hirenj

7 ms·

31.
by hirenj 2y ago
Possibly a dumb question - but are these models useful for homology finding? If you have two homologous genes, do they have similar embeddings? The reason I ask is I have a bunch of genes where I can’t get much better than a 1:many ortholog
32.
by hirenj 2y ago
On this topic, you might be interested in this article and the related discussion regarding novel anatomy. https://news.ycombinator.com/item?id=41517059
33.
by hirenj 2y ago
The phrasing seems weird because of how knowledge is acquired in this area. The first achievement was discovering that indeed some blood group antigen exists, and the second is figuring out what that antigen is. As an analogy, a bug can be
34.
by hirenj 2y ago
This paper is going in the hall of fame as being at the intersection of all my interests - mucus-like secretions, bio-adhesion, LEGO bricks, sugars and Galectins. Also nice that they cite one of the tools I made to predict glycosylation!
35.
by hirenj 2y ago
I read a great piece from Michael Bronstein about this very topic earlier this year. https://towardsdatascience.com/the-road-to-biology-2-0-will-... I think an important point raised here is the distinction between good dat
36.
by hirenj 2y ago
The PTM situation is a bit worse actually. First, of all the PTMs, high mannose N-glycans can be recapitulated (with the right knockouts). It’s the complex/hybrid that are completely missing. Second, the O-glycans are completely differ
37.
by hirenj 2y ago
This is my favourite bit of research regarding the grandmother effect - linking pathogen evasion to neuroprotective activities in old age, all at the molecular level, in an evolutionary context. https://pubmed.ncbi.nlm.nih.gov&#x
38.
by hirenj 2y ago
I actually am beginning to worry about this from a scientific publishing point of view. Yeah I know there’s editorial board meetings where articles are discussed for publication, but given that the content is being pushed out increasingly
39.
by hirenj 3y ago
These results are both interesting and unsurprising at the same time. Firstly unsurprising as the COG proteins are already well known to be important in animals, linked to a whole family of diseases, the congenital disorders of glycosylatio
40.
by hirenj 3y ago
I had a go at something like this when my kids were born. We were after names that could be pronounced in both Danish and Gujarati. After grabbing name lists from various websites, I generated phonetic translations of each name, and then lo
41.
by hirenj 3y ago
If anyone is wondering, this looks a bit like a syndromic set of phenotypes resulting from the mutation(s) in DHDDS. The mutations are hitting a really bad part in the glycosylation pathways, where I can imagine impacts on a massive number
42.
by hirenj 3y ago
NDST1 is a bifunctional sulfotransferase and de-acetylase. It’s a gatekeeper enzyme (well as much as it can gatekeep with other isoenzymes), that catalyses a sulfation on heparan sulfate (HS) chains. HS makes up a big chunk of the extracell
43.
by hirenj 3y ago
NDST1 is a funny one in the list. In principle it shouldn’t be out in circulation, so it’s probably a sign that actually what you are seeing is a dysregulation in activity of SPPL3 in shedding of this enzyme from the Golgi. More on reflecti
44.
by hirenj 3y ago
I’d be a little skeptical about spraying in a bunch of heparin and hoping it binds enough of the spike protein. This whole idea is predicated on the binding of heparin (a sulfated polysaccharide) to the spike. It’s known to be a co-receptor
45.
by hirenj 3y ago
As far as I know, there’s no receptor for GAGs on cells to mediate their uptake specifically. Usually they hitchhike on some other protein that has a specific receptor/co-receptor. Heparin is actually a sulfated polysaccharide, and not
46.
by hirenj 3y ago
Here’s a relevant thread on Twitter announcing a dataset of glucose measurements for healthy people. https://twitter.com/segal_eran/status/1649061705115115521?s=... The data lives here: http://humanphen
47.
by hirenj 4y ago
I mean if you want to go down the path of indiscriminately competitively binding Siglecs, I would read up about how NeuGc (which is found on meats) gets incorporated on our cells. Of course then you might end up in trouble with inflammatio
48.
by hirenj 4y ago
The receptors have these floppy loops which are great for bending into the right conformation to recognise different things. It turns out that if they have a few aromatic residues they just happen to recognise carbon nanotubes. It’s unlikel
49.
by hirenj 4y ago
Siglecs are SUPER important immune receptors that normally antagonise or induce tolerance in the immune system. Normally they recognise different sialic acids (e.g., the same ones recognised by hemaglutinin in influenza) and depending on th
50.
by hirenj 4y ago
I've been using the secure version of this knot for a few years now, and I've been entirely satisfied with how it holds up in the real world! https://www.fieggen.com/shoelace/secureknot.htm
51.
by hirenj 4y ago
The immune system needs to sample and test whatever is in the cerebrospinal fluid so that it knows when to activate.
52.
by hirenj 4y ago
He’s at my department at the Uni (well up until he retired), and the crazy thing is he’s been employed at the Uni for his whole adult life, since starting as a student helper at around 18.
53.
by hirenj 4y ago
I have been wondering if a better representation of a cell would actually be a large centralised message “queue”, which represents the state of the cell somehow (one entry for each metabolite molecule, or for each proteoform). The enzymes&#
54.
by hirenj 4y ago
Wow, this is a really nice little tool! I usually end up manually traversing Wiki entries to get to this info, so it’s a great shortcut!
55.
by hirenj 4y ago
A specific example would describe Bertozzi's work - where sugars with a chemical "handle" are installed on to the cell surface. You can then click something like a fluorophore onto the sugars with handles to figure out where
56.
by hirenj 4y ago
I've been using a library to knit Rmarkdown files to OneNote API compatible HTML ( https://github.com/CopenhagenCenterForGlycomics/knoter ), which lets me output PDF figures (that I can download to go into Illustrat
57.
by hirenj 4y ago
So what they’ve got is a bunch of barcoded synthetic peptides, which they use to assay for protease activity (is there even enough specificity information for each protease?). Based on the signature of activity they fit some model to tell o
58.
by hirenj 4y ago
Host protease activity classifies pneumonia etiology. Anahar et al. (2022), PNAS https://www.pnas.org/doi/10.1073/pnas.2121778119
59.
by hirenj 4y ago
If there’s a connection, it might be via hyaluronan, another glycan polymer, which is abundant in the vitreous humor in the eye. I don’t know much about how it’s regulated. Generally, I don’t think we know enough about how metabolite levels
60.
by hirenj 4y ago
Glucosamine is both a precursor metabolite and major component of complex carbohydrates in the cell. Glucosamine (GlcN) gets acetylated to form GlcNAc, which is found in pretty much all the complex carbohydrate types in humans. It’s also t

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