/sci/ - Science & Math

cyroEM is the best!

replies are always appreciated

>>6921598
u may be interested in the sauce for these then.
http://virology.wisc.edu/virusworld/viruslist.php?virus=hiv

this image is just the baseplate of a bacteria phage. i dont have any good pics of the whole virus. if anyone finds one its needed in this thread

heres that image that weve all seen all over the news. ebola virus (not cryo EM this time). i find it cool that the family filoviridae doesnt have an icosahedral capsid like most other viruses.

i love me some infographics

heres a good one of a pussy ass macrophage getting fucked up by some HIV

heres some more aids to infect /sci/ with

anybody out there on /sci/ liking these pics?

remember when ppl gave a shit about west nile?

These are nice. I'd love some gifs.

>>6921656
its a bit late for me to be making some gifs tonight. maybe if this thread is still alive tomorrow ill make some. this my first time on /sci/ in like 2 years lol

>>6921663
>this my first time on /sci/ in like 2 years lol
>lol

if u think these structures are cool check this vid out if u have an hour to kill
https://www.youtube.com/watch?v=_vBgwMDMjkM&index=4&list=PLGhmZX2NKiNlN0vnCLxkYrm5M1jtg4VBN

>>6921679
it is. last time i was here it was full of ppl looking for help on their homework. also was full of a bunch of math shit that i dont feel like doing in my spare time

Why do viruses have icosahedral symmetry?

>>6921596
Damn viruses be scary

>>6922498
this. its making my dick hard. viruses know true art.

Mech Eng here. Loving this stuff. Ignore the idiots, drop more please. And thx.

>>6921663
I will bump this at 4 hr intervals

>>6922498
Harder for the immune system to recognize the viruses.

>>6922498
>>6922894
not entirely sure why the symmetry. I believe that the capsid is a protein crystal and maybe that arrangement is most efficient for packing and unpacking the viral genome during replication cycle. Although as u can see not all viruses are icosahedral like the family filoviridea (including ebola). These are alpha helical in structure

>>6922498
Heres a diagram of a bacteria phage. note the complex structure under the head. Thats there to pierce the cell wall of a bacteria so that the genome can be injected into the cytoplasm. the capsid stays outside the cell bec the cell wall wont let the whole particle pass

OP is not a fag. Keep 'em coming, great thread.

>>6921612
this is the bottom of a bacteria phage that is used to peirce the cell wall.

>>6923542
thanks for ur bump. in return i give u yellow fever

heres a particularly cool virus called mimivirus. one of the largest ones known. note the smooth surface and the perfect 5 fold axis of summitry. also based on the scale in the image its around 4000 angstroms across

>>6921596
Awesome thread. How were the structures of these viruses found? X-Ray crystallography?

>>6923591
i think they used to use x ray crystolography back in the day but now its cryo-EM like in this pic

>>6923600
Ah cool, I learnt something today

>>6921655
do they not.
I just went over it in Microbio today lol.

the background of this image depicts the the way that the bases are paired in the (ssRNA) genome of rhinovirus. pretty cool that viruses dont need DNA and that their genome is not arranged in a double helix shape like ours is

>>6923607
lol i remember when it was all over the news here in canada a few years ago but then everyone forgot about it. Its not like west nile virus went away

Hold on folks, why the flying fuck do viruses look so fractal-like?

I mean, Hepititis E may as well be a frigging Mandelbulb.

If there are any 3Dfags here, you can take PDB files, import them into JMOL then export them in whatever visualization form (cartoon, stick, ball & stick, Van der Waals, ect.) you want as a WRL file for use in your standard 3D software. Pic related is bacterial DNA polymerase.

Thanks, OP, I didn't realise you could get whole virus coats as pdb files, this could be fun/useful for an assignment.

>>6923633
because unlike cells viruses are made of a set number of amino acid bases creating crystalline protein shells around the genome. this results in a highly ordered structure

>>6923635
glad to help and i prob will go DL JMOL again now that u mention it and start playing around with some of these structures

>>6923651
You might need a pretty beastly machine (RAM-wise) to import a WRL ball and stick model of an entire protein coat. Start off with cartoon representations and, if that works smoothly, progress to B&S. Even a model of insulin makes my 4770k with 16GB of RAM chuck a bit in C4D.

>>6923660
yeah good point. not a chance ill get anything done on this 3 year old laptop. also keep ur pics coming i like em

>>6921625

Due to geometric limitations, Viral nucleocapsids are either Helical like Ebola or Icosahedral (generally with other coatings outside the nucleocapsid like the twinned inner/outer capsule structures you can see in >>6921663 or >>6921628) - so it's a quite a common shape for viruses, it's just that most animal virae are Icosahedral because helical capsids can generally only handle genomes stored in single stranded RNA/DNA format, and you often have much less complex outer protein capsules... with the exception of yandere shit like ebola, which has a single protein for its capsid, then has a still vaguely "simple" complex outer capsule of just two proteins that fit together in a repeating pattern to form the sausage shape of the whole outercapsid then, but then as a final fuck you to its victims proceeds to wear the outer membrane of the animal cells it kills as a disguise to confuse the immune system and has a load of special molecules inside that turn off large chunks of the internal anti-viral systems of cells.

>>6923684
great explanation. heres some nodamura virus for u.

would look nice on my Christmas tree

>>6923678
Thanks, Needle section of the Type III secretion system from Y. pestis (plague). This bastard lets the bacteria pierce the membrane of immune cells and deliver cytotoxins directly into them, hampering the ability of the body to develop antibodies against them and bypassing the need for the toxins to be absorbed by the target cell. A modified form is used by PVL+ S. aureus to lyse cells but, rather than being anchored in the bacterial wall, it's spat out like an angry junky throwing used needles at a cop.

>>6923712
yeah true. i wana 3D print one so bad.

>>6923719
A little more simple, the (S) enantiomer of thalidomide (teratogenic), this was done for the cover of a paper, the author asked for something "Like a Dorling Kindersley book".

>>6923719
jebus crapes, nature just wont give us a break.

>>6923735
ohh is that the stuff that cause deformations in babies?

looks like im all outa images to dump. I do however have this khan academy on viruses witch was what sparked my interest in the subject
https://www.youtube.com/watch?v=0h5Jd7sgQWY

>>6923591
this >>6923546 is electron tunneling, to get pictures as clear as >>6923556
or >>6923593 or
>>6923600 you need to use Atomic Force Microscopy plus a lot of computing power - basically take the needle of a vinyl turntable, reduce it to an atomic scale then wave it over the surface of a thing and measure how much the needle dips based on atomic interactions.

>>6923611

Well some of them are - viral classification looks at 1) are they DNA or RNA based? 2) is it single stranded or double stranded? 2.5) if single stranded, what sense is the strand?
>>6923633

The outside of a virus is made up of generally a small handful of proteins, that fit together in a regular way, and indeed will automatically form these shapes of their own accord this if you dump them into a solution without any other proteins and the right pH levels.

Obviously back in the day when biologists were arguing over "protein" or "DNA" based genetic heredity this confused a few people, who'd isolate a DNA virus, seperate the capsid proteins from the DNA, then dumped the capsid proteins into a beaker seperate from the DNA and not only would the "infectious particles" seem to be produced but they'd then inject tons of the capsid proteins into animals and when the immune system reacted and caused symptoms they'd quite wrongly claim they'd found the hereditary agent.

Of course Viruses are genetically stingey as fuck, so you sometimes get viruses using a single protein to produce more than one geometric shape at a time, based on how their capsid proteins fit together into what are known as capsomeres - if there's say 5 capsid proteins to a face of the end point geometric structure you usually have an icosehedron, but you can then attach the same proteins pairs to form long strings, or arches, or vast helical spiral structures or elongated icosohedrons like >>6923546 and>>6923536.

>>6923750
That's the one. This happy little bugger is cholera toxin, it prevents certain G-protein coupled receptors from deactivating, ultimately leading to massive amounts of water being dumped by the mucus membranes and causing the bloody awful diarrhea you get with cholera. The same GPCR is targeted by pertussis (whooping cough) toxin which does the opposite, thickening the mucus, particularly in the lungs, to the point where it can't be shifted and the bacteria can go hog wild.

Cholera is one of the possible reasons why cystic fibrosis has persisted as a genetic disorder for so long, it gives the affected individual some resilience against cholera because they are less able to move water into their mucus membranes. Therefore, while it may give poor long term prospects, the affected individual can at least potentially survive a cholera infection without shitting themselves to death and go on to reproduce before dying from consumption around age 30.

>>6923546
that's fucking crazy

>>6923847

Bacterias have weird stuff coating their outermembranes that require phages to turn their genetic material into needles to peices through it - Viruses can get into animal and plant cells by pretending to be gianormous parcels, like a burglar hiding in a cardboard box with the house's address on it and ringing the door bell to break into a house.

>>6921596
Hey kid. Those images are not cryo TEM (theres a T in there, by the way, wiki article is not very accurate on this one but at least it does mention that its transmission electron microscopy, hence TEM).

TEM cant make 3D images because the electrons travel straight thru the specimen, giving a projection of the entire virus onto a plane.

Your 'images' are computer models in a popular protein modelling software suite, hence why they have 'PDB' sources on them, which stands for protein data base. This data comes from protein crystalography and neutron diffraction, for the most part, as SEM can do 3D but doesnt have the angstrom resolution of these 'images'.

Source: I do research on an ETEM as my job.

>>6921625
ironically, this image is almost certainly cryoTEM

>>6923881
Nature is so fucking hostile it really surprises me that complicated multicellular life can even exist.

>>6923782
you cant do AFM with this kind of resolution on deep structured objects like viruses, the probe tip would never be able to probe a 3D structure like this with any kind of detail, even if you could avoid thermal noise/drift, which in the case of a virus, you couldn't.

>>6923901
That's precisely why it exists, so you can have cells devoted to hunting down and murdering the fuck out of pathogens and any host cell foolish enough to even look like it's hiding one.

The existence of viruses really spook me. Why do they do what they do? Why does a jumble of DNA/RNA want to spread? At least bacteria and other single celled organisms respond to stimuli but viruses just are. I know these types of question get a little metaphysical but for a little while now I've bothered by this shit.

>>6923964
They're just another form of life (or something very close to it) that found a way to do what all genes do, spread themselves around.

>>6923881

>>6923973
>you don't see snake

>>6923886
good to know. i have no background in biology im just interested in the subject atm. looks like ur right about cryo TEM (or EM) and that these are not cryo images. thought they somehow generated a 3D model from the data obtained from cryo to make these.

>>6923929
>That's precisely why it exists, so you can have cells devoted to hunting down and murdering the fuck out of pathogens and any host cell foolish enough to even look like it's hiding one.
>mfw rebellious cell
>goes on to 'thug out'
>signals get sent for it to 'straighten up'
>ignores them
>signals get sent to test if it still knows its function
>ignores them
>finally, signals get sent to tell it to suicide
>ignores them
>tfw 20 macrophages hold it down, penetrate it, then break it apart into small molecules and lysosomes

>>6924265
the seedy underbelly of our cellular society needs macrophges to police it. sometimes the criminal HIV pathogens send signals to bribe the macrophages to look the other way and then they take over without an amune response. this can cause a collaps of the society as a whole.

these viruses are organized criminals that need to be stopped!

>>6924323
>"What about escalation?"
>"Escalation?"
>"We start producing phagocytes, they start producing peptidoglycan layers"
>"We start producing antibodies, they alter their surface markers"
>"Yeah"
>"And you're producing antibiotics"
>"Now take this guy, violent septicemia, two deaths, got a taste for novel compounds, like you, leaves a sensitivity card"
>"I'll look into it"

>>6923556
Can a virus prey on another virus?

>>6924781

No, those are by definition viroids, not viruses - those need to steal the polymerases and transcription factors of other viruses and smuggle themselves inside those viruses capsids to get in and out of cells.

Basically Viruses are parasites of cellular translation mechanisms to make proteins, Viroids are parasites of the viral transcription systems.

>>6923651
Are you telling me that viruses are crystal robots?

>>6923635
JMOL is for entry level fags. Use vmd.

God. I fucking love microbiology.
I knew this would be a gold mine of cool shit.

>>6925166
Thanks, wasn't aware of VMD. I've alwayed used JMOL because it did the job when I first searched for the right tool 8 years ago and no alternatives popped up.

>>6923546
They look like fucking aliens

Also, great thread OP

love this thread. hopefully I'll get to do some EM in grad school.

>>6924874
a viroid isnt exactly as u describe. viroids are naked ssRNA with no protein coat or membrane making them much smaller than a virus but still infectious particles.
a satellite virus is the closest thing to a virus that "preys" on another virus. for example the only way to get hepatitis D is if u already have hep B. this is due to the fact that hep
D needs some of hep B's proteins to propagate itself.

here is an interesting figure i found showing the entire genome of citrus exocortis (viroid). its insane that it carries enough information encoded in a genome no more than 350 bases long to replicate itself.

Fig. 2. (a) Nucleotide sequence and structure of CEVd variants. (i) CEVd-t (Semancik et al., 1993); (ii) CEVd D-92 (Semancik et al., 1994); (iii) CEVd D-104 (Semancik & Duran-Vila, 1999); (iv) CEVd D-87; (v) CEVd D-76. Nucleotide changes compared with D-92 are indicated. Molecular structures are presented as the minimum free energy form predicted at 24 °C (Zuker, 1989). The five structural domains T1, P, C, V and T2 (Keese & Symons, 1985), terminal repeated regions U1, U2, L1 and L2, the AGCU tetrads (horizontal bars) (Semancik et al., 1994) and the hairpin II (HPII) stems (Steger & Riesner, 2003) are indicated. (b) Modelling of the CEVd D-forms D-38 (i), D-40 (ii) and D-43 (iii), with quasicomplementary sequence insertions (hatched areas) compared with the D-92 sequence to complete a hypothetical stable structure of the minimum free energy form predicted at 24 °C (Zuker, 1989). Nucleotide changes compared with CEVd D-92 are indicated.

What do you think came first, the virus or the archaebacterium?

>>6929751
very good question. although viruses seem like simpler "organisms" they are all host obligate parasites. so in my opinion they must have come after archaebacterium bec they need some form of host to propogate

pic related its the effects of Potato spindle tuber viroid

>>6925057
thats exactly what im telling you. and theyre coming for u. ull never see them coming and once u notice their effects its far to late.

Multiple anthrax bacteria (green) are being enveloped by an immune system cell (purple).

>>6929875
raph?!?! is that u? also nice pic.
this is an image of a viroid. cant believe that that thing can manage to evade imune system of plants and propogate

This human T cell (blue) is under attack by HIV (yellow),

>>6925166
>not arguslab
>not cbd ultra

Great thread though

>>6929815
PST viroid genome

Virusoids are circular single-stranded RNAs dependent on plant viruses for replication and encapsidation.[1] The genome of virusoids consist of several hundred nucleotides and does not code for any proteins.
Virusoids are similar to viroids in size, structure and means of replication (Rolling circle replication).
Virusoids, while being studied in virology, are not considered as viruses but as subviral particles. Since they depend on helper viruses, they are classified as satellites. In the virological taxonomy they appear as Satellites/Satellite nucleic acids/Subgroup 3: Circular satellite RNAs.
The term virusoid is also sometimes used more generally to refer to all satellites.

-wikipedia

didnt know these were a thing until I just read this right now