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 30, 2011

Hard Biology

Pleurosigma

Pleurosigma (a marine diatom). Credit: Michael
Stringer, Westcliff-on-Sea, Essex, UK. Source.

by Elio

For some time, I've had the urge to learn something about diatoms. They are dazzlingly beautiful, relatively easy to manipulate, and have left a fossil record immense in quantity. I never had followed up on this yen, so here’s my chance. A recent paper shed light on the way they make their hard shells.

Diatoms are busy creatures, accounting by their photosynthesis for about 20% of the global primary production of organic material, an amount comparable to that produced by the tropical rain forests. They are single cells contained within a shell made up of glass (silica), which is what gives many of them often stunning shapes. Silica does not readily decompose and fossil diatom shells accumulate in prodigious quantities. Such deposits can be hundreds of meters deep in some places (fossils by the truckload!). Diatomaceous earth, as the rock consisting of fossil diatoms is called, has a large number of industrial uses, such as filtering pool water, absorbing oil spills, as a mechanical insecticide, as a mild abrasive (it may well be in your toothpaste!), and even as a component of dynamite! And, as we will see below, diatoms also have novel and unexpected uses.

Continue reading "Hard Biology" »

May 26, 2011

Talmudic Question #75

What would the world be like without the Archaea?

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.

 

May 19, 2011

Of Terms in Biology: Aptamer

by Elio

Aptamer

A DNA aptamer nestled on its
target. Source.

Picture yourself looking for a molecule that specifically inhibits an enzyme, impairs the binding of a ligand to a receptor, or does some other such wonder. Classically, one thinks of antibodies, but these require a lot of work and are not easy to come by. Easier is to fish out the desired molecule from a large pool of oligonucleotides or peptides. You do this by mixing the gemisch with whatever target you have in mind and looking for what binds to it. In the case of oligonucleotides, the candidate molecules can then be readily amplified. What you get are called aptamers. Typically, aptamers bind to their targets with high affinity and specificity, comparable to that of monoclonal antibodies.

The term "aptamer" derives from the Latin aptus, to fit. RNA and DNA aptamers have the ability to form complex 3-D structures, which endows them with a high degree of specificity for the target molecule. Aptamers can detect very small structural changes in their targets, such as the presence or absence of a methyl or hydroxyl group, or different enantiomers. For example, an aptamer to theophylline binds with 10,000-fold lower affinity to caffeine—two molecules that differ by only a single methyl group (1,3-dimethylxanthine and 1,3,7-trimethylxanthine, respectively).

To look for nucleic acid aptamers, one screens a large library of oligos (containing as many as 1020 different ones, each usually 40-60 nucleotides long) by repeated rounds of selection and amplification. This is called the SELEX process. Since this is all done in a test tube, one can select for aptamers that work under specific binding conditions, such as salt concentration, pH, and temperature. SELEX can be automated. Usually, aptamers have a long shelf life plus they have other attributes that make them good candidates for therapeutics.

For a more detailed account, click here or here. If you want to see videos of live people playing the aptamer game or animations thereof, search for “aptamer” with Google Video.

 

May 16, 2011

Frost Flowers Come to Life

by Jody Deming

1_frost_flowers

Figure 1. Frost flowers growing on thin new sea ice in the
Amundsen Gulf, as observed from the CCG research icebreaker
Amundsen in December, 2007, during the International Polar
Year (IPY) Circumpolar Flaw Lead (CFL) system study. Credit:
Eric Collins.

Biofilms are the hallmark of microbial life in all manner of natural and engineered settings. The defining features of a mature biofilm include high densities of microbes, association with a surface, and extracellular polysaccharide substances (EPS)—often very specific compounds—that give architectural structure to these habitats. But what about early stages of biofilm formation. How many microbes does it take to make a biofilm, and how much of what type of EPS to provide structure? What if the involved surface can provide enough architectural structure itself yet is always changing? What if that “surface” is sea ice?

For literally centuries, polar explorers have been aware that in the springtime the bottom of seasonal sea ice becomes visible discolored. Today we know that what they were seeing is a photosynthesis-based biofilm of grand proportions. By March, when the sun spends enough time above the horizon to initiate the ice-algal bloom, the sea ice cover over the Arctic Ocean alone (sea ice also surrounds Antarctica, of course) extends more than 14 million square kilometers, even in this era of climate-driven reductions in the cryosphere. Only in the last decade, however, have we realized that this highly porous sea ice, flushed at its ice-water interface with seawater from below, is also filled with EPS, the sticky exudates of microscopic algae and bacteria that partially account for their entrapment in the ice as it forms in autumn and through winter. These compounds, which partition into the brine phase of the ice along with the microbes and other “impurities” of seawater, are now understood to serve a myriad of biological functions within the ice, from cryo- and osmoprotection to possible viral defense. As winter progresses and the ice chills to temperatures below –20 °C near its upper surface, this porous habitat undergoes marked physical changes. Whereas the warmer (–2 °C) bottom ice is still about 20% liquid, in the upper deeply frozen horizons of the ice the inhabitable volume is reduced to 2% or less. As a result of this temperature-driven process, microbes and everything entrapped in the ice with them become concentrated into increasingly small, cold, and briny pore spaces, with no obvious outlets even as ice crystals encroach.

Continue reading "Frost Flowers Come to Life" »

May 13, 2011

A Beef

EYECHART
A bovine eye chart. Source.

by Elio

I have a complaint. Scientific papers can be quite demanding to read. So, why make life more difficult by making the legends of the figures so hard to read? My big complaint is that when a legend pertains to multiple parts, the letters corresponding to them are nearly invisible. Try finding the (c), (d), or (e) in the legend. For heaven’s sake, what is so hard about showing these in bold letters? Besides, life would be simpler if there were fewer images or if they weren’t grouped so tightly.

Next time you write a paper, tell the editor that you want the letters in figure legends to be in bold face. Thank you in the name of all of us.

May 12, 2011

Fine Reading: When Microbial Conversations Get Physical

by Elio

In a recent Opinion piece in Trends in Microbiology, Gemma Reguera invites us to think outside the box. The box in question harbors the notion that communication between microbes is chemical, and only chemical. Here, the author cuts through the confines of this perspective to point out that microbial communication also takes place via physical interactions.

By physical, Reguera means sound waves, electromagnetic radiation (mainly light), and electric currents. The latter, thanks to recent work on the function microbial nanowires, is the more familiar one. (Incidentally, this paper’s brief overview of the nanowire business is as clear as any I’ve seen.) Nanowires form grids between cells, clearly constituting an effective mechanism of communication. But further, Reguera proposes that many other microbes may communicate electrically, all being polarizable and many being known to respond to electrical reorientation (i.e., galvanotaxis).

Continue reading "Fine Reading: When Microbial Conversations Get Physical" »

May 09, 2011

A Protection Racket

by Merry

R-M_balance

Source.

First, something about R-M systems. The modification part of an R-M system is a DNA methyltransferase (aka methylase) that recognizes a 4–8 bp palindromic sequence of double-stranded DNA and methylates the cytosine or adenine bases therein. The preferred substrate for these methylases is the hemimethylated DNA that is produced by replication of the host chromosome. A bacterial chromosome typically contains hundreds of recognition sequences. All of these sites need to be methylated at all times to protect the cell from the other half of the R-M system—the restriction endonuclease. This endonuclease recognizes the same sequence as its cognate methylase and makes a double-strand cut if the site is not methylated. The methylases need to be abundant and fast as one such cut, unrepaired, means death to the cell. When a DNA phage genome or other foreign DNA containing unmethylated target sequences enters the cell, it is subject to cleavage by the host's endonuclease. It can also be methylated by the resident methylases, although this proceeds far more slowly than methylation of the hemimethylated host chromosome. Usually the endonuclease strikes before the methylase finishes its job.

Type_II

Action of a Type II R-M system. (A) The restriction endonuclease makes double-stranded cuts at unmethylated recognition sequences, whereas methylation of that target sequence protects the DNA from cleavage. (B) Incoming DNA with unmethylated target sequences is cleaved by the host's endonuclease, while the host's own methylated genome is immune. (C, upper panel) A bacterial cell with an R-M system. Its chromosome is fully methylated and thus is protected from the endonucleases present. (C, lower panel) After loss of the R-M genes, the methylase is eliminated first, DNA methylation decreases, and the persisting endonucleases attack unprotected sites, usually killing the cell. Sometimes chromosome breakage is repaired, with or without genome rearrangement. Source.

Several types of R-M systems are known. The most studied ones are the Type II systems composed of two or three separate proteins: the endonuclease, the methylase, and sometimes a controller protein. Most of what follows applies specifically to this type. The hundreds of different restriction endonucleases known show no significant amino acid sequence similarity to each other—not even those that recognize the same target sequence. However, some structural similarities can be detected. This is interpreted as possible evidence of their rapid evolution from a common ancestor.

In  a 1995 paper, Kusano and colleagues note: It is widely accepted that the evolution and maintenance of restriction-modification (RM) systems have been driven by the protection from foreign DNA that they afford to cells. This view has been frequently echoed by others. How effective are these R-M systems as a phage defense outside the lab?

Continue reading "A Protection Racket" »

May 05, 2011

Going to Great Lengths

by Merry

Tapir_knot

Source.

Given the streamlined genomes and the frugal nature of the Bacteria and Archaea, one might expect their proteins to be short and to the point. However, a survey of the 580 prokaryotic sequenced genomes available in 2008 found many genes apparently encoding large proteins. Specifically, 0.2% of the ORFs (3732 genes) were longer than 5 kb. Of those, 80 were truly giants—more than 20 kb! These mammoths were found scattered about in 47 taxa in 8 different phyla. The longest two, both from the green sulfur bacterium Chlorobium chlorochromatii CaD3, encode proteins containing 36,806 and 20,647 amino acids, respectively.

Does this set an all-domain record? Not quite. They are bested by one of our own, ttn, the gene for titin, an abundant protein of critical importance in vertebrate striated muscles. This single gene encodes 363 exons that, upon translation, yields a protein with 38,138 amino acid residues with 244 individually folded protein domains. Each titin molecule spans half the length of an entire sarcomere. Score one for the eukaryotes.

Continue reading "Going to Great Lengths" »

May 02, 2011

Designer Genes for Special Bacterial Lifestyles

by S. Marvin Friedman

Burkholderia

Burkholderia under a scanning EM. Source.

Thanks to the extensive research of the past ten years, we've become aware that many prokaryotic endosymbionts and habitual intracellular pathogens have undergone genome reduction over evolutionary time. Characteristic of this process, termed reductive convergent evolution, is the discarding of genes involved in metabolic pathways and regulatory functions that have become superfluous now that cells can scavenge host nutrients. The high percentage of noncoding DNA (including pseudogenes) found in many of these genomes probably represent obsolete genes on their way out. At the same time, there is an increase of transporter genes needed for the uptake of host-derived metabolites.

Continue reading "Designer Genes for Special Bacterial Lifestyles" »

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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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