. However, without E. coli... Read more →
by Merry Youle
Bacterial microcompartments were a great innovation. As Alan Derman explained, these protein-bounded structures assist with diverse metabolic processes by housing the requisite enzymes along with their substrates, sequestering potentially toxic intermediates, and allowing the products to exit. But the story does not end there. Enter the nanocompartment.
These are the simplest variation known so far on the theme of bacterial compartments. Like the micro version, these nano structures are thin, icosahedral protein shells that enclose a specific protein payload. Read more →
by Brandon Kim and Jon Sin To a pathogenic microbe, the human body is a foreboding environment filled with bacteriocidal immune cells ready to seek out and destroy foreign invaders. When a leukocyte detects the presence of pathogen-associated molecular patterns (PAMPs) present on the surface of pathogenic bacteria, it releases... Read more →
Note: Please note today's date. If people go to heaven does their microbiome go with them? Ramy Aziz, Merry, and Elio already provided some imagined responses. An answer from Rome: Only microbes that don't engage in immoral horizontal gene transfer or illegitimate recombination. A moralist’s answer: Each microbe will be... Read more →
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.