Leah

@hoxinsocks.bsky.social

2560 Followers 14505 Following

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)

Eliseo pointing at L9 on a large ribosome model
More line diagrams of amino acids that kinda sorta look vaguely reminiscent of the aforementioned Duchamp painting. PDB IDs for each picture: 2L9C, 7LP4, 8SXM, and 2L9C again. https://www.rcsb.org/structure/2L9C https://www.rcsb.org/structure/7LP4 https://www.rcsb.org/structure/8SXM
Duchamp's 1912 painting Nude Descending a Staircase (No. 2). A figure, painted in shades of gold, walks down a staircase; but the figure is shown at several points in time, so all the different versions of the figure overlap in the coolest ways. The other pictures feature an amino acid (gold/yellow/white tyrosine in the first two protein pictures, green phenylalanine in the last picture) that has been visualized at angles/in a style that is kind of reminiscent of that painting. The pictures are of PDB ID 7L8V, 1A66, and 7LNS, respectively. https://www.rcsb.org/structure/7L8V https://www.rcsb.org/structure/1A66 https://www.rcsb.org/structure/7LNS
The figure referenced in the quoted picture. Its top image, showing vesicles on a membrane, is what was stamped in bleach onto a shirt. The paper's description of the figure is below: Figure 8. Connection of main body AZM macromolecules to synaptic vesicles at activated active zones. A) 10 nm thick surface model from an active zone sectioned in the median plane. It includes a row of vesicles from one side of an active zone ridge and the presynaptic membrane. Two of the vesicles are docked on the presynaptic membrane, one is fused with the membrane and one is an undocked vesicle 16 nm from a vacated docking site on the membrane. The color boundary at the interface of the fused vesicle membrane with the presynaptic membrane is arbitrary. B) An 80 nm thick surface model of the same vesicles in A that includes the vesicle surface facing the AZM. Connection sites of ribs (yellow gold), spars (red) and booms (purple) are indicated by ∼3 nm long stretches of each. C) A 25 nm thick surface model from an active zone sectioned in the transverse plane. A former docked vesicle that has fused with the presynaptic membrane is connected to ribs, a spar and booms. D) A 2.4 nm thick virtual slice, which was summed from 2 successive 1.2 nm thick virtual slices, of an activated active zone sectioned in the transverse plane. A former docked vesicle that is fused with the presynaptic membrane is connected not only to main body AZM macromolecules (asterisk), but also to non-AZM macromolecules (arrows) that link it to undocked vesicles (V1 and V2). One of the vesicles (V2) was linked to a topmast in other virtual slices. E) The undocked vesicle on the right of the AZM is 10 nm from a vacated docking site on the presynaptic membrane and has rib, spar, and boom connections as does the docked vesicle on the left. F) Undocked vesicles 10 nm and 15 nm from vacated docking sites on the presynaptic membrane with connection sites of ribs, spars and booms marked by ∼3 nm long stretches of each.
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 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.”
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.
My thumb and forefinger holding a tiny blue plastic spring (about 1/4" long and 1/4" wide). It is cute.
A line diagram of cyanorhodopsin, in purple, with squiggly yellow ligands (mostly alkanes). https://www.rcsb.org/3d-view/6LM1
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.
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.
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.
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.
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
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.)
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]
A smoothed carbon backbone model of one of the chains in the structure linked above (PDB ID 9SW6), covered in little filament wisps (whatever, don't @ me), held in one hand by its very conveniently evolved handle, being sproinged with the other hand like the sproinger it is.
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
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.
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).
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.
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
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.
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.
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.
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.
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.
A photograph of a handwritten note. It reads: -Flipase, flopase, scramblase!!! -they are real! (The 'real' is thrice underlined.)
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.
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).
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.
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.
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)
A cluster of about 30 pea-sized white plastic spheroids, each sitting on a thin white brim that spans about 3/4" in diameter. They overlap in a cool scaly way and are very fun to fiddle with.
A small backlit model of ~half a virus (2VF1, I'm pretty sure, which is picobirnavirus), held with a thumb and finger in front of a flashlight. There is a yellow pentamer in the center, surrounded by 5 pink trimers; and then, at the edges of the glowball, 5 more yellow tetramers. Because it is backlit, you can't see just how terribly strandy it is.
A plastic model of a T4 bacteriophage, with a second capsid where its "legs" (long tail fibers) should be. Ain't I a stinker?
A line diagram of a vaguely similar toxin (see link for more info), zoomed in on to show three sulfur atoms joined to each other
Ribbon diagrams showing the backbone of Murinotoxin-1, in dark purple (too dark...), with a dot for each alpha carbon. Six sulfur atoms are shown in yellow. The top two sulfur atoms are bonded to each other, like one is used to seeing in proteins like these; but the other four sulfur atoms are all joined together, which is much less common. What a weirdo!
A photograph of purple acrylic letters in a bed of yellow pear-shaped acrylic cell silhouettes. The letters say, in all caps, beef scout.
An old metal tool in a display case. It's about 20" long and pretty thin. On one end there is a point that looks...pointy...but is not very sharp. A few inches in from that are some serrations. Then there is a curved section with some teeth. Near the midpoint, two short arms with pointy ends are attached to the item, on either side, sandwiching it; the arms can rotate. After that there is a segment with some curves and points; then the last bit of the item gets round and wider, seeming like it would lead to a shaft-type situation.
The same pink model as in the previous two pictures, turned upside down and filled with three whole Werther's Originals. There are also some tiny green specks lining the inside of the glowball. Don't worry about them.
Two backlit plastic glowballs, each about 2" in diameter. The one on the right shows a virus-like particle from a nodavirus that causes white tail disease in prawns (PDB ID 6JJD). It is printed in three colors: a greenish star/pentamer (of which there are 6 visible in the picture); translucent ice blue blades that jut out from each green pentamer to form five-pointed stars, and light blue everywhere else. It is pretty. The model on the left shows three colors: six yellowish small pentamers, each surrounded by five flower-petal-like clear chains, and pink triangle-ish chains between them. (The clear chains are actually split up into bluish-clear and whitish-clear, but that's not obvious in the picture.)
A backlit plastic model of a somewhat spherical macromolecule (cut in half). Three colors are shown: five yellowish small pentamers, each surrounded by five flower-petal-like clear chains, and pink triangle-ish chains between them. (The clear chains are actually split up into bluish-clear and whitish-clear, but that's not obvious in the picture.)
Half of a glowball, about 2" in diameter and backlit in the dark. It is a model of a virus-like particle from a nodavirus that causes white tail disease in prawns. It is printed in three colors: a greenish star/pentamer (of which there are 6 visible in the picture); translucent ice blue blades that jut out from each green pentamer to form five-pointed stars, and light blue everywhere else. It is pretty.
A hand holding two models of a larval fruit fly nervous system, each about an inch long, glowing green in the dark.
Two identical models, shown at different angles, of a proposed molecular structure. Each is about the size of a tennis ball. Gray, blue, red, white, and orange atoms are shown. (I kind of want to let people guess what it is.)
A small 3D print, backlit by a cell phone, showing the suspiciously-virus-shaped form Arc takes (see https://pdb101.rcsb.org/motm/308 for more). Its chains are printed in light yellowish (raised pentagon, there are 6 shown in this view), clear (a 5-pointed star around each pentagon), and light blue (everything else).
A table full of models showing tRNA, ribosomes, and associates. (And also a GLP-1 receptor and a handful of water molecules, because everybody's gotta be somewhere.) Behind the table is a "Life is Complicated" poster, and in the distance is a wall display holding more models.
A hand holding a plaster buckyball model. The model is about the size of a baseball, each atom is about the size of the tip of my thumb, and the color scheme is very everlasting-gobstopper-like.
A swooshy ribbon diagram of a salmonella phage, except it's all scattered and funky with random bits everywhere. Helices and sheets are light purple, and everything else is white, against a black background. It kind of has a texture like thick frosting. If you squint.
A hand, in the dark, holding a plastic model of a suspiciously-virus-like structure formed by an Arc homolog (see MOTM link above). Different chains have been printed in different colors, resulting in six green glowing five-pointed stars (each with a darker pentameric center) separated by jagged streaks of black. It looks cool.
A 3D print of the suspiciously-virus-shaped form Arc takes (described in the molecule of the month article linked above). Its chains are printed in blue (raised pentagon, there are 6 shown in this view), teal (a 5-pointed star around each pentagon), and yellow (everything else).
Four line diagrams of different models. 3 models show RNA, and one shows DNA. For each model, multiple conformers have been laid on top of each other so the resulting image is kind of fuzzy and spiky.
A screenshot of a notes document. The text reads: Save as GFP_11-15_v0_sameas_GFP-from-magics-v10_v4 Make a mental note to never criticize anyone’s naming conventions ever again; except from a place of empathy and support
The same picture as in the first two posts, but with different color backgrounds added to make its top half orange-yellow and its bottom half blue. Here is the description of the first picture: A hand holding a backlit circular lithophane in a Petri dish. The lithophane shows a cerebellar section from figure 2 of chapter 6 of Ramon y Cajal's Recuerdos de mi Vida. The bottom half(ish) of the lithophane is striped horizontally with parallel fibers; a blue background has been added there to make the parallel fibers look more like waves.
The same picture in the previous post, but with more color added to make its top half purple and its bottom half darker blue. Here is the description of that previous picture: A hand holding a backlit circular lithophane in a Petri dish. The lithophane shows a cerebellar section from figure 2 of chapter 6 of Ramon y Cajal's Recuerdos de mi Vida. The bottom half(ish) of the lithophane is striped horizontally with parallel fibers; a blue background has been added there to make the parallel fibers look more like waves.
A hand holding a backlit circular lithophane in a Petri dish. The lithophane shows a cerebellar section from figure 2 of chapter 6 of Ramon y Cajal's Recuerdos de mi Vida. The bottom half(ish) of the lithophane is striped horizontally with parallel fibers; a blue background has been added there to make the parallel fibers look more like waves.
A photograph of a backlit blue-green partially translucent phage virion model
A flyer containing information about the thesis defense, information which is also found in the link. It is almost all text, except for a picture of the defendant. The flyer reads: THESIS DEFENSE Edward Lopatto Program in Plant and Microbial Biosciences Laboratory of Dr. Scott Hultgren Department of Molecular Microbiology and Microbial Pathogenesis Chaperone-Usher Pathway Pili Adhesin Conformations and Inhibitors in Urinary Tract Infections June 18, 2025 EPNEC Seminar Room B 11:00 AM ZOOM LINK Contact Edward e.lopatto@wustl.edu WashU The Roy and Diana Vagelos Division of Biology and Biomedical Sciences