Small Things Considered

Talmudic Question #77

Both marine phages and predatory protists prey on bacteria. Something has been written about how phages may help bacteria escape protist predation. Click here for an erudite treatment. Is something known about the converse, namely communication between protists and phages? For instance, do protists make compounds that diminish predation by phages, e.g., by making phage-inhibitory substances?

Now That's Using Your Head!

by Merry

Legend: TEM of bacteriophage φCbK negatively stained with 1%
uranyl acetate. The arrows indicate tail filaments (TF) and head
filaments (HF). (Click to enlarge.) Source.

Something bizarre can be seen in TEMs of a Caulobacter crescentus phage, φCbK. This was first reported in a paper published back in 1972 (see the image to the right). In most respects, φCbK is your typical ho-hum siphovirus with an elongated head (60 nm diameter, 200 nm long) sporting a 290 nm long non-contractile tail with the usual tail fibers. But even with the limited imaging techniques available in 1972 these researchers could see that this phage has a single long filament protruding from the tip of its head! And there the story sat until the recent PNAS paper by Ricardo Guerrero-Ferreira and colleagues. These researchers took a close look and found that φCbK uses its head filament to make initial contact with its host, much as other phages use their long tail fibers.

Vital or Not Vital: That Is the Question

by Gemma Reguera

Sleep, by Salvador Dali. Source. ‘Dali's painting of Sleep
is successful in its suggestion of the precarious balance
of sleep. We realize that if a single crutch were to fall,
the dreamer will awake.’ Source.

If you are as a stubborn as I am, you probably just cannot let go of things easily. That is exactly what happened with me a few months ago when I sent a paper for peer-review that included results obtained using a commercial ‘vitality’ assay. The kit uses a fluorogenic redox dye that fluoresces when modified by bacterial reductases. Since the respiratory chain of the cell envelope contributes most of the cell's reductase activity, by measuring the respiratory activity this kit also, indirectly, assesses cell envelope integrity. When I got the reviews back, one reviewer asked what ‘vitality’ meant. I was sure that this would be an easy comment to address. However, I started to have a change of heart when I could not find any definition of vitality in any microbiology textbook at my disposal. A PubMed search retrieved mostly references to human vitality (or physical activity) and general aspects of bacterial viability.

I could have caved in and replaced the word ‘vitality’ with ‘viability.’ That would have been easier. After all, vital functions of the cell such as the respiratory activity of the cell envelope determine whether a cell is viable or not. However, in my mind, viability was a quality of the cell reflecting its potential to grow, while vitality referred to the measurable activities that make a cell viable. But what are the vital functions that make a cell viable? Out of desperation, I Googled the word ‘vitality’. All I could see as remotely related to my search was the Merriam-Webster definition of vitality. It is there where I opened Pandora’s box.... These are the three definitions that I found to be most applicable to microorganisms:

1. the peculiarity distinguishing the living from the nonliving
2. capacity to live and develop
3. power of enduring

Rafting Through Time

by Elio

Source.

In the placid old days, cell membranes were assumed to be fairly simple affairs: lipid bilayers with some proteins floating in them like corks. This “fluid mosaic” arrangement took a beating around the 1970’s, when biophysicists suggested that membranes may be composed of microdomains, where certain lipids and proteins become segregated into what became known as lipid rafts. With further work, these turned out to be places where specific lipids such as steroids and sphingolipids concentrate. The size of the rafts is supposedly in the 10-200 nm range. Lipid rafts are said to be involved in signal transduction, protein trafficking, and more. Some viruses, e.g. influenza, are assembled at lipid rafts, and the rafts play a role in prion development and transmission. The subject is not without controversy but it has many adherents.

Lipid raft organization in eukaryotic cells. Region (1) is standard lipid
bilayer, while region (2) is a lipid raft. (3) and (4) are membrane proteins.
Source.

So let’s ask, do bacterial membranes have lipid rafts? That they are not wholly homogeneous has been suspected for some time. Many proteins are localized at particular sites along the membrane, suggesting that specialized microdomains may be a feature of bacterial membranes as well. A recent paper by López and Kolter opens the door to such a possibility. It was known that bacteria possess proteins homologous to some involved in the lipid rafts of eukaryotic cells. One of them, FloT of B. subtilis, is related to Flotillin-1 (also known as Reggie, funny enough), a protein involved in eukaryotic vesicle trafficking and cytoskeleton rearrangement. FloT is distributed heterogeneously in the membrane and a fusion with yellow fluorescent protein can be seen under the microscope as dots along the whole cell. (See here and here.) Mutants lacking this protein are slow in growth and inefficient in sporulating. Bacteria also encode other proteins in the Flotillin family.

Did van Leeuwenhoek Spend His Youth in France?

by Nanne Nanninga

Figure 1. Young Antoni making a basket.
Illustration by Charles Pickard in The
Cleere Observer.

This title might be unexpected. Yet it is not without logic after reading a little book, The Cleere Observer: A Biography of Antoni van Leeuwenhoek, by Alma Smith Payne, published in 1970 by Macmillan in London. The booklet is amply and skillfully illustrated by Charles Pickard. According to the back flap Alma Smith Payne hopes she has managed to bring him (vL.) alive for young people. The booklet is well written and is very informative for persons not so young any more. In the booklet we read on page 23: Antoni’s father was a basket maker, as his father has been before him. This makes it plausible that young Antoni did make some baskets himself. Anyway, this is what we see on page 25 (figure 1). Presumably, to give it some Dutch flavor we see a canal and a drawbridge.

I am probably not the only one for whom this illustration rings a bell. In fact, it represents the drawbridge painted by van Gogh in Arles (France) in 1888 (figure 2). So there is a Dutch connection, although the connection is tenuous. A quick Google-search for the bridge in Arles brings one to a gasoline station named “van Gogh.”

Figure 2. Drawbridge (Pont de l’Anglois) at Arles in France as
painted by Vincent van Gogh in 1888. Source: Van Gogh Museum
Amsterdam, 1973.

 

 

 

 

 

 

 

 

 

 

 

 

 

Viruses that Infect Parasites that Infect Us: The Matryoshka Dolls of Human Pathogens

by Jamie Schafer

Source.

We’re all too familiar with the viruses that can infect us, from the common cold to yellow fever virus to the endogenous retroviruses that make up a chunk of our genome. Many of us are also acquainted with parasites, such as tape worms or Giardia, that like to set up camp in the human body. But the world of parasites and viruses does not end there. Many parasites or endosymbionts can be infected with viruses. A classic example is Paramecium, which can harbor an endosymbiotic bacterium, Caedibacter, which in turn carries phages involved in making a toxin. But from the human point of view, things start to get particularly interesting when we consider the viruses that infect parasites of humans and how those viral infections—inside of a parasite inside of a person, somewhat like a Matryoshka nesting doll—may modulate the parasite’s interaction with its human host. Several protozoan parasites, including Leishmania and Trichomonas, are in turn parasitized by viruses, namely leishmania RNA virus-1 (LRV-1) and Trichomonasviruses, respectively. A commonality among such viruses is that they all have dsRNA genomes. It remains to be seen whether they also share the practice of exacerbating parasitic infection of the host as was recently reported for LRV-1 infection of Leishmania guyanensis.

Taking Bugs Out For a Spin

How life may have arrived from elsewhere. Source.

by Linh Truong and Shabana Din

Microbes are the most robust of all life forms inhabiting our planet. Their ability to proliferate in extreme temperatures, pH, pressure, and radiation is well documented. They not only withstand but grow at physical extremes, which makes us wonder about the physical bounds for life not only on our planet, but on others as well.

How We Tell The Good Bacteria From The Bad

by Micah Manary

Recently, Yale’s Richard Flavell led a team of researchers into the most talked about and yet one of the least understood of microbial environments—the human gut. Rather than present the usual metagenomic characterization of the microbial population, he teamed up with Jeff Gordon at Washington University in Saint Louis and others to investigate one of the most important questions in the field: how does the host organism detect and respond to the replacement of its ‘normal’ gut bacteria with ‘abnormal?’

To get into this topic we need to spend a minute on the innate immune response and, specifically, the inflammasomes. These components of the innate immune system are multiprotein complexes that sense damage to the host. As the name suggests, they foster inflammation by promoting the maturation of precursors of cytokines involved in inflammation, such as interleukin 1-β and interleukin 18. When inflammasomes recognize one of many relevant signals, they assemble into a multiprotein complex, usually together with an adaptor protein called ASC (for apoptosis-associated speck-like protein containing a CARD). This complex governs activation of the protease caspase-1 with subsequent cleavage of the proinflammatory cytokines (including pro-IL-1β and pro-IL-18) into their active forms.