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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July 30, 2012

The Rise of Genomic Superspreaders

by Steven Quistad


The common ancestor of placental mammals probably looked like Eomaia scansoria, the earliest known placental mammal, shown here in an artist's reconstruction based on a 125-million-year-old fossil skeleton found in China in 2002. Source.

One hundred million years ago the earth’s climate was much warmer than today and vast inland seas stretched across entire continents. The land was dominated by charismatic megafauna that would one day serve as inspiration for Sir Arthur Conan Doyle’s novel The Lost World. This period is commonly referred to as the age of reptiles as our placental ancestors were barely visible. Yet it was during this period that something significant happened to them, something that would become a major part of who we are today. One hundred million years ago retroviruses infected our ancestors’ germline and hitched a ride through evolution into the present day where their DNA still exists in all of our genomes. In fact, such retrovirus infections occurred ~31 separate times in our evolution and these endogenous retroviruses (ERV’s) expanded and now make up an astounding 8% of our entire genome. This means that we owe ~240,000,000 bp of our DNA to these retroviruses!

Continue reading "The Rise of Genomic Superspreaders" »

July 26, 2012

Seeing Biology Through the Eyes of Visually-Impaired Students

by Amy Cheng Vollmer


Lettuce centrifuge. Source.

I have been teaching introductory biology in higher Ed since 1985, my first four years at Mills College and now at Swarthmore College since 1989. At both institutions, these courses (lecture + laboratory, taught by faculty members) were open to majors and non-majors. Through these years, it has been amazing to see the evolution of visual resources offered by textbook publishers. First the text illustrations became more sophisticated, reflecting our increased understanding of cells, molecules, organisms, and ecosystems. We were keen to make black and white copies of those illustrations onto transparencies, being careful to purchase the kind of acetate films that wouldn’t melt on the drum of the copier! Then came the wonderful transparencies with figures and tables from the texts in color—better than sliced bread! Shortly thereafter, these were arriving on CDs, and now they are accessible at websites in .pdf and .ppt formats. And oh, the animations available from publishers and from many research laboratory websites! There are some great YouTube videos about glycolysis, the TCA cycle—even the classic Protein Synthesis movie. Among my favorites for teaching introductory biology are the Oster laboratory (UC Berkeley) animations of the ATP synthase, for me there being no better way to integrate protein structure/function and proton motive force/oxidative phosphorylation. Check out the animations from his laboratory here.

Continue reading "Seeing Biology Through the Eyes of Visually-Impaired Students" »

July 23, 2012

An Evolutionary Tale of Zombie Ants and Fungal Villains & Knights

by Gemma Reguera

Infected ant with spore stalk

Fig. 1: An ant infected by O. unilateralis bites the underside of a
leaf. The fungal stroma emerges from the back of the ant’s head and
develops a fruiting body with a capsule full of spores. Once matured,
the capsule is released and the spores disperse on the forest floor.
Courtesy of David P. Hughes. Source.

In a recent post I shared with you some amazing things I had learnt about coprophilous (‘dung-loving’) fungi that spit their spores like pros. What I did not tell you then is that my six-year-old son also fell in love with the spitting fungi (dung + spit = child’s interest!) and wanted to learn more. So we spent hours watching online videos until we stumbled upon a BBC’s Planet Earth video narrated by the great David Attenborough about ant parasitic fungi in the genus Cordyceps. The video shows a carpenter ant (genus Camponotus) that has been infected by spores of the fungus Ophiocordyceps unilateralis. The spores germinate inside the ant’s respiratory track and the mycelia grow towards the brain while feeding on soft tissues. Once the fungus reaches the brain, it induces behavioral changes such that the ant climbs up vegetation and bites the underside of the leaves. There the ant awaits its death while the fungus continues to grow within. The stroma stalk of the fungus eventually protrudes from the back of the ant’s head and a fruiting body bearing a capsule filled with spores forms near its tip (Fig. 1). Once the spores are sexually mature, the capsule is released, and then explodes, either in the air or upon hitting the ground. This delivers the spores into the path of healthy ants, there to start a new cycle of infection.

Continue reading "An Evolutionary Tale of Zombie Ants and Fungal Villains & Knights" »

July 16, 2012

Blog Evolution


by Elio


Merry notes: I first stumbled across STC
when reading a book by Elio’s friend,
Lynn Margulis, in which she mentioned
the ectosymbionts of Euplotidium.
Googling for that critter by name brought
me to Elio’s 2007 post about this hand-
some ciliate.

I am sorry and sad that Merry will have to relinquish her partnership in this blog. She has been oxygen to me. Besides the fact, evident to readers of this blog, that she is a remarkably gifted writer, are less visible attributes. She has been an imaginative and creative editor, a critic of the scene, and a keeper of this blog’s moral compass. Beyond that, she is someone with whom I have discussed matters with trust and the knowledge that she will provide deep insights. I have seldom if ever had such a friend in science. I’ll try to soldier on, but it won't be the same.

 Our story is indeed unusual. After an initial flurry of emails, starting about 5½ years ago, we somewhat timorously began a Skype (audio only!) exchange that at least served us to become acquainted with the timbre of one another’s voice. And so it has stood—we have not seen each other in person yet. For all our reliance on media, we have developed a unique working relationship, where we acted symbiotically, respected our foibles and relied on the other for important as well as simpler judgments. It goes beyond that. In a short span of time, Merry has become a seasoned microbiologist, especially when it comes to the viruses. Her understanding is stunning, her perspicacity, dizzying. I will miss her companionship.

My thanks, Merry.


by Merry

I had no idea. Five-plus years ago I knocked on the virtual door of the blog and Elio invited me in. If I’d had a crystal ball that showed me what these five years would bring, I’d not have believed it. It is still hard to believe.

At first I timidly proofread Elio’s posts, then started tweaking the layout of the published articles. Soon we found that I could relieve him of some of the inevitable rewriting without distorting his message, and I even enjoyed doing this! After all, not only do I take pleasure in finding the right words, but I was getting an education in microbiology and in writing from one who knows both well. One of the most valued things he has taught me is how to find the story in a detailed research paper and then retell it in a digestible written form. I intend to express my appreciation for this gift in the very best way, that is by using what he has taught me as I continue to use written words to speak for The Small Things.

Another of Elio’s qualities was key to both my arrival at the blog and my enthusiastic participation. Some years before I discovered STC, I had read an essay by him in a microbiology textbook, one of perhaps twenty written by researchers in the field telling students something about what it is like to be a microbiologist. I remembered only his. Only he spoke with respect and appreciation for the microbes he studied. That attitude continues to infuse STC and sets it apart from the numerous other microbiology blogs.

Step by step, he encouraged me to participate in more aspects of the blog, authoring posts and then joining him in the masthead as co-blogger. Many other opportunities also came to me through his mentoring and sharing. I know he will miss me now, as I will miss him.

Also five years ago I had no idea that post-polio syndrome would ever take such a chunk out of my time and my energy, and surely not this soon. Back then I was still moving lava rocks by the ton, mixing concrete, and tending a large veggie garden that climbed up the mountainside. Today it is time for me to become STC’s first Blogger Emeritus. My work here will be completed at the end of August.

On the other hand, Elio is still going strong, and ASM is ever more committed to supporting STC. I know I will enjoy visiting STC for many years to come. Elio will never run out of fascinating microbial stories to share.

from her lava tube on the Big Island

July 12, 2012

Galectin 8: The Cell’s New Sheriff?


a, b, Early after the pathogenic bacterium
S. typhimurium invades host cells (a), it resides
in a cytoplasmic vesicle known as a Salmonella-
containing vacuole (SCV; b). c, The bacterium
can damage the vacuole membrane, exposing
host sugar molecules to the cytoplasm.
Thurston et al.
report that the host protein
galectin 8 binds to these sugars and triggers
autophagy, by which the invading bacteria are
destroyed. Specifically, the authors found
that galectin 8 recruits another protein, NDP52,
by direct interaction. NDP52, in turn, binds to
the protein LC3 and recruits other components
of the autophagy machinery to the damaged
SCV. d, Eventually, the bacterium is enclosed in
a specialized vesicle known as an auto-
phagosome, which forms from the isolation
membrane. e, Other vesicles (lysosomes) con-
taining digestive enzymes can then fuse with
the autophagosome, forming the autolysosome
within which the pathogen is destroyed. f,
The authors found that osmotic damage to
cytoplasmic vesicles, in the absence of
bacteria, also exposes host sugars that
recruit galectin 8. Source.

by Andy Cutting

Bacterial pathogens that invade a host cell either destroy it or persist within it. One of the most important defense mechanisms that mammalian cells have developed against such bacteria is the process of autophagy or “self-eating.” This is a widely studied system that cells use to degrade some of their own components as well as foreign invaders such as bacteria and viruses. So important is this process that it merits its own journal! And simple it isn’t.

A bacterial pathogen traveling through the mammalian cytosol is eventually detained within a double membrane structure, the autophagosome. How they get there varies for different bacteria. For instance, Salmonella enterica serovar typhimurium (S. typhimurium for short), a facultative intracellular pathogen, arrives within a phagosome, which is now termed the salmonella containing vesicle (SCV). It escapes from the SCV using its type III secretion system, and enters the host cytosol where, like other undesirable elements, it becomes coated with ubiquitin. This labels the bacteria as “cargo” for autophagy. When an autophagy receptor, optineurin, becomes phosphorylated it promotes selective autophagy of the ubiquitin-coated salmonella. Another mechanism for destruction of bacteria via autophagy employs proteins that directly bind to an adaptor protein coupled to the autophagosomal membrane, That should be the end of the would-be invaders. But, as we’ll see below, there is a third way to kill invading pathogens.

During autophagy, the first step is the formation of an autophagosome that contains the pathogen to be destroyed. This vesicle fuses with a lysosome whose enzymes work on degrading the pathogen within. In the paper at hand, the authors tried to figure out how autophagy combats S. typhimurium infection in HeLa cells. What they found is a novel ubiquitin-independent pathway.

Continue reading "Galectin 8: The Cell’s New Sheriff?" »

July 09, 2012

Fishing With Algae For Malaria Vaccines

by James Gregory


An algae farm—a potential site of vaccine production.

Malaria is a big killer and a major worldwide health concern. The number of malaria-related deaths has fallen to approximately 650,000 in 2010, from well over 1 million just ten years ago, thanks to the World Health Organization (WHO) and to philanthropic organizations, including the Bill and Melinda Gates Foundation. This effort, composed of drug-based treatment and insecticide-treated bed nets (ITNs), was nothing short of heroic, but unfortunately it is not sustainable. Malaria strains have been resistant to chloroquinones for decades and the emergence of artemisinin resistant strains is threatening the last effective drugs in our arsenal click here and here. The story is similar for insecticides. Countries with insecticide-resistant mosquitos far outnumber those without. For instance, mosquitos in Cote D’Ivoire are resistant to four classes of insecticides, those in India, to three.

Malaria fig 1

Figure 1. Malaria causing Plasmodium species undergo a complex
three-stage life cycle. Each stage of the life cycle could potentially
be targeted for vaccine intervention. Pre-erythrocytic vaccines –
protection for the vaccinated individual (RTS,S is a pre-erythro-
cytic vaccine). Blood – reduce the severity of malaria infections.
Mosquito – block malaria transmission by preventing mosquito
infection. Source.

In response, the Malaria Vaccine Initiative was established in 1999 by a grant from the Bill and Melinda Gates foundation to accelerate the development of effective malaria vaccines. Vaccines are the single most cost effective means of disease prevention, but, for malaria, coming up with one has not been easy. The most deadly form of human malaria is caused by the protist, Plasmodium falciparum, which has about 5300 genes and three distinct developmental stages each housed in a different environment—liver, blood, and mosquito (Fig. 1). P. falciparum spends the majority of its time hidden in liver cells and red blood cells. Here it is sequestered from the antigen-presenting cells that would trigger an adaptive immune response. Furthermore, P. falciparum is a moving target; its cell surface proteins are highly polymorphic, likely a response to the selective pressure imposed by the immune system. It seems that in this arms race the parasite is winning, but there is hope.

Continue reading "Fishing With Algae For Malaria Vaccines" »

July 05, 2012

Book Review: Microbes and Evolution


Microbes and Evolution: The World
That Darwin Never Saw.
Edited by
Roberto Kolter and Stanley Maloy.
ASM Press. A measly $14.95.
Amazon has lower shipping charges.

by Elio

Maybe it’s the lava fields in the Galapagos, maybe it's the giant tortoises, but something caused a bunch of microbiological luminaries to come out of their shells and write a bit about what they think and feel regarding evolution. A meeting held in those islands in 2009—being Darwin’s 200th birthday—brought together some 40 people instructed to discuss microbes and evolution. Out of this came a thin and extraordinary volume, an anthology of lively essays that largely succeeded in laying bare the personal reflections of the participants. And they wrote in plain English. This is quite an unusual book in the history of scientific writing. Although many people have written notable personal accounts of how they relate to their science, rarely has there been such a successful convergent effort.

The book encompasses a large variety of topics related to the subject at hand. Relatively few chapters actually focus on evolution directly, but this probably reflects the relative newness and paucity of laboratory studies in evolutionary microbiology. In some cases, the connection seems to be a bit of a stretch, based perhaps on the Dobzanskyian dictum. By stating that Nothing in biology makes sense except in the light of evolution, Dobzansky forced all biologists to pay at least lip service to connections between their work and the Big E. This is not always an easy thing to do, and in some cases, the efforts in the book can be called intrepid. But even in the seemingly less-related chapters, the nexus is not perfunctory and Darwin’s presence is keenly felt. And the ideas are consistently presented in a readable, ever stimulating fashion. In the end, about half of the participants had something to say about Darwin; the other half, what Darwin would have said about them.

To give you the flavor of what's inside this book, here are a few bons mots, chosen almost at random.

Whether viewed from the bow of the Beagle or through the lens of the microscope, all life is bound by the same evolutionary rules. P. 41

Please don't tell my mother, but for years I’ve wanted to be Charles Darwin. P. 263

...we can expect natural environments to contain a lumpy continuum of microbial genotypes and phenotypes. P. 273

So most of the evolution on this planet is actually being carried out by entities Darwin never imagined and at a scale he never could have considered. P. 69

I found this a most satisfying book, laced with charm and sharp insights. Buy it, treasure it, and keep it for your grandchildren. It will wear well. And, at the price, this is a bargain you may never see again.

July 02, 2012

Oddly Microbial: 86 Million Year-Old Deep Seabed Mystery Cells

by Marcia Stone

Editor’s Note: This is the third in what is expected to be an ongoing series about cells that might not come immediately to mind when you think “microbe.” The first two were Oddly Microbial: Ribocytes and Oddly Microbial: Cancer Cells. Comments and suggestions are encouraged.

Sediment thickness_lge

Life in a high-pressured environment with practically nothing to eat might be ok for high-fashion models, but it’s an unlikely lifestyle choice for a single cell whose usual overriding goal is to become two cells. Yet the largest living ecosystem on Earth—the deep biosphere—is comprised of microbes so energy starved that the average cell divides only once every thousand or even several thousand years.

Continue reading "Oddly Microbial: 86 Million Year-Old Deep Seabed Mystery Cells" »

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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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