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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December 16, 2013

Retrospective, December 2013

We continue our semi-annual ritual and post this quick tour of our featured blog posts published since June 2013.

Figure1
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Evolution

Microbial ‘Starstuff’. Associate blogger Gemma Reguera tells us how the remnants of a dying star become transmuted into microbial stuff, including cellular structures such as magnetosomes. One universe it is.

Who Would Have Thought? Biggest Flower, Biggest Gene Thief. The world’s largest flowers, about 1 meter across, are chock-full of genes acquired by lateral transfer. The plants that make these flowers are parasites of other plants, which may have something to do with this wholesale theft.

Parallel ERV-Mediated Evolution of Blue Egg Color in Chickens. We reprint here a delightful blog piece by Robert Gifford on how the blue color of eggs of the native chickens in Chile is due to an endogenous retrovirus. Moreover, a separate ERV insertion accounts for the blue egg color in Asian chickens. Many other avian genes are also affected by ERVs.

Fine Reading: Exploring the Microbial Dark Matter. Merry discusses the huge blank regions in our canvas depicting the microbial world. How much is left to explore!

Figure2
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Structure and Function

Oddly Microbial: Programmed Cell Death. There’s evidence thateukaryotic apoptosis evolved from the bacterial forerunner. Microbe sleuth Marcia Stone uncovers the little known fact that bacteria carry metacaspases, the prokaryotic equivalents of caspases, the eukaryotic agents of apoptosis, and tells us why this matters.

Programmed Cell Death. Associate Blogger Marvin looks at the different ways that various bacteria manage their own programmed cell death. This prompts one to ponder what happens in nature, where bacterial populations are almost always mixed.

 

It’s Time for Salmonella. Ah, circadian rhythms…Chronobiologist extraordinaire Susan Golden tells us that the circadian rhythm of the mouse determines Salmonella pathogenicity, with serious consequences for the outcome of their attempted invasion of the gut.

Vesiculation: Another Bacterial Skill. Most Gram-negatives shed bits of their outer membrane in the form of spherical vesicles. These packages function as a delivery mechanism for cellular proteins and DNA—a mode of chemical communication with other bacteria and host cells.

The Microscopic Flash Mob. Micrococcus makes waves. That is, they form ripples during their life cycle. Graduate student Melissa Wilks explains how and maybe why.

A Bacterial Body Clock: Cryptic Periodic Reversals In Paenibacillus dendritiformis.Graduate student Monika Buczek relates that these amazing motile creatures reverse  directions every 20 seconds while swarming. Both the how and the reason why remain elusive.

Figure3
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Pathogenesis

Aggregatibacter actinomycetemcomitans: A Unique Exotoxin-Producing Oral Bacterium. We borrowed this piece on an interesting oral pathogen from the blog Microbios by Pedro Valero Guillén. This organism clings to other bacteria and makes some fascinating toxins.

Polymicrobial Infections: Perhaps the Rule, Not the Exception. Graduate student Katy Patras notes that there are good reasons why many successful microbial infections are polymicrobial. Working together, relying on a variety of molecular mechanisms to confound our immune system and increase virulence, pays off for many pathogens.

Mtb Craves Sweets. There seems to be no end to the list of bacterial virulence factors. To the ones known for the tubercle bacilli, add protein-O-mannosylation of surface proteins. Associate Blogger Marvin explains.

Seeing How Antibiotics Work. Using sophisticated microscopy and clever thinking, the Pogliano labs develop a quick, high throughput way to screen compounds for antimicrobials and then characterize their mode of action.

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Microbial Diversity

The Planctomycetes, Tricky Gram-negatives Awaiting Genetic Manipulation. The planctos are a weird group of bacteria—outliers, you might say. Graduate student Marco Allemann discusses how they may differ from other Gram-negatives, how they may be the same.

A Whiff of Taxonomy – Archaeoglobus fulgidus. Hyperthermophilic archaea are always interesting, and this one is no exception. It excels at reducing perchlorate.

Figure5
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Ecology

Fine Reading: The Second Skin – Ecological Role Of Epibiotic Biofilms On Marine Organisms. Nice place, the ocean, for microbes to thrive. And thrive they do, especially in biofilms, as per a paper that discusses this in some detail.

Antarctica's Deep Lake: A Frigid Home for Steadfast Archaea. There is a lake in Antarctica so salty that it never freezes. Here live a relatively small number of Archaea, particularly adept at wholesale gene swapping.

Let There Be Light! Associate Blogger Marvin discusses how bioluminescence produced by symbiotic bacteria regulates the circadian rhythm of their host, the Hawaiian Bobtail Squid.

Weathering the Storm…the Archaeal Way. Graduate student Mike Manzella introduces us to the world of Archaea that have been trapped in salt crystals for eons, only to be reawakened some 30,00 years later. When convinced to grow in culture, they change in shape and ATP content from their crystal-encased state, pointing to physiological challenges for survival in such conditions, but also challenging researchers to prove their authenticity.

E. coli Keeps Its Powder Dry. Strangely enough, E. coli carries genes for the degradation of some sugars but does not express them in the lab. Marvin discusses a finding by S. Mahadevan’s lab that explains what’s going on. In the environment, the bacteria cleave plant sugars to make aglycones that inhibit both bacteria-eating slime molds and worms.

Figure6
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Viruses

Teaching Pseudomonas to Endocytose. Endocytosis seldom happens in the prokaryotic world, butRNA phages of Pseudomonas syringae enter their host by just such a mechanism. In sharing this story, Merry Youle suggests that bacterial membranes are not loath to invaginate, given a little prompting by a phage.

Oddly Microbial: Giant Viruses. Marcia Stone explores the stunning world of the megaviruses whose virions are larger than many bacteria and whose genomes provide food for ample evolutionary thoughts.

Figure7
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Fungi

Mycorrhizal Fungi: The World’s Biggest Drinking Straws and Largest Unseen Communication System. High on the list of amazing feats of life is the formation of continuous networks of mycorrhizal filaments spanning areas approaching a whole continent. In addition to carrying water and nutrients, they serve as conduits for signaling molecules between plants.

FUNGUS WEEK
A Whiff of Gastronomy. Truffle oil—is it worth spritzing it on your food? Elio thinks so, as long as you’re aware that it’s not quite the real thing.

Count Your Mushrooms. You knew all along that the mycelia of mushrooms far outweigh the mushrooms they produce, but here are some numbers.

Radiation Ahead? Eat a Black Mushroom! Incredible! Fungi can use radiation as a source of energy, with melanin as the antenna! It follows that ingested black mushrooms containing melanin should be radioprotective. They are, when fed to mice.

Miscellanea

Figure8
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Recommendese. Elio grouses about inflation in letters of recommendation but offers no solution to this problem.

Gut Lecture. Elio is being cantankerous again and tells us that he doesn't like to lecture on the human microbiome and why.

Recalling the Good in the Good Old Days. Elio recalls how Salvador Luria chose to present other people’s work at a seminar instead of his own.

Good Old Days # 2. Bob Murray reminisces about the way science used to be done, often in the middle of the night, plus he shares a letter to him from Josh Lederberg.

Books for the Giving Season: Viral Readings. Daniel Haeusser reviews two books on viruses written for the general public, in time for your holiday shopping.

Abigail Salyers (1942-2013). We acknowledge the passing of an outstanding microbiologist.

June 17, 2013

Retrospective, June 2013

We continue our semi-annual ritual and post this quick tour of our blog posts published since December, 2012.

Figure1
Pretty picture. Source.

Pictures Considered

Our new section dealing with “pictures that made a difference but may be nearly forgotten by now” seems to be off to a good start. Please send us suggestions of pictures you think should be considered.

 #1. Visualizing Coupled Transcription and Translation in E. coli. A single EM demonstrates that transcription and translation are coupled in prokaryotic cells.

 #2. The E. coli Chromosome Caught in the Act of Replicating. One radioautograph suffices to show that the E. coli chromosome is circular.

 #3. How Do You Know There Is a Nucleoid? Nucleoids are visualized in living E. coli cells by using the simple optical trick of increasing the refractive index of the medium.

#4. Koch’s Development of Early InstaGram Positive Photography. Associate blogger Daniel unearths one of the earliest photomicrographs of bacteria, taken by none other than Robert Koch.

#5. The Birth of the FtsZ Ring. Using gold-labeled antibodies, FtsZ, the mother of bacterial cytoskeletal proteins, was found to localize at the septum of E. coli during cell division.

Continue reading "Retrospective, June 2013" »

December 17, 2012

Retrospective, December 2012

We continue our semi-annual ritual and offer this quick tour of our blog postings since our June 2012 Retrospective.

Figure1
Mosquito larvae. Source.

Pathogenesis

Galectin 8: The Cell’s New Sheriff?
Graduate student Andy Cutting delves into the arcana of autophagy and explains why it matters to Salmonella.

Fishing With Algae For Malaria Vaccines
Making a vaccine for malaria, one of humanity’s scourges is a matter of great urgency.  James Gregory discussed how algae can be used to make an effective antimalarial vaccine.

A Kick in the Midgut
Another strategy for subduing malaria would be to kill the parasite as it wanders though the mosquito. Fellow blogger Marvin Friedman tells us about a pertinent experiment.  Be prepared for some mosquito anatomy.

Continue reading "Retrospective, December 2012" »

June 04, 2012

Retrospective, June 2012

We continue our semi-annual ritual and post this quick tour of featured blog postings since our December, 2011, Retrospective.

Computer virus

Source.

Viruses

It’s Raining Viruses! (Merry) Metabolic genes acquired from their hosts are one strategy used by baculoviruses to convert one caterpillar host into more than 109 progeny viruses.

The Immunological Synapse Goes Viral. (Merry) Once again, a virus coopts some of the sophisticated functions of our immune system and turns them against us. In this case, HTLV-1 gains an efficient mechanism for cell-to-cell transfer.

Onboard a Flying Syringe. (Merry) Insect vectors carry viruses that infect our crops as well as us. Metagenomics provides a way to query the insects and find out who is onboard.

Wily Phage Trumps Host Toxin. (Merry) Toxin-antitoxin systems are part of the bacterial arsenal of anti-phage defenses, but phage T4 carries its own antitoxin.

Ecology_lichen

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Ecology

That Scary Restroom Microbiota. Josh Fierer and Elio take exception to the scary news headlines generated by a metagenomic study of bacterial DNA in a restroom. Bugs in a bathroom? Surprise!

The Paenibacillus Moving Company. (Elio) This master swarmer can carry cargo, in this case fungal spores. It can also move across space on bridges made of fungal filaments.

Peer Pressure Induces Biofilm Production. Biofilm formation, cannibalism… anything to postpone sporulation. Marvin Friedman explains.

What’s the Score on the Microbiome? (Elio) Is the human intestinal microbiome a good thing or a bad one? We kept score for a little while.

Green Flypaper. (Merry) Social spiders use yeast to attract more flies to their web. This strategy works so well than local people bring the webs into their homes to act as flypaper.

One If by Land and Two If by Sea. Marvin tells us how bacteria abandoned the oceans and wandered on land, genome-wise.

Keystone_arch_224

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Function and Structure

Pushing the Thermodynamic Envelope into the Proteomic Edge. Why is the temperature for maximum growth rate of bacteria so close to the one at which they die? Graduate student Tracey McDole explains this in terms of entropy, enthalpy, molecular crowding, and other goodies.

Microtubules in the Verrucomicrobial Closet. Once again, cryo-electrontomography comes to the rescue, here revealing the existence of tubulin-containing filaments in a prosthecate bacterium. Daniel Haeusser explains

The Three Faces of Thiomargarita. (Merry) Sulfur-oxidizing Thiomargarita may form clusters or chains or live as sessile cells with a complex life cycle, and all three ‘faces’ of these “sulfur pearls” are beautiful.

Polar Enchantment. (Elio) How to isolate proteins that prefer to be at the poles of bacteria, thanks to a clever technique from the Kevin Young lab.

If It Walks Like DNA, and Talks Like DNA… (Merry) Both plasmids and phages have mastered the art of making proteins that mimic DNA, thus confusing host restriction endonucleases that would otherwise destroy their incoming DNA.

Living On the Edge…of the swarm. Gemma Reguera describes tricky aspects of the physics of bacteria swarming on agar.

Cell Division Through DNA Curtains. FtsK is a somewhat mysterious protein that couples chromosome replication with segregation. Gemma introduces a clever single-molecule technique that allows one to visualize FtsK’s gymnastics. 

Bacterial diversity cell phones and shoes

Bacterial diversity of cell phones and shoes. Source.

Microbial diversity

Fine Reading: Houses Made by Protists. (Elio) Single cell architects make stunningly large and complex structures for protection.

Ovobacter propellens, Not Your Average Boring Bacterium. (Elio) The fastest known swimmer among bacteria, this poor fellow has not received its due attention.

Pathogenesis

Salmonella’s Exclusive Intestinal Restaurant. (Elio) Salmonella has a unique skill: it can use tetrathionate as an electron acceptor. It’s also pretty good at oxidizing an abundant i substrate in the gut, ethanolamine.

Are Phages the Answer? Given that more ways of fighting bacterial pathogens are needed, the old idea of using phages reemerges, thanks to both Pseudomonas biofilms and a mouse study, as discussed by Marvin.

Fine Reading: Autophagy & the Cytoskeleton. (Elio) Escaping into the cytoplasm of host cells is a device used by some bacteria to avoid autophagy. The host cells respond by coating the bacteria with a protein called septin, which makes them autophagiable.

TB or not TB? Graduate students Jaime Zlamal, Andy Cutting, and Steven Quistad describe the asymmetric cell division of mycobacteria and why this may matter with regard to therapy.

What Happened to Our Friendly Enterococci? (Merry) Pathogens can gain by losing their CRISPR loci, as this makes it easier to pick up plasmids and other mobile elements bringing antibiotic resistance factors.

Evol_graph

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Evolution and Genetics

Oddly Microbial. Marcia Stone reviews a book by Michael Yarus, Life From an RNA World, with emphasis on ribocytes, those elusive early cells postulated to have existed “way back.”

The Bacterial Resistome is Both Ancient and Surprising. Marvin tells us that bacteria from caves that have been isolated for eons possess antibiotic resistance genes, including resistance against our new drugs.

How to Reform a Resistant Bacterium. (Merry) Picture this strategy: use temperate phages to deliver dominant antibiotic sensitivity genes into antibiotic resistant pathogens. These researchers offer this as a way to reduce antibiotic-resistant nosocomial infections in hospitals. 

Fine Reading: Nematodes & HGT. (Elio) Nematodes are good at acquiring bacterial genes. Horizontal gene transfer across domains?

Sex to the Rescue. (Elio) Hyperthermophilic archaea, when treated with DNA-damaging UV radiation, sprout pili and make cell aggregates that promote recombination between cells.

On Retrons. Habib Maroon introduces us to features of these mysterious prokaryotic retroelements, also known as multicopy single-stranded DNA/RNA hybrid molecules.

Fine Reading: Small Wonders. Merry offers a fine review by McCutcheon and Moran on why and how bacterial endosymbionts end up with such puny genomes.

Miscellanea

What Is This Link to Mushrooms in Works of Art? Well, that’s one of Elio’s interests. He thinks one can learn about the connection between people and mushrooms by looking at paintings.

Where Mathematicians & Biologists Meet. Biomathematician Joe Mahaffy enlightens us about the distinguished historical connection between biology and mathematics.

The Two Quantitative Steps in the Biology Growth Curve. (Elio) Biology has been invaded twice by physicists and mathematicians in the last several decades. The first wave led to the advent of molecular biology, the second (now) to a lot of useful model making.

December 19, 2011

Retrospective, December 2011

We’ve prepared this quick tour for you, with brief visits to all the major articles we posted since our May, 2011, retrospective.

BehaviorBasedInterview
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Microbial Behavior

Are You Me or Am I You?  Proteus mirabilis is one sentient bug: it can distinguish itself from its parents and relatives.

Ringing a Microbial Dinner Bell.  Bacteria make smelly stuff, some of which provides appetizing cues for insects. Associate blogger Mark Martin explains.

Labeled-microscope-diagram

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Structure and Function

Hard Biology.  How do diatoms make their glass-hard shells? Well, they assemble subunits within the cells, then export them and insert them into preformed structures.

Some Like It Curved.  How do bacteria make curves in their cell wall? It turns out that cardiolipin is a curved and curve-inducing lipid molecule found in the curvilinear cell poles of rod-shaped bacteria.

Rafting Through Time.  Do bacteria have lipid rafts in their membranes, a la eukaryotic cells? Possibly.

Vital or Not Vital: That Is the Question.  Guest Gemma Reguera clarifies the confusion about what is viable and what is vital, including what ‘vital dyes’ tell us about such states.

Virus_collage
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Viruses

Virus Hacks Intercellular Communications Network.  Cells of our immune system talk to each other when mobilizing a defense, but vaccinia has many clever ways to tamper with those messages for its own benefit.

Is a Good Offense the Best Defense? Yeasts have to choose between having RNAi to defend against incoming viruses and such, or hosting killer viruses that eliminate the competition.

Phage Lambda’s Polar Expedition.  Are all regions on the surface of an E. coli equally inviting to an adsorbing lambda phage, or does lambda have a preference?

Phage DNA: Going with the FlowTo launch an infection, a phage needs to transfer its DNA into the host cell, but a phage is not a hypodermic needle.

And We Thought We Knew What CRISPRs Do!  Here’s a new twist. A prophage in Pseudomonas aeruginosa inhibits biofilm formation and the host’s CRISPRs are required.  

Now That's Using Your Head!  We thought all tailed phages use their tails to recognize and attach to their host cells, but here’s one that uses its head instead.

Viruses that Infect Parasites that Infect Us: The Matryoshka Dolls of Human Pathogens.  Graduate student Jamie Schafer takes us, layer by layer, through two stories of viruses that infect parasites that infect us, both with possible clinical implications.

Food-borne
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Pathogenesis

A Pestis from the Past.  Associate blogger Marvin Friedman recounts the history of the Great Plague, as illuminated by recent genomic studies of old bones.

The Lyme Disease Spirochete Feasts on Tick Antifreeze.  A fellow blogger, Microbe Fan, allowed us to use his article on how borrelias use of antifreeze in ticks as a nutrient. Who would have thought?

The Janus Bug.  And you thought that Helicobacter pylori  was a bad bug, causing ulcers and cancer! Well, it may also stimulate the immune response to protect people from asthma.

Going Next Door Without Getting Your Feet Wet.  By using novel techniques, Daniel Portnoy’s lab can introduce Burkholderia into a cell, thus bypassing early stages of infection and isolating later ones. New pathogenesis mechanisms are now revealed.

A Clever Bug That Is Difficile to Control.  Marvin Friedman discusses how Clostridium difficile adenylates its teichoic acids to ward off the action of host defensive peptides.

How We Tell The Good Bacteria From The Bad.  MD/PhD student Micah Manary tells us how the inflammasome (which some of us need to look up) is involved in selecting members of the intestinal microbiome.

Test-tube
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Genomics and Evolution

The Façade of E. coli K-12.  Nothing was thought to be less dangerous than the K-12 strain of E. coli. Guess again. It’s full of genes encoding factors that can be turned on in HU protein mutants.

Fine Reading:  Microbial Evolution.  On the 150th anniversary of publication of On the Origin of Species, 34 microbiologists met in the Galapagos to discuss the role of microbes in evolution.

Bacteria Activate Fungal Gene Clusters.  Cross-talk among very different organisms are the rage. Marvin Friedman presents another exciting example.

What’s Old is New: Genome Wide Manipulation of the Bacterial Chromosome in VivoGuest Michael Schmidt discusses a novel and clever way of manipulating the bacterial chromosome on genome-wide basis.

Ecology
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Ecology

Shipwreck Microbiology.  One shipwreck can devastate a coral reef for decades. The culprit? Iron leached from the wreckage.

One Size Sometimes Can Fit All.  And this is of great concern when it is one antibiotic resistance factor that can counter every antibiotic in our arsenal.

Some Like it Cold.  Marvin Friedman explains that the trigger factor protein (a chaperone involved in keeping nascent peptides from folding prematurely) is selectively upregulated in the cold.

Taking Bugs Out For a Spin.  Graduate students Linh Truong and Shabana Din describe the unexpected resistance of bacteria to very high g forces.

A Microbe By Any Other Name Would Smell As Sweet…  Mark Martin waxes eloquent on the subject of smells emanating form bacteria and their uses.

Symbiosis

Symbiosis-fish
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A Bug in a Bug in a BugBacteria living inside bacteria? Astounding as this sounds, you find them as nested endosymbionts of mealy bugs.

Wolbachia: The Difference Between a Nuisance and a Threat?  Graduate student Jamie Shafer tells a great story about a phage altering how the endosymbiont Wolbachia affects its insect host.

A Wormful of Bugs.  Here’s another example of an animal that considers a gut obsolete. Instead, it employs a sack of densely packed bacteria that feed it by oxidizing sulfur.

Fungi0012
Source.

Fungi

The King of the FungiImagine a fungus half the size of a bowling alley growing from a fallen tree. A big tree.

Fungi That Spit Like Baseball PlayersGuest Gemma Reguera reveals new insights on how mushrooms shed their spores. Fast! Very fast!

How to Escape a Deadly EmbraceThere lurk fungi in soils that can trap nematodes. Aha! The nematodes have evolved an escape tactic.

Curiosa
Source.

Miscellanea

How to Improve Vaccines (or Not), 1912 StyleAntibodies, it turns out, make a toxic vaccine less toxic. So it was thought 100 years ago, and now we find out that this holds up.

Fine Reading: Microbial Genomics and Infectious DiseasesWe call attention to a seminal paper by David Relman on this topic.

Preaching to a Prokaryotic ChoirMark Martin directed some probing questions about the microbial world to students in his undergraduate micro class and shares with us the results.

Of Terms in Biology: RiboswitchTwenty classes of these talented RNAs are known, and they do interesting and diverse jobs.

The Microbial Weltanschauung. Elio muses on the effect of knowing that there are so many prokaryotic cells on this planet.

May 23, 2011

Retrospective, May 2011

From December 16, 2010, to May 16, 2011.
Another six months, another 50-plus posts, another retrospective.

Biofilm
Biofilm. Source.


Ecology and Evolution

Energetics of the Eukaryotic Edge. Frank Harold discusses why eukaryotes have differentiated so much more than prokaryotes. They have a way of making more energy available per genomethe mitochondria.

Frost Flowers Come to Life.  Jody Deming introduces us to unexpected microbial communities: biofilms under ice. A heartwarming finding!

Cyanobacteria:  Growing a Green Future Around the Clock.  Graduate students Spencer Diamond and Britt Flaherty explain how cyanobacteria break down their inactive photosynthetic enzymes at night and their nitrogen fixing ones during the day, all for the sake of saving their precious limited cache of iron.

Fine Reading:  When Microbial Conversations Get Physical.  We called attention to an inspired article by Gemma Reguera about how bacteria communicate via physical signals, not just chemical ones.

Bacterial History Found in Ancient Mud Scrolls.  Did you ever wonder why dry mud cakes curl up? It’s because of the goo made by cyanobacteria.

A New Game for a New Year.  Arsenic DNA? What ever happened to that?

My Geological Ignorance.  Elio admits to having spent most of his life in blissful ignorance of geological matters and tells us why this is a dirty shame. 

Geobacter: Microbial Superhero.  Suzanne Winter tells us of the marvels of this metal-eating bacterium and its glories, including its electrical skills.


Prokaryotic Structure and Function

Ecoli2
E. coli. Source.

Beyond the Bacterial Microcompartment.  Smaller still, these nanocomparments are porous icosahedral protein shells are still large enough to enclose a protein payload and sequester a metabolic activity. Their structural similarities to viral capsids raise intriguing questions.

Coping with Hard Times: Death as an Option.  The toxin-antitoxin system is not only widespread in the bacterial world, but it also depends on quorum sensing. It’s turning out to be a big deal.

Precious Metals.  What if you cast a wide net to look for unexpected metals in bacteria and archaea? You would find twenty-one of them!

Hedging Your Bets.  Bacteria that are born genetically equal aren't necessarily phenotypically the same. Simple regulatory circuits can lead to mixed populations of cells in different stable states, thus making the population better able to cope with environmental changes.

A Protection Racket.  Restriction-modification (R-M) systems can protect a bacterium from infection by some phages, but it could be the "selfish" R-M systems that benefit the most.

Going to Great Lengths.  Bacteria are indeed small things, but they have some very large genes encoding some exceedingly large proteins.

Microbial Embraces.  The Borrelia of Lyme disease embrace one another by fusing stretches of their outer membrane. Is this biologically relevant?

Some Like it Hot.  Marvin Friedman, our newest associate blogger, returns to the age old question of how proteins of hyperthermophiles are so stable. Posttranslational methylation of lysines may be involved.

Influenza
Influenza virions. Source.


Viruses

Endless Forms Most Viral.  In his Perspective piece originally published in PLoS Genetics, Welkin Johnson introduces the exciting evolutionary stories being unearthed in genomes by paleovirologists.

Worms Have Viruses, Too!  Once again we borrowed a post from the blog by Manuel Sánchez, Curiosidades de la Microbiología, this one reporting that viruses have now been found that infect that stellar model organism, C. elegans.

A Viral Pyramid Scheme.  The archaeoviruses that infect Crenarchaeota in volcanic hot springs are eccentric from start to finish. To lyse their host cells and release their virions, they form distinctive 7-sided pyramids on the cell surface.

Six Questions About CRISPRs.  In the three years since our previous post on these anti-viral defenses, much has been learned about how CRISPRs protect Bacteria and Archaea from viral infection. Researchers, too, are using CRISPRs as a "fossil" record that reveals the evolutionary history and previous viral encounters of their host cells.

Haeckel-array-1
Haeckel’s Radiolaria.


Eukaryotic Microbes

Farmer Joe Dictyostelium.  This slime mold feeds on bacteria. To ensure that future generations will be provided with this food, they carry some of the bacteria as “seeds” during differentiation.

Candida's Unstable Chromosomes & Unorthodox Sex.  Dean Dawson discusses this yeast’s unorthodox sex life. Here, fusion of diploid cells leads to a vast array of chromosomal rearrangements. 

Targeting an Achilles' Heel of Plasmodium.  Marvin Friedman reports how P. falciparum obtains its isoleucine and why this matters to their drug resistance.


Pathogens, In And Out of Humans

Pathogenesis
Source.

Pneumococcus:  Nature’s Tiniest Cheat.  Graduate students Brandon Kim and Jon Sin discuss the guiles of the pneumococcus, how it removes sialic acid residues from competing bacteria, thus keeping them from adhering to host cells.

Designer Genes for Special Bacterial Lifestyles.  Marvin Friedman discusses how some pathogens underwent genome reduction, others didn’t. It depends on their lifestyle.

Gut Microbes and the Infant Brain: A Surprising Symbiosis. Micah Manary,  an MD/PhD student, delves into the finding that the gut microbiota influences the development of the nervous system, no less.


Miscellanea

Miscellanea-warehouse-L
Source.

We’ve Figured It Out!  After many decades, Elio thinks he and his friends have figured out a novel way to teach a graduate coursehave an expert present each lecture!

Highlights of 2010.  Some friends and colleagues answer our query and tell us what was their favorite microbiology research paper in 2010.

Of Terms of Biology:  Colloids. Stefan Klumpp explains the meanings of this venerable term.

 

December 13, 2010

Retrospective, December 2010

This blog is now entering its fifth calendar year, surely a respectable age for a blog, perhaps bordering on the venerable. With the passage of time, our blend of posts has included more and more contributions from guest writers, some from young students, others from experienced and distinguished microbiologists. In other words, this blog has become a bit of a forum where people of different backgrounds and experience can share their excitement for the world of small things. We hope that as this blog enters its next year it will continue to provide you with microbial joys.

As is our tradition, we present here a lightly annotated list that includes most of our posts from the past half year.

Flu_virus

False colorized influenza viruses in DCK cells.
Credit: Centers for Disease Control/C. Goldsmith,
J. Katz, and S. Zaki. Source.

Virology

Physical VirologyManuel Sanchez tells us how physical measurement can be carried out on a single virus particle, revealing differences in how far a virus can be pushed around. We borrowed this piece from his blog, Curiosidades de la Microbiología.

Tales of DeathSome Bacteria have turned the burden of viral infection into an opportunity. They have co-opted the elaborate phage tail structures for their own use, for killing specific target Bacteria and, sometimes, even larger game.

 A Giant Among GiantsMimivirus made a big splash, but a whole host of giant viruses have been found, mostly in aquatic environments, and more are being discovered all the time. Their genomes carry hundreds of genes, many of them unexpected for a virus.

A Fastidious BacteriophageMichael Yarmolinsky brings back phage Chi from near oblivion. This coliphage attaches to a host's flagellum and then makes its way to the cell surface, taking advantage of the flagellar rotation.

Dr. Rous’s Prize-Winning Chicken.  Welkin Johnson celebrates the 100th anniversary of Peyton Rous's discovery of an oncogenic virus, now known as the Rous sarcoma virus.

When the End Is the StoryWelkin Johnson tells us that HHV-6 is unique among human hespesviruses in being integrated into our chromosomes. Not only that, it prefers the telomeres!

Promiscuous Bacteria & Viral PlayboysOccasionally, phages carry bacterial genes from host to host—one of the mechanisms for horizontal gene transfer between Bacteria. Looking at single bacterial cells, researchers found that genes were delivered more often than we realized, and even to non-hosts.

Continue reading "Retrospective, December 2010" »

May 24, 2010

Retrospective, May 2010

As is our tradition, we present here a lightly annotated list that includes most of our posts from the past half year.

Jiang-bacteriophage
Phage Epsilon15 at a resolution of 4.5 Ǻ. Source.

Viruses

Viral Turtles. Viruses with dsRNA genomes enter host cells, capsid and all, and then keep their capsid intact as a safe workshop in which to transcribe their genes. A neat strategy for evading host defenses!

Paleovirology. Associate blogger Welkin Johnson takes along on a historical tour of the endogenous retroviruses of mammals, and from there it is but a short hop to the surprising recent discovery of Bornavirus sequences in the human genome.

A Most Lively Virus. How about that? A virus that sprouts two l-o-n-g tails all on its own, after exiting from its host. Just another one of those wonders from the world of hyperthermophilic archaea and their viruses.

A Holin One. Holins, phage-encoded enzymes that lyse the host cell by making holes in the membrane, don't just make small pores. They make huge fissures that allow other phage enzymes to rapidly attack the cell wall and let the phages out.

Time’s Up. Phage infections are precisely orchestrated, even to timing the moment of cell lysis. We visit holin-land, and there learn that these small proteins end the game at just the right time.

Prophage Masquerade. Does that bacterium have any prophages on board? Not an easy question to answer. Prophages come in various forms, some inducible and some not. Some may even have been co-opted by their host and put to work as gene transfer agents for their genes.

Five Questions About Lysogeny. We found some intriguing answers to our questions. Lysogeny can benefit both phage and host, and may even play a key role in microbial evolution.

Symbiosis

Clown fish2
Source.

Autumn Leaves. Leaves of your favorite tree are turning yellow, thus shutting down your pantry (if you’re a caterpillar ensconced inside a leaf). What to do? Use your endosymbiotic Wolbachia to produce cytokines that keep an island of the leaf green (and nutritious).

Leaf-Cutters Get Their Fix (nitrogen fix, that is). You know that leaf-cutting ants are terrific at eating the fungi they cultivate in their gardens. But where do they get their nitrogen from? Could it be from nitrogen-fixing bacteria? Looks that way.

Genomics

And The Winner Is… The most abundant gene in the known universe? Transposase!

Microscope

Source: Museum of the History of
Science, Oxford.

History

Did van Leeuwenhoek Observe Yeast Cells in 1680? Nanne Nanninga examined letters and other historical material, then concluded that “our founder” actually saw yeast cells in his beer.

A Matter of Timing: Yellow Fever and the Mosquito Hypothesis. Associate blogger Welkin Johnson leads us through the maze of how yellow fever is transmitted and points to the role that this discovery played in the birth of modern virology.

A Close Encounter of the Enological Kind. John Ingraham regales us with a story of how he discovered the wine taste-correcting bacterium, Oenococcus oeni, of malolactic fermentation fame.

How Proteomics Got Started. The first to use proteomics to study bacterial physiology, Fred Neidhardt shares with us tales from those early days.

Biohazard-symbol-logo-danger-3
Source.

Pathogens

All Is Fair in Love and Warfarin. Graduate students Shigeki Miyake-Stoner and Spencer Diamond found it exciting that tubercle bacilli have a homologue of a protein called Vitamin K epoxide reductase, the target for warfarin. Sure enough, this drug affects the growth of M. tuberculosis.

Eukaryotes

Naegleria’s Split Morphology Disorder. Borrowed from the blog Skeptic Wonder by Psi Wavefunction is this tantalizing description of the cellular shenanigans of Naegleria that enjoys changing from an amoeba to a flagellate in a short two hours.

Mother’s Love. Budding yeasts have an advantage over cells that divide by mere binary fission: the bud and the mother cell are distinctive physical entities with different fates. Damaged proteins are removed from the buds and sequestered in the mother cells.

True or False: All Metazoans Need O2. False. Small metazoans called Loricifera thrive in an anaerobic brine lake at the bottom of the sea off Crete.

Physiology & Cell Structure

LatticeArchipelogics_1

From the Latent Utopias exhibition from the
Steirischer Herbst in Graz, Austria. Source.

Everyone Rowing in the Same Direction. We revisit the multicellular prokaryotes, this time focusing on the recently-described group that navigates by negative phototaxis rather than magnetotaxis.

When Crenarchaeota Divide, They Multiply. Graduate students Jenn Tsau and Suzy Szumowski tell us of another archaea-eukarya connection: they both have ESCRT proteins. In eukaryotes, these act as an “endosomal sorting complex required for transport,” but in some archaea they may participate in cell division.

On the Continuity of Biological Membranes. Frank Harold, whose concepts of the cell have influenced the thinking of many, has graced our pages with another insightful and discerning essay on the origin of membranes. A must read, if you missed it before!

Of Archaeal Periplasm & Iconoclasm. Elio likes to think he is an iconoclast, and he is in good microbial company. Counted among the iconoclasts surely would be the thermophilic archaeon Ignicoccus hospitalis, which has energy producing-machinery on the outer of its two membranes.

Measuring the Strength and Speed of the Microbial Grappling Hook. Graduate student Amber Pollack-Berti (the blogger of Tiny Topics) describes how to measure the force exerted by a bacterium when it retracts its Type IV pili.

Through the Looking Glass: Silicate in Bacterial Spores. Silica and anthrax—sounds familiar? Weaponized spores? Peter Setlow explains that silicates are found naturally on such spores.

Mysteries of the Bacterial L–Form: Can Some of Them Be Unveiled? Hans Martin enlightens us about the mysterious survival abilities of these aberrant bacterial forms. They seem to make some peptidoglycan in the presence of penicillin, using drug-resistant enzymes.

Kryptonian Vision. Frequent contributor to this blog, grad student Jennifer Gutierrez explains (somewhat heroically) how an X-ray microscope works and what we might be able to see with X-ray vision.

Ecology
Source.

Ecology

You Are What You Eat. Eat seaweeds and you're apt to have gut bacteria that have acquired genes for the enzymes needed to digest their unique polysaccharides. So write graduate students Karen Schwarzberg and Mike Gurney.

Cryptic Life in the Antarctic Dry Valleys. We contemplate the microbial life in the most barren of lands in Antarctica. A surprisingly diverse group of stalwart organisms eke out a sheltered existence within the crevices of the rocks, and even beneath translucent stones.

Odds_8
Source.

Odds & Ends

State Microbes. In the wake of Elio's interviews on National Public Radio‘s All Things Considered about official state microbes, we’re having fun hearing from readers which microbes they deem most suited for their state (or city or country). Our favorite? Actually a “City Microbe,” Clostridium botulinum, for Los Angeles, for providing botox to embellish the locals.

The Attendee's Guide to Scientific Meetings, Part II. A second installment from Julian Davies counseling us on how to survive (and even thrive) at large meetings. Good advice presented in a humorous capsule.

Of Terms in Biology: Gene Ontology. The au courant bioinformatics-savvy phylogenomicist knows that this is how you categorize all that information.

December 14, 2009

Retrospective, December 2009

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

Methodology

Old_microscope

Exciting Resolution. Forget what you learned in school about the limits of the resolving power of the optical microscope. We can now go beyond that. Jennifer Gutierrez explains how it’s done (without breaking the laws of physics!)

The Ten Minute Leeuwenhoek Microscope. Patrick Keeling shows you how to have fun in class with all hands busy making functional microscopes.

The Limitations of LB Medium. Hiroshi Nikaido sets us straight on reasons why, if you just made a batch of LB broth by carefully weighing the ingredients, adjusting the pH, and autoclaving it, you should now pour it down the drain.

Ecology_splash

Source.

Ecology

Marine Archaea and the Nitrogen Cycle. Doug Bartlett reveals that archaeal consortia in the bottom of the sea fix nitrogen and contribute to the nitrogen cycle.

There’s Gold in That Periplasm. Bacteria mine gold. They convert toxic Au(III) complexes to insoluble (and mineable) Au0.

Small Friends of Fungi. Animals eat plants, big animals eat small ones. End of story, right? Not so fast, says Bob Mesibov. Most plant detritus (leaves, twigs, etc) is consumed by fungi and bacteria, what he calls the Dead Plant Society, and not by the Green Feeders Guild.

The Spider's Guide to Predator Deception. Some spiders make conspicuous decoys that look like themselves. Predators beware!

Crocodile-plover2

Source.

Symbiosis

Condominium plant. Some plants in tropical rainforests provide both food and living accommodations for their ant symbionts in exchange for protection from herbivory.

All For One and One For All. Plants that grow at 50°C? Would you believe that to do it they need the help not only from a fungus but also from its viruses. Mark Martin explains.

Good Guys, Bad Guys. Pea aphids (bad guys) feed on our crop plants and are, in turn, preyed upon by parasitoid wasps (good guys). Not to be so readily defeated, some aphids host an anti-wasp defense team: a bacterial endosymbiont that carries a toxin-producing phage.

Myco-kleptomaniacs. Bark beetles grow fungi on the walls of the channels they make in trees. One species doesn't bother to schlep fungal spores to its young. Instead, it swipes the fungi collected by other species.

Playing the Light Organ Two Ways. The light organ of squids that contains bioluminescent bacteria also is photosensitive. This allows for cross-talk between host and symbiont, and suggests possible mechanisms for regulating light emission.

An Iconoclastic Endosymbiont. Living within the Arizona cicada is an endosymbiont that has taken genome reduction very seriously. It currently holds the record for the smallest bacterial genome, a performance that raises more questions about genome evolution than it answers.

Life in a Big Mac. Numerous endosymbionts call the macronucleus of paramecia home. When their host digests its macronuclei following mating, the endosymbionts differentiate into an infectious form and go off in search of a new host.

Pathogens

Genomic Secrets of Phytophthora infestans. How come the Potato Blight Mold has a genome that is 3 to 6 times larger than that of its cousins?

A Mold That Changed The Course of History. The Great Potato Famine in Ireland caused the migration of millions of people to the US, all thanks to a lowly mold.

Natural bact colonies

Source.

Microbial Diversity

Five Questions About Oomycetes. They may look like fungi, but fungi they're not. Some even have ways to actively shoot their spores into a passing soon-to-be host.

Five Questions About Microsporidia. Patrick Keeling answers some of our questions, such as: Are they protists, fungi, or what? We learn that their genomes are small, their mitochondria but relicts—two factors that make them highly dependent on their host cell.

Physiology & Genetics

Getting a Handle on Cell Organization. Frank Harold examines two recent reviews on the organization of cells from the point of view of self-organization and experimental cell reconstitution. He brings to this task his keen insight and his way with words.

Location, Location, Location. The localisome (the intracellular location of everything) is being well studied in Caulobacter. Alan Derman takes us through what to believe and what message to take home.

Mycobacteria Make Spores? Peter Setlow examines critically this surprising claim.

Computer-viruses
Source.

Viruses

Mad Dogs and Microbiologists. The amazing story of Pasteur’s invention and use of the rabies vaccine is recounted by virologist/historian Bill Summers.

Smallest Things Considered. Viroids are infectious agents known to infect some plants where they replicate and sometimes cause symptoms of disease. Quite an accomplishment for a naked, single-stranded RNA molecule containing 246 nucleotides.

The Viral Selenoprotein Theory. Chitra Rajakuberan tells a story of surprises in the HIV genome. Pseudoknots allow making three unexpected proteins, all of which contain selenocysteine. Does this have to do with HIV infection? Do these proteins sequester selenium in patients?

A Matter of Timing: Yellow Fever and the Mosquito Hypothesis. Welkin Johnson recounts the sleuthing that demonstrated the transmission of yellow fever by mosquitos before the infectious agent itself had been identified. We are reminded that this pioneering work cost the lives of researchers and volunteer subjects alike.

Beaks-finch
Source.

Evolution

It Was the Worst of Times, It Was the Best of Times. Plants and animals died by the droves about 250 million years ago. What happened to their carcasses? Did fungi thrive on them?

Antibiotics

The Three Stages of My Experience in Discovering the Mode of Action of Penicillin. Ted Park takes us step by step though his discovery of how penicillin acts on bacteria—a rare glimpse into the workings of a creative mind.

A Call From Arms. Julian Davies argues convincingly that antibiotics did not evolve as microbial weapons, but rather as signaling molecules.

Protists

The Genes, The Whole Genes, & Nothing But The Genes. Ciliates are skilled genomic gymnasts. They disassemble, shuffle, and then selectively reassemble their germline genome to create a new workaday macronucleus.

Mushroom man

Source.

Fungi

Mycodiesel. Don't sell your oil stocks yet, but a tropical mold can make (some) diesel fuel from cellulose.

Fungal Stars in the Forest Dark. Some fungi give off an eerie light. We don't know why, but hunting for them, as Dennis Desjardins does, is illuminating.

A Thing of Beauty. Fossil fungi in amber are known to happen, but one specimen containing an Aspergillus is of rare beauty.

Lai_atlas_supporting_atlas

Source.

Fine Reading

The Good-Enough Clockus of Prochlorococcus. Unlike Synechococcus, the better-studied model of circadian rhythmicity, prochlorococci have a simpler clock, as elucidated by Ilka Axmann and colleagues.

The Biocentric View of the Microbial World. Ramy Aziz reminds us that by fancying ourselves to be the center of the biological world, we miss a lot.

In the Company of Ciliates. Ciliates and their resident bacteria furnish us with a profusion of tales of symbioses. The best studied ones are recounted here—to whet your appetite for more.

Of Terms in Biology

  • Neuston (a new one for you?)
  • Planktonic (as opposed to sessile. Bet you know these.)
  • Sympatric and Allopatric (familiar terms for those trained in classical ecology, and increasingly relevant for microbiologists)

Bikes

Source.

Odds & Ends

Biology By the Numbers. This is where to quickly find the numbers amassed by the counting or measuring of all things biological. But beware! Go here to retrieve one number, and you're apt to be lured into exploring farther.

The Leopard and the Mouse. Just when you thought you had seen everything, here’s a leopard in captivity that doesn't mind a mouse eating its food.

Fiddling with Fungi: And the
Winner Is…
Does fungal decomposition of wood make for better violins? You bet it can, given the right fungi.

June 15, 2009

Retrospective, June 2009

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

Language

Source

Of Terms in Biology

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

Question: Is this useful? Should we continue this?

Biodiversity2_2

Source

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.

Symbiosis_plant

Source

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.

Books

Source

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.

Darwintree

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.

Suited Up

Source

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.

Ecology-Man

Source

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.

Odds&ends

Source


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.

Teachers' Corner

Podcast

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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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