106 posts · 64,146 views
On Small Things Considered we share our appreciation for the width and depth of microbial activities on this planet. We enjoy writing about unusual and unexpected phenomena in the microbial world. Fortunately, these come our way with great frequency. We rely on contributors with all levels of experience, from undergraduate and graduate students to distinguished microbiologists. Our "Teachers’ Corner" facilitates the use of the blog in the classroom. Some of our blog’s idiosyncratic features include our "Talmudic Questions" (queries that cannot be answered by simply looking them up with Google), "Of Terms in Biology," and our "Fine Reading" posts, each of which features an exceptional research paper. Small Things Considered is sponsored by the American Society for Microbiology.
Elio Schaechter
12 posts
Merry Youle
2 posts
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- April 16, 2012
- 01:00 PM
- 47 views
The Immunological Synapse Goes Viral
by Moselio Schaechter in Small Things Considered
by Merry Youle
Here’s yet another tale of how a cunning virus has converted one of our antiviral defenses into a tool for its own purposes. The co-opted mechanism is one used by cytotoxic T-cells to kill virus-infected cells: the immunological synapse. More on this in a moment. The virus is Human T-Lymphotropic Virus Type I (HTLV-1). The appropriated tactic enables the virus to spread efficiently to new host cells.
When discovered in 1977, HTLV-1 was the first known human retrovirus (HIV not being identified until six years later). While not as devastating as HIV, it currently infects 10–20 million people, 2–3% of whom will develop adult T-cell leukemia/lymphoma while another 2-3% develop a chronic inflammatory condition (HAM/TSP). Like HIV, it infects primarily CD4+ T cells. And like HIV, HTLV-1 also transmits from one person to the next in blood, milk, or semen. But just how it does this was puzzling because, unlike HIV, few free virions are found in the blood and, of those, only one virion in a million is infectious. More clues: Only enveloped HTLV-1 virions are infectious and they acquire their envelope from the lymphocyte plasma membrane as they bud from their host cell. Efficient transfer of the virus between cells requires cell-cell contact, both in vitro and in vivo.
Combined these observations suggest that perhaps the virions bud from one cell and immediately enter their next host cell without ever wandering free in the liquid milieu. What would such a strategy require? ... Read more »
Igakura, T. (2003) Spread of HTLV-I Between Lymphocytes by Virus-Induced Polarization of the Cytoskeleton. Science, 299(5613), 1713-1716. DOI: 10.1126/science.1080115
Majorovits E, Nejmeddine M, Tanaka Y, Taylor GP, Fuller SD, & Bangham CR. (2008) Human T-lymphotropic virus-1 visualized at the virological synapse by electron tomography. PloS one, 3(5). PMID: 18509526
- April 5, 2012
- 04:15 PM
- 95 views
Wiley Phage Trumps Host Toxin
by Merry Youle in Small Things Considered
by Merry Youle.
Toxin-antitoxin (TA) systems are a dime a dozen. They are found on plasmids and chromosomes within many prokaryote groups—even those with an intracellular lifestyle. Each is a two-gene operon, one gene encoding a toxin protein, the other the cognate antitoxin. Key to their function is the differential stability of the two gene products, the antitoxin degrading more...... Read more »
Otsuka Y, & Yonesaki T. (2012) Dmd of bacteriophage T4 functions as an antitoxin against Escherichia coli LsoA and RnlA toxins. Molecular microbiology, 83(4), 669-81. PMID: 22403819
- April 2, 2012
- 01:00 PM
- 100 views
Living On the Edge…of the swarm
by Moselio Schaechter in Small Things Considered
by Gemma Reguera
If anybody knows how to move, it’s bacteria. They swim in liquids using rotating flagella, but they also know how to twitch, glide, and slide on surfaces. The mechanisms that power their surface motility are varied, ranging from energy-intensive processes such as the extension and retraction of type IV pili (twitching) to movement via focal-adhesion complexes of the cell’s outer surface (gliding) or growth-induced translocation aided by surfactants (sliding). Some flagellated bacteria can also use the rotating motion of the flagellum to move across moist surfaces, a process known as swarming motility. As the word indicates, swarming is a collective behavior. Swarming cells move side-by-side in regular or irregular formations known as rafts or swarms. See, for example, previous blog posts showing the regular rafts produced by Paenibacillus or the distinctive, irregular terraces formed by Proteus. And even E. coli does it, too! ... Read more »
Wu Y, Hosu BG, & Berg HC. (2011) Microbubbles reveal chiral fluid flows in bacterial swarms. Proceedings of the National Academy of Sciences of the United States of America, 108(10), 4147-51. PMID: 21300887
Wu Y, & Berg HC. (2012) Water reservoir maintained by cell growth fuels the spreading of a bacterial swarm. Proceedings of the National Academy of Sciences of the United States of America, 109(11), 4128-33. PMID: 22371567
- April 2, 2012
- 01:18 AM
- 93 views
Sex to the Rescue
by Moselio Schaechter in Small Things Considered
by Elio
Life is tough out there. If chemistry (via oxidizing radicals) doesn’t get you, sunlight (via UV irradiation) will. No wonder that cells, both prokaryotic and eukaryotic, have an intense preoccupation with keeping their DNA intact. In most organisms, a considerable portion of the...... Read more »
Ajon M, Fröls S, van Wolferen M, Stoecker K, Teichmann D, Driessen AJ, Grogan DW, Albers SV, & Schleper C. (2011) UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili. Molecular microbiology, 82(4), 807-17. PMID: 21999488
- March 12, 2012
- 01:00 PM
- 92 views
Salmonella’s Exclusive Intestinal Restaurant
by Moselio Schaechter in Small Things Considered
by Elio
Interesting, how we get carried away by exciting concepts. I am thinking about how the study of pathogens has focused so much on the microbes’ virulence factors, by which we mean...... Read more »
Winter SE, Thiennimitr P, Winter MG, Butler BP, Huseby DL, Crawford RW, Russell JM, Bevins CL, Adams LG, Tsolis RM.... (2010) Gut inflammation provides a respiratory electron acceptor for Salmonella. Nature, 467(7314), 426-9. PMID: 20864996
- March 5, 2012
- 12:00 PM
- 43 views
How to Reform a Resistant Bacterium
by Merry Youle in Small Things Considered
by Merry Youle
A recent paper by Edgar and colleagues captured my attention with a new twist on how to combat antibiotic resistance: Our overall goal in this study is to provide a proof of principle for a genetic system that is able to restore drug sensitivity to drug-resistant pathogens residing on hospital surfaces. And these researchers propose using my favorite life form, bacteriophages, to do the job.
The seed of their idea goes back to a 1951 paper by Lederberg. He reported that in heterozygous diploids of E. coli K-12, the wild-type (wt) allele conferring streptomycin sensitivity is fully dominant to mutant streptomycin resistant alleles. This suggests that if you introduce a wt sensitive gene into a resistant bacterium by any method, you would then have a streptomycin sensitive bacterium. You don’t even have to eliminate or alter the resident resistant gene. However, once you have such a bacterium, you need to provide some selection pressure that favors it over the antibiotic resistant multitude.
The Edgar team saw this as a potential mechanism for reversing the rising tide of antibiotic resistance, especially as manifested in the form of multiple-drug resistant nosocomial infections. Resistant bacteria can survive for extended periods on hospital “touch surfaces” from where they can be transported, directly or indirectly, to their next host. The researchers envision using temperate phages sprayed on these surfaces to introduce the genes to reform their hosts. Could this work? In their paper, they provide proof of principle for such a system.... Read more »
Edgar R, Friedman N, Molshanski-Mor S, & Qimron U. (2012) Reversing bacterial resistance to antibiotics by phage-mediated delivery of dominant sensitive genes. Applied and environmental microbiology, 78(3), 744-51. PMID: 22113912
- March 1, 2012
- 12:00 PM
- 98 views
Onboard a Flying Syringe
by Merry Youle in Small Things Considered
by Merry Youle.
The face of a rugose spiraling whitefly in southern Florida. This particular species recently hitchhiked to Florida on people or plants traveling from Central America. Although whiteflies feed on plant phloem, the greatest impact on crop plants caused by many species is due to their vectoring numerous viral plant diseases. Source. Each year we spend vast sums of...... Read more »
Ng TF, Duffy S, Polston JE, Bixby E, Vallad GE, & Breitbart M. (2011) Exploring the diversity of plant DNA viruses and their satellites using vector-enabled metagenomics on whiteflies. PloS One, 6(4). PMID: 21544196
Ng TF, Willner DL, Lim YW, Schmieder R, Chau B, Nilsson C, Anthony S, Ruan Y, Rohwer F, & Breitbart M. (2011) Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes. PloS one, 6(6). PMID: 21674005
- December 13, 2011
- 10:02 PM
- 230 views
A Wormful of Bugs
by Moselio Schaechter in Small Things Considered
by Elio
Let’s start out with a little quiz. What examples can you name of endosymbiotic bacteria so tightly packed that they’re nearly wall-to-wall within cells of their host? If you said legume root nodules, you can claim a prize. (Ask someone else for it, as we don’t have any.) You would get bonus points if you also mentioned the bacteria-filled bacteriocytes of certain insects or the celebrated giant tube worms found near the deep sea black smokers. By the way, the root nodule symbioses, though not mandatory, are highly beneficial to the host, but the other two are obligatory.
Here is another recently described example to add to this thought-provoking repertoire. In the sandy bottoms beneath shallow ocean waters one finds worms that have neither a mouth nor a gut. Although such areas seem sparse in life, in fact they’re home to a rather rich biota. Microbes, both pro– and eukaryotic, are present in abundance and so are animals, such as the worms we’re talking about here. So, how can animals be mouthless and gutless?... Read more »
Gruber-Vodicka HR, Dirks U, Leisch N, Baranyi C, Stoecker K, Bulgheresi S, Heindl NR, Horn M, Lott C, Loy A.... (2011) Paracatenula, an ancient symbiosis between thiotrophic Alphaproteobacteria and catenulid flatworms. Proceedings of the National Academy of Sciences of the United States of America, 108(29), 12078-83. PMID: 21709249
Leisch N, Dirks U, Gruber-Vodicka HR, Schmid M, Sterrer W, & Ott JA. (2011) Microanatomy of the trophosome region of Paracatenula cf. polyhymnia (Catenulida, Platyhelminthes) and its intracellular symbionts. Zoomorphology, 130(4), 261-271. PMID: 22131640
- November 30, 2011
- 11:41 PM
- 393 views
Is a Good Offense the Best Defense?
by Moselio Schaechter in Small Things Considered
by Merry Youle
Most eukaryotes possess an RNA interference system (RNAi) that they use to regulate gene expression and to defend against viruses and other mobile elements. However, some budding yeasts, such as Saccharomyces cerevisiae, appear to get along just fine without it even though RNAi has benefited other yeasts by silencing transposons in particular. How do these yeasts that lack functional RNAi systems compete with closely related species that do? And how come they don’t have RNAi when RNAi arose in an early eukaryote ancestor and is conserved throughout most of the fungi?... Read more »
Drinnenberg IA, Fink GR, & Bartel DP. (2011) Compatibility with killer explains the rise of RNAi-deficient fungi. Science (New York, N.Y.), 333(6049), 1592. PMID: 21921191
- November 30, 2011
- 11:39 PM
- 326 views
Virus Hacks Intercellular Communications Network
by Moselio Schaechter in Small Things Considered
by Merry Youle
What do monocytes, lymphocytes, and neutrophils all have in common? Well, yes, they are all leucocytes and part of our immune system, but what else? They all can be prompted to migrate to the site of infection...... Read more »
Alcami, A., & Lira, S. (2010) Modulation of chemokine activity by viruses. Current Opinion in Immunology, 22(4), 482-487. DOI: 10.1016/j.coi.2010.06.004
- November 30, 2011
- 11:39 PM
- 295 views
A Pestis from the Past
by Moselio Schaechter in Small Things Considered
by S. Marvin Friedman
In recent decades we’ve come to realize that victory goes not to the swift or to the strong, but to the immune. The introduction of agents of deadly diseases into immunologically naïve populations determined momentous events in human history. The conquest of the Americas resulted in good part from the decimation of native people by diseases brought by the Spaniards, such as smallpox and measles. Two seminal books, one by William McNeill and the other by Jared Diamond, come to mind, followed recently by one by Irwin Sherman. It follows that students of historical human affairs need also a solid background in the affairs of microbes. The methods now available to paleomicrobiologists allow us to travel back in time and probe microbial events that took place in the distant past. One approach, determining the genetic sequence of ancient microbes, while still a daunting task, is providing exciting glimpses into the history of humans and their pathogens, as shown in a paper I will discuss here.... Read more »
Bos KI, Schuenemann VJ, Golding GB, Burbano HA, Waglechner N, Coombes BK, McPhee JB, DeWitte SN, Meyer M, Schmedes S.... (2011) A draft genome of Yersinia pestis from victims of the Black Death. Nature, 478(7370), 506-10. PMID: 21993626
- November 30, 2011
- 11:37 PM
- 310 views
The Lyme Disease Spirochete Feasts on Tick Antifreeze
by Moselio Schaechter in Small Things Considered
This article is lightly modified from one published in the blog Spirochetes Unwound by Microbe Fan. With kind permission of the author.
by Microbe Fan
In the northeastern United States the Lyme disease spirochete Borrelia burgdorferi spreads from one white-footed mouse to another by hitching a...... Read more »
Pappas CJ, Iyer R, Petzke MM, Caimano MJ, Radolf JD, & Schwartz I. (2011) Borrelia burgdorferi requires glycerol for maximum fitness during the tick phase of the enzootic cycle. PLoS pathogens, 7(7). PMID: 21750672
- November 30, 2011
- 11:35 PM
- 348 views
Phage Lambda’s Polar Expedition
by Moselio Schaechter in Small Things Considered
by Merry Youle
For a long, long time, phage lambda (λ) has known that its E. coli host was not simply ‘a well-stirred bag of enzymes’ (something we’ve come to appreciate only relatively recently). This is vital information for lambda since it needs to interact with two particular host proteins in order to launch an infection. One is its receptor (LamB) located on the outer membrane (OM), the other is an inner membrane protein, ManY.
ManY works for E. coli as part of the inner membrane mannose transporter, whereas for lambda it is required for entry of the phage’s DNA into the cell. And ManY is not part of that imaginary stirred gemisch. Using a ManY-GFP fusion protein and fluorescence microscopy, Edgar and colleagues demonstrated that ManY is localized at the cell poles and at cell division sites (future cell poles) in living cells.
They also found that at low MOI (a Multiplicity Of Infection of 0.5–5) lambda, too, prefers the polar regions, ‘binding’ preferentially at the poles and future poles (mid-cell).... Read more »
Edgar R, Rokney A, Feeney M, Semsey S, Kessel M, Goldberg MB, Adhya S, & Oppenheim AB. (2008) Bacteriophage infection is targeted to cellular poles. Molecular microbiology, 68(5), 1107-16. PMID: 18363799
Gibbs, K., Isaac, D., Xu, J., Hendrix, R., Silhavy, T., & Theriot, J. (2004) Complex spatial distribution and dynamics of an abundant Escherichia coli outer membrane protein, LamB. Molecular Microbiology, 53(6), 1771-1783. DOI: 10.1111/j.1365-2958.2004.04242.x
- November 30, 2011
- 11:34 PM
- 428 views
Bacteria Living Without Phages?
by Moselio Schaechter in Small Things Considered
By Merry Youle
Are there environments where there are abundant bacteria and no phages? Sounds like one of our Talmudic Questions, but this one has a specific answer, and that answer is Yes. That environment was found within a cystic fibrosis (CF) lung.
This story comes from a pair of papers recently published by a group of microbial ecologists reporting their survey of the microbes and DNA viruses present in the lungs of two late-stage CF patients. Previous studies had all relied on sampled sputum or bronchial alveolar lavage fluid. These researchers instead took advantage of the opportunity to investigate the explant lungs from a CF patient who received a lung transplant. They dissected the lungs, isolated the microbes and viruses separately from each lobe, and then extracted the DNA. This approach enabled them to determine not only the diversity within each lobe, but also to ask whether each lobe housed its own distinctive community.
... Read more »
Willner D, Haynes MR, Furlan M, Hanson N, Kirby B, Lim YW, Rainey PB, Schmieder R, Youle M, Conrad D.... (2011) Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung. American journal of respiratory cell and molecular biology. PMID: 21980056
- November 28, 2011
- 12:00 PM
- 256 views
Are You Me or Am I You?
by Moselio Schaechter in Small Things Considered
by Elio
When one cell meets another, it must make decisions. This extends itself to practically every attribute of living things, from avoiding mating with self to the establishment of territorial boundaries. Do we fuse? Will you attack me? Are you a potential mate or are you lunch? And, in the bodies of vertebrates, are you something that my immune system should recognize as foreign? Microbes are not exempted from these quandaries, being that they carry out lively conversations for purposes as diverse as feeding, differentiating into biofilms or fruiting bodies, moving, surviving in a host, or sensing their own numbers. As with the social insects, microbes converse in a chemical language. As Strassman et al. say in an insightful review: Recognition seems likely to be particularly important to microbes because they undertake many processes extracellularly in the public sphere that larger organisms privatize inside.
In studying such microbial interactions, one can choose among a number of interesting models. The Gram-negative bacillus, Proteus mirabilis, practically begs us to select it. ... Read more »
Gibbs KA, Wenren LM, & Greenberg EP. (2011) Identity gene expression in Proteus mirabilis. Journal of bacteriology, 193(13), 3286-92. PMID: 21551301
- November 21, 2011
- 12:00 PM
- 334 views
Ringing a Microbial Dinner Bell
by Moselio Schaechter in Small Things Considered
by Mark Martin
A few weeks ago, I wrote a short Small Things Considered essay describing the diverse roles that odors can play in microbiology. Articles here and there written by others attest to a growing interest in sociomicrobiology. As for myself, I have long suspected that microbes are constantly sending and responding to a wide communication ‘bandwidth’ of rich chemical chatter, and that other organisms can use or eavesdrop on those signals. Such communication is common in the eukaryotic world, conveyed by a variety of chemical messages or semiochemicals with myriad effects.
Thus, I was charmed by a recent article by Pascal Leroy and coworkers, as well as the accompanying Research Highlights essay. The researchers report how it is that the hoverfly Episyrphus balteatus is able to locate its prey, the pea aphid Ayrthrosiphon pisum. As you might guess, reading this blog, there is indeed a microbial component to this story.... Read more »
Leroy PD, Sabri A, Heuskin S, Thonart P, Lognay G, Verheggen FJ, Francis F, Brostaux Y, Felton GW, & Haubruge E. (2011) Microorganisms from aphid honeydew attract and enhance the efficacy of natural enemies. Nature communications, 348. PMID: 21673669
- August 22, 2011
- 01:00 PM
- 616 views
Going Next Door Without Getting Your Feet Wet
by Moselio Schaechter in Small Things Considered
by Elio
Intracellular life has its perks. Inside host cells, bacteria are protected from neutrophils, complement, antibodies, some antibiotics, and the other unpleasant things floating around in tissue fluids. In addition, here they have access to ample food. But there is a catch, namely how to infect other cells and other hosts.
Intracellular life has ancient and distinguished origins. When unicellular eukaryotes first arose, not only did they arise because someone (whoever it was) ingested a prokaryotic cell, but soon thereafter the emerging protists must have learned to go after the abundant food microbial around them. The prey, in turn learned to cope with this and to survive inside the predator cells, something some bacteria do successfully to this very day. Consider how these overcome the destructive forces of phagocytes and other cells. The repertoire of ways they do it is impressive indeed. Of course, not all bacteria live intracellularly, but all viruses must do so at some stage, so this subject is old hat to virologists.
For both bacteria and viruses, the intracellular lifestyle presents a problem. How do they infect their next host? ... Read more »
French CT, Toesca IJ, Wu TH, Teslaa T, Beaty SM, Wong W, Liu M, Schröder I, Chiou PY, Teitell MA.... (2011) Dissection of the Burkholderia intracellular life cycle using a photothermal nanoblade. Proceedings of the National Academy of Sciences of the United States of America, 108(29), 12095-100. PMID: 21730143
- August 15, 2011
- 01:00 PM
- 496 views
And We Thought We Knew What CRISPRs Do!
by Moselio Schaechter in Small Things Considered
by Merry Youle
Imagine that you have been growing Pseudomonas aeruginosa strain PA14 in your lab for some time, studying biofilm formation among other things. A student in your lab isolates a phage, dubbed DMS3, that mediates generalized transduction between this and other P. aeruginosa strains. Oddly, this strain, when lysogenized by DMS3, no longer forms biofilms or swarms, both group behaviors. Odd indeed. This is what actually happened in the O'Toole lab at Dartmouth, and this occurrence led these researchers to the discovery of a new function for CRISPRs. (For an introduction to CRISPRs, see our two earlier posts here and here. For a recent commentary on several papers from the O'Toole lab, see here.)
Here's how they tried to figure out what’s going on...... Read more »
Zegans ME, Wagner JC, Cady KC, Murphy DM, Hammond JH, & O'Toole GA. (2009) Interaction between bacteriophage DMS3 and host CRISPR region inhibits group behaviors of Pseudomonas aeruginosa. Journal of bacteriology, 191(1), 210-9. PMID: 18952788
Cady KC, White AS, Hammond JH, Abendroth MD, Karthikeyan RS, Lalitha P, Zegans ME, & O'Toole GA. (2011) Prevalence, conservation and functional analysis of Yersinia and Escherichia CRISPR regions in clinical Pseudomonas aeruginosa isolates. Microbiology (Reading, England), 157(Pt 2), 430-7. PMID: 21081758
- August 8, 2011
- 01:00 PM
- 721 views
Some Like it Cold
by Moselio Schaechter in Small Things Considered
by S. Marvin Friedman
About 70% of Earth’s surface is ocean. In all of them, the temperature at depths of 1000 meters or more is a constant 4 °C, constituting a vast environment populated by a diverse group of psychrophilic (“cold-loving”) microorganisms. Much of terra firma also lies in the realm of the psychrophiles: more than 20% of all soils are permafrost. Scattered about are a variety of other specialized psychrophilic environments, including cryopegs (saltwater pockets within permafrost at –10 °C that have remained liquid for 10,000 years), Antarctic dry valleys, liquid brine veins among sea-ice crystals, and cryoconite holes on the surface of glaciers. Thus psychrophiles may be the most abundant extremophiles on the planet. Yet research on these fascinating microbes has lagged behind studies on thermophiles (“heat-loving”) and halophiles (“salt-loving”).
Much of what is known about psychrophiles concerns enzymes and membranes.... Read more »
Piette F, D'Amico S, Struvay C, Mazzucchelli G, Renaut J, Tutino ML, Danchin A, Leprince P, & Feller G. (2010) Proteomics of life at low temperatures: trigger factor is the primary chaperone in the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125. Molecular microbiology, 76(1), 120-32. PMID: 20199592
- August 1, 2011
- 01:00 PM
- 696 views
The Janus Bug
by Moselio Schaechter in Small Things Considered
If you wonder what I do with myself when I'm not blogging, well I'll tell you. Among other things, I participate in an ASM-sponsored podcast called This Week In Microbiology (TWIM). It’s posted every two weeks and is easily accessible by clicking here or going to the MicrobeWorld home page. Under the leadership of Columbia University’s podcaster extraordinaire Vincent Racaniello, we sit before our computers and schmooze away about a couple of papers that caught our fancy. Recently, one of the podcasters, Margaret McFall-Ngai, went over a paper with the puzzling title Helicobacter pylori infection prevents allergic asthma in mouse models through the induction of regulatory T cells. You see why this caught Margaret’s attention. Helicobacter and asthma? A bacterium that lives in the stomach has an effect on the respiratory tract? Makes you wonder.
To put this story in context, it is part of a broader concern, to wit the multiple natures of members of our “normal” microbiota. ... Read more »
Arnold IC, Dehzad N, Reuter S, Martin H, Becher B, Taube C, & Müller A. (2011) Helicobacter pylori infection prevents allergic asthma in mouse models through the induction of regulatory T cells. The Journal of clinical investigation. PMID: 21737881
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