by the STC Team
In keeping with tradition, here is the list of our posts from the last half year (the images are taken from the posts with titles marked in bold).
Evolution
E. coli Proto-Genes by Roberto — How do bacteria come up with new genes? I intentionally did not use the phrase "acquire new genes" because, as most STC readers might know, horizontal gene transfer is likely the most frequent way new genes end up in a bacterium's genome. What I ask now is different. After more than four billion years of evolution, are bacteria still giving birth to new genes 'de novo' ?
Protists
L. olor cellular features. Top: the long "neck" of L. olor. Source Middle: the distinct cell morphologies between active contracted and active elongated states in live cells imaged using differential interference contrast (DIC) microscopy. Scale bar, 40 μm. Source Bottom: confocal fluorescence z-stack projection of an α-tubulin–stained fixed cell reveals the helically arranged cortical cytoskeleton. Source
A Whiff of Taxonomy – Lacrymaria olor by Roberto — I was recently made aware of one of Earth's "most interesting living beings owing primarily to its power of elongation, its wonderful elasticity and its great freedom of movement." Thus begins a captivating 1911 article by S. O. Mast, describing the amazing features of the ciliate Lacrymaria olor.
Physiology & Genetics
Pseudouridine, antibiotics, and blue by Janie — Pseudouridine, an isomer of uridine, is perhaps now most widely known for its critical role in the success of the COVID-19 mRNA vaccines. Three years ago on STC, Roberto wrote an appreciative note about this key feature of the vaccines, the N1-methylpseudouridine that acts a bit like an invisibility cloak...
Through The Pilus by Roberto — Among the many mechanisms of bacterial horizontal gene transfer, conjugation, the plasmid-mediated cell-to-cell movement of DNA, holds a special place in the heart of this old-timer E. coli geneticist. Its discovery not only allowed genetic mapping through "interrupted mating" experiments, it also opened the door to studies on the regulation of gene expression (witness the famed PaJaMo experiment).
A Whiff of Taxonomy – Pendulisporaceae by Christoph — Microbiologists have always been fascinated by myxobacteria, that is for over a hundred years, because of their lifestyle, coordinated swarm hunting, and their ability to form spore‑containing fruiting bodies, an easily visible but unique differentiation feat among bacteria. And for just as long, microbiologists have been tearing their hair out over the difficulties of cultivating these hunter-gatherers in the lab...
A Whiff of ...Replication – Pendulisporaceae by Christoph — Just to quote myself here: When microbiologists describe a previously unknown bacterium, they are mainly interested in its lifestyle, metabolism, morphology and cell cycle. And to continue with the self-quotation: For me, "getting to know" newbies always involves finding out how they initiate the replication of their chromosome(s)…
(A) Phase-contrast micrograph of a rosette of P. bekefii, showing non-cellular stalks radiating towards a central phase-light granule from spherical cells at the rosette circumference, some of which possess buds. Micrograph taken during collaborative research of the author and J. T. Staley (Dept. of Microbiology, University of Washington). Bar,10 µm. Source. (B) Pg, a rosette of P. gracilis with at least 11 visible filaments ; Pb, a small, three-membered rosette of P. bekefii, the type species of the genus Planctomyces and morphotype la of the Blastocaulis-Planctomyces group of budding and nonprosthecately appendaged bacteria. Bar, 5.0 μm (Not visible in this cutout). Source
Rosette is a rosette is a... (1|3) by Christoph — I dare say that every biologist was blown away when they, a decade ago or so, first saw pictures of spherical rosettes that choanoflagellates can and readily do form. Is this emergent multicellularity? Skilled microscopists had long been aware of such "rosettes" among (some) bacteria, but they never made it into the canon of bacterial shapes as they only form under certain growth conditions.
...rosette is a rosette is a... (2|3) by Christoph — I like to imagine that microscopists in the late 19th century who looked at water samples were happily surprised when they saw organized structures of cell clusters in the whole tangle of protists and bacteria, which they then liked to call “rosettes” because these were structures known from botany. And on closer inspection, it turned out that some of them were actually bacterial rosettes…
...rosette is a rosette. (3|3) by Christoph — Among the Alphaproteobacteria, a number of species from phylogenetically distantly related orders are known for forming rosettes during growth. Despite commonalities, they all have their own peculiarities when it comes to the first cell‑cell contact(s) during "rosetting". Phaeobacter inhibens (order Rhodobacterales) cells attach to each other by their "sticky ends" at one pole...
Thoughts on O-Antigen Variation by Roberto — The O-side chains of lipopolysaccharides (LPS), the outer most feature of most Gram-negative's outer membrane, are highly variable in terms of their chain length and chemical composition. In my last post, I described how the O-side chain of some bacterial strains serve as a settlement and metamorphosis cue for a marine invertebrate. My thoughts immediately took me to this question: What was the early evolutionary history of O-side chain variability?
How to grow shrubs by Christoph — Exactly eight years ago today, we introduced you to the 'Hedgehogs In Your Garden'. No, we had not turned our backs on the Small Things and became gardeners instead. Again today, it is not about gardening activities, namely, 'How to grow shrubs'. Let me explain...
A lesson from the comb jelly, deep-sea bacteria, and some obliging E. coli on how to thrive under pressure by Janie — I sometimes google "Small Things Considered + a biological term of choice" looking for older articles, to see if any paradigms have changed in the span of a decade or so. In doing so, I came across this post from 2010 on plasmalogens, membrane lipids with an ether bond linking the glycerol...
Odds & Ends
On Forgetting by Mechas — A recent essay by Melissa Kirsch of the New York Times highlights what seems to be a prevalent concern: forgetfulness. The constant exposure to an ever-growing barrage of media, especially as we grow old(er), has its toll. Even though remembering and forgetting are essential to processing information and learning as we meander through life, an excess of data can result in overflow and storage problems.
The Deep Biosphere – A Video by Roberto — It may be because it carries on so very slowly or because it is so deeply buried. Who knows, but I find the abundant microbial life of the deep biosphere thoroughly mesmerizing. That's why I was thrilled by a video on the subject that Memo Berkmen – long-time friend and STC fan – brought to my attention. It's only natural that I now share it with you.
Fig. 1. A published (but rarely seen) illustration by Angelina Hesse from a 1884 publication from Walther Hesse about quantifying microbes in the air showing colonies of fungi and bacteria on solid media. Plate XI from source.
Have you ever heard of Fanny Angelina Hesse? by Corrado Nai — A graphic novel about this forgotten woman in science is on its way – but it's unlikely to make an impact without the strong support from the microbiology community. If you have never heard Fanny Angelina Hesse's name, what's your excuse?
«Anything that can be regulated... by Christoph — ...will be regulated» Thus goes a lesser‑known but tried-and-tested amendment of Murphy's law among molecular biologists. Practitioners, especially students struggling with their own first PCR and cloning experiments in the lab, are familiar with the original «Anythings that can go wrong will go wrong, and at the worst possible time.» I don't need to dwell...
Digital Sequence Information by Mechas — Microbiologists regularly use sequence data without giving it much thought. What will surprise many scientists is that its use is now being hotly debated in international scenarios such as the Convention on Biological Diversity (CBD).
How E. coli Rose to Prominence – An Addendum by Roberto — In an era of microbiology largely dominated by research surrounding previously unimaginable extent of microbial diversity, here at STC we still have a strong affection for the advances made investigating model bacteria; prime amongst these is E. coli. Thus, it is no surprise that we are fascinated by the history of E. coli research.
How E. coli Rose to Prominence – Just One More Addendum (1|2) by Christoph — While Roberto looked deep into the fascinating past of 'How E. coli rose to prominence' in two of his recent posts, I will take a look around ahead here in 'Just One More Addendum', and a wider look around in 'Again, One More Addendum' in an upcoming post. But that was it for the time being with this 'Ecolimania' here in STC...
How E. coli Rose to Prominence – Again, One More Addendum (2|2) by Christoph — In the fourth and, for the time being, last episode of this 'Ecolimania' in STC, I take a look around: Do we know the diversity of the species E. coli ? And what can we learn from analyses of its pangenome ?
Extreme ORFs by Roberto — If you were to plot the frequency of all known open reading frames (ORFs) as a function of the number codons they contain you'd see a broad distribution showing an average of about three hundred codons and a long tail of very long ORFs. Just for fun, what are the very end points of the graph? What is the longest ORF known? And the shortest?
Genomes by AI by Roberto — Two years ago I played, simultaneously amused and bemused, with ChatGPT. It was clear artificial intelligence (AI) had taken a quantum leap. While I did not get to play with it, reading about Evo last week evoked similar feelings; it left me both in awe and slightly unnerved. In case you missed it, Evo does with genome sequences what ChatGPT does with words, i.e., almost everything.
Ecology & Evolution
Sequencing en Masse by Roberto — For someone who learned how to determine a short DNA sequence, say 50 bases, by first transcribing a DNA fragment into RNA and then sequencing the RNA using the laborious fingerprinting approach (that was 1975), current DNA sequencing is nothing short of miraculous.
From Life at the Edge of Sight by Scott Chimileski & Roberto Kolter
Larval Settlement by Roberto — Animals originate, evolve, and undergo development in a microbial world. A beautiful example of how animal development is guided by bacterial chemical cues is the metamorphosis of the bottom dwelling marine worm Hydroides elegans.
Of Terms in Biology: Edaphon by Roberto — Soil, the material on the surface of the ground on which plants grow, is itself teeming with life. And there's a term that unifies all that life as an interconnected whole: edaphon. Though it is seldom found in the scientific literature, I will argue that it should be more widely taught and used.
The Dawn of Molecular Ecology by Roberto — Almost exactly one year ago, I wrote a post on the key role played by a group of Spanish scientists in the early development of microbial molecular ecology. My main point was to drive home how the work they carried out in the early 1970s on species successions in the human gut...
Microbial Solutions for Climate Change by Mechas — News media are packed with warnings about climate change – those long–term shifts in temperature and weather patterns that today are largely attributed to human activities. Microbes, inextricably linked and key to planetary health, offer sustainable solutions.
Pictures Considered
Pictures Considered #62 : Myxococcus swarm‑hunting E. coli by Christoph — It is boring to look at swarm-hunting Myxococcus bacteria in still images, you don't get any impression of their speedy efficacy. Therefore this is, again, not a "pictures" considered here, but a time‑lapse recording as video clip.
Pictures Considered #63: Images Can Shape Us by Roberto — It used to be that, when I closed my eyes and thought back, searching for a defining moment that sparked my life-long passion for molecular biology, this image came vividly to mind. Most memories lie buried, coming back only mysteriously, and often without cue. This one, though, is clear.
Pictures Considered #64: Emergent Properties by Roberto — Some years ago, when Scott Chimileski wrote 'Life at the Edge of Sight', we wanted to present two images that displayed emergent properties of organisms expressing collective behavior. We came up with this pair of photographs, whose scales differ by seven orders of magnitude.
Methodology
When shattered glass art evokes a scientific paper? by Janie — Recently I stumbled across Simon Berger's shattered glass artwork, and was reminded of RNA-seq and transcriptomics, of all things. The Swiss artist's pieces each begin with a large pane of glass. He shatters the pane, sometimes by heavy blows via hammer that generate large fragments...
B. bigelowii/UCYN-A organization. Structural characterization during the light cycle: (Left) Differential interference contrast (DIC) micrograph displays the whole alga and showcases UCYN-A spheroid body (SB) and plastids (Pls) in the FR21 culture; the correspondent 4′,6-diamidino-2-phenylindole (DAPI) staining reveals the cell nucleus (Nu). In both images, the UCYN-A spheroid body (SB) is identified above the nucleus. Scale bars, 5 mm. (Right) Orthoslice from soft X-ray tomography (SXT) data; color-coded 3D renderings of subcellular components. Adapted from Source
Symbioses
The Nitroplast, a Nitrogen-Fixing Organelle by Mechas — The ability to fix nitrogen is usually regarded as a property of only a few diazotrophic bacteria and archaea. A new study now shows that some eukaryotes may be capable of fixing nitrogen via the newly described nitroplast, an organelle that has evolved from an endosymbiont.
Fungus Helps Carnivorous Plant Digest Prey by Kevin Blake — It is well-established that microorganisms help vertebrates digest food, such as the bacteria in our gut breaking down complex carbohydrates. But do carnivorous plants engage in similar digestive collaborations?
Endophytic Streptomyces & Plant Growth by Roberto — Because of the deleterious effects on soil due to the prolonged use and overuse of synthetic fertilizers, the quest for bacteria able to promote plant growth is an ongoing pursuit. Yet, these searches are usually focused on members of a few genera, prime amongst these Bacillus and Pseudomonas. What about the Streptomyces?
Pathogens
Outpaced in the Evolutionary Arms Race by Kevin Blake — Reports on antibiotic resistance almost invariably begin with a roll call of several very big numbers. 4.95 million deaths per year globally, calculates the World Health Organization. 2.8 million infections per year in the United States resulting in 35,000 deaths, per the US Centers for Disease Control. 10 million deaths per year by 2050 globally costing $100 trillion to the global economy, estimates the Wellcome Trust...
Viruses
Dengue on the Rise by Mechas — Dengue fever, a rapidly spreading disease caused by the dengue virus, is ranked among the top 10 threats to global health. Despite being restricted mainly to tropical and subtropical regions, concern about its spread is growing.
Phage & Bacteria: A Space for Mutual Co-Existence by Roberto — Phage-bacteria population dynamics can be remarkably complex. This is reflected in the natural history of both; new phage defense systems in bacteria and anti-defense systems in phage seem to be discovered daily. Behind these intricate strategies to help in the reproductive success of each lies the basic problem of any predator-prey relationship.
Searching for ΦX174 The search for ΦX174 was the task that our fellow blogger naturepoker set himself some time ago. His search was not in some largely forgotten and iced-over box in the back corner of a –80°C freezer. Instead, he searched the literature as to when and where this bacteriophage was first described. Naturepoker has recorded the result of this sleuthing...
Genomic Dark Matter by Mechas — Discovering microscopic organisms and elements that exist at the edge of sight is no easy task. New tools designed to explore this mysterious world reveal previously unknown elements and uncover a complex web of forms whose secrets remain to be fully unraveled.
Talmudic Questions
Talmudic Question #212 In the same spirit as Talmudic Question #4, posted on December 19, 2006, here's another similarly "crazy" one: What if all the hydrogen bonds of a cell decided to go on strike and stop their duties all at once? Which cellular process would be affected first? How long would it take for the cell to die?
Lost & Found
Lost & Found #1 by Christoph — STC will be leaving 𝕏 (formerly Twitter) in the near future. Over the coming months, at irregular intervals, I'll be sifting through my bookmarks on 𝕏 and share with you what I found, two or three tweets at a time. This is 'Lost & Found #1'.
Lost & Found #2 by Christoph — On our way out of 𝕏 (formerly Twitter), we look through our soon-to-be-obsolete "bookmarks" and show you what shouldn't just end up in the bin. Here are three more salvaged bookmarks in 'Lost & Found #2'.
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