#rnase

[bio-basic-inc]

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[monopeptide]

last night as I was about to do the Very Last Step with my flow cell the pipette tip fell off. with my sample in it

[unibiotech]

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[cytgen]

Abstract Currently, there are approximately 6500 species of viruses known in the world, among which more than 1500 are plant viruses. Most of them are capable of causing epiphytoties, which lead to decreased yields, reduced product quality, and sometimes put valuable commercial varieties or even entire plant species at risk of extinction. The global spread of viruses leads to the need to strengthen phytosanitary and quarantine restrictions, which requires additional financial costs. Understanding of viral biology and the principles of its propagation is a key factor in the formation of strategies and methods for combating these pathogens. Among the newest approaches are the genetic engineering technologies. Their use made it possible to create a number of plant varieties with increased resistance to viruses. However, the problem of creating virus-resistant plants still remains one of the most urgent since viruses acquire the ability to bypass defense mechanisms with time and there is a need to obtain new resistant varieties. There are several main approaches for obtaining of transgenic plants with increased resistance to viruses. They are based on RNA interference, resistance associated with viral capsid proteins, RNA-satellites, antisense RNAs, replicases, RNA-dependent RNA polymerase, the action of ribonucleases, ribosome-inactivating proteins, hammerhead ribozymes, miRNAs, plant antibodies, etc. One of the approaches to creating virus-resistant plants is the use of ribonuclease genes. The genes encoding ribonucleases have different origin and belong to a wide range of hosts: bacteria, fungi, plants, and animals. In particular, extracellular ribonucleases are able to cut nonspecifically molecules of viral RNA in apoplast that allows for creating plants with increased resistance to various plant viruses. This review is focused on the study of various genetic engineering approaches and the prospects of their use for the creation of virus-resistant plants. Emphasis is placed on the study of heterologous ribonuclease genes influence.

[hellsite-proteins]

also, do you know any other fun proteins where the amino acids react with eachother to form a new chemical? like residues 65-67 in GFP cyclysing to form the chromophore?

to start, i had a bit of a hard time finding the right search terms for this question, and a lot of what i found is more focused on synthetic or enzymatic methods used in labs, rather than lists of natural examples. if anything is wrong or missing as always pls lmk! i rambled a lot so that info is going to get hidden under the cut, but here is the tl;dr of three relevant PTMs

one takeaway I had from trying to find things is just how unique GFP actually is! it has been important enough for studying biological systems that its discovery was awarded the nobel prize in 2008, and a lot of incredible chemistry went into modifying its structure to make other fluorescent proteins in different colours. this is important if you want to look at more than one thing by fluorescent microscopy, and was done by altering residues around the chromophore to influence its protonation state/pKa through the local environment.

disulphide bonds:

so many proteins: insulin. RNAse A. chymotrypsin. etc.

isopeptide bonds:

the collagen-binding domain of S. aureus Cna and probably several bacterial pili have intramolecular isopeptide bonds

Vibrio cholerae, which causes cholera, makes isopeptide bonds to cross-link actin in its host

there are more examples of isopeptide bonds on wiki

biaryl ethers:

a lot of these are not made by ribosomes, and it looks like all of them are fairly small and funky looking peptides, but i think that has to count at least a little bit. here are a couple:

patellamide A

telomestatin (the wiki page on this one is so short and as far as i could tell, we aren't even sure yet if this is made by ribosomes or not so i'm really pushing things here on what counts)

letter sequence in this ask matching protein-coding amino acids:

alsdyknwanytherfnprteinswheretheaminacidsreactwitheachthertfrmanewchemicallikeresidesinGFPcyclysingtfrmthechrmphre

protein guy analysis:

for all the time i spent on this post, the protein itself is kind of underwhelming. its a shorter one with three alpha helices and a small, two strand antiparallel beta sheet, with some loops in between. this could be a real peptide, or it could just be the confused ramblings of an algorithm trying to make shapes out of an input. the confidence score is pretty low, so as usual my bet would be on the latter option, but who knows? maybe this could stably exist in real life? dream big and all that

predicted protein structure:

the main keyword i was using was 'protein cyclization', so i'm sure i missed a lot, and most of what i found is focused more on synthetic methods, but i was still able to get some good information.

this first article here gives a nice overview of protein cyclization, and a lot of different and super neat ways it can be done. if anyone wants me to give a more detailed breakdown of this article i would be happy to, since i'm not sure how clear it is to people without much of an organic chemistry background.

this next article gives an overview of post translational modifications, and also looks like a good resource with a lot of information. there are so many different PTMs out there, so if you'd like me to discuss one in particular a little more, let me know as well.

this gave me a few specific PTMs to find examples of.

the first and most obvious is disulphide bonds, which are what you are describing, but far less unique, so i also want to give some other examples

another example is isopeptide bonds, which are formed between an amine and carboxyl group just like a regular peptide bond, except that these amine and/or carboxyl groups are part of the side chain, not the peptide backbone

and finally, i found biaryl ethers, which i had never actually heard of before, and are only made by microbes and scientists, and are interesting for pharmaceuticals

there are more examples that involve cyclization with the backbone, and other types of PTMs beyond cyclization, but i've already spent too long on this, so if you want something more specific then you have to ask for it

[lost-rxverie]

tuesday | june 24 18/100 dop steps: 14.5k

i carried out a successful RNA extraction today! this was my first time working with RNA and i know it can be tricky, so i'm pleased to report that everything went smoothly (and yes, i was anxiously spraying down my gloves with RNase Zap at every possible opportunity). my research project is finally off and running!

plus: started the day with a 4 mile run, went to a lab dinner with my housemates, and finally did that laundry i'd been putting off since Saturday.

[mindblowingscience]

Researchers at the Department of Cell and Molecular Biology, Karolinska Institutet have made a major discovery in how human cells produce energy. Their study, published in The EMBO Journal, reveals the detailed mechanisms of how mitochondria process transfer RNA (tRNA) molecules, which are essential for energy production. Mitochondria need properly processed tRNAs to make proteins for energy. Problems in tRNA processing can lead to serious mitochondrial diseases. Until now, the exact process of tRNA maturation in mitochondria was not well understood. "Our study reveals, at a molecular level, how the mitochondrial RNase Z complex recognizes and processes tRNA molecules," said Genís Valentín Gesé, the first author of the study. "By using advanced cryo-electron microscopy, we've been able to visualize the complex in action, capturing snapshots of tRNA at different stages of maturation. This is a significant step forward in understanding how our cells produce energy and maintain healthy function."

Continue Reading.

[welcome-to-cell-hell]

WORLDBUILDING NOTES: RED BLOOD CELL DENUCLEATION

So a while back I made a big post talking about how in this AU, the nucleus (specifically, the DNA in it) is like a cell’s brain, as well as how that works. I wrote that whole thing and RBCs did not cross my mind ONCE. Well now that it has traversed by cranium, here’s what I got.

IRL, red blood cells lose their nuclei and all of their organelles when they leave the bone marrow. If this were to happen in the AU tho, that means all the working RBCs would be eternally wobbling around like squishy drones. Never thinking, never feeling, never speaking.. just doing their jobs exactly as programmed until they die. And that isn’t what I had in mind.

So instead, the RBCs don’t literally lose their nuclei, but they do lose its function. On denucleation day, part of the graduation ceremony involves the cell taking a shot of a special enzyme complex. This includes RNAse and a bunch of fictional (i.e. “undiscovered by humans”) enzymes called deoxystaticases. Together, they break down any and all proteins related to the transcription and replication of DNA, rendering the chromosomes static, as the name implies. This way, they can still serve their functions as the cell’s “brain,” but can’t do anything biologically significant anymore. The complex is a herbal green color, and tastes REALLY bad- meme videos of graduating RBCs overreacting to the putrid taste pop up on the internet every now and then.

As for the organelles, they DO literally lose those. In the past, a toxin was added to the enzyme complex that made the cell violently exocytosize them, but that method is now considered cruel and unnecessary. Nowadays, a simple (and much safer) surgery removes them. And yes, they still only eat ice cream after this. If you ever go on a date with one, expect a lengthy Häagen Dazs trip.. and maybe bring your own food.

[didanawisgi]

https://publichealthpolicyjournal.com/biontech-rna-based-covid-19-injections-contain-large-amounts-of-residual-dna-including-an-sv40-promoter-enhancer-sequence/

BioNTech RNA-Based COVID-19 Injections Contain Large Amounts Of Residual DNA Including An SV40 Promoter/Enhancer Sequence

Abstract

Background: BNT162b2 RNA-based COVID-19 injections are specified to transfect human cells to efficiently produce spike proteins for an immune response.

Methods: We analyzed four German BNT162b2 lots applying HEK293 cell culture, immunohistochemistry, ELISA, PCR, and mass spectrometry.

Results: We demonstrate successful transfection of nucleoside-modified mRNA (modRNA) biologicals into HEK293 cells and show robust levels of spike proteins over several days of cell culture. Secretion into cell supernatants occurred predominantly via extracellular vesicles enriched for exosome markers. We further analyzed RNA and DNA contents of these vials and identified large amounts of DNA after RNase A digestion in all lots with concentrations ranging from 32.7 ng to 43.4 ng per clinical dose. This far exceeds the maximal acceptable concentration of 10 ng per clinical dose that has been set by international regulatory authorities. Gene analyses with selected PCR primer pairs proved that residual DNA represents not only fragments of the DNA matrices coding for the spike gene, but all genes from the plasmid including the SV40 promoter/enhancer and the antibiotic resistance gene.

Conclusion: Our results raise grave concerns regarding the safety of the BNT162b2 vaccine and call for an immediate halt of all RNA biologicals unless these concerns can be dispelled.

[nitw]

thank you for keeping my fume hood RNase-free with your big ears mr fennec fox sir

doin my part!!

[cupcraft]

Anyway to distract myself I'm going to talk about my science at work right now. I am currently about to prepare to get rna from tumor samples.

So basically our tumor samples have a lot of proteins that degrade rna called rnases. Rnases exist everywhere even on our own skin so but the tumor samples from skin which is an rnase heavy tissue. Anyway so how to prevent the rnases degrading and to grt good quality rna I literally have a giant bottle of liquid nitrogen and pour that into a ceramic mortar and pestle and then I do the same with the tumor. And powder that ahit up like God's cursed seasoning. Then I like put it into a trizol solution because thay allows you to purify rna from other junk.

Anyway wish me and my rna luck don't burn yourself on liquid nitrogen be safe fellow biology ppl

[darkmaga-returns]

By Nicolas Hulscher, MPH

In the very first episode of the new show, Daily Pulse with Maria Zeee, we first discuss the peer-reviewed study by Kammerer et al published in the journal Science, Public Health Policy and the Law titled, BioNTech RNA-Based COVID-19 Injections Contain Large Amounts Of Residual DNA Including An SV40 Promoter/Enhancer Sequence:

They found DNA contamination (SV40 and Spike gene) in COVID-19 mRNA injections exceeding regulatory limits by over 300% after RNase A digestion, leading them to call for an immediate halt of all RNA biologicals. The presence of this DNA raises serious concern about possible integration into the human genome, potentially leading to permanent Spike protein production and increased cancer risk.

Currently, the FDA views peanut contamination in protein bars as a bigger threat than cancer-linked DNA contamination in widely administered genetic injections. While allergen contamination is obviously dangerous for some, this contrast reveals grave concerns:

[reportsofawartime]

自粛マスク蛋白マン

@1A48wvlkQc6mVdR

·

16時間

もともとDNAのデオキシリボースは、水酸基が存在しないためにより安定した構造を持ち、酸素分子との反応性が低くなっています。一方、リボースは水酸基が存在するため、酸素分子と反応しやすく、酸化反応を起こしやすい性質を持っています。

自粛マスク蛋白マン

@1A48wvlkQc6mVdR

·

16時間

核酸の安定性としてそのような差があり、DNaseとRNaseの反応性の違いは構造の違いを酵素が認識している。よって、DNaseIではⅿRNAを分解はできず、DNAだけを分解するということになっているのですが、強固に結合していた場合は、それによってDNAが守られてしまいます。ご理解いただけますよね。

[unibiotech]

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[transgenderer]

Virus latency (or viral latency) is the ability of a pathogenic virus to lie dormant (latent) within a cell, denoted as the lysogenic part of the viral life cycle.[1] A latent viral infection is a type of persistent viral infection which is distinguished from a chronic viral infection. Latency is the phase in certain viruses' life cycles in which, after initial infection, proliferation of virus particles ceases. However, the viral genome is not eradicated. The virus can reactivate and begin producing large amounts of viral progeny (the lytic part of the viral life cycle) without the host becoming reinfected by new outside virus, and stays within the host indefinitely.[2]

Episomal latency refers to the use of genetic episomes during latency. In this latency type, viral genes are stabilized, floating in the cytoplasm or nucleus as distinct objects, either as linear or lariat structures. Episomal latency is more vulnerable to ribozymes or host foreign gene degradation than proviral latency (see below).

Advantages of episomal latency include the fact that the virus may not need to enter the cell nucleus, and hence may avoid nuclear domain 10 (ND10) from activating interferon via that pathway. Disadvantages include more exposure to cellular defenses, leading to possible degradation of viral gene via cellular enzymes.[12]

Proviral latency: A provirus is a virus genome that is integrated into the DNA of a host cell

All interferons share several common effects: they are antiviral agents and they modulate functions of the immune system. Administration of Type I IFN has been shown experimentally to inhibit tumor growth in animals, but the beneficial action in human tumors has not been widely documented. A virus-infected cell releases viral particles that can infect nearby cells. However, the infected cell can protect neighboring cells against a potential infection of the virus by releasing interferons. In response to interferon, cells produce large amounts of an enzyme known as protein kinase R (PKR). This enzyme phosphorylates a protein known as eIF-2 in response to new viral infections; the phosphorylated eIF-2 forms an inactive complex with another protein, called eIF2B, to reduce protein synthesis within the cell. Another cellular enzyme, RNAse L—also induced by interferon action—destroys RNA within the cells to further reduce protein synthesis of both viral and host genes. Inhibited protein synthesis impairs both virus replication and infected host cells. In addition, interferons induce production of hundreds of other proteins—known collectively as interferon-stimulated genes (ISGs)—that have roles in combating viruses and other actions produced by interferon.[13][14] They also limit viral spread by increasing p53 activity, which kills virus-infected cells by promoting apoptosis.[15][16] The effect of IFN on p53 is also linked to its protective role against certain cancers.[15]

Another function of interferons is to up-regulate major histocompatibility complex molecules, MHC I and MHC II, and increase immunoproteasome activity. All interferons significantly enhance the presentation of MHC I dependent antigens. Interferon gamma (IFN-gamma) also significantly stimulates the MHC II-dependent presentation of antigens. Higher MHC I expression increases presentation of viral and abnormal peptides from cancer cells to cytotoxic T cells, while the immunoproteasome processes these peptides for loading onto the MHC I molecule, thereby increasing the recognition and killing of infected or malignant cells. Higher MHC II expression increases presentation of these peptides to helper T cells; these cells release cytokines (such as more interferons and interleukins, among others) that signal to and co-ordinate the activity of other immune cells.[17][18][19]

Epstein–Barr virus lytic reactivation (which can be due to chemotherapy or radiation) can result in genome instability and cancer.[5]

HSV reactivates upon even minor chromatin loosening with stress,[7] although the chromatin compacts (becomes latent) upon oxygen and nutrient deprivation.[8]

Cytomegalovirus (CMV) establishes latency in myeloid progenitor cells, and is reactivated by inflammation.[9] Immunosuppression and critical illness (sepsis in particular) often results in CMV reactivation.[10] CMV reactivation is commonly seen in patients with severe colitis.[11]

viral latency is so fucked up

[mush-dooms]

I soaked a stir bar in RNAse-away to mix up some buffer today not thinking that I have nothing that is RNAse free to put the stupid stir bar inside of. fuck you RNA why do you have to be everywhere