Retrospective, December 2017

by Elio
 

As is our custom, we provide a lightly annotated list of most of our posts (with links) from the past half year.
 

Evolution

• Evolutionary Ways
  Merry discussed how, when it comes to her beloved phages and their hosts, evo­lu­tionary leaps follow a sequence of small beneficial steps.

• Old Enzymes Tell Stories
  Elio presents two papers that propose that the lack of specificity of early enzymes may be put to good use.

• In the Beginning… there were Stromatolites
  Graduate student Gillian Belk discusses a paper showing how stromatolites are formed in real time. Today!.

• Accidental Complexity
  Christoph brings up how yeast enzymes reveal the role of 'accidental complexity' in evolution. Read it to find out what this means..

• Celebrating Woese – Forty Years and Entirely New Views of the Microbial World
  Roberto and Elio schmooze about the exciting things that have happened in microbiology since Woese.

• Fine Reading: A Chalk Talk
  Roberto brings up a glorious piece of writing by the early evolutionist Thomas Henry Huxley, whose 'manifesto' is a must read if there ever was one.

• To Not Get Lost in the Trees of Life (ToL)
  Christoph enlightens us about the intricacies of modern day tree-making.

Diversity

• Curioser and Curioser
  If you never heard of Kakabekia barg­hoor­ni­ana, don't worry. Here is where you can remedy that.

• A Lakeside Tale
  Christoph tells of the good time he had looking at the largest non-marine bacterium, Achromatium oxaliferum, which of all things, has many dozen nucleoids that are genetically different, all in the same cell!.

• Heat, Hydrogen, and Togas
  How a heat-loving bacterium may help turn garbage into hydrogen in a big way. Elio says that, according to Tunisian and French researchers, you just add seawater.

• Stalking Caulobacter
  Christoph has fun with the stalk of this organism and its amazing tensile strength. Not only that, it can be used to study how Caulobacter ages.

• A Whiff of Taxonomy: The Life and Times of Deinococcus, "Conan the Bacterium"
  Graduate student Alex Neu focuses on Deinococcus radiodurans and its endurance and how it may help mankind.

Ecology

• Who Dares Doubt The Decomposing Powers Of Fungi?
  David Lipson, an old friend of this blog, discusses a paper that debunks the idea that it took some 120 million years for fungi to learn to decompose plant material.

• My Home is My Microbial Castle
  Roberto tells two tales of the microbiology of the built environment, one comparing urbanized and low-income housing, the other showing the distinctions arising from different agricultural practices.

• A Fascination with Caves
  Elio, hardly a speleologist, is nonetheless taken by the ways of microbes in caves. Here, he talks of making 'moonmilk.' Find out what that is.

• Voyage to See What's at the Bottom
  Roberto and Elio worry that the DNA from decaying organisms falling to the sea bottom may greatly distort metagenomic studies.

• Living Off Air
  Roberto celebrates the climactic aspects of the season by describing what microbial life in the Arctic is like in the absence of obvious sources of carbon.

Friends and Foes

• The Spell of Coxiella
  This fascinating parasite reveals further surprises. As Elio discusses, it undergoes horizontals gene transfer, which is strange thing to do for a strict intracellular parasite.

• Let's Get Ready, Xylella Has Arrived in Europe
  Our friend in Spain, Mercé Piqueras warns of the possible onslaught of olive trees by the bacterium Xylella fastidiosa, and what could be done about it.

• Why Be Intracellular and Be Motile?
  A conundrum: why are some strict intracellular parasites motile? Where do they think they’re going? Not so simple, as Elio discusses here.

• A Bacterial Aphrodisiac
  According to Elio, sex is complicated, especially among the choanoflagellates, and it involves their bacterial friends.

Physiology

• Microbial Physiology and Diversity: What Was Old is New Again
  George O'Toole celebrates the wonders of microbial physiology and its current renaissance.

• News From the Missing Methanogenic Archaea Front
  Methanogenic archaea (are there any other kinds of methanogens?) are said to derive from halophiles. Elio says that a halophilic archaeon that makes methane has finally been found.

• "We Are What We Are"
  Christoph discusses how CRISPR is activated by quorum sensing. Two great topics come together, not surprisingly, in that versatile microbe, Pseudomonas.

• Investing in Diversification: Transport of Vitamin B₁₂ Analogs by Microbes of the Human Gut
  Daniel and Elio discuss the great diversification of vitamin B₁₂ and its relatives and speculate that they may act as signaling molecules between bacterial species.

• The Human Circadian Rhythm is a Microbial Business
  Elio presents a paper showing a perhaps unexpected relationship between our microbiota, circadian clock, and metabolism.

Viruses

• When it comes to HERV-K, I beg to differ
  Jamie discusses the 'insertional polymorphism' of human endogenous retroviruses and why more may be lurking in the human genome. Human genomicists, take note.

• tRNA Chop Shop: Retrotransposons Beware
  Jamie talks about the silencing of endogenous retroviruses by small RNAs, this time in mice. Epigenetics is involved.

• The Phage Meeting – Conferencing with Ice Cream in America's Dairyland
  Graduate student Ananya San attended this illustrious conference and tried to quench her feverish enthusiasm with ice cream.

• Phage Phactories
  Merry tells of a fascinating story that connects phage replication and structural proteins. The plot thickens – the result are structures with an eerie resemblance to eukaryotic nuclei!

Reviews

• Life at the Edge of Sight – Review of a Book by Scott Chimileski and Roberto Kolter
  Brian Barry, a retired nuclear engineer and a friend of microbes, explains why this book works so well for laymen as well as for microbiologists.

• A Star-Studded Phantastic Voyage of Phages
  Jamie had the joy of reviewing a masterpiece of a book, our own Merry Youle's 'Thinking Like a Phage.' In the spirit of the title, she worked that out.

• E Pluribus Duo: A Review of Two Recent Books on Microbiomes
  Daniel discussed two books written for the general public, ‘I Contain Multitudes’ by Ed Yong and ‘The Hidden Half of Nature’ by David Montgomery and Anne Biklé.

• Fine Reading: No Growth!
  Roberto shares his enthusiasm for a gem of review on bacterial growth by Dianne Newman and colleagues.

• Voices and Perspectives from the Past: Memoirs of Scientists and Departmental Histories
  Daniel discusses general issues concerning historical books and highlights two: 'To Make the World Intelligible' by Frank Harold, and 'Microbes at OHSU: History and Stories,' by Linda Crosa.

Miscellanea

• Miraculous Microbes
  STC bloggers decided that some phenomena are close to miraculous. See for yourself.

• Thinking About Science
  Roberto muses about such issues as funding, publishing, and job security (not his).

• How to Calculate Avogadro's Number
  We revisited the odd coincidence that 'the number' is close to that obtained by multiplying the (probable) number of bacteria in the body of one human by the number of humans (which, alas, is a moveable feast).

• Plimpton v. Muybridge
  Christoph has a romp about how DNA compares with Babylonian clay tablets as an information storage system.

• Scientific Publishing – A Conversation
  George O’Toole and Roberto have an animated chat about the many sides to scientific publication in today's turbulent world.

• Robert E. Hungate – Grandfather of Anaerobic Microbiology
  Graduate student Jonathan Lin presents a lively discussion of this pioneer in anaerobic microbiology, 'Mr. Rumen' in his time.

• Of Terms in Biology
  We had two this period: FRET and Zoospore.

• My Favorite Talmudic Questions
  Claiming that he is sometimes asked which are his favorites, Elio reveals this well-kept secret.

• Talmudic Questions
  We posted Talmudic Questions #147 – 150 in this period.