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 21, 2009

How Proteomics Got Started

by Fred Neidhardt

A-van_gogh-starry-night2

Van Gogh's Starry Night. (1889)

The following is a personal account of the beginning years of what is now called proteomics. Odd that I, almost a Luddite, should be writing about the origin of a field initiated by a dramatic technical advance; I tend to avoid complex new scientific instruments and techniques. As a graduate student under Boris Magasanik at Harvard Medical School during the early 1950s, I was glad that my project (induced enzyme synthesis in bacteria) could readily be approached with simple technology. Bacterial growth could be monitored turbidimetrically with a Klett colorimeter; the same instrument could provide colorimetric assays of enzyme activities. Only the phage geneticists of that era, using sterile toothpicks to pick viral recombinants or mutants from plaques on Petri dishes, had it technologically easier.

Around me at that time in Harvard University’s Department of Bacteriology and Immunology (now Microbiology and Molecular Genetics) were gifted individuals who on occasion were forced to purify proteins using laborious and personally onerous techniques. Not a life for me, I decided, even though H. Edwin Umbarger assured me that purifying an enzyme “developed character.”

Beside laziness, there was a second, more fundamental, reason I never purified a protein. Cell growth was the biological event that had hooked me as a graduate student, and work that began by smashing cells into little bits seemed inappropriate.

Nevertheless, within the next six years I would find myself absorbed in two major aspects of cell growth physiology that involved proteins, and these subjects would prove more intractable than the purification of proteins. Catabolite repression (or, more generally, how bacterial cells choose to utilize multiple carbon sources), and growth rate modulation (how bacterial cell size and composition are interrelated with growth rate) were two processes directly related to cell growth rate.

Continue reading "How Proteomics Got Started" »

December 17, 2009

Bacteria of a Feather…

Hoopoe

Common Hoopoe (Upapa epops) in Hodal, India. Source.

by Elio

Just when we thought we'd heard it all, along came a study on the bacterial degradation of bird feathers. We admit we hadn't previously spent much time contemplating the possibility that feathers would be susceptible to bacterial degradation, just like any other keratin-containing structure. But to a bird, this is a matter of vital importance.

Several bacteria, chiefly Bacillus licheniformis, live in the barbules, the terminal branches of the barbs of a feather. Feathers are 90% keratin; B. licheniformis secretes a keratinase. In the laboratory, B. licheniformis can completely degrade a feather in 24 hours, and this demolition occurs in vivo (or “in avis”), as well. But birds have powerful defenses against such pterophagia (“feather eating” from the Greek pteron, "wing," and phagein, "to eat"), including chemicals in the preening secretion they use for feather grooming. The bird does not face this confrontation alone. Bacteria such as enterococci that reside in its preening gland (known as the uropygial gland) produce anti-licheniformis bacteriocins. That these enterococci are present only in nestlings and females (and in the latter only during the breeding season) suggests that the interaction matters mainly while the birds are confined to the nest—a hole in a tree—because, perhaps, of the greater likelihood of infection then.

Continue reading "Bacteria of a Feather… " »

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.

December 10, 2009

Talmudic Question #56

The genie has returned. (He first visited here.) During a moonlit walk on the beach, you stub your toe against a bottle, which rolls against a rock and shatters. A genie is liberated, eager to grant you one wish. You ask for a microbiological laboratory fully equipped to your specifications. The genie grants you that but with the condition that you can study only one organism. Which would you choose?

December 08, 2009

Ways to Go

by Elio

The special issue of Science of 27 November 2009 (Volume 326, Issue 5957) focusing on Spatial Cell Biology contains a larger than usual number of items with a microbial focus. Although only one1 of the six featured Reviews on the topic in question is microbial, three of six Perspectives2, one of two Research Articles3, and three of twelve Reports4 fit the bill.

Readers of this blog need not be reminded that if Science reported on the living world in proportion to the numbers and to the past and present importance of living organisms, the biological portion of each issue would be at least 90% microbial in content!

1L. Shapiro et al., Why and How Bacteria Localize Proteins.
2Norman Letvin, Moving Forward in HIV Vaccine Development; J.F. Banfield and M. Young, Variety—the Splice of Life—in Microbial Communities; H. Ochman and R. Raghvan, Excavating the Functional Landscape of Bacterial Cells.
3S. Kühner et al., Proteome Organization in a Genome-Reduced Bacterium (Mycoplasma).
4E. Yus et al., Impact of Genome Reduction on Bacterial Metabolism and Its Regulation; M. Güell et al., Transcriptome Complexity in a Genome-Reduced Bacterium (Mycoplasma); R.G. Tawar et al., Crystal Structure of a Nucleocapsid-Like Nucleoprotein-RNA Complex of Respiratory Syncytial Virus.

December 07, 2009

A Matter of Timing: Yellow Fever and the Mosquito Hypothesis

by Welkin Johnson

Over half a century ago, initiation of worldwide vaccination programs drastically curtailed the spread of yellow fever. In recent years, however, the disease has re-emerged, with Central and West Africa being hit particularly hard. Last month, the WHO’s Yellow Fever Initiative launched a campaign aimed at vaccinating 12 million persons in Benin, Liberia and Sierra Leone. In light of these events, it seemed an appropriate moment to look back on the year 1900 and the role yellow fever played at the birth of virology as a scientific discipline.

Telegram

Telegram from J.R. Kean to Mabel Lazear. Courtesy of
Historical Collections Services, Claude Moore Health
Sciences Library, University of Virginia. Source.

On September 26, 1900, Major Jefferson Randall Kean, an army surgeon stationed in Cuba, sent a message by telegram to Mabel H. Lazear of Beverly, Massachussets. Painfully brief, his words belied a major discovery in the annals of microbiology: Dr. Lazear died at 8 this morning – Kean.

Jesse Lazear was a member of the U.S. Army’s Yellow Fever Commission in Cuba, a team headed by U.S. Army surgeon Walter Reed and including, in addition to Dr. Lazear, James Carroll and the Cuban Aristides Agramonte. In the weeks preceding his illness, Lazear experimentally transmitted yellow fever to a handful of human subjects by exposing them to the bites of mosquitoes that had previously fed on patients with yellow fever. Experiments conducted by others had failed and the mosquito hypothesis, championed since 1881 by the Cuban physician Carlos Findlay, had fallen out of contention. Although Lazear’s notes are unclear on the point, Reed and others believe he played a hand in his own death, intentionally including himself among the experimental subjects.

Continue reading "A Matter of Timing: Yellow Fever and the Mosquito Hypothesis" »

December 03, 2009

The Attendee's Guide to Scientific Meetings

by Julian Davies

IMG_0299

A balcony is the ideal place from which to scope out a
group before joining the melee.

There are many aspects to the business of going to a scientific meeting. Different protocols are required for meetings of different sizes and classifications. A general meeting, such as the massive ASM or ASBC gatherings, attract many people with many justifications for attending; it is difficult to provide guidelines for meetings of this type unless you are an invited speaker or a poster presenter. In these latter cases, being as you are there as an invitee, you must make the effort to justify your invitation. You are there to perform, to present your scientific efforts to a larger audience for evaluation. As a privileged attendee, it is your responsibility to showcase your work in the best possible manner. If giving a talk, rehashing old PowerPoint slides simply will not do; your audience is expecting something new, interesting and stimulating (more on this to come later).

Attending one of the mammoth meetings, such as the ASM general meeting, year after year is common practice for many people—perhaps for you. This may be due to the fact that when you are a member of a committee or an Editorial Board, the annual meeting is a convenient place to meet and discuss why the impact factor of your journal is going down, when everyone else’s is going up. However, there is another, perhaps more compelling reason to attend these large congregations, and that is to see old friends and to make new ones.

Continue reading "The Attendee's Guide to Scientific Meetings" »

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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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