Lightnews — Scholar-powered news

Jamie Heather

@jamieheather.bsky.social

2.4K followers 1.7K following 170 posts

🇬🇧 immunulogist in 🇺🇸 | instructor @ MGH/HMS | TCRs and pMHC Technically a James | ʤeɪmi hɛðə˞ | he/him @jamimmunology in the old place papers, tools, & 3d printed labware here: https://jamieheather.github.io/

jamieheather.github.io

Posts Media Videos Starter Packs

Pinned

Jamie Heather @jamieheather.bsky.social · Sep 1

I've got a PSA to the T cell receptor researchers of #immunosky to let you know about a new paper we've just got out: doi.org/10.1016/j.im...

This covers how our field is handling the sets of germline #TCR genes used in our research. Maybe not the most glamorous topic, but it’s kind of a big deal…

A screenshot of the old style '10 PM, do you know where your children are?' PSA poster, with the 'children are?' scribbled out and 'TCR germline gene reference comes from?' crudely pasted over the top.

1 7 14

Reposted by Jamie Heather

Alan McNally @alanmcn1.bsky.social · 1d

And in the process destroying UK HE

Times Higher Education (THE) @timeshighered.bsky.social · 1d

Tory leader Kemi Badenoch is expected to announce plans to cut the number of UK university places by about 100,000 annually by reintroducing student number controls, reports Patrick Jack #edusky
https://www.timeshighereducation.com/news/badenochs-number-caps-plan-would-cut-100000-university-places

1 2 3

Jamie Heather @jamieheather.bsky.social · 6d

Top tier lab trickery here, delightfully clever approach

Victor Tatarskiy @greenrat.bsky.social · 6d

Neat trick if you polycolonal ab's suck. Incubate them with fixed cells with a KO of your protein of interest, then spin. Protocol here: www.med.upenn.edu/markslab/ass...
I was amazed how well it worked on first try (I'm sure that I can completely eliminate unspecific bands)
#WesternBlot #cellsky

On the left - western blot of B16F10 cells wt and KO for CDK8. Our in house produced antibodies give a lot of unspecific bands. On the right same probes with antibodies preincubated with fixed CDK8 KO cells - there is a specific band and faint unspecific bands, which can be probably eliminated with increase of amount of KO cells.

1 5

Jamie Heather @jamieheather.bsky.social · 6d

Pearl bones for the hot new look 2035

Reposted by Jamie Heather

Prof Christina Pagel @chrischirp.bsky.social · 10d

Just fuck off with this. How about start the conversation by highlighting how much immigrants contribute to the UK - not least by propping up the NHS and social care system!

Also - forced volunteering is not volunteering, it's unpaid labour.

250 1.4K 4.9K

Reposted by Jamie Heather

Jeremy Berg @jeremymberg.bsky.social · 9d

When I was at NIH and shutdowns loomed, it was discovered that the administration was planning to shut down PubMed. The head of NCBI called the powers that be and pointed out that this would threaten patient safety

Who knows what will happen now

Just in case, remember Euruope-PMC
(europepmc.org )

a cartoon of donald trump with the words be prepared above him

ALT: a cartoon of donald trump with the words be prepared above him

media.tenor.com

8 91 170

Jamie Heather @jamieheather.bsky.social · 15d

Took my kid to a science festival at the weekend, she was absolutely over the moon to do a ‘real experiment’ extracting DNA (from some blueberries), just like her dad.

She’s going to be absolutely devastated when I sit her down and explain how rubbish her absorbance ratios are.

On the left there's a photo of a 1.5 ml Eppendorf tube with ~500 ul of pinkish liquid. On the right there's a photo of a nanodrop results screen, with an admittedly decent DNA concentration (~200 ng/ul) and some garbage ratios (260/280 = 0.95, 260/230 = 0.14).

3 2 46

Jamie Heather @jamieheather.bsky.social · 16d

I'm going to solve all my problems by only buying winning lottery tickets

1 1 4

Reposted by Jamie Heather

Adrian Liston @labliston.bsky.social · 19d

For our #flowcytometry peeps, would you like to have a single fix/perm protocol that is optimised for everything? One that preserves fluorophores while allowing simultaneous TF and cytokine staining? How about 100-fold cheaper?

You got it:
currentprotocols.onlinelibrary.wiley.com/doi/10.1002/...

currentprotocols.onlinelibrary.wiley.com

8 69 150

Reposted by Jamie Heather

BK. Titanji @boghuma.bsky.social · 22d

We have 2 vaccines that prevent cancer, the HBV vaccine that prevents hepatitis B related liver cancer and the HPV vaccine that prevents cervical cancer and other HPV associated cancers.
On Thursday, RFK.JR's ACIP will attack one of these vaccines (HBV) and restrict access to it.
Let that sink in!

20 250 590

Jamie Heather @jamieheather.bsky.social · 21d

The amount of autocorrect-produced gnomes (genome) and gremlins (germline) that manage to survive into my penultimate drafts of things is terrifyingly high.

Reposted by Jamie Heather

🌈Dr. Franken Frizzle 🎃 @swilua.bsky.social · 22d

you don’t understand bro, if we didn’t lie, no one would buy our product 😩

Consider the implications if ChatGPT started saying "I don't know" to even 30% of queries
- a conservative estimate based on the paper's analysis of factual uncertainty in training data. Users accustomed to receiving confident answers to virtually any question would likely abandon such systems rapidly.

53 1K 2.9K

Jamie Heather @jamieheather.bsky.social · 22d

Blimey.

Reminds me of this post I saw yesterday: www.reddit.com/r/mildlyinfu...

From the mildlyinfuriating community on Reddit: My 9 year old son's Math teacher marked this wrong

Explore this post and more from the mildlyinfuriating community

www.reddit.com

1 1

Jamie Heather @jamieheather.bsky.social · 23d

Slack may work, but I've DM'd you some emails

Jamie Heather @jamieheather.bsky.social · 23d

I bet the AIRR-C ML working group would be interested in talking about this, having arranged similar competitions for other TCR/BCR prediction stuff.

(I don't have an in silico TCR design tool horse in this race, but very invested in scaling TCR validation efforts!)

1 1

Reposted by Jamie Heather

Alex Rubinsteyn @alexr.bsky.social · 23d

Thinking about running a TCR generation contest:

We give you a set of pMHCs without known cognate TCRs

You give us your top k in silico TCR designs

We test them for cytotoxicity as TCR-Ts against cancer cells that are validated to express the target

Who’s in?

1 2 5

Jamie Heather @jamieheather.bsky.social · 23d

The drosophila Dscam1 gene presumably evolved specifically to mess with bioinformaticians

PLOS Biology @plosbiology.org · 23d

The #Drosophila Dscam1 gene generates 10000s of isoforms, but only a small fraction supports neuronal functions. This study shows that #fitness & #immunity are the likely primary evolutionary drivers of Dscam1 isoform diversity in #arthropods @plosbiology.org 🧪 plos.io/4gp8cWd

Top: Dscam1 gene structure and isoform diversity in pancrustacean species. Top: Schematic diagrams of Drosophila melanogaster Dscam1 gene and protein structure. The variable exons or domains are shown in color, while the constant exons or domains are shown in gray. Middle: Phylogenetic distribution of Dscam1 isoform diversity. A phylogenetic tree of Pancrustacean species is shown in the lower panel. The upper panel shows distribution of the number of exons in variable exon 4, exon 6, or exon 9 clusters in Pancrustacean species, with variable exon clusters shown in different colors. The middle panel shows distribution of the number of potential ectodomains diversity, where species with a special number of diversities are highlighted. Bottom: Reducing the Dscam1 diversity affects adult survival upon Beauveria bassiana infection. Survival curves after Triton or B. bassiana infection for wild-type and exon 4 (left), exon 6 (middle), and exon 9 (right) mutants are shown, respectively. The Triton groups (control) are represented by solid lines, while the B. bassiana groups are represented by dashed lines.

1 7

Reposted by Jamie Heather

Heng Li @lh3lh3.bsky.social · 23d

And learn what fully AI-generated websites look like. Avoid them, as they are more likely to be scam.

1 3 9

Reposted by Jamie Heather

Ewan Birney @ewanbirney.bsky.social · 24d

Bioinformaticians / computational biologists take note - know where you should take your OS tool chain from and do not introduce backdoors.

James Bonfield @jbonfield.bsky.social · 24d

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.

Ie: it's not us (Samtools team)! Be warned

3 19 34

Jamie Heather @jamieheather.bsky.social · 23d

Exactly my fear - especially as the first ELN I tried back in my PhD got similarly acquired and I lost a bunch of records!

Jamie Heather @jamieheather.bsky.social · Sep 8

This is a cool story that I've watched with great interest - making big steps in the field of de novo TCR generation! Great work @dkarthikey1.bsky.social / @benjamingvincent.bsky.social / @alexr.bsky.social et al

Waggoner Lab @labwaggoner.bsky.social · Sep 8

Conditional generation of real antigen-specific T cell receptor sequences @natmachintell.nature.com
www.nature.com/articles/s42...

2 4 10

Reposted by Jamie Heather

Adrian Liston @labliston.bsky.social · Sep 3

🧵How to write and manage your first research budgets

The point of funding is to convert it into quality research. A well-spent research budget should fund the idea it was raised on, plus revision experiments, plus preliminary data for the next grant. So you need to spend, while avoiding waste.

3 37 110

Reposted by Jamie Heather

Elizabeth Jacobs, PhD @elizabethjacobs.bsky.social · Sep 3

It doesn’t matter if you feed your kids organic foods, MAHA moms.

It doesn’t matter if you lift every day, bro.

It doesn’t matter how many supplements you consume.

When polio, diphtheria, measles, mumps, and whooping cough come a calling, all that matters is if you are vaccinated or not.

160 1.8K 6K

Jamie Heather @jamieheather.bsky.social · Sep 3

A nice reminder that even the most fundamental 'rules' of biology are basically just strong suggestions

Nature @nature.com · Sep 3

A common type of ant in Europe breaks a fundamental rule in biology: its queens can produce male offspring that are a whole different species

go.nature.com/4mOb5T9

‘Almost unimaginable’: these ants are different species but share a mother

Ant queens of one species clone ants of another to create hybrid workers that do their bidding.

go.nature.com

3 16 37

Jamie Heather @jamieheather.bsky.social · Sep 2

Is this a new meaning of woke? I can't see how that relates to being aware of social or racial justice issues.

(Also, is atherosclerosis having an autoimmune component controversial? I thought there was a bunch of known autoantigens in the mix)

Jamie Heather @jamieheather.bsky.social · Sep 2

How is this 'woke thinking'?