Retrospective, June 2016

by Elio

We continue our custom of listing the posts from the last half year, lightly annotated. Could retrospection lead to introspection?

Arts and the Microbes

Photo Credit: Unhindered by Talent

• Art about Small Things. Christoph introduces artist Lindsay Olson and muses about art and science.

• Working on Art about Small Things. Lindsay Olson tells us how she consults with biologist to draw lovely images of protists.

• Agar Art Contest an All-Around Winner. Co-blogger Jamie Henzy explains that ASM has sponsored a contest of Petri dish art. The contest continues.

• Movies & Bugs: The movie The Martian is reviewed by Manuel Sánchez. Lots of microbial wrinkles.

• Movies & Bugs: Medicine Man. Manuel reviews another movie with microbial connections.

The World Out There

• A Sphere of Free Food. Graduate student Rachel Diner discussed recent advances in the interaction of bacteria and the marine phytoplankton, clever fmicrofluidic devices and all.

• Who Feasts on Volcanic Fluids? Recent graduate Than Kyaw introduces the "snowblower vents" which spew white flocs of bacterial. Interesting orange flocs of iron bacteria are found nearby.

• Raindrops Keep Falling On Their Heads (Thanks To Mushroom Spores, That Is). Elio discusses a paper by Ni Money and colleagues that studies the possible role of fungal spores in making raindrops. Lots of such spores in the air.

• Gulliver and the Lilliputians, revisited. Christoph tells us that bacteria in some natural environments are tiny indeed, but not before making a detour into "metagenomic binning." Evolutionary musings ensue. He gives us a close up view of these Lilliputians.

• New Bug in Old Bottles. Christoph tells us of good news on the plastic degradation front. Meet Ideonella sakaiensis 201-F6, a Be­ta­pro­teobacterium from the larger Co­ma­mo­nas family, that can degrade PET. Marine organisms should feel relieved.

Bugs and Us

• A Passing Observation. Elio points out that "fecal microbiome" and "intestinal microbiome" should not be used interchangeably.

• Weakening The Mycolic Acid Fortress of M. tuberculosis. City University of New York graduate student Monika Buczek discusses the genetics of mycolic acid synthesis, the tubercle bacillus defensive armor.

• How Can Microbes Contribute to the "War on Cancer?" Elio wonders how microbes can contribute to the White House newly announced war on cancer.

• The Enemy of My Enemy is My Friend - A Microbial Solution to The Emperor of all Maladies. Elie Diner gives examples of how this may be done: bacteria hone in to the inside of tumors where the conditions are often anaerobic, and other bacteria may help diagnosis cancers.

How Things Work

• Seeing from the Bacterial Point of View. UC San Diego graduate student Mizu Ota and Professor Susan Golden tell us how round cyanobacterial cells work as a lens to focus light on side opposite the light soruce. This helps them tell which way to move.

• The Red Queen – Running Uphill. Christoph explains how to think about the "fitness landscape" that is explored by bacteria in their evolution. Lenski’s lab explores what happens over 50,00 generations, using competition experiments, and alternative models.

• Evolution? Who Needs It Now That We Have CRISPR/Cas9s? Science writer Marcia Stone and her Vogon friends bring up the point that CRISPR technology may be a way around evolution. But let’s be careful…

• Let's eat! Bdellovibrio bacteriovorus couples predation with replication. UC San Diego undergrad Jacky Lu discusses work done with “ghost cells” to recognize the cues used by these predator bacteria to select their prey.

• An Electrifying Chemiosmotic Exchange. Margaret Lee, a professor at Ohlone College asked: How do Gram positive bacteria carry out chemiosmosis while seeming lacking an enclosed (periplasmic) membrane space? This led to a lively exchange with expert Frank Harold.

• The Evolution of Death or: Is There Anything that the Eukaryotes Invented? Co-blogger Jamie Henzy introduces us to the notion that the SOS response responds differently to the extent of DNA damage. Strong activation happens via the RecA system, moderate activation via the MazEF pathway. Complicated but exciting.

Viruses, Viruses

• Active Lysogeny Regulatory Switches: Scars That Can Make Genes Whole. Co-blogger Daniel explains the concept of "active lysogeny regulatory switch." It deals with the fact that "even if temporary, provides an ecological window for the evolution of mutually beneficial functions." The frequency of genomic rearrangements attests to that.

• Need Protection? Hire a Virus! Co-blogger Jamie Henzy has a way with viruses. Parasitoid wasps lay their eggs in insect larvae, where they must cope with the resident immune system. How to handle this? Use a virus, one inserted into the wasp’s genome.

• Need protection? Hire a virus! – Part Deux. Jamie, still on the topic of genome integrated viral sequences, explains that depending of where it integrates, a virus will alter the expression pattern of host transcription factors, ergo influence the expression of multiple host genes in a coordinated fashion.

New Approaches

• Opening Windows into the Cell. UC San Diego graduate student Kanika Khanna introduces a technique for making thick objects visible by cryo-electrontomography. Abrade away some of the material until the object becomes thin enough! The technique is called Focus-Ion Beam Milling.

• How to Make a Photosynthetic Bacterium in One Simple Step. Elio isn't kidding. Coat an ordinary non- photosynthetic bacterium with cadmium sulfate beads and it can fix CO2! It makes acetate with it, then biomass.

Bits of History

• Leftover Science. Some results from anyone’s lab in time hit a wall, there to lie dormant and forgotten. Elio recounts one such.

• How did E. coli  get named K-12? Mehmet Berkmen and Paul Riggs had a good time trying to figure this out, even if they weren’t entirely successful.

• Van Leeuwenhoek's freshwater microorganisms in 1674. Spirogyra or Anabaena? Nanne Nanninga tell us that a Dutch microphotographer, Wim van Egmond reinterpreted what Leeuwenhoek saw when he looked a coiled filamentous organisms: they were probably the bacteria Anabaena, not the algae Spirogyra. Once again, prokaryotes came first!

• In the Company of Microbes: Ten Years of Small Things Considered. This is Elio’s newest book, consisting of excerpts from this blog. He favored items of general interest, such as musing, historical perspectives, and the likes. With doodles from his artist daughter Judith. A kind comment in Amazon.com says, among other things: "A refreshing and motivating quick read that makes it seem as if the reader is at the bar eavesdropping on a great conversation." Muchas gracias.

Miscellanea

• How All Living Things Are Connected (In An Exam). A collection of 11 papers written for the midterm exam of the UCSD/SDSU graduate course Integrative Microbiology that Doug Bartlett and I teach. We gave students the option of answering this Talmudic-type, open-ended question: How would you go about defending the statement that "all living things are connected to other living things" to an educated lay audience? What examples would you present to illustrate how pervasive this is in the living world?’

• Take your kids to the bugs on a Sunday afternoon – Micropia, the world's only microbe zoo in Amsterdam. Mathias Grote, a microbiologist turned historian of science, takes on a tour of Micropia in central Amsterdam.

• At first, 4.6 million sounds like a lot, but in term of moles, it's nothing… Elio mentions that Bernd Heinrich in his book “The Trees in My Forest” notes that one cell in his tree takes up 4.6 million CO2 molecules a second, which sounds like a lot (but isn't really).

• Fine Reading: Insights Into How We Got Here. By Elio. Bernie Strauss wrote a fine account of how Beadle and Tatum revolutionized genetics.

Minibits

• A Snippet: Oceanic Conversations. By Elio

• A Snippet of Recent Microbial Reads. By Daniel Haeusser

Pictures Considered

• Pictures Considered #33. Viral Abundance and Diversity. By Elio

• Pictures Considered #34. The first look at the two membranes of Gram-negatives. By Elio

• Pictures Considered #35. The Isolation of the Inner and Outer Membrane of E. coli. By Elio

• Pictures Considered #36. The Discovery of Bacterial Minicells. By Elio

• Pictures Considered #37. The Queen's Necklaces. By Christoph