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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- February 14, 2011
- 12:00 PM
- 1,185 views
The Great Epidemic
by Merry Youle in Small Things Considered
When you read the title—The Great Epidemic—what came to mind? The Black Death (Yersinia pestis) that in two years killed 20 million people in Europe—approximately 30-60% of the population? The 1918 flu pandemic with its tally of 50 million dead in three years? AIDS, with a death toll projected to reach 200 million by 2025? Or perhaps that 20th century epidemic that struck down over three and a half billion in North America in the space of a few decades—the American chestn........ Read more »
Dawe AL, & Nuss DL. (2001) Hypoviruses and chestnut blight: exploiting viruses to understand and modulate fungal pathogenesis. Annual review of genetics, 1-29. PMID: 11700275
- November 20, 2009
- 09:54 AM
- 1,176 views
Genomic Secrets of P. infestans, the Master of Potato Blight
by Merry Youle in Small Things Considered
No fungicide has ever been found to which P. infestans could not ultimately adjust…Indeed, no potato has ever been developed with defenses that Phytophthora could not ultimately breach.
More than 150 years after the historic Irish potato famine LINK 2, the deadly pathogen responsible for potato blight, Phytophthora infestans, is now destroying more than $3 billion worth of potatoes each year. What is the secret of it's pathogenic success? Hoping to find some answers in its genome, a team o........ Read more »
Haas BJ, Kamoun S, Zody MC, Jiang RH, Handsaker RE, Cano LM, Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T.... (2009) Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature, 461(7262), 393-8. PMID: 19741609
- February 21, 2011
- 12:00 PM
- 1,119 views
Candida's Unstable Chromosomes & Unorthodox Sex
by Dean Dawson in Small Things Considered
Who hasn't heard of Candida? It’s one of the most common fungal pathogens of humans. It is also a commensal organism, living mainly in people’s gastrointestinal tract. The diseases it causes range from a fairly mild vaginitis to deadly opportunistic systemic infections. In fact, Candida species are a major cause of nosocomial bloodstream infections. Candidas are close relatives of the baker’s yeast, Saccharomyces cerevisiae, but live by very different rules.
Candida has been the focus o........ Read more »
Poláková S, Blume C, Zárate JA, Mentel M, Jørck-Ramberg D, Stenderup J, & Piskur J. (2009) Formation of new chromosomes as a virulence mechanism in yeast Candida glabrata. Proceedings of the National Academy of Sciences of the United States of America, 106(8), 2688-93. PMID: 19204294
Bennett, R. (2010) Coming of Age—Sexual Reproduction in Candida Species. PLoS Pathogens, 6(12). DOI: 10.1371/journal.ppat.1001155
- February 11, 2010
- 08:12 PM
- 1,101 views
Measuring the Strength and Speed of the Microbial Grappling Hook
by Moselio Schaechter in Small Things Considered
by Amber Pollack-Berti I’ll admit, I’ve been in love with the type IV pili (T4P) for a long time. After memorizing all those complex pathways for regulation and metabolism, there was something so refreshing and accessible about pili. These bacterial surface appendages are, by their nature, mechanical structures. They are easy to visualize. Their composition is simple: a Type...... Read more »
Clausen M, Jakovljevic V, Søgaard-Andersen L, & Maier B. (2009) High-force generation is a conserved property of type IV pilus systems. Journal of bacteriology, 191(14), 4633-8. PMID: 19429611
- June 1, 2009
- 10:14 AM
- 1,098 views
Say, Brother, Can You Spare a DNA?
by Merry Youle in Small Things Considered
Mention horizontal gene transfer (HGT) in bacteria, and what comes to mind is the acquisition of new traits and capabilities across large evolutionary distances. Not so for the neisseriae. For them, HGT is a means to swap genes with other members of the species and to maintain the status quo in the face of assault on their genome by host defenses.
Infection by the human pathogen N. gonorrhoeae is met by the rapid recruitment of polymorphonuclear leukocytes (PMNs) to the site. PMNs are profess........ Read more »
Davidsen, T. (2004) Biased distribution of DNA uptake sequences towards genome maintenance genes. Nucleic Acids Research, 32(3), 1050-1058. DOI: 10.1093/nar/gkh255
Hamilton, H., Dominguez, N., Schwartz, K., Hackett, K., & Dillard, J. (2005) Neisseria gonorrhoeae secretes chromosomal DNA via a novel type IV secretion system. Molecular Microbiology, 55(6), 1704-1721. DOI: 10.1111/j.1365-2958.2005.04521.x
- July 11, 2011
- 01:00 PM
- 1,061 views
Viruses that Infect Parasites that Infect Us: The Matryoshka Dolls of Human Pathogens
by Moselio Schaechter in Small Things Considered
by Jamie Schafer
We’re all too familiar with the viruses that can infect us, from the common cold to yellow fever virus to the endogenous retroviruses that make up a chunk of our genome. Many of us are also acquainted with parasites, such as tape worms or Giardia, that like to set up camp in the human body. But the world of parasites and viruses does not end there. Many parasites or endosymbionts can be infected with viruses. A classic example is Paramecium, which can harbor an endosymbiotic ........ Read more »
Ives A, Ronet C, Prevel F, Ruzzante G, Fuertes-Marraco S, Schutz F, Zangger H, Revaz-Breton M, Lye LF, Hickerson SM.... (2011) Leishmania RNA virus controls the severity of mucocutaneous leishmaniasis. Science (New York, N.Y.), 331(6018), 775-8. PMID: 21311023
- January 3, 2011
- 12:00 PM
- 1,006 views
Precious Metals
by Moselio Schaechter in Small Things Considered
Now that news of the arsenic-eating bacteria has saturated cyberspace, the airwaves, and even old-fashioned newsprint, we step back to raise a larger question: Why have so few elements from the periodic table made it into living things? You seldom hear about anything past the first few rows in the table. Turns out this is a gross oversight. Many more elements, previously unsuspected, are to be found in a large number of metalloproteins. So, move over, arsenic and make room for other elements.
U........ Read more »
Cvetkovic A, Menon AL, Thorgersen MP, Scott JW, Poole FL 2nd, Jenney FE Jr, Lancaster WA, Praissman JL, Shanmukh S, Vaccaro BJ.... (2010) Microbial metalloproteomes are largely uncharacterized. Nature, 466(7307), 779-82. PMID: 20639861
- February 18, 2010
- 11:45 AM
- 991 views
Prophage Masquerade
by Merry Youle in Small Things Considered
Roseovarius nubinhibens recently joined the exclusive club of about a thousand bacteria whose genomes have been sequenced. Why this honor? It’s a member of one of the most ubiquitous and most intensely studied clades of α-Proteobacteria, the marine roseobacters. This populous group participates in important jobs, including the global cycling of sulfur, climate regulation, and even modulation...... Read more »
Zhao Y, Wang K, Ackermann HW, Halden RU, Jiao N, & Chen F. (2010) Searching for a "hidden" prophage in a marine bacterium. Applied and environmental microbiology, 76(2), 589-95. PMID: 19948862
- November 22, 2010
- 02:18 PM
- 980 views
Physical Virology
by Manuel Sánchez in Small Things Considered
Physical Virology. Such is the title of the article that appeared in Nature Physics. This is the name for a new discipline that is under development. Its focus is the study of viruses from a physical perspective. Seen this way, viruses are natural nanoparticles with distinct mechanical and thermodynamic properties
Professors W. Ross and G.J.L Wuite of the Foundation For Fundamental Research On Matter of the University of Amsterdam and R. Bruinsma of the Physics Department at UCLA summarize in........ Read more »
Roos, W., Bruinsma, R., & Wuite, G. (2010) Physical virology. Nature Physics, 6(10), 733-743. DOI: 10.1038/nphys1797
- June 21, 2010
- 01:00 PM
- 979 views
Our Counterintelligence Staph
by Moselio Schaechter in Small Things Considered
by Karen Schwarzberg, Mike Gurney, and Nikos Gurfield S. aureus biofilm formed overnight on silicon elastomer, a material used in catheters. Bar = 10 µm. Source. Typically, when one thinks about the commensal bacteria living with us, what comes to mind are the benefits they provide by aiding in food metabolism, producing vitamins, and preventing colonization by invading pathogenic bacteria....... Read more »
Iwase T, Uehara Y, Shinji H, Tajima A, Seo H, Takada K, Agata T, & Mizunoe Y. (2010) Staphylococcus epidermidis Esp inhibits Staphylococcus aureus biofilm formation and nasal colonization. Nature, 465(7296), 346-9. PMID: 20485435
- April 7, 2011
- 03:45 PM
- 951 views
Beyond the Bacterial Microcompartment
by Merry Youle in Small Things Considered
Bacterial microcompartments were a great innovation. As Alan Derman explained, these protein-bounded structures assist with diverse metabolic processes by housing the requisite enzymes along with their substrates, sequestering potentially toxic intermediates, and allowing the products to exit. But the story does not end there. Enter the nanocompartment.
These are the simplest variation known so far on the theme of bacterial compartments. Like the micro version, these nano structures are thin........ Read more »
Sutter M, Boehringer D, Gutmann S, Günther S, Prangishvili D, Loessner MJ, Stetter KO, Weber-Ban E, & Ban N. (2008) Structural basis of enzyme encapsulation into a bacterial nanocompartment. Nature structural , 15(9), 939-47. PMID: 19172747
- November 4, 2010
- 01:00 PM
- 940 views
One Symbiont Is Good, Two Are Better: The Forever Fascinating Story of the Leaf-Cutting Ants and Their Bacteria
by Moselio Schaechter in Small Things Considered
by Elio
Now here’s a question you’ve been asking all along about the interaction between the leaf cutting (Attine) ants, the fungi they cultivate, and the bacteria that make antifungals against unwanted fungal species. Have these bacteria evolved along with the ants to protect their gardens from unwanted "weeds," or do the ants pick up such bacteria from their environment? New data suggest both things happen.
To remind you, leaf-cutting ants practice fungiculture, and have been doing this ........ Read more »
Barke J, Seipke RF, Grüschow S, Heavens D, Drou N, Bibb MJ, Goss RJ, Yu DW, & Hutchings MI. (2010) A mixed community of actinomycetes produce multiple antibiotics for the fungus farming ant Acromyrmex octospinosus. BMC biology, 109. PMID: 20796277
Poulsen M, & Currie CR. (2010) Symbiont interactions in a tripartite mutualism: exploring the presence and impact of antagonism between two fungus-growing ant mutualists. PloS one, 5(1). PMID: 20090958
- September 17, 2009
- 09:56 AM
- 933 views
Fine Reading: The Good-Enough Clockus of Prochlorococcus
by Moselio Schaechter in Small Things Considered
by Elio
The very first post on this blog (It Don't Mean a Thing If It Ain't Got That Swing) LINK 1 was about the circadian rhythm of cyanobacteria. They turn their photosynthetic apparatus on and off to match the daily course of light and dark. This is a true clock-driven circadian rhythm because it manifests whether or not the light is on or off, thus is not just a response to a stimulus.
What fascinated us then and continues to bedazzle us now is that this rhythm has an understandable b........ Read more »
Axmann, I., Duhring, U., Seeliger, L., Arnold, A., Vanselow, J., Kramer, A., & Wilde, A. (2009) Biochemical Evidence for a Timing Mechanism in Prochlorococcus. Journal of Bacteriology, 191(17), 5342-5347. DOI: 10.1128/JB.00419-09
- November 8, 2010
- 12:00 PM
- 921 views
Fattening Up Microbial Geological Biomarkers
by Paula Welander in Small Things Considered
by Paula Welander
First Evolved! Last Extinct! This prokaryotic pride motto was coined by my undergraduate advisor (and good friend) Prof. Mark Martin. As a microbiologist, I love this motto for many reasons, but especially because it alludes to one of the underlying principles of my current research. Microbes were indeed the first to evolve and the metabolic inventions of ancient microbes greatly influenced the ancient Earth’s environment and the evolution of life. The interaction between ........ Read more »
Welander PV, Coleman ML, Sessions AL, Summons RE, & Newman DK. (2010) Identification of a methylase required for 2-methylhopanoid production and implications for the interpretation of sedimentary hopanes. Proceedings of the National Academy of Sciences of the United States of America, 107(19), 8537-42. PMID: 20421508
- June 4, 2009
- 10:13 AM
- 898 views
A Nuclear Family
by Merry Youle in Small Things Considered
Certain mussels called “bathymodiolins” are part of the spellbinding fauna of the dark world of oceanic hydrothermal vents and cold seeps. Similar to other metazoans in that realm, they rely on chemosynthetic bacteria for their nutrition. These mussels possess symbionts from two clades of γ-proteobacteria: chemoautotrophic sulfur oxidizers that fix CO2 using sulfide or thiosulfate as their energy source, and methane oxidizers that use methane for both carbon and energy. The symbionts are we........ Read more »
Zielinski, F., Pernthaler, A., Duperron, S., Raggi, L., Giere, O., Borowski, C., & Dubilier, N. (2009) Widespread occurrence of an intranuclear bacterial parasite in vent and seep bathymodiolin mussels. Environmental Microbiology, 11(5), 1150-1167. DOI: 10.1111/j.1462-2920.2008.01847.x
- February 28, 2011
- 12:51 PM
- 869 views
Farmer Joe Dictyostelium
by Moselio Schaechter in Small Things Considered
The practice of agriculture is not limited to humans: ants, termites, and snails all grow fungi, and who knows who else do something similar. But not many have claimed that such activities are to be found among simpler organisms. Now we have a report that slime molds have also gone down the road to agriculture. Dictyostelium discoideum, the best studied of the cellular slime molds, is a social amoeba that thrives by grazing on bacteria. Given ample bacterial food, these organisms grow as single ........ Read more »
Brock DA, Douglas TE, Queller DC, & Strassmann JE. (2011) Primitive agriculture in a social amoeba. Nature, 469(7330), 393-6. PMID: 21248849
- June 27, 2011
- 01:00 PM
- 867 views
Some Like It Curved
by Moselio Schaechter in Small Things Considered
by Elio Think about it: understanding what goes on inside any cell is hard enough. Add to that the complexities of being rod-shaped, and the mind starts to boggle. People have wondered about this aplenty. For sure, many expeditions have set out to explore the poles of rod-shaped bacilli—how they are created, what molecules prefer to reside at this site...... Read more »
Renner LD, & Weibel DB. (2011) Cardiolipin microdomains localize to negatively curved regions of Escherichia coli membranes. Proceedings of the National Academy of Sciences of the United States of America, 108(15), 6264-9. PMID: 21444798
- August 30, 2010
- 01:00 PM
- 862 views
Plasmalogens Have Evolved Twice
by Moselio Schaechter in Small Things Considered
by Howard Goldfine.
Some biologists go blissfully through life without paying much attention to lipids. They do this at their own risk, because there are innumerable things to be learned from their study, including, as we will see here, many relevant to the understanding of evolution. Lipids come in unexpected and exciting varieties, a point that has been acknowledged in this blog (for examples, see here and here)
The lipids that make up the membranes of prokaryotes are polar, that is, they ha........ Read more »
Goldfine, H. (2010) The appearance, disappearance and reappearance of plasmalogens in evolution. Progress in Lipid Research. DOI: 10.1016/j.plipres.2010.07.003
- May 9, 2011
- 01:00 PM
- 857 views
A Protection Racket
by Moselio Schaechter in Small Things Considered
by Merry Youle
Two review papers published last year (click here and here) each devoted many pages to recounting the numerous ways that bacteria avoid becoming phage food. The list of defenses attests not only to the intense selection pressure exerted by phages, but also to the evolutionary quick-footedness of their intended hosts. Because restriction-modification systems (R-M systems) were first detected by their ability to reduce phage infection, they are often present as a shining example ........ Read more »
Stern A, & Sorek R. (2011) The phage-host arms race: shaping the evolution of microbes. BioEssays : news and reviews in molecular, cellular and developmental biology, 33(1), 43-51. PMID: 20979102
Labrie, S., Samson, J., & Moineau, S. (2010) Bacteriophage resistance mechanisms. Nature Reviews Microbiology, 8(5), 317-327. DOI: 10.1038/nrmicro2315
- April 18, 2011
- 12:31 PM
- 843 views
Six Questions About CRISPRs
by Merry Youle in Small Things Considered
Phage predation on bacteria is intense, but bacteria are not defenseless sitting ducks. They make use of a repertoire of diverse strategies to stay even with even the wiliest of phages. First line defenses are those that block phage entry at the door. Often these involve modifying a surface component that is used by the phages as a recognition, attachment, or entry site. Such changes typically carry fitness costs, by impacting essential transporters for example; as a result, phage sensitive stra........ Read more »
Horvath, P., & Barrangou, R. (2010) CRISPR/Cas, the Immune System of Bacteria and Archaea. Science, 327(5962), 167-170. DOI: 10.1126/science.1179555
Karginov FV, & Hannon GJ. (2010) The CRISPR system: small RNA-guided defense in bacteria and archaea. Molecular cell, 37(1), 7-19. PMID: 20129051
Marraffini LA, & Sontheimer EJ. (2010) CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nature reviews. Genetics, 11(3), 181-190. PMID: 20125085
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