Leah

@hoxinsocks

I just really love shapes. I love it when things are shapes. And I love it even more when shapes are things (Molecular model printer @3dmoleculardesigns.bsky.social‬‬, former rodent botherer, perennial cell enjoyer)

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Leah@hoxinsocks· 24d

Ah hell, why not post the rest of that set? I used to have...opinions...about behavioral assays. I still do, but I used to, too.

A sketch of a human in an elevated plus maze. (That's a ~common test for anxiety-related behavior in rodents and some other nonhuman animals.) To the left of it is Maria Bamford's description of anxiety: "It's like we're at, like, a wonderful party--it's just a regular party; everybody's having a good time--and then all of a sudden, somebody shows up in a pretty frighteningly realistic Dracula costume. And you know it's just fuckin' Steve Benaquist. Right? And everyone says, 'Oh yeah, it's Steve Benaquist.' But he won't say he's Steve Benaquist. And then he starts chasing you."

A simplified sketch of a person in a social preference test, which is usually run using mice. One person stands in the middle of two caged people. Below, a Louis CK description of related phenomena reads: "You ever see somebody that you don't know...again?"

A sketch of a person hanging upside down from a swingset-like frame by one leg, arms dangling. It represents the tail suspension test, which has been used in rodents to study depression-related behaviors.

Leah@hoxinsocks· 25d

‘Melancholy’ is today’s #ArtRepostJuly prompt. The sucrose preference test is often used to study anhedonia-related behaviors in rodents. It is represented here next to a description of anhedonia from Hyperbole and a Half. 🐡

A drawing of a stick figure looking at two glasses of water (one which contains sucrose), next to a written description of anhedonia by Allie Brosh (the author of Hyperbole and a Half, which I highly recommend reading in book or blog form). That description reads: “I tried to get out more, but most fun activities just left me existentially confused or frustrated with my inability to enjoy them.”

Leah@hoxinsocks· 29d

'Colorful' for today's #ArtRepostJuly prompt, plus bonus pics of the same model (protein chunk + methylated DNA) (www.rcsb.org/3d-view/2KY8)

Line diagrams of PDB entry 2KY8, showing a chunk of protein bound to a chunk of methylated DNA. It is a solution NMR structure, with multiple conformers laid on top of each other, so it has a messy sketch-like feel to it.

Leah@hoxinsocks· Jul 11

One of the summer students makes these little springs out of purging filament 🥺

My thumb and forefinger holding a tiny blue plastic spring (about 1/4" long and 1/4" wide). It is cute.

Leah@hoxinsocks· Jul 6

Today's #ArtRepostJuly prompt is 'dry'--a friend on Ye Olde Twitter noted that the crispies on this cyanorhodopsin look like uncooked ramen. Which they do!!

A line diagram of cyanorhodopsin, in purple, with squiggly yellow ligands (mostly alkanes). https://www.rcsb.org/3d-view/6LM1

Leah@hoxinsocks· Jul 6

Leland Melvin's portrait is my Tom Holland's Rihanna's Umbrella

NASA astronaut Leland D. Melvin's 2009 professional portrait, in which he is smiling one of the happiest smiles I've ever seen a person smile, while one of his dogs mouths his ear and his other dog looks on with a Very Amusing Dog Expression.

Leah@hoxinsocks· Jul 2

Whoop and I don't think I ever posted the business end of the phage glowball! Heh heh heh...heh heh heh...heh heh heh heh heh... www.rcsb.org/structure/7LHD

Four photographs of the same plastic glowball from the picture in the previous post, but turned upside down so you can see its RNA innards. Lots of pale, twisty RNA bits (think Kraft mac & cheese spirals) festoon the insides of the jagged blue protein coat. The next few pictures show the same model backlit, zoomed in on, and glowing in the dark, respectively.

Leah@hoxinsocks· Jun 10

Big models like these can make Jmol sad, which makes my eyeballs very, very happy

Two screenshots of a carbon backbone model of the virus linked above in the above post, with the carbon backbone thickened all to hell for prettiness purposes, as viewed with a slightly glitchy Jmol. There are a bunch of enlarged model pieces strewn around the screen because I zoomed in or out too fast. I dig it.

Leah@hoxinsocks· Jun 2

An image from the linked page. Its description reads: Left: JBD30 is a siphophage that infects Pseudomonas aeruginosa by attaching to hair-like pili on the bacterial surface. This illustration was created by combining pdb_00008rkc, pdb_00008rkb, pdb_00008rk9, pdb_00008rk8, pdb_00008rk7, pdb_00008rk6,pdb_00008rk5, and pdb_00008rk4. Right: Andhra is a podophage that infects Staphylococcus epidermidis. This illustration was created by combining pdb_00008egt, pdb_00008egs, pdb_00008egr, and pdb_00008ej5.

Another image from the linked page. It reads: The E217 is a myophage that infects Pseudomonas aeruginosa, a pathogen which is naturally resistant to antibiotics. It has been used in an experimental cocktail developed to treat Pseduomonas infections. Illustrations was created by combining multiple structures: pdb_00008frs, pdb_00008eon, pdb_00008fuv, and pdb_00008fvh. Tail fibers, which were not resolved experimentally, have been drawn in.

Another image from the linked page. Its description reads: Most phage recognize host cells through the specific interaction between receptor binding proteins, or RBPs, at the end of their tail or tail fibers, and proteins or other molecules, such as sugars, on the host cell surface. Take a closer look at a few examples of phage RBPs bound to bacterial host proteins by clicking on the jsMol tab. The first example shows the RBP of T5 phage binding to the FhuA transporter of E. coli (pdb_00008a8c and pdb_00008b14), the second shows the receptor binding domain of λ phage's RBP, called gpJ, binding to the LamB porin of Shigella sonnei (pdb_00008xcj), and the third shows the binding of Oekolampad phage's tail RBP to the LptDE translocon, from Shigella flexneri (pdb_00009rpt). In all cases, the phage RBP is shown in magenta and the bacterial receptor shown in white.

A plastic model of a T4 bacteriophage, with a second capsid where its "legs" (long tail fibers) should be. Ain't I a stinker? --And not to be that guy, but 3DMD does sell T4 bacteriophage models: https://shop.3dmoleculardesigns.com/products/t4-bacteriophage-mighty-model%C2%A9

Leah@hoxinsocks· May 24

These pictures are old and insufficiently contextualized. But so are you. That's fine. It's fine.

The first three pictures are the carbon backbone, at varying angles/levels of zoom, of Protein Data Bank entry 9VVJ: erlin1/2 complex.
https://www.rcsb.org/structure/9VVJ

A potassium channel structure from 25 years ago (PDB ID: 1F6G)
https://www.rcsb.org/structure/1F6G

Leah@hoxinsocks· May 11

📢 MILWAUKEE SUMMER JOB 📢 Working at 3DMD is life-changing for anyone who loves bio or chem. Or art. Or plastics. Or shapes. But I'm biased... Ideal resume-builder for young scientists! No prior experience in science or manufacturing needed; just attention to detail. www.indeed.com/job/producti...

Part of the summer workshop area, showing a plethora of molecular models. Some are made of injection-molded plastic, some are made of cut foam, some are made of 3D-printed parts. Summer production staff made and processed those parts. That could be you! (Also, some models are made of plaster and other things, don't worry about those.)

Dynamic DNA model, made of injection-molded parts. During summer workshops, production staff get to see parts go from their hands into the hands of happy teachers. It is extremely satisfying.

A potassium channel model, made of 3D-printed parts, with an augmented reality animation showing how potassium transport through the channel (emphasizing the role of oxygen atoms in water and oxygen atoms on the protein in shlorping the potassium along). Production staff cleans the support material from these parts and glues them together. That could be you!

Aside from standard models, production staff also helps process 3D printed parts for custom models, like this huge antibody that went to Paris for the 2024 Olympics (!). That was a fun summer. Pictured here is Mark Hoelzer, one of the coolest humans I've ever met, who has several lifetime's worth of weird projects under his belt.

Leah@hoxinsocks· May 3

Which, 1) fund basic science, you assholes and b) that led me to this

This picture and the next show a screenshot of a Nature letter (1891) by F. Gowland Hopkins, titled Pigment in Yellow Butterflies.
It reads:
Apropos of the interesting discussion on comparative palatability and warning colours (NATURE, November 19, p. 53; November 26, p. 78), it may be of interest to your readers if I restate in your columns some of the properties of the yellow pigment contained in the wings of the common brimstone and many other butterflies; the possible significance of which in conferring protective unpalatability is suggested by Mr. Beddard. My paper on the subject, to which Mr. Beddard refers, was read before the Chemical Society in June 1889; but, being more or less of a preliminary nature, it was published only in the abstracts of that Society's proceedings (Abst. Proc. Chem. Soc., vol. v., 1889, p. 117; vide also NATURE, vol. xl. p. 335).
[cont.'d in next picture]

The pigment is freely soluble in hot water, though quite insoluble in cold water, and in most organic solvents. Its aqueous solution is strongly acid to litmus; and, though it appears to be quite innocuous to frogs when injected under the skin, it may well be ungrateful to the ranine palate. At the same time it must be noted in this regard that its solubility in the secretions of the frog's mouth is but very slight.
The substance is, as I have shown, undoubtedly a derivative of uric acid, yielding the latter body as one of its products of hydrolysis. It gives the murexide reaction direct. It forms quite definite salts with metals, its compounds with the alkalies being soluble bodies.
Having regard to the wide-spread presence of the body in the scales of diurnal Lepidoptera, I have ventured to call it lepidotic acid. In its physical properties it closely resembles mycomelic acid, a yellow derivative of uric acid; and, in my original paper, I ventured to suggest a formula for the body. I hope shortly to publish a more complete account of the subject, and to assign a formula to lepidotic acid based upon fuller evidence. Meanwhile, in common with many others of your readers, I am looking forward to the appearance of Mr. Beddard's book. The literature of the subject of animal coloration is not easily accessible, and a text-book thereon will be a valuable acquisition. We have, it is true, the interesting work of Mr. Poulton; but the subject is there treated from what is, perhaps, a somewhat limited standpoint.
F. Gowland Hopkins.
Sir Wm. Gull Research Laboratory,
Guy's Hospital, December 16.

Then a bit of the next letter is shown. It reads:
The Chromosphere Line lambda 6676˙9.
In response to Father Cortie's implied question as to the identification of this line as belonging to the spectrum of iron,...

Leah@hoxinsocks· May 1

Update: The sproinger sproings! The sproinger always sproings. #3dThursday

Leah@hoxinsocks· Apr 21

#TubulinTuesday!

Picture from the linked article, which includes this description:

Sleeping parasites. Trypanosomid flagellates (Blechomonas lauriereadi) are parasites that live in the extracellular spaces — typically in their hosts’ blood plasma and body fluids. The parasites can cause sleeping sickness if they infect humans, and animal trypanosomiasis in cattle and horses. Here, the organisms’ microtubules are labelled in pink and their extensive mitochondria in green, using expansion microscopy. The images are part of ongoing efforts to build an atlas of microbial eukaryotes.

Felix Mikus, Dudin & Dey Labs

Leah@hoxinsocks· Apr 20

Disinteglobins: A meditation on wholeness. $900 OBO

Three pictures, from different angles, showing the same thing: a plate of globin misprints in which the support filament jammed partway through the print. Out of yellowish support blocks arises a thicket of sturdy but disconnected snakelike carbon backbones, partially printed side chains, and squiggly strands of errant filament strewn about like Easter basket grass.

Leah@hoxinsocks· Mar 29

Oop, surprise pocket urea!

A plastic model of urea, with a carbon atom about the size of my thumbnail, painted hastily in cute colors (yellow's a bit too yellow and pink's a bit too pale, whatever).

Leah@hoxinsocks· Mar 12

Well...I do like puzzles...

Two alpha-globin models, side by side, from the 3DMD hemoglobin mighty model. The one on the left is intact on a base. The one on the right has been smashed into about 34 pieces.

Leah@hoxinsocks· Mar 6

!! Fungus cluster, fern sora, tomato, tomato! SHAPES!

Fern sorus (spore factory), taken by Rogelio Moreno, 2nd place winner of Nikon's photomicrography competition 2018. It looks...very reminiscent of the fungus picture in the quoted post's image. More: https://www.nikonsmallworld.com/galleries/2018-photomicrography-competition/fern-sorus-structures-producing-and-containing-spores

Leah@hoxinsocks· Jan 28

And ever deeper we sink into...

A scan of page 110 from Vaught's Practical Character Reader. It shows a diagram of a frowning man's bald head, with a drawn-on band running from his eyebrows to the back/base of his head. This band is labeled: The Torrid Zone. The caption reads: The torrid zone of human nature.

Leah@hoxinsocks· Jan 27

From a friend in Minneapolis:

A screenshot of my friend's post. It reads:

I have been getting messages from people outside of the cities telling me to stay safe and avoid protests where things could get violent. I want people to understand that a protest is honestly one of the safest places to be, because ICE are cowards and they aren't grabbing people where there's a crowd.

The dangerous place to be is driving to the gym. Walking to the grocery store. Getting a fucking donut, apparently. When you're by yourself, or with just one or two people, and someone could get kidnapped right in front of you.

There is no way to be 100% safe when ICE tries to kidnap your neighbor unless you look away, turn away, and do nothing. I will never do that, so I cannot be safe until they leave.

Leah@hoxinsocks· Jan 18

My boyfriend saw this, asked me for the picture, and then sent me benotafraid.jpg

The same green-yellow-red structure as in the previous picture, except it's more artfully added to an ethereal depiction of a many-winged "biblically accurate" angel.

Leah@hoxinsocks· Jan 17

Ahahahaha that rocks! I, for one, welcome our new molecular overlords

A stock photo of a flying saucer that has had the aforementioned NOMPC ion channel expertly, EXPERTLY, added to it. The green (more hydrophobic) chunk of the channel is "embedded" in the flying saucer as in a lipid nanodisc, and its long sproingy tentacles are sprawling down with the saucer's beam.

Leah@hoxinsocks· Jan 15

Myriad errors have occurred, but I have Learned

A 3D-printed model, part PLA and part water-soluble PVA, soaking its supports off in water. It shows the same weird sproingy tetramer as the previous posts mention (PDB ID 5VKQ). Three of its squiggly carbon backbone chains are lime green, and one is orange. The orange is not supposed to be the only long chain. There was a layer shift Incident, which the green chains might have survived if the backbone were thicker and there were more struts added. The colors were chosen approximately randomly (an actually important build was using those colors, and it had extra plate space), but I kind of like them. I think.

Leah@hoxinsocks· Jan 6

That reminds me of this note from a teacher workshop, which makes me smile every time I walk past it

A photograph of a handwritten note. It reads:
-Flipase, flopase, scramblase!!!
-they are real!

(The 'real' is thrice underlined.)

Leah@hoxinsocks· Dec 30

This is nuts on several levels! Also, how am I even supposed to photograph this thing?

A coiled green plastic model, about 3/4” in diameter and 6” long unstretched, showing the carbon backbone of a super mega long ankyrin repeat from the ion channel shown above (PDB: 5VKQ). It’s a weird one, even for me.

Leah@hoxinsocks· Dec 18

I started looking for dynein and got distracted by what a good sproinger this chunk would make

A ribbon diagram showing the carbon backbones of two protein chunks. It is a Protein Data Bank structure, as text indicates:

6L4P | pdb_00006I4p
Crystal structure of the complex between the axonemal outer-arm dynein light chain-1 and microtubule binding domain of gamma heavy chain

The top protein chunk, in green, looks a lot like the sproingy 3D printed protein chunk that I'm holding in the next picture. But that one is an ice-binding protein from a carrot (PDB ID 6W78).

Leah@hoxinsocks· Nov 14

Henry Wrinkler is going to San Diego; muahahahaha

A plastic finger puppet, held up in front of an airplane wall/windows, a model of the upper chunk of a mouse embryo (mostly head and forepaws). E14.5. From GigaScience. The model is about 2" tall and is a light peach color.

Leah@hoxinsocks· Oct 24

Heh. Heh heh. Ho ho ho. Happy mole day!

A partially finished sign for 3D Molecular Designs. The 'molecular' is in progress, so it reads 3D mole designs. It's as clever as it needs to be, and I think that's beautiful.

Leah@hoxinsocks· Sep 25

I see the news, it seems Shakespearean, I post a doodle of a virion

A diagram showing the carbon backbone of a phage, shown as a cross-section. Its protein shell is light purple, and its nucleic innards are light orange. (PDB ID 7LHD; https://www.rcsb.org/structure/7LHD)

Leah@hoxinsocks· Sep 12

Printing these caps with brims was a bit excessive, but I'm glad I did, because a) I'd rather deal with brims than spiders, and--more importantly--b) now I've got inspiration for some kinda scaly knobby something something