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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March 17, 2014

The Bacterial Chromosome: A Physical Biologist's Apology. A Perspective.

by Suckjoon Jun

I entered the bacterial chromosome field in 2004 as a fresh Ph.D. trained in theoretical physics. Ten years is not long enough for one to gain the depth and breadth of a scientific discipline of long history, certainly not for an early career scientist to write an essay of the status of A Mathematician’s Apology (Hardy 1940). Nevertheless, I agreed to write this Perspective as a physicist who entered biology, because my colleagues are often curious to know what drives physicists to become (physical) biologists, and make them stay in biology despite many challenges. I also wanted to share several lessons I have learned because, while some of them are personal and specific to my field, I have a good reason to believe that they might resonate with many future travelers. This Perspective is for them.

I would like to start with the story of one of the most familiar and yet mysterious forces in nature—gravity. Galileo is said to have dropped two balls of different masses from leaning Tower of Pisa in Italy some five hundred years ago. His experiment was to demonstrate that, on the contrary to Aristotle’s theory, the falling rate of the balls was independent of their mass. A modern version of this experiment was performed on the Moon by the Commander of Apollo 15 with a hammer and a feather. For a movie of this experience, click here. When released from the same height at the same time, the two falling bodies hit the surface of the Moon simultaneously! On the Earth, however, the feather would have fluttered, as if alive, because of the air.

Initially attracted to the beauty of Amsterdam, I started my post-doctoral research at AMOLF, an interdisciplinary research institute known for exciting interactions at the interface between physical and biological sciences. The forces I was interested in were much less tangible than gravity. In particular, I was supposed to explain the driving force underlying segregation of a replicating chromosome in Escherichia coli. It sounded simple to me, except that I barely knew anything about bacteria, certainly without realizing that it was one of the long-standing problems in biology. I knew the DNA biophysics literature fairly well, but when I saw the beautiful 1992 illustration of E. coli in Goodsell, it was obvious that something like the wormlike chain model was not going to be very useful to understand segregation of the whole chromosome. What worried me was the directionality—if I were a small protein sitting on a replicating chromosome, could I tell which DNA segment belongs to which sister DNA? Physicists like questions like that, whether they are rooted in physics or biology.

Continue reading "The Bacterial Chromosome: A Physical Biologist's Apology. A Perspective." »

March 13, 2014

Pictures Considered #14. Rickettsia undergoing binary fission (from a paper authored by Elio in 1957)

Figure1

The series of photomicrographs illustrates part of the cytoplasm of a mouse fibroblast cell containing two rickettsiae “A” and “B,” each of which divides into two daughter organisms. During the 20-minute period between the photographs shown in the right corner of each figure. Phase photomicrographs, magnification 2000X.  Source.

March 10, 2014

The Cold Side Of Microbial Life

by Gemma Reguera

The Cold Side Of The Earth

Figure1 Figure 1. The Arctic and boreal regions of the Earth (or Northern lands) are shown in color, each color corresponding to a different type of above-ground vegetation. Source.

In the midst of one of the worst Michigan winters on record, I felt inspired to learn more about how microbes cope with the cold (it is true: misery does indeed like company). So it happens that the polar vortex that has visited our northern states a few times this season has given us a glimpse at the subzero temperatures that prevail in the northern lands of our planet, sometimes all year round. The most northern areas are what we generally know as the Arctic, a treeless region that is either barren of vegetation or limited to tundra (shrubs, grass, lichens, etc.). As you continue going south, you enter the boreal region, characterized by its thick coniferous forests. The soils in these northern lands are called permafrost because they remain frozen for long periods of time. The almost permanent frozen state of these soils limits microbial activity and the turnover of organic matter. Not surprisingly, permafrost soils store approximately 25% of all of the planet’s soil organic matter.

For all their frigid circumstances, do not assume that permafrost microbes are in a perpetual state of hibernation. These frozen soils harbor a broad diversity of microbes. Furthermore, bulk measurements indicate that there is microbial metabolic activity despite the subzero temperature regimes. Just how much, we don’t know. Scientists fear that global warming will continue to thaw large areas of permafrost, promoting microbial activities and the turnover of the large quantities of organic matter trapped in the soils. This could lead to the release of substantial amounts of carbon into the atmosphere in the form of carbon dioxide and the greenhouse gas methane. However, with the limited information we have, it is difficult to predict how the permafrost microbial communities will respond to global warming.

Continue reading "The Cold Side Of Microbial Life" »

March 06, 2014

Talmudic Question #106

What may be the reason why E. coli is usually the most abundant facultative anaerobe in mammalian feces?

March 03, 2014

A Mouthful Of Microbes

by Gemma Reguera

Smile (or not)!

Figure1 Figure 1. One of our ancient relatives? Source.

After watching Hollywood movies of medieval knights with neat haircuts and bright smiles, it may shock you to be reminded that our dear medieval cousins looked anything but clean. The truth is that hygiene was not a top priority in the Middle Ages and germs were in heaven. This was a time in which cities lacked sewage systems and feces, urine, and garbage were dumped onto the streets or into the castle moat. Not surprisingly, outbreaks of water-borne diseases were a frequent occurrence. Add to that religious concerns about nudity, and it will not surprise you to know that even the most illustrious doctors recommended not taking baths regularly. As a result, everybody, from the lowest peasant to the most powerful king, stank like a smelly animal.

In this era of complete disregard for personal hygiene, people did pay some attention to dental hygiene. Why? Because toothache was a widespread malady and people would result to anything in their power to prevent it and alleviate it. They would rub on their teeth, for example, mixtures of fresh or burned scented herbs such as parsley, mint, and rosemary, and then rinse their mouths with solutions made of herbs, vinegar, wine, and/or alum (the latter is still use by many as a home remedy for sore throat). Alas, these practices were not effective enough to prevent dental bacteria from growing and causing cavities and infections. I also read that our medieval ancestors were advised to clean their teeth in the morning, rather than at night. I imagine this was done to ensure they had good (better?) breath. However, the morning practice left the oral microbes free to roam and proliferate throughout the long night hours. Hence, cavities and abscesses were very common and medieval barbers found a profitable side job: pulling out teeth!

Continue reading "A Mouthful Of Microbes" »

February 28, 2014

TWiM #73: Eyeing Root Nodule Development

Hosts: Vincent RacanielloMichael Schmidt and Michele Swanson.

Vincent, Michael, and Michele discuss how soil-dwelling bacteria induce the formation of root nodules on legumes via a protein called CYCLOPS. 

Right click to download TWiM #73 (57.5 MB .mp3, 80 minutes).

Subscribe to TWiM (free) on iTunesZune Marketplace, via RSS feed, by email or listen on your mobile device with the Microbeworld app.

Send your microbiology questions and comments (email or mp3 file) to twim@twiv.tv, or call them in to 908-312-0760. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twim.

February 27, 2014

A Failed Experiment

by Elio

Figure1 Figure 1. Source.

In 1956 I joined Ole Maaløe’s laboratory in Copenhagen for a two year postdoc. We worked on the connection between the rate of growth of Salmonella and its macromolecular composition, arriving at the conclusion that there was indeed a simple linear correlation between the cells’ nucleic acid and protein content and how fast they were growing. In trying to interpret this, Ole was influenced by the experiments coming from the labs of quite a few people, showing that the synthesis of many biosynthetic enzymes becomes repressed when the end product of their pathway is added to the medium. If, say, arginine is added to a culture, the enzymes involved in arginine biosynthesis will not be made. If so, in cultures grown in a rich broth, many biosynthetic genes should indeed be silenced. These should include all the operons for amino acid biosynthesis and for other building blocks present in this medium.

Figure2
Figure 2. Ole Maaløe. Source.

Ole reckoned that if he kept a culture growing steadily for a long time in rich broth, the cells might shed some of biosynthetic genes because they would not be needed under these conditions. So he did the following experiment: He inoculated a large flask containing perhaps 3 or 4 liters of a very rich broth. As an aside, the kitchen at the State Serum Institute where Ole worked until he became professor at the University of Copenhagen was known for making exquisitely rich media. The ladies who worked there prepared their own meat infusion using the best Danish veal meat in the market and added to it carefully selected batches of peptone. Their broth allowed Salmonella to growth at a superfast 16 minute doubling time (try that with dehydrated commercial media!) So, you can expect that the cultures in such a superrich medium might be super-repressed.

Ole’s inoculum was small enough that the culture was still in exponential growth by the time it was time to go home. I ‘m quite sure that in order to slow down the growth he kept the culture at a temperature lower than the 37° optimum (but don't remember what it was). Before leaving the lab, he inoculated a second flask using a small aliquot from the first flask. The next morning he did the same thing, and he kept up this series of twice-a-day inoculations for (I think) one week. By the end of this time, the culture had been growing exponentially for perhaps 500 generations. He reasoned that this careful protocol was necessary to avoid the genes reawakening in the stationary phase, where they may be needed. Thus even an incipient entry into stationary phase had to be studiously avoided.

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February 24, 2014

On Finding Jewels in the Junk

by Christoph Weigel

By good tradition, posts in the STC blog come with subtitles to let our readers have a (short) break to breathe deeply before diving into the next paragraph. The subtitles of this post come as—yes!—music titles, in a more oblique way referring to the content of the following paragraph and with the invitation to the readers to enjoy listening while having a break.

Take #1 - Caravan (Duke Ellington)

Figure1 Figure 1. Transcriptional regulation in eukaryotes. Source.

In prokaryotes, it only takes a small jazz band to get the music grooving: piano and a rhythm section suffice. The promoter region of a gene is a tiny stage on which RNA polymerase (p) and few transcription factors (dr, b) improvise on a tune, i.e. they initiate or skip transcription. By contrast, it takes a big band in eukaryotes to perform Duke Ellington's 'Caravan'. And since not all the musicians fit to the narrow stage trombones and saxophones are placed elsewhere in the concert hall: transcription factors (tb, sax) bind to sites—enhancer or silencer elements—that are found upstream and downstream of genes and also within introns.

In its typical textbook style, figure 1 oversimplifies the complex interplay of RNA polymerase II with the various transcription factors at a eukaryotic promoter by reducing it to a two-dimensional array, suspiciously omitting downstream located 'gene regulatory sequences'. This flatters our human ability to perceive 2D-maps at a glance but it ain't got that swing. Admittedly, only a 3D-animation could catch the groove of the spatial intricacies that bring enhancer-bound transcription factors into the proximity necessary for the multiple protein-protein interactions that orchestrate eukaryotic transcription initiation. Let alone the possibility that transcription factors bound to one enhancer interact with protein complexes at two or more promoters simultaneously. Please note in figure 1 the stippled grey line tagged 'spacer DNA', we will come to this later.

Continue reading "On Finding Jewels in the Junk" »

February 20, 2014

Good Old Days #3. Van Niel and Pacific Grove

by Bernard Strauss

Figure1 Figure 1. The Hopkins Martine Station in Pacific Grove, California. Source.

In 1949, at the end of my second year at Caltech the faculty seems to have decided that I really needed to learn some biology. The method the Caltech faculty adopted was to send me to the summer course in microbiology given at the Hopkins Marine Station of Stanford University by Cornelis van Niel.

The van Niel course consisted of a summer’s work of classes and laboratory. I was given an office, which I shared with Ruth Sager. The class would meet with van Niel for lecture and discussion and we would then do laboratory work based on the discussion. An idea of the course can be gained from the first exercise. The class suspended some bakers yeast in water and using a microscope looked at the suspension. Van Niel would then go around the room asking students one by one what they saw. Invariably the answer would be yeast cells and the process would continue until some student (possibly warned by those with experience from past years) would say "I see little circles." This was the answer van Niel wanted in order to illustrate the difference between observation and conclusion (I saw circles but van Niel was convinced I had been warned!).

Van Niel was a master at maneuvering class discussion. Again and again he would have the class "design" an experiment, making corrections and inserting controls and then when we were all finished and satisfied with "our" design, Wolf Vishniac, the TA, would wheel in carts with the equipment, media and strains to do exactly the experiment that “we” had designed. (Wolf was the son of the photographer, Roman Vishniac best known for his photographs of pre World War II Eastern Jews but also an accomplished biological photographer).

Continue reading "Good Old Days #3. Van Niel and Pacific Grove" »

February 17, 2014

The Fungus That Killed Darwin’s Frog

by Gemma Reguera

A Mouthful of Kids

Figure1 Figure 1. A ‘pregnant’ male Darwin frog carries its babies in the vocal pouch (left) until they are big enough to be spat out (right). Sources here and here.

In his second expedition to South America, Darwin discovered many new species of animals and plants. The field observations obtained throughout this 5-year expedition provided the intellectual framework for the maturation of his ideas on evolution. It also introduced the world to a tiny (2-3 cm in length) frog known as Darwin’s frog. The group includes the northern (Rhinoderma rufum) and the southern (Rhinoderma darwinii) species, which inhabit the central and southern forests of Chile (and adjacent areas of Argentina), respectively. As in many other amphibians, fecundation is external. However, Darwin’s frogs do not leave the fecundated eggs on the ground and exposed to environmental insults and predators. The males scoop them with their mouths and incubate them in their vocal sac. The dedicated dads feed their offspring after the eggs hatch, producing secretions analogous to milk that allow the tadpoles to grow in a protected environment, sometimes until they have fully developed into froglets. When the young are mature enough to fend for themselves, the male frog literally spits them out. You can see a short video describing this amazing reproductive strategy following this link. This behavior, generally known as neomelia, allows the male ‘surrogates’ to care for the eggs and then the young, maximizing survival throughout the critical tadpole stage. Unfortunately, deforestation in the regions inhabited by these frogs has resulted in vast habitat losses, leaving Darwin’s frogs in precarious conditions. The last sight of a northern Darwin frog was reported in 1980, leading researchers to suspect that this particular species went extinct years ago. The species has been tagged as ‘possibly extinct’. The southern species, R. darwinii, which has traditionally occupied a much larger region, has been able to survive, but population numbers have declined dramatically.

Continue reading "The Fungus That Killed Darwin’s Frog" »

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