Small Things Considered

Talmudic Question #61

Endocytosis is said to be an exclusively eukaryotic property. Why did prokaryotes not develop this ability?

True or False: All Metazoans Need O2

by Elio

I am the Lorax, and I'll yell and I'll shout for the fine things on earth that are on their way out!
                                                                                                                  Dr. Seuss

A loriciferan from L’Atalante Basin. Scale
bar: 50 mµ. Source.

Life without air—a term coined by Louis Pasteur, the discoverer of anaerobiosis—has been thought to be exclusively a property of microbes, be they prokaryotic or eukaryotic. Multicellular organisms were thought to lack this talent. Until recently that is, when an Italian and Danish group led by Roberto Danovaro looked at an unusual-sounding habitat, a brine “lake” at the bottom of the Mediterranean, nearly 200 km from Crete. Called L’Atalante Basin, this area was formed when salt dissolved from the sea’s subsurface and accumulated in underwater depressions. Eight times more saline than seawater, this layer does not mix with the water column above it and, like the underlying sediment, is completely anoxic. This particular site is not unique; so-called oxygen minimum zones are found in all the oceans at fairly shallow depths as such things go, usually from 200 m to 1,500 m. Characteristically, they have very low available oxygen and lots of sulfide.

Extremophilic archaea and bacteria are common in such inhospitable-sounding environments, and so are a few eukaryotic microbes, notably protozoa. The news is that one can also find small multicellular living animals at this site. These include members of the Loricifera, metazoans less than a millimeter in length that are common inhabitants of the more usual marine sediments. Their name, sounding like something from Dr. Seuss, actually stems from their exoskeleton that serves as armor (lorica in Latin). Loriciferans have been found in hypersaline marine sites before, but they were presumed to be remnants of dead organisms falling from above (the “rain of cadavers”). However, although they are abundant in the anoxic zone, in the last 40 years only two specimens had been found in the deep Mediterranean Sea above it. This new report shows that these little animals are actually alive, as demonstrated by their life-like morphology, their uptake of radioactive leucine, and their staining with “vital” dyes. Some had eggs in them. Other kinds of metazoans in the same samples were clearly dead.

So, how do these anaerobic loriciferans harvest their energy?

The Attendee's Guide to Scientific Meetings, Part II

by Julian Davies

Source.

To begin with, attending a scientific meeting should be considered a privilege, especially if you have been invited to speak or present a poster. In accepting the invitation you are representing yourself, your lab, your colleagues, your institute or university, even your country. A poster is a living publication; this should not be taken lightly.

It may seem like it at times (i.e. the opening mixer) but a scientific conference is not to be considered in the same way as hockey game; improper behavior in a crowd of your fellow microbiologists will be noted. If you are giving a presentation, you must prepare adequately; ill-prepared talks or posters make a presentation into a bad impression!

Posters are important, you must have seen posters that have impressed you in the past and you should use these as models. They should have no more than four columns (three is best) and limited to nine figures and tables; the latter should be self-explanatory and uncluttered. Complex tables and figures should be avoided. The introductory text should be the submitted abstract and the concluding text should tell people what you have found, why it is important and what you will do next. A bold title will attract the passers-by. But, please, please, no photos of your children, parents, or partners!

Autumn Leaves

by Merry

Late Phyllonorycter blancardella leaf mine on an apple
leaf. This species makes a "blotch" mine, as opposed
to the squiggly white trails of others that you might
have seen in your garden. Visible are the layer of silk
spun by the larva on the mine floor and its pupal case
in the corner. Source.

Each autumn, as the leaves on the apple trees in the Loire Valley turn from green to gold, observant orchardists notice islands of healthy green within the otherwise yellow leaves. These islands coincide with the site of leaf mines created by the larvae of a small moth, the apple leafminer Phyllonorycter blancardella. A group of French researchers have been taking a closer look at this for some years, and they have recently struck gold.

First a little background. Each apple leafminer begins life as a fertilized egg deposited within an apple tree leaf. There, confined between the two leaf epidermal layers in a plot bounded by adjacent leaf veins, the larval caterpillar feeds, develops through several instars, pupates, and, if all goes well, emerges as an adult moth. As it feeds on the plant tissue and deposits frass, it forms the "mine" visible from the outside. This endophagous strategy affords some protection from parasitoids that aim to deposit their own eggs inside the developing caterpillar inside the leaf. It also gives the larvae ready access to the more nutritious and less defended inner leaf tissues. But judging from the large size of the holes made by even just one very small caterpillar in my garden, I doubted that the limited area encompassed by a mine could provide enough food for the development of even this tiny moth.

Apparently it can't.

Of Terms in Biology: Gene Ontology

by Elio

Not to be confused with ontogeny (the study of a multicellular organism’s development, usually from an egg into maturity, as in “ontogeny recapitulates phylogeny”), ontology is a term used by philosophers that has now been appropriated by bioinformaticists. Here it denotes the categorization of knowledge within a certain domain. Proponents of a consortium called Gene Ontology wrote: The goal of the Consortium is to produce a structured, precisely defined, common, controlled vocabulary for describing the roles of genes and gene products in any organism. This group is starting modestly, working with the databases for three model eukaryotes: drosophila, mouse, and yeast. The high degree of conservation of both sequence and function observed, particularly for core cellular functions, often makes it possible to transfer knowledge acquired from one organism to others.

From Gene Ontology, a portion of the biological process ontology describing DNA
metabolism. Note that a node may have more than one parent. For example, DNA
ligation has three: DNA-dependent DNA replication, DNA repair and DNA recom-
bination. Source.

Several websites are concerned with ontological approaches. Not all are readily penetrable. The Open Biological and Biomedical Ontologies tells us: The OBO Foundry is a collaborative experiment involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain.

Gene ontology is being used widely and is destined to become part of every biologist’s vocabulary.

Paleovirology

Stromatolites from the Proterozoic (2.3 billion years
ago) found in the Andes of Bolivia. Source.

by Welkin Johnson

How does one even begin to investigate the natural history of viruses? The dinosaurs bequeathed a motley assortment of bones, teeth, footprints striding 'cross ancient riverbeds, fossilized eggs, the occasional coprolite. The tiny trilobite left lasting and ubiquitous impressions, finding its way into textbooks and museum gift shops. Even prehistoric cyanobacteria, miniscule and boneless, are abundantly memorialized by gatherings of statue-like stromatolites.

As a scientist fascinated with the evolutionary interplay between viruses and their hosts, I admit to considerable professional envy. The paleontologists have it good. What, if anything, does a virus leave behind? My study subjects are utterly lacking in bony, fossilizable material, are too tiny to leave informative impressions in stone, and, unlike bacteria, produce no telltale geochemical signatures. By necessity, viral prehistory is traditionally inferred indirectly from phylogenetic reconstruction, typically based on aligned sequences of highly conserved subdomains shared by many viral polymerases. But these are genetic sequences, obtained from modern viral species, and the inferred ancestors aren't "real;" they are simply averages, each one a best-guess consensus. More importantly, this approach is limited to viruses with living modern descendents; it tells us nothing about extinct viral lineages. (Most likely T. Rex had its own contingent of obligate intracellular parasites?).

In this regard, the retroviruses are the notable exception.

Did van Leeuwenhoek Observe Yeast Cells in 1680?

by Nanne Nanninga

Source.

It is common knowledge that beer was produced by the ancient Egyptians and that van Leeuwenhoek (1632-1723) was the first to see yeast cells. However, what was defined as yeast in the seventeenth century is different from that of today. So did van Leeuwenhoek really observe yeast? In attempting to answer this question it might be helpful to describe some fundamental work on yeast by Charles Cagnard-Latour (1777-1859) published in 1838. (Recall that the cell theory dates from 1839). This tells us of the beer brewing and wine making state of the art around that time. It was known that the addition of yeast to properly treated grains of cereals would produce alcohol and carbon dioxide from the extracted malt sugars. In the times of van Leeuwenhoek yeast was considered an inanimate paste with no connection to living cells. What did Cagnard-Latour see? It is important to use the term “see” because, as he emphasized, he wished to approach yeast research in a new way, that is, by employing a microscope. (This approach was also followed by F. T. Kützig and Th. A. Schwann at the same time.)

Cagnard-Latour went to an English style brewery in Paris where every hour he took a sample for study from the container in which the beer was being produced. Initially he observed globules of different sizes, later he saw small vesicles protruding from the globules that had arisen through budding (Fr. par bourgeons), and finally, after four hours, only doublets were present. He concluded the initial small vesicles had increased in size through growth. If so, the doublets should not be adventious aggregates. To test this he forcibly shook his microscopic preparation with a kind of thorn (Fr. poinçon) and observed that the doublets remained intact. Remarkably, he noticed that upon dissolution of the doublets a scar remained at a variable place on the globule’s surface. He used the terms cicatrice (Fr. for scar) and marque ombilicale (Fr. for navel).

The number of globules increased in time, as did their total weight. His general conclusion was that beer brewing or fermentation involves the growth and proliferation of an organism. He also observed that commercial yeast contains singlets exclusively. So at this stage yeast was redefined, changing from an inanimate to an animate object. But was it an animal or a plant? Here he used the same approach as van Leeuwenhoek. The “little animals” of the latter were considered animals because they exhibited autonomous movement. Because yeast did not, Cagnard-Latour classified his growing globules as plants. Cagnard-Latour made another observation that I find highly relevant to the interpretation of van Leeuwenhoek's data. He saw his globules emit gas bubbles which caused individual globules to rise to the surface of the fermenting fluid in the fermentation vat.

Now, what about the observations of van Leeuwenhoek?

A Most Lively Virus

by Merry Youle

TEMs of a variety of viruses and virus-like particles ob-
served in a single enrichment culture established from
a sample collected at a Yellowstone hot acidic spring
(85°C, pH 1.5–2.0). Bar = 200 nm (100 nm for insets).
Source.

Morphologically speaking, the viruses of mesophilic and moderately thermophilic bacteria and archaea are a dull bunch. Of 5,100 surveyed, 97% are ho-hum head-and-tail phages—icosahedral heads with helical tails. The remainder were tailless icosahedra or filaments, except for two spindle-shaped oddballs. If you'd like more structural excitement, best to go virus hunting in geothermally-heated aquatic environments above 80 ºC—the hot springs, mud holes, and deep-sea hydrothermal vents—and be prepared to be astonished.

Here the statistics are reversed. Only 6% resemble typical head-and-tail phages; another 6% are tailless icosahedrons; about two-thirds are filamentous, rod-shaped, or spindle-shaped; the rest are truly unique. The oddest ones are viruses of hyperthermophilic Crenarchaeota of the genera Sulfolobus, Acidianus, Pyrobaculum and Thermoproteus. About two dozen of these have been isolated and char acterized, calling for the creation of seven new viral families to house them. All have dsDNA genomes, some linear and some circular. Almost all eschew host lysis, opting instead for a stable lysogenic relationship. Maybe life outside is just a little too tough.

Talmudic Question #60

Are there more different viral "species" or different plasmid genomes on Earth?