#Genomics Research Laboratory

[theloverstomb]

‘Fragile Microbiomes’ by bio-artist Anna Dumitriu

1. SYPHILIS DRESS- This dress is embroidered with images of the corkscrew-shaped bacterium which causes the sexually transmitted disease syphilis. These embroideries are impregnated with the sterilised DNA of the Nichols strain of the bacterium - Treponema pallidum subsp. pallidum - which Dumitriu extracted with her collaborators.

2. MICROBE MOUTH- The tooth at the centre of this necklace was grown in the lab using an extremophile bacterium which is part of the species called Serratia (Serratia N14) that can produce hydroxyapatite, the same substance that tooth enamel is made from.

The handmade porcelain teeth that make up this necklace have been coated with glazes derived from various bacterial species that live in our mouths and cause tooth decay and gum disease, including Porphyromonas gingivalis, which can introduce an iron-containing light brown stain to the glaze.

3. TEETH MARKS: THE MOST PROFOUND MYSTERY- In his 1845 essay “On Artificial Teeth”, W.H. Mortimer described false teeth as “the most profound mystery” because they were never discussed. Instead, people would hide the stigma of bad teeth and foul breath using fans.

This altered antique fan is made from animal bone and has been mended with gold wire, both materials historically used to construct false teeth (which would also sometimes incorporate human teeth). The silk of the fan and ribbon has been grown and patterned with two species of oral pathogens: Prevotella intermedia and Porphyromonas gingivalis. These bacteria cause gum disease and bad breath, and the latter has also recently been linked to Alzheimer’s disease.

4. PLAGUE DRESS- This 1665-style 'Plague Dress' is made from raw silk, hand-dyed with walnut husks in reference to the famous herbalist of the era Nicholas Culpeper, who recommended walnuts as a treatment for plague. It has been appliquéd with original 17th-century embroideries, impregnated with the DNA of Yersinia pestis bacteria (plague). The artist extracted this from killed bacteria in the laboratory of the National Collection of Type Cultures at the UK Health Security Agency.

The dress is stuffed and surrounded by lavender, which people carried during the Great Plague of London to cover the stench of infection and to prevent the disease, which was believed to be caused by 'bad air' or 'miasmas'. The silk of the dress references the Silk Road, a key vector for the spread of plague.

5. BACTERIAL BAPTISM- based on a vintage christening gown which has been altered by the artist to tell the story of research into how the microbiomes of babies develop, with a focus on the bacterium Clostridioides difficile, originally discovered by Hall and O’Toole in 1935 and presented in their paper “Intestinal flora in new-born infants”. It was named Bacillus difficilis because it was difficult to grow, and in the 1970s it was recognised as causing conditions from mild antibiotic-associated diarrhoea to life-threatening intestinal inflammation. The embroidery silk is dyed using stains used in the study of the gut microbiome and the gown is decorated with hand-crocheted linen lace grown in lab with (sterilised) C. difficile biofilms. The piece also considers how new-borns become colonised by bacteria during birth in what has been described as ‘bacterial baptism’.

6. ZENEXTON- Around 1570, Swiss physician and alchemist Theophrastus Paracelsus coined the term ‘Zenexton’, meaning an amulet worn around the neck to protect from the plague. Until then, amulets had a more general purpose of warding off (unspecified) disease, rather like the difference today between ‘broad spectrum’ antibiotics and antibiotics informed by genomics approaches which target a specific organism.

Over the next century, several ideas were put forward as to what this amulet might contain: a paste made of powdered toads, sapphires that would turn black when they leeched the pestilence from the body, or menstrual blood. Bizarre improvements were later made: “of course, the toad should be finely powdered”; “the menstrual blood from a virgin”; “collected on a full moon”.

This very modern Zenexton has been 3D printed and offers the wearer something that genuinely protects: the recently developed vaccine against Yersinia pestis, the bacterium that causes plague.

[reasonsforhope]

"An international research team has found almost a million potential sources of antibiotics in the natural world.

Research published in the journal Cell by a team including Queensland University of Technology (QUT) computational biologist Associate Professor Luis Pedro Coelho has used machine learning to identify 863,498 promising antimicrobial peptides -- small molecules that can kill or inhibit the growth of infectious microbes.

The findings of the study come with a renewed global focus on combatting antimicrobial resistance (AMR) as humanity contends with the growing number of superbugs resistant to current drugs.

"There is an urgent need for new methods for antibiotic discovery," Professor Coelho, a researcher at the QUT Centre for Microbiome Research, said. The centre studies the structure and function of microbial communities from around the globe.

"It is one of the top public health threats, killing 1.27 million people each year." ...

"Using artificial intelligence to understand and harness the power of the global microbiome will hopefully drive innovative research for better public health outcomes," he said.

The team verified the machine predictions by testing 100 laboratory-made peptides against clinically significant pathogens. They found 79 disrupted bacterial membranes and 63 specifically targeted antibiotic-resistant bacteria such as Staphylococcus aureus and Escherichia coli.

"Moreover, some peptides helped to eliminate infections in mice; two in particular reduced bacteria by up to four orders of magnitude," Professor Coelho said.

In a preclinical model, tested on infected mice, treatment with these peptides produced results similar to the effects of polymyxin B -- a commercially available antibiotic which is used to treat meningitis, pneumonia, sepsis and urinary tract infections.

More than 60,000 metagenomes (a collection of genomes within a specific environment), which together contained the genetic makeup of over one million organisms, were analysed to get these results. They came from sources across the globe including marine and soil environments, and human and animal guts.

The resulting AMPSphere -- a comprehensive database comprising these novel peptides -- has been published as a publicly available, open-access resource for new antibiotic discovery.

[Note: !!! Love it. Open access research databases my beloved.]"

-via Science Daily, June 5, 2024

[covid-safer-hotties]

Also preserved on our archive

First detection of XEC in Virginia

By Jean Jadhon

ROANOKE, Va. (WDBJ) - A new COVID-19 variant has been detected in half of U.S. states, including Virginia.

It’s the X.E.C. variant.

Some of the earliest cases were reported from samples tested at the Fralin Biomedical Research Institute at Virginia Tech Carilion in Roanoke.

Carla Finkielstein is the director of the Molecular Diagnostics Laboratory and professor at Virginia Tech’s Fralin Biomedical Research Institute. She oversees the lab where they’re tracking the virus.

“We have detected a new variant that is called XEC,” said Finkieltein. The cases we identified all came from Southwest Virginia.”

But Finkielstein says the virus may not have originated here.

“I want to make sure we don’t link the cases to Southwest Virginia because this could be simply people that traveled to Europe and arrived [back] and they live in Southwest Virginia.

Scientists at the Fralin Biomedical Research Institute at Virginia Tech Carilion in Roanoke have been testing samples since the pandemic began; the tests are completed in the same day in an intricate process.

Here they conduct genomic surveillance, tracking the virus at the molecular level. The idea is to catch any changes in the virus early.

“The reason is you want to catch something that is super new immediately that pops up,” said Finkielstein. “So you can report it to the health department.”

The information is also entered into a federal database.

So far Finkielstein says the new variant doesn’t seem to present in patients much differently than past variants of COVID-19.

“It shows kind of the typical symptoms of COVID we’ve seen before. Maybe this one seems to have a little bit more of a sore throat which is a little different,” said Finkielstein.

The lab tests samples from all over Virginia. Finkielstein predicts a surge in COVID cases this winter and is advising everyone to get their COVID vaccine and to wear a mask if you feel sick out of courtesy to your co-workers and friends and to help prevent the spread of the virus.

[fishyfishyfishtimes]

Daily fish fact #564

Zebrafish!

They’re one of the most common animals used in laboratories for research! This is due to many reasons, like their fast maturing rate and embryonic development time, their well-known behaviour and development, and their genome that has been fully sequenced!

[chaosticbraindo]

Kaijune - day 23: Flourish 🌺🫀

Biollante is technically the entire hollow earth the size of the continent itself. This is technically just the core of her.

Chaos Biollante

Nearing the end of humanity’s collapse, all of the world’s leadership put down their differences to form an alignment. Although mankind has been able to buy themselves some time by pitting the kaijus together, the very same kaijus that “protect” them are also extremely dangerous themselves. Therefore, a number of plans and projects to push back the damage of the kaijus were put in motion. Among these projects, one notable course of action is nicknamed project-Biollante.

It is stated that the project, lead by Dr. Genshiro Shiragami, was experimenting with combining Kaiju cells with that of some floral and fauna- with some rumored that it even includes human DNA despite not having any prove. What is certained, however, is that by splicing together various floral genome with the cells within Gojira, these plants can feeds off the constant source of energy emitted and grow non stop. Adding in Mothra’s scale which accelerate growth and it is hoped that these mutated plants would grow fast enough to survive the destruction of the kaijus. With it being effectively a bio-bomb however, the laboratory is moved deep underground to keep Biollante contained in case things went wrong… and sadly went wrong it did.

Through unknown reasons- perhaps coincidental, Baragon burrows down to a zone nearby the underground research station. With a skeleton hot enough to melt stone, its heat caused major damage to the lab and break electrical instruments, causing malfunction and accidentally releasing Biollante out of its containment tank. With this being an unstable prototype, the plant start absorbing heat and grow unhindered- soon taking over the entire station after Baragon left. Although a number of the human researchers evacuated to the surface, the majority of them was left behind when the lab was sealed, leaving them at the mercy of the plant and countless animals subjects that are also freed from containment.

the station was completely sealed off in fear of Biollante devastating humanity’s only safe haven on the surface… until a few decades later when the human within Mothra’s domain was instructed by her to open the vault and venture downward. what they see was unbelievable. Biollante has grown to the size of a continent, its body taking in dirt and convert it to bio-mater underneath the surface and creating an entire hidden world. this world is populated by the man and beast left behind all those years ago and have evolved beyond anyone’s wildest imagination. And luckily, Biollante have seems to reach a size where it stabilized itself, using its body to support this ecosystem and leaving a new world for the surface inhabitants to discover. A world that was commonly called the Hollow Earth.

[mskenway97]

What about TFA waspinator encountering a human scientist(reader) the rest is up to your imagination.(Safe vore please)

Peaceful investigation

Tfa Waspinator x Fem!human!reader

Words : 1,145

Summary: You found yourself on a journey, researching species, but what you didn't know was that this fascination would take you to the most unlikely places.

Warning: g/t content, safe vore, soft vore, protection vore

You had always been fascinated by the evolution of the species, you had studied too much and now that you know that aliens also exist thanks to the Detroit autobots. You wanted to know even more since there were some things that looked like them… But they will also have fauna, their flora. Your research had come to fruition thanks to the collaboration of Prowl in certain parts that he had commented with you about the Dinobots, Optimus told you something about Blackarania but not much because of his past. That made me even more curious. Knowing about it made your curiosity grow more and more that you were attentive to any new discoveries. You had notes, lots of notes… The other researchers were beginning to think you were going crazy. But there was something your notes didn't give you a being to investigate closely. Since Prowl wouldn't let you get close to the Dinobots, no matter how many times you tried. Even sneaking around the ninja bot had always caught you. One day they told you that they had discovered a huge being in the Amazon that resembled the descriptions you had given. They called you to see if you could help in their mystery. You were looking forward to this trip at least, you wouldn't be interrupted in case you could see a new species or at worst if they were messing with you for investigating something like this. The climate of the Amazon was complicated to what you were used to in Detroit, besides the fact that here you could be the prey.

You didn't think much of it since you weren't far away from your escort who was watching. The damage caused to some structures, there were some trees that were broken, others were filled with a viscous substance that you did not recognize. It was purple, unlike any fluid you had ever seen. You told your companions about it but they did not give importance to the discovery you made. You tried to analyze it in the laboratory, the results took some time but the only thing you identified was that it was 30% bee DNA and 70% unknown DNA… Unknown, something already told you that this being that roamed the Amazon was no longer common. You tried to describe the unknown genome with different chemicals but all of them were failing. It's like it was mutated or something. You were even more eager to know what was going on but at the same time in your last visits to the affected area, you felt like you were being watched. Until one day they decided to do an expedition at night, they told you that it was completely safe and there would be no problem. You are not so sure, if the fauna detected an easy prey, no matter how many security measures they put in place, they would get whatever they could. But despite the risk you accepted because maybe you could find your specimen. At night you were in your tent still trying once again to get the unknown DNA data out of the sample you took. You ran over 40 tests but this one seemed to be something…. Then you started to hear a rumbling outside they had attacked the camp you were in, you didn't understand what was going on but they took you to safety as best they could so you ran after them, the grunting noises around you left you with goose bumps, feeling your heart in a fist. The men didn't know what to do so they told you to head for a cave to be safe. You didn't object so you went into that cave trying to find a safe place. Some time passed in which you stayed in the cave just listening to the silence of the night and little else. Then you heard a noise at the back of the cave. Your logical side told you not to approach but your curious side wanted to know who was making the noise. So you decided to see what was going on at the bottom of that place that was getting bigger and bigger until it showed you a grotto, illuminated in blue, you were fascinated by the place until you felt something rise in front of you. You screamed for a moment when you didn't recognize what animal had caught you, wait, was it an animal? You focused your sight better to see not a wild animal but… A giant robot and not just any insect looking bumblebee with purple optics, that was staring at you.

-Not to be a threat to waspinator… What to do here, human?

You are trembling, in the servos of that enormous being…. as I took a closer look at you.

-I recognize… Waspinator to see you near dangerous zone. You go where you shouldn't - said Waspinator while I tried to keep calm. You didn't know exactly what its intentions were but if you made a false move it could be fatal.

-I was investigating… It seems to have led me to you… What exactly are you? What do you transform into? - you asked curiously but quite carefully. it felt you were sniffing me out - Waspinator being from Cybertron… You have no fear… That's weird - said Waspinator as he put you on the ground.

-Oh are you an autobot? Or Decepticon? - you asked a little scared while he denied and watched every move you made.

-I'm neither. Being traitors…

-I understand, I'd like to know more about you but I have to get back to camp… - you said as he picked you up again in his servos. I didn't understand why he did it.

-Not leaving is not safe… I'll get you to safety, inside… - said Waspinator you didn't understand until you were getting close to what seemed to be his mouth, you started to move frantically trying to get as far away as you could from that mouth but it was stronger than you. When you realized you were between the jaws of the huge beast that was massaging you with its tongue and crushing your chest a little on the roof of your mouth making you gasp for a moment before it swallowed you. Waspinator felt a pleasant sensation in his tanks.

Waspinator felt a pleasant sensation in his tanks, feeling that you were safe. It wasn't safe for someone as small as you to be alone in the Amazon and his tanks, his body would protect you from harm. He sensed that you were still moving… so he generated some movement.

-Not to worry… Waspinator will protect you - said Waspinator as he moved away to hide in the middle of the night. Where you wouldn't know for sure when you would see the light again.

[mindblowingscience]

Investigators from the laboratory of Ali Shilatifard, Ph.D., the Robert Francis Furchgott Professor and chair of Biochemistry and Molecular Genetics, have discovered a new repeat gene cluster sequence that is exclusively expressed in humans and non-human primates. The discovery, detailed in a study published in Science Advances, is a breakthrough for human genome biology and has wide-ranging implications for future research in transcriptional regulation, human evolution, and the study of repetitive DNA sequences, according to the authors. "This is an unbelievable discovery of the first elongation factor that is repeated within the human genome and is very primate-specific," said Shilatifard, who is also director of the Simpson Querrey Institute for Epigenetics and a professor of Pediatrics. Over the last two decades, rapid advancements in genome sequencing technologies have accelerated research exploring the genetic structure of various regions throughout the human genome. Larger regions of the human genome are composed of repetitive DNA sequences, dubbed genetic "dark matter" by experts, which until recently was unidentifiable using traditional short-read DNA sequencing technology.

Continue Reading.

[goodfish-bowl]

What Little Remains

Chapter 2: Cooking by the Book

Ectoberhaunt 2024 Day 15: Science Fiction

AO3 Link (to be updated) Chapter 1 Link (read for context)

Summary: Dr. Reeden is considered a specialist in the technology for many reasons. The investors really should've expected this when they allowed them to join T.Z.A.P

Warnings: gore, human experimentation

Words: 3,045

After compiling the research and finally reading the papers they had obtained from the laboratory, Reeden needed a new pack of smokes. Those papers had been some of the most unscientific research papers Reeden had ever encountered, which was saying a lot considering their past working experience. But these papers in particular made them determined to create physical copies of the papers just to burn them with. They weren’t even an archaeologist like the other four people left on this team, but a geneticist who specialized in researching the humanoid genome throughout the past millennia and the resulting variation in humanoids and the occasional tangentials across the galaxy. Not quite archeology, in their opinion, but a type of genetic tracking a bit closer to the ancient discipline of paleontology instead. They had just wanted to get a good look at a pre-nuclear human genome for their latest paper, the original template would be invaluable for perspective. It was the only reason they had agreed to be on the T.Z.A.P team in the first place. 

What had ended up in Reeden’s lap instead was a variation of tangential DNA sequence from before that branch of humanity even existed. Void of space, that would make the kid the first tangential, the first variation and deviation. Now they only wished they could figure out what the actual fuck was going on with the kid’s DNA sequence. There were at least two different sets, impossible in and of itself, with holes in each, where the other filled in, like some paradoxical basket weaving. But there were more holes, which neither set of DNA contained the answers to. 

With the Head Doctor’s approval, Reeden had free access to most of the samples, not the core for obvious reasons, but the other genetic and biological ones were all they needed. They think the Doctor had put the intern on the unfortunate project of inspecting the core. From the other samples, they were able to reconstruct most of the boy’s DNA sequences with the D.R.C.R.A. (that Reeden was specially trained in) at the expense of only one of the intact vials. There were red blood cells mixed in with the… ectoplasm(?) the kid possessed. Each set contained the complete recipe for an entire being with only pieces of each actually being used. One was closer to what Reeden imagined the original human genome was like and the other was similar but based on ectoplasm instead of carbon. There was no transition between the two and no way the kid should’ve been able to switch between them… unless they were secretly hiding a form in-between. 

Reeden practically leaped from their seat and pulled up that awful video, the final one of the set, and scrubbed through it, finding the exact timestamp where the kid switched forms. Then, writing it down on their hand, went back to the vials, intact and otherwise, any of the samples really. The in-between. That was where the missing DNA must be. 

Reeden found one sample, ripped it open, and tossed the entire sample into the D.R.C.R.A. It was that ectoplasmic-isotopic solution that made their life that much easier, as it seemed to prevent the degradation of DNA unlike any other preservative Reeden had ever encountered. They powered up the machine and let it record the entire transition as the sample suddenly started to degrade after being removed from the solution. It switched from ectoplasmic to carbon and Reeden almost lost focus watching the visible reaction take place through the viewing window of the D.R.C.R.A. The machine slowly but surely began piecing the DNA sequences together, along with that they had already fed it. It would take a while, but Reeden could already see the third DNA sequence filling in the final gaps. They now had the complete recipe, as mixed up and convoluted as it was. It was an interesting challenge just putting it together, it made Reeden almost excited for the next part. 

Reeden left their lab, intent to grab something with a resemblance to food and to see if the final piece was in place. They needed a break anyway. With the hiss of the door, Reeden entered the cafeteria and put in the code for their order. Just their luck, that one intern, Zavier(?) was sitting with his head on the table. The Head Doctor had taken a liking to the intern. She wouldn’t have let him work on this project otherwise. The kid wasn’t leaving her supervision any time soon. 

Reeden dropped their tray with a metallic slap to the table, and the intern snapped his head up. 

“Greetings. How goes it go with the glowy orb?” Reeden asked casually. 

Zavier slowly lowered his head back to the table, shoulders shaking and muttering quietly to the point Reeden couldn’t make sense of it. That hadn’t been the reaction they’d been expecting. They’d intended to tease the intern a bit, but he already seemed ready to cry. That wouldn’t do at all. 

“What is it? I can’t hear you.”

“It’s a brain in a jar,” Zavier whimpered, and Reeden stopped dead. “And that’s not even the worst part.” 

Reeden blinked, slowly wrapping their head around what the intern had said. It made sense based on the ectoplasmic DNA sequence and the horrible papers, but actually facing the fact was a different matter.

“And what would be the ‘worst part’?”

“They're still alive in there. Dreaming, or some other kind of deep comatose, unconscious state, but they're still there, after over 3,000 Terran years.” 

Reeden whistled under their breath, “Fattest nap of the ages, right there. Can’t imagine it’s been good for their mental state though,” they commented, “But that’s good, in its own way. Means we’ve got all the pieces to toss in the D.R.C.R.A.”

“What is that anyway? A D.R.C.R.A.?” Zavier asked. 

“DNA Reader and Cellular Reconstruction Apparatus. It’s normally a piece of medical technology used to regrow limbs and organs, but with a talented geneticist like myself, it has other uses as well,” Reeden explained. 

Sure, there were a few gray areas with the tech, especially with what the apparatus was originally designed for, and this was coming pretty damn close to its original use. Cloning was a messy and frankly pointless business overall. They weren’t particularly worried about the moral obligations of things. Was never their style. 

“No way… that… you can’t use it to bring people back to life. That’s just-”

“Nope, you can’t make a complete person. It’s a body sure, but no one’s home. Basically a living corpse. That’s why it’s a good thing that the core is intact. Can’t really recreate something that’s built up over time. But with the core being a ‘brain in a jar’, we have all of the ingredients to cook by the book.” 

“We’re really reviving them” Zavier gasped, stuck somewhere between awe and shock. 

“Yep.”

Reeden wanted a smoke. 

All five of the researchers on project “Phantom”, as it had been unofficially dubbed, were shoved into the operating room of the D.R.C.R.A. staring intently at the main chamber of the machine, the orb suspended in position. 

“You know, this might be the first time an entire being has been reconstructed in this thing, right?” Someone commented. Reeden didn’t correct them.

“Then let’s make sure this event is properly recorded so that when I report it, our success will cushion the consequences,” the Head Doctor stated. Reeden grinned, they had figured as much. 

“Wait, are we not approved to be doing this?” Zavier asked, a panicked expression on his face.

Reeden laughed, “I think this is more of a ‘forgiveness than permission’ sort of situation. Besides, they let us use the D.R.C.R.A. in the first place knowing I was here. With an opportunity like this, it would be a waste to do otherwise, approval or not.”

Reeden double-checked, making sure that everything was being recorded before beginning. 

“My name is Doctor Reeden del Orcutus, lead geneticist of the Terra Zero Archeology Project. We are currently attempting to reconstruct an individual from circa 2000 AD Terra Zero after finding a complete and viable DNA sequence. However, the individual being reconstructed is not only a tangential, but possesses three separate DNA sequences, only one of which is carbon-based, while the others are ectoplasmically-based. This is the energy source of interest to the Terra Zero project. An attempt at ‘revival’ is being made after the discovery of an additional organ, functioning as a secondary brain, shown to contain the subject’s intact consciousness. Reviving and communicating with this individual aligns with the majority of T.Z.A.P’s goals and is now considered tantamount to the project.” Reeden stated for the recording, sure to include just enough logical evidence for if they were to get investigated later. 

Their investors really shouldn’t have included this much wiggle room in the statement of T.Z.A.P's mission. Now they had a legal loophole to escape culpability. The Head Doctor kept them around for a reason, and it wasn’t just for their specialty or to steal their smokes every now and again.

“Beginning calibration for cellular reconstruction now.” 

The D.R.C.R.A. gave a low thrum and the chamber inside slowly filled with light, sterilizing it in preparation for the initial regeneration. Reeden gave a cursory glance over to the supply tanks, checking to make sure that there were enough materials to make a full person. It wasn’t good to run out mid-way after all. It took forever to clean blood out of a machine this complicated. Luckily, everything was there, even the additional elements that had to be added for the multiple DNA sequences. 

The machine pinged and Reeden gave a wide grin. 

“Sanitation and calibration complete, beginning reconstruction.”

Danny awoke slowly. His entire body felt heavy, and his head clouded. There was a disconnect between what he was experiencing and what he expected. Something in his head denied it all, like this couldn’t be real. Danny couldn’t find it in himself to really care if it was real or not, just that he had a body, and heavy or not, he could move it. The experience seemed both novel and extremely foreign for reasons he couldn’t remember or palace.

Danny began slowly, twitching a finger, stretching his toes, and slowly readjusting each limb, until he built up to opening his eyes. He immediately closed them. Pins-and-needles spread to every part of Danny’s body and Danny let out a sharp breath. This caused him to start coughing. Everything hurt. Everything was so sensitive. He felt raw and exposed. 

Danny squinted his eyes, shielding them behind a hand, struggling just to hold his hand up. The light wasn’t that bright but his eyes struggled to adjust to it either way. With his other arm, Danny forced himself to sit up with a groan before placing his arm in his lap as he leaned against the headboard. Blurry eyes caught on his right hand in his lap. Something seemed… not right with that. He couldn’t remember what. 

It took several more minutes for his eyes to finally allow him to see, and Danny glanced around the room. It was weird in a way he couldn't really place. ‘It was like if a hospital room was a furniture store display’, was the only way he could describe it. At least, Danny figured it was a hospital room, if one with a really weird feel to it. The gray color of the walls instead of the standard white or off-yellow didn’t help. It made the whole thing seem like a Twilight Zone episode with the monochrome pallet. Here Danny was, sitting in a strange hospital room, in a place he had no idea where, feeling really bugged out in his own skin, all by himself. 

Danny took an additional moment to check himself over, something like panic causing him to sputter. He was fine. Not a single scratch or scar on him. He didn’t know why he expected any in the first place, or that the fact there were none at all weirded him out so much. He wasn’t supposed to be covered in scars. This was fine. He was okay. 

There was a sound, a hydraulic kind of hiss, and Danny snapped to it, practically jumping in fright. The doorway was now open, the door sliding cleanly into the wall all on its own, a person standing behind it. 

Danny would like to say he was the strangest person he had ever encountered, but somehow, he couldn’t seem to. He didn’t think he had encountered anyone weirder than the person with gray skin with matching ashy hair in front of him, but his lack of reaction left him uncertain. He felt like he was missing a lot of things, really. 

The gray-skinned person blinked owlishly at him, leading to something of a staring contest before the stranger became flustered, digging through the pockets of a patch-covered lab coat and pulling out a handheld device before shoving it back into the coat pockets. 

“Sorry!” He apologized. “We didn’t think you would be awake this early. We expected you’d be comatose for a week at least before waking up.” 

Danny continued staring. He wasn’t shocked by the stranger's appearance and he decided that was the weirdest part. He couldn’t remember. 

“How’d I get here?” Danny blurted. 

The stranger paused, apparently not expecting the question. “Umm, I’m not sure what I’m supposed to tell you, so it might be better to save questions like… that until the Head Doctor and Dr. Reeden get here,” he explained. My name’s Zavier,” he added. 

Danny wanted to ask more. He was forgetting something, a lot of something, and it freaked him out. But ‘Zavier’ couldn’t answer his questions. 

There was a ping, and Zavier pulled out the device again, reading something on it. It almost looked like a cell phone, if cell phones were sleek bricks instead of being phone-shaped. 

“Since you’re awake, we’d like to confirm a few things while the Head Doctor is on her way to answer your questions. Is that alright?”

Danny nodded. He found it weird that he had to be the one to confirm the questions. Usually, medical professionals just ask Jazz or his parents. Did that mean he was here alone? 

“Okay. Your name is ‘Danny’, right? Also, what’s your last name?” Zavier began. 

They didn’t know his name. Danny had definitely been brought here alone from… wherever he had been before. 

“My name’s Danny Fenton,” he confirmed. 

“Birth date?”

“June 14th, 1990.”

“Tests show that you’re around 17 years old, is that right?”

Danny blinked. That… that didn’t make sense. 

“I… I’m 17?” Danny ended up asking instead.

Danny had some memories still intact, but he could for the life of him remember what he had been doing before. He was just about to start high school wasn’t he? If he was supposed to be 17, then that would’ve been years ago. Anything from that point forward was blank, while things from before that were blurry at best. 

Zavier looked up from his device, frowning and meeting Danny’s eyes. Zavier’s eyes were a blue so pale that they almost blended into the whites of his eyes. It looked like he should be blind, but he met Danny’s gaze just fine and didn't seem to have any trouble reading on his weird phone. 

“Some memory loss was to be expected but… but that’s a lot.”

Danny looked down at his own hands. They didn’t seem different, but were larger and slenderer than he remembered, despite not feeling like there was anything off with the proportions of his body. But he was three years older now. He was older than Jazz was, wasn’t he? No, Jazz would be 19, probably off at some fancy university doing whatever know-it-alls did there. (Something in his gut told him that wasn’t true, he ignored it). Danny wanted to go look in a mirror, just to see what he looked like. 

“Do you know what happened?” Danny asked. 

Zavier twitched, which was more than Danny had honestly expected. He looked nauseous at the thought, if anything. Something had happened, something really bad that was horrible enough that it made sense if Danny forgot. 

“I… can’t tell you that, either.” The answer was expected enough. 

The door hissed open a second time and two more people entered the room, both seeming older than Zavier by at least a decade, just from the way they carried themselves alone. 

The first to enter was a shorter, round woman with skin so dark it was almost black, but having warmer hues to it than the cool greys of Zavier’s. Her hair clung tightly to her head before exploding out behind her in a dense orb of gray curls. Her lab coat was even more heavily decorated than Zavier’s as well, but she wore them like military badges instead of quirky patches. Following her was a person who looked like they had been pulled through a taffy machine, slender in every way, with a gaunt face and dark hair contrasting a pale complexion, like an inverse of the other two. 

“Head Doctor, Doctor Reeden,” Zavier greeted. 

The Head Doctor, the woman, who Danny assumed was in charge of everything, gave Zavier a quick nod before approaching Danny and looking over him. Danny fought the urge to squirm. Dr. Reeden snickered in the background. Once she was apparently satisfied, from a bag Danny hadn’t noticed when she walked in, she pulled out a thick binder and held it out to him. He just let it sit in his lap, unable to hold it up. It was heavy. 

“It’s nice to meet you, Danny Fenton. Your existence here is groundbreaking and we have much to talk about, but first, welcome to the Terra Zero Archeology Project. Here’s the basics of what you need to know for a time 3,000 years after your own.” 

If the binder hadn’t already been sitting in Danny’s lap, he would’ve dropped it.

Ectoberhaunt 2024 Masterpost

[todaysbug]

February 11th, 2024

The Worm (Caenorhabiditis elegans)

Distribution: Found in temperate regions worldwide.

Habitat: Terrestrial; lives in humid soils with moderate oxygen contents and low-to-medium clay contents.

Diet: Microbivorous; feed on bacteria that lives in soil and on rotting vegetation, but can also feed on various species of yeast.

Description: C. elegans is aptly nicknamed "the worm" because it is a very common laboratory model; in fact, it's used as the model organism for all eukaryotic organisms! These worms are very easy to study due to the transparency of their body, as well as their limited number of cells, having only 131 cells in their entire bodies. They were the first multicellular organisms to have their entire genome sequenced (as they only have 6 chromosomes and approximately 20,000 genes). Common research on these worms include the processes of embryogenesis, development, disease and aging (especially in the form of programmed cell death). By understanding how their genes are involved in the aging process, we can hopefully have a better idea of the processes involved in human aging, too!

Most of these worms are self-fertilizing hermaphrodites, though males are also present (composing only about 1/1000 worms). Though their anatomy is quite simple, they do possess a simple brain and nervous system (one third of their cells are neurons). They're also capable of rudimentary learning, as well as using chemoreceptors to orient themselves, and respond minimally to light (living in dark environments, they don't have much need for good eyesight).

Image by K. Bradnam and gif by Bob Goldstein.

[petervintonjr]

Meet the unsung contributor to revolutionary breakthroughs in treating polio, cancer, HPV, and even COVID-19: Henrietta Lacks. Born in 1920 Roanoke, Virginia, Henrietta's mother Eliza died when she was only four, and she was ultimately raised by her maternal grandfather in Clover, Virginia. Henrietta worked as a tobacco farmer and attended a segregated school until the age of 14, when she gave birth to a son, Lawrence. A daughter, Elsie, was born three years later --to compound the family's difficulties, Elsie had cerebral palsy and epilepsy. Henrietta and her now-husband David Lacks moved to Turner Station (now Dundalk), Maryland where David had landed a job with a nearby steel plant. At the time Turner Station was one of the oldest African-American communities in Baltimore County and there was sufficient community support for the family to buy a house and produce three more children.

In 1951 at the age of 31, Henrietta died at Johns Hopkins Hospital of cervical cancer, mere months after the birth of the family's youngest son. But before her death --and without her or her family's consent-- during a biopsy two tumour cell samples were taken from Henrietta's cervix and sent to Johns Hopkins researchers. Hernietta's cells carried a unique trait: an ability to rapidly multiply, producing a new generation every 24 hours; a breakthrough that no other human cell had achieved. Prior to this discovery, only cells that had been transformed by viruses or genetic mutations carried such a characteristic. With the prospect of now being able to work with what amounted to the first-ever naturally-occurring immortal human cells, researchers created a patent on the HeLa cell line but hid the donor's true identity under a fake name: Helen Lane.

It is no exaggeration to state that in the 70 years since her death, Henrietta's cells have been bought, sold, packaged, and shipped by thousands of laboratories; with her cells being used as a baseline in as many as 74,000 different studies (including some Nobel Prize winners). Her cells have even been sent into space to study the effects of microgravity, and were instrumental in the Human Genome Project. While no actual law (or even a code of ethics) necessarily required doctors to ask permission before taking tissue from a terminal patient, there was a very clear Maryland state law on the books that forbade tissue removal from the dead without permission, throwing the situation into something of a legal grey area. However because Henrietta was poor, minimally educated, and Black, this standard was quietly (and easily) circumvented and she was never recognized for her monumental contributions to science and medicine ...and her family was never compensated. The family remained unaware of Henrietta's contribution until 1975, when the HeLa line's provenance finally became public. Henrietta had been buried in an unmarked grave in the family cemetery in Clover, Virginia but in 2010 a new headstone was donated and dedicated, acknowledging her phenomenal contribution. That same year the John Hopkins Institute for Clinical and Translational Research established a new Henrietta Lacks Memorial lecture series. A statue of Lacks was commissioned in 2022, to be erected in Lacks's birthplace of Roanoke, Virginia --pointedly replacing a previous statue of Confederate Gen. Robert E. Lee, which had been removed following nationwide protests over the murder of George Floyd.

Dive into The Immortal Life of Henrietta Lacks by Rebecca Skloot, originally published in 2011 and subsequently adapted into an HBO movie in 2017, starring Oprah Winfrey as Henrietta's daughter Deborah and Renee Elise Goldberry as Henrietta. (And yes, this book has been challenged and banned in more than one school district.)

[reasonsforhope]

"Similar to the expeditions of a hundred or two hundred years ago, the Tara Pacific expedition lasted over two years. Its goal was to research the conditions for life and survival of corals. The ship crossed the entire Pacific Ocean, assembling the largest genetic inventory conducted in any marine system to date. The team's 70 scientists from eight countries took around 58,000 samples from the hundred coral reefs studied.

The first results of the analysis have now been published in Nature Communications. This largest-ever data set collection on coral reef ecosystems is freely available, and for years to come, will be the basis for elucidating the living conditions for corals and finding a way for them to survive climate change.

Important first results of the expedition show that global microbial biodiversity is much higher than previously thought. The impacts of the environment on evolutionary adaptation are species-specific, and important genes in corals are duplicated.

Global biodiversity ten times higher than assumed

Coral reefs are the most biologically diverse marine ecosystem on Earth. Although they cover only 0.16% of the world's oceans, they are home to about 35% of known marine species. Using a genetic marker-based data set, the researchers found that all of the globally estimated bacterial biodiversity is already contained in the microorganisms of coral reefs.

"We have been completely underestimating the global microbial biodiversity," says Christian Voolstra, professor of genetics of adaptation in aquatic systems at the University of Konstanz and scientific coordinator of the Tara Pacific expedition. He says the current estimate of biodiversity (approximately five million bacteria) is underestimated by about a factor of 10.

Impacts of the environment on evolutionary adaptation are species-specific

The 32 archipelagos studied serve as natural laboratories and provide a wide range of environmental conditions, allowing scientists to disentangle the relationships between environmental and genetic parameters across large spatial scales. This led to another important finding: The effects the environment has on evolutionary adaptation trajectories of corals are species-specific. To determine this, the researchers examined the telomeres, the ends of chromosomes that are the carriers of genetic information, for the first time.

In humans, the length of telomeres decreases during life; that is, with an increasing number of cell divisions, suggesting that biological age is closely linked to the length of telomeres. Researchers on the Tara Pacific expedition have now found that the telomeres in very stress-resistant corals are always the same length. "They apparently have a mechanism to preserve the lengths of their telomeres," Voolstra concludes...

Important genes are duplicated

Research data from the Tara Pacific expedition brought to light that the long life of some coral species may have yet another reason: the duplication of certain genes. Many important genes are present multiple times in the genome. The researchers were able to determine this through sequencing of coral genomes employing a new high-resolution technique.

This technique, called long-read sequencing, makes it possible to not only determine the set of genes present, but also to look at their order in the genome. According to Voolstra, the pervasive presence of gene duplication could be a possible explanation for why corals can live for thousands of years despite being exposed, for instance, to extreme UV radiation in shallow waters.

The entire data collection is freely accessible

All data sets are openly accessible and fully described with accompanying physical and chemical measurements to provide them as a scientific resource to all researchers.

"This is unique," Voolstra says. "It is the largest data set collection on coral reefs ever collected and it is completely open access." The aspiration is that this data collection will serve as a foundation and inventory to guide future study of coral reefs worldwide for many years."

-via Phys.org, June 26, 2023

[covid-safer-hotties]

Dutch participatory surveillance framework for evaluating evolutionary changes on SARS-CoV-2 affecting Rapid Diagnostic Test sensitivity in 2022 –2023 - Preprint Posted Sept 10, 2024

An interesting preprint that shows us water does indeed make things wet: The majority of rapid test negatives come from human error (first and foremost, not using RATs to serial test)

Abstract Background Rapid Diagnostic Tests (RDTs) have been pivotal in the diagnostics for SARS-CoV-2 and policies surrounding self-isolation. When self-testing policies are in place a decreased sensitivity of the virus to RDTs can give benefits for viral spread. However, to monitor for reduced sensitivity of RDTs we rely on the collection of SARS-CoV-2 positive samples from RDT negative patients. Infectieradar, a national participatory surveillance that registers influenza-like symptoms is used as a framework to study false-negative RDT results due to emergence of new virus variants.

Methods Participants report weekly on RDT use and symptoms linked to Acute Respiratory Illness (ARI). Each week, all RDT positive and a sample of 200 among RDT negative but symptomatic participants were invited to send in nose throat swabs (NTS). SARS-CoV-2 Ct-values are determined using RT-PCR on NTS samples for RDT positive and RDT (false) negative participants and compared. Sequencing is performed on all eligible samples for phylogenetic analysis of the SARS-CoV-2 nucleocapsid protein and the whole genome sequence. NTS samples of participants with discordant RT-PCR and RDT results are also analyzed using RDTs by professionals in the laboratory.

Results Between October 2022 and October 2023, our study had 16,893 participants and we collected 1,757 self-test-positive/NTS PCR positive samples and 359 self-test-negative/NTS PCR positive samples (RDT-/PCR+). These participants were asked to take a SARS-CoV-2 RDT upon symptoms. Within SARS-CoV-2 PCR positive participants, we did not find characteristics that differ in SARS-CoV-2 RDT negative versus positive participants. There were no associations with specific changes in the N protein nor did our phylogenetic analysis show clustering of RDT negative samples.

Conclusion Evaluating brand-specific RDT performance in Dutch population and false-negative RDT analyses, led to no evidence for SARS-CoV-2 evolution affecting RDT sensitivity. The participatory surveillance program Infectieradar is a powerful tool for our national surveillance on acute respiratory illnesses, as well as for research purposes. Since this framework offered both self-testing and the gold standard of PCR testing results.

[thescienceofequus]

Dr. Orlando, who has spent years mapping the domestication history of horses, is an author of the paper, which he hopes will jump-start research on the humble donkey and restore some of its dignity. He and researchers from 37 laboratories around the world analyzed the genomes of 207 modern donkeys, living in 31 countries. They also sequenced DNA from the skeletons of 31 early donkeys, some of which date as far back as 4,500 years.

Scholars had previously identified three potential centers of domestication, in the Near East, northeast Africa (including Egypt) and the Arabian Peninsula. But Dr. Orlando’s team concluded that donkeys — humanity’s first land-based transport — were domesticated only once, around 5,000 B.C., when herders in the Horn of Africa and present-day Kenya began to tame wild asses. That date is about 400 years before the earliest archaeological evidence of tamed donkeys from El Omari, near Cairo, and nearly three millenniums before horses were first harnessed.

[darkmaga-returns]

I am sympathetic to the view that human-contagious-disease-causing viruses have not been demonstrated to exist. So far, these demonstrations have not convinced me, despite my earnest study.

I tend to agree with the Drs Bailey who have laid out their views on this and many aspects of the Corona declared pandemic in their brilliant new (and amply referenced) small book “The Final Pandemic”. And I tend to agree with the most influential critical textbooks on the question, which I have listed here

I am a career scientist with deep relevant expertise: CV and description of expertise. I ran a large university research group and had an electron microscope and many spectrometers and other instruments in my well-funded laboratory. I specialized, among many areas, in environmental nanoparticles, including their interactions with bacteria.

Anyway, after reading many state-of-the-art science articles about disease-causing virus “isolation” and characterization, I remain firmly unconvinced.

The main counter argument to my skepticism appears to be that PCR genome characterization is robust and specific. I plan to deep dive into PCR technology, eventually, but right now I am far from convinced of that counter argument also.

I remain highly suspicious of a wet chemical method (PCR) that relies on controlled thermal degradation to amplify a molecular fragment a kazillion times, which could not otherwise be detected. And I remain skeptical that thus obtained genome sequences are particularly relevant to biology. That’s me.

I mean, I think the PCR jockeys and the molecular-theory immunologists take up way too much space. And of course they are rewarded for their brilliant efforts.

But these are not my main topic today. Today, I want to say that I think some of the criticism of “germ theory” goes too far.