#meta genomics

[cbirt]

In the vast and intricate realm of metagenomics, where microbial communities unveil a wealth of biomedical knowledge, a groundbreaking development has emerged. Scientists from Pennsylvania State University introduced MetagenomicKG, a new knowledge graph built to take the exploration of metagenomic data to unprecedented heights. This revolutionary resource has the potential to change how researchers address the complexity of microbial ecosystems and provides a comprehensive and interconnected framework tailored to the unique needs of this emerging field.

The large amount and diversity of genomic content in microbial communities make metagenomics an affluent area of ​​biomedical knowledge. However, traversing these complex societies and their vast unknowns often depends on a variety of reference libraries, each with a specific analytical purpose. From the Genome Taxonomy Database (GTDB) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) to the Bacteria and Viruses Bioinformatics Resource Center (BV-BRC), these repositories are essential for the genetic and functional annotation of microbial communities.

Despite their valuable contributions, inconsistent nomenclature or identifiers between these repositories present challenges for effective integration, representation, and use. Enter the Knowledge Graph, a powerful solution that organizes biological entities and their relationships into a coherent network, revealing hidden patterns and enriching our biological understanding with deeper insights.

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#bioinformatics #genomics #meta genomics #microbiome #knowledge graph #science news

[oculusxcaro]

🍉 - What is something they have done that they feel the most guilt over? How do they handle this guilt?  Does the guilt ever get resolved?

Random Headcanons

One of if not the biggest thing Khare feels like utter shit about even to this very day? Not helping the other people unfortunate to get locked up and experimented on alongside her. Not while escaping, not going straight to the authorities and telling them about the place the moment she walked free, Khare did absolutely nothing, focusing purely on saving her own hide and the guilt eats away at her every single day. It wasn't as though they were friends but she watched for months as others were subjected to countless experiments and injections like her with many of them dying, if they hadn't been grossly mutated beyond recognition or driven mad as a result. Some of them were like her, young people snatched from the streets by chance. Some were older with families of their own, wondering if they'll ever see their loved ones again. Many were barely teenagers, runaways or problem children who wouldn't be missed. It was a horrible time for them all, wondering who would be next to go, be it in a body bag or on the autopsy table as their captors investigaged their findings more thoroughly. As soon as the opportunity to escape presented itself, Khare grabbed the chance, snatching the keycard and running off into the wilderness where the facility had been hidden deep in the mountains, away from prying eyes. It took a while to find civilisation and when she did... Khare said nothing to anybody, focusing purely on making her way down south, to put as much distance between herself and her captors, in case they were still pursuing her. Where the facility actually was, Khare is unable to recall and not a day goes by where she doesn't think of those left behind, still being tortured and warped beyond recognition as their tormentors focus on their sick goal of creating their own metahumans, of finding out how to bestow powers onto ordinary human beings. Could she have grabbed a few survivors? Could she have unlocked their cells and led a rebellion against their captors? Or could it have all failed and she'd be yet another corpse for them to study, making them one step closer to their plans?

The what-if's and could-be's keep her up most days, and it's a relief when she finally goes into torpor if only to stop thinking for a while.

#themckaytriarchy #memes ;; random headcanons #🌈 || headcanons #If there's one thing Khare will always hate herself for it's this #She always imagined it would be like in a movie where you'd valiantly fight back or lead the authorities back to help #But the reality was so much worse #Especially as somebody who was no longer supposed to be in the country #And after what they did to her she was very much afraid of getting found again #And who would believe her anyway? #Even if she could retrace her steps hundreds of hundreds of miles up north? #The authorities or FBI might just sling her on the dissection table themselves after what her body's been put through #This group was all about experimenting on the human genome and finding out how to reactivate meta genes #Or implant them into people who didn't have them #Make super soldiers if you will #Khare's genes were just stable enough to endure everything they did to her until escaping #She feels like utter shit for being such a coward :/ #human experimentation tw #human experimentation cw #human trafficking tw #human trafficking cw

[chaotic-archaeologist]

I feel a little silly asking for advice about this, but how do you deal with not doing a hard science? I do literature studies and meta-studies and I like the heritage side of archaeology too, but I've internalized the idea of non-STEM not being science so much that I feel like a fraud, who is not actually doing an academic thing and I hate that I can't be proud of my work and accomplishments, but I also don't know how to fully let go of it. Any tips?

Listen, I don't think this is a silly question at all! And my advice for you more or less boils down to:

You gotta stop caring about what other people think.

That's it. There's no winning this rat race. We live in a society which has (over) prioritized what it defines as "hard sciences" and it sucks. I could write a whole essay on why it sucks—and plenty of people both more educated and eloquent than I already have.

Give yourself the freedom to stop comparing yourself to other disciplines. Find the joy in what you do, and pay attention to that. Celebrate the ways in which your discipline is changing the world, even in the smallest of ways. That stuff matters!

Humanity needs experts of every shape, size, and kind—we'd be in a world of trouble if people only ever became physicists or chemists biologists. Thank goodness some of us grow up to be art historians or sociologists or music theorists or any one of the thousands of jobs that aren't an academic field but are nonetheless incredibly important!

Because, also—c'mere, lemme whisper something in your ear: academia and "academics" are kind of bullshit. It's a made up system based on made up constructs that has been given made up meaning and yet manages to manifest itself in very real ways. What is a real academic anyway? Ask a hundred different people and you'll get a hundred different answers.

Sure, your brand of academia (and mine) might not involve a particle accelerator or a dissection lab or a genome sequencer, but that's fine because it's all made up anyways! And just like players on team sports, our positions all look different because we're performing different functions.

Let your own preoccupation with the hard sciences go. Focus on your own work and passions. I think it'll make your life a lot happier.

-Reid

#he speaks #academic advice #life advice #internet brother

[spaceaudyssey]

One thing that I think no one has pointed out yet about this doctor who episode (the star beast) is it's take on the genetic memory theory

According to Wikipedia:

In psychology, genetic memory is a theorized phenomenon in which certain kinds of memories could be inherited, being present at birth in the absence of any associated sensory experience, and that such memories could be incorporated into the genome over long spans of time.

And BBC news:

Behaviour can be affected by events in previous generations which have been passed on through a form of genetic memory, animal studies suggest. Experiments showed that a traumatic event could affect the DNA in sperm and alter the brains and behaviour of subsequent generations.Dec 1, 2013

While there is more studying that needs to be conducted in order for this to be fully proven, it has been theorized as a possible reason as to why people may be born with certain fears or phobias to which there is no other explanation for. ADHD and other forms of neuro divergence are another human trait that has been theorized to be as a result of genetic memory. Again, it has not been fully proven, so I don't want anyone who reads this, to think that this is 100% fact. Read this with caution.

In the case of Rose in the star beast episode, She grew up her whole life, subconsciously remembering little things her mother experienced, and a lot of those experiences have fully affected Rose's own life, from the toys she makes, to how she even chose her own name.

Before I go on, I want to add that, on the comment of gender, from what very brief research I have done, I will not speak on behalf of gender when It comes to genetic memory, as I have not seen studies conducting gender identity in connection to genetic memory. While it could be possible that Rose is experiencing this gender identity because of the DoctorDonna meta crisis effect, this does not mean that she definitely is experiencing this because of DDME or genetic memory in general. Gender on its own is a complicated concept, a social construct, and that's its own set of scientific research that should be respectfully explored before we even consider that genetic memory can interfere in any part of one's gender identity. Also this is a work of fiction. Keep that in mind.

As I have stated before, The DDME is a major part as to why she has made the toys that she has made. It has basically become present in her imagination and probably her dreams. And without knowing it consciously, she helps out in saving London by pressing buttons she never pressed and saying words she's never said before. The instinct (DoctorDonna) in her mind and body kicked in when it needed to. In addition she shares this connection with her mother and it's all because of her mother, and the doctor. It was a connection she didn't even know that she had until it happened.

While I don't think it was done on purpose, the DDME is in a lot of ways a more fictional and exaggerated metaphor for genetic memory theory. While I don't think people can remember the exact things that their parents and grandparents experienced, and y'know, glow and start acting completely different, I feel that any kind of traumatic experience that is very intense to any individual, has the possibility to change the brain chemistry of future offspring and create more or less, a defense mechanism. I.E. the body keeps the score. It can also have the ability to give future offspring the similar likes, interests, and abilities of their predecessors, but to a lesser degree (because there are a lot of other factors that need to be considered when it comes to the development of an individual person's personality, such as their environment, and who they're friends with etc).

At the end , Rose states that basically she feels like herself now. Part of that is in comment to her gender identity, but it's more than that, because now she realizes why she has made those toys, why Rose is her name, and maybe other things that we didn't see in the episode, like maybe her personality, her dreams, her imagination, any reasonings behind decisions she's made in the past (similar to her mother giving her lottery money away), and maybe anything about her that might come across to others as "different". The main difference between her and someone in the real world, is that she has a major answer as to why. We people of the real world can only make a guess as to why we are the way we are. But Rose has the gift of having that answer (or the answer to some things she might have questioned, but probably not everything). And now she is fully embracing it and feels at peace with herself. It has also probably made the bond between her and her mother even stronger because of those shared experiences.

Basically I'm just fascinated in the topic of genetic memory theory, and this episode really brought it back up for me. After noticing the behavioral patterns of women on my maternal side, and how it made us connected in a way, I started to think that the possible reasons for why I have anxiety (or partly) could be due to traumatic experiences of past ancestors. This might not be true, but it would be quite a life changer if it actually was proven. Being able to have that knowledge in general would be quite powerful in the studies of mental health.

Oh and one more thing, in river song's case, I don't know if it's the same or not. The tardis interfered with her genetics, but idk if it shaped her personality, or her regular non-timelord abilities or whatever, but I guess it's possible. It's also been a while since I've watched any of her episodes. I just thought I'd bring that up because that's another person that has been affected by the doctor since before birth in some way.

#doctor who #the star beast #genetic memory #im just obsessed with this topic #let me talk about it okay

[starseneyes]

Spock / Nurse Christine Chapel - Star Trek: Strange New Worlds S1

Your resident shipper of ships here with yet another edition of Meta analysis. I’ll begin by saying I understand the canon of these characters (from what we’ve seen), so I have a fairly good sense of what is and is not possible for the future. That said, I’m enjoying the ride and I’m curious what our fearless leaders will do with what I consider is some considerable wiggle room in the saga.

But, I’m getting ahead of myself.

I know there are many ship combinations out there, and I respect them all! I mean no disrespect to any ship in the Star Trek universe. I only wish to highlight and discuss one that has surprisingly become one of my favorites throughout this season.

This is a Meta. I will spoil the entire season of Star Trek: Strange New Worlds. Turn back now if you wish to remain un-spoiled! Otherwise, welcome to the ramblings of the girl with stars in her eyes. This one’s going to be fun!

“I’m gonna mess with your genome. You first.”

Their first interaction. Nurse Christine Chapel is a civilian on-loan with a heckuva lot of intel and attitude. She has grit and guts, but she also has a wild side.

I love the way she looks to Spock, immediately zeroing in on him as the one to flirt with. My guess is that since she’s mentioned previous friendships with Vulcans, it’s one of those things she likes to do—flirt with the Vulcan to see if she gets a reaction. Kind of like those people who take photos with the Queen’s Guard in London eager to get them to twitch.

Spock notes the extra attention and looks to Pike, who offers a “it is what it is” smirk. Nobody’s going to rescue him from this.

From everything we learn of Christine in season one, she struggled with commitment, romantic relationships, and opening herself up. She uses humor and intelligence as defenses. Flirting with an emotionally unavailable (see what I did there?) Vulcan is insignificant to her at this point. It’s just a flirt. No harm, no foul, right?

“You ready for this?” “I am more than capable of managing any pain you can induce.”

A casual exchange with a factual response from Mr. Spock. But Christine Chapel can’t resist the opportunity to needle him a little.

“Mr. Spock! Now you’re just toying with me.”

Watch Uhura’s reaction. After just the “Mr. Spock” she’s already clued into the massive flirting going on right in front of her. It’s blatant! It’s in the open!

Again, for Christine this is no big deal. This is harmless flirting and it’s never going anywhere. I spent years in the theater, and this reminds me of a lot of us who might have flirted with one another at various times but had zero interest in hooking up or a committed relationship. It was just fun to flirt! Christine strikes me as one of us, at her core—battered, broken, but still finding the fun.

Of course, the implications of a little rough sex might have flown over Spock’s head, but the raised eyebrow suggests to me that it did not.

“That was not my intention.” “I’ve noticed.”

Uhura is still looking back at them like, “What the hell did I just witness?” and I love it. It’s like when you bring someone from outside the theater world backstage where half the cast’s naked, one guy’s randomly dry-humping friends for fun, and the rest are performing choreographed musical numbers from another show in the hallway. It’s mayhem and from the outside looks like madness.

But to us, it’s just a bit of fun. Same for Christine here... it’s just a bit of fun.

After episode 2, these two don’t see each other again until episode 5.

“Um, sorry, I really need to go and check on my friend. I’ll call you later, okay?”

Ortegas had offered to be there as a backup with Lt. Devers, but Christine thought she was in the clear. To her great horror, Devers doesn’t want to hook up in the back, but wants to get his hooks into her and bring her over to his ship. The overwhelm strikes her and she’s desperate for an out.

This isn’t about her seeking another guy to get away from one guy. This is looking for an out—any out—to get out of a bad situation. Because, from her point of view, it can’t get much worse than this.

Spock is her excuse. And I think the ONLY reason Devers doesn’t abandon the bar right then and there is that he sees Christine’s headed over to talk to a Vulcan, and few red-blooded (red-shirted) men would be concerned about their human girl having any real sparks with an emotionless green-blooded Vulcan.

I say few, because I’m sure there are some men out there who might think something could happen. But, from what I gauge of Devers, he is not that man.

“But you’re also an idiot.” “I feel I should have seen that coming. Please, elucidate.”

Clearly, they’ve been talking a bit, and he genuinely seeks insight. Though he has only had a few interactions with Christine at this point, he’s known her to be truthful (”This is going to be painful”), thorough, direct, and consistent. Her calling him out in this manner only emphasizes what he already believes to be true about her.

Vulcans, by their very nature, tend to be honest. We’ve heard many times in this series how Vulcans cannot lie in the way that humans do. Christine is a human who has the option to lie, in Spock’s eyes, but in this moment she’s chosen to be truthful about her assessment. That is why I believe he asks for more.

“You’re supposed to put her ahead of your duties. That’s what being in a relationship is. It’s mutual sacrifice. Pretty much why I avoid them.”

Christine is a strong, independent woman who wants to continue her current quality of life. There’s absolutely nothing wrong with that! But she knows that being tied down to someone would get in the way of her getting to lead that life. She’s consciously choosing not to engage in a dedicated, committed relationship.

Spock, on the other hand, is very much engaged. And Christine genuinely wants to help him see the other side in this. She’s coming at it as a friend, especially considering her friend-with-benefits is still pining for her at the bar over her shoulder.

Then, Spock drops the bombshell—he’s worried T’Pring thinks he’s too human.

“Okay.”

I love this little moment. She doesn’t offer judgment. She doesn’t try to discount it. She says “Okay” and nods to him, a nonverbal cue asking him to continue. She’s making space for him to say his piece, and I think that’s a very important part of how Christine sees friendship—it’s a give and take.

Then, he starts to open up, to share about the isolation he felt as a child living on Vulcan. Christine leans forward, her body weight shifting as she relates to their shared experiences of bullying. It’s the first real thing between them, the first connection point.

“Teenage Spock had a pretty lousy time of it, huh?” “I was bonded to my pet shlat I-Chaya.” “I had a malamute named Milo who may or may not have bitten this girl who called me stupid. Sharp teeth.”

And with that, this conversation has completely shifted. Instead of Christine coming in as a sounding board for Spock, she’s now engaging with him. They’re trading stories. They’re connecting. They’re bonding over very real aspects of their lives, and they don’t even realize it.

“I hope the girl did not repeat the mistake again.”

There’s the hint of a smile in his face as he says it. It’s the closest she’s seen to his human side coming out, and she catches herself smiling back at him. Oh, no. In her mind, he’s becoming a friend. Yes, she likes to flirt with him, but that’s completely one-sided and not at all indicative of anything real.

But that moment between them is the first real moment of connection. It was honest. It came out of nowhere. But it happened.

And Christine wants none of that.

So, she shifts the conversation back to T’Pring and away from the two of them. Helping Spock with his relationship helps put that wedge between him and Christine back in place. It’s a defense mechanism.

“What are friends for?”

Again, she’s putting that line of friendship out hard to remind herself that it exists. That’s all they can be, just friends.

“What are friends for...” “That was a rhetorical, Spock.” “Oh, I know. Humans are almost as easy to tease as Vulcans.”

And there’s that hint of a smile, again. He played a trick on her. Yes, a small one, but enough to get an honest smile out of her. She ducks her head, looking away, but, darnit, that was cute and she can’t deny it.

“Is that Spock’s girlfriend? Hard to tell, but does she look pissed?”

Spock (in T’Pring’s body) is sprinting to Christine for help. Christine thinks she’s looking at the real T’Pring, the fiancée of her friend, and she is nervous. She really meant all of her advice to Spock in good faith, but you never know how it’s going to turn out, or how a woman might feel about their man talking to another woman about their issues.

SIDE NOTE: And can we talk about this location? The two seats encircling toward one another, separated, but identical in shape and form. Can there be a more perfect metaphor for where Spock and Chapel are in this series?

They are very alike, in some ways, and while each of them feels a pull toward the other, like the chairs that do not touch, they can never truly be joined. Whoever was the set designer or location team is breaking my heart today. It’s perfect.

“You clearly have a relationship opportunity.”

Leave it to Christine to find the silver lining in this mess. T’Pring is trying to save his career, so she encourages him to help T’Pring out. It’s the mutual sacrifice she was talking about, but now he gets to live it.

“It is well known that you are betrothed to the son of Sarek... you defend Vulcan ideals with one hand, insult them with the other.” “Hey.”

Both Spock and Christine are getting a little upset here. Poor Spock has had to endure this BS his whole life. Now he’s seeing that it can impact T’Pring, too. From Christine’s point of view, she just learned this week how much people like this hurt her friend, and she doesn’t want to let it happen, again.

“You know what? I work with Spock. He’s twice the Vulcan you are.”

Spock (as T’Pring) tries not to react, but you can tell he appreciates her stepping in to defend him. I doubt many did when he was a child.

“Humans evolved from apes, did they not? You’ve kept many of their charming qualities, it would seem.” “I would caution you to stop insulting my companion.”

And now it’s Spock’s turn. By comparing Christine to an ape, this man is essentially trying to diminish her, much like the girl who called her “stupid” as a child.

“To tell you the truth, I came here today with every intention of considering rehabilitation, but the company you keep changed my mind.”

That’s it. Spock’s had enough.

Because Christine is more than his shipmate. She is a friend. She is a companion. She is someone who has accepted him, listened to him, helped him, and defended him... all without ever offering judgment on his validity as a being worthy of existence.

And this sh*thead just went too far.

The human side of Spock that feels kinship and appreciation for Christine asserts itself in the form of a right hook that sends Vulcan pea-brain sprawling.

Christine was ready to defend herself, but her friend stepped in.

Think about that. The girl whose malamute was her only defense against bullies has a friend who stepped up to defend her. He came through for her. That’s no small thing for Christine.

“Perhaps we should keep the details of how exactly we captured Barjan between us. My response was a tad too human.” “I’d say just the right amount.”

The look Christine gives him is so... nuanced. There’s gratitude. There’s admiration. There’s appreciation. And, again, she’s not condemning a single part of him. She’s accepting him just as he is. And he’s not used to that.

“Nurse Chapel.” “You know you can call me Christine.” “Christine.”

Hearing him say her name has an unexpected impact. She was content to continue working when he called her Nurse Chapel, but her first name on his lips draws her eyes to his. There’s a weight to it that hits unexpectedly.

“I want to thank you again for your help.” “Hey, no big deal.”

She puts distance between them physically, attempting to disengage from the impact.

“Perhaps not. But for me the deal was very big, very big indeed.”

The whole experience has bonded them even more than that conversation. He came to her in confidence, and she kept his confidence. She helped him do T’Pring’s job. She defended him. She was there for him.

And she’s trying to help him be honest with himself. That’s always been tricky for him, especially with being raised on Vulcan around Vulcans. But Christine’s words get through to him, and he is honest with himself and with T’Pring.

Christine is having an impact on him. At this point, it’s only friendship, but it’s a growing friendship. She has proven herself reliable, and he’s done the same for her. They are going to help one another, defend one another, protect one another. There are no doubts on that front. And having that foundation is a beautiful thing.

But, as is the case with these two, it can also be a little dangerous.

“Be honest” “It would have to be the right guy... I, uh... No.”

She can’t say it. Because our homegirl is starting to get a crush and she knows it. That dinner together was the start of something, but she thought she nipped it in the bud. At the end of the episode when she and Spock were talking in Sickbay... there was a new layer to everything.

The tone completely shifted from the two of them talking at a table in a busy restaurant/bar... to nobody else being in the room. No other sounds. No distractions. Just two people sharing a quiet moment of honesty.

And Christine values honesty almost as much as Spock. He showed appreciation for her, gratitude, and genuine caring. It flustered her, though she wishes it didn’t.

And that’s why she can’t say a word to Ortegas about it. Putting it out there in the world as a spoken thought would give it too much powers... and Christine still wants to stamp this out before it goes outside her comfort zone.

“Earth to Spock!” “I am sorry. I am distracted.”

It’s another few episodes before the pair share a significant moment. I find it fascinating (excuse the word choice, but that’s the one that popped out) that we transition from our virtual chat between T’Pring and Spock to an in-person one with Christine.

On a stroll to meet Dr. Aspen, Christine notes Spock’s complete lack of focus. From his very first reaction, she can tell that something is off. I love that she knows him so well that she can tell when he’s completely in his head.

“I need... a friend.” “Ah, spill it.”

Christine seems to be ducking out of the latest T’Pring/Spock drama, but when he pulls out the “friend” card, she gives in. This is fully within the limits that she has set, and she really does want to help.

“T’Pring has been researching human sexuality. She has been quite thorough.” “That doesn’t sound so bad.” “One would imagine.” “But...”

I love that “But”. From her perspective, sexuality is not a bad thing! It’s not a bad thing to research and be aware of at all. But, she can sense that “but” coming, and she wants to give him space to say what he needs to say.

It reminds me of the “Okay” and nod from the dinner conversation in Spock Amuck. She recognizes he has more to say, even if he’s still formulating in his mind how to say it. It’s a way of not rushing him to the point, while acknowledging she knows there’s one coming.

“She appears more eager to explore my humanity than I am.” “Spock, are you telling me your girlfriend is moving too fast for you?” “Reconciling my divergent cultures of origin is complex. The journey is challenging.”

This friendship is deep. He’s opening up about some scary stuff. But he also has the experiences of Spock Amuck to inform him. He’s told her before about the bullying, and she got to see some of the disdain first-hand. She defended him, even. So, he knows that he can talk to her about this without judgment.

“Spock, do you know why it’s fun to be friends with Vulcans? Because Vulcans are honest. Don’t try to be smarter than the truth. That’s what got you in trouble last time.”

I love this. If you recall, T’Pring is trying really hard to be accepting of Spock’s Human side, and each time Christine has reminded him to try addressing T’Pring as a Vulcan. That’s what she’s saying here... not that he has to be a Vulcan to be honest, but that Vulcans are intrinsically honest beings. Leaning into that will help him with T’Pring.

And he knows Christine is right.

“Also, pro tip, pay better attention to me when I’m talking... because?” “You are very charming and I am completely missing it?” “Progress. You’re learning.”

I love this return to flirting. After the weirdness at the end of Spock Amuck, Christine truly believes she’s regained her friendship footing with Spock. He’s clearly parroting back something she once spoke to him (or many times, for all we know), and she’s flashing a flirtatious smile his way in response.

Box achieved. From both their points of view, the rhythm is back and nothing’s going to shake it.

You see where this is going, right? Of course you do. You understand just when a character gets comfortable, it’s time to shake them up somehow.

“I lost the man I love, even if it was to a Vulcan prison, not pirates.” “You stole a Federation ship, and are blackmailing Vulcans for love?”

I love the absolute disdain in Christine’s voice. to her, this is a lot further than she’s ever considered going for love. Then again, Christine bolts before love has a chance to take hold.

“I apologize in advance for any liberties I take. Please follow my lead. “Okay.”

This is that trust I was mentioning before. Christine has no idea what’s in his head, but she’s going along with it.

“I have been giving in to my human side. More so than I wish to admit. I cannot deny the emotions within me any longer. Nurse Chapel and I-”

Christine gets it. She doesn’t get why he’s doing it, but she already told him she was going to follow his lead, so she’s following. She can tell he’s faltering and steps in to help.

Side Note: WHY is he faltering NOW and not earlier in the declaration? Why was he able to get through the rest of that without struggle? I believe because a small part of him knows it’s true. A small part of him is aware of the growing connection between himself and Nurse Chapel. He never would have otherwise admitted it, but it serves the needs of the moment.

“He’s trying to tell you that we’re having an affair.”

The framing is gorgeous. Christine steps alongside Spock, and you can see a confused T’Pring in the center, watching them. There’s the distance of her watching through a screen while Spock and Christine stand nearly shoulder-to-shoulder.

“We’re in love. I’m sorry.”

Angel isn’t buying it. Not for a second.

“No, I...”

Nope. Words aren’t coming. Why aren’t they coming? We can argue that his Vulcan nature is stepping over his human nature, making it difficult to lie. But, rather, I think he doesn’t know how he really feels to even make a declaration, and that’s tripping him up.

That’s why he resorts to physical affection—to showing T’Pring something that might sway her.

Spock awkwardly brings Christine to face him, then leans in to kiss her, thin-lipped. Her hand instinctively rises to his neck, but her eyes remain open. Gotta stay disassociated, Christine. Don’t feel. Don’t feel.

But she feels.

Her eyes close as the kiss deepens. Her right hand shifts from his side to his back, and as it does, everything in Spock shifts.

He can feel her. He can feel her desire for him, and that sends off a cascade of feelings within him. His hands glide over her back, his right hand plunging lower as he shifts from thin lips to open-mouth.

He shifts sides, lips parted, tongue touching hers as she leans up on her toes, hand grabbing tighter around his neck as her brow furrows.

They pull apart slowly, lips parted.

That’s important. At least, it is to me. They entered into this kiss completely thin-lipped, two friends embarking on a mission to deceive. Instead, they exit it more open to one another than they’d anticipated, and the ones they’re deceiving now are each other and themselves...

Their eyes flicker open, and Christine’s come to rest on his lips, processing what just happened. That wasn’t some thin-lipped peck.

There was Spock tongue. Repeat, there was Spock tongue!

Her eyes travel up to meet his, wide and terrified. That felt right. Why did it feel right? It wasn’t supposed to feel right! All the boxes and zones she had in place for Spock are shattered... and she knows it.

Spock’s response is more muted, of course, but it’s there. The way his eyes flicker away and then back, again. He knows that something in him has shifted toward her... something he couldn’t have anticipated.

Spock turns back to the monitor as Christine’s hands awkwardly fall away from his chest. She and Spock can’t look at one another. Her job done, she goes back to her post over his left shoulder while Spock and T’Pring decouple.

“I think there’s more to life than logic... and so, I suspect, do you.”

Watch Angel in that little pause, how their eyes trail to Christine, then back to Spock. I really do worry that’s going to come back to bite them at some point. Much as Angel was able to call Spock’s plan, it’s impossible to watch that kiss and think there was nothing behind it (unless, of course, you’re T’Pring).

“I apologize for the... incident between Nurse Chapel and I.” “Why apologize? It was an impressive gambit...” “You knew?” “Of course. I never actually believed you could have feelings for Nurse Chapel.”

Watch. His. Face.

Because, truthfully, Spock himself isn’t so certain. He wants to be committed to this relationship completely, and has done everything he can to do so. The times he has spent the most time with “Nurse Chapel” have actually been in service to his relationship with T’Pring, whether discussing his relationship or assisting T’Pring’s career during the body-swap.

I honestly think he hadn’t considered having feelings for Christine until T’Pring speaks it. It’s part of my whole theory that words have power. Christine couldn’t tell Ortegas about having a crush on Spock. Spock couldn’t consider having feelings for Christine until someone else said it aloud.

Because he was faced with having to either refute or confirm the assertion, he then had to consider it.

And I don’t think he’d ever considered it before.

“Of course not.”

Oh, sweet baby Vulcan... You’re in denial, my friend.

“Your human side can be a source of strength. There is no way you could have sold the passion of that kiss without it.”

She earnestly believes this. She believes he tapped into some ability to deceive that he had been hiding rather than the truth—he quite accidentally tapped into his human side that he’s been suppressing.

Think about it. He started this episode talking about his reluctance to explore human sexuality. No blaming or shaming here. I’m known as a prude around my friends and family because I’m a demi-sexual who gets SUPER uncomfortable with sex scenes to this day. So, seriously, no judgment!

But he encounters human sexuality in a subtle way with that kiss... and I doubt he expected himself to respond in the way that he did. I doubt he’s ever actually kissed a human before... and when he felt Christine’s response to him, something in him responded to her.

That passion wasn’t an act. But, he’s willing to let T’Pring (and, to a degree, himself) believe it. I don’t think he truly wishes to deceive his fiancée in this moment. Rather, he wants to believe what she’s saying. It’s simpler if he can be a half Vulcan/half Human who has the ability to lie about feeling anything for Nurse Chapel rather than... really feeling what he feels.

That’s messy. That’s complicated.

“Thank you. You know me well.”

I feel like this is... a wish. Because, if she truly knows him well, then what she is saying is truth and he can believe it. He can trust it. He can ignore the part of him that’s questioning everything.

But, as so many have pointed out... he doesn’t even know himself.

“I came here to thank you and applaud your performance on the Bridge.”

Watch Christine... she has a nice little rhythm with what she’s doing, but as soon as she hears his voice, her pacing slowed. She had hoped she’d avoid this talk. I mean, it took her several chances with Dever to finally be open and honest with him about not wanting to be with him... THIS is not her strong suit—talking about her own feelings.

“I thought because you are human you might need to discuss your feelings.”

When I was a little girl, I didn’t like to ask for my mother’s time. She was a hair and makeup artist in the film industry and always working. When she was home, she was exhausted and often on edge... as a single mother of two young kids, she had a lot to handle. So, I never told her when I needed to talk to her about something.

I’d ask her if she needed to talk. “Momma, do you need to talk?”

I see the same thing here in Spock. Yes, he does think that she needs to talk, but he’s using it as a cover for the fact that he really needs to talk, too.

As I said, I think when T’Pring said it was impossible for Spock to have feelings for Christine, he actually had to consider if he did... and was left confused. Even the phrasing here, “your feelings” echoes back to T’Pring’s verbiage.

“Spock, like I said earlier, I like Vulcans. I know where I stand with you. You’re an honest man. You’re not the guy who would chase after another woman while you have a girlfriend. So I know for certain there’s no feeling between us.”

Some have argued the Christine put Spock in the “Vulcan box” with this speech, but I disagree. Yes, she references their earlier conversation and leans into the inherently truthful nature of Vulcans. But then she says, “You’re an honest man.”

The term “Man” is not typically used to describe a Vulcan. I went on a whole research binge on gender and Vulcans. While there are names that traditionally had a male or female gender connotation, those conventions do not hold across canon.

Plus, we’ve been told in canon that TRUE Vulcan names are almost impossible for non-Vulcans to pronounce, even with the help of Universal Translators. So, these names that we’ve come to know them by are not even their given Vulcan names.

Merriam-Webster defines “man” as “an adult male human being.“

Human.

So, in her speech, she is actually acknowledging both parts of him and pulling them into the whole—a person who she will not let out of the friend-zone.

It’s not so much about defining him as it is about defining where they stand. We have already seen that Christine is fiercely loyal to her friends, and with that comes a sort of trust that she refuses to break, let alone let another break it.

Spock has trusted Christine with a great deal, and she has trusted him as well. And now they must trust one another not to overstep boundaries that must stay in place... for so many reasons.

“I’m glad to hear it. You know me well.”

This is the echo of what he told T’Pring, likely because he hears reflected back to him what he wanted to hear—there’s nothing between them. He wants to believe these two women know him better than he knows himself... because he struggles so much with knowing who he is on his own.

Eventually, he’s going to have to stop relying on other people to tell him who he is, and find a way to reconcile all the pieces of himself into... Spock. But, that’s a topic for another blog!

“You’re a good friend, Mr. Spock.” “As are you, Nurse Chapel.”

She puts up that friend-zone firmly, even going so far as to step into formalities. And from her point of view, he seems to get the message, as he answers back in kind.

“Spock, one last thing.”

And in the next breath, she’s fallen back into the informal and he comes running when she calls. No, it’s not a sign of “oh my GOSH they’re going to FALL INTO EACH OTHER’S ARMS and MAKE LOVE ON THE FLOOR OF SICKBAY”. I’m not deluded. But it does show how easy it is for them to trust one another. There’s no hesitation.

“You said that on the Bridge you suddenly realized the identity of the prisoner that Angel was trying to free.”

This is where that trust comes in, again. Spock answers her freely. He holds nothing back. He shares with her intimate details of his own family by telling her about his brother.

Because, no matter what is going on between these two, they have tightly woven a cord of trust. That’s the foundation. That’s the basis. They trust one another explicitly.

“Lieutenant Duke. He did not account for potential instabilities in the Jeffries Tube.” “Duke wasn’t paying attention.” “Indeed.”

Two episodes later and we get a few small interactions at the beginning of the episode (and an important one at the end), but I love the subtlety of this one. We saw in the previous scene that Christine is more than willing to be his guide through Human culture (the drinking game) while everyone else just ignored his confusion.

Here, Spock is able to talk in a manner that Christine automatically understands what he really means. She understands him on a very deep level, and a small interaction like that really shows it.

“I understand that, uh, Vulcans have a strong, hidden primal nature. I bet you’re a tempest when you’re angry.”

Of course, this whole conversation is to set up Spock’s arc in this episode... what happens when he lets out a little emotion? A little anger? A little rage?

“It is true without proper mindfulness Vulcan emotion is dangerous. We use logic to not succumb to anger.” “It’s good to get mad sometimes.”

This reminds me so strongly of T’Pol from Enterprise. While my least favorite Star Trek series of those I’ve seen, T’Pol and Trip held a very special place in my heart both apart and as a couple. Her journey of trying to more deeply understand pure Vulcan emotion was incredible to watch. But, like Spock, letting out that first little bit was incredibly dangerous.

From everything I understand of Vulcans, they are taught to suppress emotions... not how to handle them, how to work through them, how to work with them. Spock is half human, too, so he’s got a wide array of emotions and hormones, no doubt, to deal with.

The loss of Hemmer is too much for him.

“The people you love the most can cause you the most pain. But it’s the people you love that can mend your heart when you feel broken. That’s what Hemmer’s purpose was. To fix what is broken. And he did.”

Spock has been standing there struggling with his emotions, clenching and unclenching his fists. Christine can see it... that he’s on the edge.

When he peels out of there, she follows. The rage bursting inside (and thinking he’s alone), he slams a fist into the bulkhead.

“Spock!” “Do not follow me.” “What’s going on?” “I’m warning you, back off!”

She raises a hand to his shoulder, but as it connects he grabs it away. He freezes, his hand around her wrist. Christine looks down at her hand, then back up to Spock.

“Tell me what’s going on.”

I love the emphasis... It’s on “me”. Because, this isn’t just anyone asking. It’s her. It’s the woman he has trusted with so much in such a short time. It’s the woman who has never judged him and won’t judge him now. It’s HER asking.

“I can’t control it.”

And in an instant, without hesitation, he tells her. It spills out of him without stops or sputters. It’s a truth he doesn’t want to carry... but more than that, I think he desperately doesn’t want to carry it alone.

Spock has the distinction of being the only of his kind... a half Human, half Vulcan raised on Vulcan with the expectations of being a “good little Vulcan”. This is not how a good little Vulcan behaves.

“I’ve let something out Rage. Pain.” “It’s your emotions.” “My mind has gotten weak.”

And there it is. “I’m broken.” “I’m wrong.” “I’m not good enough.” It’s all there. All these perceptions of who he is supposed to be and how he is supposed to act. He’s not supposed to give into his human side. He’s not supposed to feel.

But he’s feeling.

“No. No.”

She reaches for his face with both hands, and you can see how he tenses and start to pull away from the touch. But as the second hand lands, he settles into it.

“It doesn’t make you weak, Spock. It makes you human.”

That’s a terrifying thought. And while some say, “Oh, now she’s trying to put him in the human box!” I don’t feel that way. When I see this, it’s more her saying that it’s not wrong. It’s simply a part of him... the part of him that’s human.

That’s what she’s trying to say... You aren’t broken, Spock. You aren’t wrong. You are good enough. This is what it is to be human. We feel things. BIG things, sometimes. And that’s okay.

She pulls him into her arms, using the power of an embrace to communicate caring. She did the same with Uhura earlier in the episode as Hemmer delivered his final words of advice. Now, she pulls Spock against her, both of her arms winding under his.

He stand there a moment, caught between his two worlds. But the longer he stands with her, the more he feels something else.

Comfort.

Spock’s eyes drift closed as he soaks in the feeling, nestling his cheek against Christine’s. His arms lift to wrap around her, settling as he leans in against her, eyes fully closed. He rests in the embrace. He rests in the feelings running through him.

Not feeling of rage or pain... but of warmth. The kind of warmth that comes from loving acceptance and caring.

They pull apart. As they do, their eyes flicker up to meet one another’s. Then, Christine’s flash to his lips and his follow to hers. Her eyes trail back up to his eyes... but his gaze is locked on her lips.

She realizes it, and as she does, he peels away... leaving her standing alone in the corridor.

Because his emotions are still close to the surface... all of them. And those emotions from Serene Squall that he’s been trying to convince himself were part of a deception aren’t as easy to push down when Pandora’s Box of emotions is cracked open.

And she knows it. She knows that look, even if she’s never seen it before on his face. She wants desperately to be his friend and him to be hers... but there are undercurrents that are growing more undeniable as time passes.

"Massive cerebral trauma. Major blood loss. Spinal fractures. Radiation burns across 40% of his body. I’m not sure that he will recover from this. But if he does... he will not be the same.”

Speaking of time passing... in the flash-forward “What if” finale, we get a glimpse of a stricken Christine frozen over the near-corpse of Spock. We don’t know what has transpired between them, but there’s obviously still caring. There’s obviously still concern.

A Sickbay full of people and she’s frozen over his bed, holding it together, but clearly distraught.

We know that’s not the future for this duo... and we know the weight of canon that implies they never find their way to one another. But, however long this journey is, it’s a joy to watch.

Ethan Peck and Jess Bush have effortless chemistry, bolstered by smart script choices and elegant directing. This season of Strange New Worlds has been a masterpiece, in this humble Trekkie’s opinion.

For context, my Freshman year of College my final persuasive speech was a 10 minute effort about why people should give Star Trek a watch... I aced it. So, this gal’s a hardcore fan.

And I’m definitely a fan of these iterations of Spock and Christine Chapel.

I’ve seen some people whine on the internet about Christine Chapel... “Who is she except a Spock love interest?“

Who else is Christine Chapel? Christine Chapel is a nurse. She is a brilliant scientist who is even interested in medieval medicine, which involves sewing people back together. She is part of an incredible initiative at the cutting edge of science to help with protecting First Contact protocols.

Her attitude is a mixture of devil-may-care and I-care-too-much with a dash of did-she-really-just-say-that. She’s not a gossip, but she does love to talk and listen.

She is incredibly competent on her own in the medical field, but also an amazing support for Dr. M’Benga. Trust me. I’ve had so many surgeries I’ve learned to watch the nurses and assistants. She’s an incredible assistant, quick on her feet, and often moving in complete rhythm with Dr. M’Benga without him having to ask.

She grew up bullied and took comfort in her pet, a welcome companion. She’s had many lovers of her choosing, and she’s afraid of commitment and relationships. Though, she shows a great understanding of what a relationship should look like, which makes me believe she grew up seeing what it shouldn’t look like. Trust me. I have first-hand experience on that one.

She is a caretaker, always asking how people are (La’an in All Those Who Wander). She’ll be the one giving you a hug (Uhura and Spock in All Those Who Wander). And she’ll let you talk when you need to talk it out. Christine is a good friend who is desperate to trust even as she is terrified to do so.

She’ll help carry your bags without being asked (Spock Amuck), and she’ll go on long walks in nature to talk about life (like with Ortegas). She can totally kick *ss with nothing but a hypospray (Serene Squall). And she is willing to join Starfleet’s cause to boldly go.

I see some of myself in her, so maybe that makes me more drawn to her and her story.

I know they’ve wrapped shooting Season 2, and I can’t wait to see what they have in store for us. If it’s anything like Season 1, then we’re all definitely in for a treat!

As always, thanks for reading! All the best to you and yours.

#Star Trek Strange New Worlds #Strange New Worlds #Ethan Peck #Jess Bush #Spock #Chapel #Nurse Chapel #christine chapel #ST:SNW #SNW #Star Trek: Strange New Worlds #Spapple #Spock x Chapel #Star Trek

[approximateknowledge]

w. whats a hoppo

*MY TIME HAS COME*

(you will regret this)

a hoppo (plural zeskoppo (it's an exonym out of necessity in the native language of the actual pov character's first klég (=language, there's another layer which im not gonna go into now because this setting has been cooking in my mind since i was like 15) because zeskoppo by definition don't have language)) is a species that is not a species that forms a greater meta-civilisation that is not in any way a civilisation at all once you actually know how it works

to explain what the fuck this all means we will have to go all the way back to their origins

a world (not a planet, the physics are different, not relevant here either) that would never get name and definitely no longer exists (it got deconstructed by its former inhabitants long ago) that was mostly dominated by a constant shifting pattern of highly symbiotic non-sophont colonies of what earth biologists would probably classify as eusocial organisms. these eusocial old dominant lifeforms (called kilok) are not the zeskoppo, except they also are.

for you see the "megafaunal" life of this nameless world is not actually multicellular in a real sense; their entire body is either inaminate "dead" tissue, or one singular incredibly complex cell-like mass, with the closest thing they have to "dna" also kind of doubling as the scaffolding of what approximates the nervous system

and here's the thing, they're "one cell", and so what is a "virus" to a cell of such a scale? well, it's a lot more subtle

a hoppo is anatomically like a stretched-out neotenic biradial (no back-belly distinction) kilok, and they "reproduce" by infecting unhatched kilok eggs with the viral agent that is actually their species

a hoppo is a kilok virocell

but it gets weirder

because remember the whole gene-nerve overlap? well the viral genome very easily bends and adapts and mutates as the individual hoppo learns, and so the copy injected into the kilok egg basically contains all the acquired memories of the hoppo injecting it at the time of injection. and it stacks

so while a hoppo in isolation isn't any more intelligent than a basic-ass kilok worker with some extra instincts, their *experience* stacks

and the thing is they don't even communicate with eachother, they're no sophont in any way shape or form! but also after a certain point they figured out that observing others brings more survivability. but then the observers kind of cheated out the non-observers and outcompeted them and so there's now an arms' race to prevent non-relatives from observing one's skills

and because memories and genetics are the same to a hoppo, the trick is that they just *think up* a "confirmation code" and all the descendants just *know* it when hatching but also you can spy on confirmations and then learn and fake them so it becomes more and more encrypted and they figure out more tricks and so on

and in the end you get a highly advanced meta-civilisation with massive data-exchanges but none of the actual entities involved are sentient and none of the data is actual communication beyond absurdly long-winded and encoded permission codes and the demonstrations buried within them

that's a simply as i can explain them there's so much more and this setting is massive

i have particle physics and conlangs cladistic trees

help

#ak goes insane #hoppo #thank you for asking! #long post

[nuadox]

World’s largest epilepsy study reveals ‘genetic architecture’ and points to new therapies

- By Luciana Constantino , Agência FAPESP -

Considered the largest genetic study of epilepsy in the world, a study published in the journal Nature Genetics reveals specific alterations in DNA that signal a greater risk of the brain disorder.

Identifying these alterations will improve diagnosis and advance the possibility of new treatments for the disease.

The researchers identified 26 different areas (loci) of the genome that are linked to epilepsy, with 29 genes thought to play an important role in the disorder. Of these genes, 17 were associated with epilepsy for the first time; ten are linked to the development of the disease when mutated or altered (known as monogenic epilepsy genes) and the other seven are known to already have approved drugs that focus on treating autism spectrum disorders.

Analysis of the subtypes revealed significantly different “genetic architectures” mainly between two subtypes of epilepsy – focal and generalized – and common variations in DNA can explain between 39.6% and 90% of the genetic risk for the latter type.

Coordinated by a consortium of the International League Against Epilepsy (ILAE) involving more than 350 scientists, the study compared data from 29,944 people with the disease to those of 52,538 control subjects. It included epilepsy cases of European (92%), African (3%) and Asian (5%) descent.

Brazil was the only Latin American representative through the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), a FAPESP Research, Innovation and Dissemination Center (RIDC) based at the State University of Campinas (UNICAMP).

“We at BRAINN were involved in all stages of the work, from the detailed characterization of the patients from a clinical, imaging and neurophysiological point of view – which we’re very good at – to planning the analyses, suggesting how they could be carried out and then checking the results. We were also actively involved in writing the article, which was submitted to the journal over a year ago. Many international studies exclude patients from Brazil because we have such great genomic diversity. However this study did a meta-analysis, which allows us to combine populations with different genomic structures. For the future, we want to expand this diversity even more,” Iscia Teresinha Lopes-Cendes, a professor at UNICAMP’s School of Medical Sciences and co-author of the BRAINN article, told Agência FAPESP.

There are an estimated 2 million Brazilians with epilepsy, at least 25% of whom are uncontrolled, according to the Ministry of Health. Worldwide, the World Health Organization (WHO) estimates that 50 million people are affected by the disorder, a third of whom are resistant to the treatments available on the market.

A highly hereditary neurological disease with no cure, epilepsy causes seizures, up to 40 or 50 a day in the most severe cases, leading to loss of consciousness and falls. Uncontrolled seizures not only disrupt the patient’s daily routine but also pose a serious risk of sudden and premature death.

Treatment involves a combination of medications, which are not always effective. Most medications reduce the activity of neurons across the board, which controls seizures, but they have side effects. An alternative is surgery to remove the part of the brain affected by the malformation.

Now, the researchers are proposing some medications that are normally used for other conditions, but act on the epilepsy risk genes identified in the study.

Knowledge over time

Recognizing the complexity of the genetic and environmental factors related to epilepsy, the consortium was formed in 2010 to collaborate on investigating large datasets at an international level.

“This is an important milestone for the ILAE Consortium on Complex Epilepsies and shows what can be achieved when scientists collaborate openly and share data from around the world,” said the league’s president, Professor Helen Cross, in a press release.

To arrive at the results suggesting different genetic architectures between focal and generalized forms of epilepsy, genetic data were combined with databases of phenotypic information, expanding the sample to more than 51,600 patients and 1 million “controls.” This discovery of the different genetic framework for the different types of epilepsy provides clues to understanding the various syndromes.

In their work, the scientists point out that the proteins that carry electrical impulses through the gaps between the brain’s neurons are part of the risk for generalized forms of epilepsy. In this sense, they emphasize the importance of accurately characterizing or classifying specific epileptic syndromes (syndromic phenotyping) in order to better understand the genetic basis of the disease.

An advocate of studies with so-called “pure data,” Lopes-Cendes says that she is now working specifically on mesial temporal lobe epilepsy (MTLE) with hippocampal atrophy. “We’ve been continuously generating data for specific research on the topic. I’d argue that in certain studies, mixing information from different types of epilepsy can ’dilute’ the data and not highlight results that might appear if the group of patients studied was more homogeneous. I think a balance is needed,” she adds.

In early 2023, the researcher and her group published another article that deepened our understanding of MTLE, considered the most common and refractory to pharmacological treatment, by evaluating, for the first time, the profile of messenger RNA (mRNA, a molecule that contains the information for the production of proteins) from surgical tissue obtained from patients.

Because of her work in genetics, Lopes-Cendes was recently invited by the WHO to join the new Technical Advisory Group on Genomics (TAG-G), which is responsible for contributing to the process of accelerating access to genomic knowledge and technologies, especially in low- and middle-income countries. The group consists of 15 scientists from different countries.

The article “GWAS meta-analysis of over 29,000 people with epilepsy identifies 26 risk loci and subtype-specific genetic architecture” can be read at: www.nature.com/articles/s41588-023-01485-w.

This text was originally published by FAPESP Agency according to Creative Commons license CC-BY-NC-ND. Read the original here.

--

Read Also

For epilepsy sufferers, cutting-edge technology offers early alerts of seizures

#epilepsy #health #medicine #genomics #seizures #seizure #brain #neuroscience #medtech #health tech #brazil

[needle-noggins]

@strawberryblackcrown 🫡 just doing my duty, friend. But seriously, there is SO MUCH MORE to be said about Trigun meta and we’re barely into the book club!! Buckle up everybody, because it’s going to get absolutely wild towards the end. Trimax is actively mutating our genomes and rewiring our brains as we speak. We’re already past the point of no return!!

#trigunbookclub #trimax

[cbirt]

Typhoid, once a disease that ravaged countries, had been considered tamed by the introduction of new antibiotics in the mid-20th century. Awareness of the importance of sanitation and hygiene also rose as literacy and higher education rates increased; however, the rise of multidrug resistance in various typhoid strains has become a cause for concern. A new consortium, the Global Typhoid Genomics Consortium, has now been formed to further our understanding of antimicrobial resistance in typhoid in different countries and regions. Enabling policymakers to make decisions utilizing genomic data from disease surveillance may make it easier to plan for disease outbreaks and treatment.

Salmonella Typhi, commonly referred to as Typhi, is the causative agent of typhoid fever, which, if left untreated, can be fatal, with mortality ratios estimated to be less than 1% in modern times but ranging from 10% to 20% in the pre-antibiotic era. Historically, the disease has been responsible for deaths on a mass scale, usually triggered by the prevalence of unhygienic conditions, as urbanization and industrialization led to overcrowded cities and unsafe living environments. While the situation has mostly improved in many parts of the world due to significant improvements in water, sanitation, and hygiene infrastructure, it is still responsible for more than 10 million infections, as well as more than 100,000 deaths annually. A large number of these deaths were in low-income countries, with patients often having less access to clean water, food, and hygiene infrastructure.

Salmonella was one of the initial pathogens to undergo sequencing in high-income countries. Public health laboratories often identify Typhi strains from patients and carriers, which serves as an informal method for monitoring the genetic makeup of pathogenic populations in countries with a high prevalence of the disease. More recently, whole genome sequencing (WGS) was utilized for disease surveillance in both endemic and non-endemic countries.

Continue Reading

#genomics #bioinformatics #typhoid fever #antimicrobial resistance #amr #global health

[thesquidkid]

Who says science isn't exciting?

4x04 Dear Mama

Hi, and welcome back to my science meta! I'm actually writing this merely a few hours after watching the finale, and I haven't gotten a chance to rewatch any of season 4. So this might get updated in the future as I intend to rewatch the entire show to give you the best science breakdown possible!

Anyway, this is not about the finale, it's about 4x04 and science. Hence I will ignore all my feelings about this episode, and focus on my favourite thing in the world: science!

So buckle your seat-belts, deconnect all your braincells, and prepare yourself to dive into some alien made-up science!

(Content warning for this meta, I talk about squids a lot, because as you can see from my username, I like that animal)

We start up with a dialogue between Isobel and Liz:

Isobel: "All right, uh, Dr. Dyson, why don't you tell me about this, uh, alien ectoplasm, hmm?"

Liz: "Oh, I prefer the term "goo," but it's technically epidermal tissue. Mm-hmm."

The ectoplasm is the outer layer of a cell's cytoplasm. The ectoplasm is usually of an elastic texture.

The cytoplasm is the all of the material in an eukaryotic cell, enclosed by the cell membrane, excluding the cell nucleus.

Euraryotic cells are cells whose nucleus is enclosed by a nuclear envelope.

The cell nucleus is what contains all of the cell's genome (all genetic information of an organism).

So, the thing is, what we see on screen looks like skin that has been shed. Which is not what ectoplasm is. And I really don't know why Isobel would mention that. I guess one could theorise that after spending many hours around people (Liz and Kyle) who talk about biology, one would absorb some of that vocabulary.

However, Liz indeed corrects her, by saying something scientifically correct! Skin is indeed epidermal tissue.

Epidermal tissue is the outmost cell layer of the primary plant body. So, really, humans are plants and therefore the outer layer of skin, since our skin is composed of 3 layers, one of which is called the epidermis (corresponding to the outer layer), which is an other word for epidermal tissue.

I know this is a weird thing to be proud of, but the fact that they used correct terms (as far as I know) is pretty cool. Just afterwards, Liz mentions the third helix and hence it is definitely alien. Which, personally, I didn't need to look at it under a microscope to tell. The skin sample glowed. Human skin, as far as I know, doesn't do that.

But, better be safe than sorry. It's always good to check your results, and give background to the results that were obtained.

***

The next science is something that kinda confused me at first, and then seemed to make some sense. Liz seems to be walking around the desert with a metal detector (spectrometer). And she says:

"Yeah. I rigged it so that it would locate the alien tech component in alien biology. I mean, at least I hope I did."

A spectrometer is a scientific instrument used to separate and measure spectral (over a spectrum) components of a physical phenomenon.

There are light spectrometers, that can separate white light (visible light) and measure the individual bands of colour that compose the light (called a spectrum). There are mass spectrometers which measure the different masses of the atoms or molecules in a gas.

There are other types of spectrometers, like a magnetic one, which is what I had initially assumes Liz had used, but turns out a magnetic spectrometer requires very specific conditions.

Then, I decided to look further into mass spectrometer. It appears that it would work on solids rather than just on gasses. We then can conclude that Liz probably used a mass spectrometer, and tweaked it so that it would "detect" the change in mass between alien DNA (which contains a third helix, which I'm guessing must affect it's mass), from the rest of the desert.

Well, she does find an odd change in mass, in, you know, a truck buried under sand. Very normal, of course.

***

Liz saying "For the first time in forever, the science doesn't make any sense to me." really really describes my constant state watching that show

***

Liz and Kyle science!

Liz: "Kyle. What if the alien cells aren't dead? What if they are only playing dead? Like an octopus does when it-it's scared and it turns into coral."

Kyle: "You're talking chromatophores."

Octopuses (I had to google the plural of octopus, and I'm just going with what google answered) wan indeed turn into coral! It's fascinating to see (here's a youtube video for you). Squids can also change their colour (which I can actually talk about a lot, I have done extensive research on squids 😅😂).

Squids and octopuses have cells called chromatophores that have the particularity of changing colour. These cells are situated just below the the surface of the skin, which is thin enough to show the colour of these cells.

Chromatophores basically work by having a center that is elastic and contains a certain colour. The elasticity means that when it stretches out, the coulour would appear brighter, and hence give the illusion of changing colour (since then the colours seems more visible). This elastic center, like a little pouch, is controlled by nerves and muscles. These cells are found in a large number, in varying sizes. Hence, it can create a full camouflage. Thing of it like pointillism, a painting made of thousands of little dots of different colour.

To go back to the alien science, basically the alien cells taken from the skin sample have the same property than squids and octopuses. I guess you could say, that I, squid kid, am an alien. (Sorry, I had to, I have been saving this from the moment I watched the episode. It is my moment to shine).

By introducing the sample from the blue eyes, it is like saying "hey don't be afraid, I'm a friend", and the squid/octopus basically reverts to their "original form".

(Moral of the story: don't scare me. I'll turn into coral 😂)

(Side note, but this is one of the reasons thesquidkid is my url)

***

I could talk about Tezca and Jones' body. But I genuinely have no idea what is going on, and I don't even want to know. However, I am always happy to talk theories and ideas!

***

This is the end of the meta for this episode! It took me most of the day ngl. I was writing in during the breaks in my lectures, because I was so excited to finally talk about how cool squids are 😂

I don't really know when I'll upload the next one, but I'll keep doing them episode by episode, instead of all in one post. I did that for the first three seasons and that was not a great idea for my sanity. You have no idea how stressful it is to write a full meta all on tumblr drafts. I was so scared it would crash and I'd lose everything. I guess I like to live dangerously 😂

#sorry not sorry for talking about squids #i have been waiting for ever for the opportunity #there wasn't much science in this ep tho #so it went quite fast to write the meta #especially since i didnt really need google for the squids part 😂 #roswell new mexico #rnm #rnm meta #rnm 4x04 #thesquidkid does meta

[scienceinenglish]

Gene associated with autoimmune illness may protect carriers from COVID-19

In findings published Thursday in PLOS Genetics, researchers from King's College London report a mysterious new balance between wolf and bug: A gene associated with increased risk of the autoimmune disease systemic lupus erythematosus (SLE) may protect carriers from severe COVID-19.

The research team performed a meta-analysis of three genome-wide association studies performed on Europeans. They found several sites associated with both SLE and severe COVID-19. The two with the tightest relationships were TYK2, which affects the production of interferon, and CLEC1A, which encodes a lectin involved in resistance to fungi and in cell-cell communication. Individuals with a mutated TYK2 were at greater risk of SLE but lower risk of severe COVID. Individuals with a mutated CLEC1A were at great risk of both severe COVID-19 and fungal infection.

The authors described their findings as "an exciting result made possible by the large genetic studies in COVID-19 and Lupus, and opens the door to our understanding of how the biology of the immune system is calibrated to protect us against infection from viruses and other infectious agents, but at the risk of developing autoimmune disease."

Read the full text of the study in PLOS Genetics.

Wang Y, Guga S, Wu K, Khaw Z, Tzoumkas K, Tombleson P, et al. (2022) COVID-19 and systemic lupus erythematosus genetics: A balance between autoimmune disease risk and protection against infection. PLoS Genet 18(11): e1010253. https://doi.org/10.1371/journal.pgen.1010253

www.lifescienceediting.com

#COVID-19 #lupus #genetics and genomics #autoimmune #science news

[psykotiskapsalmer]

Väggar som pratar med väggar

Jag är trött på själviskt samtalande

vill inte höra om ditt jobb, ditt barn, 

din semester eller senaste fester. 

Ställer ändå en följdfråga och ler

“hur kändes det?”, “berätta mer”. 

Hoppas du förstår och ser,

att de är en tjänst jag gör

genom att lyssna och ge gehör

att jag inte bryr mig, 

men vet att du gör. 

Men den tanken har inte slagit dig. 

Som det mesta, för meta, 

det flyger över ditt huvud. 

Självupptagen, så uppe i dig, så tagen i dig själv. 

Åh, så behagligt med ett lyssnande öra!

Omedveten om att det är ett jobb, en tjänst, ett jävla göra. 

Så skönt för dig att få lyfta, lufta, 

uttrycka, bearbeta, sätta ord på

säga säga säga,

säga dig själv till existens. 

Externalisera dig själv. 

Helt utan kärna. Förlägger allt det interna. 

Du håller låda, 

monologer i minuter – ja varför inte timmar 

jag slutade lyssna, hjälp, jag tror jag svimmar!

Tills du är så van vid ljudet av din egna röst

att det blir din enda tröst. 

att du förlorat hemmet i ditt eget bröst. 

Du märker inte längre när du avbryter

märker inte hur en viskning ofta ryter 

i en vädjan,

den trevligaste formen av HÅLL KÄFT

ingen vill va din obetalda terapeut. 

Eller,

ställ en fråga och våga, 

håll in dig själv. 

Ge tid till eftertanke, täpp till din holk, 

prata med och inte på folk. 

Svälter du utan uppmärksamhet?

Vari finns din identitet? 

Blir du stissig utan nickningar och instämmanden?

Oförmågen att bekräfta din egen person.  

Jag hade tagit det som en personlig lektion…

Visst kan du snacka! Men

så liten,

så ensamt.

Till och med

pinsamt.  

Ja och jo,

jag låter väl dig hållas då. 

“Jaså?”, “Visst är det så”, “Hej och hå och apropå”

Är väl snäll då, 

startar samtal, till och med på eget bevåg

låtsas delta i din ensidiga dialog.

#långdikt #dikt #utvalddikt #reflektioner

[twiainsurancegroup]

[leedsomics]

Long term co-circulation of multiple arboviruses in southeast Australia revealed by xeno-monitoring of mosquitoes and metatranscriptomics

Arbovirus surveillance of wild-caught mosquitoes is an affordable and sensitive means of monitoring virus transmission dynamics at various spatial-temporal scales, and emergence and re-emergence during epidemic and interepidemic periods. A variety of molecular diagnostics for arbovirus screening of mosquitoes (known as xeno-monitoring) are available, but most provide limited information about virus diversity. PCR-based screening coupled with metatranscriptomics is an increasingly affordable and sensitive pipeline for integrating complete viral genome sequencing into surveillance programs. This enables large-scale, high-throughput arbovirus screening from diverse samples. We collected mosquitoes in CO2-baited light traps from five urban parks in Brisbane from March 2021 to May 2022. Mosquito pools of [≤]200 specimens were screened for alphaviruses and orthoflaviviruses using virus genus-specific primers and reverse transcription quantitative PCR (qRT-PCR). A subset of virus-positive samples was then processed using a mosquito-specific ribosomal RNA depletion method and then sequenced on the Illumina NextSeq. Overall, 54,670 mosquitoes, representing 26 species were screened in 382 pools. Thirty detections of arboviruses were made in 28 pools. Twenty of these positive pools were further characterised using meta-transcriptomics generating 18 full-length genomes. These full-length sequences belonged to four medically relevant arboviruses: Barmah Forest, Ross River, Sindbis-like and Stratford viruses. Phylogenetic and evolutionary analyses revealed the evolutionary progression of arbovirus lineages over the last 100 years, highlighting long-distance dispersal across the Australian continent and continuous circulation characterised by constant turnover of virus lineages. http://dlvr.it/T4sKzP