Retrospective, July to December 2022
by the STC team
Keeping with tradition, here is a lightly annotated list of our forty-seven posts from the last half year.
Protists
A Dinoflagellate and its Mucosphere by Christoph
There are strikingly different table manners among human cultures past and present when it comes to food ingestion, who wouldn't know. Not so with our single-celled eukaryotic relatives, the protists, who gobble up everything that feels and smells about right? Wrong. Engulfment, as biologists call this behavioral process is a bit like putting a bowl of ramen noodles to your lips and...
In the Company of Bacteria: Amoebae by Christoph
In times long past, highly evolved eukaryotes, for example biochemists, occasionally quipped that bacteria were nothing more than a bag of enzymes. Well, from the perspective of bacteria, one could easily return the compliment: eukaryotes, for example single-celled amoebae, are little more than a...
The first illustration of an amoeboid, from Roesel von Rosenhof's Insecten-Belustigung (1755). Source
Luciferin in Scintillons at Sea by Janie
Summer through autumn is the time of year for marine dinoflagellates' famed light festivals. If the conditions are just right, the roll of an ocean wave or the push of a kayak paddle or the sway of your legs as you wade in deeper is enough to set the waters...
Symbioses
Green Sloths and Robots by Roberto
... in the case of red parrot feathers the pigment has the added benefit of protecting the plumage from bacterial degradation. Today I stay on the topic of animal coloration by describing the peculiar pelage pigment of sloths. Exactly what constitutes an eye-catching color is, of course, in the eye of the beholder.
Ecology
Thinking outside the rod (or coccus) by Roberto
With kind permission by the organizers, we reproduce here an edited transcript of Roberto's talk (via live video) at the meeting on 'Major ideas in quantitative microbial physiology: Past, Present and Future', held in June this year in København, Denmark...
Stream in Isle of Skye, Scotland. Image Roberto Kolter
Psittacofulvin: Polly's Peculiar Plumage Pigment by Janie
In macro-fauna, eye-catching colors typically serve two purposes: to woo potential mates, or to signal that the creature is not a snack and will in fact poison you. This is where parrots diverge – and get embroiled in connections to microbiology...
Is Pseudomonas aeruginosa ubiquitous? by Roberto
Going back several decades I tried to argue that, contrary to popular belief, Pseudomonas aeruginosa is not a ubiquitous bacterium. This was based on our difficulties in obtaining strains from pristine environments, conversations with many colleagues describing similar experiences, and...
Physiology & Genetics
An antibiotic honeycomb by Manuel Sánchez
Atomic force microscopy (AFM) is one of the most powerful tools in studying the surfaces of any material. So it should come as no surprise that it has been used in the study of viral envelopes and biological membranes. One of its great advantages...
Heavy‑duty Traffic, Microscale by Christoph
Mention "flagella" and we microbiologists instantly think of these ingenious appendages that bacterial cells use to propel themselves through fluids of varying viscosities (archaea do this, too, with their archaella). We rarely think of them as an accessory to transport cargo. Yes "cargo," you read correctly, but maybe you remember...
Two head-to-tail oriented E. coli cells moving within a lipid tube (lipid vesicle not visible in the upper right corner). Source
"Off with Their (tRNA) Heads" by Janie
Some bacterial molecules have the social graces of certain 1700s French revolutionaries, or Shakespeare's Richard III, or the Queen of Hearts from Alice's Adventures in Wonderland – in that all share a penchant for beheading those they encounter! In the microbial case...
Shepherding bacteria with specks of light by Helena Massana-Cid
The celebrity among bacteria Escherichia coli, as many other swimming cells, inspects its surroundings by moving in zigzag motion while searching for "greener pastures." Thus, if a group is swimming in a homogeneous area they will fill all available space uniformly...
I → Y → II ? by Christoph
Don't worry, STC won't switch to cuneiform without warning. What vaguely resembles a chemical formula or a cuneiform text is meant to keep the title as short as possible. More verbose: I will take a closer look at Y‑shaped bacteria to see if their "irregular" shape points to their mode of cell division...
Once more: I → Y → II ? by Christoph
In part 1, I looked at Bifidobacterium bifidum to see if the occasionally observed Y‑shape of these bacteria gives any hint on their mode of cell division ─ maybe longitudinal division? No, there is no tangible clue that they divide by splitting their Y zipper-like between the "arms". Here now I ask the same...
How Fairy Tales Taught Us to Think about Science by Chelsi Cassilly
In the tale of the Princess and the Pea, the royalty of a young princess is confirmed by her ability to detect a single pea under 20 mattresses and 20 quilts. This remarkable sensitivity, while likely creating an unbearable life for this princess, pays dividends in the world of immunology where appropriate responses are absolutely crucial.
Escherichia coli – Flagship Bacterium of Molecular Biology by Roberto
There is little doubt that Escherichia coli is a favorite of ours here at STC. E. coli fans from around the world seem to get a special thrill when we post any new development arising from studies on this astonishing model bacterium. We are so taken by it that our coverage has gone beyond describing research. Previously on STC...
Lichen in Roth. ©2021 Christoph Weigel
A Whiff of Taxonomy – Biostraticola tofi by Christoph
No, Biostraticola tofi is not a "flagship bacterium" of molecular biology like E. coli, which was recently celebrated by Roberto. In fact, it's hardly known even among hardcore microbiologists! Yet this species is a close relative of E. coli, loosely speaking a first cousin. But as it goes...
The Very Bacterial Caterpillar by Jennifer Frazer
Glued to the inside of your mouth this very moment (there's a 50% chance) may be plump bacterial caterpillars. They cling to your cheek with paired little holdfasts, like the feet of a tomato hornworm resolutely clasping its stem. Of course, rather than tomatoes and tomato leaves, the diet of these bacteria...
Kitasatospora, a bacterium promoted to honorary amoeba by Christoph
A decade ago, Elio wound up a post on endocytosis by E. coli with the bold remark: "If indeed E. coli is only one protein away from endocytosis, perhaps this work will compel us to cross endocytosis off the list of physiological traits that are exclusive attributes of the eukaryotic cell plan." For sure, expressing human caveolin‑1 in E. coli to force it...
Ice Ice Maybe by Janie
The ability to trigger ice formation is a property shared by certain particles both organic and inorganic, including bacteria, viruses, phytoplankton, pollen, soot, dust. These little particles help water molecules come together and form ice at warmer temperatures than freezing point...
Methodology
Of Terms in Biology: DGGE by Christoph
DGGE, to keep the title short, stands for denaturing gradient gel electrophoresis. You may wonder what an electrophoresis technique is doing in our 'of Terms in Biology' section, but it was once a nifty way to explore microbial diversity in environmental samples. And sometimes it still is, which struck me...
Viruses and Phages
Giant Soil Viruses by Abigail Curtis
My first niche microbiological interest came freshman year of high school, when I discovered that viruses don't solely infect animals. Indeed, viruses are pervasive in every ecosystem, including the smallest ones in the ground. The aspect of viruses in microbial ecosystems...
Retrons Resolved by Mechas Zambrano
Just like solving a crossword puzzle or a sudoku, it is also greatly gratifying when apparently obscure scientific observations are figured out. There are many examples in microbiology of observations that, though they hint at some biological...
Odds & Ends
Rose is a rose is a rose is a... roseota? by Roberto
Give me a chance to quote Gertrude Stein and I'll do so gladly. This time the opportunity was handed to me on a silver platter. On October 2021, almost out of the blue, the International Committee on Systematics of Prokaryotes (ICSP) published a paper with the "names and formal descriptions...
A Rose. Photo by Mechas Zambrano
Consider Keeping Small Things in Perspective by Roberto
Our previous post was a bit unusual for STC, the transcription of a talk I had given a few weeks earlier. First and foremost, I want to express my gratitude to Christoph who proposed the idea for that post. Let me also elaborate on the ending of that presentation...
Applied Molecular Microbiology at Dubrovnik by Roberto
If you are interested in any subject related to small molecule natural products of microbial origin, the "John Innes/Rudjer Bošković Summer School in Applied Molecular Microbiology" is for you. I know that course name is a mouthful so when I am describing the school to microbiologists, I refer to it simply as the "Dubrovnik School."...
Winogradsky Rothko by Christoph
Winogradsky ─ you rightly expect the name of Sergei Winogradsky (1856–1953) to come up occasionally in a blog that Considers Small Things. But Rothko ? One of the luminaries of post-WWII abstract expressionism in the US, the Latvian‑American painter Mark Rothko (1903─1970) is best known for his color field paintings...
No Title [just a very brief rant] by Christoph
We "emphasize the unusual and the unexpected phenomena for which we have a special fascination." And in fact, there are so many exciting troves in the recent scientific literature ─ and in the older no less! ─ that we could easily blog three times a week... at least. But there are, occasionally, dregs of garbage we...
A Message to the Attendees by Elio
With kind permission by the organizers, we reproduce here Elio's message to the attendees of the meeting on 'Major ideas in quantitative microbial physiology: Past, Present and Future' held in June this year in København, Denmark.
The Krebs (Bi)Cycle by Christoph
Today I'm taking you on a short tour, a (bi)cycle tour. Don't be alarmed, it won't be a long ride. And no previous fitness check! You can cycle directly on your screen. A minimum of brain activity is expected though. You guessed it, it's about the Krebs cycle. More precisely: The Krebs (Bi)Cycle. Let's pedal!
The Krebs Cycle. Anonymous. Source The University of Sheffield
Sulfur disproportionation is exergonic in the vicinity of marine hydrothermal vents by Elio
Now that's a title of a paper for you. I confess, it baffled me. At a minimum, I had to look up "disproportionation". What is it? Also known as "dismutation", this refers to a redox reaction in which a compound that is partly oxidized converts to two compounds...
Gram versus Derm by Elio
As you well know, bacteria are divided into two groups, historically known as Gram positives and Gram negatives (Archaea are all Gram negative as they lack the telling peptidoglycan). By and large, Gram positives have a cell envelope consisting of a single membrane and a thick layer of...
Doing Science in Memory of a Bygone Era by Christopher Rensing
In the spring of 1986, I started my studies at the Free University of Berlin. I was accompanied by two friends from Bremen in Northern Germany, Ingo Haar and Roland Beckmann. Roland later performed wonderful work elucidating structure and function of the ribosome.
Nature's Drug Factories: Visualising the Invisible by Munro Passmore
For general audiences, science can often seem impenetrable to understand because of its inherent scale and complexity. This is particularly true in the field of natural products – where we seek to understand the processes microscopic organisms undertake to make molecules we later use as...
Microbes Warming Up to Climate Change by Mechas Zambrano
A week of unusually warm weather for November in Boston, MA, and an online presentation on the perils of climate change have triggered my inner alarm in anticipation of troubles to come. We are well within the epoch recognized by some as the "Anthropocene," in which humans have become the major force behind global change.
Summer Courses in Microbiology by Roberto
These days in New England – specifically in Cambridge, where I am now – the air is crisp as the temperatures are beginning to drop and the leaves are already displaying magnificent colors. Fall is in full swing, and summer is a memory. But this past summer, once again, left me with the delightful memory...
Spetses "The New Microbiology" Summer School by Roberto
Participants of the Spetses Summer School first travel to Athens and then embark on a nearly three-hour ferry ride across the Saronic Gulf to reach Spetses. Consequently, almost everyone is tired upon arrival. But no matter how exhausted, everyone feels invigorated by the magical feeling of...
Scientific Publishing – eLife's Reviewed Preprints by Roberto
Just over five years ago, George O'Toole and I had a conversation about scientific publishing which we posted at STC. After some harsh comments critiquing for-profit scientific publishers, journal impact factors, and predatory journals, we turned to thinking about solutions. George indicated some guarded enthusiasm for the...
Book Reviews & Fine Reading
Fine Reading: Antonie van Leeuwenhoek by Mechas Zambrano and Roberto
The earliest roots of science can be traced to ancient times in which so-called natural philosophers attempted to explain the world around them. However, the word science, coined in the 14th century, and the concept of science as the pursuit of knowledge...
Replica of a Leeuwenhoek single-lens microscope. Photo credit: Scott Chimileski
Primo Levi's periodic table, and when scientists write fiction by Janie
There are lots of fantastic books that convey love of a science, depict the braided lines of logic and intuition and luck in experimentation, and depict scientists' lives both in and beyond the lab. Memoir, fiction, biography. Science as metaphor for life, these books will frequently allude to...
Book Review: Transformer by Janie
Here is a quote from the Hungarian biochemist Albert Szent-Györgyi: "Life is nothing but an electron looking for a place to rest." Bold statement with a good point, encapsulating the energetics and chemistry that underlies all life... This is the angle of viewing life on Earth that...
In Memoriam
Angela Restrepo — Living on Through Memory by Mechas Zambrano
Today we can easily bring to mind the names of many women scientists who serve as inspiration and role models. But this was not always the case. Even in the mid-20th century, women in science were few and far between, especially in developing nations...
Pepe Casadesús (1951─2022) by Roberto
If you ever visited the Department of Genetics at the University of Sevilla, Spain, you most likely met Josep Casadesús; Pepe as he was universally known. If you were so very fortunate, I am sure you still have lasting and wonderful memories of that encounter. Doubtless, you will remember how he...
Talmudic Questions
#197 Why aren't any Archaea known to make spores?
#198 Biologists are often criticized because they do not have a watertight definition of 'life.' Is that really so bad? Does that make biology a 'lesser' science?
#199 Biosynthetic genes for many antibiotics evolved hundreds of millions of years ago. Resistance genes evolved concurrently among neighboring bacteria. If most neighbors to antibiotic producers are resistant, what is...
#200 what is the leading cause of bacterial or archaeal death?
#200 ─ Our Twitter Poll To celebrate our two hundredth Talmudic Question "What is the leading cause of bacterial or archaeal death?" we made a poll on Twitter. Thanks to our followers we received more than 100 votes, wow! We suggested the following as possible answers, presented here...
#201 Given that today is the day that the US celebrates Thanksgiving... What is Pseudomonas syringae pv phaseolicola – inhabitants of the green beans used for the traditional casserole – most thankful for?
