Moselio Schaechter


  • 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.

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May 31, 2012

Quotes from the Grab Bag

by Elio

Late this Tuesday, Merry pointed out that we didn't have a piece for our Thursday posting. As aficionados of this blog may have noticed, we reserve the weightier pieces for Mondays, and publish shorter, lighter ones on Thursdays. In panic, I had to dig into my grab bag, looking for something to post. In lieu of something original, I came up with quotes that have spoken to me at different times. Please send in your cherished quotes and, before too long, we will post them as well.


If a thing is not worth doing, it is not worth doing well.
Salvador Luria

The juvenile sea squirt wanders through the sea searching for a suitable rock or hunk of coral to cling to and make its home for life. For this task, it has a rudimentary nervous system. When it finds its spot and takes root, it doesn't need its brain anymore so it eats it! It's rather like getting tenure.
Daniel Dennett (from Consciousness Explained

A theory that fits all the facts is bound to be wrong as some of the facts will be wrong.
Francis Crick

It is a very good morning exercise for a research scientist to discard a pet hypothesis every day before breakfast.
Konrad Lorenz (from On Aggression)

The prototype [of the great pathologist]is not the liberator releasing slaves, the good Samaritan lifting up the fallen, but the dog sniffing tremendously at an infinite series of rat-holes.
H.L. Mencken

A theory is a policy rather than a creed.
Joseph J. Thomson

The capacity to blunder slightly is the real marvel of DNA. Without this special attribute, we would still be anaerobic bacteria and there would be no music.
Lewis Thomas

Viruses are viruses
André Lwoff (1957)

Life would not long be possible in the absence of microbes.
Louis Pasteur

out of every 30,000 bacteria in the United States, 29,999 are harmless, useful, or even necessary for our lives while one is a disease bacterium. That is not a bad record compared with that of the human race. In 1942, there were 7,569 persons convicted of murder in the United States, or 1 out of every 17,000. Considering that the proportion of harmful bacteria in our estimate is certainly too high, it would be only fair to admit that bacteria are no more dangerous to humanity than man himself.
Otto Rahn (from The 1941 Census of Bacteria in the United States, in Microbes of Merit, 1945)

Louis Pasteur's theory of germs is ridiculous fiction.
Pierre Pachet, Professor of Physiology at Toulouse, 1872

The primary aim of bacteriology as taught in this department is to equip the student to do, and of hygiene to live, rightly. The power of observation, the indefinite refining value upon the individual sometimes called culture, the ability to concentrate the mind, the capacity to study, —all belong to this subject
Bacteriology and Hygiene Department curriculum, 1902-1903 Michigan State University Catalog.


And a few more…

Visual_quote

(Right) A visual quote from Hollis who blogs at In the Company of Plants and Rocks. The statue is of the anti-evolutionist Louis Agassiz himself! Head plant courtesy of Mother Nature via 1906 San Francisco earthquake.

Vincent Racaniello, blogmaster of Virology blog and podcast host of TWiV, TWiP, and TWiM contributes:

I have little patience with scientists who take a board of wood, look for its thinnest part, and drill a great number of holes where drilling is easy.
Albert Einstein

And, saying that it is the only quote hanging in his office for the past 30 years:

There is no expedient to which a man will not resort to avoid the real labor of thinking.
Thomas A. Edison

May 28, 2012

Cell Division Through DNA Curtains

by Gemma Reguera

Despite the apparent simplicity of bacterial cells, their cell division cycle is a complex developmental program that couples cellular growth to the replication and segregation of chromosomes and the division of the cell’s cytoplasm (aka cytokinesis) (Fig. 1). The bacterial cell division cycle starts with the commitment of the cell to reproduce. This is the step in which, forgive the pun, size truly matters. During active growth, the cell’s size changes to accommodate increases in mass, volume, and biosynthetic capacity. When the cell reaches a critical size, essential cellular functions such as intracellular transport and nutrient uptake are constrained and optimal growth can no longer be supported. Provided conditions are adequate for growth, cell division is undertaken to allow the bacterium to regain its individual cellular fitness.

BinaryFission

Fig. 1: As the cell grows in size, the chromosome is replicated and segregated. A constricting septum forms at midcell to divide the cell’s cytoplasm and produce two daughter cells. Source.

Continue reading "Cell Division Through DNA Curtains" »

May 24, 2012

Fine Reading: Endogenous Retroviruses

by Elio

I can't think of anything more startling, more promising, and more intractable in biology than the business of endogenous retroviruses. They seem to be ubiquitous in both invertebrates and vertebrates, and even in plants. In humans, they make up at least 8% of the genome, plus some bits and pieces. They are ancient; in our lineage they go back perhaps 100 million years. Let's face it, if we hadn't been told about them, we could never have conjured up such a strange story. It’s like hearing that you possess a limb or an organ that you didn't know about.

The very existence of endogenous retroviruses (ERVs) touches us in a number of ways. How is evolution shaped by the acquisition of such viral packets of genes? How often has it happened? Did it arise by infection, as seems likely? Is this an ongoing process that leads to further evolution? What does this have to do with the evolution of viruses? What does it reveal about the regulation of gene expression? On balance, do they do more good or more harm? All these questions have arisen elsewhere, but they are brought to the fore by these strange entities.

Continue reading "Fine Reading: Endogenous Retroviruses" »

May 21, 2012

Where Mathematicians & Biologists Meet

by Joe Mahaffy

Math_cartoon

Source.

Mathematics and Biology have a long history together. It goes back to early studies on epidemiology (such as John Snow‘s on cholera and the Broad Street pump), and includes Ross’s quantitative studies that show how malaria can be controlled by careful analysis of data. And, of course, there are many others. In the early 20th century, population models with differential equations were developed to describe the dynamics of populations, such as the studies of Alfred Lotka, who felt that natural selection could be quantified by physical laws, and Vito Volterra, who created a model to explain the predator-prey ratios in the Italian fish markets. These early models provide excellent tools because in their simplicity they show biologists how mathematics can help explain noteworthy biological phenomena. Mathematicians enjoy such models because the examples themselves make it easier to explain what the equations are describing.

Continue reading "Where Mathematicians & Biologists Meet" »

May 17, 2012

The Bacterial Resistome is Both Ancient and Surprising

by S. Marvin Friedman

Soda_Straw_room_raw

The Soda Straw Room in the Lechuguilla Cave. These pencil-thin
stalactites are called soda straws from their size and the fact
they have a central canal through which mineral-laden water flows.
Although it is not uncommon for soda straws to grow three to five
feet long, the ones in this room are as long as 15 feet. Credit: Norm
Thompson. Source.

One of the many interesting controversies that microbiologists can ponder today is whether the alarming proliferation of antibiotic-resistant strains is primarily a consequence of the widespread use of antibiotics in humans and in animal husbandry. An examination of bacteria isolated from terrestrial animals in the Galapagos, a remote location with limited exposure to humans, revealed  an absence of antibiotic resistance genes. Likewise, plasmids from bacterial collections that predate the antibiotic era were mostly devoid of resistance elements. Furthermore, a study of Dutch soil samples showed an increase in antibiotic resistance genes in contemporary samplings as compared to those from the pre-antibiotic era. On the other hand, antibiotic resistance genes were both abundant and diverse in ancient DNA recovered from Pleistocene deposits (30,000 years ago). Likewise, a survey of present-day actinomycetes revealed that multidrug resistance was prevalent even though human sources of antibiotics were presumed absent in this environment. It should be noted, however, that the actinomycetes are prolific antibiotic producers and thus it is not surprising to find resistance elements enriched in this group.

Continue reading "The Bacterial Resistome is Both Ancient and Surprising" »

May 14, 2012

If It Walks Like DNA, and Talks Like DNA…

by Merry Youle

Hawk moth caterpillar

The Hawk Moth Caterpillar inflates its thorax as a
defense mechanism, resulting in a snakelike appearance,
complete with false eyes. Source.

Conjugative plasmids and transposons have been found guilty of spreading antibiotic resistance genes from pathogen to pathogen.  But how do they get past the bacterial defenses against incoming foreign DNA? Most bacteria have some sort of restriction-modification system to take care of just such molecular invaders. With such a system, they modify their own chromosomal DNA by adding methyl groups to specific residues within a short recognition sequence which is different for different enzymes. Incoming DNA that doesn’t have those particular sites methylated is “restricted,” i.e., cleaved, by the restriction endonuclease. This is end of game for an incoming phage or other mobile element that had replicated in a different strain or species.

Continue reading "If It Walks Like DNA, and Talks Like DNA…" »

May 10, 2012

Talmudic Question #87

By John Ingraham

Can you think of a species that has been wiped out by an infectious agent?

May 07, 2012

Polar Enchantment

by Elio

Auroras-Over-Both-Earth-Poles

NASA's Polar spacecraft captured the first-ever movie of
auroras dancing simultaneously around both of Earth's
polar regions. Source.

All bacteria, even those that are spherical, display geometric asymmetries during at least part of their life cycle, and it appears that cells take advantage of these asymmetries to localize cellular components to specific sites. So begins a paper by Li and Young that describes a novel approach for detecting E. coli proteins that preferentially localize to the cell poles. There is already a considerable catalog of “polar” proteins in various bacteria, some involved in chemotaxis, signaling, regulation of septation, flagella synthesis, phage attachment, and a raft of other phenomena. Pretty soon you may be tempted to ask which proteins do not localize to the poles. This may sound facetious, but it illustrates the recent changes in mindset regarding the structural complexities of the prokaryotic cell. But many questions remain. We readily subscribe to the notion that bacteria are not bags of enzymes but this begs the broad question “what are they?”

Continue reading "Polar Enchantment" »

May 03, 2012

What Happened to Our Friendly Enterococci?

by Merry

Enterococci had been generally regarded as benign commensals, a part of our healthy intestinal microbiota. They were even invited in, being used as probiotics. But then, in the late 1970s, the first multiple drug-resistant strains appeared, and vancomycin-resistant strains followed in 1981. In recent decades, they have taken center stage as one of the pathogens most commonly associated with nosocomial infections. Enterococcal infections are particularly difficult to manage now because these bugs have accumulated numerous virulence genes and antibiotic resistance factors. What happened?

First, a few facts about these organisms. Enterococcus is a genus of Gram-positive lactic acid bacteria in the phylum Firmicutes. They used to be called streptococci because their typically paired cells look so similar. The two species found in our intestines, E. faecalis (90–95%) and E. faecium (5–10%), are facultative anaerobes.

Now here’s your first clue as to their change into pathogens. Hospital-adapted strains have more DNA than their benign relations—more than 600 kb of additional coding potential, enough for hundreds of genes—mostly in the form of acquired mobile elements. The first enterococcus to have its genome sequenced was one such hospital-adapted E. faecalis strain. I’ll have more to say about this strain (V583) later. One quarter of its genome is composed of mobile elements, including three independently replicating plasmids, three chromosomally integrated plasmid remnants, seven prophages, and a pathogenicity island. Here reside several virulence genes as well as antibiotic resistance factors.

Continue reading "What Happened to Our Friendly Enterococci?" »

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  • We welcome readers to answer queries and comment on our musings. To leave a comment or view others, remarks, click the "Comments" link in red following each blog post. We also occasionally publish guest blog posts from microbiologists, students, and others with a relevant story to share. If you are interested in authoring an article, please email us at elios179 at gmail dot com.

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