#Functional genomics

[cbirt]

Unstudied areas of life sciences, including uncharacterized or less characterized genes and proteins, have an exclusively dedicated repository through the recent works of scientists affiliated with the MRC Laboratory of Molecular Biology, Cambridge; the University of Cambridge and the University of Oxford, United Kingdom. The open source database ‘Unknome’ is now the repertoire of organism’s “unknome” and encompasses the Genome Ontology (GO) annotations-based “knownness” score of those poorly understood proteins, representing the extent of information that is known about the protein. Apart from that, the study reveals that shifting attention from well-established proteins towards less-characterized proteins is extremely promising for maturing current knowledge about cellular developmental and regulatory processes, rectifying misannotations, and extending the scope for achieving novel druggable targets.

The inquisitiveness and surge in technological advancement have boosted and equipped the science community for meticulous investigation of the realm of proteins, and the venture has enriched the biological sciences with the discovery of different proteins and an understanding of their biological significance, especially functions.

Despite this, the unwrapping of the functions and roles of innumerable proteins is yet to be done. As the author mentions, most of the studies and databases are focused on proteins and genes, which are already well-studied and well-designated. Conceivably, this pattern is attributed to the undersupply of funding from the authority, the associated risk of expense, preconceived speculation of unsuccess, and the inconvenience of assays in laboratory settings.

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[autodidacticpolymath-blog]

A Policy arm @ Cambridge had VERY interesting use of "confidential" patient data for Genomic & Medical Research during and post COVID.

20 15 Pathogen genomics into practice Data sharing to support UK clinical genetics and genomics services Genetic screening programmes: an international review of assessment criteria 2017 Personalised prevention in breast cancer – the policy landscape Developing effective ctDNA testing services for lung cancer Linking and sharing routine health data for research Variant classification and…

[netbiopub]

Rescue of neuropsychiatric phenotypes in a mouse model of 16p11.2 duplication syndrome by genetic correction of an epilepsy network hub. Nat Commun. 2023; 14: 825.

[markscherz]

Quick, while the frog purists aren't looking, what's your favorite salamander?

No question, salamanders of the genus Thorius, the smallest salamanders in the world.

[Thorius pennatulus — src]

[Thorius sp. — src]

Truly astonishing creatures.

[opens-up-4-nobody]

...

[catboybiologist]

“As a biologist, the terms biological woman and man don’t make any sense to me” okay then you’re an idiot and a terrible biologist. I swear to god, morons like you only become biologists just so you can hold it over others, when in reality, if biology deniers like you can become biologists, then being one really doesn’t mean much anyway. But this probably just gave an autogynophile like you a boner to read, anyway.

Oh fun! Haven't gotten one of these in a while. Disregarding the fact that you somehow think the qualification for being a biologist entirely hinges on defining womanhood, I do need to ask some clarification. I know I'm feeding the trolls here, but here we go: does your definition of "biological woman" mean:

Sociological woman? Eh, context dependent, I'm not fully out of the closet, but oftentimes, I am and present femme. So let's call that one 50/50.

Psychological woman? Because I am one.

Neurological woman? Because I am one [1].

Physical woman? My soft tissue redistribution is handling that well.

Hormonal woman? My blood tests are within cis female ranges.

Transcriptional woman? As a signalling molecule, the downstream effects of estrogen have broad transcriptional effects, completely changing the profile of gene expression and functional genomics of my cells. [2]

Genetic woman? I mean, see my above point- as far as my genes that are actually active, I have all of the same transcripts being produced, controlling which genes are expressed.

Karyotypic woman? I actually have a few signs pre-HRT that might point to a non-XY chromosome pair, but I haven't had a karyotype. We'll put that down as unknown. And hell, even if its XY, there's plenty of cis women who are karyotypically XY, with suppressed sry or complete androgen insensitivity. Interestingly enough, a completely androgen insesitive woman can go her whole life without knowing- and functionally, is very similar to a trans woman, actually. Fancy that. [3]

Reproductive woman? I can't produce an egg cell, but neither can significant fractions of cis women. Also, this is all gonna change soon, which is fun. [4]

There's also a lot of understudied aspects to the biology of HRT and even pre-HRT that are emerging, largely demonstrating widespread cellular and genetic remodeling of trans individuals undergoing hormone therapy. The field is a bit behind due to constant political pressure to revoke funding, but a lot of the results are extremely exciting in both testosterone and estrogen hormone therapies. I'm sure that, as a self professed biology As someone who presumably has a lot of expertise in biology, I'm assuming that you're aware of all of this cutting edge research, and are keeping up with modern papers, including but not limited to these cool findings:

Trans men on HRT exhibit significant genetic and transcriptional changes that make them biochemically male. [5][6]. It's a good hypothesis that the same happens with estrogen treatment, but those studies don't exist yet- I'm sure you're reserving judgment until more publications exist, of course.

Trans men on HRT develop male cell types and tissues. [7]

Trans women experience muscular and blood cell changes that align with cis women moreso than cis men [8]

And many, many more! This is an exciting, underserved, and groundbreaking field of research, and I'm sure you're keeping up with the latest in scientific journals about it.

I'm sure, of course, that you understand that it becomes impossible to draw a distinct line anywhere in here, and that words like "woman" are shorthand for the myriad of traits that invisibly synthesize in our mind and in society to represent a concept? I'm sure you understand that science is fundamentally descriptive, not prescriptive? I'm sure that you understand that these findings, while really cool and interesting, actually don't mean jack shit about what the word "woman" means or not?

As someone who is the ultimate decider in what a biologist is, I'm sure you know that bioessentiallism is a childish mindset that completely ignores and disregards the constantly changing, dynamic nature of biological systems, something that extends well beyond biological sex and its relation to gender.

I'm sure that also, that you understand that beyond just this, that the role of science in society is to advise how to achieve our moral principles, not create moral principles in themselves. And I'm sure that understanding means you know that trans affirming healthcare and supportive societal treatment leads to reduced mortality and increased happiness for everyone, right?

So great to talk to someone who is surely a scientist on this. You are a biologist, if you're talking like this, I assume? I assume you're not going to spit complete misreadings of scientific language from the background sections of these papers that only reveal you've never read a scientific paper in your life if you're thinking this way? I assume you have experience interpreting data like this?

Also, imagining my genitalia while writing this? Ew. Please stop projecting your fetishes into my inbox.

Works cited:

Kurth F, Gaser C, Sánchez FJ, Luders E. Brain Sex in Transgender Women Is Shifted towards Gender Identity. J Clin Med. 2022 Mar 13;11(6):1582. doi: 10.3390/jcm11061582. PMID: 35329908; PMCID: PMC8955456.

Fuentes N, Silveyra P. Estrogen receptor signaling mechanisms. Adv Protein Chem Struct Biol. 2019;116:135-170. doi: 10.1016/bs.apcsb.2019.01.001. Epub 2019 Feb 4. PMID: 31036290; PMCID: PMC6533072.

Gottlieb B, Trifiro MA. Androgen Insensitivity Syndrome. 1999 Mar 24 [Updated 2017 May 11]. In: Adam MP, Feldman J, Mirzaa GM, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1429/

Murakami, K., Hamazaki, N., Hamada, N. et al. Generation of functional oocytes from male mice in vitro. Nature 615, 900–906 (2023). https://doi.org/10.1038/s41586-023-05834-x

Pallotti F, Senofonte G, Konstantinidou F, Di Chiano S, Faja F, Rizzo F, Cargnelutti F, Krausz C, Paoli D, Lenzi A, Stuppia L, Gatta V, Lombardo F. Epigenetic Effects of Gender-Affirming Hormone Treatment: A Pilot Study of the ESR2 Promoter's Methylation in AFAB People. Biomedicines. 2022 Feb 16;10(2):459. doi: 10.3390/biomedicines10020459. PMID: 35203670; PMCID: PMC8962414.

Florian Raths, Mehran Karimzadeh, Nathan Ing, Andrew Martinez, Yoona Yang, Ying Qu, Tian-Yu Lee, Brianna Mulligan, Suzanne Devkota, Wayne T. Tilley, Theresa E. Hickey, Bo Wang, Armando E. Giuliano, Shikha Bose, Hani Goodarzi, Edward C. Ray, Xiaojiang Cui, Simon R.V. Knott, The molecular consequences of androgen activity in the human breast, Cell Genomics, Volume 3, Issue 3, 2023, 100272, ISSN 2666-979X, https://doi.org/10.1016/j.xgen.2023.100272. (https://www.sciencedirect.com/science/article/pii/S2666979X23000320)

Xu R, Diamond DA, Borer JG, Estrada C, Yu R, Anderson WJ, Vargas SO. Prostatic metaplasia of the vagina in transmasculine individuals. World J Urol. 2022 Mar;40(3):849-855. doi: 10.1007/s00345-021-03907-y. Epub 2022 Jan 16. PMID: 35034167.

Harper J, O'Donnell E, Sorouri Khorashad B, McDermott H, Witcomb GL. How does hormone transition in transgender women change body composition, muscle strength and haemoglobin? Systematic review with a focus on the implications for sport participation. Br J Sports Med. 2021 Aug;55(15):865-872. doi: 10.1136/bjsports-2020-103106. Epub 2021 Mar 1. PMID: 33648944; PMCID: PMC8311086.

[faultfalha]

The Solanum americanum genome has been used to discover immune receptors that detect potato late blight pathogen effectors. The discovery could lead to the development of new, more effective ways to fight the late blight pathogen.

[wilwheaton]

Scientists at UC Riverside have demonstrated a new, RNA-based vaccine strategy that is effective against any strain of a virus and can be used safely even by babies or the immunocompromised.  Their flu vaccine will also likely be delivered in the form of a spray, as many people have an aversion to needles. “Respiratory infections move through the nose, so a spray might be an easier delivery system,” Hai said. Additionally, the researchers say there is little chance of a virus mutating to avoid this vaccination strategy. “Viruses may mutate in regions not targeted by traditional vaccines. However, we are targeting their whole genome with thousands of small RNAs. They cannot escape this,” Hai said. Ultimately, the researchers believe they can ‘cut and paste’ this strategy to make a one-and-done vaccine for any number of viruses. “There are several well-known human pathogens; dengue, SARS, COVID. They all have similar viral functions,” Ding said. “This should be applicable to these viruses in an easy transfer of knowledge.”

Vaccine breakthrough means no more chasing strains

This is HUGE. This will fundamentally change how we get inoculated.

[guiltyidealist]

I haven't been able to stop thinking about ADHD Ammy since it was brought to my awareness

It's so fucking like. it could not possibly be more canonical without a character straight up saying "Ammy has ADHD". everything points to it

and I like to think Chibi is autistic too

[why-animals-do-the-thing]

Do you have a snoot noodle or other variation of sighthound? If yes, there’s new heart health research for the breed happening!

A researcher at Texas A&M whose work I’m familiar with is starting a new study looking at genetic factors contributing to heart disease in Borzoi and related breeds. They just put out a call for dog owners who are willing to submit saliva samples & (noodle) medical records. Studies like this need a big sample size! They’re accepting new sign-ups starting now until March 1, 2025, for dogs both in the US and internationally.

Let’s help make some science!

From the study page:

“Background and purpose

Recent research in Borzoi dogs has revealed that dogs of this breed experience sudden, unexplained death. About 85% of sudden, unexplained deaths in humans are linked to an underlying heart disease. Our existing research in Borzoi dogs has shown that they are predisposed to developing arrhythmias (abnormal heart rhythms) and dilated cardiomyopathy (a heart muscle disease causing dilated heart chambers and weak pumping function).

Due to our documentation of the frequency of these conditions in Borzoi dogs, we seek to identify responsible genetic variations similar to what is seen in humans with electrical cardiac diseases that trigger arrhythmias and dilated cardiomyopathy.

The objective of our study is to identify genetic mutations associated with heart disease in Borzoi dogs and document their existence in other sighthound breeds.

What happens in this study

We are collecting saliva samples from both healthy Borzoi and Borzoi dogs affected with arrhythmias and/or dilated cardiomyopathy. We will also collect saliva samples from any other sighthound breeds.

We will extract DNA from these samples and perform genomic sequencing on a select number while retaining the remainder for further screening.By analyzing the sequencing data, we can compare the genes of healthy and affected Borzoi dogs and identify variants linked to their heart conditions. We will also compare the findings in Borzoi dogs to results from other sighthound breeds.

Pet owner responsibilities

A swab kit will be sent to you for at home use along with a link to an instructional video on how to properly obtain a swab of the mouth. The kit will contain equipment to collect the saliva swab, a history form for your pet, a client consent form and a shipping label to return samples to us.

Participation requirements

To participate, you must have a Borzoi dog or a sighthound breed that is either healthy or affected by arrhythmias and/or dilated cardiomyopathy. Pets may be any age or sex. Electronic or paper veterinary medical records will need to be provided.

Benefits and risks of participating

There is little to no risk for taking a brief swab of the mouth for saliva collection if procedures outlined in the video are followed. No individual genetic test results will be provided to study participants.

Compensation

There is no cost to the owner for participating in this study. No compensation will be provided.”

[cbirt]

The ground-breaking study introduces functional genomics analysis’s foundation model, Genomics-FM. This versatile and data-efficient model overcomes the limitations of traditional AI approaches. Genomics is a field that has seen a transformative shift due to the introduction of artificial intelligence. Researchers are increasingly using AI to unveil the intricacies of genomes, from understanding genetic diseases to devising new therapies. Nevertheless, there is always an enormous challenge as these AI models require a lot of labeled data to train them.

Genomic information can be analyzed using Genomics-FM, an advanced AI model developed specifically for this purpose. Traditional AI models largely depend on carefully annotated datasets, unlike Genomics-FM, which can learn from vast amounts of unlabelled genomic information. This process, called pre-training, enables the model to possess a basic comprehension of complex patterns and relationships existing in genomic data.

Ensemble genomic vocabulary is a critical innovation behind Genomics-FM. It implies that the model learns from different representations of genomic information, enabling it to be adaptable and versatile for various genomic tasks. After pre-training, Genomics-FM can be easily adapted to specific tasks with little labeled data via fine-tuning.

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[hellsitegenetics]

just wanna say i love the contrast between this blog and @hellsite-proteins. Here the results are always a lovely surprise! Whether a post is an obscure bacteria or a creature amusingly related to its post, it's always a treat to see what kind of funny little thing a post may be. In contrast, hellsite-proteins' results almost always have a chaotic tone to them (affectionate). Unnecessarily long and stringy loops everywhere. i cheer when a protein is actually, confidently functional. the differing moods of each blog is amusing

String identified: t aa a t ctat t t g a @t-t. t t a aa a ! t a t a c acta a cat ag at t t t, t' aa a tat t at tt tg a t a . ctat, t-t' t at aa a a catc t t t (actat). ca g a tg . c a t acta, ct cta. t g ac g ag

Closest match: Boloria euphrosyne genome assembly, chromosome: 27 Common name: Pearl-bordered fritillary

(image source)

[enneegon]

hello hello.. here's the complete reference for hifsamotud. the space thang! the supership! some more information below the cut

HIFSAMOTUD stands for Hollow Intercession, Falling Space, All Mundane Order Towards Unawakened Discovery (or simply Discovery for short, to refer to it as a whole) which is by all means.... a ridiculously long name! every couple words is meant to represent each of its minds.

originally, it was restricted to travelling a specific distance away from the planet - a taboo that it managed to break, along with rewriting its genomes in such a way that expanded its range of communication. it functions like a massive satellite for iterators on ground, allowing them to send signals to other iterators who would usually be out of their radius.

discovery is unfortunately not as large as a moon, but it's very fun to depict it as a gargantuan, otherworldly being that i think it would be perceived as :) in reality it is just very very curious about everything down below..

[icarusredwings]

This has been on my mind for NO Fucking reason so to make it shut up, lets talk about it.

"Why doesn't Wade just do chemotherapy?"

In this essay, I will explain the answer to that question, looking at Germ cancer cells and testicular cancer rates to decide-

Can Wade have biological kids?

Let's start with the basic facts.

What a germ cell tumor?

A germ cell tumor is a mass made of reproductive cells, also called germ cells. “Germ” is short for “germinate,” which means to mature. For men and people assigned male at birth (AMAB), germ cells mature into sperm. Related, germ cell tumors most often form where eggs get made (ovaries) and where sperm gets made (testicles).

[ https://my.clevelandclinic.org/health/diseases/23505-germ-cell-tumor]

Testicular cancer.

Most testicular cancers start in cells known as germ cells and are called germ cell tumours. Germ cells in men produce sperm. Testicular germ cell tumours can develop from germ cell neoplasia in situ (GCNIS). GCNIS means that there are abnormal cells in the testicle.

[https://www.cancerresearchuk.org/about-cancer/testicular-cancer/types#:~:text=Most%20testicular%20cancers%20start%20in,abnormal%20cells%20in%20the%20testicle.]

More than 90% of testicular cancer start in the germ cells, which are cells in the testicles and develop into sperm. This type of cancer is known as testicular germ cell cancer. Testicular germ cell cancer can be classified as either seminomas or nonseminomas, which may be identified by microscopy.

[https://www.cancer.gov/ccg/research/genome-sequencing/tcga/studied-cancers/testicular-germ-cell-study ]

Treatments.

At the moment there is not a lot of options, the most common are:

Chemotherapy

Radiation

Surgery

Chemotherapy.

Chemotherapy works by stopping or slowing the growth of cancer cells, which grow and divide quickly. Because of his healing factor, this would probably not work and if anything cause Wade more illness seeing as Chemo causes

Fatigue

Hair loss

Easy bruising and bleeding

Infection

Anemia (low red blood cell counts)

Nausea and vomiting

Appetite changes

Constipation

Diarrhea

Mouth, tongue, and throat problems such as sores and pain with swallowing

Peripheral neuropathy or other nerve problems, such as numbness, tingling, and pain

Skin and nail changes such as dry skin and color change

Urine and bladder changes and kidney problems

Weight changes

Chemo brain, which can affect concentration and focus (serve mind fog)

Mood changes

Changes in libido and sexual function

And last but not least Fertility problems

[https://www.cancer.org/cancer/managing-cancer/treatment-types/chemotherapy/chemotherapy-side-effects.html ]

Radiation.

At high doses, radiation therapy kills cancer cells or slows their growth by damaging their DNA. Cancer cells whose DNA is damaged beyond repair stop dividing or die. When the damaged cells die, they are broken down and removed by the body. In theory this would work a little bit, for about 12 minutes and then he immediately would have all of those dead cells back because while the radiology killed one spot, cancer spreads. Quickly. With his healing factor its MUCH quicker too. All that pain for nothing.

Fatigue

Hair loss

Memory or concentration problems

Throat problems, such as trouble swallowing

Cough

Shortness of breath

Taste changes

Skin changes (such as burning and peeling)

Less active thyroid gland

Sexual problems

Fertility problems

Urinary and bladder problems

[https://www.cancer.gov/about-cancer/treatment/types/radiation-therapy]

Surgery.

I dont even need any sources for this. We saw what happened to his legs when ripped off. They just grew back. And if removing cancer cells makes newer cancer cells? That's useless.

Summary.

Wades entire body is cancerous. Yes. His ENTIRE body. Every arm, toe, and fingernail on this man is cancerous. His healing factor is literally just having rapid cancer growth (amongst other things)

Chemotherapy and radiation will not work on him. Chemotherapy works by killing cancerous cells in order to grow healtheir ones. Except Wade can only produce cancerous cells. Yes, while they are new and much more likely in the very early stages, it's still cancerous.

This being said, there is no cure or treatment for Wades Cancer (that we know of at this time) Its quite physically the only thing keeping him with super hero powers yet still remains even after his powers are taken.

Hate to say it.

I hate to say it but statistically removing older, more advanced cells to replace with newer, less progressive cells (aka removing or ripping off his limbs/ parts of his body so they can grow back as new and fresh) is probably the best 'treatment' Wade has right now. Radiology would work the same, right?

Yes, but A. Not as B. Too many side effects that he he'll have to deal with MORE making him even more crazy and sick. Why would he do that when he can just tease Logan into slicing a hurt leg off and go from there?

Will the treatment help him be fertile?

Realistically, without his powers, he probably would be dead in a week, perhaps less due to just HOW much cancer this man truly has.

Chemo would also make it worse. So much worse, in fact. Both pain wise and his chances at ever biologically having a child.

Result(s) Before the cancer was diagnosed, (66%) 79/120 couples who attempted to conceive succeeded within 1 year. After (Cancer) treatment, (43%) 38/88 couples conceived within 1 year.

[https://www.fertstert.org/article/S0015-0282(03)00335-2/fulltext]

Testical Germ Cell Tumors are associated with semen abnormalities before orchiectomy. This review shows an increase in abnormal semen parameters among men with TGCT even outside the treatment effects of orchiectomy, radiation, or chemotherapy.

[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4270136/ ]

The way that TGCT affects the sperm is that it's very common for not only lower sperm count (obviously, it's hard to produce when you're fighting an entire body illness) but also changes the shape of the sperm which makes it very difficult to reach the egg. Sperm with crooked tails, double tails, double heads, or even broken sperm have a very hard time reaching the egg (think of it like natural selection) and die off before they get anywhere. If you already have low countage and most of them can't make it?

Well that's much lower chances of fertility.

In the comics.

In the comics, Wade has a daughter named Eleanor Camacho in which he was unaware of because her mother saw his face and ran away in terror. The entire thing is that her mother thought she was going to die and decided fuck it, if im gonna die Im gonna die happy so decided to spend these last moments with wade (who she literally just met- if that aint weird in itself idk what is).

She only ever found him to demand child support, and he refused to believe such a beautiful child could he his given his stance of insecurity and well- Just utter shock anyway, I think. He is right. Eleanor is gorgeous as a baby and as an adult.

(There's actually a whole comic where he's trying to fight death so his daughter doesn't die before him because he "couldn't bear the thought of living without her" so they activate a bomb "with the power of a black hole" and comit death together. It's very sweet)

TLDR

In conclusion.

Yes, Wade can have children, but he has a better chance at being successful if he removes his lower half and regrows it so that its *less* cancerous than before cells, therefore hes more likely to have normal shaped sperm and probably more of it during the process.

No, chemotherapy, radiation, and surgery would not be effective. Unfortunately, the most effective thing for him is ripping his limbs off sometimes.

"Forest- why the fuck did you write this?"

You know... I really don't know. I wanted to become a bio geneticist, and here I am. Writing about some bald guys' balls on the Internet. Siiigghh... anyway. Use this. however you want, I don't even care at this point.

[microbes-in-hats]

Daphnia pulex (Water flea)

Photo credit: Paul Hebert

Source: Functional Genomics Thickens the Biological Plot. Gewin V, PLoS Biology Vol. 3/6/2005, e219. doi:10.1371/journal.pbio.0030219