by the STC Team
In keeping with tradition, here is the list of our posts from the last half year.
Physiology & Genetics
Of Terms in Biology: "Synonymous Substitution", part 1|2 by Christoph — We are occasionally warned not to compare apples with pears (sorry, English speakers, not with oranges this time). Sure, both are pome fruits, and both plants belong to the Rosaceae family, but they differ notably in shape, feel, smell and taste. Geneticists may well need a similar warning when they sometimes use the terms silent mutation and synonymous substitution interchangeably.
Of Terms in Biology: "Silent Mutation", part 2|2 by Christoph — To continue with the comparison of apples and pears from the first part, here is an example of a synonymous mutation that can rightly be described as a silent mutation...
Small predators that could save our lives by Jéssica Gil Serna — The world of predatory bacteria is a true reflection of the David versus Goliath story. A small cell needs to kill its large prey to ensure its own survival. This is the case of bacteria of the genus Bdellovibrio whose importance has been highlighted in recent years as a possible alternative to defeat antibiotic-resistant superbugs.
A Whiff of Taxonomy – Atribacter laminatus by Christoph — The image is way too large to show it here, but when you join me and Hug et al. (2016) for "A new view of the tree of life" here, you can spot a bunch of names of bacterial phyla in the top left corner that sound unfamiliar. One of those, Atribacteria, is at the top of the column with Aquificae, Calescamantes, ... , Fusobacteria. Atribacter laminatus, the first cultivated representative of the phylum Atribacteria, is the subject...
A Whiff of... Replication – Atribacter laminatus by Christoph — When microbiologists describe a previously unknown bacterium, they are mainly interested in its lifestyle, metabolism, morphology and cell cycle. For me, "getting to know" a newbie always involves – let's call it an addiction – reading its genome sequence and finding out how it initiates the replication of its chromosome(s).
Never a Dull Enzyme by Roberto — The tricarboxylic acid cycle enzyme citrate synthase from Synechocous ccelongatus has the remarkable feature that it self-assembles into multimeric fractal shapes, specifically Sierpiński triangles. As Arthur Kornberg would have said: "Never a dull enzyme!"...
Hey flagellum, shift into reverse gear! by Christoph — In a classical manual gearbox, a gearwheel is inserted between the countershaft and the drive shaft. This reverses the direction of rotation of the drive shaft. Flagella have found a smart solution to do without an additional gearwheel in their gearbox: They run their engine along the outside of a gearwheel or, if they reverse the direction of rotation, on its inside...
Oscillibacter and Cholesterol by Roberto — From its humble beginnings as an inhabitant of the Japanese corbicula clam alimentary canal to center stage attention-getter as a cholesterol-lowering resident of the human gut, Oscillibacter has experienced a meteoric rise to stardom.
Odds & Ends
Butyribacterium, E. coli and the Elephant – A Snippet and an Adumbration by Roberto — I could not help myself. As I begin another year of blogging at STC, I had to start with this recurring theme of elephants. It does have the feeling of a blogger's equivalent to a composer's ostinato (think obstinate) – a motif that persistently repeats. Oh, but what wonderfully alluring motif, E. coli and Elephants!
The Early Days of Restriction Enzymes by John Collins — In the early 1960s, Werner Arber in Switzerland discovered that foreign DNA entering a bacterial cell could be cleaved on both strands by restriction endonucleases (restriction enzymes). This was part of the host's defense against viral attack. For this discovery he shared the 1978 Nobel Prize with Hamilton Smith and Daniel Nathans.
Bacterial Sounds by Roberto — Towards the end of last century, I read a short but provocative note entitled "Do bacteria sing?" With a title like that, who's not going to read it? As is usually the case, that reading led to more reading. I discovered several papers describing how some bacteria could be stimulated to form colonies more efficiently following sound stimulation.
Serendipity in Science by Roberto — Serendipity. I feel it is one of the most beautiful words in English; it's so melodic and loaded with meaning. Perhaps I'm fascinated by it because it is difficult to translate into my native Spanish. Regardless, it does seem that quite often scientific discoveries happen serendipitously.
Inactive Ingredients Meet Gut Microbes by Janie — Among all the human microbiome's kaleidoscopic effects on human health, one likely less frequently thought about by prescribing medical professionals is the ability to chemically alter the medications we take. It's well-established that our gut residents are teeming with enzymes...
Women: An Unfolding Story by Mechas — International Women’s Day, celebrated on March 8, commemorates women's struggle for equality, celebrates achievements, and raises awareness about discrimination and disparity.
Gut Microbes and Exercise by Roberto — These days there seems to be an ever-growing number of studies aiming to associate diverse human behaviors with gut microbiome composition. My curiosity has been particularly piqued by studies involving exercise.
Requiem for an Apparatus by Roberto — Have you ever seen the type of apparatus that Carl Woese and colleagues used to obtain data to support their conclusion that Bacteria and Archaea were so distant phylogenetically as to merit being different domains of life?
SIMPLIFY Science Writing by Roberto — Writing is an essential part of all scientific endeavors. Yet it is rare to find a scientist that finds it easy, not to mention joyful. I am not much different. But after many years at it, I have learned to take certain steps that make the process at least less daunting, even simple.
Lubert Stryer (1938–2024) by Roberto — Second semester, senior year at Carnegie-Mellon. Newly minted Assistant Professor Bill Brown, with whom I was learning to do peptide mapping, ran into the lab with a huge smile and holding a deep blue book with a mesmerizing structure on its cover. "Look at what Stryer has done, this is just so beautiful!"
Test Your STC Knowledge It's been almost a year since our last puzzle, here's another one. Quite appropriate to have a test at the end of the semester. If you've kept up your STC reading, this may prove an easy test. If you haven't... Well, this is your chance to catch up.
Ecology & Evolution
Of Terms in Biology: Teleonomy by Roberto — Read the following two phrases: In the presence of lactose, E. coli induces beta–galactosidase in order to use the sugar. In the presence of lactose, E. coli induces beta–galactosidase and thereby uses the sugar. Which one would you use? Do you see the fundamental difference between them?
Earth History – Microbial Numbers and Impact by Roberto — I find solace in putting my life in perspective. And one of my favorite ways to approach this is to consider life at scales that are orders of magnitude away from my direct experience. Since all the life we know of is on Earth, here are a few of Earth's basic numbers...
Origins of Multicellularity Revisited by Roberto — In the early years of STC, Elio wrote two posts on multicellularity. Why? Because "we lovers of microbes delight in the complexity of multicellular bacteria such as the actinomycetes, the myxobacteria, and some cyanobacteria," said he. Why do I write about this again? I'll argue that those three bacterial types are only the tip of the iceberg, bacterial multicellularity is the norm.
Enlightened by Microbial Rhodopsins by Mechas — The cold and dark northern winter days evoke nostalgia for the comfort and warmth of sunshine. We may take the sun for granted or even shun its scorching rays in hot weather, but we seldom think about the complex process of building life from solar energy, the foundation of our existence.
A Breath of Fresh Air – More than Just Oxygen by Mechas — Our lives are stitched from numerous activities, many of which go largely unnoticed. One of these is breathing, which is essential but only occasionally acknowledged.
Microbes and Methane by Roberto — If you're looking for a primer on microbes and methane (as was I, recently) I direct you to a timely report from an American Academy of Microbiology (AAM) colloquium on the subject. It's excellent reading as it contains a treasure trove of information along with an impressive list of references, for those who want to take a deeper dive into the subject.
Extremely Slow Growth in the Seabed by Roberto — Estimates are that, at the global scale, there are more microbial cells – maybe 5 x 1029 – in the seabed than in the water column above. These cells are not just near the seafloor, many of them lie buried deep in the sediment. Very deep indeed, as deep as 2.5 kilometers. And they've been there for a long time, even millions of years.
A Whiff of Taxonomy – Altiarchaeum hamiconexum by Roberto — Altiarchaeum hamiconexum is a relatively recent addition to the growing list of microbial primary producers, i.e. those that fix CO2. Its first sightings date back only a little more than twenty years and its ability to fix carbon was recognized only the last decade. And, as so many microbes, it has thus far resisted cultivation.
[da capo] The Tyranny of Phylogeny: An Exhortation by Elio — (Re-posted today to celebrate Elio's birthday!) There are days when I wish that the Woesian Three Domain scheme were wrong. Not that I would be happier if there were four or five or whatever number of domains. What would please me would be an escape from what I feel is an unnecessarily oppressive way of thinking, the seating…
Traveling E. coli by Roberto — Whether it is to attend meetings, carry out collaborative research, visit family, or simply explore exotic locations, scientists tend to do a lot of international travel (myself very much included). And one thing we do not want to experience during or after such travel is any sort of intestinal malfunction.
On the Origin of (the Word) Species by Roberto — Systematic classification of organisms is a fundamental part of biology. Yet, despite its being essential, the species concept has a problem; there is still no universally accepted definition.
Microbial Community Ecology by Roberto — Many present-day microbial ecology studies involve some sort of sequencing effort to determine which microbes are present in a sample. It seems that during the last three decades, every conceivable ecosystem of Earth and its inhabitants has been thus explored. But, what have we learned?
Of Terms in Biology: Ecological Drift by Roberto — In last Monday's post I presented Mike Vellend's "Theory of Community Ecology," which posits that selection, drift, speciation, and dispersal are the processes that interact to determine community dynamics. Today I'm going to expand on the process of "ecological drift." What is that?
Methodology
Viable Counts – A Conical Approach by Roberto — How many living cells in my culture? There are times when optical densities will not suffice, when you will want to have an accurate assay that determines viable cell counts. It's no wonder one of the first things a student of microbiology learns is the age-old concept of using "colony forming units" (aka as CFU) as a viability assay...
A Solar Eclipse (and the Weight of Paper) by Christoph — Last week I had in mind to write a short hommage to a venerable lab instrument, the flatbed chart recorder, but then the solar eclipse got in the way. More precisely, not the eclipse, but the map of the USA that went viral on social media, with the booking numbers...
Of Terms in Biology: Kymogram by Christoph — In his presentation at a meeting in Copenhagen last year, Johan Elf showed several kymograms. No, these are not fancy versions of pie charts that everyone knows, but an intuitively accessible visualization of the localization of macromolecular complexes in living bacterial cells as they change over time.
Pathogens
Wastewater Microbiology by Mechas — Using wastewater to monitor human populations is a growing trend. The waste products found in the water discarded after domestic, commercial, or industrial use reflects the habits and consumptions of society and provide a pool of information on our customs and behaviors.
Coley's Toxins Revisited by Roberto — In the last few years, immunotherapy has quickly become the emerging "fourth pillar" in cancer treatment, joining surgery, radiation therapy and chemotherapy. The basic concept behind the development of immune checkpoint inhibitors as anti-cancer therapeutics is that activating the immune system can sometimes result in the body ridding itself of malignant cells.
Viruses
Filamentous Phage Shields by Roberto — Elaborate mechanisms that protect bacteria against phage are well known, with CRISPR leading the way. Less familiar but equally fascinating is the fact that, somewhat unexpectedly, phages themselves sometimes offer bacteria protection in harsh environments. Filamentous phages do just that.
Of Terms in Biology: Phage–Plasmid (1|2) by Christoph — Once you think again about horizontal gene transfer (HGT) and how genomic DNA can pass from one cell to another, you may soon feel quite medieval and ruminate «mille viae ducunt hominem per saecula Romam». One of the main routes of chromosomal and extra‑chromosomal DNA (to Rome) is via transduction by bacteriophages, another via conjugation by plasmids, but there are other main roads too...
Of Terms in Biology: Phage–Plasmid (2|2) by Christoph — In the first part of this piece on phage–plasmids (P–Ps), I focused on examples that are well known today, and on the fact that they are representatives of larger families with dozens of members, rather than peculiar solitary cases. Here now, in the second part, I will introduce some lesser-known examples of phage–plasmids.
Talmudic Questions
Talmudic Question #210 The endosymbiosis of a cyanobacterium led to the formation of the photosynthetic organelle, the chloroplast. Along evolutionary history this organelle proved quite plastic; there are many non-photosynthetic variants with very different functions...
Talmudic Question #211 Contributed by Seth Bordenstein — What is the craziest thing a phage enzyme can do to eukaryotic hosts?
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