Small Things Considered

Making Waves at Asilomar

by Elio

Asilomar breakers. Source.

It’s seldom that a bug has a negative effect on me. It's usually just the opposite: bugs make my day. But this time, some kind of bronchitis virus prevented me from going to a meeting that I would have truly loved to attend. The Integrated Microbial Biodiversity Program, under the umbrella of the Canadian Institute For Advanced Research (CIFAR), recently held their annual meeting in Asilomar, California. The location speaks to their willingness to transcend national barriers; the program, their transcending of conventional academic barriers, as well. The papers covering numerous ecological and evolutionary aspects of microbial life were presented by leading investigators from Canada and beyond. Included were such luminaries as Tom Cavalier-Smith, Ford Doolittle, Jonathan Eisen, Patrick Keeling, Forest Rohwer, and Curtis Suttle, to name just a few.

I had been asked to present stories from this blog, something that I have done with pleasure at several other venues. But this one would have been extra special. On all accounts, I missed out on what was truly my kind of meeting.

A few words about CIFAR from their website:

CIFAR has assembled a team of leading researchers from across Canada and around the world that is capable of taking on the monumental task of exploring this astounding universe of bacteria, viruses, and other microbes.

CIFAR’s Integrated Microbial Biodiversity program is transforming human understanding of the web of life, and changing the way we approach medicine and health, environmental sustainability, and evolutionary biology itself.

About Our Talmudic Questions

by Elio

Source.

We have now posted Talmudic Question #50, so this may be a time to reflect on this endeavor. True to our intent, these have been questions that have no definitive answers but most of the responses offered thoughtful conjectures. The pleasure resides in contemplating the question. What deeper meaning lies therein?

As an aside, the question “how many angels can dance on the head of a pin” may sound Talmudic but actually has a totally different origin, as discussed here.

The source of these Talmudic Questions? Notably, about one quarter were submitted by aficionados among our readers, and we are mighty glad for it. Those are among the very best. The rest arose from an inventory of questions carried along through the years, or that popped up at night during moments of wakefulness. As always, we have several more waiting in the wings. The well seems inexhaustible.

We hope that you enjoy this exercise and that you will share your answers with us. Better yet, consider sending us your own Talmudic questions. We know that there is at least one taking shape in each of you.

Talmudic Question #50

What do you think are the most interesting questions in present day microbiology?

Retrospective, June 2009

We present here a lightly annotated list that includes most of our posts from the past half year.

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Of Terms in Biology

We inaugurated this department in recent months. Terms in the spotlight so far:

• Eremacausis (here’s a new one for you)
• Metabolomics (its ins and outs)
• Obligate Parasite (which should have stirred a spirited controversy but barely did)
• Orthologs (to help you distinguish them from those other relations—paralogs)
• Panmictic (do you know this one?)

Question: Is this useful? Should we continue this?

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Microbial Diversity

The Microbe That Could Be Seen: Epulopiscium, that leviathan among bacteria, yields some of the secrets of its gigantism. With hundreds of thousands of copies of some of its genes, no wonder it can make so much of itself!

What You Didn’t Know About Janthinobacterium: Jenna Tabor-Godwin, Rhona Stuart, Rosa I. León Zayas, and Chitra Rajakuberan, students at San Diego State University and UC San Diego, tell us of a colorful bacterium that makes antibiotics that help its salamander host withstand fungal infection.

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Symbiosis

The Bacterium That Doesn't Know How To Tie Its Own Shoelaces: Carsonella is an endosymbiont of insects. With a genome of 160 kb, it barely qualifies as a bacterium—but it’s not yet an organelle. Strange-looking, too.

A Hot Happy Couple: The genome of Ignococcus hospitalis, the host to Nanoearchaeum equitans, has been sequenced, allowing a deep contemplation of the goings-on in this high temperature archaeal consortium.

Happy Together… Life of the Bacterial Consortium Chlorochromatium aggregatum: Mark Martin regales us with thoughts and facts about this misnamed lake-dwelling consortium composed of a chemoheterotrophic motile bacterium surrounded by a cadre of green-sulfur bacterial epibionts.

The Two Faces of Photorhabdus: This famed symbiont of nematodes is both a mutualist and a pathogen. It depends on which host you ask, the nematode or the insect. And it glows in the dark.

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The View From Here

Constructing a Synthetic Mycoplasma: Shmuel Razin recollected early thoughts on making a synthetic mycoplasma. Some things come around…

Fine Readings

Horizontal Gene Transfer in Eukaryotic Evolution: Patrick Keeling and Jeffrey Palmer discuss intriguing examples, exploring how they may have shaped the evolution of eukaryotes.

Emma Darwin: With all the bicentennial hoopla, did Mrs. Darwin get a fair shake? A broader view is presented by Mercé Piqueras.

Charles Darwin's sketch from 1837
captured how organisms evolve. Source.

Evolution

The Scandalous Bdelloid Rotifers: Rare among metazoans, they lack sex. But they have engaged in frequent horizontal gene transfer, which may have something to do with their extreme resistance to drying and irradiation.

Viruses and the Tree of Life: We reprinted Vincent Racaniello’s synopsis of a paper by Moreira and López-García that offered ten reasons why viruses should not be included in the Tree of Life.

The World is Pleiotropic: Our sales pitch for the notion that most biological macromolecules are multifunctional, using ribosomal proteins as examples.

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Pathogens

Coxiella Escapes from Cell! Coxiella burnetii, has been coaxed into growing in cell-free media. Scratch that one from the list of "obligate intracellular parasites."

A Pathogen's Swiss Army Knife: Maren von Köckritz-Blickwede discusses staph’s Protein A, a multifunctional protein that does a number of things to thwart the immune system.

Killer Prophage for Hire: Hydrogen peroxide made by pneumococci kills staphylococci by inducing their prophages.

30,000 Parasitoids Can't Be Wrong: These wasps deposit their eggs within other insect’s larvae. Why are the eggs not killed? This raises the issue of when a virus-like particle is not a virus.

Say, Brother, Can You Spare a DNA? Does DNA obtained by transformation help gonococci mend their ROS-damaged genome? And how do they take up useable genes but exclude potentially damaging foreign DNA?

Collateral Damage: Corals can be killed when folliculinid ciliates find them to be a convenient substrate on which to settle. No harm intended.

A Nuclear Family: In the dark world of hydrothermal vents, bathymodiolin mussels are host to essential bacterial symbionts, but also to a γ-proteobacterium free-loader. This critter invades the nuclei of gill cells where it reproduces, at the expense of the cell.

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Ecology

No Phosphorus? No Problem! (There’s More Than One Way to Skin a Phytoplankton): Cyanobacteria and small marine eukaryotes make do with little phosphorus in their environment by making sulpholipids instead.

A Fly in the Frozen Custard: 500,000 years is a long time to survive in glacial ice. But instead of being dormant, bacteria have been repairing their DNA all along. But were they actually frozen all that time?

The Secret Under the Ice: We reprinted a fine piece from the Spanish blog of Manuel Sanchez, Curiosidades de la Microbiología, on the Antarctic "blood falls," a curious outpouring of bright red ferric iron-rich material, a by-product of the work of sulfate-reducing bacteria.

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Odds & Ends

Music to the Tune of a Protein: Do you want to translate a protein sequence into music? Ask Stephen Zielinski.

Acoustic Mimicry: A rare non-microbial post. It’s about butterfly larvae that mimic the sounds made by queen ants.

Fine Reading: Emma Darwin

by Elio

Portrait of Emma Darwin
from the late 1830s by
George Richmond. Source.

Just when you thought that everything conceivable has been written about Charles Darwin on his bicentennial, a revealing perspective on his wife, Emma, appeared in the journal International Microbiology. Written by the distinguished science writer Mercé Piqueras, the article sheds light on many aspects of the relationship between Charles and Emma, including their correspondence while he was traveling on the Beagle. Of particular interest is the clash between her theistic beliefs and his agnosticism. They both learned to live with it.

Mercè also offers a rich eclectic blog in Catalan, La lectora corrent (The Common Reader, à la Virginia Woolf) where she shares her passion for language, science, and spreading the word. It’s also available in English and Spanish, but beware! It’s machine-translated.

The World Is Pleiotropic

by Elio

The bacterial ribosome is composed of three
different RNA molecules and more than 50
different proteins. Source.

So there! By this rash assertion I mean that in the biological world almost every macromolecular constituent is likely to function in more than just one way, i.e., is pleiotropic. One and the same protein may be enzymatic, regulatory, and structural; one nucleic acid, informational, structural, and regulatory; and so on. Clarence Jeffery called this “moonlighting.”

Most biologists know this, but how many think it’s a big deal? I do, based on little more than the belief that living things are parsimonious and make efficient use of their parts. Doesn’t it seem reasonable that our own 30,000 or so genes (a puny number, one would think) each encode many functions?

A Nuclear Family

by Merry

(E) TEM of swollen nucleus with endonukes in longitudinal and cross-
section. The chromatin has been reduced to narrow remnants along
the nuclear membrane. (G) TEM of endonukes showing electron
dense particles distributed throughout the cells. Source.

Certain mussels called “bathymodiolins” are part of the spellbinding fauna of the dark world of oceanic hydrothermal vents and cold seeps. Similar to other metazoans in that realm, they rely on chemosynthetic bacteria for their nutrition. These mussels possess symbionts from two clades of γ-proteobacteria: chemoautotrophic sulfur oxidizers that fix CO₂ using sulfide or thiosulfate as their energy source, and methane oxidizers that use methane for both carbon and energy. The symbionts are well-housed in specialized cells (bacteriocytes) in the gills of the mussels where the constant flow of water brings the needed substrates to them. A pleasant mutualistic arrangement.

Say, Brother, Can You Spare a DNA?

by Merry

N. gonorrhoeae is a Gram-negative coccus,
usually seen in pairs with adjacent flattened
sides. Pili, extending several micrometers from
the cell surface, play a major role in adherence.
Source.

Mention horizontal gene transfer (HGT) in bacteria, and what comes to mind is the acquisition of new traits and capabilities across large evolutionary distances. Not so for the neisseriae. For them, HGT is a means to swap genes with other members of the species and to maintain the status quo in the face of assault on their genome by host defenses.

Infection by the human pathogen N. gonorrhoeae is met by the rapid recruitment of polymorphonuclear leukocytes (PMNs) to the site. PMNs are professional phagocytes that use a combination of antimicrobial proteins and reactive oxygen species (ROSs) to kill the engulfed invaders. Their ROS attack is effective against the gonococci and quickly kills the majority of them. However, a subpopulation not only survives within the phagosomes, it also replicates. A number of factors enable the gonococci to do this. An important one is having a means to repair the DNA damaged by the ROSs. This is where the HGT comes in.