#halophilous

[mistandbluemoon]

oh. so that's why it's called whalefall city

[anyajkramer]

some geophilomorph centipedes are littoral! And they eat barnacles!!!

[hellsite-proteins]

Featured Protein: Bacteriorhodopsin

this fantastic protein was suggested by @imperialinquisition, and i'm so excited i finally got around to putting together some information about it!

this protein is found in archaea – specifically Halobacterium salinarum, which are halophilic (live in extremely salty environments) obligate aerobes (need oxygen to function). it has 7 transmembrane domains and is an analog to human rhodopsin (a G-protein-coupled receptor protein in the rod cells of our eyes *note: bacteriorhodopsin is NOT a G-protein-coupled receptor, but is still in the 7TM receptor family) and forms distinct purple coloured parts of the cell membrane. this protein is also the source of a lot of interest from an engineering and biotechnology perspective.

this is one of several types of proton pumps, which transport protons across a cell membrane against an electrochemical gradient. however, the feature that makes this one so interesting is that it is powered by sunlight. when a photon of light is absorbed, all-trans-retinal (one molecule attached to each of 3 protein chains) is isomerised to 13-cis-retinal. this induces conformational changes in the rest of the protein through a 9-stage photocycle, altering the pKa values of a few conserved residues and allowing one proton to be transferred outside the cell. through this action, the inside of the cell is made 10,000-fold more basic than outside the membrane! this proton gradient is used to power ATP synthase, making most of the cell's ATP

sources:

i wasn't able to download a version of the structure with all three chains, but i found some cool images of the structure:

as always, if i made any mistakes, please let me know!

[rainbowsylvie]

There are probably Pokémon adapted to environments so hyperspecific that even if people did find them they’d never be able to actually have them due to not being able to survive outside it, just like some life in the real world

It would be nice to see them in spin-off games though, like a new game that’s something like Pokémon snap and legends arceus where you’re sent to document Pokémon such as these, maybe you’re given a Pokémon that can withstand such environment but don’t necessarily need them to surviveoh fuck tardigrade Pokémon this is how they can introduce tardigrade Pokémon this is how tardigrade Pokémon can STILL WIN!

Anyway. Areas like this can include obvious places like the deep sea or high up in the mountains where oxygen is thin, as well as places with high radiation or high up in the atmosphere where rayquaza lives(could be a late or endgame area because of that), hot springs and places on the extreme ends of the ph scale may be difficult to document but they may be worth it

Pokémon could include pallas cats(could be a variant or a new Pokémon), blobfish(do NOT remove them you know damn well what happens), yeti crabs(perhaps a deep sea crabominable variant), that snail with the iron shell, brittle stars and perhaps some Pokémon based on lesser known eukaryotes, such as halophilic fungi, and even Pokémon that live in places real life creatures have no chance in. This is a fantasy world, do whatever.

Now the creatures that live in these areas are usually, well, Fucking Tiny, but if a tick can be 4 inches, I think they can make microscopic creatures be inch big Pokémon. This can also be where the camera comes in, it will have a big zoom function so you can get up really close to the little guys without having to act get near them. The aforementioned tardigrade Pokémon could help you interact with the environment if you’re unable to for whatever reason, such as a hot spring or a place too radioactive for most life or you’re in a small submersible in the ocean or That Is Actual Fucking Lava. You could also be supplied with a ditto to help you with further documentation, since while you can’t use the actual Pokémon, a ditto can help fill in the gaps pretty well if they’re just as able to withstand the environment as well as the Pokémon they’re copying.

The game won’t be focused in one specific region, but various areas around the world, both preexisting and new regions. I have a thought for a tiny, undiscovered Pokémon near the hot springs in hoenn, or something that only lives within stark mountain in the battle zone near sinnoh, perhaps even a Pokémon that somehow migrated there from firespit island from the hisui days, and you can’t tell me paldea’s area zero Doesn’t have some hyperadapted Pokémon in there, maybe in the water at the bottom, though I don’t think you’d be allowed there for a While(lategame area probably). Pokémon world Antarctica, Iceland, and Yellowstone are not safe from documentation. When exploring regions, only small parts will be available to you, such as the locations previously mentioned.

Now a lot of people probably wouldn’t like a game with almost entirely new Pokémon look at black and white’s initial reception and variants, almost none of which that you can even use not counting ditto copies, but since this would be a spinoff mostly used to help with world building, I’d say those people can Suck It Up and let us have our fun, pokemon doesn’t have to cater to you specifically all the time, you may like the battles, but some of us enjoy worldbuilding and speculative biology.

I don’t have any concept art at the moment as I started writing this down shortly before dinner, but I’ll reblog this post with some once I have enough.

[teratocrat]

When I first came to Ajax, when I stepped out of the red-and-yellow shuttle to plant my feet in the planet's sand, what I noticed before anything else was how pale the buildings are. On Mars, even in the warmest and most equatorial provinces, human habitation is universally black (or its best approximation), built from fulcrete and basalt and painted wood, to absorb the warmth of the sun against the bitter cold. On Ajax, far closer to its sun than Mars or even Earth, and with its 39-hour days, they must build for the opposite, towers of white or reflective silver with burrowed basements and sub-basements and sub-sub-basements underneath. The Ajactes live in cities the color of bone. The second thing I noticed, the thing that probably any other person would notice first, was the surfeit of salt in the air. I noticed this because it stung my eyes, like the threat of tears. As it happens, Ajax's oceans are significantly more saline than Earth's or Emieni's, and even its topsoil is a kind of hardpan composed of sand and dust cemented in a salt matrix. For the first several centuries of its habitiforming, it hosted an extremely carefully managed tight ecosystem of halophilic algae, bacteria and lichen painstakingly shipped from Earth and Mars, fed upon by a few species of brine shrimp. Gradually, the Hesperides introduced more species as the previous ones found their foothold: turtleweed and saltbush and cordgrasses, periwinkles and blue crabs and flamingos, suites of genetically-modified mangroves whose knees whistled in the morning and evening hours, bananas and maize and halotolerant rice. Most recently (within the last two hundred and fifty years) the Ajax Planetary Authority had grown increasingly bold and experimental: a breed of sheep brought out of cryogenic vaults on Old Earth to eat the masses of seaweed that washed ashore around the Southernmost Continent, whitetail deer both to manage the turtleweed scrubland that was covering the northern half of the Great Continent and to provide a stable meat source more robust than flamingos and periwinkles, a kind of gopher tortoise/diamondback terrapin hybrid that had proved encouragingly robust in the prairies of Mars, and even tigers to laze about in the shade of the forests that bordered saltmeadows full of bounding deer. All the Ajactes I spoke to seemed both personally invested in and extraordinarily proud of these tigers, showing me images and videos on their utility wedges, and several of the state television channels would cut away to live feeds of the animals sleeping or bathing their cubs or stalking prey.

[nightbunnysong]

11/50 Day Productivity Challenge

1. Exercise

2/2 rest day

2. Reading

20 minutes (book on the history of my hometown)

3. Diet and weight loss

breakfast: green tea, fruit, sourdough bread with homemade fig jam

lunch: vegetable soup and sourdough bread, herbal tea

dinner: kinda lost the appetite and didn't eat

4. Academic goals

Today I was discouraged and I did lost motivation but not my discipline.

- 3h repeat aloud halophile systems etc

- i'm now taking more notes

5. Personal growth

Today, I was very disciplined and assertive with others, even though I was feeling a bit down. I also got a new conditioner that smells like cocoa, and I can't stop sniffing my hair because it smells so good lol.

[bacteriashowdown]

Verrucomicrobiota

Group: Hydrobacteria; PVC Group

Gram-stain: Negative

Etymology: For Verrucomicrobium spinosum. From Latin "verruca", meaning "wart", and neo-Latin "microbium", meaning a microbe. This is not because they cause warts, but because they are bumpy.

About: Verrucomicrobiota is small phylum, with few well-described species. These come from a range of environments, having been found in soil, freshwater, coastal springs, human feces, insects, and geothermal environments. As with other members of the PVC superphylum (see Planctomycetota), they have inner membranes that form organelle-like compartments. Verrucomicrobiota use these in order to break down complex carbohydrates: the compartments safely store toxic compounds that are produced as byproducts during the degradation of sugars. Verrucomicrobiota are found in seasonal algae blooms, where they are able to break down the tougher components of the algae, while the other bacteria can only gobble up the easy stuff.

This phylum also contains its fair share of extremophiles. There are halophiles, which thrive in environments with high concentrations of salt, as well as thermophiles and some of the most extremely acidophilic bacteria out there. The polyextremophiles Methylacidiphilum infernorum are both thermophilic and acidophilic, as well as obligately methanotrophic. Methanotrophy is a pretty unique quality: it means that they feed on methane, and as such require a high concentration in their surrounding environment. 

[myrebelancestorsdiedforme]

Lake Hillier, located on Middle Island in Western Australia, is renowned for its bright pink hue. This distinctive color results from the presence of microorganisms such as the micro-algae Dunaliella salina and halophilic bacteria. Unlike other colored lakes, the water of Lake Hillier retains its pink color even when collected in a container.

[marlowethelibrarian]

hey!

🐍- How do you deal with it when you come across a plothole?

🕳️- Talk about a research rabbit hole you fell down!

Anyways, No pressure

Take your Time!

hello!!

Haha well historically I've just abandoned things because of plot holes, but I'm trying to sit down and commit to a long form work I've already put a lot of effort in!! So usually I'll just talk it through with some friends to try and find a solution. Sometimes it's just as simple as adding or removing an element from the worldbuilding.

As for research rabbit holes....

well, let's see I've also done some dives into Andean and Vietnamese agriculture to try and figure out food in project cannibalism. Quinoa plants are really fucking pretty guys. It grows in six foot stalks that can turn a range of colors from red to purple. The Hmong population in Vietnam also has indigenous strains of corn that they grind down and steam- a lot of them are in danger of extinction due to hybridization. It's an important staple crop for them!!

I've also looked into halophytes, plants adapted to high levels of salt, of which there are a large variety and some are edible! There's a "green salt" salt replacement that's just a dried halophillic sea pea plant, which I think is really interesting. There's also a database at ehaloph.uc.pt that's literally just for halophytes which even includes a filter for economic uses!

[spacenutspod]

5 Min Read Why is Methane Seeping on Mars? NASA Scientists Have New Ideas Filled with briny lakes, the Quisquiro salt flat in South America’s Altiplano region represents the kind of landscape that scientists think may have existed in Gale Crater on Mars, which NASA’s Curiosity Rover is exploring. Credits: Maksym Bocharov The most surprising revelation from NASA’s Curiosity Mars Rover — that methane is seeping from the surface of Gale Crater — has scientists scratching their heads. Living creatures produce most of the methane on Earth. But scientists haven’t found convincing signs of current or ancient life on Mars, and thus didn’t expect to find methane there. Yet, the portable chemistry lab aboard Curiosity, known as SAM, or Sample Analysis at Mars, has continually sniffed out traces of the gas near the surface of Gale Crater, the only place on the surface of Mars where methane has been detected thus far. Its likely source, scientists assume, are geological mechanisms that involve water and rocks deep underground. If that were the whole story, things would be easy. However, SAM has found that methane behaves in unexpected ways in Gale Crater. It appears at night and disappears during the day. It fluctuates seasonally, and sometimes spikes to levels 40 times higher than usual. Surprisingly, the methane also isn’t accumulating in the atmosphere: ESA’s (the European Space Agency) ExoMars Trace Gas Orbiter, sent to Mars specifically to study the gas in the atmosphere, has detected no methane. Why do some science instruments detect methane on the Red Planet while others don’t? “It’s a story with a lot of plot twists,” said Ashwin Vasavada, Curiosity’s project scientist at NASA’s Jet Propulsion Laboratory in Southern California, which leads Curiosity’s mission. Methane keeps Mars scientists busy with lab work and computer modeling projects that aim to explain why the gas behaves strangely and is detected only in Gale Crater. A NASA research group recently shared an interesting proposal. Reporting in a March paper in the Journal of Geophysical Research: Planets, the group suggested that methane — no matter how it’s produced — could be sealed under solidified salt that might form in Martian regolith, which is “soil” made of broken rock and dust. When temperature rises during warmer seasons or times of day, weakening the seal, the methane could seep out. Led by Alexander Pavlov, a planetary scientist at NASA’s Goddard Space Flight Center in Greenbelt, Maryland, the researchers suggest the gas also can erupt in puffs when seals crack under the pressure of, say, a rover the size of a small SUV driving over it. The team’s hypothesis may help explain why methane is detected only in Gale Crater, Pavlov said, given that’s it’s one of two places on Mars where a robot is roving and drilling the surface. (The other is Jezero Crater, where NASA’s Perseverance rover is working, though that rover doesn’t have a methane-detecting instrument.) Pavlov traces the origin of this hypothesis to an unrelated experiment he led in 2017, which involved growing microorganisms in a simulated Martian permafrost (frozen soil) infused with salt, as much of Martian permafrost is. Pavlov and his colleagues tested whether bacteria known as halophiles, which live in saltwater lakes and other salt-rich environments on Earth, could thrive in similar conditions on Mars. The microbe-growing results proved inconclusive, he said, but the researchers noticed something unexpected: The top layer of soil formed a salt crust as salty ice sublimated, turning from a solid to a gas and leaving the salt behind. Permafrost on Mars and Earth “We didn’t think much of it at the moment,” Pavlov said, but he remembered the soil crust in 2019, when SAM’s tunable laser spectrometer detected a methane burst no one could explain. “That’s when it clicked in my mind,” Pavlov said. And that’s when he and a team began testing the conditions that could form and crack hardened salt seals. Pavlov’s team tested five samples of permafrost infused with varying concentrations of a salt called perchlorate that’s widespread on Mars. (There’s likely no permafrost in Gale Crater today, but the seals could have formed long ago when Gale was colder and icier.) The scientists exposed each sample to different temperatures and air pressure inside a Mars simulation chamber at NASA Goddard. Periodically, Pavlov’s team injected neon, a methane analog, underneath the soil sample and measured the gas pressure below and above it. Higher pressure beneath the sample implied the gas was trapped. Ultimately, a seal formed under Mars-like conditions within three to 13 days only in samples with 5% to 10% perchlorate concentration. This is a sample of mock Martian regolith, which is “soil” made of broken rock and dust. It’s one of five samples that scientists infused with varying concentrations of a salt called perchlorate that’s widespread on Mars. They exposed each sample to Mars-like conditions in the Mars simulation chamber at NASA’s Goddard Space Flight Center in Greenbelt, Maryland. The brittle clumps in the sample above show that a seal of salt did not form in this sample because the concentration of salt was too low. NASA/Alexander Pavlov This image is of another sample of mock Martian “soil” after it was removed from the Mars simulation chamber. The surface is sealed with a solid crust of salt. Alexander Pavlov and his team found that a seal formed after a sample spent three to 13 days under Mars-like conditions, and only if it had 5% to 10% perchlorate salt concentration. The color is lighter in the center where the sample was scratched with a metal pick. The light color indicates a drier soil underneath the top layer, which absorbed moisture from the air as soon as the sample was removed from the simulation chamber, turning brown. NASA/Alexander Pavlov That’s a much higher salt concentration than Curiosity has measured in Gale Crater. But regolith there is rich in a different type of salt minerals called sulfates, which Pavlov’s team wants to test next to see if they can also form seals. Curiosity rover has arrived at a region believed to have formed as Mars’ climate was drying. Improving our understanding of methane generation and destruction processes on Mars is a key recommendation from the 2022 NASA Planetary Mission Senior Review, and theoretical work like Pavlov’s is critical to this effort. However, scientists say they also need more consistent methane measurements. SAM sniffs for methane only several times a year because it is otherwise busy doing its primary job of drilling samples from the surface and analyzing their chemical makeup. In 2018, NASA announced that the Sample Analysis at Mars chemistry lab aboard the Curiosity Rover discovered ancient organic molecules that had been preserved in rocks for billions of years. Findings like this one help scientists understand the habitability of early Mars and pave the way for future missions to the Red Planet.Credit: NASA’s Goddard Space Flight CenterDownload this video in HD formats from NASA Goddard’s Scientific Visualization Studio “Methane experiments are resource intensive, so we have to be very strategic when we decide to do them,” said Goddard’s Charles Malespin, principal investigator for SAM. Yet, to test how often methane levels spike, for instance, would require a new generation of surface instruments that measure methane continuously from many locations across Mars, scientists say. “Some of the methane work will have to be left to future surface spacecraft that are more focused on answering these specific questions,” Vasavada said. By Lonnie ShekhtmanNASA’s Goddard Space Flight Center, Greenbelt, Md. Share Details Last Updated Apr 22, 2024 Contact Lonnie Shekhtman lonnie.shekhtman@nasa.gov Location Goddard Space Flight Center Related Terms Curiosity (Rover) Goddard Space Flight Center Mars Mars Exploration Program Mars Science Laboratory (MSL) Missions NASA Directorates Planetary Science Division Science Mission Directorate The Solar System

[stephenjaymorrisblog]

America is Republic, not a Theocracy.

Part 2

Stephen Jay Morris

9/29/2023

© Scientific Morality.

For some time, I was aspiring writer. I wrote fictional stories. One was called, “The Flag and the Cross 2084.” It was a futuristic story about America conquering all countries on earth. America was this gigantic empire under which the residents of all countries had to learn English or be killed. They were also required to believe in fundamentalist Christianity or be killed. White Anglo Saxion Protestants were privileged citizens. Government was replaced by a corporate board of directors to run the planet. Only Aryan men were allowed to vote and only White men were permitted to be rich. It had an intergalactic space force called “God’s Aryan Warriors,” which mission was to conquer the universe by space invasions. It was revealed that so called UFOs were advance mode flying saucers, spying on all citizens.

The Christian Church of America oversaw law and order. In 2054, the Constitution was abolished and was replaced by the King James Bible as the official constitution of the planet. All other religions were abolished. Jews were forced to denounce their religion and accept Jesus as their lord and savior. If not, they were put into human sized, microwave ovens. White Women had to become baby producing machine for the Aryan race. In 2070, women lost their right to vote and were not permitted to be in the work force. They were relegated to being homemakers. In 2080, 40 million LBGTQ+ people died in Christian death camps. And yes, there were flying cars! Oh, I almost forgot: all citizens’ brains were injected with microchips that showed authorities their whereabouts at all times.  Pretty apocalyptic totalitarian future, yes? One more thing about this futuristic nightmare: only married people were allowed to have sex. If you were caught, you were put in Jesus camps, otherwise known as prisons. And yes, masturbation was illegal.

Times have changed and history has made a liar out of me--thankfully. Someday I will do a third rewrite of my manuscript.

Back to the past of 2023. What is interesting about my story is that all Islamic theocracies were destroyed and replaced with Christian theocracies. Now I ask you? What’s the difference between Islamic theocracy and Christian theocracy? Answer: Most Christians are White. However, it doesn’t matter which religion controls a country. In any case, it is an authoritarian nightmare. If America became a theocracy, people would be swimming to Communist Cuba to become American exiles! Is Iran worse than North Korea? Not really. Left wing authoritarianism and Right wing totalitarianism both suck! That is the problem with absolutism: you are either against the Left or against the Right. If you believe in black and white vision, then you will never see a rainbow. That is why the religious Right hates rainbows; they see everything in black and white!

Some think that…I mean, “feel,” that a Chistian nation would be this Pollyanna society, wherein everybody is a sweetheart! Everybody follows God’s rules, everybody feels and thinks the same. A lily white, pure society. Wrong! Some Christians subscribe to the proposition that violence solves all problems. That freedom is reserved for Christians only. Is there taxation in this Christian society? Oh, fuck yeah, there is! Except it’s called, “tithing.” In this new society, you will have to pay 75% of your income. If you should have a heart attack, your pastor will say a prayer for you. If you masturbate, the God Squad will send you to Jesus’ camp. Do you want that? Good! Stay the fuck away from me!

I am not engaging in drollery here. To jerk off, I need a halophile environment. If the theocrats win, the American experiment is over. Plus, the bastards don’t believe in scientific methodology.

We don’t need religion. Really!  Freedom is for all, not just a chosen few.

[earaercircular]

Researchers: 'First genetically engineered bacterium that eats plastic from seawater'

Researchers have found a way to genetically engineer a marine microorganism, allowing it to break down plastic in saltwater. Is this the solution to the plastic problem?

A group of scientists from the University of North Carolina worked with two types of bacteria: Vibrio natriegens[1] and Ideonella sakaiensis[2]. The former thrives in saltwater and reproduces quickly. The second bacterium is remarkable because it produces enzymes that can break down and eat polyethylene terephthalate – better known as PET.

Combine bacteria

By combining the two bacteria, the researchers were able to combine fast reproduction and saltwater ability with the property of the plastic-eating enzyme. The genetically engineered bacterium can break down PET in a saltwater environment at room temperature.

And that is a breakthrough, the researchers say. “It is scientifically exciting because this is the first time anyone has managed to combine cells from the  Vibrio natriegens with those of Ideonella sakaiensis,” said Nathan Crook, co-author of the study. [3]

Economically achieveable

“From a practical point of view, this is also the first genetically engineered organism capable of degrading PET microplastics in saltwater,” said Tianyu Li, first author of the paper. “That is important because it is not economically feasible to remove plastic from the ocean.” The salt must first be removed from the water before the plastic can be filtered out on an industrial scale.

Obstacles

Although this is an important step for the researchers, there are still obstacles before the research can be further scaled up. For example, the modified bacteria must be further modified so that it can also feed on other products besides plastic. In addition, according to the researchers, it would be even more beneficial if the bacteria produced a useful raw material from the eaten plastic.

The researchers would like to talk to companies from the industry. “For example, which molecules are desirable for industry?” Crook asks. Once they know this, the researchers can focus specifically on whether they can modify the bacterium in such a way that it can produce that molecule.

Limit on plastic production

Plastic-eating bacteria are not new[4]. In recent years, scientists have increasingly discovered animals with a hunger for plastic.[5] For example, German scientists found an enzyme in a cemetery compost heap that can break down plastic[6], and AI helped researchers[7] build the ultimate plastic-eating bacteria. All those plastic-eating organisms may help solve plastic pollution, but the best solution is still a limit on plastic production, researchers wrote in an open letter.[8]

Source

Romy de Weert, Onderzoekers: 'Eerste genetisch gemanipuleerde bacterie die plastic uit zeewater eet', in: Change Inc, 18-09-2023, https://www.change.inc/circulaire-economie/onderzoekers-eerste-genetisch-gemanipuleerde-bacterie-die-plastic-uit-zeewater-eet-40407

[1] Vibrio natriegens is a Gram-negative marine bacterium.[3][5] It was first isolated from salt marsh mud. It is a salt-loving organism (halophile) requiring about 2% NaCl for growth. It reacts well to the presence of sodium ions which appear to stimulate growth in Vibrio species, to stabilise the cell membrane, and to affect sodium-dependent transport and mobility. Under optimum conditions, and all nutrients provided, the doubling time of V. natriegens can be less than 10 minutes. V. natriegens is able to successfully live and rapidly divide in its coastal areas due its large range of metabolic fuel. Recent research has displayed that Vibrio natriegens has a flexible metabolism, which allows it to consume a large variety of carbon substrates, reduce nitrates, and even fix nitrogen from the atmosphere under nitrogen-limiting and anaerobic conditions.[6] In the laboratory, the growth medium can be easily changed, thus affecting the growth rate of a culture.[7][8] V. natriegens is commonly found in estuarine mud. S.I. Paul et al. (2021)[5] isolated and identified many strains of Vibrio natriegens from marine sponges of the Saint Martin's Island Area of the Bay of Bengal, Bangladesh.

[2] Ideonella sakaiensis is a bacterium from the genus Ideonella and family Comamonadaceae capable of breaking down and consuming the plastic polyethylene terephthalate (PET) using it as both a carbon and energy source. The bacterium was originally isolated from a sediment sample taken outside of a plastic bottle recycling facility in Sakai City, Japan.

[3] Poly(ethylene terephthalate) (PET) is a highly recyclable plastic that has been extensively used and manufactured. Like other plastics, PET resists natural degradation, thus accumulating in the environment. Several recycling strategies have been applied to PET, but these tend to result in downcycled products that eventually end up in landfills. This accumulation of landfilled PET waste contributes to the formation of microplastics, which pose a serious threat to marine life and ecosystems, and potentially to human health. To address this issue, our project leveraged synthetic biology to develop a whole-cell biocatalyst capable of depolymerizing PET in seawater environments by using the fast-growing, nonpathogenic, moderate halophile Vibrio natriegens. By leveraging a two-enzyme system—comprising a chimera of IsPETase and IsMHETase from Ideonella sakaiensis—displayed on V. natriegens, we constructed whole-cell catalysts that depolymerize PET and convert it into its monomers in salt-containing media and at a temperature of 30°C. https://aiche.onlinelibrary.wiley.com/doi/full/10.1002/aic.18228?_ga=2.34308516.464140274.1695118704-1472931476.1658240840

[4] Read also: https://www.tumblr.com/earaercircular/707410638839971840/this-bacteria-likes-plastic-but-not-plastic-soup?source=share & https://www.tumblr.com/earaercircular/710350099144949760/these-green-start-ups-indicate-the-way-to-a?source=share

[5] We are still pumping more and more plastic waste into the world. Only a small part is recycled, while the majority ends up in the garbage heap. But there is hope. Science is increasingly discovering animals with plastic cravings. Five examples of creatures with a tasty appetite for plastic.https://www.change.inc/circulaire-economie/plastic-recyclen-2-0-vijf-diertjes-met-een-honger-naar-kunststof-38551

[6]German researchers found an enzyme in a cemetery compost heap that can break down plastic. The enzyme dissolves a plastic grape container within sixteen hours until a watery substance remains. That substance can be used to make new plastic. https://www.change.inc/circulaire-economie/doorbraak-enzym-eet-binnen-16-uur-plastic-op-38376

[7] Artificial intelligence helped researchers build the ultimate plastic-eating bacteria. By improving the molecular structure of the plastic-digesting enzyme via the computer, there is now a version that eats plastic in one day at low temperatures.https://www.change.inc/circulaire-economie/ai-maakt-enzym-dat-in-24-uur-plastic-opeet-38180

[8] Scientists around the world warn in a letter that there must be a limit on plastic production. According to the researchers, an upper limit is the only solution to stop the growing threat of plastic waste to the environment and ourselves. https://www.change.inc/circulaire-economie/wetenschappers-waarschuwen-limiet-op-plasticproductie-is-enige-redmiddel-38186

[jesus-died-for-mycins]

Lasso peptides are a really cool family of peptides that have a very unique knotted structure and are chronically understudied and poorly understood. Lasso peptides get their name from the way the N-terminus wraps back around the peptide chain and forms an isopeptide bond with the carbonyl of a Glu/Asp residue, forming a literal lasso like shape:

This is a deceptively tricky reaction to study, let alone replicate. At the minute, most studies done on identifying and isolating these molecules use overexpression, chemical or even biosynthetic strategies are inaccessible, which is a real shame because the unusual topologies of these peptides gives them excellent protease resistance and much better pharmacokinetics than linear, or even standard cyclic peptides.

More detailed images of the peptides reveal some interesting quirks of how they adopt this unique shape:

This stick model on the left show the whole lasso peptide, with the section forming the ring highlighted in green. The sequence that is ‘lasso’d’ so to speak is quite interesting, and is shown on the right. The C terminal tryptophan-phenylalanine motif is common among lasso peptides and acts as a ‘stopper’ and provides a, frankly massive, steric barrier to unfolding the lasso. The encapsulated section is comprised of glycine which is pretty easy to rationalise because glycine doesn’t have a side chain, thus making it the most suitable for threading through a ring. I’ve also highlighted the proline, which is also common among lasso peptides, it is though that the proline is important to preorganising the lasso before the ring is completed, proline is a much more restricted amino acid than the others and often adopts this role as a conformational guide.

Its worth remembering just how tight this whole arrangement is, threading a peptide though a 7 residue ring is no small feat, and here’s the space filling model to highlight that fact:

There is no wiggle room at all, and that is key to understanding why these things are so hard to make, they incur a huge entropic and steric penalties for being in these tightly wound conformations and aren’t offsetting that by forming covalent bonds or massive protein scale stabilising interactions. As such I think they’re pretty remarkable and definitely worth studying more.

References:

1. Tan, S., Moore, G., and Nodwell, J. (2019) Put a bow on it: Knotted antibiotics take center stage. Antibiotics 8, 117.

2. Liu, T., Ma, X., Yu, J., Yang, W., Wang, G., Wang, Z., Ge, Y., Song, J., Han, H., Zhang, W., Yang, D., Liu, X., and Ma, M. (2021) Rational generation of lasso peptides based on biosynthetic gene mutations and site-selective chemical modifications. Chemical Science 12, 12353–12364.

3. Structure, bioactivity, and resistance mechanism of streptomonomicin, an unusual lasso peptide from an understudied halophilic actinomycete. Chemistry & Biology. Cell Press.