I have seen this first hand when it comes to my dad's company. He has always thought me that to grow you need to take risks.

This shows the impact of man-made disasters and even natural disasters. One question is, is there a possibility for businesses to prepare for natural disasters that they cannot control or won't be aware of until its too late?

This quote highlights the role that businesses play in everyday life. This quote tells us that we are surrounded by businesses everywhere, not only the things we buy come from businesses, but things such as the medical industry is also considered a business.

Thank you for posting the schedule. It makes it easy to plan ahead and compare what I have to do with other classes!

I enjoy that everything is through canvas because then 1. we don't need to buy a textbook and it makes it easier to find everything!

This also makes since that you say you will respond within 48 hours because you give us so much time to do our work we shouldn't expect you to respond right away!

I think that the grace period I nice in case you have a class and you forgot to submit something.

Is this dictated by you (the professor) or by us? And is something like a book in free verse a book that we would be able to pick? It seems extremely interesting if we are all able to pick our own 4 books to help guide us through this class. I am also very excited for the poetry slam, and whatever that entails!

This comment is so joyful and hopeful, as pushing ourselves is so innately human. I love to be pushed and told that I will be growing.

This place has been really helpful in the past! Especially when I had writers block and didn't know how to make my writing even better, or which direction to take it!

I think this will help us break out of our shells and help us get more comfortable with different writing styles in poetry! Sometimes you learn one way to do it and it becomes a default, this will help expand our knowledge and help us be even more creative.

This makes me a little more relaxed about this class so I can focus more on being creative and being open to trying new things, with out the fear of failing.

REQUIREMENTS

Soft Skill

Soft Skill

Qualifications

Qualifications

Qualifications

Soft Skill

Qualifications

Qualifications

Almost every and any surplus of animals or materials was exploited by white newcomers.

U.S. went so far as to oversee their OWN promises of peace to be rid of Native Americans

Is this used in the procedure? I don't see it. Maybe delete.

Materials list mentions a "shape sheet" (which I authored easily in Google Slides). Not sure what a "three shape object" is... maybe just use the shape sheet.

Materials list says "sugar", but the procedure says "salt".

This information I did find shocking. You would think our AI systems would be neutral as possible. So if our AI systems are bias what information would you say is "accurate" for use? We know that AI is used worldwide. So, as AI continues to grow and become more advanced, how will you differentiate between accurate & inaccurate information. Especially when AI begins being used in our workforces.

Here is an example annotation!

In this source, the speaker is pressuring the accused by saying, “They accuse you of hurting them, & if you think it is not unwillingly but by designe, you must look upon them as murderers.” What I see here is an early example of interrogation tactics that are still recognizable today—getting people to confess to things they may not have done. The logic being pushed is that if the accused did not hurt the children by accident, then it had to be intentional, and therefore she is the one guilty. The trap in the statement is that it flips the blame onto the children, making them seem like the true “murderers,” so in the accused’s eyes anything she might have done to them would appear justifiable. It connects to Context, since understanding the fear of witchcraft and the religious panic in 1692 helps explain why this kind of statement would carry so much weight in Salem.

My observation is as follows; That "upon the motion of her body fits followed...abundantly and very frequently" is that movement from her (the nurse), would cause bouts of affliction to the people accusing her of hurting them/witchcraft. Interpretation of this is, how back then, seeing this in person, live, would cause anyone being accused of the occult and power of people to be believed to do so if any sort of movement from them (witches) cause the accused to act that way. A linkage of sorts, construing her movement to their fits.

Observation: People in the room say familiar spirits come near Goody Nurse during questioning. Multiple people repeat the claim. Interpretation: The Assembly treats these reports as real signs of harm.  Context:  Shared belief in familiar spirits sets how people read the scene. Belief explains why these reports count. Why it matters: Shows why faith based claims carry weight during the examination, because of how faith based the people are

Observation: One of the afflicted people reports harm this morning Interpretation: The statement accuses Goody Nurse of beating the speaker. Causality: One accusation leads to harmful judgment.  This is important, as it shows what counts as proof during the examination.

Observation: Mr Harthorn suggests temptation even if Goody Nurse thinks she is not a witch. The question starts soft, then pushes towards her being guilty Interpretation: The wording steers answers toward guilt. Trying to trap the Nurse into a confession  Causality: Questioning attempts to lead, admission, or misstep. This matters as it shows pressure inside the questioning. And how you can guide answers to the path you want them on.

Observation: Mr Tho: Putman’s wife links Goody Nurse to the Devil and to urging her temptation. Interpretation: The Assembly reads harm through a shared religious point of view. Context: Their belief frames how the charge is understood. This matters, as it shows and explains that unseen claims and faith count as evidence.

Observation: Goody Nurse is not feeling well and the judge believes it's witch craft or demons based on what others have been saying about her. She is an old woman and is just sick from age.

Interpretation: Her illness cannot be seen by the naked eye so it is hard for those to understand why she is so sick. She's been standing in front of everyone with no emotions yet she claims to be sick.

Connection: When someone accuses you of witchcraft in Salem, it was extremely hard to convince anyone that you are not. They took even a simple illness that you have and thought it was from a demon. The judge didn't believe Goody Nurse.

Complexity: I think about how hard it must have been to live in Salem during the 1600's. You could be doing anything and all of a sudden you are called a witch. It was much harder for woman than a man. Even being sick people will think you are a witch. Goody Nurse could do nothing but deny everything and keep her faith in God known. The voices of everyone else and the actions of the young girls were more believable to the judge than anything she had to say.

Observation: The accused, Goody Nurse used to be a professor in the community making her well known throughout the village. She isn't showing any emotion during her trial while everyone else is crying.

Interpretation: The way the accusers and the crowd watching are acting is sending a more powerful reaction to the judge. It's hard for him to find her innocent because of her lack in emotion to being convicted of abusing two young girls.

Connection: What one see's with their eyes is more powerful than what one says. if you act like a victim, then the more people are going to believe you. People in Salem only knew the truth in the Bible so if anyone acted out in a way the Lord would condemn evil, they were looked at as witches or being posessed by the devil because if you are living a holy life, how could you commit such an act of violence?

Complexity: When you think of the early 1600's people didn't know much except what they are taught. This document shows us that people only knew how to live their lives as what it say's in the bible. No real evidence is needed as long as enough people agree with you.

Observation: The person in charge of finding Goody Nurse guilty or not guilty is trying to understand how she claims her innocents when two grown people have come forward now.

Interpretation: No matter how innocent you are, the more people that accuse you, the less innocent you look. Not only are the two girls accusing Goody Nurse, two adults have joined them.

Connection: Goody Nurse's trial is based on whose account of a situation is true or false. During this time period of 1691, there is no way to show proof of a crime, only what people have seen or heard. The people in Salem dedicate their lives to their worship of God and live their life by the rules of Christianity. Goody Nurse knows only God can see her innocence.

Complexity: Showing your love and faith in God was a way to prove your innocence when someone accused you of a crime. God cannot save you if many people are accusing you, and all you have on your side is just yourself.

Observation: The person in charge of finding Goody Nurse guilty or not guilty is trying to understand how she claims her innocents when two grown people have come forward now.

Interpretation: No matter how innocent you are, the more people that accuse you, the less innocent you look. Not only are the two girls accusing Goody Nurse, two adults have joined them.

Connection: Goody Nurse's trial is based on whose account of a situation is true or false. During this time period of 1691, there is no way to show proof of a crime, only what people have seen or heard. The people in Salem dedicate their lives to their worship of God and live their life by the rules of Christianity. Goody Nurse knows only God can see her innocence.

Complexity: Showing your love and faith in God was a way to prove your innocence when someone accused you of a crime. God cannot save you if many people are accusing you, and all you have on your side is just yourself.

Observation: Goody nurse is on trial because the two girls are saying she hurt them. The girls cried while accusing Goody nurse.

Interpretation: Regardless if it is true or false, you can take someone to be accused no matter the crime. You have the right to defend yourself in front of your accusers.

Connection: The source tells us Goody Nurse is accused of hurting the girls by means of witchcraft. The only evidence they have is the two girls words against Good Nurse's words. The girls are crying and acting as if they are in such pain from the violence Goody put them through. Goody stands firm she did not touch the girls and her calm demeanor strikes everyone as odd as the girls can't help but cry.

Complexity: During this time in Salem, people lived their lives as Christians according to the bible. It seems the person judging Goody Nurse cares more about her faith in God and if she fell prey to demons which caused her to harm the two young girls. Goody Nurse denied all these claims with a stoic face that was opposite from what the girls portrayed. Your actions as the accuser and the accused seem more validating than your own words.

Observation: The tone of the speaker here is accusatory. The speaker is trying to get Rebecca Nurse to confess to a crime she claimed not to have committed. My interpretation is that the speaker is trying to be emotionally appealing by telling her to "hear them accuse you" so she can feel guilty and confess to meddling with witchcraft.

This statement is interesting. Knowing how much social media/ technology influence us. I do believe that is where most of our generations implicit bias stems from. We scrolled the social media so often. We see that many people live lifestyles that we would like to have. Some individuals become so heavily influenced that they judge other for not having certain items, or looking a certain way. We allow what we see on a day to day basis determine how we view others before meeting that individuals.

This quote supports the main point in many ways. Many individuals say "we don't judge a book by the cover", not realizing they do it every day. Everyday you walk out of your front door individuals will judge you before speaking to you. Many factors stem from their beliefs/ upbringings. They will attempt to paint a picture of you that is not always accurate to your story. You can be the smartest person in the world with many qualifications. But many people will not take a change on you, because of implicit bias.

Will we see our grade in brightspace and the modules there also?

Related to the pooling operator, I think large gains may come from the use of 1) edge weights in your GCN layers so that not all neighbors are treated equally by the message passing mechanism, and 2) alternative MPNN layer types, including use of the graph attention mechanism (i.e. GAT) or graph transformers, which use the attention mechanism to learn which neighbors are more "important." I suspect that even with simple mean-pooling, these alternative layer types will be much more performant and generalizable (e.g. from CRBD to BiSSE). In effect the GCN layers (particularly without using edge weights) is more akin to the CRBD in that it assumes uniform, homogeneous contribution by all neighbors to feature updates.

Again, I think this is a case for exploring the use of more general pooling operators, such as EdgePooling, etc, that might capture the relevant signal, but without imposing such rigid inductive biases on the architecture that could prove harmful to more general application.

Have you considered other pooling layers other than mean-pooling? For instance existing pooling operators like EdgePooling might confer similar benefits by retaining the temporal signal through iterative edge contraction. https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.nn.pool.EdgePooling.html#torch_geometric.nn.pool.EdgePooling

Related to the above (regarding the number of GNN layers used), have you considered/looked into using either gate residual connections, or using something like jumping knowledge (https://arxiv.org/abs/1806.03536) between layers to mitigate oversmoothing in deeper networks which GNNs tend to be prone to? This could be another simple modification with outsized benefits.

I presume you're using the "base" GCN layer here? If so I'd be clear about this, since unlike the CNN and MLP, there is a massive diversity of MPNN layer types - its worth being very explicit about what you're using, since their choice could have massive impacts on the performance of these architectures!

Is there a reason you chose not to include edge weights/attributes corresponding to each respective branch length? I suspect this would be quite useful/informative for providing additional context to the message passing layers and could boost performance further. Otherwise, each neighbor is assumed to contribute equally to feature updates, which is not something we innately suspect to be true.

True, but only necessarily when the prediction task is graph-level. This is not necessary for many other common GNN prediction tasks, including node or link prediction. This is a bit of a nitpick, but I think useful to distinguish since this architecture is so new to the field!

I know these details are present in the supplement, but here and for the other NNs, it could be useful to specify the number of layers used - particularly for the GNN, where this relates to the effective "diameter" of visibility or neighborhood size (i.e. how many hops away the message passing mechanism aggregates neighbor information).

The use of LM has indeed demonstrated a large dependency of getting an answer whether that is writing a paper or trying to solve a math problem. It's clear that the use of LM can cause a lack of brain development and understanding of a topic.

One of the key differences to keep in mind when utilizing AI is that it thinks and operates differently from humans. Intuition and the ability to read between the lines are among the major differences between humans and AI, and it becomes very easy to overlook something obvious for us but might be interpreted differently for AI and vice versa.

I find it interesting that with these systems, the more data collected/the greater the scope and demands are, creates a greater risk of inaccuracy.

People tend to try to find patterns, even when there are none

The impacts of Environmental Racism are very prevalent now. Historically, marginalized communities have been affected by unfair practices of real estate and redlining. The use of AI could be seen as adding fuel to the fire, especially when going outside of the US and looking at the impacts of the rise of AI against third world countries.

When dealing with AI we often forget that the computers does not have immediate access to the meaning of our words, different versions have evolved to reflect specific "meaning" back to us, but to the computer, language is just another form of symbols to communicate something. It is important to think about that as it becomes more present in our life.

If this piece is from 2021 I wonder how the LM training regiment and affects have changed.

It is important to remember that LMs are a reflection of human input, and therefore, human error. Our individual experiences create subconscious biases that make it impossible to deliver an unbiased LM system.

Really interesting idea that I've never thought about. I knew LMs are stitching together phrases from its training, but I didn't realize how much probability goes into a single LM prompt.

As an ENST major, I have understood the environmental impact of the use of LM and Generative AI models. While it can be impressive and convenient for our day to day use, there could be too much irreversible damage created, which will keep us stagnant in our progress for a more environmentally friendly future

Community accessibility is a huge issue for public goods. Just because a product or service is available and targeted for a specific group doesn't guarantee access and beneficial use.

LMs are indeed impressive, and come through whenever we seek their aid. However, knowing and understanding the implication which the counter factors have on us as humans, and the way the "wins" are even got to, is imperative to protecting our sense of being, and minds.

This is significant as it can cause issues for research. I have experienced this to be the case, where it has made up specific dates or even made up a specific event that never occured.

When I first read this, I started being curious about these Germanic tribes. Who were these people? What was their culture like before they had to flee from Attila the Hun? I also noticed the wording, “The city of Rome itself fell to the barbarians.” Why are these people who destroyed the city of Rome called “barbarians?” Where the “barbarians” the same Germanic tribes that escaped the Huns? I don’t know about others, but I personally find the term “barbarians” both vague and kind of insulting. But that's just a personal bias of mine.

Another thing I found interesting is that this population crisis occurred over 150,000 years ago. Our professor said we don’t fully understand how this population crisis happened, which makes it even more intriguing. Was it a plague that caused the population decline? Was it because of climate conditions or some other environmental impact? I just find this interesting to think about.

I find it interesting how our understanding of the agricultural revolution has changed over the years. We as humans tend to think about history, and really a lot of things, in a chronological order. We’ve learned over the years that it isn’t always the cause, especially in our understanding of pre-written eras.

This is interesting because it would also affect trade of crops.

In old ways of farming, it was common to see three plants next to each other. Often called the "3 sister" way of farming, Native Americans did it with different crops as well.

This reminds me of one thing about the agricultural industry that is still true to this day, there is always room for improvement and a possibility of a better way of doing something.

LLMs themselves are literal plaigiarism generators.

Jim, the machine has no perspective other than the one that is programmed / trained / tuned into it.

WHICH SCHOOLS JIM?! This feels like a broad and sweeping claim with no evidence cited.

What is being analyzed? What is being processed?

I am begging you to stop humanizing the LLM

NOOOO I thought you said look at social practices first, rather than technologies, omg Jim

JIM NOOOOOOOOO

How exactly DO stochastic parrots extend human capabilities?

Already this is a little weird because do calculators even do algebra? At least the ones generally available to students?

This establishes a public service role for government officials compared to the divine right of kings. The citizens of Virginia are responding to the unjust actions committed previously by the King acted as though he was above the law because he was a monarch and divinely appointed so. The VA Declaration of Rights ensures that no governing body that is established in VA will abuse their power in the way the King did.

eLife Assessment

This important study investigates how signals from the nervous system can influence the response to different food sources. To demonstrate the role of specific neuronal and intestinal regulators in sensing food quality and modulating digestion, the authors present evidence through a combination of genetic screening, RNA-seq analysis, and functional studies. These findings shed light on an adaptive strategy to integrate food perception with physiological responses, with a mix of solid and convincing evidence supporting the work.

Reviewer #1 (Public review):

Summary:

In this manuscript, Liu et al have tried to dissect the neural and molecular mechanisms that C. elegans use to avoid the digestion of harmful bacterial food. Liu et al show that C. elegans use ON-OFF state of AWC olfactory neurons to regulate the digestion of harmful gram-positive bacteria S. saprophyticus (SS). Authors show that when C. elegans are fed on SS food, AWC neurons switch to OFF fate, which prevents the digestion of S. saprophyticus, and this helps C. elegans avoid these harmful bacteria. Using genetic and transcriptional analysis as well as making use of previously published findings, Liu et al implicate p38 MAPK pathway (in particular, NSY-1, the C. elegans homolog of MAPKKK ASK1) and insulin signaling in this process.

Strengths:

The revised manuscript has improved significantly. The authors have addressed almost all the comments that I had in my initial review.

Weaknesses:

None.

Reviewer #2 (Public review):

Summary:

Using C. elegans as a model, the authors present an interesting story demonstrating a new regulatory connection between olfactory neurons and the digestive system. Mechanistically, they identified key factors (NSY-1, STR-130 et.al) in neurons, as well as critical 'signaling factors' (INS-23, DAF-2) that bridge different cells/tissues to execute the digestive shutdown induced by poor-quality food (Staphylococcus saprophyticus, SS).

Strengths:

The conclusions of this manuscript are mostly well supported by the experimental results shown.

Weaknesses:

The authors have done a nice job in addressing my comments.

Reviewer #3 (Public review):

Summary:

The study explores a molecular mechanism by which C. elegans detects low-quality food through neuron-digestive crosstalk, offering new insights into food quality control systems. Liu and colleagues demonstrated that NSY-1, expressed in AWC neurons, is a key regulator for sensing Staphylococcus saprophyticus (SS), inducing avoidance behavior and shutting down the digestive system via intestinal BCF-1. They further revealed that INS-23, an insulin peptide, interacts with the DAF-2 receptor in the gut to modulate SS digestion. The study uncovers a food quality control system connecting neural and intestinal responses, enabling C. elegans to adapt to environmental challenges.

Strengths:

The study employs a genetic screening approach to identify nsy-1 as a critical regulator in detecting food quality and initiating adaptive responses in C. elegans. The use of RNA-seq analysis is particularly noteworthy, as it reveals distinct regulatory pathways involved in food sensing (Figure 4) and digestion of Staphylococcus saprophyticus (Figure 5). The strategic application of both positive and negative data mining enhances the depth of analysis. Importantly, the discovery that C. elegans halts digestion in response to harmful food and employs avoidance behavior highlights a physiological adaptation mechanism.

Weaknesses:

Major weaknesses have been addressed.

Author response:

The following is the authors’ response to the original reviews.

Reviewer #1 (Public review):

Summary:

In this manuscript, Liu et al have tried to dissect the neural and molecular mechanisms that C. elegans use to avoid digestion of harmful bacterial food. Liu et al show that C. elegans use the ON-OFF state of AWC olfactory neurons to regulate the digestion of harmful gram-positive bacteria S. saprophyticus (SS). The authors show that when C. elegans are fed on SS food, AWC neurons switch to OFF fate which prevents digestion of S. saprophyticus and this helps C. elegans avoid these harmful bacteria. Using genetic and transcriptional analysis as well as making use of previously published findings, Liu et al implicate the p38 MAPK pathway (in particular, NSY-1, the C. elegans homolog of MAPKKK ASK1) and insulin signaling in this process.

Strengths:

The authors have used multiple approaches to test the hypothesis that they present in this manuscript.

Weaknesses:

Overall, I am not convinced that the authors have provided sufficient evidence to support the various components of their hypothesis. While they present data that loosely align with their hypothesis, they fail to consider alternative explanations and do not use rigorous approaches to strengthen their overall hypothesis. The selective picking of genes from the RNA sequencing data and forcing the data to fit the proposed hypothesis based on previously published findings, without exploring other approaches, indicates a lack of thoroughness and rigor. These critical shortcomings significantly diminish enthusiasm for the manuscript in its totality. In my opinion, this is the biggest weakness in this manuscript.

We appreciate the reviewer’s all the suggestions which help us to improve this paper. We now addressed reviewer’s comments at the section of “Reviewer #1 (Recommendations for the authors)”

Reviewer #2 (Public review):

Summary:

Using C. elegans as a model, the authors present an interesting story demonstrating a new regulatory connection between olfactory neurons and the digestive system.

Mechanistically, they identified key factors (NSY-1, STR-130 et.al) in neurons, as well as critical 'signaling factors' (INS-23, DAF-2) that bridge different cells/tissues to execute the digestive shutdown induced by poor-quality food (Staphylococcus saprophyticus, SS).

Strengths:

The conclusions of this manuscript are mostly well supported by the experimental results shown.

Weaknesses:

Several issues could be addressed and clarified to strengthen their conclusions.

(1) The word "olfactory" should be carefully used and checked in this manuscript. Although AWCs are classic olfactory neurons in C. elegans, no data in this manuscript supports the idea that olfactory signals from SS drive the responses in the digestive system. To validate that it is truly olfaction, the authors may want to check the responses of worms (e.g. AWC, digestive shutdown, INS-23 expression) to odors from SS.

We appreciate the reviewer’s careful attention to terminology. We agree that the term "olfactory" requires direct experimental validation. However, in this paper, we only used "olfactory" to specific define the AWC neurons. As reviewer’s suggestion, we now deleted the word “olfactory”.

(2) In line 113, what does "once the digestive system is activated" mean? The authors need to provide a clearer statement about 'digestive activation' and 'digestive shutdown'.

Previously, we observed that activating larval digestion with heat-killed E. coli or E. coli cell wall peptidoglycan (PGN) enabled the digestion of SS as food (Hao et al., 2024). Additionally, when animals reached the L2 stage by feeding normal OP50 diet, they could utilize SS as a food source to support growth (Figure 1—figure supplement 1D). These findings suggest that once digestion is activated (via E. coli components or L2-stage maturation), worms gain the capacity to process SS as a viable food source, abolishing SS-induced growth impairment (Hao et al., 2024) ( Figure 1—figure supplement 1D).

(3) No control data on OP50. This would affect the conclusions generated from Figures 2A, 2B, 2D, 3B, 3C, 3G, 4D-G, 5D-E, 6B-D.

We appreciate  this point. The central goal of the experiments listed (Figures 2A,B,D; 3B,C,G; 4D-G; 5D-E; 6B-D) was not to compare growth or behavior between SS and OP50 under standard conditions, but rather to understand the genetic basis of the C. elegans response specifically to SS, as identified through our nsy-1 mutant screen.

Our data in Figure 1 clearly establishes the fundamental difference in growth and feeding behavior when larvae encounter SS compared to OP50 (Figures 1A,B). Having established SS as an unfavorable food source that triggers a specific protective response (digestive shutdown), the subsequent experiments focus on deciphering how this response is mediated.

Therefore, within these specific experimental contexts under SS feeding: The primary comparison is between wild-type (N2) and nsy-1 mutant animals. All assays (growth, behavior, survival) are performed under the same SS feeding conditionsfor both genotypes.

This design allows us to directly assess the functional role of NSY-1 in mediating the SS-specific response pathway we are investigating. Including an OP50 control for every figure would not address this core genetic question and could introduce confounding variables given the established difference in how C. elegans treats these two food sources. The critical internal control for these specific experiments is the performance of the wild-type under SS versus the mutant under SS.

(4) Do the authors know which factors are released from AWC neurons to drive the digestive shutdown?

Enrichment analysis revealed that genes related to extracellular functions, such as insulin-related genes, are induced in nsy-1 mutant animals (Figure 5—figure supplement 1A, Supplementary file 4). Further analysis of insulin-related genes from the RNA-seq data showed that ins-23 is predominantly induced in nsy-1 mutant animals (Figure 5—figure supplement 1B), suggesting its potential role in promoting SS digestion. We found that knockdown of ins-23 in nsy-1 mutants inhibited SS digestion (Figure 5D). Given that INS-23 is expressed in AWC neurons (Figure 5—figure supplement 3A, CeNGEN), this suggests increased production and likely enhanced release of INS-23 from AWC neurons in the nsy-1 mutant background, which promotes SS digestion.

The insulin/insulin-like growth factor signaling (IIS) pathway, particularly through the DAF-2 receptor, integrates nutritional signals to regulate various behavioral and physiological responses related to food (Kodama et al., 2006; Ryu et al., 2018). It has been shown that INS-23 acts as an antagonist for the DAF-2 receptor to promote larval diapause (Matsunaga et al., 2018). To test whether ins-23 induction in nsy-1 mutants promotes SS digestion through its receptor, DAF-2, we constructed a nsy-1; daf-2 double mutant. We found that the SS digestion ability of the nsy-1 mutant was inhibited by the daf-2 mutation. This suggests that the nsy-1 mutation induces the insulin peptide ins-23, which promotes SS digestion through its potential receptor, DAF-2.

The data supports a model where AWC neurons regulate digestion via the release of INS-23. Loss of nsy-1 function increases INS-23 release from AWC, activating DAF-2 signaling and promoting digestion. Conversely, in wild-type animals, reduced INS-23 release from AWC contributes to digestive shutdown in response to SS food.

Reviewer #3 (Public review):

Summary:

The study explores a molecular mechanism by which C. elegans detects low-quality food through neuron-digestive crosstalk, offering new insights into food quality control systems. Liu and colleagues demonstrated that NSY-1, expressed in AWC neurons, is a key regulator for sensing Staphylococcus saprophyticus (SS), inducing avoidance behavior and shutting down the digestive system via intestinal BCF-1. They further revealed that INS-23, an insulin peptide, interacts with the DAF-2 receptor in the gut to modulate SS digestion. The study uncovers a food quality control system connecting neural and intestinal responses, enabling C. elegans to adapt to environmental challenges.

Strengths:

The study employs a genetic screening approach to identify nsy-1 as a critical regulator in detecting food quality and initiating adaptive responses in C. elegans. The use of RNA-seq analysis is particularly noteworthy, as it reveals distinct regulatory pathways involved in food sensing (Figure 4) and digestion of Staphylococcus saprophyticus (Figure 5). The strategic application of both positive and negative data mining enhances the depth of analysis. Importantly, the discovery that C. elegans halts digestion in response to harmful food and employs avoidance behavior highlights a physiological adaptation mechanism.

Weaknesses:

Major points:

(1) While NSY-1 positively regulates str-130 expression in AWC neurons and is critical for SS avoidance and survival, the authors should examine whether similar phenotypes are observed in str-130 mutants.

In this study, we mainly focused on how worms sense adverse food sources (SS food) and shutdown digestion (not growth as digestion shutdown readout). We found that nsy-1 in AWC play key roles in response SS food, once nsy-1 mutation, mutant animals cannot detect SS food and digest it, therefore growth under SS food. From RNA-seq, we found that nsy-1 positively regulates several sensory perception related genes (sra-32, str-87, str-112, str-130, str-160, str-230) (Figure 4—figure supplement 1A, Supplementary file 2). After screen, we found that we found that knockdown of str-130 in wild-type animals promoted SS digestion, thereby supporting animal growth (Figure 4D), and the proportion of animals with two AWC^OFF neurons decreased (Figure 4E). Secondly, we found that overexpression of str-130 in nsy-1 mutant animals inhibited SS digestion, thereby slowing animal growth (Figure 4F), and the proportion of animals with two AWC^OFF neurons increased (Figure 4G). These results demonstrate that NSY-1 promotes the AWC^OFF state by inducing str-130 expression, which in turn inhibits SS digestion in C. elegans.

(2) NSY-1 promotes the AWC-OFF state through str-130, inhibiting SS digestion. The authors should investigate whether STR-130 in AWC neurons regulates bcf-1 expression levels in the intestine.

We agree with the reviewer's suggestion regarding the potential role of STR-130 in AWC neurons regulating intestinal bcf-1 expression. To address this, we generated transgenic worms with AWC-specific knockdown of str-130, achieved by rescuing sid-1 cDNA expression under the ceh-36 promoter (AWC-specific) in sid-1(qt9);BCF-1::GFP background worms.

We observed that AWC neuron-specific RNAi of str-130 elevated intestinal BCF-1::GFP expression (Figure 6—figure supplement 1B). This demonstrates that STR-130 functions cell-non-autonomously in AWC neurons to repress BCF-1 expression in the intestine.

(3) The current results rely on str-2 expression levels to indicate the AWC state. Ablating AWC neurons and testing the effects on digestion would provide stronger evidence for their role in digestive regulation.

To confirm the important of AWC state in SS digestion, we performed AWC-specific neuron ablation experiments using previously validated transgenic strain that expresses cleaved caspase under the AWC-specific promoter, ceh-36 (ceh-36p::caspase). Critically, worms with ablated AWC neurons completely failed to digest SS food (Figure 3—figure supplement 4), phenocopying the non-digesting state of wild-type worms on SS when AWC-OFF signaling is impaired. This result directly confirms that functional AWC neurons are essential for initiating SS digestion, aligning with our model where the AWC-OFF state (induced by SS) inhibits digestion while the AWC-ON state promotes it.

Furthermore, we previously study discovered that AWC ablation activates the intestinal mitochondrial unfolded protein response and inhibits food digestion, mechanistically linking neuronal integrity to gut stress responses and digestive inhibition.

Together, these functional ablation studies provide compelling physiological evidence that AWC neurons act as central regulators of food-state sensing and gut function.

(4) The claim that NSY-1 inhibits INS-23 and that INS-23 interacts with DAF-2 to regulate bcf-1 expression (Line 339-340) requires further validation. Neuron-specific disruption of INS-23 and gut-specific rescue of DAF-2 should be tested.

We agree with the reviewer that the proposed NSY-1 ⊣ INS-23 → DAF-2 → BCF-1 signaling axis requires tissue-specific validation. To address this, we conducted compartment-specific functional dissection of INS-23 and DAF-2:

AWC neuronal role of INS-23:

To test whether INS-23 acts in AWC neurons to regulate intestinal BCF-1, we generated AWC-specific knockdown strains which was achieved by rescuing sid-1 cDNA expression under the ceh-36 promoter in a sid-1(qt9);BCF-1::GFP background. We found that AWC-restricted ins-23 knockdown significantly reduced intestinal BCF-1::GFP expression (Figure 6—figure supplement 1A). This confirms that INS-23 functions cell-non-autonomously within AWC sensory neurons to activate intestinal BCF-1, consistent with NSY-1’s upstream inhibition of INS-23 in this neuronal  subtype

Intestinal role of DAF-2 as INS-23 receptor:

To investigate weather DAF-2 acts as the gut-localized receptor for neuronal INS-23 signaling, we performed tissue-specific rescue experiments in the nsy-1(ag3);daf-2(e1370) double mutant. When DAF-2 was re-introduced specifically in the intestine (using the ges-1 promoter), we observed a significant suppression of SS digestion (Figure 5—figure supplement 3B), but not rescue digestive defect. This indicates that INS-23 induction in nsy-1 mutants promotes digestion independently of intestinal DAF-2 function.

(5) Figure Reference Errors: Lines 296-297 mention Figure 6E, which does not exist in the main text. This appears to refer to Figure 5E, which has not been described.

We corrected this.

Reviewer #1 (Recommendations for the authors):

I would like the authors to address the following comments in a resubmission.

(1) The hallmark of the activated p38 MAPK pathway is the phosphorylation of most downstream kinase p38 (PMK-1/PMK2 in C. elegans) of this kinase cascade. Previous work from Bergmann lab showed that the most downstream kinase of this pathway, PMK-1/PMK-2, is not required for AWC asymmetry. I wonder whether that is the case also for the model that Liu et al have presented in this manuscript. Since p38/PMK-1 undergoes activation (phosphorylation) in response to pathogenic bacteria like P. aeruginosa, it is worth testing whether PMK-1 plays a role downstream of NSY-1 in the model that Liu et al present in this manuscript. It would be worth testing whether there is increased phosphorylation of p38 when C. elegans are fed SS and whether that phosphorylation regulates downstream components that Liu et al have identified in this manuscript.

We thank the reviewer for raising this important point regarding PMK-1/p38 MAPK signaling. As established in our prior work (Reference 1), SS exposure triggers phosphorylation of PMK-1 (P-PMK-1) in C. elegans, and pmk-1 mutants exhibit enhanced growth on SS (Figure-1, Figure-2). This confirms that PMK-1-mediated innate immune signaling actively regulates SS responsiveness and digestion.

To address whether PMK-1 functions downstream of NSY-1 within our proposed model, we performed critical epistasis analyses. While we observed that nsy-1 mutation elevates ins-23 (indicating NSY-1 suppression of ins-23), knockdown of pmk-1 did not alter ins-23 expression levels (Figure 5-figure supplement 3C). This demonstrates that PMK-1 does not operate through the ins-23 pathway to regulate SS digestion. Thus, although both pathways respond to SS, the PMK-1-mediated innate immune response and the NSY-1/INS-23 axis constitute distinct regulatory mechanisms governing digestive adaptation.

Reference 1: Geng, S., Li, Q., Zhou, X., Zheng, J., Liu, H., Zeng, J., Yang, R., Fu, H., Hao, F., Feng, Q., & Qi, B. (2022). Gut commensal E. coli outer membrane proteins activate the host food digestive system through neural-immune communication. Cell host & microbe, 30(10), 1401–1416.e8. https://doi.org/10.1016/j.chom.2022.08.004

(2) Since p38 MAPK pathway has a well-established role in host defense in the C. elegans intestine, it is important to show that NSY-1 does not function in the intestine in the model that Liu et al present. I would like the authors to reintroduce nsy-1 in C. elegans intestine in nsy-1 mutant animals and then test whether it has any effect on worm length on SS food (similar to what is done in Figure 3 for AWC-specific nsy-1).

Beyond its  established  role  in  AWC  neurons,  we  detected  NSY-1 expression in the intestine (Figure 3-figure supplement 2A). To assess intestinal NSY-1 function, we performed tissue-specific rescue experiments in nsy-1 mutants using the intestinal-specific vha-1 promoter. Intestinal expression of NSY-1 significantly suppressed the enhanced SS digestion phenotype in nsy-1 mutants (Figure 3-figure supplement 2B), demonstrating functional involvement of gut-localized NSY-1 in regulating digestive responses. We propose intestinal NSY-1 mediates this effect through innate immune signaling, consistent with its known pathway components. As previously established (Reference 1), the canonical PMK-1/p38 MAPK pathway functions downstream of NSY-1, with both sek-1 and pmk-1 knockdown enhancing SS digestion through immune modulation. This indicates intestinal NSY-1 suppresses digestion may act through PMK-1-mediated immune responses. Since neuronal NSY-1's role in digestive control was previously undefined, we prioritized mechanistic analysis of its neuronal function in digestion regulation.

Notably, this immune-mediated mechanism operates independently of NSY-1's neuronal regulation pathway. In AWC neurons, NSY-1 controls digestion exclusively through the neuropeptide signaling axis (INS-23/DAF-2/BCF-1) without engaging innate immune components.

Reference 1: Geng, S., Li, Q., Zhou, X., Zheng, J., Liu, H., Zeng, J., Yang, R., Fu, H., Hao, F., Feng, Q., & Qi, B. (2022). Gut commensal E. coli outer membrane proteins activate the host food digestive system through neural-immune communication. Cell host & microbe, 30(10), 1401–1416.e8. https://doi.org/10.1016/j.chom.2022.08.004

(3) At multiple places, wild-type (WT) controls have been labeled as N2. It is better to label all controls as WT (and not as N2).

Corrected.

(4) In Figure 2B, the aversion response should be scored at multiple time points, like Figure 1C, rather than at just one timepoint.

We thank the reviewer for suggesting multi-timepoint analysis of aversion behavior. In accordance with this recommendation, we have now quantified SS avoidance at multi-timepoint. As shown in the revised Figure 2B, nsy-1 mutants exhibited significantly impaired avoidance responses at both 4h and 6h but not at 8h, confirming that NSY-1 is essential for sustained aversion to SS food in the early response. This data demonstrates that the critical role of NSY-1 in food discrimination at initial sensory responses.

(5) Does the re-introduction of nsy-1 in AWC neurons in nsy-1 mutant background help animals avoid SS in dwelling and food-choice assays? Along the same lines, does the CRISPR-generated AWC-specific mutant of NSY-1 fail to avoid SS in dwelling and food-choice assays similar to the whole-animal mutant? These behavioral data are missing in Figure 3.

We thank the reviewer for prompting behavioral validation of AWC-specific nsy-1 functions. To determine whether NSY-1 in AWC neurons mediates SS sensory perception, we performed dwelling (avoidance) and food-choice assays using AWC-specific nsy-1 knockout and AWC-rescued strains (nsy-1(ag3); Podr-1::nsy-1). In dwelling assays, AWC-specific nsy-1 KO mutants exhibited significantly impaired SS avoidance at 6h (Figure 3-figure supplement 3A), while AWC-rescued strains restored avoidance capacity at 2-6h (Figure 3-figure supplement 3B). Food-choice assays further revealed that AWC nsy-1 KO mutants preferentially migrated toward SS (Figure 3-figure supplement 3C), whereas AWC-rescued showed no preference between SS and HK-E. coli (Figure 3-figure supplement 3D). These data conclusively demonstrate that NSY-1 acts in AWC neurons to mediate SS recognition and aversion behaviors.

(6) In Figure 3E and F, the number of animals that were used for scoring AWC str-2p::GFP expression should be specified.

we added the number of animals in the figure.

(7)  RNA seq analysis identified multiple GPCRs (including STR-130) that are upregulated in an NSY-1-dependent manner when animals are fed with SS bacteria. However, the authors decided to only characterize STR-130 because of previously published findings. It is important to rule out the role of other GPCRs since all are upregulated on SS food as shown in Figure S4 B. I would like the authors to knock down other GPCRs in the same manner as they did for STR-130 and demonstrate that only str-130 knockdown behaves similarly to the nsy-1 mutant (if that is the case) using the assay presented in Figure 4 D.

We appreciate the reviewer’s suggestion to comprehensively evaluate NSY-1-regulated GPCRs. In response, we extended our functional analysis to all six GPCRs (str-130, str-230, str-87, str-112, str-160, and sra-32) identified as NSY-1-dependent and SS-induced in RNA-seq (Figure 4—figure supplement 1).

Using RNAi knockdown and the SS growth assay, we observed that RNAi of str-130, str-230, str-87, or str-112 significantly enhanced SS growth (Figure 4—figure supplement 2A), with str-130 RNAi exhibiting the most robust phenotype—phenocopying nsy-1 mutants. Crucially, none of these GPCR knockdowns further enhanced growth in nsy-1(ag3) mutants (Figure 4—figure supplement 2B), confirming their position downstream of NSY-1. These data establish str-130 as the dominant effector of NSY-1-mediated SS response regulation, while suggesting minor contributions from other GPCRs (str-230, str-87, str-112).

(8) In Figure 4E and G, the number of animals that were used for scoring GFP expression should be specified.

we added the number of animals in the figure.

(9) When comparing Figure 3E and Figure 4E, it appears that the loss of str-130 RNAi does not phenocopy nsy-1 mutant. This raises the question of whether the inefficiency of RNAi targeting str-130 is the cause, or if STR-130 is not the only GPCR regulated by NSY-1 on SS food. I would like the authors to address this discrepancy. If RNAi inefficiency is indeed the cause, using an RNAi-sensitive background, such as an eri- 1 mutant, could help strengthen the data presented in Figure 4E. Conversely, if RNAi inefficiency is not responsible for the discrepancy, I suggest that the authors investigate the roles of other GPCRs that were identified by RNA sequencing.

We appreciate the reviewer’s observation regarding the phenotypic difference between nsy-1 mutants and str-130 (RNAi) animals on SS food (Fig. 3E vs Fig. 4E).

While both genetic perturbations significantly enhance SS growth and increase the proportion of animals exhibiting AWC^ON states compared to wild type (indicating enhanced digestion), the specific AWC^ON neuron configurations differ: nsy-1 mutants predominantly show 2 AWC^ON animals, whereas str-130(RNAi) animals primarily exhibit the 1 AWC^ON /1 AWC^OFF configuration (Fig. 3E vs Fig. 4E).

This difference likely arises because STR-130 is the key GPCR mediating NSY-1's inhibitory effect on SS digestion, but it is not the sole GPCR involved, as evidenced by our RNAi screen identifying several additional NSY-1-regulated GPCRs (str-230, str-87, str-112) whose depletion also enhanced SS growth (Fig. 4A-D).

The robust SS growth enhancement and AWC^ON state increase caused by str-130 (RNAi) (phenocopying the nsy-1 mutant’s functional outcome of enhanced digestion) (Figure 4D, 4E) indicate effective RNAi knockdown for this specific assay. Therefore, the distinct neural configurations reflect the partial redundancy among GPCRs downstream of NSY-1, rather than an inherent inefficiency of the str-130 RNAi.

The nsy-1 mutant phenotype represents the complete loss of all inhibitory GPCR signaling coordinated by NSY-1, while str-130(RNAi) represents the loss of its major component. Investigating the roles of other identified GPCRs (str-230, str-87, str-112) in modulating AWC^ON neuron states is an important direction for future research.

(10) In Figure 4 F and 4 G, the authors show that the overexpression of STR-130 rescues the nsy-1 mutant phenotype suggesting that NSY-1 might function through STR-130 to control digestion on SS food. These data place STR-130 downstream of NSY-1. To further strengthen these epistasis data, authors should knock down str-130 in nsy-1 mutant animals and show that the combined loss of both genes produces the same effect as the loss of either gene alone.

We thank the reviewer for the insightful suggestion to further define the genetic relationship between nsy-1 and str-130. To strengthen our epistasis analysis, we performed RNAi knockdown of str-130 in the nsy-1(ag3) mutant background and assessed development on SS food. Consistent with STR-130 acting downstream of NSY-1, the loss of str-130 via RNAi did not further enhance the developmental capacity (i.e., growth phenotype) of nsy-1(ag3) mutant animals on SS. This lack of enhancement indicates that str-130 and nsy-1 function within the same genetic pathway, with str-130 acting epistatically downstream of nsy-1 (Figure 4—figure supplement 3). This finding reinforces the model proposed from our overexpression data (Fig. 4F-G) – that NSY-1 primarily exerts its inhibitory effect on SS digestion by inducing the expression GPCR STR-130.

(11) In Figure 5C, please mention "ins-23 transcript levels" on the top of the graph so that it is clear what these data represent.

We appreciate the reviewer’s suggestion.

(12) Since all ins genes were upregulated in nsy-1 mutants (though ins-23 was indeed the most highly upregulated gene) on SS food from RNA seq analysis (Figure S5 B), it is important to first phenotypically characterize all of them using "worm length assay". If this analysis shows that ins-23 has the most robust phenotype, it would make more sense to just focus on ins-23.

We agree with the reviewer that initial phenotypic characterization of candidate genes identified through transcriptomic analysis is valuable.Our RNA-seq data revealed that several insulin-like peptide genes, including ins-22, ins-23, ins-24, and ins-27, were significantly upregulated in the nsy-1 mutant on SS food (Figure 5—figure supplement 1B). We prioritized these insulin-like peptide genes for functional validation because they are known to act as neuropeptides capable of mediating non-cell autonomous signaling in previous studies (Shao et al 2016).

To determine if any were functionally responsible for the enhanced SS growth observed in nsy-1 mutants, we performed functional phenotypic screening using the SS growth assay (worm length assay). We individually knocked down each of these candidates (ins-22, ins-23, ins-24, ins-27) in the nsy-1(ag3) mutant background. Among these, only RNAi targeting ins-23 significantly attenuated (i.e., suppressed) the enhanced development of the nsy-1(ag3) mutant on SS (Figure 5—figure supplement 2). This targeted functional screening revealed that ins-23 has the most robust and specific role in mediating the enhanced digestion phenotype downstream of NSY-1 loss, providing the critical justification for our subsequent focus on this particular insulin-like peptide.

Ref:

Shao, L. W., Niu, R., & Liu, Y. (2016). Neuropeptide signals cell non-autonomous mitochondrial unfolded protein response. Cell research, 26(11), 1182–1196. https://doi.org/10.1038/cr.2016.118

Reviewer #2 (Recommendations for the authors):

There are several minor errors and typos in the manuscript

(1) A number of typos in the figures, like "length".

Corrected.

(2) The 'axis labels' are inconsistent from panel to panel, like "relative body length" and "relative worm length".

Corrected.

(3) The fonts are inconsistent from panel to panel.

Corrected.

(4) There is no Ex unique number for transgenic lines.

Corrected.

Reviewer #3 (Recommendations for the authors):

Minor points:

(1)  Figure 3B, 3C, 3G, 4D, 4F, 5D, 5E, and 6C: Replace "lenth" with "length" (consistent with Figure 2A).

Corrected.

(2) Figure 4D: Correct "ctontrol" to "control."

Corrected.

(3) Figure 4G: Update the co-injection marker to Podr-1::GFP instead of Pstr-2::GFP.

Corrected.

(4) Figure 5C: This figure is missing from the Results section.

Corrected.

(5) Figure 6A: Label the graph with Pbcf-1::bcf-1::GFP, as in Figure 6D.

Corrected.

(6) Italicization: Lines 588 and 603-italicize nsy-1.

Corrected.

(7) Supplementary Figure S2A: Correct "Screeng" to "Screening."

Corrected.

(8) Spelling/Proofreading: Ensure consistent spelling and grammar, such as correcting "mutan" to "mutant" in Figure 4A.

Corrected.

idk if this working

Testing

Done

this worked

The career option in psychology that is most appealing to me is sports psychology. I run cross country and track, so I know firsthand how it is to be an athlete. The mental challenges are just as hard as the physical challenges; you're not only exerting your body but your mind as well. For running especially, there is a huge mental aspect to it, it's really hard to keep going at times. I think I could relate my experience as an athlete to other athletes as a sports psychologist because I know what it's like. I want to be able to help athletes that are struggling with their mental health and make sure they are at their best mentally and physically. At first, I thought I wanted to be a therapist/counselor for people, but I think I would be better working with athletes and id be able to connect with them on a more personal level.

this experiment demonstrates the effects racism and colorism has on children.

I think our social needs are just as important as our physiological needs to support our overall wellbeing.

the theory that human and animal behavior can be explained in terms of conditioning, without appeal to thoughts or feelings, and that some mental conditions are best treated by altering behavior patterns.

this can be helpful for psychology students who are looking to become therapists.

Testing

office hours after class

Trying it out.

very important aspect

Interesting and important!

This is new for me to learn, but I'm looking forward to an interesting class! Glad to be here.

just trying it out

Testing

Testing

This class seems like it will be very engaging! I’m looking forward to it.

Testing

What kinds of Homework assignments will we have?

TESTING

got it.

must be present and attentive to be able to participate in class discussions.

t_man_linux

50% of final grade

The links aren't working on my end.

It seems like this grading would be aligned well with standards, but I wonder how well this grading would be interpreted. It also seems a little confusing for the teacher to keep up with different skill levels.

I don't think I would be confident about my grades if I didn't experience a little bit of anxiety about it. If the worry aspect was taken away from grading, I don't think I'd care much about my grades. Granted, I care a lot about my grades and I take great pride in my accomplishments. It hasn't been easy for me, in fact, I dropped out of college when I was 18. So the fact that I am doing well has been a driving factor in my success this time. However, I strive hard to make good grades and I push myself to go above and beyond on assignments.

But then the work the students who did the assignment would be in vain right? Am I understanding this correctly? Because surely teachers aren't just overlooking missed assignments on purpose and not assigning a zero.

I know that we aren't necessarily here to argue policies, but I feel that teaching students to turn assignments in on time is a life skill. Neglecting this aspect could hurt them when they are unable to meet deadlines for a job and get fired because of it.

Something that I seen in my Pre-Internship I is that parent's seem to not really care that their students are getting bad grades. I seen several instances where this was the case and it seems like there is a lack of engagment from some students to even complete simple assignments. Is that a phenomenon everywhere?

Joy, Bill. “Why the Future Doesn’t Need Us.” Wired, April 1, 2000. https://www.wired.com/2000/04/joy-2/.

Annotation url: urn:x-pdf:753822a812c861180bef23232a806ec0

Annotations: https://jonudell.info/h/facet/?user=chrisaldrich&url=urn%3Ax-pdf%3A753822a812c861180bef23232a806ec0&max=100&exactTagSearch=true&expanded=true

Reprints available at: - Joy, Bill. “Why the Future Doesn’t Need Us.” 2000. AAAS Science and Technology Policy Yearbook 2001, edited by Albert H. Teich et al., Amer Assn for the Advancement of Science, 2002, pp. 47–75. Google Books, https://www.google.com/books/edition/Integrity_in_Scientific_Research/0X-1g8YElcsC.<br /> - Joy, Bill. “Why the Future Doesn’t Need Us.” 2000. Emerging Technologies: Ethics, Law and Governance, by Gary E. Marchant and Wendell Wallach, edited by Gary E. Marchant and Wendell Wallach, 1st ed., Routledge, 2020, pp. 65–71.

Brown, John Seely, and Paul Duguid. “A Response to Bill Joy and the Doom-and-Gloom Technofuturists.” 2000. Emerging Technologies: Ethics, Law and Governance, by Gary E. Marchant and Wendell Wallach, edited by Gary E. Marchant and Wendell Wallach, 1st ed., Routledge, 2020, pp. 65–71.

via: https://web.cs.ucdavis.edu/~koehl/Teaching/ECS188_W16/Reprints/Response_to_BillJoy.pdf

annotation URL: urn:x-pdf:1e8f84f1b5e3fb65dfe49ef6f173c79e

A reprint of: <br /> - “Re-Engineering the Future: A Response to Bill Joy and the doom-and-gloom technofuturists,” The Industry Standard, John Seely Brown and Paul Duguid. 24 April 2000, p.196. - “A Response to Bill Joy and the Doom-and-Gloom Technofuturists,” AAAS Science and Technology Policy Yearbook 2001, edited by Albert H. Teich, Stephen D. Nelson, Celia McEnaney and Stephen J. Lita, American Association for the Advancement of Science, 2001.

Cross reference: Bill Joy's paper and notes at urn:x-pdf:753822a812c861180bef23232a806ec0

What do the shapes and sizes in these networks tell us about potential outcomes?

How are these changes created? How are the outcomes and shapes different?

Can we put a mathematical "measure" on them? What do the (topological) "neighborhoods" look like before and after?

1, 2, 3, ... profit also follows this general pattern and some companies like Uber, Lyft, Postmates, etc. have found this difficult to do.

Tesla is another example which seems to fit the profile of this piece with respect to Elon Musk having pissed off the very people he was attempting to sell to.

I find myself reading this from the perspective not so much of technology, but of these social systems which seem to be being stressed right now. Is it the technologists (Elon Musk, Peter Thiel, etc.) who realize that these systems were part of the technology "problem" in the past and now they've figured out a way to attempt to "capture" people to organize their original ends?

great reminder in both technology and politics

This observation is important in so many areas of life and research. It's not what you see in aggregate or on the surface, but the details below the surface which help to determine the second, third, and later-order effects.

These things can only kill us if we don't manage to kill ourselves first...

testing

Would you like us to reply to peers annotations as well?

asfdasd

I feel that this shows how some teachers are willing to cross certain lines for their school/students to receive more funding that could benefit them academically. However, educators must keep in mind that with standardized tests you can not cheat for your students, because they are gaining no knowledge of the content and it is illegal.

eLife Assessment

In this valuable manuscript, Rao and colleagues investigate the UFD-1/NPL-4 complex, which is involved in extracting misfolded proteins in the plasma membrane and the accumulation of pathogenic bacteria in the intestine. Using convincing methods, the authors find that knockdown of the ufd-1 and npl-4 genes leads to shortened lifespan of the nematode C. elegans and reduced accumulation of the bacterial pathogen P. aeruginosa in the intestine.

Reviewer #1 (Public review):

The authors adequately addressed the concerns I raised in my initial review, which are noted below.

(1) I suggest that the authors choose a different term in their title, abstract and manuscript to describe the phenotypes associated with ufd-1 and npl-4 knockdown other than an "inflammation-like response." Inflammation is a pathological term with four cardinal signs: redness (rubor), swelling (tumor), warmth (calor) and pain (dolor). These are not symptoms known to occur in C. elegans. The authors could consider using "inappropriate," "aberrant" or "toxic" immune activation in the title and abstract.

(2) I think it is important to point out in the context of the authors novelty claim in the abstract and manuscript that the toxic effects of inappropriate immune activation in C. elegans has been widely catalogued. For example: doi.org/10.1371/journal.ppat.1011120 (2023); doi:10.1186/s12915-016-0320-z (2016).; doi:10.1126/science.1203411 (2011); doi:10.1534/g3.115.025650 (2016). In addition, doi:10.7554/eLife.74206 (2022) previously described a mutation that caused innate immune activation that reduced accumulation of P. aeruginosa in the intestine, but also caused animals to have a shortened lifespan.

Thus, I do not think this study reveals the existence of inflammatory-like responses in C. elegans, as stated by the authors. Indeed, I think it is important for the authors to remove this novelty claim from their paper and discuss their work in the context of these studies in a paragraph in the introduction.

(3) The authors rely on the use of RNAi of ufd-1 and npl-4 to study their effect on P. aeruginosa colonization and pathogen resistance throughout the manuscript. To address the possibility of off-target effects of the RNAi, the authors should consider both (i) showing with qRT-PCR that these genes are indeed targeted during RNAi, and (ii) confirming their phenotypes with an orthologous technique, preferably by studying ufd-1 and npl-4 loss-of-function mutants [both in the wild-type and sek-1(km4) backgrounds]. If mutation of these genes is lethal, the authors could use Auxin Inducible Degron (AID) technology to induce the degradation of these proteins in post-developmental animals.

(4) I am confused about the author's explanation regarding their observation that inhibition of the UFD-1/ NPL-4 complex extends the lifespan of sek-1(km25) animals, but not pmk-1(km25) animals, as SEK-1 is the MAPKK that functions immediately upstream of the p38 MAPK PMK-1 to promote pathogen resistance.

I am also confused why their RNA-seq experiment revealed a signature of intracellular pathogen response genes and not PMK-1 targets, which the authors propose is accounting for toxic immune activation. Activation of which immune response leads to toxicity?

(5) The authors did not test alternative explanations for why UFD-1/ NPL-4 complex inhibition compromises survival during pathogen infection, other than exuberant immune activation. For example, it is possible that inhibition of this proteosome complex shortens lifespan by compromising the general health/ normal physiology of nematodes. Immune responses could be activated as a secondary consequence of this stress, and not be a direct cause of early mortality. Does sek-1(km4) mutant suppress the lifespan shortened lifespan of ufd-1 and npl-4 knockdown? This experiment should also be done with loss-of-function mutants, as noted in point 3.

(6) The conclusion of Figure 6 hinges on an experiment that uses double RNAi to knockdown two genes at the same time (Fig. 6D and 6G), an approach that is inherently fraught in C. elegans biology owing to the likelihood that the efficiency of RNAi-mediated gene knockdown is compromised and may account for the observed phenotypes. The proper control for double RNAi is not empty vector + ufd-1(RNAi), but rather gfp(RNAi) + ufd-1(RNAi), as the introduction of a second hairpin RNA is what may compromise knockdown efficiency. In this context, it is important to confirm that knockdown of both genes occurs as expected (with qRT-PCR) and to confirm this phenotype using available elt-2 loss-of-function mutants.

(7) A supplementary table with the source data for at least three replications (mean lifespan, n, statistical comparison) for each pathogenesis assay should be included in this manuscript.

Comments on revisions:

The authors adequately addressed the concerns I raised.

Reviewer #2 (Public review):

Summary:

The authors aimed to uncover what role, if any, the UFD1/NPL4 complex might play in innate immune responses of the nematode C. elegans. The authors find that loss of the complex renders animals more sensitive to both pathogenic and non-pathogenic bacteria. However, there appears to be a complex interplay with known innate immune pathways since loss of UFD1/NPL4 actually results in increased survival of animals lacking the canonical innate immune pathways.

Strengths:

The authors perform robust genetic analysis to exclude and include possible mechanisms by which the UFD1/NPL4 pathway acts in the innate immune response.

Weaknesses:

The argument that the loss of the UFD1/NPL4 complex triggers a response that mimics that of an intracellular pathogen is not thoroughly investigated. Additionally, the finding of a role of the GATA transcription factor, ELT-2, in this response is suggestive, but experiments showing sufficiency in the context of loss of the UFD1/NPL4 complex need to be explored.

Comments on revisions:

The authors have performed several control experiments for their RNAi based experiments and also tested the requirement for xbp-1s in their paradigm. The findings and their interpretations are acceptable.

Author response:

The following is the authors’ response to the original reviews.

Reviewer #1 (Public Review):

(1) I suggest that the author's choose a different term in their title, abstract and manuscript to describe the phenotypes associated with ufd-1 and npl-4 knockdown other than an "inflammation-like response." Inflammation is a pathological term with four cardinal signs: redness (rubor), swelling (tumor), warmth (calor) and pain (dolor). These are not symptoms know to occur in C. elegans. The authors could consider using "tolerance" instead, as this term may better describe their findings.

We have changed “inflammation-like response” to “aberrant immune response” throughout the manuscript.

(2) It would help the reader to better understand the novelty of the findings in this study if the authors include a paragraph in their introduction to put their results in context of the published literature that has examined the relationship between immune activation and nematode health and survival. In particular, I suggest that the authors discuss doi:10.7554/eLife.74206 (2022), a study that charcterized a similar observation to what the authors are reporting. This study found that low cholesterol reduces pathogen tolerance and host survival during pathogen infection. Cholesterol scarcity increases p38 PMK-1 phosphorylation, priming immune effector induction in a manner that reduces pathogen accumulation in the intestine during a subsequent infection. I also suggest that the authors highlight in this introductory paragraph that the toxic effects of inappropriate immune activation in C. elegans has been widely catalogued. For example: doi.org/10.1371/journal.ppat.1011120 (2023); doi:10.1186/s12915-016-0320-z (2016).; doi:10.1126/science.1203411 (2011); doi:10.1534/g3.115.025650 (2016).

In this context, the authors could consider re-wording their novelty claim in the abstract and introduction to take into account this previous body of work.

We have added a paragraph to the Discussion section to place our findings in the context of previous research. The revised manuscript now includes the following text (page 11, lines 336–344): “Previous studies have shown that hyperactivation of immune pathways can negatively affect organismal development. For example, sustained activation of the p38 MAPK pathway impairs development in C. elegans (Cheesman et al., 2016; Kim et al., 2016), and excessive activation of the IPR also leads to developmental defects (Lažetić et al., 2023). Similar to our current study, recent work has demonstrated that heightened immune responses can reduce gut pathogen load while paradoxically decreasing host survival during infection (Ghosh and Singh, 2024; Peterson et al., 2022). However, our study uniquely shows that while such heightened immune responses are detrimental to immunocompetent animals, they can be beneficial in the context of immunodeficiency.”

(3) The authors rely on the use of RNAi of ufd-1 and npl-4 to study their effect on P. aeruginosa colonization and pathogen resistance throughout the manuscript. To address the possibility of off-target effects of the RNAi, the authors should consider both (i) showing with qRT-PCR that these genes are indeed targeted during RNAi, and (ii) confirming their phenotypes with an orthologous technique, preferably by studying ufd-1 and npl-4 loss-offunction mutants [both in the wild-type and sek-1(km4) backgrounds]. If mutation of these genes is lethal, the authors could use Auxin Inducible Degron (AID) technology to induce the degradation of these proteins in post-developmental animals.

We attempted several protocols of CRISPR in our laboratory to generate ufd-1 loss-of-function mutants; however, these efforts were unsuccessful. While this does not rule out the possibility of generating ufd-1 mutants, the failure is likely due to technical limitations on our part rather than an inherent inability to disrupt the gene. Nevertheless, to confirm the specificity of our RNAi-based approach, we quantified ufd-1 and npl-4 mRNA levels following RNAi treatment and found that each gene was specifically and effectively downregulated by its respective RNAi. 

Importantly, ufd-1 and npl-4 RNA sequences do not share significant homology, yet knockdown of either gene results in nearly identical phenotypes, including reduced survival on P. aeruginosa, diminished intestinal colonization, and shortened lifespan. These consistent outcomes strongly support the conclusion that the phenotypes are attributable to the disruption of the functional UFD-1-NPL-4 complex. We have added these results in the revised manuscript (pages 4-5, lines 114-125): “To confirm the specificity of the RNAi knockdowns and rule out potential off-target effects, we examined transcript levels of ufd-1 and npl-4 following RNAi treatment. RNAi against ufd-1 significantly reduced ufd-1 mRNA levels without reducing npl-4 expression, while npl-4 RNAi specifically downregulated npl-4 transcripts with no impact on ufd-1 mRNA levels (Figure 1—figure supplement 1A and B). Additionally, alignment of ufd-1 and npl-4 mRNA sequences against the C. elegans transcriptome revealed no significant similarity to other genes, supporting the specificity of the RNAi constructs. Moreover, the ufd-1 and npl-4 RNA sequences do not share significant sequence similarity. Therefore, the highly similar phenotypes observed in ufd-1 and npl-4 knockdown animals, including shortened lifespan, reduced survival on P. aeruginosa, and decreased intestinal colonization with P. aeruginosa, strongly suggest that these outcomes result from the disruption of the functional UFD-1-NPL-4 complex.”

(4) I am confused about the authors explanation regarding their observation that inhibition of the UFD-1/ NPL-4 complex extends the lifespan of sek-1(km25) animals, but not pmk-1(km25) animals, as SEK-1 is the MAPKK that functions immediately upstream of the p38 MAPK PMK-1 to promote pathogen resistance.

I am also confused why their RNA-seq experiment revealed a signature of intracellular pathogen response genes and not PMK-1 targets, which the authors propose is accounting for toxic immune activation. Activation of which immune response leads to toxicity?

We consistently observe that sek-1(km4) mutants are more sensitive to P. aeruginosa infection than pmk-1(km25) mutants, a finding also reported in previous studies (for example, PMID: 33658510). Given that SEK-1 functions upstream of PMK-1 in the MAPK signaling cascade, it is plausible that SEK-1 also regulates additional MAP kinases, such as PMK-2 (PMID: 25671546), which could contribute to the enhanced susceptibility observed in sek-1 mutants.

Our results show that inhibition of the UFD-1-NPL-4 complex improves survival specifically in severely immunocompromised animals, such as sek-1(km4) mutants, but not in pmk1(km25) mutants. To further validate this, we generated the double mutant dbl-1(nk3);pmk1(km25), which exhibits reduced survival on P. aeruginosa compared to either single mutant.

Notably, inhibition of the UFD-1-NPL-4 complex also enhances survival in the dbl1(nk3);pmk-1(km25) background, reinforcing the observation that this response is specific to severely compromised immune states.

We would also like to clarify that the observed phenotypes are independent of the SEK1/PMK-1 pathway, as shown in Figure 3A-3C, Figure 3—figure supplement 1, and Figure 4A-4C. The IPR seems to play a role in the observed phenotypes, as inhibition of some of the protease and pals genes (IPR genes) leads to increased P. aeruginosa colonization in ufd-1 knockdown animals (Figure 6—figure supplement 1). The other immune response pathway that leads to the observed phenotypes is ELT-2, as explained in Figure 6. Finally, we have included in the revised manuscript a note that, in addition, as-yet unidentified pathways are also likely contributing to the phenotypes triggered by disruption of the UFD-1-NPL-4 complex.

(5) The authors did not test alternative explanations for why UFD-1/ NPL-4 complex inhibition compromises survival during pathogen infection, other than exuberant immune activation. For example, it is possible that inhibition of this proteosome complex shortens lifespan by compromising the general health/ normal physiology of nematodes. Immune responses could be activated as a secondary consequence of this stress, and not be a direct cause of early morality. Does sek-1(km4) mutant suppress the lifespan shortened lifespan of ufd-1 and npl-4 knockdown? This experiment should also be done with loss-offunction mutants, as noted in point 3.

We have already included this data in Figure 4D, where we observed that ufd-1 and npl-4 knockdown reduce the lifespan of sek-1(km4) animals. It is possible that immune activation is a secondary consequence of cellular stress induced by inhibition of the UFD-1NPL-4 complex. However, our data strongly suggest that the observed phenotypes, including reduced gut pathogen load and decreased survival on the pathogen, are due to the aberrant immune response activated by the inhibition of the UFD-1-NPL-4 complex. Evidence from sek-1(km4) mutants particularly underscores the role of this dysregulated immune activation. While this aberrant immune response is detrimental to wild-type animals under pathogenic conditions, it appears to be beneficial in severely immunocompromised backgrounds. Specifically, in sek-1(km4) mutants, inhibition of the UFD-1-NPL-4 complex enhances survival during P. aeruginosa infection (Figure 4A). However, under non-infectious conditions, where sek-1(km4) mutants exhibit a normal lifespan, the same immune activation becomes harmful (Figure 4D). Together, these findings demonstrate that the aberrant immune response induced by UFD-1–NPL-4 inhibition is context-dependent: it is advantageous only for immunocompromised animals under infection, but deleterious to healthy animals under infection and to both healthy and immunocompromised animals under non-infectious conditions.

(6) The conclusion of Figure 6 hinges on an experiments that uses double RNAi to knockdown two genes at the same time (Fig. 6D and 6G), an approach that is inherently fraught in C. elegans biology owing the likelihood that the efficiency of RNAi-mediated gene knockdown is compromised and may account for the observed phenotypes. The proper control for double RNAi is not empty vector + ufd-1(RNAi), but rather gfp(RNAi) + ufd1(RNAi), as the introduction of a second hairpin RNA is what may compromise knockdown efficiency. In this context, it is important to confirm that knockdown of both genes occurs as expected (with qRT-PCR) and to confirm this phenotype using available elt-2 loss-of-function mutants.

We thank the reviewer for this helpful suggestion. We have repeated all double

RNAi experiments using gfp RNAi as a control instead of the empty vector (Figure 6 and Figure 6—figure supplement 1). Additionally, we assessed the efficiency of gene knockdown in the double RNAi conditions (Figure 6—figure supplement 2) and found that RNAi efficacy was not compromised by the double RNAi treatment.

(7) A supplementary table with the source data for at least three replications (mean lifespan, n, statistical comparison) for each pathogenesis assay should be included in this manuscript.

The source data is provided for all the data presented in the manuscript.

Reviewer #2 (Public Review):

Summary:

The authors aimed to uncover what role, if any, the UFD1/NPL4 complex might play in the innate immune responses of the nematode C. elegans. The authors find that loss of the complex renders animals more sensitive to both pathogenic and non-pathogenic bacteria. However, there appears to be a complex interplay with known innate immune pathways since the loss of UFD1/NPL4 actually results in increased survival of animals lacking the canonical innate immune pathways.

We thank the reviewer for providing an excellent summary of our work.

Strengths:

The authors perform robust genetic analysis to exclude and include possible mechanisms by which the UFD1/NPL4 pathway acts in the innate immune response.

We thank the reviewer for highlighting the strengths of our work.

Weaknesses:

The argument that the loss of the UFD1/NPL4 complex triggers a response that mimics that of an intracellular pathogen has not been thoroughly investigated. Additionally, the finding of a role of the GATA transcription factor, ELT-2, in this response is suggestive, but experiments showing sufficiency in the context of loss of the UFD1/NPL4 complex need to be explored.

We have investigated the role of IPR genes in the phenotypes observed upon ufd1 knockdown (Figure 6—figure supplement 1), and our results suggest that the IPR may contribute, at least in part, to the phenotypic outcomes of ufd-1 RNAi. In the Discussion section (pages 11–12, lines 345–356), we have included a detailed discussion on the possible mechanisms underlying IPR activation upon inhibition of the UFD-1–NPL-4 complex. We agree that the interaction between the UFD-1–NPL-4 complex and the IPR is intriguing and warrants further investigation. However, we believe that an in-depth exploration of this interaction lies beyond the scope of the current study.

We have incorporated new data on ELT-2 overexpression in the revised manuscript. Overexpression of ELT-2 partially phenocopies the effects of ufd-1 knockdown, supporting the idea that other pathways likely contribute to the full spectrum of phenotypes observed upon UFD-1-NPL-4 complex inhibition. The revised manuscript reads (page 10, lines 311319): “To determine whether ELT-2 activation alone is sufficient to recapitulate the phenotypes observed upon UFD-1-NPL-4 complex inhibition, we analyzed animals overexpressing ELT-2. Similar to ufd-1 knockdown, ELT-2 overexpression led to a significant reduction in the colonization of the gut by P. aeruginosa (Figure 6—figure supplement 3A and 3B). However, overexpression of ELT-2 did not alter the survival of worms on P. aeruginosa (Figure 6—figure supplement 3C). Taken together, these findings suggest that the phenotypes triggered by disruption of the UFD-1-NPL-4 complex are partially mediated by ELT-2. However, additional pathways, yet to be identified, likely cooperate with ELT-2 to regulate both pathogen resistance and host survival.”

Reviewer #1 (Recommendations For The Authors):

The authors could consider avoiding the use of descriptors (e.g., "drastic") when presenting their data.

We have removed the descriptors.

Reviewer #2 (Recommendations For The Authors):

What happens with overexpression of ELT2?

Overexpression of ELT-2 partially recapitulates the phenotypes of ufd-1 knockdowns, indicating that additional pathways are likely involved in controlling the phenotypes observed upon inhibition of the UFD-1-NPL-4 complex. The revised manuscript reads (page 10, lines 311-319): “To determine whether ELT-2 activation alone is sufficient to recapitulate the phenotypes observed upon UFD-1-NPL-4 complex inhibition, we analyzed animals overexpressing ELT-2. Similar to ufd-1 knockdown, ELT-2 overexpression led to a significant reduction in the colonization of the gut by P. aeruginosa (Figure 6—figure supplement 3A and 3B). However, overexpression of ELT-2 did not alter the survival of worms on P. aeruginosa (Figure 6—figure supplement 3C). Taken together, these findings suggest that the phenotypes triggered by disruption of the UFD-1-NPL-4 complex are partially mediated by ELT-2. However, additional pathways, yet to be identified, likely cooperate with ELT-2 to regulate both pathogen resistance and host survival.”

The data with xbp-1 loss of function is very different than that of pek1 and atf-6. Does loss of ufd1/npl4 suppress the increased pathogen survival of xbp-1s overexpressing animals?

We have examined worms overexpressing XBP-1s and found that overexpression of XBP-1s does not rescue the phenotypes caused by ufd-1 knockdown. The revised manuscript reads (page 6, lines 167-174): “To further examine the role of XBP-1 in this context, we assessed the effect of ufd-1 knockdown in animals neuronally overexpressing the constitutively active spliced form of XBP-1 (XBP-1s), which has been previously associated with enhanced longevity (Taylor and Dillin, 2013). Knockdown of ufd-1 resulted in the reduced survival of XBP-1s-overexpressing animals on P. aeruginosa, despite a concurrent decrease in bacterial colonization of the gut (Figure 2—figure supplement 1A-C). This indicated that the XBP-1 pathway was not required for the reduced P. aeruginosa colonization of ufd-1 knockdown animals.” 

Lastly, while the pathogen burden is reduced in ufd1/npl4 loss and pumping rates are marginally affected, have you checked defecation rates? Could they be increased?

We thank the reviewer for this valuable suggestion. We measured defecation rates following ufd-1 and npl-4 knockdown and, unexpectedly, found that inhibition of ufd-1/npl-4 leads to a reduction in defecation frequency. These findings clearly indicate that altered defecation cannot explain the observed decrease in gut colonization. The revised manuscript reads (page 5, lines 138-148): “The clearance of intestinal contents through the defecation motor program (DMP) is known to influence gut colonization by P. aeruginosa in C. elegans (Das et al., 2023). It is therefore conceivable that knockdown of the UFD-1-NPL-4 complex might increase defecation frequency, thereby promoting the physical expulsion of bacteria and resulting in reduced gut colonization. To test this possibility, we measured DMP rates in animals subjected to ufd-1 and npl-4 RNAi. Contrary to this hypothesis, both ufd-1 and npl-4 knockdown animals exhibited a significant reduction in defecation frequency compared to control RNAi-treated animals (Figure 1—figure supplement 2C). This reduction in DMP rate persisted even after 12 hours of exposure to P. aeruginosa (Figure 1—figure supplement 2D). Thus, the change in the DMP rate in ufd-1 and npl-4 knockdown animals is unlikely to be the reason for the reduced gut colonization by P. aeruginosa.”

In summary, we would like to thank the reviewers again for providing constructive and thoughtful feedback. We believe we have fully addressed all the concerns of the reviewers by carrying out several new experiments and modifying the text. The manuscript has undergone substantial revision and has thereby improved significantly. We do hope that the evidence in support of the conclusions is found to be complete in the revised manuscript.

Studying is a quest to remember and understand what we read. The real breakthrough in learning is in applying the material to real-world situations. Employers and teachers don't care that you know something like the back of your hand, they care what you do with that information. Regurgitating information because you are well studied is no longer relevant; experiential learning is the future. People don't have fond memories of that time they studied; fond memories derive from beneficial experiences.

The uniqueness of a thought is a beautiful thing. Devotion to a narrative isn't as persuasive and pervasive as an idea that is wholly unique and compelling. As free thinkers, we must challenge our notions of what is true by asking questions (even if those questions sometimes lead us astray). Part of a learning journey is finding your way to another place (Friere's act of becoming), even if you sometimes get lost in the process.)

To truly care about a subject, there has to be a connection that is made between the reader and the author. Without that human connection, there is no motivation to hear what a person has to say. It contributes to their ethos when you feel connected to them.

Within every learner, at some point, they must face their failings and confront their concept of reality; to truly question who they are and who they want to be. When someone endures this process, they can then achieve anything that they set their mind towards with conviction and zeal.

eLife Assessment

The identification of RBMX2 as a novel regulator linking mycobacterial infection to Epithelial-Mesenchymal Transition and cancer progression are fundamental findings that advance our understanding of a major research question about the link between infectious and non-infectious diseases, microbiology and oncology. It does so by introducing RBMX2 as a novel host factor, a potential therapeutic target and biomarker for both TB and lung cancer. The evidence provided is convincing because it is appropriate and the validated multi-omics methodologies used are in line with the current state of the art. This study will be of interest to scientists working in the fields of drug discovery, microbiology and oncology.

Reviewer #1 (Public review):

The authors have addressed all my concerns and have addressed them to my satisfaction.

Reviewer #3 (Public review):

Summary:

This study investigates the role of the host protein RBMX2 in regulating the response to Mycobacterium bovis infection and its connection to epithelial-mesenchymal transition (EMT), a key pathway in cancer progression. Using bovine and human cell models, the authors have wisely shown that RBMX2 expression is upregulated following M. bovis infection and promotes bacterial adhesion, invasion, and survival by disrupting epithelial tight junctions via the p65/MMP-9 signaling pathway. They also demonstrate that RBMX2 facilitates EMT and is overexpressed in human lung cancers, suggesting a potential link between chronic infection and tumor progression. The study highlights RBMX2 as a novel host factor that could serve as a therapeutic target for both TB pathogenesis and infection-related cancer risk.

Strengths:

The major strengths lie in its multi-omics integration (transcriptomics, proteomics, metabolomics) to map RBMX2's impact on host pathways, combined with rigorous functional assays (knockout/knockdown, adhesion/invasion, barrier tests) that establish causality through the p65/MMP-9 axis. Validation across bovine and human cell models and in clinical tissue samples enhances translational relevance. Finally, identifying RBMX2 as a novel regulator linking mycobacterial infection to EMT and cancer progression opens exciting therapeutic avenues.

Weaknesses:

There are a few minor weaknesses like grammatical errors, spelling mistakes. Also, the manuscript is too dense; improving the narratives in the Results and Discussion section could help readers follow the logic of the experimental design and conclusions.

Author response:

The following is the authors’ response to the original reviews.

Reviewer #1 (Public review):

Summary:

This manuscript presents a compelling study identifying RBMX2 as a novel host factor upregulated during Mycobacterium bovis infection.

The study demonstrates that RBMX2 plays a role in:

(1) Facilitating M. bovis adhesion, invasion, and survival in epithelial cells.

(2) Disrupting tight junctions and promoting EMT.

(3) Contributing to inflammatory responses and possibly predisposing infected tissue to lung cancer development.

By using a combination of CRISPR-Cas9 library screening, multi-omics, coculture models, and bioinformatics, the authors establish a detailed mechanistic link between M. bovis infection and cancer-related EMT through the p65/MMP-9 signaling axis. Identification of RBMX2 as a bridge between TB infection and EMT is novel.

Strengths:

This topic and data are both novel and significant, expanding the understanding of transcriptomic diversity beyond RBM2 in M. bovis responsive functions.

Weaknesses:

(1) The abstract and introduction sometimes suggest RBMX2 has protective anti-TB functions, yet results show it facilitates pathogen adhesion and survival. The authors need to rephrase claims to avoid contradiction.

We sincerely appreciate the reviewer's valuable feedback regarding the need to clarify RBMX2's role throughout the manuscript. We have carefully revised the text to ensure consistent messaging about RBMX2's function in promoting M. bovis infection. Below we detail the specific modifications made:\

(1) Introduction Revisions:

Changed "The objective of this study was to elucidate the correlation between host genes and the susceptibility of M.bovis infection" to "The objective of this study was to identify host factors that promote susceptibility to M.bovis infection"

Revised "RBMX2 polyclonal and monoclonal cell lines exhibited favorable phenotypes" to "RBMX2 knockout cell lines showed reduced bacterial survival"

Replaced "The immune regulatory mechanism of RBMX2" with "The role of RBMX2 in facilitating M.bovis immune evasion"

(2) Results Revisions:

Modified "RBMX2 fails to affect cell morphology and the ability to proliferate and promotes M.bovis infection" to "RBMX2 does not alter cell viability but significantly enhances M.bovis infection"

Strengthened conclusion in Figure 4: "RBMX2 actively disrupts tight junctions to facilitate bacterial invasion"

(3) Discussion Revisions:

Revised screening description: "We screened host factors affecting M.bovis susceptibility and identified RBMX2 as a key promoter of infection"

Strengthened concluding statement: "In summary, RBMX2 drives TB pathogenesis by compromising epithelial barriers and inducing EMT"

These targeted revisions ensure that:

All sections consistently present RBMX2 as promoting infection; the language aligns with our experimental finding; potential protective interpretations have been eliminated. We believe these modifications have successfully addressed the reviewer's concern while maintaining the manuscript's original structure and scientific content. We appreciate the opportunity to improve our manuscript and thank the reviewer for this constructive suggestion.

(2) While p65/MMP-9 is convincingly implicated, the role of MAPK/p38 and JNK is less clearly resolved.

We sincerely appreciate the reviewer's insightful comment regarding the roles of MAPK/p38 and JNK in our study. Our experimental data clearly demonstrated that RBMX2 knockout significantly reduced phosphorylation levels of p65, p38, and JNK (Fig. 5A), indicating potential involvement of all three pathways in RBMX2-mediated regulation.

Through systematic functional validation, we obtained several important findings:

In pathway inhibition experiments, p65 activation (PMA treatment) showed the most dramatic effects on both tight junction disruption (ZO-1, OCLN reduction) and EMT marker regulation (E-cadherin downregulation, N-cadherin upregulation);p38 activation (ML141 treatment) exhibited moderate effects on these processes; JNK activation (Anisomycin treatment) displayed minimal impact.

Most conclusively, siRNA-mediated silencing of p65 alone was sufficient to:

Restore epithelial barrier function

Reverse EMT marker expression

Reduce bacterial adhesion and invasion

These results establish a clear hierarchy in pathway importance: p65 serves as the primary mediator of RBMX2's effects, while p38 plays a secondary role and JNK appears non-essential under our experimental conditions. We have now clarified this relationship in the revised Discussion section to strengthen this conclusion.

This refined understanding of pathway hierarchy provides important mechanistic insights while maintaining consistency with all our experimental data. We thank the reviewer for this valuable suggestion that helped improve our manuscript.

(3) Metabolomics results are interesting but not integrated deeply into the main EMT narrative.

Thank you for this constructive suggestion. In this article, we detected the metabolome of RBMX2 knockout and wild-type cells after Mycobacterium bovis infection, which mainly served as supporting evidence for our EMT model. However, we did not conduct an in-depth discussion of these findings. We have now added a detailed discussion of this section to further support our EMT model.

ADD:Meanwhile, metabolic pathways enriched after RBMX2 deletion, such as nucleotide metabolism, nucleotide sugar synthesis, and pentose interconversion, primarily support cell proliferation and migration during EMT by providing energy precursors, regulating glycosylation modifications, and maintaining redox balance; cofactor synthesis and amino sugar metabolism participate in EMT regulation through influencing metabolic remodeling and extracellular matrix interactions; chemokine and cGMP-PKG signaling pathways may further mediate inflammatory responses and cytoskeletal rearrangements, collectively promoting the EMT process.

(4) A key finding and starting point of this study is the upregulation of RBMX2 upon M. bovis infection. However, the authors have only assessed RBMX2 expression at the mRNA level following infection with M. bovis and BCG. To strengthen this conclusion, it is essential to validate RBMX2 expression at the protein level through techniques such as Western blotting or immunofluorescence. This would significantly enhance the credibility and impact of the study's foundational observation.

Thank you for your comment. We have supplemented the experiments in this part and found that Mycobacterium bovis infection can significantly enhance the expression level of RBMX2 protein.

(5) The manuscript would benefit from a more in-depth discussion of the relationship between tuberculosis (TB) and lung cancer. While the study provides experimental evidence suggesting a link via EMT induction, integrating current literature on the epidemiological and mechanistic connections between chronic TB infection and lung tumorigenesis would provide important context and reinforce the translational relevance of the findings.

We sincerely appreciate the valuable comments from the reviewer. We fully agree with your suggestion to further explore the relationship between tuberculosis (TB) and lung cancer. In the revised manuscript, we will add a new paragraph in the Discussion section to systematically integrate the current literature on the epidemiological and mechanistic links between chronic tuberculosis infection and lung cancer development, including the potential bridging roles of chronic inflammation, tissue damage repair, immune microenvironment remodeling, and the epithelial-mesenchymal transition (EMT) pathway. This addition will help more comprehensively interpret the clinical implications of the observed EMT activation in the context of our study, thereby enhancing the biological plausibility and clinical translational value of our findings.

ADD:There is growing epidemiological evidence suggesting that chronic TB infection represents a potential risk factor for the development of lung cancer. Studies have shown that individuals with a history of TB exhibit a significantly increased risk of lung cancer, particularly in areas of the lung with pre-existing fibrotic scars, indicating that chronic inflammation, tissue repair, and immune microenvironment remodeling may collectively contribute to malignant transformation 74. Moreover, EMT not only endows epithelial cells with mesenchymal features that enhance migratory and invasive capacity but is also associated with the acquisition of cancer stem cell-like properties and therapeutic resistance 75. Therefore, EMT may serve as a crucial molecular link connecting chronic TB infection with the malignant transformation of lung epithelial cells, warranting further investigation in the intersection of infection and tumorigenesis.

Reviewer #2 (Public review):

Summary:

I am not familiar with cancer biology, so my review mainly focuses on the infection part of the manuscript. Wang et al identified an RNA-binding protein RBMX2 that links the Mycobacterium bovis infection to the epithelial-Mesenchymal transition and lung cancer progression. Upon mycobacterium infection, the expression of RBMX2 was moderately increased in multiple bovine and human cell lines, as well as bovine lung and liver tissues. Using global approaches, including RNA-seq and proteomics, the authors identified differential gene expression caused by the RBMX2 knockout during M. bovis infection. Knockout of RBMX2 led to significant upregulations of tight-junction related genes such as CLDN-5, OCLN, ZO-1, whereas M. bovis infection affects the integrity of epithelial cell tight junctions and inflammatory responses. This study establishes that RBMX2 is an important host factor that modulates the infection process of M. bovis.

Strengths:

(1) This study tested multiple types of bovine and human cells, including macrophages, epithelial cells, and clinical tissues at multiple timepoints, and firmly confirmed the induced expression of RBMX2 upon M. bovis infection.

(2) The authors have generated the monoclonal RBMX2 knockout cell lines and comprehensively characterized the RBMX2-dependent gene expression changes using a combination of global omics approaches. The study has validated the impact of RBMX2 knockout on the tight-junction pathway and on the M. bovis infection, establishing RBMX2 as a crucial host factor.

Weaknesses:

(1) The RBMX2 was only moderately induced (less than 2-fold) upon M. bovis infection, arguing its contribution may be small. Its value as a therapeutic target is not justified. How RBMX2 was activated by M. bovis infection was unclear.

Thank you for your valuable and constructive comments. In this study, we primarily utilized the CRISPR whole-genome screening approach to identify key factors involved in bovine tuberculosis infection. Through four rounds of screening using a whole-genome knockout cell line of bovine lung epithelial cells infected with Mycobacterium bovis, we identified RBMX2 as a critical factor.

Although the transcriptional level change of RBMX2 was less than two-fold, following the suggestion of Reviewer 1, we examined its expression at the protein level, where the change was more pronounced, and we have added these results to the manuscript.

Regarding the mechanism by which RBMX2 is activated upon M. bovis infection, we previously screened for interacting proteins using a Mycobacterium tuberculosis secreted and membrane protein library, but unfortunately, we did not identify any direct interacting proteins from M. tuberculosis (https://doi.org/10.1093/nar/gkx1173).

(2) Although multiple time points have been included in the study, most analyses lack temporal resolution. It is difficult to appreciate the impact/consequence of M. bovis infection on the analyzed pathways and processes.

We appreciate the valuable comments from the reviewers. Although our study included multiple time points post-infection, in our experimental design we focused on different biological processes and phenotypes at distinct time points:

During the early phase (e.g., 2 hours post-infection), we focused on barrier phenotypes during the intermediate phase (e.g., 24 hours post-infection), we concentrated more on pathway activation and EMT phenotypes;

And during the later phase (e.g., 48–72 hours post-infection), we focused more on cell death phenotypes, which were validated in another FII article (https://doi.org/10.3389/fimmu.2024.1431207).

We also examined the impact of varying infection durations on RBMX2 knockout EBL cellular lines via GO analysis. At 0 hpi, genes were primarily related to the pathways of cell junctions, extracellular regions, and cell junction organization. At 24 hpi, genes were mainly associated with pathways of the basement membrane, cell adhesion, integrin binding and cell migration By 48 hpi, genes were annotated into epithelial cell differentiation and were negatively regulated during epithelial cell proliferation. This indicated that RBMX2 can regulate cellular connectivity throughout the stages of M. bovis infection.

For KEGG analysis, genes linked to the MAPK signaling pathway, chemical carcinogen-DNA adducts, and chemical carcinogen-receptor activation were observed at 0 hpi. At 24 hpi, significant enrichment was found in the ECM-receptor interaction, PI3K-Akt signaling pathway, and focal adhesion. Upon enrichment analysis at 48 hpi, significant enrichment was noted in the TGF-beta signaling pathway, transcriptional misregulation in cancer, microRNAs in cancer, small cell lung cancer, and p53 signaling pathway.

Reviewer #3 (Public review):

Summary:

This study investigates the role of the host protein RBMX2 in regulating the response to Mycobacterium bovis infection and its connection to epithelial-mesenchymal transition (EMT), a key pathway in cancer progression. Using bovine and human cell models, the authors have wisely shown that RBMX2 expression is upregulated following M. bovis infection and promotes bacterial adhesion, invasion, and survival by disrupting epithelial tight junctions via the p65/MMP-9 signaling pathway. They also demonstrate that RBMX2 facilitates EMT and is overexpressed in human lung cancers, suggesting a potential link between chronic infection and tumor progression. The study highlights RBMX2 as a novel host factor that could serve as a therapeutic target for both TB pathogenesis and infection-related cancer risk.

Strengths:

The major strengths lie in its multi-omics integration (transcriptomics, proteomics, metabolomics) to map RBMX2's impact on host pathways, combined with rigorous functional assays (knockout/knockdown, adhesion/invasion, barrier tests) that establish causality through the p65/MMP-9 axis. Validation across bovine and human cell models and in clinical tissue samples enhances translational relevance. Finally, identifying RBMX2 as a novel regulator linking mycobacterial infection to EMT and cancer progression opens exciting therapeutic avenues.

Weaknesses:

Although it's a solid study, there are a few weaknesses noted below.

(1) In the transcriptomics analysis, the authors performed (GO/KEGG) to explore biological functions. Did they perform the search locally or globally? If the search was performed with a global reference, then I would recommend doing a local search. That would give more relevant results. What is the logic behind highlighting some of the enriched pathways (in red), and how are they relevant to the current study?

We appreciate the reviewer's thoughtful questions regarding our transcriptomic analysis. In this study, we employed a localized enrichment approach focusing specifically on gene expression profiles from our bovine lung epithelial cell system. This cell-type-specific analysis provides more biologically relevant results than global database searches alone.

Regarding the highlighted pathways, these represent:

Temporally significant pathways showing strongest enrichment at each stage:

(1) 0h: Cell junction organization (immediate barrier response)

(2) 24h: ECM-receptor interaction (early EMT initiation)

(3) 48h: TGF-β signaling (chronic remodeling)

Mechanistically linked to our core findings about RBMX2's role in:

(1) Epithelial barrier disruption

(2) Mesenchymal transition

(3) Chronic infection outcomes

We selected these particular pathways because they:

(1) Showed the most statistically significant changes (FDR <0.001)

(2) Formed a coherent biological narrative across infection stages

(3) Were independently validated in our functional assays

This targeted approach allows us to focus on the most infection-relevant pathways while maintaining statistical rigor.

(2) While the authors show that RBMX2 expression correlates with EMT-related gene expression and barrier dysfunction, the evidence for direct association remains limited in this study. How does RBMX2 activate p65? Does it bind directly to p65 or modulate any upstream kinases? Could ChIP-seq or CLIP-seq provide further evidence for direct RNA or DNA targets of RBMX2 that drive EMT or NF-κB signaling?

We sincerely appreciate the reviewer's in-depth questions regarding the mechanisms by which RBMX2 activates p65 and its association with EMT. Although the molecular mechanism remains to be fully elucidated, our study has provided experimental evidence supporting a direct regulatory relationship between RBMX2 and the p65 subunit of the NF-κB pathway. Specifically, we investigated whether the transcription factor p65 could directly bind to the promoter region of RBMX2 using CHIP experiments. The results demonstrated that the transcription factor p65 can physically bind to the RBMX2 region.

Furthermore, dual-luciferase reporter assays were conducted, showing that p65 significantly enhances the transcriptional activity of the RBMX2 promoter, indicating a direct regulatory effect of RBMX2 on p65 expression.

These findings support our hypothesis that RBMX2 activates the NF-κB signaling pathway through direct interaction with the p65 protein, thereby participating in the regulation of EMT progression and barrier function.

In our subsequent work papers, we will also employ experiments such as CLIP to further investigate the specific mechanisms through which RBMX2 exerts its regulatory functions.

ADD and Revise in Results:

To thoroughly verify the regulatory mechanism between RBMX2 and p65, we initiated our investigation by conducting an in-depth analysis of the RBMX2 promoter region to identify potential interactions with the transcription factor p65. Initially, we performed molecular docking simulations to predict the binding affinity and interaction patterns between RBMX2 and p65 proteins. These simulations revealed multiple amino acid residues within the RBMX2 protein that formed strong, stable interactions with p65. The docking analysis yielded a high docking score of 1978.643 (Fig. 7K), indicating a significant likelihood of a direct physical interaction between these two proteins.

To complement the protein-protein interaction analysis, we next investigated whether p65 could directly bind to the promoter region of the RBMX2 gene at the transcriptional level. Using the JASPAR database, a comprehensive resource for transcription factor binding profiles, we queried the RBMX2 promoter sequence for potential p65 binding sites. This analysis identified several putative binding motifs, suggesting that p65 may act as a transcriptional regulator of RBMX2 expression.

To experimentally validate this transcriptional regulatory relationship, we employed a dual-luciferase reporter assay. We cloned the RBMX2 promoter region containing the predicted p65 binding sites into a luciferase reporter plasmid. This construct was then co-transfected into cultured cells along with a plasmid expressing p65. The luciferase activity was significantly increased in cells expressing p65 compared to control groups, providing functional evidence that p65 enhances the transcriptional activity of the RBMX2 promoter (Fig. 7I).

Furthermore, to confirm the direct binding of p65 to the RBMX2 promoter in a chromatin context, we performed chromatin immunoprecipitation followed by quantitative PCR (ChIP-qPCR). In this assay, we used specific antibodies against p65 to immunoprecipitate chromatin fragments containing p65-bound DNA. The enriched DNA fragments were then analyzed using primers targeting the RBMX2 promoter region. Our results demonstrated a significant enrichment of the RBMX2 promoter in the p65 immunoprecipitated samples compared to the IgG control, thereby confirming that p65 physically associates with the RBMX2 promoter in vivo (Fig. 7J). Collectively, these findings-ranging from computational docking predictions to transcriptional reporter assays and ChIP validation-provide strong evidence supporting a direct regulatory interaction between p65 and RBMX2. This regulatory mechanism may play a critical role in the biological pathways involving these two molecules, particularly in contexts such as inflammation, immune response, or cellular stress, where p65 (a subunit of NF-κB) is known to be prominently involved.

(3) The manuscript suggests that RBMX2 enhances adhesion/invasion of several bacterial species (e.g., E. coli, Salmonella), not just M. bovis. This raises questions about the specificity of RBMX2's role in Mycobacterium-specific pathogenesis. Is RBMX2 a general epithelial barrier regulator or does it exhibit preferential effects in mycobacterial infection contexts? How does this generality affect its potential as a TB-specific therapeutic target?

Thank you for your valuable comments. When we initially designed this experiment, we were interested in whether the RBMX2 knockout cell line could confer effective resistance not only against Mycobacterium bovis but also against Gram-negative and Gram-positive bacteria. Surprisingly, we indeed observed resistance to the invasion of these pathogens, albeit weaker compared to that against Mycobacterium bovis.

Nevertheless, we believe these findings merit publication in eLife. Moreover, RBMX2 knockout does not affect the phenotype of epithelial barrier disruption under normal conditions; its significant regulatory effect on barrier function is only evident upon infection with Mycobacterium bovis.

Importantly, during our genome-wide knockout library screening, RBMX2 was not identified in the screening models for Salmonella or Escherichia coli, but was consistently detected across multiple rounds of screening in the Mycobacterium bovis model.

(4) The quality of the figures is very poor. High-resolution images should be provided.

Thank you for your feedback; we provided higher-resolution images.

(5) The methods are not very descriptive, particularly the omics section.

Thank you for your comments; we have revised the description of the sequencing section.

(6) The manuscript is too dense, with extensive multi-omics data (transcriptomics, proteomics, metabolomics) but relatively little mechanistic integration. The authors should have focused on the key mechanistic pathways in the figures. Improving the narratives in the Results and Discussion section could help readers follow the logic of the experimental design and conclusions.

Thank you for your valuable comments. We have streamlined the figures and revised the description of the results section accordingly.

Reviewer #2 (Recommendations for the authors):

(1) The first part of the results and the major conclusions largely overlap with the previous paper by the same authors (Frontiers in Immunology, https://doi.org/10.3389/fimmu.2024.1431207). The previous paper has already established that RBMX2 is induced upon infection as a host factor, and its knockout led to cell proliferation. Thus, the current paper should focus more on the mechanisms rather than repeating the previous story.

We appreciate the reviewer's careful reading and constructive feedback. We fully acknowledge the foundational work published in our Frontiers in Immunology paper (doi:10.3389/fimmu.2024.1431207), which established RBMX2 as an infection-induced host factor affecting cell proliferation. The current study represents a significant mechanistic extension of these initial findings, with the following key advances:

(1) Novel Mechanistic Insights (Current Study Focus):

Discovery of the p65/MMP-9 pathway as the central mechanism mediating RBMX2's effects on EMT (Figs. 4-6)

First demonstration of RBMX2's role in epithelial barrier disruption (Figs. 2-3)

Identification of temporal regulation patterns during infection progression (Fig. 7)

(2) Expanded Biological Scope:

Demonstration of RBMX2's function in both bovine and human cell systems (vs. previous bovine-only data)

Clinical correlation with TB lesions

Therapeutic potential assessment through pathway inhibition

(3) Technical Advancements:

CRISPR-based mechanistic validation (vs. previous siRNA approach)

Multi-omics integration (transcriptomics + metabolomics)

Advanced live-cell imaging

We have now:

Removed redundant proliferation data from Results

Sharpened the Introduction to highlight mechanistic questions

Added explicit discussion comparing both studies

The current work provides the first comprehensive mechanistic framework for RBMX2's role in TB pathogenesis, moving substantially beyond the initial observational findings. We believe these new insights into the molecular pathways and therapeutic implications represent an important advance for the field..

(2) Line 107-110: The CRISPR screening results are not provided. Has it been published, or is it an unpublished dataset? RBMX2 knockout cells exhibited 'significant' resistance to the infection. How significant? Data?

Thank you for your valuable comments. The library mentioned, along with data on another host factor, TOP1, is being submitted by another researcher from our laboratory to a journal, and we will cite each other in the future. RBMX2 ranked second in terms of enrichment among all the identified genes, and its knockout cell line exhibited the second highest anti-infective capacity among all the host factors.

(3) Line 152: The RNA-seq analysis has already been performed/reported in the previous Frontiers paper. Therein, 173 genes were found to be differentially expressed. In the current paper, 42 genes were differentially expressed in all three time points. If the addition of new time points were the highlight of this paper, why would the authors focus on differentially expressed genes from all three time points?

Thank you for your valuable comments.

In the newly added data, we aimed to investigate the temporal changes during Mycobacterium bovis infection of host cells.

Previous study (Frontiers): Single 24h timepoint → 173 DEGs

Current study: Three timepoints (0h, 24h, 48h) with 42 consistently regulated genes → Reveals temporally stable core regulators of infection response

On one hand, we briefly described in the manuscript those important genes that exhibited changes across all time points.

On the other hand, in the supplementary materials, we also focused on the enriched genes at each individual time point, to better understand the temporal dynamics regulated by RBMX2.

(4) Line 153: The '0 h' time point is in fact 2 h post-infection. Why did the authors skip the real 0h time point? All the analysis and data should be relative to the 0h pi, rather than relative to the WT at each time point.

We appreciate the reviewer's important question regarding our timepoint nomenclature. The experimental timeline was designed as follows:

(1) Infection Protocol:

2h to 0h: Bacterial co-culture (MOI 20:1)

0h: Gentamicin (100 μg/ml) added to kill extracellular bacteria

0h+: Monitored intracellular survival

(2) Rationale for "0h" Designation:

This marks the onset of intracellular infection phase when Extracellular bacteria are eliminated (validated by plating)Host cell responses to intracellular pathogens begin All subsequent measurements reflect genuine infection (not attachment)

(3)Technical Validation:

Confirmed complete extracellular killing by:

Culture supernatant plating (0 CFU after gentamycin)

Microscopy ( no surface-associated bacteria)

(4) Comparative Analysis:

All data are presented as:

Fold-change relative to uninfected controls at each timepoint

We have now:

Clarified the timeline in Methods

Specified "0h = post-gentamicin" in all figure legends

This standardized approach aligns with established intracellular pathogen studies (e.g., Cell Microbiol. 2018;20:e12840). We're happy to adjust terminology if "0hpi (post-invasion)" would be clearer.

(5) Figure 2F: The data should be compared to the 0h pi, and show the temporal changes of gene expression.

Thank you for your suggestion. We have added additional information to this section. At the same time, we also aim to focus on the changes in gene expression between RBMX2 knockout and wild-type (WT) samples.

We have now:

Added temporal expression profiles relative to 0hpi baseline (SFig.4C).

Clarified the dual normalization approach in Methods

Maintained original between-group comparisons for phenotypic correlation

(6) Line 207. Not all the proteins were down-regulated post-infection.

Thank you for your comment. The overall level of the Tight junction related protein is downregulated, although it may not show a significant change at a specific time point.

We have revised our description, changing the keyword from "All" to "Most."

(7) Line 278, the introduction of the H1299 cell line should appear earlier when it was mentioned for the first time in the manuscript.

Thank you for your comment. We have provided a description in the abstract and Result1.

ADD:

Abstrat: Meanwhile, we also validated the EMT process in human lung epithelial cancer cells H1299.

Result 1: Furthermore, RBMX2-silenced H1299 cells exhibited a higher survival rate compared to H1299 ShNc cells after M. bovis infection (Fig. 1H).

(8) Figure 4 is huge and almost illegible, which may be divided into two figures.

Thank you for your valuable comments. We have streamlined the figures and revised the description of the results section accordingly.

Reviewer #3 (Recommendations for the authors):

I encountered frequent grammatical and syntactic issues. Thoroughly revising the manuscript for English language and clarity, preferably with professional editing assistance, could increase the quality of the paper.

Thank you for your valuable comments; we will invite a professional editor to polish the language.

eLife Assessment

The article presents important findings describing the role of IL27 in maintaining HSCs at steady state, and in emergency haematopoiesis in response to T. goodii by limiting the inflammatory monocyte outcomes. The evidence provided are solid and support that IL27 acts at the level of HSCs and not downstream. This study will be of interest to immunologists and hematologists, as well as infectious disease researchers.

Reviewer #1 (Public review):

In the manuscript, Aldridge and colleagues investigate the role of IL-27 in regulating hematopoiesis during T. gondii infection. Using loss-of-function approaches, reporter mice, and the generation of serial chimeric mice, they elegantly demonstrate that IL-27 induction plays a critical role in modulating bone marrow myelopoiesis and monocyte generation to the infection site. The study is well-designed, with clear experimental approaches that effectively address the mechanisms by which IL-27 regulates bone marrow myelopoiesis and prevents HSC exhaustion. I have two minor comments that could enhance the conceptual framework of this study:

(1) The authors indirectly show that IL-27R expression on HSPCs is necessary for regulating HSC proliferation and preventing exhaustion. However, given that they have access to IL-27RFlox mice, they could cross these with Fgd5Cre mice to specifically delete IL-27R on long-term HSCs. This would provide direct evidence for the role of IL-27 signaling in LTHSCs during infection.

(2) Since memory T and B cells often home to the bone marrow, it would be interesting to consider the potential cross-talk between these cells, HSPCs, and IL-27 signaling during secondary T. gondii infection. A brief discussion of this possibility would strengthen the study's broader implications.

Reviewer #2 (Public review):

Aldridge et al. demonstrate the important role of IL-27 in limiting emergency myelopoiesis in response to Toxoplasma gondii infection. Interestingly, IL-27 acts specifically at the level of early haematopoietic progenitors, inducing STAT signalling, which, in this case, dampens proliferation and preserves HSC fitness.

They used different mouse genetic models such as HSC lineage tracing, IL27 and IL27R-deficient mice to show that :

HSCs actively participate in emergency myelopoiesis during Toxoplasma gondii infection.

The absence of IL27 and IL27R increases monocyte progenitors and monocytes, mainly inflammatory monocytes CCR2hi.

At steady state, loss of IL27 impairs HSC fitness as competitive transplantation shows long-term engraftment deficiency of IL27 BM cells. This impairment is exacerbated after infection.

IL27 is produced by various BM and other tissue cells at steady state and its expression increases with infection, mainly by increasing the number of monocytes producing it.

This article highlights a new mechanism that acts directly at the level of early hematopoietic cells to limit over-inflammation during infection.

Author response:

The following is the authors’ response to the original reviews.

Reviewer #1 (Public review):

In the manuscript, Aldridge and colleagues investigate the role of IL-27 in regulating hematopoiesis during T. gondii infection. Using loss-of-function approaches, reporter mice, and the generation of serial chimeric mice, they elegantly demonstrate that IL-27 induction plays a critical role in modulating bone marrow myelopoiesis and monocyte generation to the infection site. The study is well-designed, with clear experimental approaches that effectively adddress the mechanisms by which IL-27 regulates bone marrow myelopoiesis and prevents HSC exhaustion.

Reviewer #2 (Public review):

Summary:

Aldridge et al. aim to demonstrate the role of IL27 in limiting emergency myelopoiesis in response to Toxoplasma gondii infection by acting directly at the level of early haematopoietic progenitors.

They used different mouse genetic models, such as HSC lineage tracing, IL27 and IL27R-deficient mice, to show that:

(1) HSCs actively participate in emergency myelopoiesis during Toxoplasma gondii infection.

(2) The absence of IL27 and IL27R increases monocyte progenitors and monocytes, mainly inflammatory monocytes CCR2hi.

(3) At steady state, loss of IL27 impairs HSC fitness as competitive transplantation shows long-term engraftment deficiency of IL27 BM cells. This impairment is exacerbated after infection.

(4) IL27 is produced by various BM and other tissue cells at steady state, and its expression increases with infection, mainly by increasing the number of monocytes producing it.

Although it is indisputable that IL27 has a role in emergency myelopoiesis by limiting the number of proinflammatory monocytes in response to infection, the authors' claim that it acts only on HSCs and not on more committed progenitors (CMP, GMP, MP) is not supported by the quality of the data presented here, as described below in the weakness section. In addition, this study highlights a role for IL27 during infection, but does not focus on trained immunity, which is the focus of the targeted elife issue.

We thank the reviewer for these comments. We did try (and perhaps failed) to highlight that all cells within the HSPC category, which includes HSCs and MPPs, have the potential to contribute. The lack of IRGM1-RFP reporter expression in CMPs (Supp Fig5C) suggests that only HSCs and MPPs are progenitors that respond to IL-27 within the bone marrow, and thus that IL-27 signaling on these contributes to the effects observed on monopoiesis and peripheral monocyte populations. We have emphasized this in the revised manuscript, particularly in the introduction (line 82) and discussion (lines 469-472). While this manuscript does not focus solely on trained immunity, the impacts of infection regulating HSC differentiation and having a long-term impact on this compartment are a central theme of trained immunity. For example, Figure 6 and the supporting supplemental figures almost exclusively focus on the differentiation potential that is programed into LTHSCs by infection and the role of IL-27 in regulating this programing. Additionally, Figure 7 shows the long-term consequences of such training. The introduction      and discussion have been modified  to emphasize these connections to trained immunity.         

Weakness

(1) In Figure 4, MFI quantification is required. This figure also shows the expression level (FACS and RNA) in progenitors (GMP and CMP, GP, MP), which is quite similar to that of HSC at this level, so it is really surprising that CMP does not respond at all to IL27 (S5C).

As requested, we have included the MFIs, calculated as a fold change over control FMOs, in the revised manuscript. While HSPCs and CMPs show relatively similar RNA expression of Il27ra (Supp. Fig. 5 A), the levels of surface IL-27R expression by CMPs is lower than HSPCs (Fig. 4C, revised). Additional downstream progenitors (including GMPs) show highly reduced RNA expression and a corresponding low expression of the receptor protein. This is now more apparent with the quantified MFIs (Fig 4-5).

(2) Total BM was used to test the direct effect of IL27 on HSC. There could be an indirect effect from other more mature BM cells, even if they show lower receptor expression than HSC. This should be done on a different sorted population to prove the direct effect of IL27 on HSC. The authors need to look more closely at some stat-dependent genes or stat itself in different sorted cell populations, not just irgm1. It is also known that Stat is associated with increased HSC proliferation in response to IFN, which is the opposite of what is observed here.

We thank the reviewer for this question. We have found that the methanol fixation required to detect pSTAT disrupted the ability to stain for HSPCs by flow cytometry. Thus, we used the IRGM1 reporter, which we have found to be a sensitive and high-fidelity reporter of STAT1 activity while preserving epitope markers of HSPCs.

We agree that the use of bulk bone marrow in the in vitro stimulations could allow for the activation of non-HSPC cell types that are IL-27R+. This is now emphasized in the text. However, there are advantages to this bulk approach as it allows simultaneous analysis of all HSPC populations and downstream progenitors in the same cultures, allowing the ability to assess how the small numbers of IL-27R expressing lymphocytes present in these cultures respond (data that are now included, Supp. Fig. 5C). These cultures also allow a direct comparison of our IL-27R expression analysis with responsiveness to IL-27. Only a selection of the populations analyzed are shown in these data; however, all populations in Figure 4A were also analyzed in Supp. Fig. 5C. These data sets directly correlate receptor expression with sensitivity to IL-27. If this effect was indirect (i.e the ability of IL-27 to induce IFN-γ) then we would expect more robust expression of the IRGM1 reporter across other cell populations. However, while IFN-γ stimulates broad expression of IRGM1, the effects of IL-27 are restricted to HSPC and mature lymphocytes (Supp. Fig. 5C). In other words, the cells that express the highest levels of the IL-27R are most responsive to IL-27.

While we do not directly measure HSPC proliferation in these cultures, we agree with the reviewer that the decreased proportions of proliferating HSPCs seen in the absence of IL-27 during infection (Fig. 7A) is a complex data set. The reviewer is also correct that interferons can promote HSC proliferations; however, they can also promote cell stress, DNA damage, and even cell death of HSCs during chronic exposure (reviewed extensively in Demerdash, Y., et al. Exp Hematol. 2021. PMID: 33571568). Thus IFNs, much like IL-27, appear to regulate HSPCs with contextual importance, inducing their proliferation but also death. The activation of STAT1 and STAT3 by IL-27 may be at the core of some of these effects observed in our data, and we point out that IL-10, another activator of STAT1+3, has been shown to limit HSC responses to inflammation (lined 58-62), but we have also presented other possibilities in the discussion.

(3) The decrease in HSC fitness in IL27R KO at steady state could be an indirect effect of the increase in proinflammatory monocytes contributing to high levels of inflammatory cytokines in the BM and thus chronic HSC activation that is enhanced in response to infection. What is the pro-Inflammatory cytokine profile of the BM of IL27 OR IL27R deficient mice and of mixed chimera mice.

We thank the reviewer for this insightful comment. This was part of our stated rationale in generating the mixed WT:IL-27R-/- BM chimeras presented in Figure 2. In this mixed setting, there remained differences between the ability of the IL-27R sufficient and deficient stem cells to generate inflammatory macrophages. These results suggest that differences in the inflammatory environment do not account for the differences observed. This conclusion is further supported by the observation that the infection-induced levels of IFN-γ in the bone marrow are equivalent in the presence or absence of IL-27 (now included in the revised manuscript, Supp. Fig. 1F).

(4) Furthermore, the FACS profile of KI67/brdu of Figure 7 is doubtful, as it is shown in different literature that KSL are not predominantly quiescent as shown here, but about 50% are KI67-. This is also inconsistent with the increase of HSC observed in Figure 1. Quantification of total BruDU+ HSC and other progenitors is also important to quantify all cells that have proliferated during infection. As the repopulation of IL27-deficient BM is also lower in the absence of infection the proliation  of HSC in IL27R KO mice in the absence of infection is also important.

The comment indicates that the reviewer is concerned that our staining for Ki67 is on the low end of reported literature (~10-50% of LSKs, depending on age of the mice and simulation (Thapa R, et al. Stem Cell Res Ther. 2023. PMID: 37280691; Nies KPH, et al. Cytometry A. 2018. PMID: 30176186)). Our stains were performed on cells from infected mice, which does alter the classic markers used to identify HSPCs. For this reason, we are stringent with our gating strategy and may be excluding more HSPCs than are included in other reports. We have included our FMO control in the revised manuscript to indicate our gating approach (Supp. Fig. 9A). While the population of Ki67+ HSPCs is low, these results were consistent between our experiments and provide data sets that are interpretable.

(5) The immunofluorescence in Figure 3 shows a high level of background and it is difficult to see the GFP and tomato positive cells. In this sense, the number of HSCs quantified as Procr+ (more than 8000 on a single BM section) is inconsistent with the total number of HSCs that a BM can contain (i.e., around 6000 per BM as quantified in Figure 1).

We agree with the reviewer and have found that there is a high level of background in these stains. We have thresholded these images, as described in our methods, to minimize this. Additionally, the increased numbers of Procr+ cells in the imaging vs our flow data is expected, and has been reported by others (Steinert, EM, et al. Cell. 2015. PMID: 25957682).

(6) The addition of arrows to the figure will help to visualise positive cells. It is also not clear why the author normalised the GFP+ cells to the tomato+ cells in Figure 3D.

We thank the reviewer for this comment and have added the suggested arrows. We have also included a more detailed explanation for our normalization strategy.

(7) Furthermore, even if monocytes represent a high proportion of IL27-producing cells, they are only 50% of the cells at 5dpi, as shown in Figure 3 and S4. Without other monocyte markers, line 307 is incorrect.

We thank the reviewer for this clarification and have adjusted the text accordingly.

(8) How do the authors explain that in Figure 1, 5-10% of labelled precursors and monocytes can give 100% of monocytes? This would mean that only labelled HSC can differentiate into PEC monocytes. 5

We thank the reviewer for their interest in this result. Monocytes and macrophages are some

Reviewer #1 (Recommendations for the authors):

I have two minor comments that could enhance the conceptual framework of this study:

(1) The authors indirectly show that IL-27R expression on HSPCs is necessary for regulating HSC proliferation and preventing exhaustion. However, given that they have access to IL-27RFlox mice, they could cross these with Fgd5Cre mice to specifically delete IL-27R on long-term HSCs. This would provide direct evidence for the role of IL-27 signaling in LTHSCs during infection.

We appreciate this comment and did attempt this experiment with several HSPC specific Cres, including the Procr-cre (used elsewhere in the manuscript) and the MDS1-cre-ERT2 (Jackson Laboratory Strain #:032863). Unfortunately, validation revealed that deletion efficiency of the IL-27R with these HSCspecific Cre lines was inefficient, and so experiments are ongoing to enhance efficiency of the deletion and test alternative Cre lines (such as the Fgd5-cre).

(2) Since memory T and B cells often home to the bone marrow, it would be interesting to consider the potential cross-talk between these cells, HSPCs, and IL-27 signaling during secondary T. gondii infection. A brief discussion of this possibility would strengthen the study's broader implications.

We thank the reviewer for this opportunity. We have previously investigated the interplay between immune cells in the bone marrow (Glatman Zaretsky A, et al. Cell Rep. 2017. PMID: 28228257) and now include these possibilities in the discussion (line 465-470).

Reviewer #2 (Recommendations for the authors):

Minor points:

(1) Figures 6F and 7B: should be shown as % of donor and not total number to clarify the lineage potency of LTHSC. The fact that the results of transplantation are separated into different figures makes it not easy to follow. To see if the increase in monocyte production by IL27 KO BM is specific, the percent of donorderived cells for other populations, such as lymphoid, but also in MP, and inflammatory monocytes, is necessary to confirm Figure 2.

Perhaps there has been a misunderstanding? In these plots, we are not analyzing mixed chimeras but single transfer chimeras into lethally irradiated hosts. Thus, the % of donor reaches ~80- 90%. However, to measure the actual output of the HSPCs, the cell number was necessary to compare amongst groups. Additional description is provided in the figure legends and in the text of the manuscript (lines 391-392, 434-436, 651-653, and 680-682).

(2) The heavy UMAP description is unnecessary. Responses As requested, we have reduced this description of how the UMAPs were derived.

As requested, we have reduced this description of how the UMAPs were derived

Alan cuddling my toddler self when I awake in the night scared of the thunder during a storm

Lying under a cosy, soft blanket and being read a story

Enjoying a nourishing drink of water after bad excrement

Basically, "duplex recovery" is calculated as: identify every dsDNA read (a read which has at least 1 read from the opposite strand); recovery is "the number of bases on all dsDNA reads divided by the number of bases on all reads". Max is 100%.

Willendorf was very cool!

Digital Media & Learning should invert the weekly rhythm of school so that praxis is not the add-on but the spine. Replacing conventional homework with community praxis blocks embedded in the timetable (regular, protected hours when learners work in the world of self-selected problems with accountable partners). Credit is earned through change logs, witness statements, and public debriefs rather than quizzes. Courses become civic studios: the city is the lab, reflection is the instrument, and transformation is the deliverable. This isn't service learning as charity; it is curriculum as collective action, where "media" includes posters, bylaw drafts, street maps, performances, and policy memos that alter conditions on the ground.

The classroom must be recast as a guild where novices and masters co-produce their craft, and authority must be demonstrated through responsiveness, not presumed by position. The asymmetry must be broken as roles need to be reversible for a learning exchange to occur.

The antidote is a "make-witness-revise" curriculum that privileges deeds over declarations. Weeks are structured around building something that did not exist on Monday, witnessing its effects in a real context by Wednesday, and revising by Friday after a public critique. Talk remains, but as residue of work rather than its substitute: critique circles, exhibition days, and field journaling become the assessment score. Media here are not slides but artifacts and arrangements (gardens, pop-up exhibits, neighborhood wayfinding, micro-museums) that readers can touch and residents can use. In this design, the volume of words matters less than their capacity to tee up a change that can be seen, felt, and contested.

DML can institutionalize the why. A weekly 'why' ticket asks each learner to pose a question that would change the next module if taken seriously; an orchestration service clusters submissions and spins up mini design sprints to chase the most generative threads. The breakthrough is curricular responsiveness as scale. The course renews itself from the questions of its participants, and questions becomes a practiced habit rather than a sporadic act of courage; building to the collective schema of the participants within the discoursal community.

This is not a poetic aside; it is an architectural requirement. In DML, the syllabus itself should be fork-able: readings, cases, datasets, and media are version-controlled, and learners submit pull requests that change the course canon in real time. The innovation is curricular co-ownership made technical. Student do not merely contribute posts in this context; they merge content into the backbone of the course, building an evidentiary trail that can be studied as a new kind of learning dataset akin to a repository of knowledge.

Passivity breeds fragmentation. Design integrative assignments that require connecting and weaving multiple perspectives into a single tapestry of human thought and expression.

Authority as scaffolding, not silencing. Provide exemplars + criteria, then get out of the way of creativity. To truly pursue education, student must be set on the path of learning as they are guided to their own unique views on topics rather than dragged along that path.

Preservation rhetoric can mask stagnation. Require students to nominate a reading with a justified alternative. Innovation leads to new perspectives and new ways of thinking which can open the door for social and educational enlightenment.

This is definitely something that I need to remember to do. Often I highlight or underline passages from a text because they have meaning in the moment and I recognize that it is something that relates to another topic in some way or form. However, I do not always leave myself notes in the margin because I feel as though I will be able to remember it or that getting through the passage is more important. Because of this, I will sometimes come back and not remember the significance of the highlighted text.

This is a great insight, as doing so will help retain information gleaned from the selection. By reading the selection twice, you are also able to catch details you may have missed, helping build a greater understanding both of the material and the style in which the author is writing.

add space btwn 12. and Copyright

add space btwn 11. and Applicable

add space btwn 10. and Minors

add space

symbolism of the eagle being the leader and the creator of man and woman

add space

add space

add space

add space

add space

add space

add space

delete?

add space

add space

add space

address should be 350 N Clark St, Suite 350, 60654

eLife Assessment

This important study describes the effect of beta-glucan innate training of macrophages and its effect on uptake of tumour cells and on the production of inflammatory cytokines. The data are convincing and show decreased phagocytic activity of apoptotic tumour cells accompanied by lower levels of secreted IL-1β, and in vivo findings are also provided in the revision. This finding has potential impact on designing potential macrophage-targeted cancer immuno-therapeutic approaches.

Reviewer #1 (Public review):

Summary:

The authors were attempting to describe if trained innate immunity would modulate antibody dependent-cellular phagocytosis (ADCP) and/or efferocytosis.

Strengths:

The use of primary murine macrophages, and not a cell line, is considered a strength.

The trained immunity mediated changes to phagocytosis affected both myeloma and breast cancer cells. The broad effect is consistent with trained immunity.

In this revised manuscript, the authors now include in vivo data to show in vivo relevance.

Weaknesses:

There are many types of cancers so it would be helpful to focus the title more for the types of cancers included in the present study, the most relevant of course would be the type of cancer used for the in vivo model.

Reviewer #3 (Public review):

Summary:

Chatzis et al showed that β-glucan trained macrophages have decreased phagocytic activity of apoptotic tumor cells and that is accompanied by lower levels of secreted IL-1β using mouse model.

Strengths:

This finding has potential impact on designing new cancer immunotherapeutic approaches by targeting macrophage efferocytosis.

The concerns have been addressed.

Author response:

The following is the authors’ response to the original reviews.

Reviewer #1 (Public review):

Summary:

The authors were attempting to describe whether trained innate immunity would modulate antibody-dependent cellular phagocytosis (ADCP) and/or efferocytosis.

Strengths:

The use of primary murine macrophages, and not a cell line, is considered a strength. The trained immunity-mediated changes to phagocytosis affected both melanoma and breast cancer cells. The broad effect is consistent with trained immunity.

Weaknesses:

The most significant weakness, also noted by the authors in the discussion, is the lack of in vivo data. Without these data, it is not possible to put the in vitro data in context. It is unknown if the described effects on efferocytosis will be relevant to the in vivo progression of cancer.

We thank the reviewer for these comments. To examine the role of trained immunity on the modulation of macrophage efferocytosis in vivo, we performed immunostaining analysis in sections from B16F10 tumour samples.

Importantly, we found that macrophage efferocytosis of apoptotic tumour cells was significantly decreased in the tumour tissue that was excised from mice treated with β-glucan 7 days prior to tumour inoculation (supplementary Figure 3). These data are consistent with our findings using co-culture assays further strengthening the impact of our key findings in this report.

Reviewer #2 (Public review):

Summary:

The authors follow up their preclinical work on beta-glucan-induced trained immunity in murine tumor models that they published in Cell in 2020. In particular, they focus on the role of trained immunity and efferocytosis of cancer cells

Strengths:

While properly conducted, the work is underwhelming and fully depends on in vitro observations performed with co-cultures of bone marrow derived macrophages from beta-glucantreated mice and tumor cell lines. From these in vitro studies, the authors conclude that trained immunity induction has no effect on antibody-dependent cellular phagocytosis, while it decreases efferocytosis.

Weaknesses:

It would be important to study these phenomena in tumor mouse models in vivo. The authors clearly have the expertise as they have shown in previous studies. Especially because the in vitro observation appears to conflict with the in vivo anti-tumor found in mice prophylactically treated with beta-glucan. Clearly, trained immunity is associated with diverse cellular responses and mechanisms, some of which may promote tumor growth, as the current manuscript suggests, but in the absence of in vivo studies, it is merely a mechanistic exercise of which the relevance is difficult to determine.

We thank the reviewer for raising this important comment. We have followed reviewer’s suggestion and examined the role of trained immunity on the modulation of macrophage efferocytosis in vivo. As mentioned in our response to Reviewer 1, we demonstrate that efferocytosis of apoptotic melanoma cells in situ was attenuated in tumour samples from ‘trained’ mice as compared to those from controltreated mice.

Efferocytosis displays a pro-tumour and immunosuppressive role, therefore both our in vitro co-culture (Figure 1) and in vivo (supplementary Figure 3) findings are consistent with our previously published in vivo data supporting the tumour-suppressive role of prophylactic treatment with β-glucan (Kalafati, Kourtzelis et al, PMID: 33125892). 

Reviewer #3 (Public review):

Summary:

Chatzis et al showed that β-glucan trained macrophages have decreased phagocytic activity of apoptotic tumor cells and that is accompanied by lower levels of secreted IL-1β using a mouse model. Strengths: This finding has a potential impact on designing new cancer immunotherapeutic approaches by targeting macrophage efferocytosis.

Weaknesses:

Whether this finding could be applied to other scenarios is underdetermined.

(1)  Does the decrease of efferocytosis also occur in human monocytes/macrophages after training?

(2)  Both β-glucan and BCG are well-trained innate immunity agents, the authors showed that β-glucan decreased efferocytosis via IL-1 β, so it is interesting to know whether BCG has a similar effect.

We thank the reviewer for these comments. Our data suggest that induction of trained immunity with β-glucan contributes to decreased macrophage efferocytosis of tumour cells based on co-culture and in vivo approaches in a mouse setting.  

We agree with the reviewer that utilisation of a human setting would be important to provide additional validation of our findings.

Induction of trained immunity entails epigenetic and metabolic reprogramming of hematopoietic stem and progenitor cells (HSPCs). As such, the elucidation of mechanisms that modulate trained immunity in human cells would require the establishment of a macrophage differentiation model based on the use of HSPCs rather than the stimulation of monocytes or macrophages with β-glucan.

Additionally, the investigation of the impact of BCG in trained immunity-dependent phagocytosis would require the assessment of all different types of phagocytic cargos (apoptotic melanoma and breast cancer cells, apoptotic neutrophils, microbial bioparticles) as we did in the case of the β-glucan.  The capacity of different molecules to induce trained immunity in the efferocytosis setting requires further investigation that would be beyond the scope of this study. Therefore, we plan to address these very interesting points in a future study.

Additional text was added in the Discussion section to clarify the reviewer's points. In addition, we provide a more specific title that reflects better the specificity of our findings.

Tin Tin sitting next to me and saying wise words to me after I have experienced bad excrement earlier before

Alan comforting me when I wake up in the night sleepless

eLife Assessment

The manuscript provides important findings on how striatal projection neurons regulate spontaneous locomotion speed in the context of implicit motivation and distinct contextual valence. The manuscript presented convincing supporting evidence for the findings. This work will be of broad interest to neuroscientists in the fields of basal ganglia, movement control, and cognition.

Reviewer #1 (Public review):

Summary:

This fundamental work employed multidisciplinary approaches and conducted rigorous experiments to study how a specific subset of neurons in the dorsal striatum (i.e., "patchy" striatal neurons) modulates locomotion speed depending on the valence of naturalistic contexts.

Strengths:

The scientific findings are novel and original and significantly advance our understanding of how the striatal circuit regulates spontaneous movement in various contexts.

Weaknesses:

This is extensive research involving various circuit manipulation approaches. Some of these circuit manipulations are not physiological. This is discussed.

Reviewer #2 (Public review):

Hawes et al. investigated the role of striatal neurons in the patch compartment of the dorsal striatum. Using Sepw1-Cre line, the authors combined a modified version of the light/dark transition box test that allows them to examine locomotor activity in different environmental valence with a variety of approaches, including cell-type-specific ablation, miniscope calcium imaging, fiber photometry, and opto-/chemogenetics. First, they found ablation of patchy striatal neurons resulted in an increase in movement vigor when mice stayed in a safe area or when they moved back from more anxiogenic to safe environments. The following miniscope imaging experiment revealed that a larger fraction of striatal patchy neurons was negatively correlated with movement speed, particularly in an anxiogenic area. Next, the authors investigated differential activity patterns of patchy neurons' axon terminals, focusing on those in GPe, GPi, and SNr, showing that the patchy axons in SNr reflect movement speed/vigor. Chemogenetic and optogenetic activation of these patchy striatal neurons suppressed the locomotor vigor, thus demonstrating their causal role in the modulation of locomotor vigor when exposed to valence differentials. Unlike the activation of striatal patches, such a suppressive effect on locomotion was absent when optogenetically activating matrix neurons by using the Calb1-Cre line, indicating distinctive roles in the control of locomotor vigor by striatal patch and matrix neurons. Together, they have concluded that nigrostriatal neurons within striatal patches negatively regulate movement vigor, dependent on behavioral contexts where motivational valence differs.

The strengths of this work include the use of multiple experimental approaches, including genetic/viral ablation of patch neurons, miniscope single-cell imaging, as well as projection-specific recording of axonal activity by fiber photometry, and causal manipulation of the neurons by chemogenetic and optogenetics. Although similar findings were reported previously, the authors' results will be of value owing to multiple levels of investigation. In my view, this study will add to the important literature by demonstrating how patch (striosomal) neurons in the striatum controls movement vigor.

Reviewer #3 (Public review):

Hawes et al. combined behavioral, optical imaging, and activity manipulation techniques to investigate the role of striatal patch SPNs in locomotion regulation. Using Sepw1-Cre transgenic mice, they found that patch SPNs encode locomotion deceleration in a light-dark box procedure through optical imaging techniques. Moreover, genetic ablation of patch SPNs increased locomotion speed, while chemogenetic activation of these neurons decreased it. The authors concluded that a subtype of patch striatonigral neurons modulates locomotion speed based on external environmental cues.

In the revision, the authors have largely addressed my concerns with additional explanation and discussion, although some of the key experiments to strengthen the authors' claim by identifying the function of specific cell populations remain to be conducted due to technical challenges. Nevertheless, the current results remain valuable and interesting to a wide audience in the field.

Author response:

The following is the authors’ response to the previous reviews

Reviewer #1 (Public review): 

Summary:

This fundamental work employed multidisciplinary approaches and conducted rigorous experiments to study how a specific subset of neurons in the dorsal striatum (i.e., "patchy" striatal neurons) modulates locomotion speed depending on the valence of the naturalistic context. 

Strengths: 

The scientific findings are novel and original and significantly advance our understanding of how the striatal circuit regulates spontaneous movement in various contexts.  Response: We appreciate the reviewer’s positive evaluation.

Weaknesses: 

This is extensive research involving various circuit manipulation approaches. Some of these circuit manipulations are not physiological. A balanced discussion of the technical strengths and limitations of the present work would be helpful and beneficial to the field. Minor issues in data presentation were also noted. 

We have incorporated the recommended discussion of technical limitations and addressed the physiological plausibility of our manipulations on Page 33 of the revised Discussion section. Specifically, we wrote: 

“Judicious interpretation of the present data must consider the technical limitations of the various methods and circuit-level manipulations applied. Patchy neurons are distributed unevenly across the extensive structure of the striatum, and their targeted manipulation is constrained by viral spread in the dorsal striatum. Somatic calcium imaging using single-photon microscopy captures activity from only a subset of patchy neurons within a narrow focal plane beneath each implanted GRIN lens. Similarly, limitations in light diffusion from optical fibers may reduce the effective population of targeted fibers in both photometry and optogenetic experiments. For example, the more modest locomotor slowing observed with optogenetic activation of striatonigral fibers in the SNr compared to the stronger effects seen with Gq-DREADD activation across the dorsal striatum could reflect limited fiber optic coverage in the SNr.Alternatively, it may suggest that non-striatonigral mechanisms also contribute to generalized slowing. Our photometry data do not support a role for striatopallidal projections from patchy neurons in movement suppression. The potential contribution of intrastriatal mechanisms, discussed earlier, remains to be empirically tested. Although the behavioral assays used were naturalistic, many of the circuit-level interventions were not. Broad ablation or widespread activation of patchy neurons and their efferent projections represent non-physiological manipulations. Nonetheless, these perturbation results are interpreted alongside more naturalistic observations, such as in vivo imaging of patchy neuron somata and axon terminals, to form a coherent understanding of their functional role”.

Reviewer #2 (Public review):

Hawes et al. investigated the role of striatal neurons in the patch compartment of the dorsal striatum. Using Sepw1-Cre line, the authors combined a modified version of the light/dark transition box test that allows them to examine locomotor activity in different environmental valence with a variety of approaches, including cell-type-specific ablation, miniscope calcium imaging, fiber photometry, and opto-/chemogenetics. First, they found ablation of patchy striatal neurons resulted in an increase in movement vigor when mice stayed in a safe area or when they moved back from more anxiogenic to safe environments. The following miniscope imaging experiment revealed that a larger fraction of striatal patchy neurons was negatively correlated with movement speed, particularly in an anxiogenic area. Next, the authors investigated differential activity patterns of patchy neurons' axon terminals, focusing on those in GPe, GPi, and SNr, showing that the patchy axons in SNr reflect movement speed/vigor. Chemogenetic and optogenetic activation of these patchy striatal neurons suppressed the locomotor vigor, thus demonstrating their causal role in the modulation of locomotor vigor when exposed to valence differentials. Unlike the activation of striatal patches, such a suppressive effect on locomotion was absent when optogenetically activating matrix neurons by using the Calb1-Cre line, indicating distinctive roles in the control of locomotor vigor by striatal patch and matrix neurons. Together, they have concluded that nigrostriatal neurons within striatal patches negatively regulate movement vigor, dependent on behavioral contexts where motivational valence differs.

We are grateful for the reviewer’s thorough summary of our main findings.

In my view, this study will add to the important literature by demonstrating how patch (striosomal) neurons in the striatum control movement vigor. This study has applied multiple approaches to investigate their functionality in locomotor behavior, and the obtained data largely support their conclusions. Nevertheless, I have some suggestions for improvements in the manuscript and figures regarding their data interpretation, accuracy, and efficacy of data presentation

We appreciate the reviewer’s overall positive assessment and have made substantial improvements to the revised manuscript in response to reviewers’ constructive suggestions.

(1) The authors found that the activation of the striatonigral pathway in the patch compartment suppresses locomotor speed, which contradicts with canonical roles of the direct pathway. It would be great if the authors could provide mechanistic explanations in the Discussion section. One possibility is that striatal D1R patch neurons directly inhibit dopaminergic cells that regulate movement vigor (Nadal et al., Sci. Rep., 2021; Okunomiya et al., J Neurosci., 2025). Providing plausible explanations will help readers infer possible physiological processes and give them ideas for future follow-up studies.

We have added the recommended data interpretation and future perspectives on Page 30 of the revised Discussion section. Specifically, we wrote:

“Potential mechanisms by which striatal patchy neurons reduce locomotion involve the supression of dopamine availability within the striatum. Dopamine, primarily supplied by neurons in the SNc and VTA,broadly facilitates locomotion (Gerfen and Surmeier 2011, Dudman and Krakauer 2016). Recent studies have shown that direct activation of patchy neurons leads to a reduction in striatal dopamine levels, accompanied by decreased walking speed (Nadel, Pawelko et al. 2021, Dong, Wang et al. 2025, Okunomiya, Watanabe et al. 2025). Patchy neuron projections terminate in structures known as “dendron bouquets”, which enwrap SNc dendrites within the SNr and can pause tonic dopamine neuron firing (Crittenden, Tillberg et al. 2016, Evans, Twedell et al. 2020). The present work highlights a role for patchy striatonigral inputs within the SN in decelerating movement, potentially through GABAergic dendron bouquets that limit dopamine release back to the striatum (Dong, Wang et al. 2025). Additionally, intrastriatal collaterals of patch spiny projection neurons (SPNs) have been shown to suppress dopamine release and associated synaptic plasticity via dynorphin-mediated activation of kappa opioid receptors on dopamine terminals (Hawes, Salinas et al. 2017). This intrastriatal mechanism may further contribute to the reduction in striatal dopamine levels and the observed decrease in locomotor speed, representing a compelling avenue for future investigation.”

(2) On page 14, Line 301, the authors stated that "Cre-dependent mCheery signals were colocalized with the patch marker (MOR1) in the dorsal striatum (Fig. 1B)". But I could not find any mCherry on that panel, so please modify it.

We have included representative images of mCherry and MOR1 staining in Supplementary Fig. S1 of the revised manuscript.

(3) From data shown in Figure 1, I've got the impression that mice ablated with striatal patch neurons were generally hyperactive, but this is probably not the case, as two separate experiments using LLbox and DDbox showed no difference in locomotor vigor between control and ablated mice. For the sake of better interpretation, it may be good to add a statement in Lines 365-366 that these experiments suggest the absence of hyperactive locomotion in general by ablating these specific neurons.

As suggested by the reviewer, we have added the following statement on Page 17 of the revised manuscript: “These data also indicate that PA elevates valence-specific speed without inducing general hyperactivity”.

(4) In Line 536, where Figure 5A was cited, the author mentioned that they used inhibitory DREADDs (AAV-DIO-hM4Di-mCherrry), but I could not find associated data on Figure 5. Please cite Figure S3, accordingly.

We have added the citation for the now Fig. S4 on Page 25 of the revised manuscript.

(5) Personally, the Figure panel labels of "Hi" and "ii" were confusing at first glance. It would be better to have alternatives.

As suggested by the reviewer, we have now labeled each figure panel with a distinct single alphabetical letter.

(6) There is a typo on Figure 4A: tdTomata → tdTomato

We have made the correction on the figure.

Reviewer #3 (Public review):

Hawes et al. combined behavioral, optical imaging, and activity manipulation techniques to investigate the role of striatal patch SPNs in locomotion regulation. Using Sepw1-Cre transgenic mice, they found that patch SPNs encode locomotion deceleration in a light-dark box procedure through optical imaging techniques. Moreover, genetic ablation of patch SPNs increased locomotion speed, while chemogenetic activation of these neurons decreased it. The authors concluded that a subtype of patch striatonigral neurons modulates locomotion speed based on external environmental cues. Below are some major concerns:

The study concludes that patch striatonigral neurons regulate locomotion speed. However, unless I missed something, very little evidence is presented to support the idea that it is specifically striatonigral neurons, rather than striatopallidal neurons, that mediate these effects. In fact, the optogenetic experiments shown in Fig. 6 suggest otherwise. What about the behavioral effects of optogenetic stimulation of striatonigral versus striatopallidal neuron somas in Sepw1-Cre mice?

Our photometry data implicate striatonigral neurons in locomotor slowing, as evidenced by a negative cross-correlation with acceleration and a negative lag, indicating that their activity reliably precedes—and may therefore contribute to—deceleration. In contrast, photometry results from striatopallidal neurons showed no clear correlation with speed or acceleration.

Figure 6 demonstrates that optogenetic manipulation within the SNr of Sepw1-Cre⁺ striatonigral axons recapitulated context-dependent locomotor changes seen with Gq-DREADD activation of both striatonigral and striatopallidal Sepw1-Cre⁺ cells in the dorsal striatum but failed to produce the broader locomotor speed change observed when targeting all Sepw1-Cre⁺ cells in the dorsal striatum using either ablation or Gq-DREADD activation. The more subtle speed-restrictive phenotype resulting from ChR activation in the SNr could, as the reviewer suggests, implicate striatopallidal neurons in broad locomotor speed regulation. However, our photometry data indicate that this scenario is unlikely, as activity of striatopallidal Sepw1-Cre⁺ fibers is not correlated with locomotor speed. Another plausible explanation is that the optogenetic approach may have affected fewer striatonigral fibers, potentially due to the limited spatial spread of light from the optical fiber within the SNr. Broad locomotor speed change in LDbox might require the recruitment of a larger number of striatonigral fibers than we were able to manipulate with optogenetics. We have added discussion of these technical limitations to the revised manuscript. Additionally, we now discuss the possibility that intrastriatal collaterals may contribute to reduced local dopamine levels by releasing dynorphin, which acts on kappa opioid receptors located on dopamine fibers (Hawes, Salinas et al. 2017), thereby suppressing dopamine release.

The reviewer also suggests an interesting experiment involving optogenetic stimulation of striatonigral versus striatopallidal somata in Sepw1-Cre mice. While we agree that this approach would yield valuable insights, we have thus far been unable to achieve reliable results using retroviral vectors. Moreover, selectively targeting striatopallidal terminals optogenetically remains technically challenging, as striatonigral fibers also traverse the pallidum, and the broad anatomical distribution of the pallidum complicates precise targeting. This proposed work will need to be pursued in a future study, either with improved retrograde viral tools or the development of additional mouse lines that offer more selective access to these neuronal populations as we documented recently (Dong, Wang et al. 2025).

In the abstract, the authors state that patch SPNs control speed without affecting valence. This claim seems to lack sufficient data to support it. Additionally, speed, velocity, and acceleration are very distinct qualities. It is necessary to clarify precisely what patch neurons encode and control in the current study.

We believe the reviewer’s interpretation pertains to a statement in the Introduction rather than the Abstract: “Our findings reveal that patchy SPNs control the speed at which mice navigate the valence differential between high- and low-anxiety zones, without affecting valence perception itself.” Throughout our study, mice consistently preferred the dark zone in the Light/Dark box, indicating intact perception of the valence differential between illuminated areas. While our manipulations altered locomotor speed, they did not affect time spent in the dark zone, supporting the conclusion that valence perception remained unaltered. We appreciate the reviewer’s insight and agree it is an intriguing possibility that locomotor responses could, over time, influence internal states such as anxiety. We addressed this in the Discussion, noting that while dark preference was robust to our manipulations, future studies are warranted to explore the relationship between anxious locomotor vigor and anxiety itself. We report changes in scalar measures of animal speed across Light/Dark box conditions and under various experimental manipulations. Separately, we show that activity in both patchy neuron somata and striatonigral fibers is negatively correlated with acceleration—indicating a positive correlation with deceleration. Notably, the direction of the cross-correlational lag between striatonigral fiber activity and acceleration suggests that this activity precedes and may causally contribute to mouse deceleration, thereby influencing reductions in speed. To clarify this, we revised a sentence in the Results section:

“Moreover, patchy neuron efferent activity at the SNr may causally contribute to deceleration, asindicated by the negative cross-correlational lag, thereby reducing animal speed.”. We also updated the Discussion to read: “Together, these data specifically implicate patchy striatonigral neurons in slowing locomotion by acting within the SNr to drive deceleration.”

One of the major results relies on chemogenetic manipulation (Figure 5). It would be helpful to demonstrate through slice electrophysiology that hM3Dq and hM4Di indeed cause changes in the activity of dorsal striatal SPNs, as intended by the DREADD system. This would support both the positive (Gq) and negative (Gi) findings, where no effects on behavior were observed.

We were unable to perform this experiment; however, hM3Dq has previously been shown to be effective in striatal neurons (Alcacer, Andreoli et al. 2017). The lack of effect observed in GiDREADD mice serves as an unintended but valuable control, helping to rule out off-target effects of the DREADD agonist JHU37160 and thereby reinforcing the specificity of hM3Dq-mediated activation in our study. We have now included an important caveat regarding the Gi-DREADD results, acknowledging the possibility that they may not have worked effectively in our target cells:

“Potential explanations for the negative results in Gi-DREADD mice include inherently low basal activity among patchy neurons or insufficient expression of GIRK channels in striatal neurons, which may limit the effectiveness of Gicoupling in suppressing neuronal activity (Shan, Fang et al. 2022).”

Finally, could the behavioral effects observed in the current study, resulting from various manipulations of patch SPNs, be due to alterations in nigrostriatal dopamine release within the dorsal striatum?

We agree that this is an important potential implication of our work, especially given that we and others have shown that patchy striatonigral neurons provide strong inhibitory input to dopaminergic neurons involved in locomotor control (Nadel, Pawelko et al. 2021, Lazaridis, Crittenden et al. 2024, Dong, Wang et al. 2025, Okunomiya, Watanabe et al. 2025). Accordingly, we have expanded the discussion section to include potential mechanistic explanations that support and contextualize our main findings.

Reviewer #1 (Recommendations for the authors):

Here are some minor issues for the authors' reference:

(1) This work supports the motor-suppressing effect of patchy SPNs, and >80% of them are direct pathway SPNs. This conclusion is not expected from the traditional basal ganglia direct/indirect pathway model. Most experiments were performed using nonphysiological approaches to suppress (i.e., ablation) or activate (i.e., continuous chemo-optogenetic stimulation). It remains uncertain if the reported observations are relevant to the normal biological function of patchy SPNs under physiological conditions. Particularly, under what circumstances an imbalanced patch/matrix activity may be induced, as proposed in the sections related to the data presented in Figure 6. A thorough discussion and clarification remain needed. Or it should be discussed as a limitation of the present work.

We have added discussion and clarification of physiological limitations in response to reviewer feedback. Additionally, we revised the opening sentence of an original paragraph in the discussion section to emphasize that it interprets our findings in the context of more physiological studies reporting natural shifts in patchy SPN activity due to cognitive conflict, stress, or training. The revised opening sentence now reads: “Together with previous studies of naturally occurring shifts in patchy neuron activation, these data illustrate ethologically relevant roles for a subgroup of genetically defined patchy neurons in behavior.”

(2) Lines 499-500: How striato-nigral cells encode speed and deceleration deserves a thorough discussion and clarification. These striatonigral cells can target both SNr GABAergic neurons and dendrites of the dopaminergic neurons. A discussion of microcircuits formed by the patchy SPNs axons in the SNr GABAergic and SNC DAergic neurons should be presented.

We have added this point at lines 499–500, including a reference to a relevant review of microcircuitry. Additionally, we expanded the discussion section to address microcircuit mechanisms that may underlie our main findings.

(3) Line 70: "BNST" should be spelled out at the first time it is mentioned.

This has been done.

(4) Line 133: only GCaMP6 was listed in the method, but GCaMP8 was also used (Figure 4). Clarification or details are needed.

Thank you for your careful attention to detail. We have corrected the typographical errors in the Methods section. Specifically, in the Stereotaxic Injections section, we corrected “GCaMP83” to “GCaMP8s.” In the Fiber Implant section, we removed the incorrect reference to “GCaMP6s” and clarified that GCaMP8s was used for photometry, and hChR2 was used for optogenetics.

(5) Line 183: Can the authors describe more precisely what "a moment" means in terms of seconds or minutes?

This has been done.

(6) Line 288: typo: missing / in ΔF

Thank you this has been fixed

(7) Line 301-302: the statement of "mCherry and MOR1 colocalization" does not match the images in Figure 1B.

This has been corrected by proving a new Supplementary Figure S1.

(8) Related to the statement between Lines 303-304: Figure 1c data may reflect changes in MOR1 protein or cell loss. Quantification of NeuN+ neurons within the MOR1 area would strengthen the conclusion of 60% of patchy cell loss in Figure 1C

Since the efficacy of AAV-FLEX-taCasp3 in cell ablation has been well established in our previous publications and those of others (Yang, Chiang et al. 2013, Wu, Kung et al. 2019), we do not believe the observed loss of MOR1 staining in Fig. 1C merely reflects reduced MOR1 expression. Moreover, a general neuronal marker such as NeuN may not reliably detect the specific loss of patchy neurons in our ablation model, given the technical limitations of conventional cell-counting methods like MBF’s StereoInvestigator, which typically exhibit a variability margin of 15–20%.

(9) Lines 313-314: "Similarly, PA mice demonstrated greater stay-time in the dark zone (Figure 1E)." Revision is needed to better reflect what is shown in Figure 1E and avoid misunderstandings.

Thank you this has been addressed.

(10) The color code in Figure 2Gi seems inconsistent with the others? Clarifications are needed

Color coding in Figure 2Gi differs from that in 2Eii out of necessity. For example, the "Light" cells depicted in light blue in 2Eii are represented by both light gray and light red dots in 2Gi. Importantly, Figure 2G does not encode specific speed relationships; instead, any association with speed is indicated by a red hue.

(11) Lines 538-539: the statement of "Over half of the patch was covered" was not supported by Figure 5C. Clarification is needed.

Thank you. For clarity, we updated the x-axis labels in Figures 1C and 5C from “% area covered” to “% DS area covered,” and defined “DS” as “dorsal striatal” in the corresponding figure legends. Additionally, we revised the sentence in question to read: “As with ablation, histological examination indicated that a substantial fraction of dorsal patch territories, identified through MOR1 staining, were impacted (Fig. 5C).”

(12) Figure 3: statistical significance in Figure 3 should be labeled in various panels.

We believe the reviewer's concern pertains to the scatter plot in panel F—specifically, whether the data points are significantly different from zero. In panel 3F, the 95% confidence interval clearly overlaps with zero, indicating that the results are not statistically significant.

(13) Figures 6D-E: no difference in the speed of control mice and ChR2 mice under continuous optical stimulation was not expected. It was different from Gq-DRADDS study in Figure 5E-F. Clarifications are needed.

For mice undergoing constant ChR2 activation of Sepw1-Cre+ SNr efferents, overall locomotor speed does not differ from controls. However, the BIL (bright-to-illuminated) effect on zone transitions isdisrupted: activating Sepw1-Cre⁺ fibers in the SNr blunts the typical increase in speed observed when mice flee from the light zone toward the dark zone. This impaired BIL-related speed increase upon exiting the light was similarly observed in the Gq-DREADD cohort. The reviewer is correct that this optogenetic manipulation within the SNr did not produce the more generalized speed reductions seen with broader Gq-DREADD activation of all Sepw1-Cre⁺ cells in the dorsal striatum. A likely explanation is the difference in targeting—ChR2 specifically activates SNr-bound terminals, whereas Gq-DREADD broadly activates entire Sepw1-Cre⁺ cells. Notably, many of the generalized speed profile changes observed with chemogenetic activation are opposite to those resulting from broad ablation of Sepw1-Cre⁺ cells. The more subtle speed-restrictive phenotype observed with ChR2 activation targeted to the SNr may suggest that fewer striatonigral fibers were affected by this technique, possibly due to the limited spread of light from the fiber optic. Broad locomotor speed change in LDbox might require the recruitment of a larger number of striatonigral fibers than we were able to manipulate with an optogenetic approach. Alternatively, it could indicate that non-striatonigral Sepw1-Cre⁺ projections—such as striatopallidal or intrastriatal pathways—play a role in more generalized slowing. If striatopallidal fibers contributed to locomotor slowing, we would expect to see non-zero cross-correlations between neural activity and speed or acceleration, along with negative lag indicating that neural activity precedes the behavioral change. However, our fiber photometry data do not support such a role for Sepw1-Cre⁺ striatopallidal fibers. We have also referenced the possibility that intrastriatal collaterals could suppress striatal dopamine levels, potentially explaining the stronger slowing phenotype observed when the entire striatal population is affected, as opposed to selectively targeting striatonigral terminals. These technical considerations and interpretive nuances have been incorporated and clarified in the revised discussion section.

(14) Lines 632: "compliment": a typo?

Yes, it should be “complement”.

(15) Figure 4 legend: descriptions of panels A and B were swapped

Thank you. This has been corrected.

(16) Friedman (2020) was listed twice in the bibliography (Lines 920-929).

Thank you. This has been corrected.

Reviewer #3 (Recommendations for the authors):

It will be helpful to label and add figure legends below each figure.

Thank you for the suggestion.

Editor's note:

Should you choose to revise your manuscript, if you have not already done so, please include full statistical reporting including exact p-values wherever possible alongside the summary statistics (test statistic and df) and, where appropriate, 95% confidence intervals. These should be reported for all key questions and not only when the p-value is less than 0.05 in the main manuscript. We noted some instances where only p values are reported.

Readers would also benefit from coding individual data points by sex and noting N/sex

We have included detailed statistical information in the revised manuscript. Both male and female mice were used in all experiments in approximately equal numbers. Since no sex-related differences were observed, we did not report the number of animals by sex.

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eLife Assessment

In this manuscript, Park et al. developed a multiplexed CRISPR construct to genetically ablate the GABA transporter GAT3 in the mouse visual cortex, with effects on population-level neuronal activity. This work is important, as it sheds light on how GAT3 controls the processing of visual information. The findings are compelling, leveraging state-of-the-art gene CRISPR/Cas9, in vivo two-photon laser scanning microscopy, and advanced statistical modeling.

Reviewer #1 (Public review):

Summary:

The authors have investigated the role of GAT3 in the visual system. First, they have developed a CRISPR/Cas9-based approach to locally knock out this transporter in the visual cortex. They then demonstrated electrophysiologically that this manipulation increases inhibitory synaptic input into layer 2/3 pyramidal cells. They further examined the functional consequences by imaging neuronal activity in the visual cortex in vivo. They found that absence of GAT3 leads to reduced spontaneous neuronal activity and attenuated neuronal responses and reliability to visual stimuli, but without an effect on orientation selectivity. Further analysis of this data suggests that Gat3 removal leads to less coordinated activity between individual neurons and in population activity patterns, thereby impaired information encoding. Overall, this is an elegant and technically advanced study that demonstrates a new and important role of GAT3 in controlling processing of visual information.

Strengths:

Development of a new approach for a local knockout (GAT3)

Important and novel insights into visual system function and its dependence on GAT3

Plausible cellular mechanism

Weaknesses:

No major weaknesses.

Reviewer #2 (Public review):

Summary:

Park et al. has made a tool for spatiotemporally restricted knockout of the astrocytic GABA transporter GAT3 leveraging CRISPR/Cas9 and viral transduction in adult mice, and evaluated the effects of GAT3 on neural encoding of visual stimulation.

Strengths:

This concise manuscript leverages state-of-the-art gene CRISPR/Cas9 technology for knocking out astrocytic genes. This has to a little degree been preformed previously in astrocytes and represents an important development in the field. Moreover they utilize in vivo two-photon imaging of neural responses to visual stimuli as a readout of neural activity, in addition to validating their data with ex vivo electrophysiology. Lastly, they use advanced statistical modeling to analyze the impact on GAT3 knockout. Overall, the study comes across as rigorous and convincing.

Weaknesses:

Adding the following experiments would potentially have strengthened the conclusions and helped interpret the findings, although may be considered outside the scope of this manuscript, and be pursued in future work:

(1) Neural activity is quite profoundly influenced by GAT3 knockout. Corroborating these relatively large changes to neural activity with in vivo electrophysiology of some sort as an additional readout would have strengthened the conclusions.

(2) Given the quite large effects on neural coding in visual cortex assessed with jRGECO imaging it would have been interesting the mouse groups could have been subjected to behavioral testing assessing the visual system.

Author response:

The following is the authors’ response to the original reviews.

Reviewer #1 (Public review):

Summary:

The authors have investigated the role of GAT3 in the visual system. First, they have developed a CRISPR/Cas9-based approach to locally knock out this transporter in the visual cortex. They then demonstrated electrophysiologically that this manipulation increases inhibitory synaptic input into layer 2/3 pyramidal cells. They further examined the functional consequences by imaging neuronal activity in the visual cortex in vivo. They found that the absence of GAT3 leads to reduced spontaneous neuronal activity and attenuated neuronal responses and reliability to visual stimuli, but without an effect on orientation selectivity. Further analysis of this data suggests that Gat3 removal leads to less coordinated activity between individual neurons and in population activity patterns, thereby impairing information encoding. Overall, this is an elegant and technically advanced study that demonstrates a new and important role of GAT3 in controlling the processing of visual information.

We are grateful to the reviewer for their positive appraisal of our work, including our technical advances and our demonstration of how cortical astrocytes play a role in visual information processing by neurons via GAT3-mediated regulation of activity.

Strengths:

(1)  Development of a new approach for a local knockout (GAT3).

(2)  Important and novel insights into visual system function and its dependence on GAT3.

(3)  Plausible cellular mechanism.

Weaknesses:

No major weaknesses were identified by this reviewer.

We thank the reviewer for highlighting the strengths of our study, including the development of a novel local knockout strategy for GAT3, the discovery of important functional consequences for visual system processing, and the identification of a plausible underlying cellular mechanism.

Reviewer #2 (Public review):

Summary:

Park et al. have made a tool for spatiotemporally restricted knockout of the astrocytic GABA transporter GAT3, leveraging CRISPR/Cas9 and viral transduction in adult mice, and evaluated the effects of GAT3 on neural encoding of visual stimulation.

Strengths:

This concise manuscript leverages state-of-the-art gene CRISPR/Cas9 technology for knocking out astrocytic genes. This has only to a small degree been performed previously in astrocytes, and it represents an important development in the field. Moreover, the authors utilize in vivo two-photon imaging of neural responses to visual stimuli as a readout of neural activity, in addition to validating their data with ex vivo electrophysiology. Lastly, they use advanced statistical modeling to analyze the impact of GAT3 knockout. Overall, the study comes across as rigorous and convincing.

We appreciate the reviewer’s endorsement of our experimental rigor and methodological innovation. We agree that combining in vivo and ex vivo measurements with rigorous analytical methods strengthens the overall conclusions of the study and demonstrates the important role of astrocytic GAT3 in cortical visual processing.

Weaknesses:

Adding the following experiments would potentially have strengthened the conclusions and helped with interpreting the findings:

(1) Neural activity is quite profoundly influenced by GAT3 knockout. Corroborating these relatively large changes to neural activity with in vivo electrophysiology of some sort as an additional readout would have strengthened the conclusions.

We agree that further investigation of neuronal activity at higher temporal resolution would provide valuable complementary data, particularly given the profound effects we observed using a pan-neuronal calcium indicator. Detailed in vivo electrophysiology—such as large-scale Neuropixel recordings—would allow assessment of single-neuron spiking dynamics and potentially cell-type specific responses following GAT3 deletion. While such an investigation is beyond the scope of the current study, we concur that it would be an important follow-up direction to further dissect the effects of GAT3 knockout on neuron activity profiles at both single-cell and population levels.

(2) Given the quite large effects on neural coding in visual cortex assessed på jRGECO imaging, it would have been interesting if the mouse groups could have been subjected to behavioral testing, assessing the visual system.

We appreciate the reviewer’s suggestion to explore potential behavioral consequences of GAT3 deletion. Based on our observed alterations in visual cortical activity, we agree that GAT3 knockout could impact visual discrimination-based behaviors. Astrocytes in the visual cortex are highly tuned to sensory and motor events and are generally known to shape behavioral outputs (Slezak et al., 2019; Kofuji & Araque, 2021). Our study suggests that regulation of inhibitory signaling via GAT3 transporters is a possible mechanism by which astrocytes influence visually guided behaviors. Although behavioral assessments fall beyond the scope of the current work, we agree with the reviewer’s suggestion and will pursue future experiments employing paradigms such as go/no-go visual detection or two-alternative forced choice to determine whether astrocytic GAT3 modulates visually guided behaviors and perceptual decisionmaking.  

Reviewer #1 (Recommendations for the authors):

It could be more clearly stated from the very beginning that a method was developed and used which, by itself, apparently has no cell type selectivity. It is highly plausible that the effects are mostly due to the absence of astrocytic GAT3, as discussed by the authors, but the distinction of what has been done and what is interpretation based on the literature is occasionally a bit blurry. This is also important because there are CRISPR/Cas9-based approaches that are astrocyte-specific (e.g., GEARBOCS).

We thank the reviewer for this helpful suggestion. As noted, our current approach does not confer celltype specificity on its own. Although our interpretation—supported by expression patterns and prior literature—attributes the observed effects primarily to astrocytic GAT3 loss, we agree that this distinction should be explicitly stated. We have revised the Introduction section (lines 83-87) to clarify that while MRCUTS allows for local gene knockout, it is not inherently cell-type specific unless combined with celltype restricted Cre drivers, as is possible in future applications.

A change of ambient GABA following GAT3 deletion is central to the proposed cellular mechanism. Demonstrating this directly would strengthen the manuscript (e.g., changed tonic GABAergic current in the absence of GAT3, and insensitivity to SNAP-5114).

While we recognize that directly quantifying ambient GABA levels would further strengthen our study, substantial evidence supports the role of GABA transporters in coordinately regulating both phasic and tonic inhibition and cellular excitability (Kinney, 2005; Keros & Hablitz, 2005; Semyanov et al. 2003).

Moreover, tonic GABA currents have been shown to strongly correlate with phasic inhibitory bursts (Glykys & Mody, 2007; Farrant & Nusser, 2005; Ataka & Gu, 2006), suggesting shared underlying regulatory mechanisms. Furthermore, as the reviewer correctly points out, alternative mechanisms such as non-vesicular GABA release or disinhibition via interneuron suppression cannot be excluded (also discussed in Kinney 2005). Given these considerations, we prioritized sIPSC measurements as a more integrative and reliable proxy for altered GABAergic signaling in L2/3 pyramidal neurons. We have revised the Discussion section (lines 329-333) to explain our choice of approach for further clarification.

We also agree it would be of interest to test whether GAT3 KO neurons exhibit insensitivity to SNAP-5114, both ex vivo and in vivo. However, based on our SNAP-5114 application experiments in vivo, which revealed only subtle effects on single-neuron properties (Figure S2A-F), we anticipate that interpreting a lack of effect in the KO condition would be challenging and potentially inconclusive.  

References

Ataka, T. & Gu, J. G. Relationship between tonic inhibitory currents and phasic inhibitory activity in the spinal cord lamina II region of adult mice. Mol. Pain. (2006).  

Bright, D. & Smart, T. Methods for recording and measuring tonic GABAA receptor-mediated inhibition. Front. Neural Circuits. 7, (2013).

Farrant, M. & Nusser, Z. Variations on an inhibitory theme: phasic and tonic activation of GABAA receptors. Nat. Rev. Neurosci. 6, 215–229 (2005).  

Glykys, J. & Mody, I. Activation of GABAA Receptors: Views from Outside the Synaptic Cleft. Neuron. 56, 763-770 (2007).

Keros, S. & Hablitz, J. J. Subtype-Specific GABA Transporter Antagonists Synergistically Modulate Phasic and Tonic GABAA Conductances in Rat Neocortex. J. Neurophysiol. 94, 2073–2085 (2005).

Kinney, G. A. GAT-3 Transporters Regulate Inhibition in the Neocortex. J. Neurophysiol. 94, 4533–4537 (2005).

Kofuji, P. & Araque, A. Astrocytes and Behavior. Annu. Rev. Neurosci. 44, 49–67 (2021).

Semyanov, A., Walker, M. & Kullmann, D. GABA uptake regulates cortical excitability via cell type–specific tonic inhibition. Nat. Neurosci. 6, 484–490 (2003).

Slezak, M., Kandler, S., Van Veldhoven, P. P., Van den Haute, C., Bonin, V. & Holt, M.G. Distinct

Mechanisms for Visual and Motor-Related Astrocyte Responses in Mouse Visual Cortex. Curr. Biol. 18, 3120-3127 (2019).

Apparently, Hardie is a brand of house siding. The implication of which I do not know.

Certainly a hook to set expectations and get readers interested

Hedging account: Account number related to Hedging transactions linked to series. If the there could be hedging transaction recorded to the series, than it must be must be set. Hedge type accounts can be selected.