Posts Tagged ‘bacteria’
“The most outstanding feature of life’s history is a constant domination by bacteria”*…
Jennifer Kahn interviews biochemist Jennifer Doudna (who won the Noel Prize for the gene-editing engine Crispr) on her new focus– our microbiomes, tackling everything from immune disorders and mental illness to climate change—all by altering microbes in the digestive tract…
… what isn’t the microbiome responsible for? It’s been all the rage for the past few years, with scientists hoping it could help treat everything from immune disorders to mental illness. How exactly that will work is something we’re just starting to explore. This spring, the effort got a boost when UC Berkeley biochemist and gene-editing pioneer Jennifer Doudna, who won a Nobel Prize in 2020 for coinventing Crispr, joined the pursuit. Her first order of business, spearheaded by Berkeley’s Innovative Genomics Institute: fine-tuning our microbiome by genetically editing the microbes it contains while they’re still inside us to prevent and treat diseases like childhood asthma. (Full disclosure: I teach at Berkeley.) Oh, she also wants to slow climate change by doing the same thing in cows, which are collectively responsible for a shocking amount of greenhouse gas.
As someone who has written about genetic engineering in the past, I have to admit that my first reaction was: No way. The gut microbiome contains around 4,500 different kinds of bacteria plus untold viruses, and even fungi (so far: in practice we’ve only just started counting) in such massive quantities that it weighs close to half a pound. (Microbes are so tiny that 30 trillion bacteria would weigh roughly 1 ounce. So half a pound is a lot.)
Figuring out which ones are responsible for which ailments is tricky. First you need to know what’s causing the problem: like maybe something is producing too much of a particular inflammatory molecule. Then you have to figure out which microbe—or microbes—is doing that, and also which gene within that microbe. Then, in theory, you can fix it. Not in a petri dish, but in situ—meaning in our fully active, roiling, squishing stomach and intestines while they continue to do all the stuff they usually do.
Until recently, it would have seemed insane—not to mention literally impossible—to edit all the microbes belonging to a species within a vast ecosystem like our gut. And to be fair, Doudna and her collaborator, Jill Banfield, still don’t know quite how it will work. But they think it can be done, and in April, TED’s Audacious Project donated $70 million to support the effort. My own gut feeling (right?) was that this was either brilliant or terrifying, or possibly both at once. Brilliant because it had the potential to head off or treat diseases in an incredibly targeted and noninvasive way. Terrifying because, well, you know … releasing a bunch of inert viruses equipped with gene-editing machinery into the vital ecosystem that is our gut microbiome—what could go wrong? With that in mind, I invited Jennifer Doudna to my house for a chat about the future of microbiome medicine…
Fascinating– and encouraging: “Crispr Pioneer Jennifer Doudna Has the Guts to Take On the Microbiome,” in @WIRED.
(Image above: source)
* Stephen Jay Gould
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As we investigate our intestines, we might spare a thought for Guido Pontecorvo; he died on this date in 1999. A geneticist, he discovered the process of genetic recombination in the common soil fungus Aspergillus— and as a result the parasexual cycle— in what became the model for the genetic studies in many other fungi. This cycle gives rise to genetic reassortment by means other than sexual reproduction; its discovery provided a method of genetically analyzing asexual fungi…. which, as noted above, populate our microbiomes.
“Life’s a little weird”…
Needs must…
You may have ridden out the pandemic in compact living quarters without, say, much natural light or air conditioning. Perhaps you lived with roommates or family in an atmosphere that, as time wore on, grew increasingly toxic.
Things could be worse! You could be a member of the Alviniconcha species—specifically, a small, spike-studded snail who thrives in an environment inhospitable to most aquatic life; mere meters from deep-sea hydrothermal vents that constantly spew toxic chemicals into the water. Think you have limited natural light? Try living nearly 10,000 feet below the surface of the ocean, where complete darkness envelops you 24 hours a day, under pressure so intense all the air pockets in your body would instantly collapse.
And forget Seamless. Forget food—at least the kind you ingest with your mouth. Your survival hinges on bacteria living in your gills (you have gills!) in a symbiotic relationship that provides you with energy, via a process called chemosynthesis. It’s like photosynthesis, but chemosynthesis is driven by chemical reactions instead of light. As there’s no sunlight and minimal oxygen present, the bacteria that dwell within Alviniconcha use hydrogen and sulfur molecules to produce sugars and other macronutrients that the animals then use as food. “There’s very little food so deep in the ocean,” says Dr. Corinna Breusing, postdoctoral researcher at the University of Rhode Island and co-author of a recent paper on the snails and their symbionts. “Having your own food-producing machine is much better than waiting for it to fall to you.” While chemosynthesis is common around hydrothermal vents, it can occur in places outside of vents, such as in cold seeps and whale falls and even salt marshes: anyplace the proper mélange of inorganic compounds is brewing.
The researchers studied Alviniconcha living at the bottom of the Lau Basin, in the southwestern Pacific Ocean, and found that the type of bacterial symbiont determined where their particular host species could live. “The symbionts have different metabolic capacities and adaptations, so we think that the symbionts influence the distribution of the animal,” Breusing says, adding that snails with Campylobacteria dominated at vents with higher concentrations of sulfide and hydrogen, while those with Gammaproteobacteria were able to thrive at sites with lower concentrations of sulfide and hydrogen. Meaning: your chef-roommate, who happens to live in your respiratory system, also decides where you hang your hat (so to speak).
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Most hydrothermal vent-dwelling animals, such the aforementioned snails and deep-sea anemones, as well as some species of mussels and tube worms, depend on bacteria that they pick up from the environment, but there is a species of deep-sea clam that passes their symbiont down from mother to offspring, like a fancy set of dinner plates. (This is rare in the marine world, Breusing says.) In the case of the deep-sea clams, where the symbiont is inherited, the symbiont cannot thrive outside the host and dies with it. But if a symbiont is taken up from the environment, it can be released back into the environment after its host dies, ready to help feed a brand-new host.
Alviniconcha might not pack the same visual punch as much marine life does much closer to the surface, but their very existence points to the origins of life on Earth. Before oxygen was free and plentiful, microbial life had to work with inorganic compounds like methane and ammonia, which over millennia dissolved into the seas. Much is still murky about how these little snails co-evolved with the bacteria that enable them to survive, but these fascinating ecosystems indicate that our education about life at the margins is just getting started…
“Life at the Edge of Impossible“: ten thousand feet under the sea, these snails thrive with a little help from their friends; from Adrienne Day (@adrienneday).
* Dr. Seuss
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As we examine extremes, we might send redefining birthday greetings to Carl Woese; he was born on this date in 1928. A microbiologist and biophysicist, he made many contributions to biology; but he is best remembered for defining the Archaea (a new domain of life).
For much of the 20th century, prokaryotes were regarded as a single group of organisms and classified based on their biochemistry, morphology and metabolism. In a highly influential 1962 paper, Roger Stanier and C. B. van Niel first established the division of cellular organization into prokaryotes and eukaryotes, defining prokaryotes as those organisms lacking a cell nucleus. It became generally assumed that all life shared a common prokaryotic (implied by the Greek root πρό [pro-], before, in front of) ancestor.
But in 1977 Woese (and his colleague George E. Fox) experimentally disproved this universally held hypothesis. They discovered a kind of microbial life which they called the “archaebacteria” (Archaea), “a third kingdom” of life as distinct from bacteria as plants are from animals, Having defined Archaea as a new “urkingdom” (later domain) which were neither bacteria nor eukaryotes, Woese redrew the taxonomic tree. His three-domain system, based on phylogenetic relationships rather than obvious morphological similarities, divided life into 23 main divisions, incorporated within three domains: Bacteria, Archaea, and Eucarya.
“Thinking within strict limits is stifling”*…
Affectionately nicknamed “Conan the Bacterium,” Deinococcus radiodurans, a so-called polyextremophile, has an uncanny ability to rapidly repair damage to its genome. As a result, it can resist the most hostile conditions, from drought to radiation to acid baths to a Martian atmosphere. And if Canadian conceptual poet Christian Bök has his way, it will compose verse that will outlive our Sun.
Bök has earned a reputation for conducting extremely difficult poetic experiments and executing them with technical wizardry. In his award-winning 2001 bestseller Eunoia , for example, he uses only a single vowel in each chapter, a constraint that produces a form known as a univocalic . The first section is composed of words that include no vowels other than a , the second includes no vowels other than e , and so on. To build an appropriate lexicon for this demanding work, Bök read through Webster’s Third International Unabridged Dictionary five times and spent six years writing. His latest poetic challenge takes him into trickier and more technically specialized territory. Taking on the very perishability of text, Bök has devised a novel solution: In composing his verse, he is employing the medium of life itself.
The Xenotext: Book 1 represents the first phase of Bök’s wildly ambitious project—nearly 15 years in the making and still ongoing—of encoding poetry into the genome of the bacterium D. radiodurans . Using a substitution cipher, Bök “translates” his poetry into what he calls a “chemical alphabet” representing a genetic sequence. After simulating the resulting protein’s folding pattern, which is essential for its functioning, Bök sends his specifications to a biotechnical lab that engineers the gene accordingly. Finally, Bök’s team of biologists transplants a plasmid carrying the gene into the bacterium.
But why introduce such complexity into the process of poetic composition? The Xenotext provocatively wagers that—in the face of global catastrophe, whether in the form of ecological collapse, drug-resistant pandemic, or nuclear war—D. radiodurans can preserve at least a bit of humanity’s poetic heritage after the apocalypse. DNA, with its remarkable storage capacity and stability, is perhaps the “natural element,” the worthy vessel for the mind’s substance that Wordsworth expresses longing for in the epigraph above…
Writing an eternal poem, one that will survive in the DNA of extremophile bacteria when all other life on the planet is extinguished: “Poetry of the Apocalypse.”
For more on exactly how Bök “writes,” see: “The Making of a Xenotext.”
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As we ponder posterity, we might send straight-forward birthday greetings to Joseph Addison; he was born on this date in 1672. A poet, playwright, and politician, Addison is probably best remembered for The Spectator, a daily publication– a “paper” as it was then called, and as it successors have been known ever since– which he founded in London with his partner Richard Steele.
The Spectator was widely read in London; indeed Jürgen Habermas suggests that the paper was instrumental in the emergence of the public sphere in 18th century England. It also had North American readers (including Benjamin Franklin and James Madison).
“Human DNA spreading out from gravity’s steep well like an oilslick”*…
Could the Earth be a life-exporting planet? That’s the curious question examined in a recent paper written by Harvard University astronomers Amir Siraj and Abraham Loeb.
The researchers take a novel twist on the controversial notion of panspermia – the idea, propelled into the mainstream in the early 1970s by astronomers Fred Hoyle and Chandra Wickramasinghe, that life might have started on Earth through microbes arriving from space.
The theory is generally discounted, although eminent astrophysicists such as Stephen Hawking conceded it was at least possible, and a major paper published in 2018 revived the topic big-time.
In their [late December, 2019] paper, Siraj and Loeb reverse the standard assumption about the direction of the microbial journey and ask whether it is possible to that at some point Earth-evolved bacteria could have been propelled away from the planet, possibly to be deposited somewhere else in the Milky Way…
Astronomers suggest microbes might hitch lifts on interstellar asteroids. More on the hypothesis and the evidence that supports it at “Earth bacteria may have colonised other solar systems.” Read the underlying paper at arXiv.
* William Gibson, Neuromancer
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As we ponder the polarity of proliferation, we might recall that it was on this date in 1921 that Albert Einstein startled his audience at the Prussian Academy of Sciences in Berlin by suggesting the possibility that the universe could be measured. His talk, “Geometry and Experience” (text here), applied some results of the relativity theory to conclude that if the real velocities of the stars (as could be actually measured) were less than the calculated velocities, then it would prove that real gravitations’ great distances were smaller than the gravitational distances demanded by the law of Newton. From that divergence, the finiteness of the universe could be proved indirectly, and could even permit the estimation of its size.
Later that year, Einstein was announced as the 1921 Nobel Laureate in Physics, an award he accepted the following year.
Einstein in 1921
Happy Birthday, Dante, Mozart, and Lewis Carroll!
“In the end everything is connected”*…
A fungus known as a Dermocybe forms part of the underground wood wide web that stitches together California’s forests [source]
Research has shown that beneath every forest and wood there is a complex underground web of roots, fungi and bacteria helping to connect trees and plants to one another.
This subterranean social network, nearly 500 million years old, has become known as the “wood wide web.”
Now, an international study has produced the first global map of the “mycorrhizal fungi networks” dominating this secretive world…
Mycorrhizal ecologist Dr Merlin Sheldrake, said, “Plants’ relationships with mycorrhizal fungi underpin much of life on land. This study … provides key information about who lives where, and why. This dataset will help researchers scale up from the very small to the very large.”…
The underground network of microbes that connects trees—charted for first time: “Wood Wide Web: trees’ social networks are mapped.”
Read the Nature release that reports the research here.
* The Book of Chameleons
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As we contemplate connection, we might spare a thought for Anders (Andreas) Dahl; he died on this date in 1789. A botanist and student of Carl Linnaeus, he is the inspiration for, the namesake of, the dahlia flower.
Dahlia, the flower named after Anders Dahl [source]
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