Also… no actually that’s it. We spend our whole time on this. Go write a comment on the proposed rule change, contact your representatives. This is it folks - American science doesn’t recover from this, at least not for a long time.

Links

• The paper (that we didn’t end up talking about): Gut microbiota promotes immune tolerance at the maternal-fetal interface

• The best summary of the new rule and what to do about it, from a former NIH insider

• A tool from the Federation of American Societies for Experimental Biology (FASEB) to help you craft an original comment with the help of AI, if you’re into that sort of thing. But don’t be lazy - make it personal!

• A guide from Stand Up For Science on how to writing a comment opposing the rule change

• NIH reporter, where you can look up everything you could ever want to know about funded grants

• If you are a professor, sign up for the American Union of University Professors

Also, we’re thick with analogies - neutrophils are by turns mobs, berserker warriors, or agents of a fascist state.

Links

• The paper: Neutrophils self-limit swarming to contain bacterial growth in vivo

• Previous episode about neutrophils and NETs: Episode 5 - When the carnies roll in

• National Geographic documentary: The Secret History of Bees

• Atlantic article about a dumb new conspiracy theory about scientists dying

Plus, Matt thinks it’s funny they’re taking tissue slices though fecal pellets and Kevin routinely says “microvillus” when he means “villus”, and pretends to know the anatomy of the intestines when he clearly doesn’t, despite being an Assistant Professor in the GI division at a hospital.

Links

• The paper - Spatial transcriptomics maps host–gut microbiome biogeography at high resolution

• The technologies - 10x Visium, StereoSeq, and CosMx

• Wikipedia - human digestive system

So should everyone rush to drip LPS and ovalbumin into their noses? Mmmm… not so fast.

Plus, we kvetch about new NIH policies for the politburo-tization of grant review. A new era of American Lysenkoism is here!

Links

• The paper: Mucosal vaccination in mice provides protection from diverse respiratory threats

• The new NIH policy on grant review - doesn’t sound so bad, but you need to read it in context.

In this paper, Matt and Kevin discuss a new paper identifying and describing a new kind of macrophage (or is it a dendritic cell?) they call “adenophages”. The cells live in salivary and other exocrine glands, and are really good at phagocytosis and antigen presentation. But they also help squeeze out spit?

Links

• The Paper: Adenophages are an atypical macrophage population in exocrine glands sustained by ILC2-derived GM-CSF

• Wikipedia article on salivary glands

In this episode, Matt and Kevin look back and look ahead. What (if anything) has Audiommunity accomplished? What (if anything) should we do going forward?

Plus, some solid rants about the importance of science, science communication, and government funding.

Links

• IMMGEN - The immunological genome

• Vanavar Bush

• The Harvard Plan Podcast

• Audiommunity episode about Stand Up for Science

It’s a long one, and we get snarky in this one folks! Buckle up!

Creating random vectors

In this episode, we spend a fair amount of time talking about the statistical implications of these methods, and Kevin says things like

if I generated a bunch of random vectors, we would still see the same thing.

But is that really true? Kevin wrote some code to find out! You can find the link to the actual code below if that’s your jam, but to give a brief summary, Kevin

1. Generated a dataset with approximately the same proportion of APOE genotypes and neurodegeneration pattern as the authors have in table S1

2. Generated a bunch of random values drawn from a normal distribution to match the number of proteins found in the SomaScan screen

3. Performed a mutual information screen and PCA as described in the paper

4. Generated a couple of random lists of proteins to test the GSEA analysis described in the paper.

Here’s what he saw:

So it’s not literally true that completely random data will segregate based on this analysis - mea culpa. But if you add even a tiny bit of underlying correlation structure (some directional noise on 1% of samples), we see the following:

Which is much closer to what it looks like in the paper. We discuss these results and the code at around minute 68, and the link to the code is below.

Links

• The Paper - APOE ε4 carriers share immune-related proteomic changes across neurodegenerative diseases

• Wikipedia on prion disease

• Code to replicate Kevin’s random number generation

In this episode, Matt and Kevin are joined by Nicole Ackermans to discuss her recent review paper tracing human thoughts about headbutting from 10,000 BCE to the present day. How are animals like bighorn sheep and woodpeckers protected from brain injury? Actually, wait... are they protected from brain injury?

It’s a wonderful romp of a paper, but with some serious undertones, since misinformation about animal biology is being commercialized and promoted to make people feel better about gladiatorial sports like football.

Links

• The Paper - A history of thought on headbutting animals

• Ologies episode with Joy Reidenberg: https://www.alieward.com/ologies/functional-morphology

• Ologies episode with Nicole: https://www.alieward.com/ologies/headbutts

• The birds aren’t real

• The actual ratio of microbes to human cells

Also, Kevin had to deal with a surprising number of attempts by the auto-transcription service of Riverside.fm to spell out “GATA3”:

• “got a three”

• “data three”

• “God of Three” (my personal favorite)

Can you guess what “tear eggs” are? What about “raw gamete”? “Iacocque”?

Links

• The paper: Neonatal regulatory T cells persist into adulthood across multiple tissues with high enrichment in the skin

• Audiommunity episode about fate-mapping B-cells in lymph nodes

• Audiommunity episode about “re-wilded” mice

Against all expectations, there’s RNA attached to the surface of cells. Why? Who knows! But it almost certainly has implications for the immune system. As Matt and Kevin discuss in this episode, it turns out that cells add sugars to these RNAs (glycosylation) to hide them from the innate immune system, especially during apoptosis.

Links

• The Paper: RNA N-glycosylation enables immune evasion and homeostatic efferocytosis

• Previous Audiommunity episode about Lupus

• Previous Audiommunity epiode about innate immunity

• Previous Audiommunity episode about cGAS

But most of this conversation is about the wildly complicated molecular biology they had to use in 1989.

Links

• The Paper: The V(D)J recombinase activating gene, RAG-1

• Previous audiommunity episode on VDJ recombination: Antibodies and Infantry

• TWiV Episode 100 - podcast interviewing Baltimore about his life and career

• David Baltimore Nobel Lecture

We now have an email address! Send your questions and comments to contact@auduommunity.org!

Matt and Kevin discuss a new paper about the “subfornical organ” which (once again) undermines the idea of immune privilege, and also points to an interesting evolutionary question: why would T-cells migrating from fat to the brain affect hunger response?

Also, Matt tries to speak through virus-mediated destruction of his trachea, and Kevin keeps trying to make Buddhist immunology a thing.

Links

• The paper: The subfornical organ is a nucleus for gut-derived T-cells that regulate behavior

• Wikipedia entry on interoception

• Audiommunity episode 17 about the then-surprising notion of lymphatics in the brain

• Audiommunity episode 19 about helminths and brain autoimmunity

In this episode Kate and Kevin discuss a new paper showing that anti-phage defenses of bacteria can provide really broad protection if they just get expressed at a higher level. So why don’t they? Trade-offs of course - always with the evolutionary trade-offs.

Links

• The paper: Expression level of anti-phage defence systems controls a trade-off between protection range and autoimmunity

• Portal protein review in Annual Reviews Virology

We now have an email address! Send your questions and comments to contact@auduommunity.org!

Matt and Kevin discuss a new paper about the “subfornical organ” which (once again) undermines the idea of immune privilege, and also points to an interesting evolutionary question: why would T-cells migrating from fat to the brain affect hunger response?

Also, Matt tries to speak through virus-mediated destruction of his trachea, and Kevin keeps trying to make Buddhist immunology a thing.

Links

• The paper: The subfornical organ is a nucleus for gut-derived T-cells that regulate behavior

• Wikipedia entry on interoception

• Audiommunity episode 17 about the then-surprising notion of lymphatics in the brain

• Audiommunity episode 19 about helminths and brain autoimmunity

Also, Kevin uses phrases like “hypercube” and “system of differential equations” as if he knows what they mean.

Links

• The paper - Modeling Reemergence of Vaccine-Eliminated Infectious Diseases Under Declining Vaccination in the US

• What’s in a vaccine?

• WHO information on vaccination effectiveness

• Our world in data - Vaccines

You can now find and subscribe to us on youtube!

Things are bleak in American academia here in 2025. Here, Matt and Kevin speak with Abbie Smith, an assistant professor at Emory’s Hope Clinic, where she researches HIV and oversees clinical trials assessing the prevention and treatment of people with HIV. As you might imagine, the current regime isn’t super happy about her work.

No paper in this episode, just some honest kvetching and an inspiring speech from Abbie about what we can aspire to.

Links

• Hope clinic at Emory

• Abbie Smith and the last time she was on Audiommunity

• Science homecoming

Also, for future reference, apparently riverside.fm’s bot transcription cannot distinguish Tregs from T-rex.

Links

• The paper

• Yes she will, Precious, she will get the hose

In this episode Matt and Kevin discuss the way that the immune system changes over the course of the menstrual cycle, and the implications this has for susceptibility to HIV infection.

Also, this is one of the more ranty episodes we’ve had in a while, prepare yourself!

Links

• The paper - Proinflammatory oscillations over the menstrual cycle drives bystander CD4 T cell recruitment and SHIV susceptibility from vaginal challenge

• Previous episode on the immune system during pregnancy - episode 19

• Journal involving the new director of the NIH about funding... “reforms”

Also, Kevin gets philosophical, and Matt compares the immune system to gardening.

Links

• The paper - Colonic goblet cell-associated antigen passages mediate physiologic and beneficial translocation of live gut bacteria in preweaning mice

• Brain lymphatics paper and audiommunity episode

• Kevin finally published that blog post about models and Buddhism - also started a substack

In this episode, we’re talking about the OAS-RNaseL virus-sensing pathway, and the passage of its product, 2,5-oligoadenylate, through gap junctions.

Also in this episode, Matt relives his gel-running trauma, Kate remembers getting scooped, and Kevin still can’t figure out his terrible, horrible, no good, very bad internet.

Links

• The paper - OAS cross-activates RNase L intercellularly through cell-to-cell transfer of 2-5A to spread innate immunity

• The beautiful cGAS and cGAMP papers Kate is constantly referencing.