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

The first illustration of an amoeboid, from Roesel von Rosenhof's Insecten-Belustigung (17­55). Source

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...

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...

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...
 

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

Stream in Isle of Skye, Scotland. Image Ro­­­berto Kolter

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...

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...

Two head-to-tail oriented E. coli cells moving within a lipid tube (lipid ve­sicle not visible in the upper right corner). Source

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...

"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...
 

Odds & Ends

A Rose. Photo by Mechas Zambrano

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...

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 Cycle. Anonymous. Source The University of Sheffield

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!

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

Replica of a Leeuwenhoek single-lens mi­cro­scope. Pho­to credit: Scott Chimileski

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...

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?