They were clearly trying to take advantage of a nice spring to prepare for summer. They were obviously hard workers from the rest of this document.

I am unsure what alders are

I am unsure what alders are.

The Catholic school I went to was St. Mary and I heard this phrase every day! It plays and clearly has always played a big role for catholics.

I wonder what this looks like. Would ours be considered 2 deck?

Sentence structure is off, probably because of the translation.

This sounds like holding out hope.

Whenever I read or watch old stuff they seem to use this phrase.

The description of the place seems kind of sad. This is super descriptive and I can picture the place. It sounds like it would be beautiful to me, though.

There are churches everywhere now, so people do not really have long commutes anymore. Despite this, less people seem to go to church or to just listen online.

Religious house decor is interesting and representative of the people.

Originally written in French, then translated to English, which is clear from this portion of author, translater.

What does this mean?

This entire paragraph was filled with lots of emotions behind it. It discussed their way of life and how it was being expressed as being a surprise to them.

It is discussed how these people are different. But it seemed as though they were accepted

This heavily connects to our topic of migration this week for our weekly journal.

How romantic! The way people would speak back in day is so different on how we proclaim love to one in another today.

Interesting way to say that they prayed.

That's interesting to read. Why did it matter if they were ugly, young, or pretty?

That is interesting to read. I have never heard of the term, " speaker ended by adding his own laugh". Maybe he was trying to ease the speech.

boundaries

Tuberculosis (Pulmonary Infection (but she doesn't have any mucus...but she does have significant weight loss) Pneumonia?

Bacterial Infection (from cuts on arm?) Pulmonary fibrosis (only because patient vapes, chance is lower) COPD Pulmonary embolism (shortness of breath)

makes a point of religion as he is against it

ABAB rhyme scheme head said bare hair the poem also talks about the lost of innocence

historical setting, we don't have really chimney-sweepers anymore

I believe Blake tries to establish a sense of direction in one's life separate from religion by introducing virtues of mercy, pity, peace, and love and how the individual is clearly influenced by these virtues. I think he’s pretty much saying that regardless of what your religion is, all humans embody these virtues internally and throughout everyday life. It’s almost like a celebration of the human spirit and the goodness we have internally.

AABB pattern happening; there is a very youthful feel around the poem and the rhyme scheme adds to that child-like voice of innocence while covering much heavier topics.

emphasis on the nature of the poem where children's innocence is being stepped from them. also give physical dialogue that the children are crying

Using the imagery of comparing the colour of soot- a black powder to Tom's white hair, before it was shaved. Showing a duality, much like the themes and message of the poem.

meaning swampy/muddy ground -- illustrates how down in the dumps the child is, probably caked in mud, sad and crying. Breaks my heart :(

"freedom from civil disorder, internal peace of a nation" Through following Christ and not organized religion, one is free from the rigidity and confines of churches as institutions

"The" Shepherd; again reference to Christ (rather than "A" shepherd, "the" important one)

Coffins of black- meaning the soot the child would be breathing in and could let to their deaths. Also, it could foreshadow the children's death as in the following two stanzas, angels. God and the setting of a funeral are mentioned.

https://sites.udel.edu/britlitwiki/chimney-sweeper/

Summer is icumin vibes

A reference to Tom's innocence, using the word lamb and reference to his white hair. https://sites.udel.edu/britlitwiki/chimney-sweeper/

"containing all that can be received", "perfect, entire, utter" Christ is empowering and entirely oriented towards goodness

"Did he smile his work to see? / Did he who made the Lamb make thee?"

of or relating to people or nations that do not practice Christianity, Judaism, or Islam.

1. old-fashioned + often disparaging : a person who is not religious or whose religion is not Judaism, Islam, or especially Christianity.

2. old-fashioned + disapproving : a nonreligious or uncultured person.

The origins of heathen and pagan are semantically similar. Heathen likely comes from a term for a country inhabitant—in particular, a “heath dweller.”

Etymology: Middle English hethen, from Old English hǣthen; akin to Old High German heidan heathen, and probably to Old English hǣth heath

the whole poem invokes a sense of loss and longing. With dark and wet imagery, it seeks to make the reader feel as uncomfortable as the fatherless child. this animates the poem and make it feel as if you can touch the dew

Themes of nature as a glorified paradise and better way of being.

Christ referred to himself as a shepherd, Blake was a devout follower of Jesus Christ (though not organized religion); celebratory poem about Christ, his teachings, and the beauty of his lifestyle

Romanticism poems often have these proclamations of vivid imagination like "rising upon clouds" and "flying through fields on the wings of a bird" (from a Wordsworth poem I think). These kinds of lines invoke a strong sense of overwhelm for the reader, an otherworld feeling that stems from a vast imagination

1540s, "a tract or region of the earth," shortening of climate (or a nativization of Latin clima). It might usefully take up the old, abandoned "horizontal region of the earth" sense of climate, but it is used chiefly by the poets, and they display no evident agreement on what they mean by it.

poem about childhood which is a feature of Romantic poetry

This first line is straightforward and starts a poem about child labourers within chimney sweepers around 1789 when the 'songs of innocence' where published, https://en.wikipedia.org/wiki/The_Chimney_Sweeper#:~:text='%20Blake%20uses%20this%20poem%20to,labor%20in%20a%20corrupt%20society.

consonance: repetition of "S" sound

very confident assertion. potentially underestimating the powerful ideological drive of NPM proponents, and the willingness of those who gain power to subvert democracy in cases where their constituents (those who should benefit from these more efficient private bureaucracies) are unsatisfied and collectively wish to return to state-run, regulated provision of services

!!!

personification of earth throughout the poem -- makes the poem feel animated

This can be reflective of how the boys parents are taking advantage of him, forcing him to work; pretending what they are doing is good when the boy is suffering

https://www.derstandard.at/story/3000000237839/september-unwetter-waren-bisher-heftigste-regenfaelle-in-zentraleuropa

dreamy, romantic idealized

Soul & star "s" + Sound & sea "s" repeating

utopian, optimistic

rebellion, individuality

Altar, sword, and pen - god, death, and creation Rule of three Contrast of sword and pen, death & creation

they all seem to use the "fake it till you make it" strategy (mentalism, mind over matter)<br /> but most are stuck in the "fake it" phase, because the british/US empire is too strong

AABB rhyme scheme going, fast boy lost.

refers to a child trapped in a dangerous situation symbolically used for emotional despair.

repittion and opening of the line creates a sense of urgency for the father to respond to his little boy

Though the poem speaks to the general hubris of man, the historical context of the Romantic era could speak specifically towards a nervousness against the Industrial Revolution, the warning of 'Nothing beside remains' still being entirely possible to this day.

Etymology is rooted from Ramses II, commonly regarded as the most successful and powerful pharaoh in Egyptian history

alliteration

Alliteration of hand/heart; personification of hand + heart to emphasize the king's power

Alliteration

Alliteration

Die rechte italienische regierung will sich an die spitze der gegner des verbrenner verbots ab zweitausend fünfunddreißig in der eu stellen under bei einem treffen zur zukunft der europäischen automobilindustrie in brüssel wird der italienische industrieminister oder so für die sogenannte technologie offenheit und für den einsatz von biokraftstoffen argumentieren punkt außerdem plädiert er für einen europäischen fonds zur stützung der autor industrie und für einen schutz der europäischen industrien punkt a beruft sich dabei auch auf die vorschläge mario dragees kommt https://www.repubblica.it/economia/2024/09/24/news/stop_motori_termici_elettrico_urso_europa_auto-423517621/

Eine neue studie ergibt komma das das schmelzen des arktischen permafrosts zu einer schnellen intensivierung der waldbrände in kanada inspirieren führen und große mengen methan freisetzen wird kommt Waldbrände haben kanada zwanzig dreiundzwanzig zum viert größten krimi tänzen der welt gemacht punkt https://www.liberation.fr/environnement/climat/climat-le-degel-des-sols-va-entrainer-une-hausse-abrupte-des-feux-de-foret-en-arctique-20240924_OPVJLA4IV5ADXM6KNZOR4BUZDU/

for - Indyweb dev - history - Gyuri and Christopher 2019 paper

1. An indication or warning of a future occurrence; an omen.
2. A feeling or intuition of what is going to occur; a presentiment.
3. Prophetic significance or meaning.

v. (prĭ-sāj, prĕsĭj) pre·saged, pre·sag·ing, pre·sag·es

1. To indicate or warn of in advance; portend.
2. To have a presentiment of.
3. To foretell or predict.

The verb presage was predated by a noun presage, meaning "omen." Both forms derive from the Latin prefix prae- combined with the adjective sagus, meaning "prophetic." Foretell, predict, forecast, prophesy, and presage all mean "to tell beforehand."

Etymology - echo, but also from to cry (Latin) develops pathos. Also references the story of Narcissus (Greek) and the nymph who was obsessed with him; pathetic, unending obsession

readers are able to put aside any skepticism of the reality of what's written (this disbelief) and take the fantastic ideas to heart to emotionally connect (poetic faith)

The emotions attached are so real that the line between reality and not is blurred by the reader, for a second they believe the supernatural poems are real, and for that second they feel all the emotions attached to it, they just have to momentarily believe it real.

This quote relates to the American Yawp as well, because it goes more in-depth to explain how slave masters became more strict and strategic with how they carried on with enslavement, due to slaves becoming more educated and knowing how to free themselves and break away from oppression.

This quote also related to the American Yawp reading as it furthermore proves how enslavement was more so. popular in the Caribbean because it was more high demand. New England didn't choose to not participate in enslavement because they cared for Africans but because it was as high demand in those areas. However, New England still participated by buying the products produced by African slaves.

This quote relates to the American Yawp reading as they have the same idea of how groups of people of the same descent, do not come in agreement with each other due to being separated through enslavement. It is hard to stand as one when you are disassociated because of such hatred.

Der sturm boris ist durch die globale heizung zweimal wahrscheinlicher geworden komme und die menge der niederschläge lag circa sieben prozent höher komma als sie es in der vorindustriellen zeit gewesen wäre punkt das sind die ergebnisse einer attribution es viel in mitteleuropa mehr niederschlag komma als je zuvor gemessen wurdestudie von.World Weather Attribution.

https://www.liberation.fr/environnement/tempete-boris-les-pluies-diluviennes-en-europe-centrale-ont-ete-rendues-deux-fois-plus-probables-par-le-rechauffement-20240925_NUD2FMRCD5F67KQV4264EX4UOQ/

This study was the first to test stress recovery using physical measurements like muscle tension, skin conductance, and blood pressure. It found that people recovered from stress faster and more completely in natural settings compared to urban environments.

Research shows that exposure to nature is good for mental health, supported by many years of studies in environmental psychology. These studies highlight how time in natural environments helps restore mental well-being.

Cities get hotter due to a lack of green spaces and water features. Green areas help by stopping surfaces from absorbing heat, reducing pollution, and cooling the air through evaporation from plants.

Ecosystems can help slow down climate change by storing carbon, but climate change is already happening. So, while we work to prevent more damage, we also need to adjust to the changes that are already here.

The loss of biodiversity takes away important sources for many current medicines and reduces the chances of finding new drugs from plants, animals, and microbes. As species disappear, we lose potential cures for diseases, limiting future medical discoveries.

put emphasis in the poem by breaking conventional rhythms. the poem also describes the nature around them.

effective

To minify JS, CSS and HTML files, comments and extra spaces need to be removed, as well as crunch variable names so as to minimize code and reduce file size. The minified file version provides the same functionality while reducing the bandwidth of network requests.

In reality

easily understood

where your program will be executed

COMPILE TIME the time window during which a language's statements are converted into binary instructions for the processor to execute.

false

a way in which something is usually done.

not to allow

a comparison between one thing and another

purpose

Not good!

for - Indyweb - hyperpost is the precursor to Indyweb

for - Indyweb development - peergos

I wonder exactly how accurate this actually is. I wonder how closely you can tell age by these factors.

While home ranges are crucial for understanding animal behavior, there is significant variability in how different animals utilize these spaces.

Frey 데이터셋에서 생성된 이미지는 선명해 보이지만, NORB 데이터셋의 경우 매우 뭉개진 형태의 이미지가 생성된 것처럼 보입니다. 동일한 gray scale의 데이터셋임에도 불구하고 이러한 차이가 나는 원인이 무엇인지 궁금합니다.

alliteration of "m" and "s"

생성 품질을 평가하기 위해 log likelihood 기반의 평가 metric을 사용한 것 같은데, log likelihood가 실제 사람이 얼마나 real data로 느끼는 지를 평가할 수 있나요?

z가 동일한 input x에 대해서 noise가 더해지면서 매 학습마다 다른 값을 가지게 되는데, decoder를 학습시킬 때, 안정적으로 수렴할 수 있음을 보증할 수 있나요?

okay so nature itself isn't social- but the concepts and laws to define it are because they were created by the collective, a bunch of individual observations and similar sensations brought together and synthesized

every concept can be derived from the social realm as all concepts were developed socially

After historically having their culture overlooked it is refreshing to see Acadians take back their culture and language, sharing it in an entertaining way. Being able to joke and make light of what could be a hard topic to speak on.

Jeremías 18:1-11 Jehova en su misericordia los trata cómo el alfarero que lo intenta una y otra vez hasta que su artesanía queda como el espera. El es igual el da oportunidad para que los que obran con maldad, puedan cambiar, si se dejan moldear por su palabra.

eLife assessment

Using microscopy experiments and theoretical modelling, the authors present convincing evidence of cellular coordination in the gliding filamentous cyanobacterium Fluctiforma draycotensis. The results are important for the understanding of cyanobacterial motility and the underlying molecular and mechanical pathways of cellular coordination.

Reviewer #1 (Public review):

Summary:

The authors use microscopy experiments to track the gliding motion of filaments of the cyanobacteria Fluctiforma draycotensis. They find that filament motion consists of back-and-forth trajectories along a "track", interspersed with reversals of movement direction, with no clear dependence between filament speed and length. It is also observed that longer filaments can buckle and form plectonemes. A computational model is used to rationalize these findings.

Strengths:

Much work in this field focuses on molecular mechanisms of motility; by tracking filament dynamics this work helps to connect molecular mechanisms to environmentally and industrially relevant ecological behavior such as aggregate formation.

The observation that filaments move on tracks is interesting and potentially ecologically significant.

The observation of rotating membrane-bound protein complexes and tubular arrangement of slime around the filament provides important clues to the mechanism of motion.

The observation that long filaments buckle has the potential to shed light on the nature of mechanical forces in the filaments, e.g. through the study of the length dependence of buckling.

Weaknesses:

The manuscript makes the interesting statement that the distribution of speed vs filament length is uniform, which would constrain the possibilities for mechanical coupling between the filaments. However, Figure 1C does not show a uniform distribution but rather an apparent lack of correlation between speed and filament length, while Figure S3 shows a dependence that is clearly increasing with filament length. Also, although it is claimed that the computational model reproduces the key features of the experiments, no data is shown for the dependence of speed on filament length in the computational model. The statement that is made about the model "all or most cells contribute to propulsive force generation, as seen from a uniform distribution of mean speed across different filament lengths", seems to be contradictory, since if each cell contributes to the force one might expect that speed would increase with filament length.

The computational model misses perhaps the most interesting aspect of the experimental results which is the coupling between rotation, slime generation, and motion. While the dependence of synchronization and reversal efficiency on internal model parameters are explored (Figure 2D), these model parameters cannot be connected with biological reality. The model predictions seem somewhat simplistic: that less coupling leads to more erratic reversal and that the number of reversals matches the expected number (which appears to be simply consistent with a filament moving backwards and forwards on a track at constant speed).

Filament buckling is not analysed in quantitative detail, which seems to be a missed opportunity to connect with the computational model, eg by predicting the length dependence of buckling.

Reviewer #2 (Public review):

Summary:

The authors combined time-lapse microscopy with biophysical modeling to study the mechanisms and timescales of gliding and reversals in filamentous cyanobacterium Fluctiforma draycotensis. They observed the highly coordinated behavior of protein complexes moving in a helical fashion on cells' surfaces and along individual filaments as well as their de-coordination, which induces buckling in long filaments.

Strengths:

The authors provided concrete experimental evidence of cellular coordination and de-coordination of motility between cells along individual filaments. The evidence is comprised of individual trajectories of filaments that glide and reverse on surfaces as well as the helical trajectories of membrane-bound protein complexes that move on individual filaments and are implicated in generating propulsive forces.

Limitations:

The biophysical model is one-dimensional and thus does not capture the buckling observed in long filaments. I expect that the buckling contains useful information since it reflects the competition between bending rigidity, the speed at which cell synchronization occurs, and the strength of the propulsion forces.

Future directions:

The study highlights the need to identify molecular and mechanical signaling pathways of cellular coordination. In analogy to the many works on the mechanisms and functions of multi-ciliary coordination, elucidating coordination in cyanobacteria may reveal a variety of dynamic strategies in different filamentous cyanobacteria.

Reviewer #3 (Public review):

Summary:

The authors present new observations related to the gliding motility of the multicellular filamentous cyanobacteria Fluctiforma draycotensis. The bacteria move forward by rotating their about their long axis, which causes points on the cell surface to move along helical paths. As filaments glide forward they form visible tracks. Filaments preferentially move within the tracks. The authors devise a simple model in which each cell in a filament exerts a force that either pushes forward or backwards. Mechanical interactions between cells cause neighboring cells to align the forces they exert. The model qualitatively reproduces the tendency of filaments to move in a concerted direction and reverse at the end of tracks.

Strengths:

The observations of the helical motion of the filament are compelling.

The biophysical model used to describe cell-cell coordination of locomotion is clear and reasonable. The qualitative consistency between theory and observation suggests that this model captures some essential qualities of the true system.

The authors suggest that molecular studies should be directly coupled to the analysis and modeling of motion. I agree.

Weaknesses:

There is very little quantitative comparison between theory and experiment. It seems plausible that mechanisms other than mechano-sensing could lead to equations similar to those in the proposed model. As there is no comparison of model parameters to measurements or similar experiments, it is not certain that the mechanisms proposed here are an accurate description of reality. Rather the model appears to be a promising hypothesis.

Author response:

Public Reviews:

Reviewer #1 (Public review):

Summary:

The authors use microscopy experiments to track the gliding motion of filaments of the cyanobacteria Fluctiforma draycotensis. They find that filament motion consists of back-and-forth trajectories along a "track", interspersed with reversals of movement direction, with no clear dependence between filament speed and length. It is also observed that longer filaments can buckle and form plectonemes. A computational model is used to rationalize these findings.

We thank the reviewer for this accurate summary of the presented work.

Strengths:

Much work in this field focuses on molecular mechanisms of motility; by tracking filament dynamics this work helps to connect molecular mechanisms to environmentally and industrially relevant ecological behavior such as aggregate formation.

The observation that filaments move on tracks is interesting and potentially ecologically significant.

The observation of rotating membrane-bound protein complexes and tubular arrangement of slime around the filament provides important clues to the mechanism of motion.

The observation that long filaments buckle has the potential to shed light on the nature of mechanical forces in the filaments, e.g. through the study of the length dependence of buckling.

We thank the reviewer for listing these positive aspects of the presented work.

Weaknesses:

The manuscript makes the interesting statement that the distribution of speed vs filament length is uniform, which would constrain the possibilities for mechanical coupling between the filaments. However, Figure 1C does not show a uniform distribution but rather an apparent lack of correlation between speed and filament length, while Figure S3 shows a dependence that is clearly increasing with filament length. Also, although it is claimed that the computational model reproduces the key features of the experiments, no data is shown for the dependence of speed on filament length in the computational model. The statement that is made about the model "all or most cells contribute to propulsive force generation, as seen from a uniform distribution of mean speed across different filament lengths", seems to be contradictory, since if each cell contributes to the force one might expect that speed would increase with filament length.

We agree that the data shows in general a lack of correlation, rather than strictly being uniform. In the revised manuscript, we intend to collect more data from observations on glass to better understand the relation between filament length and speed. 

In considering longer filaments, one also needs to consider the increased drag created by each additional cell - in other words, overall friction will either increase or be constant as filament length increases. Therefore, if only one cell (or few cells) are generating motility forces, then adding more cells in longer filaments would decrease speed.

Since the current data does not show any decrease in speed with increasing filament length, we stand by the argument that the data supports that all (or most) cells in a filament are involved in force generation for motility. We would revise the manuscript to make this point - and our arguments about assuming multiple / most cells in a filament contributing to motility - clear.

The computational model misses perhaps the most interesting aspect of the experimental results which is the coupling between rotation, slime generation, and motion. While the dependence of synchronization and reversal efficiency on internal model parameters are explored (Figure 2D), these model parameters cannot be connected with biological reality. The model predictions seem somewhat simplistic: that less coupling leads to more erratic reversal and that the number of reversals matches the expected number (which appears to be simply consistent with a filament moving backwards and forwards on a track at constant speed).

We agree that the coupling between rotation, slime generation and motion is interesting and important when studying the specific mechanism leading to filament motion. However, we believe it even more fundamental to consider the intercellular coordination that is needed to realise this motion. Individual filaments are a collection of independent cells. This raises the question of how they can coordinate their thrust generation in such a way that the whole filament can both move and reverse direction of motion as a single unit. With the presented model, we want to start addressing precisely this point.

The model allows us to qualitatively understand the relation between coupling strength and reversals (erratic vs. coordinated motion of the filament). It also provides a hint about the possibility of de-coordination, which we then look for and identify in longer filaments.

While the model results seem obvious in hindsight, the analysis of the model allows phrasing the question of cell-to-cell coordination, which has not been brought up previously when considering the inherently multi-cell process of filament motility.

Filament buckling is not analysed in quantitative detail, which seems to be a missed opportunity to connect with the computational model, eg by predicting the length dependence of buckling.

Please note that Figure S10 provides an analysis of filament length and number of buckling instances observed. This suggests that buckling happens only in filaments above a certain length.

We do agree that further analyses of buckling - both experimentally and through modelling would be interesting.  This study, however,  focussed on cell-to-cell coupling / coordination during filament motility. We have identified the possibility of de-coordination through the use of a simple 1D model of motion, and found evidence of such de-coordination in experiments. Notice that the buckling we report does not depend on the filament hitting an external object. It is a direct result of a filament activity which, in this context, serves as evidence of cellular de-coordination.

Now that we have observed buckling and plectoneme formation, these processes need to be analysed with additional experiments and modelling. The appropriate model for this process needs to be 3D, and should ideally include torques arising from filament rotation. Experimentally, we need to identify means of influencing filament length and motion and see if we can measure buckling frequency and position across different filament lengths. These works are ongoing and will have to be summarised in a separate, future publication.

Reviewer #2 (Public review):

Summary:

The authors combined time-lapse microscopy with biophysical modeling to study the mechanisms and timescales of gliding and reversals in filamentous cyanobacterium Fluctiforma draycotensis. They observed the highly coordinated behavior of protein complexes moving in a helical fashion on cells' surfaces and along individual filaments as well as their de-coordination, which induces buckling in long filaments.

We thank the reviewer for this accurate summary of the presented work.

Strengths:

The authors provided concrete experimental evidence of cellular coordination and de-coordination of motility between cells along individual filaments. The evidence is comprised of individual trajectories of filaments that glide and reverse on surfaces as well as the helical trajectories of membrane-bound protein complexes that move on individual filaments and are implicated in generating propulsive forces.

We thank the reviewer for listing these positive aspects of the presented work.

Limitations:

The biophysical model is one-dimensional and thus does not capture the buckling observed in long filaments. I expect that the buckling contains useful information since it reflects the competition between bending rigidity, the speed at which cell synchronization occurs, and the strength of the propulsion forces.

Cell-to-cell coordination is a more fundamental phenomenon than the buckling and twisting of longer filaments, in that the latter is a consequence of limits of the former. In this sense, we are focussing here on something that we think is the necessary first step to understand filament gliding. The 3D motion of filaments (bending, plectoneme formation) is fascinating and can have important consequences for collective behaviour and macroscopic structure formation. As a consequence of cellular coupling, however, it is beyond the scope of the present paper.

Please also see our response above. We believe that the detailed analysis of buckling and plectoneme formation requires (and merits) dedicated experiments and modelling which go beyond the focus of the current study (on cellular coordination) and will constitute a separate analysis that stands on its own. We are currently working in that direction.

Future directions:

The study highlights the need to identify molecular and mechanical signaling pathways of cellular coordination. In analogy to the many works on the mechanisms and functions of multi-ciliary coordination, elucidating coordination in cyanobacteria may reveal a variety of dynamic strategies in different filamentous cyanobacteria.

We thank the reviewer for highlighting this point again and seeing the value in combining molecular and dynamical approaches.

Reviewer #3 (Public review):

Summary:

The authors present new observations related to the gliding motility of the multicellular filamentous cyanobacteria Fluctiforma draycotensis. The bacteria move forward by rotating their about their long axis, which causes points on the cell surface to move along helical paths. As filaments glide forward they form visible tracks. Filaments preferentially move within the tracks. The authors devise a simple model in which each cell in a filament exerts a force that either pushes forward or backwards. Mechanical interactions between cells cause neighboring cells to align the forces they exert. The model qualitatively reproduces the tendency of filaments to move in a concerted direction and reverse at the end of tracks.

We thank the reviewer for this accurate summary of the presented work.

Strengths:

The observations of the helical motion of the filament are compelling.

The biophysical model used to describe cell-cell coordination of locomotion is clear and reasonable. The qualitative consistency between theory and observation suggests that this model captures some essential qualities of the true system.

The authors suggest that molecular studies should be directly coupled to the analysis and modeling of motion. I agree.

We thank the reviewer for listing these positive aspects of the presented work and highlighting the need for combining molecular and biophysical approaches.

Weaknesses:

There is very little quantitative comparison between theory and experiment. It seems plausible that mechanisms other than mechano-sensing could lead to equations similar to those in the proposed model. As there is no comparison of model parameters to measurements or similar experiments, it is not certain that the mechanisms proposed here are an accurate description of reality. Rather the model appears to be a promising hypothesis.

We agree with the referee that the model we put forward is one of several possible. We note, however, that the assumption of mechanosensing by each cell - as done in this model - results in capturing both the alignment of cells within a filament (with some flexibility) and reversal dynamics. We have explored an even more minimal 1D model, where the cell’s direction of force generation is treated as an Ising-like spin and coupled between nearest neighbours (without assuming any specific physico-chemical basis). We found that this model was not fully able to capture both phenomena. In that model, we found that alignment required high levels of coupling (which is hard to justify except for mechanical coupling) and reversals were not readily explainable (and required additional assumptions). These points led us to the current, mechanically motivated model.

The parameterisation of the current model would require measuring cellular forces. To this end, a recent study has attempted to measure some of the physical parameters in a different filamentous cyanobacteria [1] and in our revision we will re-evaluate model parameters and dynamics in light of that study. We will also attempt to directly verify the presence of mechano-sensing by obstructing the movement of filaments.

eLife assessment

The authors present a solid statistical framework for using sibling phenotype data to assess whether there is evidence for de-novo or rare variants causing extreme trait values. Their valuable method is promising and will be of interest to researchers studying complex trait genetics.

Reviewer #1 (Public review):

This is a clever and well-done paper. The authors sought to craft a method, applicable to biobank-scale data but without necessarily using genotyping or sequencing, to detect the presence of de novo mutations and rare variants that stand out from the polygenic background of a given trait. Their method depends essentially on sibling pairs where one sibling is in an extreme tail of the phenotypic distribution and whether the other sibling's regression to the mean shows a systematic deviation from what is expected under a simple polygenic architecture.

Their method is successful in that it builds on a compelling intuition, rests on a rigorous derivation, and seems to show reasonable statistical power in the UK Biobank. (More biobanks of this size will probably become available in the near future.) It is somewhat unsuccessful in that rejection of the null hypothesis does not necessarily point to the favored hypothesis of de novo or rare variants. The authors discuss the alternative possibility of rare environmental events of large effect.

Comments on current version:

The authors have addressed the concerns of the reviewers. I have no further comments.

Author response:

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

eLife assessment

The authors present valuable findings on how to determine the genetic architecture of extreme phenotype values by using data on sibling pairs. While the authors' derivations of the method are correct, the scenarios considered are incomplete, making it difficult to have confidence in the interpretation of the results as demonstrating the influence of de-novo or Mendelian (rare, penetrant-variant) architectures. The method nevertheless shows promise and will be of interest to researchers studying complex trait genetics. 

A.1: We have now expanded our consideration of the scenarios and we have ensured that we do not over-interpret our results as being due to de novo or Mendelian architectures. Instead, we make clear that our statistical tests are powered to identify these architectures but that there are other potential causes of significant results (e.g. measurement error or uncontrolled environmental factors from heavy-tailed distributions), making follow-up validation studies necessary before underlying architectures can be confirmed. We consider this to be typical of observational research, in which significant results may indicate causal effects unless uncontrolled confounding factors explain the observed associations, requiring experimental/trial follow-up for validation. We believe that our tests are useful for providing initial inference, and that in some settings – e.g. prioritising samples for sequencing to identify rare variants – could be useful as an initial screening step to increase the efficacy of a planned analysis or study.

Additionally, we have now developed “SibArc”, an openly available software tool that takes input sibling trait data and estimates conditional sibling heritability across the trait distribution. Then - based on our theoretical framework developed and described in the paper - for each tail of the trait distribution, estimates effect sizes and generates P-values corresponding to our de novo and Mendelian tests, and performs a Kolmogorov-Smirnov test to identify general departures from our null model. Furthermore, SibArc also provides additional functionality for users under preliminary beta form, for example, running an iterative optimisation routine to infer approximate relative degrees of polygenic, de novo, and Mendelian architectures prevailing in each trait tail. We have made this software tool, Quick Start tutorial, and sample data available online at Github and are hosting these on a dedicated website: www.sibarc.net.

Reviewer #1 (Public Review):

This is a clever and well-done paper that should be published. The authors sought to craft a method, applicable to biobank-scale data but without necessarily using genotyping or sequencing, to detect the presence of de novo mutations and rare variants that stand out from the polygenic background of a given trait. Their method depends essentially on sibling pairs where one sibling is in an extreme tail of the phenotypic distribution and whether the other sibling's regression to the mean shows a systematic deviation from what is expected under a simple polygenic architecture. 

Their method is successful in that it builds on a compelling intuition, rests on a rigorous derivation, and seems to show reasonable statistical power in the UK Biobank. (More biobanks of this size will probably become available in the near future.)  It is somewhat unsuccessful in that rejection of the null hypothesis does not necessarily point to the favored hypothesis of de novo or rare variants. The authors discuss the alternative possibility of rare environmental events of large effect. Maybe attention should be drawn to this in the abstract or the introduction of the paper. Nevertheless, since either of these possibilities is interesting, the method remains valuable. 

A.2: We agree with the reviewer that we should have made it clearer that - while our statistical tests are powered to identify de novo and Mendelian architectures – significant findings from our tests could also be explained by rare environmental events of large effect (specifically by uncontrolled environmental factors with heavy-tailed distributions). We have now made this clear throughout the manuscript (see A.1).

Moreover, we agree with the reviewer that whether the cause of deviations from expectations are due to de novo or rare variants, or environmental factors, either possibility is interesting. For example, in either scenario, our results can highlight inaccuracy in PRS prediction of extreme trait values for certain traits, and also provides a relative measure across different traits of large effects impacting on the trait tails, irrespective of whether genetic or environmental. We now place more emphasis on this point throughout the manuscript.

Reviewer #2 (Public Review):

Souaiaia et al. attempt to use sibling phenotype data to infer aspects of genetic architecture affecting the extremes of the trait distribution. They do this by considering deviations from the expected joint distribution of siblings' phenotypes under the standard additive genetic model, which forms their null model. They ascribe excess similarity compared to the null as due to rare variants shared between siblings (which they term 'Mendelian') and excess dissimilarity as due to de-novo variants. While this is a nice idea, there can be many explanations for rejection of their null model, which clouds interpretation of Souaiaia et al.'s empirical results.

A.3: We agree with the reviewer that we should have made clearer that there are other explanations for significant results from our tests and we have now fully addressed this point – (see A.1, A.2, A.4, A.5 for more detail).  In addition, we now elaborate on exactly what our null hypothesis is: which is not only that the expected joint distribution of siblings’ phenotypes is governed by the standard additive genetic model, but that environmental effects are either controlled for or else their combined effect is approximately Gaussian. Furthermore, by selecting only those traits whose raw trait distribution most closely corresponds to a Gaussian distribution from the UK Biobank, we increase the probability that significant results from our tests are due to rare variants (shared or unshared among siblings).

The authors present their method as detecting aspects of genetic architecture affecting the extremes of the trait distribution. However, I think it would be better to characterize the method as detecting whether siblings are more or less likely to be aggregated in the extremes of the phenotype distribution than would be predicted under a common variant, additive genetic model.

A.4: As discussed above we should have stated more clearly that significant results could be due to non-genetic factors, we have now addressed this.

However, we do not think that it would be appropriate to characterise our tests as merely corresponding to over and under aggregation of siblings in the tails. Firstly, environmental factors should be controlled for as part of our testing, increasing the probability that significant results are due to genetic, and not environmental factors. Secondly, tests for identifying broad over and under aggregation of siblings in the tails should be designed differently and, accordingly, the tests that we have developed here would not be optimal to detect over/under aggregation of siblings in trait tails. Our test for inference of de novo variants, for example, exploits the fact that de novo alleles of large effect result in one sibling being extreme and all others being drawn from the background distribution, so that the mean of other siblings is relatively low – not merely that other siblings are less likely to be found in the tail. For more discussion on this issue in relation to one of reviewer 1’s points, see A.9.

Exactly how the rareness and penetrance of a genetic variant influence the conditional sibling phenotype distribution at the extremes is not made clear. The contrast between de-novo and 'Mendelian' architectures is somewhat odd since these are highly related phenomena: a 'Mendelian' architecture could be due to a de-novo variant of the previous generation. The fact that these two phenomena are surmised to give opposing signatures in the authors' statistical tests seems suboptimal to me: would it not be better to specify a parameter that characterizes the degree or sharing between siblings of rare factors of large effect? This could be related to the mixture components in the bimodal distribution displayed in Fig 1. In fact, won't the extremes of all phenotypes be influenced by all three types of variants (common, rare, de-novo) to greater or lesser degree? By framing the problem as a hypothesis testing problem, I think the authors are obscuring the fact that the extremes of real phenotypes likely reflect a mixture of causes: common, de-novo, and rare variants (and shared and non-shared environmental factors). 

A.5: We absolutely recognise that there will typically be a complex and continuous mix of genetic architectures underlying complex traits in their tails, dictated by the 2-dimensional relationship between allele frequency and effect size. We did consider developing a fully Bayesian statistical framework to model this, but soon realised that doing this properly would require a substantial amount of model development, accounting for multiple factors in ways that would require a great deal of further investigation; for example, performing a range of complex simulations to investigate the effects of different selective pressures over time, different patterns of assortative mating, and effect size generating distributions. We are in the process of applying for funding for a multi-year project that will perform exactly these investigations as a step towards developing more sophisticated models of inference. In the meantime, we do believe that the simpler hypothesis-testing framework that we have developed here does have important value. Assuming that environmental factors are accounted for, or that any that are not accounted for have combined Gaussian effects, then our tests will indeed infer enrichments of de novo and ‘Mendelian’ rare alleles of large effect in the tails of complex traits. Results from these tests can also be compared within and across traits to compare the relative degree of such enrichments among traits. For some traits we observe significant results from both tests, and for other traits we observe highly significant results from one of our tests but not the other. Thus, while our tests do not provide a complete picture about the genetic architecture in the tails of complex traits, they do offer some intriguing initial insights into tail architecture, important given the enrichment of disease in trait tails.

To better enable interpretation of the results of this method, a more comprehensive set of simulations is needed. Factors that may influence the conditional distribution of siblings' phenotypes beyond those considered include: non-normal distribution, assortative mating, shared environment, interactions between genetic and shared environmental factors, and genetic interactions. 

A.6: As described above (see A.5) we do agree that a more comprehensive set of simulations is exactly what is needed to further extend this work. However, we believe that the tests that we have developed so far, which make some simplifying assumptions that we think would often hold in practice, is a useful start to what is an entirely novel approach to inferring genetic architecture from family trait-only (non-genetic) data. Our work could already be useful for method developers who may wish to extend our approach in ways that we may not think of. It could also be useful for applied scientists focusing on specific traits who will be able to gain initial, inference-level, insights by applying our tests to their data, while the results of applying our tests may even guide study design of rare variant mapping studies.

In summary, I think this is a promising method that is revealing something interesting about extreme values of phenotypes. Determining exactly what is being revealed is going to take a lot more work, however. 

A.7: We thank the reviewer for highlighting the promise in our approach and agree that it is revealing something interesting about complex traits. We also agree that it is going to take a lot more work to reveal exactly what that is for different traits, which we plan to work on ourselves and hope that this paper will help other interested scientists to follow-up on and extend as well.

Recommendations for the authors:

Reviewer #1 (Recommendations For The Authors):

R.1.1: Why these particular traits (body fat, mean corpuscular haemoglobin, neuroticism, heel bone mineral density, monocyte count, sitting height)? 

A.8: Traits were initially selected to cover a variety of traits (anthropometric, metabolic, personality..) and to illustrate different examples of tail architecture. However, in response to a point from reviewer 2 (see A.17), we have now overhauled our quality control of traits to ensure that only traits closely matching Gaussian distributions are included. In total, 18 traits were selected, with detailed results presented in Appendix 4 and results corresponding to 6 of the traits presented in the main text (Figure 6) to show examples of different types of tail architecture.

R.1.2: Why are there separate tests for de novo and Mendelian architectures? It seems that one could use either of the derived tests for both purposes, simply by switching to a two-sided test for each tail. My guess is that the score test of whether alpha is zero would be the more statistically powerful test. 

A.9: The score test of whether alpha is zero has limited power to detect Mendelian architectures. This is because under Mendelian effects, half the siblings in a family have trait values reflecting the background distribution, such that the mean of sibling trait values is not so different from the polygenic expectation (i.e. alpha close to 0). The Mendelian score test that we developed is substantially more powerful because it evaluates co-occurrence of siblings in the tails, which is far higher under Mendelian architecture in the tail than compared to polygenic architecture.

However, in order test for general departures from our null model, including those of non-Gaussian environmental factors, we now include results from performing a Kolmogorov-Smirnoff test of difference from the expected distribution, and also provide this test as an option in our ‘SibArc’ software tool.

R.1.3: This method assumes that assortative mating is absent. I worry that sitting height might not be a good trait to analyze, since there is some assortative mating (~0.3) for height (e.g., Yengo et al., 2018). Perhaps this trait should not be included among those that are analyzed in this paper. Then again, it is possible that there is less assortative mating for sitting height than total height (i.e., leg length) (Jensen & Sinha, 1993). 

A.10:  It is true that our method assumes random mating. We note that while  assortative mating increases sibling similarity relative to expectation, if it is stable across the trait distribution it will also bias heritability estimation upward which is likely it’s potential impact in our framework.  However, if assortative mating is more prevalent in the tails of the distribution, it can result in excess kurtosis – an impact that can increase false positive Mendelian tests and false negative de novo tests.  Given that the trait distribution for Sitting Height has only moderate excess Kurtosis (~0.4, see Fig 9, Appendix 4) and we inferred de novo architecture only for this trait, we feel that including it in the paper is appropriate. 

R.1.4: I wonder if it's possible to discuss the impact of non-additive genetic variance on the method. How does this affect the estimation of heritability, which calibrates the expectation for regression to the mean? Can non-additive genetic deviations explain a rejection of the null hypothesis of simple polygenicity? 

A.11: Yes, the heritability estimation, which calibrates expectation for regression to the mean, assumes additivity of effects, as do the most popular estimators of heritability from GWAS data in the field: GCTA-GREML, LD Score regression and LDAK. Accordingly, non-additive genetic effects could result in rejection of the null hypothesis. We have highlighted this point in the Discussion. However, we also point out that current evidence suggests that the contribution of non-additive genetic effects to complex trait variation is relatively small (Hivert 2021) and that non-additive genetic effects that have a similar impact across the trait distribution should not be a problem for our approach (only those that have an increasing effect towards the tails would be).

R.1.5: p.5: Maybe a more realistic way to simulate a genetic architecture is to draw the MAF from the distribution [MAF(1 - MAF)]^{-1} and then an effect of the minor allele from some mound-shaped distribution (e.g., mixture of normals). The absolute or squared effect of the minor allele should increases as the MAF decreases, and there have been some papers trying to estimate this relationship (e.g., Zeng et al., 2021). Maybe make the number of causal SNPs 10,000. I don't rate this as an urgent suggestion because my sense is that the method should be robust, making adequate even a fairly minimal simulation confirming its accuracy. 

A.11: In separate work, we have performed a comprehensive simulation study using the forward-in-time population genetic simulator SLIM-3 (Haller and Messer, 2019), which generates genetic effects according to Gaussian and Gamma distributions and models different selective pressures on complex traits. We plan to publish this work shortly and also extend the simulations to family data, from which we will be able to test the performance of our methods here under a range of different scenarios of genetic variation generation, including a variety of relationships between allele frequency and effect sizes. We agree with the reviewer that at this point, however, our minimal simulation should be sufficient to confirm our tests’ general robustness and so we will perform further testing once we have extended our more sophisticated simulation study.

R.1.6: p.6: Step D seems to leave out a normalization of G to have unit variance. Also, the last part should say "the square of the correlation between the genetic liability and the trait is equal to the heritability." 

A.12: Corrected – we thank the reviewer for spotting this.

R.1.7: Figure 5: The power being adequate if roughly 1 of a 1000 index siblings with an extreme trait value owes their values to de novo mutations makes me think that there should be a discussion of the prior probability. The average person carries about 80 de novo mutations. How many of these are likely to affect, e.g., height? Zeng et al. (2021) gave estimates of mutational targets. Given that a mutation affects height, will its likely effect size be large enough to be detected with the method? Kemper et al. (2012) discussed this point in a perhaps useful way. 

A.13: We find the work investigating mutational target sizes and generating effect sizes of different mutations (de novo or rare) to be extremely interesting and critical for understanding the causes of observed genetic variation. However, we think that this work is insufficiently progressed at this point to build on directly here for making more nuanced interpretation of our results. We are, however, exploring the impact of mutational target sizes, effect size distributions and selection effects, on the genetic architecture of complex traits via population genetic simulations (see A.11), and so we hope to be able to provide more in-depth interpretation of our results in the future.

R.1.8: Figure 6: The number in the tables for Mendelian architecture are presumably observed and expected counts. But what about the numbers for de novo architecture? Those don't look like counts. Maybe they are conditional expectations of standardized trait values. Whatever the case may be, the caption should provide an explanation. 

A.14: The observed and expected values for the de novo statistical test represent the expected and observed mean standardized trait values for siblings of individuals in the bottom and top 1% of the distribution. We have now made this clear in our updated figure.

R.1.9: p. 16: Element (2,1) in the precision matrix after Equation 15 is missing a negative sign. 

A.15: Corrected – we thank the reviewer for spotting this.

R.1.10: p. 20: Shouldn't Equation 20 place an exponent of n on the factor outside of the exponential? 

A.16: Corrected – we thank the reviewer for spotting this.

Reviewer #2 (Recommendations For The Authors):

R.2.1: The first concern that I have is that their statistical tests rely heavily on an assumption of bivariate normal distribution for sibling pair's phenotypes. Real phenotypes do not have such a distribution in general. The authors rely upon an inverse-normal transform when applying their method to real data. While the inverse-normal transform will ensure that the siblings' phenotypes have a marginal normal distribution, such a transform does not ensure that the joint distribution is bivariate normal. The authors should examine their procedure for simulated phenotypes with a non-normal distribution to see if their statistical tests remain properly calibrated. Related to this, I am concerned about applying an inverse normal transform to the neuroticism phenotype that contains only 13 unique values in UKB. How does the transform deal with tied values? Can we sensibly talk about extreme trait values for such a set of observations? 

A.17: The reviewer is correct that a bivariate normal distribution for sibling pairs’ trait values does not necessarily hold, and only does so if the assumptions of our null model are met (polygenic effects, Gaussian environmental effects, random mating..). We have now more clearly described the assumptions of our null model, and to increase the matching of our selected traits to those assumptions we have expanded our analyses and now present results on traits that are close to Gaussian. As part of this more strict quality control, only traits with more than 50 unique values are included, meaning that neuroticism is excluded in our final analysis. We also now note that performing an inverse normal transformation on the traits only increases the robustness of the tests to some of our modelling assumptions. In future work we plan to investigate how best to model the conditional sibling distribution under a variety of non-Gaussian environmental effects and different non-random patterns of mating.

R.2.2: The joint sibling phenotype distribution (Equation 4) can be derived by applying the formula for the conditional distribution of a multivariate Gaussian to the standard additive genetic model. The authors' derivation is unnecessarily complex. Furthermore, many of the formulae have been used in Shai Carmi's work on embryo screening, but this work is not cited. 

A.18: We now state in the text that the conditional sibling distribution can also be derived from the joint trait distribution of related individuals, which we use in our extension to the 3-sibling scenario, and cite Shai Carmi’s work where this is used. The joint distribution is a more straightforward way to derive the conditional sibling distribution, but our derivation based on considering mid-parents is generalisable to cases where assumptions of random mating, Gaussian population trait distribution and no selection do not hold. We also think that our mid-parent based derivation will be more intuitive to many readers, leading to greater understanding and potential for extension. Therefore, overall we believe that its presentation is worthwhile and we have now elaborated on this in the Methods.

R.2.3: Equation 8: this probability should be conditional on s1 

A.19: Corrected – we thank the reviewer for spotting this.

R.2.4: The empirical application to UKB data is lacking methodological details. Also, the number of siblings used is low compared to the number of available sibling pairs. Around 19k sibling pairs are available in the UKB white British subsample, but only 10k were used for height. Why? Also, why are extreme values excluded? Isn't this removing the signal the authors are looking to explain?

A.20: We have now provided more methodological details throughout the Methods section, in particular in relation to the samples used and quality control performed. The removal of individuals with extreme values, in particular, is because unusually low/high trait values are more likely to be due to measurement error (e.g. due to imperfect measuring device, or storage/assaying) than for typical values, and so while this may also result in some loss in power (albeit small due to few individuals having values +/- 8 s.d. trait means) we consider it worth it for the potential reduction in type I error. In performing our newly expanded analysis (described above), and accounting for the reviewer’s point here about sample size, we did find a bug in our pipeline that meant that we did not include as many sibling pairs as available. We thank the reviewer for spotting this, since this contributed to our new analysis being substantially more powerful than the original (including up to ~17k sibling pairs depending on completeness of trait data).

Benjamin C Haller, Phillip W Messer. SLiM 3: Forward Genetic Simulations Beyond the Wright–Fisher Model. Molecular Biology and Evolution. 2019. 36(3): 632-637.

SD Whiteman, SM McHale, A Soli. Theoretical Perspectives on Sibling Relationships. J Fam Theory Rev. 2011 Jun 1;3(2):124-139.

Nicholas H Barton, Alison M Etheridge, and Amandine Véber. The infinitesimal model: Definition, derivation, and implications. Theoretical population biology, 118:50–73, 2017.

Valentin Hivert et al. “Estimation of non-additive genetic variance in human complex traits from a large sample of unrelated individuals.” American journal of human genetics vol. 108,5 (2021)

Author response:

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

Public Reviews:

Reviewer #1 (Public Review):

Summary:

The authors demonstrate that it is possible to carry out eQTL experiments for the model eukaryote S. cerevisiae, in "one pot" preparations, by using single-cell sequencing technologies to simultaneously genotype and measure expression. This is a very appealing approach for investigators studying genetic variation in single-celled and other microbial systems, and will likely inspire similar approaches in non-microbial systems where comparable cell mixtures of genetically heterogeneous individuals could be achieved.

Strengths:

While eQTL experiments have been done for nearly two decades (the corresponding author's lab are pioneers in this field), this single-cell approach creates the possibility for new insights about cell biology that would be extremely challenging to infer using bulk sequencing approaches. The major motivating application shown here is to discover cell occupancy QTL, i.e. loci where genetic variation contributes to differences in the relative occupancy of different cell cycle stages. The authors dissect and validate one such cell cycle occupancy QTL, involving the gene GPA1, a G-protein subunit that plays a role in regulating the mating response MAPK pathway. They show that variation at GPA1 is associated with proportional differences in the fraction of cells in the G1 stage of the cell cycle. Furthermore, they show that this bias is associated with differences in mating efficiency.

Weaknesses:

While the experimental validation of the role of GPA1 variation is well done, the novel cell cycle occupancy QTL aspect of the study is somewhat underexploited. The cell occupancy QTLs that are mentioned all involve loci that the authors have identified in prior studies that involved the same yeast crosses used here. It would be interesting to know what new insights, besides the "usual suspects", the analysis reveals. For example, in Cross B there is another large effect cell occupancy QTL on Chr XI that affects the G1/S stage. What candidate genes and alleles are at this locus? And since cell cycle stages are not biologically independent (a delay in G1, could have a knock-on effect on the frequency of cells with that genotype in G1/S), it would seem important to consider the set of QTLs in concert.

We thank the reviewer for this suggested clarification. We have modified the text to make it clear that cell cycle occupancy is a compositional phenotype. Like the reviewer, we also noticed the distal trans eQTL hotspot on Chr XI in Cross B, but we were not able to identify compelling candidate gene(s) or variant(s) despite extensive effort.

Reviewer #2 (Public Review):

Boocock and colleagues present an approach whereby eQTL analysis can be carried out by scRNA-Seq alone, in a one-pot-shot experiment, due to genotypes being able to be inferred from SNPs identified in RNA-Seq reads. This approach obviates the need to isolate individual spores, genotype them separately by low-coverage sequencing, and then perform RNA-Seq on each spore separately. This is a substantial advance and opens up the possibility to straightforwardly identify eQTLs over many conditions in a cost-efficient manner. Overall, I found the paper to be well-written and well-motivated, and have no issues with either the methodological/analytical approach (though eQTL analysis is not my expertise), or with the manuscript's conclusions.

I do have several questions/comments.

393 segregant experiment:

For the experiment with the 393 previously genotyped segregants, did the authors examine whether averaging the expression by genotype for single cells gave expression profiles similar to the bulk RNA-Seq data generated from those genotypes? Also, is it possible (and maybe not, due to the asynchronous nature of the cell culture) to use the expression data to aid in genotyping for those cells whose genotypes are ambiguous? I presume it might be if one has a sufficient number of cells for each genotype, though, for the subsequent one-pot experiments, this is a moot point.

As mentioned in our preliminary response, while it is possible to expand the analysis along these lines, this is not relevant for the subsequent one-pot experiments. We have made all the data available so that anyone interested can try these analyses.

Figure 1B:

Is UMAP necessary to observe an ellipse/circle - I wouldn't be surprised if a simple PCA would have sufficed, and given the current discussion about whether UMAP is ever appropriate for interpreting scRNA-Seq (or ancestry) data, it seems the PCA would be a preferable approach. I would expect that the periodic elements are contained in 2 of the first 3 principal components. Also, it would be nice if there were a supplementary figure similar to Figure 4 of Macosko et al (PMID 26000488) to indeed show the cell cycle dependent expression.

We have added two new figures (S2 and S3) that represent alternative visualizations of the cell-cycle that are not dependent on UMAP. Figure S2 shows plots of different pairs of principal components, with each cell colored by its assigned cell-cycle stage. We do not observe a periodic pattern in the first 3 principal components as the reviewer expected, but when we explore the first 6 principal components, we see combinations of components that clearly separate the cell cycle clusters. We emphasize that the clusters were generated using the Louvain algorithm and assigned to cell-cycle stages using marker genes, and that UMAP was used only for visualization.

We could not create a figure similar to Macosko et al. because of differences between the cell cycle categories we used and those of Spellman et al (PMID 9843569). We instead created Figure S3 to address the reviewer's comment. This figure uses a heatmap in a style similar to that of Macosko et al. to display cell-cycle-dependent expression of the 22 genes we used as cell cycle markers across each of the five cell cycle stages (M/G1, G1, G1/S, S, G2/M).

We have renumbered the supplementary figures after incorporating these two additional supplementary figures into the manuscript.

Aging, growth rate, and bet-hedging:

The mention of bet-hedging reminded me of Levy et al (PMID 22589700), where they saw that Tsl1 expression changed as cells aged and that this impacted a cell's ability to survive heat stress. This bet-hedging strategy meant that the older, slower-growing cells were more likely to survive, so I wondered a couple of things. It is possible from single-cell data to identify either an aging, or a growth rate signature? A number of papers from David Botstein's group culminated in a paper that showed that they could use a gene expression signature to predict instantaneous growth rate (PMID 19119411) and I wondered if a) this is possible from single-cell data, and b) whether in the slower growing cells, they see markers of aging, whether these two signatures might impact the ability to detect eQTLs, and if they are detected, whether they could in some way be accounted for to improve detection.

As mentioned in our preliminary response, we are not sure how to look for gene expression signatures of aging in yeast scRNA-seq data. We believe that the proposed analyses are beyond the scope of the current paper. As noted above, we have made all the data available so that anyone interested can explore these hypotheses.

AIL vs. F2 segregants:

I'm curious if the authors have given thought to the trade-offs of developing advanced intercross lines for scRNA-Seq eQTL analysis. My impression is that AIL provides better mapping resolution, but at the expense of having to generate the lines. It might be useful to see some discussion on that.

We thank the reviewer for the comments. We believe that a discussion of trade-offs between different approaches for constructing mapping populations, such as AIL and F2 segregants, is beyond the scope of this paper.

10x vs SPLit-Seq

10x is a well established, but fairly expensive approach for scRNA-Seq - I wondered how the cost of the 10x approach compares to the previously used approach of genotyping segregants and performing bulk RNA-Seq, and how those costs would change if one used SPLiT-Seq (see PMID 38282330).

We thank the reviewer for the comments. We believe that a discussion of cost trade-offs between 10x and other approaches is beyond the scope of this paper, especially given the rapidly evolving costs of different technologies.

Recommendations for the authors:

Reviewer #1 (Recommendations For The Authors):

Throughout the results section the authors point to File S1 for additional information. This file is a tarball with about 20 Excel documents in it, each with several sheets embedded. The authors should provide a detailed README describing how to understand the organizations of the files in File S1 and the many embedded sheets in each file. Statements made in the manuscript about File S1 should explicitly direct the reader to a specific spreadsheet and table to refer to.

We have added an additional README file to the tarball that explains the organization of File S1 and describes the data contained in each sheet. Throughout the text, we now reference specific spreadsheets to assist the reader. In addition, these spreadsheets have been added to a github repository https://github.com/theboocock/finemapping_spreadsheets_single_cell

Neither of the two GitHub repositories referenced under "Code availability" has adequate documentation that would allow a reader to try and reproduce the analyses presented here. The one entitled https://github.com/joshsbloom/single_cell_eQTL has no functional README, while https://github.com/theboocock/yeast_single_cell_post_analysis is somewhat better but still hard to navigate. Basic information on expected inputs, file formats, file organization, output types, and formats, etc. is required to get any of these pipelines to run and should be provided at a minimum.

We thank the reviewer for the comment. In response, we have refactored both GitHub repositories and added extensive documentation to improve usability. We updated the versions of software and packages, this has been reflected in the methods section.

S. cerevisiae strains are preferentially diploid in nature and many genes involved in the mating pathway are differentially regulated in diploids vs haploids. Have the authors explored the fitness effects of the GPA1 82R allele in diploids? What is the dominance relationship between 82W and 82R?

We thank the reviewer for the comment. In diploid yeast, the mating pathway is repressed, and thus we would not expect there to be any fitness consequences due to the presence of different alleles of GPA1.

The diploid expression profiling (page 5 and Table S9) doesn't implicate GPA1; can you the authors comment on this in light of their finding in haploids?

The mating pathway, including GPA1, is repressed in diploids, and hence the expression of GPA1 cannot be studied in these strains (PMID: 3113739). In addition, allele-specific expression differences only identify cis-regulatory effects. We know that the GPA1 variant results in a protein-coding change, which may or may not influence the levels of mRNA in cis, so that even if GPA1 were expressed in diploids, there would be no expectation of an allele-specific difference in expression.

With respect to the candidate CYR1 QTL -- note that strains with compromised Cyr1 function also generally show increased sporulation rates and/or sporulation in rich media conditions (cAMP-PKA signaling represses sporulation). Is this the case in diploids with the CBS2888 allele at CYR1? If the CBS2888 allele is a CYR1 defect one might expect reduced cAMP levels. It is possible to estimate adenylate cyclase levels using a fairly straightforward ELISA assay. This would provide more convincing evidence of the causal mechanism of the alleles identified.

We thank the reviewer for the comment, and we agree that a functional study of the CYR1 alleles would provide more convincing evidence for the causal mechanism of the connection between cell cycle occupancy, cAMP levels, and growth. However, we believe that the proposed experiments are beyond the scope of our current study. The evidence we provide is sufficient to establish that CYR1 is a strong candidate gene for the eQTL hotspot.

Re: CYR1 candidate QTL -- The authors should reference the work of [Patrick Van Dijck] (https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Van+Dijck+P&cauthor_id= 20924200) and [Johan M Thevelein] (https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Thevelein+JM&cauth or_id=20924200) on CYR1 allelic variation, and other papers besides the Matsumoto/ Ishikawa papers, as the effects of cAMP-PKA signaling on stress can be quite variable. cAMP pathway variants, including in CYR1, have popped up in quite a few other yeast QTL mapping and experimental evolution papers. These should be referenced as well.

We thank the reviewer for these references; we have added a comment about the relationship between stress tolerance and CYR1 variation, and cited the relevant references accordingly.

Figure S10 - the subfigure showing the frequency of the GPA 82R compared to 82W suggests a fairly large and deleterious fitness effect of this allele; on the order of 7-8% fewer cells per cell cycle stage than the 82W allele. Can the authors reconcile this with the more modest growth rate effect they report on page 8?

Figure S12C displays the allele frequency of the 82R allele across the cell cycle in the single-cell data from allele-replacement strains. These strains were grown separately and processed using two individual 10x chromium runs. The resulting sequenced library had 11,695 cells with the 82R allele and 14,894 cells with the 82W allele. The 7-8% difference in the number of cells is due to slight differences in the number of captured cells per run, not due to growth differences, because we attempted to pool cells in equal numbers from separate mid-log cultures.

The proportion of cells in G1 increases by ~3% in strains with the 82R allele relative to the baseline proportion of cells in the experiment, which, to the reviewers point, is still larger than the ~1% growth difference we observed. Cell cycle occupancy is a compositional phenotype. As shown in figure S12C, the 82R variant increases the fraction of cells in G1 and slightly decreases the fraction of cells in M/G1. There is no obvious expectation for quantitatively translating a change in cell cycle occupancy to a change in growth rate.

The authors refer to the Lang et al. 2009 paper w/respect to GPA1 variant S469I but that paper seems to have explored a different GPA1 allele, GPA1-G1406T, with respect to growth rates.

We thank the reviewer for their comment. The S469I variant is the same as the G1406T variant, one denoting the amino acid change at position 469 in the protein and the other denoting the corresponding nucleotide change at position 1406 in the DNA coding sequence. We have altered the text to make this clear to the reader.

Reviewer #2 (Recommendations For The Authors):

I make no recommendations as to additional work for the authors. The manuscript is complete. I suggested some things I would like to see in my review, but it's up to them to decide whether they think any of those would further enhance the manuscript.

However, I do have I have some pedantic formatting notes:

- Microliters are variously presented as uL, ul, and µl - it should be µL

- Similarly, milliliters are presented as ml and ML - it should be mL

- Also, there should be a space between the number and the unit, e.g. 10 µL

- Some gene names in the manuscript are not italicized in all instances, e.g., GPA1

We thank the reviewer for these formatting suggestions, we have made these changes throughout the text.

eLife assessment

This manuscript describes the mapping of natural DNA sequence variants that affect gene expression and its noise, as well as cell cycle timing, using as input single-cell RNA-sequencing of progeny from crosses between wild yeast strains. The method represents an important advance in the study of natural genetic variation. The findings, especially given the follow-up validation of the phenotypic impact of a mapped locus of major effect, provide convincing support for the rigor and utility of the method.

Reviewer #1 (Public Review):

The authors demonstrate that it is possible to carry out eQTL experiments for the model eukaryote S. cerevisiae, in "one pot" preparations, by using single-cell sequencing technologies to simultaneously genotype and measure expression. This is a very appealing approach for investigators studying genetic variation in single-celled and other microbial systems, and will likely inspire similar approaches in non-microbial systems where comparable cell mixtures of genetically heterogeneous individuals could be achieved.

While eQTL experiments have been done for nearly two decades (the corresponding author's lab are pioneers in this field), this single-cell approach creates the possibility for new insights about cell biology that would be extremely challenging to infer using bulk sequencing approaches. The major motivating application shown here is to discover cell occupancy QTL, i.e. loci where genetic variation contributes to differences in the relative occupancy of different cell cycle stages. The authors dissect and validate one such cell cycle occupancy QTL, involving the gene GPA1, a G-protein subunit that plays a role in regulating the mating response MAPK pathway. They show that variation at GPA1 is associated with proportional differences in the fraction of cells in the G1 stage of the cell cycle. Furthermore, they show that this bias is associated with differences in mating efficiency.

Reviewer #2 (Public Review):

Boocock and colleagues present an approach whereby eQTL analysis can be carried out by scRNA-Seq alone, in a one-pot-shot experiment, due to genotypes being able to be inferred from SNPs identified in RNA-Seq reads. This approach obviates the need to isolate individual spores, genotype them separately by low-coverage sequencing, and then perform RNA-Seq on each spore separately. This is a substantial advance and opens up the possibility to straightforwardly identify eQTLs over many conditions in a cost-efficient manner. Overall, I found the paper to be well-written and well-motivated, and have no issues with either the methodological/analytical approach (though eQTL analysis is not my expertise), or with the manuscript's conclusions.

eLife assessment

This important study investigates neurobiological mechanisms underlying the maintenance of stable, functionally appropriate rhythmic motor patterns during changing environmental conditions - temperature in this study in the crab Cancer borealis stomatogastric central neural pattern generating circuits producing the rhythmic pyloric motor pattern, which is naturally subjected to temperature perturbations over a substantial range. The authors present compelling evidence that the neuronal hyperpolarization-activated inward current (Ih), known to contribute to rhythm control, plays a vital role in the ability of these circuits to appropriately adjust the frequency of rhythmic neural activity in a smooth monotonic fashion while maintaining the relative timing of different phases of the activity pattern that determines proper functional motor coordination transiently and persistently to temperature perturbations. This study will be of interest to neurobiologists studying rhythmic motor circuits and systems and their physiological adaptations.

Reviewer #1 (Public review):

Summary:

This important study investigates the neurobiological mechanisms underlying the stable operation and maintenance of functionally appropriate rhythmic motor patterns during changing environmental conditions - temperature in this study in the crab Cancer borealis stomatogastric neural pattern generating network producing the pyloric motor rhythm, which is naturally subjected to temperature perturbations over a substantial range. This study is relevant to the general problem that some rhythmic motor systems adjust to changing environmental conditions and state changes by increasing the cycle frequency in a smooth monotonic fashion while maintaining the relative timing of different network activity pattern phases that determine proper motor coordination. How this is achieved mechanistically in complex dynamic motor networks is not understood, particularly how the frequency and phase adjustments are achieved as conditions change while avoiding operational instabilities on different time scales. The authors specifically studied the contributions of the hyperpolarization-activated inward current (Ih), which is involved in rhythm control, to the adjustments of frequency and phases in the pyloric rhythmic pattern as the temperature was altered from 11 degrees C to 21 degrees C. They present compelling evidence that this current is a critical biophysical feature in the ability of this system to adjust transiently and persistently to temperature perturbations appropriately. After blocking Ih in the pyloric network with cesium, the network was unable to reliably produce its characteristic rapid and smooth increase in the frequency of the triphasic rhythmic motor pattern in response to increasing temperature or its typical steady-state increase in frequency over this Q10 temperature range.

Strengths:

(1) The authors addressed this problem by technically rigorous experiments in the crab Cancer borealis stomatogastric ganglion (STG) in vitro, which readily allows for neuronal activity recording in a behaviorally and architecturally defined rhythmic neural circuit in conjunction with the application of blockers of Ih and synaptic receptors to disrupt circuit interactions. This approach is an effective way to experimentally investigate how complex rhythmic networks, at least in poikilotherms, mechanistically adjust to environmental perturbations such as temperature.

(2) While previous work demonstrated that Ih increases in pyloric neurons as temperature increases, the authors here establish that this increase is necessary for normal responses of STG neural activity to temperature, which consist of a smooth monotonic increase in the frequency of rhythmic activity with increasing temperature.

(3) The data shows that blocking Ih with cesium causes the frequency to transiently decrease ("jags") when the temperature increases and then increases after the temperature stabilizes at a steady state, revealing a non-monotonic frequency response to temperature perturbations.

(4) The authors dissect some of the underlying neuronal and circuit dynamics, presenting evidence that after blocking Ih, the non-monotonic jags in the frequency response are mediated by intrinsic properties of pacemaker neurons, while in the steady state, Ih determined the overall frequency change (i.e., temperature sensitivity) through network interactions.

(5) The authors' results highlight more complex dynamic responses to increasing temperature for the first time, suggesting a longer timescale process than previously recognized that may result from interactions between multiple channels and/or ion channel kinetics.

Weaknesses:

(1) The involvement of Ih in achieving the frequency and phase adjustments as conditions change and allowing smooth transitions to avoid operational instabilities in other complex rhythmic motor networks, for example, in homeotherms, is not established, so the present results may have limited general extrapolations.

Reviewer #2 (Public review):

Summary:

Using the crustacean stomatogastric nervous system (STNS), the authors present an interesting study wherein the contribution of the Ih current to temperature-induced changes in the frequency of a rhythmically active neural circuit is evaluated. Ih is a hyperpolarization-activated cation current that depolarizes neurons. Under normal conditions, increasing the temperature of the STNS increases the frequency of the spontaneously active pyloric rhythm. Notably, under normal conditions, as temperature systematically increases, the concomitant increase in pyloric frequency is smooth (i.e., monotonic). By contrast, blocking Ih with extracellular cesium produces temperature-induced pyloric frequency changes that follow a characteristic sawtooth response (i.e., non-monotonic). That is, in cesium, increasing temperature initially results in a transient drop in pyloric frequency that then stabilizes at a higher frequency. Thus, the authors conclude that Ih establishes a mechanism that ensures smooth changes in neural network frequency during environmental disturbances, a feature that likely bestows advantages to the animal's function.

The study describes several surprising and interesting findings. In general, the study's primary observation of the cesium-induced sawtooth response is remarkable. To my knowledge, this type of response has not yet been described in neurobiological systems, and I suspect that the unexpected response will be of interest to many readers.

At first glance, I had some concerns regarding the use of extracellular cesium to understand network phenomena. Yes, extracellular cesium blocks Ih. But extracellular cesium has also been shown to block astrocytic potassium channels, at least in mammalian systems (i.e., K-IR, PMID: 10601465), and such a blockade can elevate extracellular potassium. I was heartened to see that the authors acknowledge the non-specificity of cesium (lines 320-325) and I agree with the authors' contention that "a first approximation most of the effects seen here can likely be attributed to Cs+ block of Ih". Upon reflecting on the potential confound, I was also reassured to see that extracellular cesium alone does not in fact increase pyloric frequency, an effect that might be expected if cesium indirectly raises [K+]outside. If the authors agree, then I suggest including that point in their discussion.

In summary, the authors present a solid investigation of a surprising biological phenomenon. In general, my comments are fairly minor. Thanks for contributing an interesting study.

Strengths:

A major strength of the study is the identification of an ionic conductance that mediates stable, monotonic changes in oscillatory frequency that accompany changes in the environment (i.e., temperature).

Weaknesses:

A potential experimental concern stems from the use of extracellular cesium to attribute network effects specifically to Ih. Previous work has shown that extracellular cesium also blocks inward-rectifier potassium channels expressed by astrocytes, and that such blockade may also elevate extracellular potassium, an action that generally depolarizes neurons. Notably, the authors address this potential concern in the discussion.

Reviewer #3 (Public review):

Summary:

This paper presents a systematic analylsis of the role of the hyperpolarization-activated inward current (the h current) in the response of the pyloric rhythm of the stomatogastric ganglion (STG) of the crab. In a detailed set of experiments, they analyze the effect of blocking h current with bath infusion of the h current blocker cesium (perfused as CsCl). They show interesting and reproducible effects that blockade of h current results in a period of frequency decrease after an upward step in temperature, followed by a slow increase in frequency. This contrasts with the normal temperature response that shows an increase in frequency with an increase in temperature without a downward "jag" in the frequency response. This is an important paper for showing the role of h current in stabilizing network dynamics in response to perturbations such as a temperature change.

Strengths of the paper:

The major effects are shown very clearly and convincingly in a range of experiments with combined intracellular recording from neurons during changes in temperature.

Weaknesses

The Marder lab has detailed models of the pyloric rhythm. These temperature effects have not yet been modeled and could be the focus of future modeling studies.

Author response:

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

Response to Public Reviews:

We thank the reviewers for their kind comments have implemented many of the suggestion their suggestions. Our paper has greatly benefited from their advice.  Like Reviewer 1, we acknowledge that while the exact involvement of Ih in allowing smooth transitions is likely not universal across all systems, our demonstration of the ways in which such currents can affect the dynamics of the response of complex rhythmic motor networks provides valuable insight. To address the concerns of Reviewer 2, we included a sentence in the discussion to highlight the fact that cesium neither increased the pyloric frequency nor caused consistent depolarization in intracellular recordings. We also highlighted that these observations suggest both that cesium is not indirectly raising [K+]outside and support the conclusion that the effects of cesium are primarily through blockade of Ih rather than other potassium channels.

Reviewer 3 raised some important points about modeling. While the lab has models that explore the effects of temperature on artificial triphasic rhythms, these models do not account for all the biophysical nuances of the full biological system. We have limited data about the exact nature of temperature-induced parameter changes and the extent to which these changes are mediated by intrinsic effects of temperature on protein structure versus protein interactions/modification by processes such as phosphorylation. With respects to the A current, Tang et al., 2010 reported that the activation and inactivation rates are differentially temperature sensitive but we do not have the data to suggest whether or not the time courses of such sensitivities are different. As such, we focus our discussion on the properties we know are modulated by temperature, i.e. activation rates. Within the discussion we now include the suggestion that future, more comprehensive modeling may be appropriate to further elucidate the ways in which reducing Ih may produce the here reported experimentally observed effects.

Reviewer #1 (Recommendations For The Authors):

Suggested revisions:

A figure showing examples of the voltage-clamp traces for the critical measurements of the extent of Ih block by 5 mM CsCl in PD and LP neurons at the temperature extremes in these preparations is not shown, and the authors should consider including such a figure, perhaps as a supplemental figure.

We have added Supplemental Figure 1 containing voltage-clamp traces demonstrating the extent of Ih block by 5mM CsCl in PD and LP neurons at 11 and 21°C.  Due to technical concerns, different preparations were used in the measurements at 11°C and 21°C, but the point that the H-current is reduced is demonstrated in all cases.

Reviewer #2 (Recommendations for The Authors):

Specific (Minor) Comments:

(1) Line 83: In Cs+ "at 11°C, the pyloric frequency was significantly decreased compared to control conditions (Saline: 1.2± 0.2 Hz; Cs+ 0.9± 0.2 Hz)".

As above, the authors often report that cesium generally reduces pyloric frequency. Figure 5A demonstrates this action quite nicely. However, cesium's effect on pyloric frequency at 11°C seems less robust in Figure 1C. Why the discrepancy?

There is variability in the effects of Cs+ on the pyloric frequency.  As noted, the standard deviation in frequency in both conditions is 0.2Hz.  As such, there are some cases in which the initial frequency drop in Cs+ compared to control was relatively small.  1C is one such case, but was selected as an example because of its clear reduction in temperature sensitivity. 

(2) I don't understand what the arrows/dashed lines are trying to convey in Figure 3C.

The arrows/dashed lines represent the criteria used to define a cycle as “decreasing in frequency” (Temperature Increasing) or “increasing in frequency” (Temperature Stable).  We have amended lines 130 and 137 in the text to hopefully clarify this point, as well as the figure legend.

(3) Lines 118/168. The description of cesium's specific action on the depolarizing portion of PD activity is a bit confusing. In my mind, "depolarization phase" refers to the point at which PD is most depolarized. Perhaps restating the phrase to "elongation of the depolarizing trajectory" is less confusing. The authors may also want to consider labeling this trajectory in Figure 2C.

We have changed “depolarization phase” to “depolarizing phase” to highlight that this is the period during which the cell is depolarizing, rather than at its most depolarized.  We consider the plateau of the slow wave and spiking (the point at which PD is most depolarized) to be the “bursting phase”.  We have labeled these phases in Figure 2C as suggested.

(4) Figure 3C legend: a few words seem to be missing. I suggest "the change in mean frequency was more likely TO decrease IN Cs+ than in saline".

Thank you for catching this typo, it has been corrected.

(5) Line 165: Awkward phrasing. “In one experiment, the decrease in frequency while temperature increased and subsequent increase in frequency after temperature stabilized was particularly apparent in Cs+ PTX”.

How about: “One Cs+ PTX experiment wherein elevating the temperature transiently decreased pyloric frequency is shown in Figure 4F.”

We have amended this sentence to read, “One Cs++PTX experiment in which elevating the temperature produced a particularly pronounced transient decrease in frequency is shown in Figure 4F.”

(6) Line 186: Awkward phrasing. "LP OFF was also significantly advanced in Cs+, although duty cycle (percent of the period a neuron is firing) was preserved".

The use of the word "although" seems a bit strange. If both LP onset and LP offset phase advance by the same amount, then isn't an unchanged duty cycle expected?

“Although” has been changed to “and subsequently”.

Reviewer #3 (Recommendations For The Authors):

Major comments:

(1) I know the Marder lab has detailed models of the pyloric rhythm. I am not saying they have to add modeling to this already extensive and detailed paper, but it would be useful to know how much of these temperature effects have been modeled, for example in the following locations.

(2) Line 259 - "Mathematically..." - Is there a computational model of H current that has shown this decrease in frequency in pyloric neurons? If you are working on one for the future, you could mention this.

There is not currently a model in which the reduction of the H-current results in the non-minimum phase dynamics in the frequency response to temperature seen experimentally. It should be noted that our existing models of pyloric activity responses to temperature are not well suited to investigate such dynamics in their current iterations.  Further work is necessary to demonstrate the principles observed experimentally in computational modeling, and we have added a sentence to the paper to reflect this point (Line 268).

(3) Line 318 - "therefore it remains unclear" - I thought they had models of the circuit rhythmicity. Do these models include temperature effects? Can they comment on whether their models of the circuit show an opposite effect to what they see in the experiment? I'm not saying they have to model these new effects as that is probably an entirely different paper, but it would be interesting to know whether current models show a different effect.

We have some models of the pyloric response to temperature, but these models were specifically selected to maintain phase across the range of temperature.  When Ih was reduced in these models, a variety of effects on phase and duty cycle were seen.  These models were selected to have the same key features of behavior as the pyloric rhythm, but do not capture all the biophysical nuances of the complete system, and therefore should not necessarily be expected to reflect the experimental findings in their current iterations.  Furthermore, these models are meant to have temperature as a static, rather than dynamic input, and thus are ill-suited to examine the conditions of our experiments.  The models in their current state are not sufficiently relevant to these experimental findings that we they can illuminate the present paper `2.

(4) "If deinactivation is more accelerated or altered by temperature than inactivation...While temperature continued to change, the difference in parameters would continue to grow" - This is described as a difference in temperature sensitivity, but it seems like it is also a function of the time course of the response to change in temperature (i.e. the different components could have the same final effect of temperature but show a different time course of the change).

We know from Tang et al, 2010, that activation and inactivation rates of the A current are differentially temperature sensitive. We have no evidence to suggest that the time course of the response to temperature of various parameters differ.  The physical actions of temperature on proteins are likely to be extremely rapid, making a time course difference on the order of tens of seconds less unlikely, though not impossible. Modeling of the biophysics might illuminate the relative plausibility of these different mechanisms of action, but we feel that our current suggested explanation is reasonable based on existing information.

(5) Is it known how temperature is altering these channel kinetics? Is it via an intrinsic rearrangement of the protein structure, or is it a process that involves phosphorylation (that could explain differences in time course?). Some mention of the mechanism of temperature changes would be useful to readers outside this field.

It is not known exactly how temperature alters channel parameters.  Invariably some, if not all, of it is due to an intrinsic rearrangement of protein structure, and our current models treat all parameter changes as an instantaneous consequence.  However, it is possible that some effects of temperature are due to longer timescale processes such as phosphorylation or cAMP interactions.  Current work in the lab is actively exploring these questions, but there is no definitive answer. Given that this paper focuses on the phenomenon and plausible biomolecular explanations based on existing data, we have not altered the paper to include more exhaustive  coverage of all the possible avenues by which temperature may alter channel properties.

Specific comments:

Title: misspelling of "Cancer" ?

We are unsure how that extra “w” got into the earliest version of the manuscript and have removed it.

Line 66 "We used 5mM CsCl" - might mention right up front that this was a bath application of the substance.

We have altered this line to read “used bath application of 5mM CsCl”.  

Figure 4 - "The only feedback synapse to the pacemaker kernel neurons, LP to PD, and is blocked by picrotoxin" - I think the word "and" should be removed from this phrase in the figure legend.

Fixed

Figure 4 legend - "Reds denote temperature...yellows denote..." - I think it should be "Red dots denote temperature...yellow dots denote...".

Done

Figure 4B - Why does the change in frequency in cesium look so different in Figure 4B compared to Figure 1C or Figure 3B? In the earlier figures, the increase of frequency is smaller but still present in cesium, whereas, in Figure 4B, cesium seems to completely block the increase in frequency. I'm not sure why this is different, but I guess it's because 3B and 4B are just mean traces from single experiments. Presumably, 4B is showing an experiment in which the cesium was subsequently combined with picrotoxin?

Figures 1C, 3B, and 4B are indeed all from different single experiments. As acknowledged in our concluding paragraph, there was substantial variability in the exact response of the pyloric rhythm to temperature while in cesium.  The most consistent effect was that the difference in frequency between cesium and saline at a particular temperature increased, as demonstrated across 21 preparations in Figure 1D. It may be noted in Figure 1E that the Q10 was not infrequently <1, meaning that there was a net decrease in frequency as temperature increased in some experiments such as seen in the example of Figure 4B.  The “fold over” (initial increase in steady-state frequency with temperature, then decrease at higher temperatures) has been observed at higher temperatures (typically around 23-30 degrees C) even under control conditions but has not been highlighted in previous publications.  The example in 4B was chosen because it demonstrated both the similarity in jags between Cs+ and Cs++PTX and an overall decrease in temperature sensitivity, even though in this instance the steady-state change in frequency with temperature was not monotonic. 

Figure 6A - "Phase 0 to 1.0" - The y-axis should provide units of phase. Presumably, these are units of radians so 1.0=2*pi radians (or 360 degrees, but probably best to avoid using degrees of phase due to confusion with degrees of temperature).

Phase, with respect to pyloric rhythm cycles, does not traditionally have units as it is a proportion rather than an angle. As such, we have not changed the figure.

Line 275 - "the pacemaker neuron can increase" - Does this indicate that the main effects of H current are in the follower neurons (i.e. LP and PY versus the driver neuron PD)?

Not necessarily.  We posit in the next paragraph that the effect of the H current on the temperature sensitivity could be due to its phase advance of LP, but that phase advance of LP is not particularly expected to increase frequency.  We favor the possibility that temperature increases Ih in the pacemaker, which in turn advances the PRC of the rhythm, allowing the frequency increase seen under normal conditions.  In Cs+, this advance does not occur, resulting in the lower temperature sensitivity.  In Cs++PTX, the lack of inhibition from LP means compensatory advance of the pacemaker PRC by Ih is unnecessary to allow increased frequency.

Line 285 - "either increase frequency have no effect" - Is there a missing "or" in this phrase?

Thank you, we have added the “or”.

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eLife assessment

This important study highlights cell types preserving long-lived proteins and lays a foundation for identifying exceptionally long-lived proteins in the ovary. Convincing evidence describes helpful data about protein turnover and identifies long-lived macromolecules in oocytes and somatic cells during mouse ovarian aging. This work will be of interest to researchers working on aging and reproductive health.

I can add a note to a higlight

fesibility?

eLife assessment

This potentially valuable study examines the role of IL17-producing Ly6G PMNs as a reservoir for Mycobacterium tuberculosis to evade host killing activated by BCG immunisation. The authors report that IL17-producing polymorphonuclear neutrophils harbour a significant bacterial load in both wild-type and IFNg-/- mice and that targeting IL17 and Cox2 improved disease outcomes whilst enhancing BCG efficacy. Although the authors suggest that targeting these pathways may improve disease outcomes in humans, the evidence as it stands is incomplete and requires additional experimentation for the study to realise its full impact.

Reviewer #1 (Public review):

Summary:

Recruitment of neutrophils to the lungs is known to drive susceptibility to infection with M. tuberculosis. In this study, the authors present data in support of the hypothesis that neutrophil production of the cytokine IL-17 underlies the detrimental effect of neutrophils on disease. They claim that neutrophils harbor a large fraction of Mtb during infection, and are a major source of IL-17. To explore the effects of blocking IL-17 signaling during primary infection, they use IL-17 blocking antibodies, SR221 (an inverse agonist of TH17 differentiation), and celecoxib, which they claim blocks Th17 differentiation, and observe modest improvements in bacterial burdens in both WT and IFN-γ deficient mice using the combination of IL-17 blockade with celecoxib during primary infection. Celecoxib enhances control of infection after BCG vaccination.

Strengths:

The most novel finding in the paper is that treatment with celecoxib significantly enhances control of infection in BCG-vaccinated mice that have been challenged with Mtb. It was already known that NSAID treatments can improve primary infection with Mtb.

Weaknesses:

The major claim of the manuscript - that neutrophils produce IL-17 that is detrimental to the host - is not strongly supported by the data. Data demonstrating neutrophil production of IL-17 lacks rigor. The experiments examining the effects of inhibitors of IL-17 on the outcome of infection are very difficult to interpret. First, treatment with IL-17 inhibitors alone has no impact on bacterial burdens in the lung, either in WT or IFN-γ KO mice. This suggests that IL-17 does not play a detrimental role during infection. Modest effects are observed using the combination of IL-17 blocking drugs and celecoxib, however, the interpretation of these results mechanistically is complicated. Celecoxib is not a specific inhibitor of Th17. Indeed, it affects levels of PGE2, which is known to have numerous impacts on Mtb infection separate from any effect on IL-17 production, as well as other eicosanoids. Finally, the human data simply demonstrates that neutrophils and IL-17 both are higher in patients who experience relapse after treatment for TB, which is expected and does not support their specific hypothesis. The use of genetic ablation of IL-17 production specifically in neutrophils and/or IL-17R in mice would greatly enhance the rigor of this study. The authors do not address the fact that numerous studies have shown that IL-17 has a protective effect in the mouse model of TB in the context of vaccination. Finally, whether and how many times each animal experiment was repeated is unclear.

Reviewer #2 (Public review):

Summary:

In this study, Sharma et al. demonstrated that Ly6G+ granulocytes (Gra cells) serve as the primary reservoirs for intracellular Mtb in infected wild-type mice and that excessive infiltration of these cells is associated with severe bacteremia in genetically susceptible IFNγ-/- mice. Notably, neutralizing IL-17 or inhibiting COX2 reversed the excessive infiltration of Ly6G+Gra cells, mitigated the associated pathology, and improved survival in these susceptible mice. Additionally, Ly6G+Gra cells were identified as a major source of IL-17 in both wild-type and IFNγ-/- mice. Inhibition of RORγt or COX2 further reduced the intracellular bacterial burden in Ly6G+Gra cells and improved lung pathology.

Of particular interest, COX2 inhibition in wild-type mice also enhanced the efficacy of the BCG vaccine by targeting the Ly6G+Gra-resident Mtb population.

Strengths:

The experimental results showing improved BCG-mediated protective immunity through targeting IL-17-producing Ly6G+ cells and COX2 are compelling and will likely generate significant interest in the field. Overall, this study presents important findings, suggesting that the IL-17-COX2 axis could be a critical target for designing innovative vaccination strategies for TB.

Weaknesses:

However, I have the following concerns regarding some of the conclusions drawn from the experiments, which require additional experimental evidence to support and strengthen the overall study.

Major Concerns:

(1) Ly6G+ Granulocytes as a Source of IL-17: The authors assert that Ly6G+ granulocytes are the major source of IL-17 in wild-type and IFN-γ KO mice based on colocalization studies of Ly6G and IL-17. In Figure 3D, they report approximately 500 Ly6G+ cells expressing IL-17 in the Mtb-infected WT lung. Are these low numbers sufficient to drive inflammatory pathology? Additionally, have the authors evaluated these numbers in IFN-γ KO mice?

(2) Role of IL-17-Producing Ly6G Granulocytes in Pathology: The authors suggest that IL-17-producing Ly6G granulocytes drive pathology in WT and IFN-γ KO mice. However, the data presented only demonstrate an association between IL-17+ Ly6G cells and disease pathology. To strengthen their conclusion, the authors should deplete neutrophils in these mice to show that IL-17 expression, and consequently the pathology, is reduced.

(3) IL-17 Secretion by Mtb-Infected Neutrophils: Do Mtb-infected neutrophils secrete IL-17 into the supernatants? This would serve as confirmation of neutrophil-derived IL-17. Additionally, are Ly6G+ cells producing IL-17 and serving as pathogenic agents exclusively in vivo? The authors should provide comments on this.

(4) Characterization of IL-17-Producing Ly6G+ Granulocytes: Are the IL-17-producing Ly6G+ granulocytes a mixed population of neutrophils and eosinophils, or are they exclusively neutrophils? Sorting these cells followed by Giemsa or eosin staining could clarify this.

Reviewer #3 (Public review):

Summary:

The authors examine how distinct cellular environments differentially control Mtb following BCG vaccination. The key findings are that IL17-producing PMNs harbor a significant Mtb load in both wild-type and IFNg-/- mice. Targeting IL17 and Cox2 improved disease and enhanced BCG efficacy over 12 weeks and neutrophils/IL17 are associated with treatment failure in humans. The authors suggest that targeting these pathways, especially in MSMD patients may improve disease outcomes.

Strengths:

The experimental approach is generally sound and consists of low-dose aerosol infections with distinct readouts including cell sorting followed by CFU, histopathology, and RNA sequencing analysis. By combining genetic approaches and chemical/antibody treatments, the authors can probe these pathways effectively.

Understanding how distinct inflammatory pathways contribute to control or worsen Mtb disease is important and thus, the results will be of great interest to the Mtb field.

Weaknesses:

A major limitation of the current study is overlooking the role of non-hematopoietic cells in the IFNg/IL17/neutrophil response. Chimera studies from Ernst and colleagues (PMCID: PMC2807991) previously described this IDO-dependent pathway following the loss of IFNg through an increased IL17 response. This study is not cited nor discussed even though it may alter the interpretation of several experiments.

Several of the key findings in mice have previously been shown (albeit with less sophisticated experimentation) and human disease and neutrophils are well described - thus the real new finding is how intracellular Mtb in neutrophils are more refractory to BCG-mediated control. However, given there are already high levels of Mtb in PMNs compared to other cell types, and there is a decrease in intracellular Mtb in PMNs following BCG immunization the strength of this finding is a bit limited.

Author response:

eLife assessment

This potentially valuable study examines the role of IL17-producing Ly6G PMNs as a reservoir for Mycobacterium tuberculosis to evade host killing activated by BCG immunisation. The authors report that IL17-producing polymorphonuclear neutrophils harbour a significant bacterial load in both wild-type and IFNg-/- mice and that targeting IL17 and Cox2 improved disease outcomes whilst enhancing BCG efficacy. Although the authors suggest that targeting these pathways may improve disease outcomes in humans, the evidence as it stands is incomplete and requires additional experimentation for the study to realise its full impact.

Thank you for evaluating our manuscript. We understand the concern related to the direct role of Ly6G+Gra-derived IL17 in TB pathogenesis. For the revised manuscript, we will provide additional experimental evidence through direct regulation of IL-17 production in Mtb-infected mice and its impact on improving BCG efficacy.

Public Reviews:

Reviewer #1 (Public review):

Summary:

Recruitment of neutrophils to the lungs is known to drive susceptibility to infection with M. tuberculosis. In this study, the authors present data in support of the hypothesis that neutrophil production of the cytokine IL-17 underlies the detrimental effect of neutrophils on disease. They claim that neutrophils harbor a large fraction of Mtb during infection, and are a major source of IL-17. To explore the effects of blocking IL-17 signaling during primary infection, they use IL-17 blocking antibodies, SR221 (an inverse agonist of TH17 differentiation), and celecoxib, which they claim blocks Th17 differentiation, and observe modest improvements in bacterial burdens in both WT and IFN-γ deficient mice using the combination of IL-17 blockade with celecoxib during primary infection. Celecoxib enhances control of infection after BCG vaccination. 

Thank you for the summary.

Strengths:

The most novel finding in the paper is that treatment with celecoxib significantly enhances control of infection in BCG-vaccinated mice that have been challenged with Mtb. It was already known that NSAID treatments can improve primary infection with Mtb.

Thank you.

Weaknesses:

The major claim of the manuscript - that neutrophils produce IL-17 that is detrimental to the host - is not strongly supported by the data. Data demonstrating neutrophil production of IL17 lacks rigor. 

Our response: Neutrophil production of IL-17 is supported by two independent methods/ techniques in the current version: 

(1) Through Flow cytometry- a large fraction of Ly6G+CD11b+ cells from the lungs of Mtb-infected mice were also positive for IL-17 (Fig. 3C).

(2) IFA co-staining of Ly6G + cells with IL-17 in the lung sections from Mtb-infected mice (Fig. 3 E_G and Fig. 4H, Fig. 5I).

However, to further strengthen this observation, we plan to analyse sorted Ly6G+Gra from the lungs of infected mice using IL-17 ELISPOT assay. This will unequivocally prove the Ly6+Gra production of IL-17. Several publications support the production of IL-17 by neutrophils (Li et al. 2010; Katayama et al. 2013; Lin et al. 2011). For example, neutrophils have been identified as a source of IL-17 in human psoriatic lesions (Lin et al. 2011), in neuroinflammation induced by traumatic brain injury (Xu et al. 2023) and in several mouse models of infectious and autoimmune inflammation (Ferretti et al. 2003; Hoshino et al. 2008) (Li et al. 2010). However, ours is the first study reporting neutrophil IL-17 production during Mtb pathology.

The experiments examining the effects of inhibitors of IL-17 on the outcome of infection are very difficult to interpret. First, treatment with IL-17 inhibitors alone has no impact on bacterial burdens in the lung, either in WT or IFN-γ KO mice. This suggests that IL-17 does not play a detrimental role during infection. Modest effects are observed using the combination of IL-17 blocking drugs and celecoxib, however, the interpretation of these results mechanistically is complicated. Celecoxib is not a specific inhibitor of Th17. Indeed, it affects levels of PGE2, which is known to have numerous impacts on Mtb infection separate from any effect on IL-17 production, as well as other eicosanoids. 

The reviewer correctly says that Celecoxib is not a specific inhibitor of Th17. However, COX-2 inhibition does have an effect on IL-17 levels, and numerous reports support this observation (Paulissen et al. 2013; Napolitani et al. 2009; Lemos et al. 2009). We elaborate on the results below for better clarity.

Firstly, in the WT mice, Celecoxib treatment led to a complete loss of IL-17 production in the lungs of Mtb-infected mice (Fig. 5D). Interestingly, IL-17 production independent of IL-23 is known to require PGE2 (Paulissen et al. 2013; Polese et al. 2021). In the WT or IFNγ KO mice, we rather noted a decline in IL-23 levels post-infection, suggesting a possible role of PGE2 in IL-17 production. However, in the lung homogenates of Mtb-infected IFNγ KO mice, Celecoxib had no effect on IL-17 levels in the lung homogenates. Thus, celecoxib controls IL-17 levels only in the Mtb-infected WT mice. Including celecoxib with anti-IL17 in the IFNγ KO mice controls pathology and extends its survival.

Second, the reviewer’s observation is only partially correct that IL-17 inhibition has a modest effect on the outcome of infection. While IL-17 neutralization and inhibition alone in the IFNγ KO mice and WT mice, respectively, did not bring down the lung CFU burden significantly, in both these cases, there was an improvement in the lung pathology. The reduced pathology coincided with reduced neutrophil recruitment and a reduced Ly6G+Graresident Mtb population in the WT mice. IL-17 neutralization alone improved IFNγ KO mice survival by ~10 days (Fig. 4F-G). 

Third, regarding the SR2211 and Celecoxib combination study, we agree with the reviewer that Celecoxib has roles independent of IL-17 regulation. However, in the results presented in this study, there are three key aspects- 1) neutrophil-derived IL-17-dependent neutrophil recruitment, 2) the presence of a large proportion of intracellular Mtb in the neutrophils and 3) dissemination of Mtb to the spleen. Celecoxib treatment alone helps reduce lung Mtb burden in the WT mice. However, SR2211 fails to do so. It is evident that celecoxib is doing more than just inhibiting IL-17 production. The result shows that celecoxib blocks neutrophil recruitment (which could be an IL-17-dependent mechanism) and also controls the intraneutrophil bacterial population. Finally, either SR2211 or celecoxib could block dissemination to the spleen. The role of neutrophils in TB dissemination is only beginning to emerge (Hult et al. 2021). We will revise the description in the results and discussion section for this data to make it easier to understand.

Finally, we have also done experiments with SR2211 in BCG-vaccinated animals, which shows the direct impact of IL-17 inhibition on the BCG vaccine efficacy. We will add this result in the revised version.

Finally, the human data simply demonstrates that neutrophils and IL-17 both are higher in patients who experience relapse after treatment for TB, which is expected and does not support their specific hypothesis. 

We disagree with the above statement. Why a higher IL-17 is expected in patients who show relapse, death or failed treatment outcomes? Classically, IL-17 is believed to be protective against TB, and the reviewer also points to that in the comments below. A very limited set of studies support the non-protective/pathological role of IL-17 in tuberculosis (Cruz et al. 2010). High IL-17 and neutrophilia at the baseline in the human subjects (i.e. at the time of recruitment in the study) highlight severe pathology in those subjects, which could have contributed to the failed treatment outcome. This observation in the human cohort strongly supports the overall theme and central observation in this study.

The use of genetic ablation of IL-17 production specifically in neutrophils and/or IL-17R in mice would greatly enhance the rigor of this study. 

The reviewer’s point is well-taken. Having a genetic ablation of IL-17 production, specifically in the neutrophils, would be excellent. At present, however, we lack this resource, and therefore, it is not feasible to do this experiment within a defined timeline. Instead, for the revised manuscript, we will present the data with SR2211, a direct inhibitor of RORgt and, therefore, IL-17, in BCG-vaccinated mice.

The authors do not address the fact that numerous studies have shown that IL-17 has a protective effect in the mouse model of TB in the context of vaccination.

Yes, there are a few articles that talk about the protective effect of IL-17 in the mouse model of TB in the context of vaccination (Khader et al. 2007; Desel et al. 2011; Choi et al. 2020). This part was discussed in the original manuscript (in the Introduction section). For the revised manuscript, we will also provide results from the experiment where we blocked IL-17 production by inhibiting RORgt using SR2211 in BCG-vaccinated mice. The results clearly show IL-17 as a negative regulator of BCG-mediated protective immunity. We believe some of the reasons for the observed differences could be 1) in our study, we analysed IL-17 levels in the lung homogenates at late phases of infection, and 2) most published studies rely on ex vivo stimulation of immune cells to measure cytokine production, whereas we actually measured the cytokine levels in the lung homogenates. We will elaborate on these points in the revised version.

Finally, whether and how many times each animal experiment was repeated is unclear.

We will provide the details of the number of experiments in the revised version. Briefly, the BCG vaccination experiment (Figure 1) and BCG vaccination with Celecoxib treatment experiment (Figure 6) were performed twice and thrice, respectively. The IL-17 neutralization experiment (Figure 4) and the SR2211 treatment experiment (Figure 5) were done once. We will add another SR2211 experiment data in the revised version. 

Reviewer #2 (Public review):

Summary:

In this study, Sharma et al. demonstrated that Ly6G+ granulocytes (Gra cells) serve as the primary reservoirs for intracellular Mtb in infected wild-type mice and that excessive infiltration of these cells is associated with severe bacteremia in genetically susceptible IFNγ/- mice. Notably, neutralizing IL-17 or inhibiting COX2 reversed the excessive infiltration of Ly6G+Gra cells, mitigated the associated pathology, and improved survival in these susceptible mice. Additionally, Ly6G+Gra cells were identified as a major source of IL-17 in both wild-type and IFNγ-/- mice. Inhibition of RORγt or COX2 further reduced the intracellular bacterial burden in Ly6G+Gra cells and improved lung pathology.

Of particular interest, COX2 inhibition in wild-type mice also enhanced the efficacy of the BCG vaccine by targeting the Ly6G+Gra-resident Mtb population.

Thank you for the summary.

Strengths:

The experimental results showing improved BCG-mediated protective immunity through targeting IL-17-producing Ly6G+ cells and COX2 are compelling and will likely generate significant interest in the field. Overall, this study presents important findings, suggesting that the IL-17-COX2 axis could be a critical target for designing innovative vaccination strategies for TB.

Thank you for highlighting the overall strengths of the study.  Weaknesses:

However, I have the following concerns regarding some of the conclusions drawn from the experiments, which require additional experimental evidence to support and strengthen the overall study.

Major Concerns:

(1) Ly6G+ Granulocytes as a Source of IL-17: The authors assert that Ly6G+ granulocytes are the major source of IL-17 in wild-type and IFN-γ KO mice based on colocalization studies of Ly6G and IL-17. In Figure 3D, they report approximately 500 Ly6G+ cells expressing IL-17 in the Mtb-infected WT lung. Are these low numbers sufficient to drive inflammatory pathology? Additionally, have the authors evaluated these numbers in IFN-γ KO mice? 

Thank you for pointing out about the numbers in Fig. 3D. It was our oversight to label the axis as No. of IL17+Ly6G+Gra/lung. For this data, only a part of the lung was used. For the revised manuscript, we will provide the number of these cells at the whole lung level from Mtb-infected WT mice. Unfortunately, we did not evaluate these numbers in IFN-γ KO mice through FACS. 

For the assertion that Ly6G+Gra are the major source of IL-17 in TB, we have used two separate strategies- a) IFA and b) FACS. 

However, as described above in response to the first reviewer, for the revision, we propose to perform an IL-17 ELISpot assay on the sorted Ly6G+Gra from the lungs of Mtb-infected WT mice.

(2) Role of IL-17-Producing Ly6G Granulocytes in Pathology: The authors suggest that IL17-producing Ly6G granulocytes drive pathology in WT and IFN-γ KO mice. However, the data presented only demonstrate an association between IL-17+ Ly6G cells and disease pathology. To strengthen their conclusion, the authors should deplete neutrophils in these mice to show that IL-17 expression, and consequently the pathology, is reduced.

Thank you for this suggestion. Others have done neutrophil depletion studies in TB, and so far, the outcomes remain inconclusive. In some studies, neutrophil depletion helps the pathogen (Rankin et al. 2022; Pedrosa et al. 2000; Appelberg et al. 1995), and in others, it helps the host (Lovewell et al. 2021; Mishra et al. 2017) ). One reason for this variability is the stage of infection when neutrophil depletion was done. However, another crucial factor is the heterogeneity in the neutrophil population. There are reports that suggest neutrophil subtypes with protective versus pathological trajectories (Nwongbouwoh Muefong et al. 2022; Lyadova 2017; Hellebrekers, Vrisekoop, and Koenderman 2018; Leliefeld et al. 2018). Depleting the entire population using anti-Ly6G could impact this heterogeneity and may impact the inferences drawn. A better approach would be to characterise this heterogeneous population, efforts towards which could be part of a separate study.

For the revised manuscript, we will provide results from the SR2211 experiment in BCG-vaccinated mice and other results to show the role of IL-17-producing Ly6G+Gra in TB pathology.   

(3) IL-17 Secretion by Mtb-Infected Neutrophils: Do Mtb-infected neutrophils secrete IL-17 into the supernatants? This would serve as confirmation of neutrophil-derived IL-17. Additionally, are Ly6G+ cells producing IL-17 and serving as pathogenic agents exclusively in vivo? The authors should provide comments on this.

We have not directly measured IL-17 secretion by neutrophils in our experiments. However, Hu et al have reported IL-17 secretion by Mtb-infected neutrophils in vitro (Hu et al. 2017). Whether there are a few neutrophil roles exclusively seen under in vivo condition is an interesting proposition. We do have some observations that suggest in vitro phenotype of Mtb-infected neutrophils is different from in vivo.

(4) Characterization of IL-17-Producing Ly6G+ Granulocytes: Are the IL-17-producing Ly6G+ granulocytes a mixed population of neutrophils and eosinophils, or are they exclusively neutrophils? Sorting these cells followed by Giemsa or eosin staining could clarify this.

This is a very important point. While usually eosinophils do not express Ly6G markers in laboratory mice, under specific contexts, including infections, eosinophils can express Ly6G. Since we have not characterized these potential Ly6G+ sub-populations, that is one of the reasons we refer to the cell types as Ly6G+ granulocytes, which do not exclude Ly6G+ eosinophils. A detailed characterization of these subsets could be taken up as a separate study.

Reviewer #3 (Public review):

Summary:

The authors examine how distinct cellular environments differentially control Mtb following BCG vaccination. The key findings are that IL17-producing PMNs harbor a significant Mtb load in both wild-type and IFNg-/- mice. Targeting IL17 and Cox2 improved disease and enhanced BCG efficacy over 12 weeks and neutrophils/IL17 are associated with treatment failure in humans. The authors suggest that targeting these pathways, especially in MSMD patients may improve disease outcomes.

Thank you.

Strengths:

The experimental approach is generally sound and consists of low-dose aerosol infections with distinct readouts including cell sorting followed by CFU, histopathology, and RNA sequencing analysis. By combining genetic approaches and chemical/antibody treatments, the authors can probe these pathways effectively.

Understanding how distinct inflammatory pathways contribute to control or worsen Mtb disease is important and thus, the results will be of great interest to the Mtb field.

Thank you.

Weaknesses:

A major limitation of the current study is overlooking the role of non-hematopoietic cells in the IFNg/IL17/neutrophil response. Chimera studies from Ernst and colleagues (PMCID: PMC2807991) previously described this IDO-dependent pathway following the loss of IFNg through an increased IL17 response. This study is not cited nor discussed even though it may alter the interpretation of several experiments.

Thank you for pointing out this earlier study, which we concede we missed discussing. We disagree on the point that results from that study may alter the interpretation of several experiments in our study. On the contrary, the main observation that loss of IFNγ causes severe IL-17 levels is aligned in both studies.

IDO1 is known to alter Th cell differentiation towards Tregs and away from Th17 (Baban et al. 2009). It is absolutely feasible for the non-hematopoietic cells to regulate these events. However, that does not rule out the neutrophil production of IL-17 and the downstream pathological effect shown in this study. We will discuss and cite this study in the revised manuscript.

Several of the key findings in mice have previously been shown (albeit with less sophisticated experimentation) and human disease and neutrophils are well described - thus the real new finding is how intracellular Mtb in neutrophils are more refractory to BCGmediated control. However, given there are already high levels of Mtb in PMNs compared to other cell types, and there is a decrease in intracellular Mtb in PMNs following BCG immunization the strength of this finding is a bit limited.

The reviewer’s interpretation of the BCG-refractory Mtb population in the neutrophil is interesting. The reviewer is right that neutrophils had a higher intracellular Mtb burden, which decreased in the BCG-vaccinated animals. Thus, on that account, the reviewer rightly mentions that BCG is able to control Mtb even in neutrophils. However, BCG almost clears intracellular burden from other cell types analysed, and therefore, the remnant pool of intracellular Mtb in the lungs of BCG-vaccinated animals could be mostly those present in the neutrophils. This is a substantial novel development in the field and attracts focus towards innate immune cells for vaccine efficacy. 

References:

Appelberg, R., A. G. Castro, S. Gomes, J. Pedrosa, and M. T. Silva. 1995. 'SuscepBbility of beige mice to Mycobacterium avium: role of neutrophils', Infect Immun, 63: 3381-7.

Baban, B., P. R. Chandler, M. D. Sharma, J. Pihkala, P. A. Koni, D. H. Munn, and A. L. Mellor. 2009. 'IDO activates regulatory T cells and blocks their conversion into Th17-like T cells', J Immunol, 183: 2475-83.

Choi, H. G., K. W. Kwon, S. Choi, Y. W. Back, H. S. Park, S. M. Kang, E. Choi, S. J. Shin, and H. J. Kim. 2020. 'AnBgen-Specific IFN-gamma/IL-17-Co-Producing CD4(+) T-Cells Are the Determinants for ProtecBve Efficacy of Tuberculosis Subunit Vaccine', Vaccines (Basel), 8.

Cruz, A., A. G. Fraga, J. J. Fountain, J. Rangel-Moreno, E. Torrado, M. Saraiva, D. R. Pereira, T. D. Randall, J. Pedrosa, A. M. Cooper, and A. G. Castro. 2010. 'Pathological role of interleukin 17 in mice subjected to repeated BCG vaccination after infection with Mycobacterium tuberculosis', J Exp Med, 207: 1609-16.

Desel, C., A. Dorhoi, S. Bandermann, L. Grode, B. Eisele, and S. H. Kaufmann. 2011. 'Recombinant BCG DeltaureC hly+ induces superior protection over parental BCG by simulating a balanced combination of type 1 and type 17 cytokine responses', J Infect Dis, 204: 1573-84.

Ferreg, S., O. Bonneau, G. R. Dubois, C. E. Jones, and A. Trifilieff. 2003. 'IL-17, produced by lymphocytes and neutrophils, is necessary for lipopolysaccharide-induced airway neutrophilia: IL-15 as a possible trigger', J Immunol, 170: 2106-12.

Hellebrekers, P., N. Vrisekoop, and L. Koenderman. 2018. 'Neutrophil phenotypes in health and disease', Eur J Clin Invest, 48 Suppl 2: e12943.

Hoshino, A., T. Nagao, N. Nagi-Miura, N. Ohno, M. Yasuhara, K. Yamamoto, T. Nakayama, and K. Suzuki. 2008. 'MPO-ANCA induces IL-17 production by activated neutrophils in vitro via classical complement pathway-dependent manner', J Autoimmun, 31: 79-89.

Hu, S., W. He, X. Du, J. Yang, Q. Wen, X. P. Zhong, and L. Ma. 2017. 'IL-17 ProducBon of Neutrophils Enhances AnBbacteria Ability but Promotes ArthriBs Development During Mycobacterium tuberculosis InfecBon', EBioMedicine, 23: 88-99.

Hult, C., J. T. Magla, H. P. Gideon, J. J. Linderman, and D. E. Kirschner. 2021. 'Neutrophil Dynamics Affect Mycobacterium tuberculosis Granuloma Outcomes and DisseminaBon', Front Immunol, 12: 712457.

Katayama, M., K. Ohmura, N. Yukawa, C. Terao, M. Hashimoto, H. Yoshifuji, D. Kawabata, T. Fujii, Y. Iwakura, and T. Mimori. 2013. 'Neutrophils are essential as a source of IL-17 in the effector phase of arthritis', PLoS One, 8: e62231.

Khader, S. A., G. K. Bell, J. E. Pearl, J. J. Fountain, J. Rangel-Moreno, G. E. Cilley, F. Shen, S. M. Eaton, S. L. Gaffen, S. L. Swain, R. M. Locksley, L. Haynes, T. D. Randall, and A. M. Cooper. 2007. 'IL-23 and IL-17 in the establishment of protective pulmonary CD4+ T cell responses after vaccination and during Mycobacterium tuberculosis challenge', Nat Immunol, 8: 369-77.

Leliefeld, P. H. C., J. Pillay, N. Vrisekoop, M. Heeres, T. Tak, M. Kox, S. H. M. Rooijakkers, T. W. Kuijpers, P. Pickkers, L. P. H. Leenen, and L. Koenderman. 2018. 'DifferenBal antibacterial control by neutrophil subsets', Blood Adv, 2: 1344-55.

Lemos, H. P., R. Grespan, S. M. Vieira, T. M. Cunha, W. A. Verri, Jr., K. S. Fernandes, F. O. Souto, I. B. McInnes, S. H. Ferreira, F. Y. Liew, and F. Q. Cunha. 2009. 'Prostaglandin mediates IL-23/IL-17induced neutrophil migraBon in inflammation by inhibiting IL-12 and IFNgamma production', Proc Natl Acad Sci U S A, 106: 5954-9.

Li, L., L. Huang, A. L. Vergis, H. Ye, A. Bajwa, V. Narayan, R. M. Strieter, D. L. Rosin, and M. D. Okusa. 2010. 'IL-17 produced by neutrophils regulates IFN-gamma-mediated neutrophil migration in mouse kidney ischemia-reperfusion injury', J Clin Invest, 120: 331-42.

Lin, A. M., C. J. Rubin, R. Khandpur, J. Y. Wang, M. Riblen, S. Yalavarthi, E. C. Villanueva, P. Shah, M. J. Kaplan, and A. T. Bruce. 2011. 'Mast cells and neutrophils release IL-17 through extracellular trap formation in psoriasis', J Immunol, 187: 490-500.

Lovewell, R. R., C. E. Baer, B. B. Mishra, C. M. Smith, and C. M. Sasseg. 2021. 'Granulocytes act as a niche for Mycobacterium tuberculosis growth', Mucosal Immunol, 14: 229-41.

Lyadova, I. V. 2017. 'Neutrophils in Tuberculosis: Heterogeneity Shapes the Way?', Mediators Inflamm, 2017: 8619307.

Mishra, B. B., R. R. Lovewell, A. J. Olive, G. Zhang, W. Wang, E. Eugenin, C. M. Smith, J. Y. Phuah, J. E. Long, M. L. Dubuke, S. G. Palace, J. D. Goguen, R. E. Baker, S. Nambi, R. Mishra, M. G. Booty, C. E. Baer, S. A. Shaffer, V. Dartois, B. A. McCormick, X. Chen, and C. M. Sasseg. 2017. 'Nitric oxide prevents a pathogen-permissive granulocytic inflammation during tuberculosis', Nat Microbiol, 2: 17072.

Napolitani, G., E. V. Acosta-Rodriguez, A. Lanzavecchia, and F. Sallusto. 2009. 'Prostaglandin E2 enhances Th17 responses via modulation of IL-17 and IFN-gamma production by memory CD4+ T cells', Eur J Immunol, 39: 1301-12.

Nwongbouwoh Muefong, C., O. Owolabi, S. Donkor, S. Charalambous, A. Bakuli, A. Rachow, C. Geldmacher, and J. S. Sutherland. 2022. 'Neutrophils Contribute to Severity of Tuberculosis Pathology and Recovery From Lung Damage Pre- and Posnreatment', Clin Infect Dis, 74: 1757-66.

Paulissen, S. M., J. P. van Hamburg, N. Davelaar, P. S. Asmawidjaja, J. M. Hazes, and E. Lubberts. 2013. 'Synovial fibroblasts directly induce Th17 pathogenicity via the cyclooxygenase/prostaglandin E2 pathway, independent of IL-23', J Immunol, 191: 1364-72.

Pedrosa, J., B. M. Saunders, R. Appelberg, I. M. Orme, M. T. Silva, and A. M. Cooper. 2000. 'Neutrophils play a protective nonphagocytic role in systemic Mycobacterium tuberculosis infection of mice', Infect Immun, 68: 577-83.

Polese, B., B. Thurairajah, H. Zhang, C. L. Soo, C. A. McMahon, G. Fontes, S. N. A. Hussain, V. Abadie, and I. L. King. 2021. 'Prostaglandin E(2) amplifies IL-17 production by gamma-delta T cells during barrier inflammation', Cell Rep, 36: 109456.

Rankin, A. N., S. V. Hendrix, S. K. Naik, and C. L. Stallings. 2022. 'Exploring the Role of Low-Density Neutrophils During Mycobacterium tuberculosis InfecBon', Front Cell Infect Microbiol, 12: 901590.

Xu, X. J., Q. Q. Ge, M. S. Yang, Y. Zhuang, B. Zhang, J. Q. Dong, F. Niu, H. Li, and B. Y. Liu. 2023. 'Neutrophil-derived interleukin-17A participates in neuroinflammation induced by traumatic brain injury', Neural Regen Res, 18: 1046-51.

Carlo Van De Roer

Carlo van de Roer

I think as theres a lot of content here i wonder if the menu could have drop downs when hovered over? And maybe use a sticky banner like we do on these https://www.education.library.manchester.ac.uk/mle/packages/writing/ when the person starts scrolling the menu reappears briefly

If possible i think we should reduce these to about 5 - one of these could be about where to find help on Linked in Learning itself?

Can we have a divider here to separate this out a little and try the grey background?

Also can you reword this to:

Further support for your development During your studies, you will receive support to develop professional skills that are relevant to your chosen career path. Building these skills takes time and is part of your lifelong learning journey. Throughout your time at university, you can return to this guide and LinkedIn Learning whenever you find it useful.

You can also access workshops and guides through the Library teaching programmes which support academics skills, research and specialist support areas such as copyright.

Reword this to:

Share Your Career Goals and Interests on LinkedIn Sharing your career goals on LinkedIn enhances your LinkedIn Learning experience by helping the platform recommend courses tailored to your goals. It also allows your network and mentors to suggest relevant resources, connect you with professionals in similar fields, and increases your visibility to recruiters. This information will help LinkedIn suggest: * Job or internship opportunities * Companies to follow * Professional groups to join for networking

Reword this to:

Build Your Professional Network

Building your LinkedIn network makes your learning more engaging and relevant by: * Offering personalised course recommendations. * Sharing new skills with recruiters. * Aligning learning with your connections' career paths. * Accessing curated content from LinkedIn Groups.

swap this order here to share your career goals and interests and build your professional network

Can networking secrtion be after benefits f listing career goals

Reduce padding above

MIssing link and reduce padding afterward but increase padding between this and transcript

This needs some text to introduce it - whats it about and why do they need to watch it?

Any instructions we should number. Rather than a transcript for demo videos can we have the video and the written instructions like this in a accordion

Make this sentence part of the previous paragraph

Reword to

We recommend you regularly review and update your LinkedIn Profile and LinkedIn Learning Path with any new goals or interests.

I would reword this to 'Update your learning path'

The heading here says playlist but the video is about collections?

I think we can keep the title much shorter too just 'Creating a collection/playlist'

I'm a little confused by this video cant watch it at the moment - is this playlists and collections or are career goals something else? If something else I think it need bullet above and any videos should be in same order as the bullets

Reword to Playlist and collections allow you to choose how you engage with LinkedIn Learning, giving you a personalised learning experience.

Reword to

• Collections are more flexible groupings of courses or resources that you can explore at your own pace, allowing you to dive into specific topics or areas of interest.

Reword to:

• Playlists are like Learning Paths, they are sets of courses or videos organised to progressively build your skills but unlike Learning Paths you can personalise them. This can be especially useful when you find learning specific topics complex.

Reword to:

You can also gather together tailored learning content based on your personal or career goals by using playlists and collections.

Change this first sentence so it incorporates the one after the bullets as follows:

Your academic may use LinkedIn Learning to create tailored Learning Paths or Collections to help guide your studies. These curated resources are designed to complement your coursework and provide additional opportunities to deepen your understanding and skills.

Delete

Reword to • Learning Paths are a structured series of courses organised to progressively build your skills, which can be especially useful when learning complex topics like coding or data analysis. You may have Learning paths created for you by your academic will usually be created by your academics. • Collections are a more flexible grouping of courses or resources that you can explore at your own pace, allowing you to dive into specific topics or areas of interest.

eLife assessment

This useful study investigates the role of Complement 3a Receptor 1 (C3aR) in the pathogenesis of Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) using mouse models with specific target deletions in various cell types. While the relevance of C3aR in inflammatory contexts has been established, the authors provide helpful but incomplete evidence that C3aR does not contribute significantly to MASLD pathogenesis in their models, a claim that would require additional experiments for support.

Reviewer #1 (Public review):

Summary:

In this paper Homan et al used mouse models of Metabolic Dysfunction-Associated Steatotic Liver Disease and different specific target deletions in cells to rule out the role of Complement 3a Receptor 1 in the pathogenesis of disease. They provided limited evidence and only descriptive results that despite C3aR being relevant in different contexts of inflammation, however, these tenets did not hold true.

Weaknesses:

(1) The results are based on readouts showing that C3aR is not involved in the pathogenesis of liver metabolic disease.

(2) The description of the mouse models they used to validate their findings is not clear. Lysm-cre mice - which are claimed to delete C3aR in (?) macrophages are not specific for these cells, and the genetic strategy to delete C3aR in Kupffer cells is not clear.

(3) Taking this into account, it is very challenging to determine the validity of these data, also considering that they are merely descriptive and correlative.

Reviewer #2 (Public review):

Summary:

Homan et al. examined the effect of macrophage- or Kupffer cell-specific C3aR1 KO on MASLD/MASH-related metabolic or liver phenotypes.

Strengths:

Established macrophage- or Kupffer cell-specific C3aR1 KO mice.

Weaknesses:

Lack of in-depth study; flaws in comparisons between KC-specific C3aR1KO and WT in the context of MASLD/MASH, because MASLD/MASH WT mice likely have a low abundance of C3aR1 on KCs.

Homan et al. reported a set of observation data from macrophage or Kupffer cell-specific C3aR1KO mice. Several questions and concerns as follows could challenge the conclusions of this study:

(1) As C3aR1 is robustly repressed in MASLD or MASH liver, GAN feeding likely reduced C3aR1 abundance in the liver of WT mice. Thus, it is not surprising that there were no significant differences in liver phenotypes between WT vs. C3aR1KO mice after prolonged GAN diet feeding. It would give more significance to the study if restoring C3aR1 abundance in KCs in the context of MASLD/MASH.

(2) Would C3aR1KO mice develop liver abnormalities after a short period of GAN diet feeding?

(3) What would be the liver macrophage phenotypes in WT vs C3aR1KO mice after GAN feeding?

(4) In Fig 1D, >25wks GAN feeding had minimal effects on female body weight gain. These GAN-fed female mice also develop NASLD/MASH liver abnormalities?

(5) Would C3aR1KO result in differences in liver phenotypes, including macrophage population/activation, liver inflammation, lipogenesis, in lean mice?

(6) The authors should provide more information regarding the generation of KC-specific C3aR1KO. Which Cre mice were used to breed with C3aR1 flox mice?

Author response:

Public Reviews:

Reviewer #1 (Public review):

Summary: 

In this paper Homan et al used mouse models of Metabolic Dysfunction-Associated Steatotic Liver Disease and different specific target deletions in cells to rule out the role of Complement 3a Receptor 1 in the pathogenesis of disease. They provided limited evidence and only descriptive results that despite C3aR being relevant in different contexts of inflammation, however, these tenets did not hold true. 

Weaknesses: 

(1) The results are based on readouts showing that C3aR is not involved in the pathogenesis of liver metabolic disease. 

(2) The description of the mouse models they used to validate their findings is not clear. Lysm-cre mice - which are claimed to delete C3aR in (?) macrophages are not specific for these cells, and the genetic strategy to delete C3aR in Kupffer cells is not clear. 

(3) Taking this into account, it is very challenging to determine the validity of these data, also considering that they are merely descriptive and correlative. 

We generated 2 different cohorts of mice using LysM-Cre (Jackson Strain #004781) to drive deletion in all macrophages and Clec4f-Cre (Jackson Strain #033296) to specifically ablate C3ar1 in Kupffer cells. We will ensure that experimental models will be clearly defined in the revised manuscript. The reviewer’s point is well taken that LysM-Cre transgene can also be active in granulocytes and some dendritic cells. Even so, despite deletion of C3ar1 in macrophages and other granulocytes, we do not see a major effect on hepatic steatosis and fibrosis in this GAN diet induced model of MASLD/MASH. This was a somewhat surprising finding. We do not agree that our findings are correlative. We specifically ablated C3aR1 in macrophages or Kupffer cells and found no significant differences in the major readouts of steatosis and fibrosis for MASLD/MASH between control and knockout mice. It is possible that in other models of liver injury that we did not test (e.g., short-term treatment with a hepatotoxin such as carbon tetrachloride), there may be differences in liver injury in mice lacking C3ar1 in macrophages, but the GAN diet model has been shown to better parallel the gene expression changes in human MAFLD/MASH.

Reviewer #2 (Public review):

Summary:

Homan et al. examined the effect of macrophage- or Kupffer cell-specific C3aR1 KO on MASLD/MASHrelated metabolic or liver phenotypes. 

Strengths:

Established macrophage- or Kupffer cell-specific C3aR1 KO mice. 

Weaknesses:

Lack of in-depth study; flaws in comparisons between KC-specific C3aR1KO and WT in the context of MASLD/MASH, because MASLD/MASH WT mice likely have a low abundance of C3aR1 on KCs. 

Homan et al. reported a set of observation data from macrophage or Kupffer cell-specific C3aR1KO mice. Several questions and concerns as follows could challenge the conclusions of this study: 

(1) As C3aR1 is robustly repressed in MASLD or MASH liver, GAN feeding likely reduced C3aR1 abundance in the liver of WT mice. Thus, it is not surprising that there were no significant differences in liver phenotypes between WT vs. C3aR1KO mice after prolonged GAN diet feeding. It would give more significance to the study if restoring C3aR1 abundance in KCs in the context of MASLD/MASH. 

GAN diet feeding resulted in higher liver C3ar1 compared to regular diet (Figure 1H). This thus became an impetus for studying the effects of C3ar1 deletion in macrophages or Kupffer cells, which are responsible for the majority of liver C3ar1 expression, in MASLD/MASH (Figures 2B and 3H).  

(2) Would C3aR1KO mice develop liver abnormalities after a short period of GAN diet feeding?  

We did not assess if short term GAN diet feeding resulted in significant differences in liver abnormalities in the C3ar1 macrophage or Kupffer cell knockout mice. Perhaps the reviewer’s point is that perhaps with shorter periods of GAN diet feeding there may be a phenotype in the KO mice. We agree that this is entirely possible, though with shorter feeding timeframes what is typically seen is hepatic steatosis without fibrosis. Nevertheless, the most important element in our opinion for a disease preventing or modifying model lies with the longer-term GAN diet feeding. With long term GAN diet feeding that has been previously shown to model human MASLD/MASH, we did not observe significant differences in liver abnormalities with the KO mice.

(3) What would be the liver macrophage phenotypes in WT vs C3aR1KO mice after GAN feeding? 

Similar to the above point, given the lack of a major MASLD/MASH phenotype in hepatic steatosis and fibrosis, we did not further profile the liver macrophage profiles of the macrophage or Kupffer cell C3ar1 KO mice with GAN feeding.  

(4) In Fig 1D, >25wks GAN feeding had minimal effects on female body weight gain. These GAN-fed female mice also develop NASLD/MASH liver abnormalities? 

We thank the reviewer for this question. In general, female GAN-fed mice develop milder MASLD/MASH abnormalities. We will include additional data in the revised manuscript.

(5) Would C3aR1KO result in differences in liver phenotypes, including macrophage population/activation, liver inflammation, lipogenesis, in lean mice? 

Likewise, we will include data further characterizing liver inflammation, lipogenesis and macrophages in macrophage C3ar1 KO mice under lean/regular diet conditions.

(6) The authors should provide more information regarding the generation of KC-specific C3aR1KO. Which Cre mice were used to breed with C3aR1 flox mice? 

Clec4f-Cre transgenic mice were used to generate Kupffer cell specific KO of C3ar1. This will be clarified and explicitly stated in the revised manuscript.

Author response:

Public Reviews:

Reviewer #1 (Public review):

Summary:

This study puts forth the model that under IFN-B stimulation, liquid-phase WTAP coordinates with the transcription factor STAT1 to recruit MTC to the promoter region of interferon-stimulated genes (ISGs), mediating the installation of m6A on newly synthesized ISG mRNAs. This model is supported by strong evidence that the phosphorylation state of WTAP, regulated by PPP4, is regulated by IFN-B stimulation, and that this results in interactions between WTAP, the m6A methyltransferase complex, and STAT1, a transcription factor that mediates activation of ISGs. This was demonstrated via a combination of microscopy, immunoprecipitations, m6A sequencing, and ChIP. These experiments converge on a set of experiments that nicely demonstrate that IFN-B stimulation increases the interaction between WTAP, METTL3, and STAT1, that this interaction is lost with the knockdown of WTAP (even in the presence of IFN-B), and that this IFN-B stimulation also induces METTL3-ISG interactions.

Strengths:

The evidence for the IFN-B stimulated interaction between METTL3 and STAT1, mediated by WTAP, is quite strong. Removal of WTAP in this system seems to be sufficient to reduce these interactions and the concomitant m6A methylation of ISGs. The conclusion that the phosphorylation state of WTAP is important in this process is also quite well supported.

Weaknesses:

The evidence that the above mechanism is fundamentally driven by different phase-separated pools of WTAP (regulated by its phosphorylation state) is weaker. These experiments rely relatively heavily on the treatment of cells with 1,6-hexanediol, which has been shown to have some off-target effects on phosphatases and kinases (PMID 33814344).

Given that the model invoked in this study depends on the phosphorylation (or lack thereof) of WTAP, this is a particularly relevant concern.

Related to this point, it is also interesting (and potentially concerning for the proposed model) that the initial region of WTAP that was predicted to be disordered is in fact not the region that the authors demonstrate is important for the different phase-separated states. Taking all the data together, it is also not clear to me that one has to invoke phase separation in the proposed mechanism.

We are grateful for the Reviewer’s positive comment and constructive feedback. In this article, we claim a novel and important mechanism that de-phosphorylation-driven solid to liquid phase transition of WTAP mediates its co-transcriptional m6A modification. We first observed that WTAP underwent phase transition during virus infection and IFN-β stimulation, and confirmed the phase transition driven force of WTAP through multiple experiments. Besides 1,6‐hexanediol (1,6-hex) treatment, we also introduced S/T to D/A mutations to mimic the phosphorylation and de-phosphorylation WTAP in vitro and in cells, identified 5ST-D mutant as SLPS mutant, and 5ST-A mutant as LLPS mutant. We then performed 1,6-hex experiment to confirm the importance of phase separation for WTAP function, and revealed that 5ST-D SLPS mutant and 5ST-A LLPS mutant had different influence on WTAP-promoter region interaction and co-transcriptional m6A modification. Following the reviewer’s suggestion, we need to further clarify the phosphorylation of WTAP phase separation. We plan to repeat the experiments by introducing potent PP4 inhibitor, fostriecin, and performed further experiments to explore the effect of WTAP IDR domain, which is reported to play a critical role for its phase separation.

1,6-hex was initially considered as the inhibitor of hydrophobic interaction which involved in various kinds of protein-protein interaction, indicating that off-target effects of 1,6-hex was inevitable. It is reported that 1,6-hex impaired RNA pol II CTD specific phosphatase and kinase activity at 5% concentration3. However, 1,6-hex is still widely used in the LLPS-associated functional studies despite its off-target effect. Related to this article, 10% 1,6-hex was reported to dissolve WTAP phase separation droplets2. Beside WTAP, 1,6-hex (5%-10% w/v) was also used to explore the phase separation characteristic and function on phosphorylated protein or even kinase, including p‐tau441, TAZ, HSF1 and so on4-6. 10% 1,6-hex inhibited the crucial role of phosphorylation-driven HSF1 LLPS in chromatin binding and transcriptional process presented by RNA-seq dataset6, indicating the function on kinase or phosphatase of 1,6-hex might not a global effect. To avoid the 1,6-hex-mediated kinase/phosphatase impairment in this project, we introduced the WTAP SLPS mutation and LLPS mutation besides 1,6-hex treatment to explore the m6A modification function of WTAP phase transition. We plan to repeat the experiments by lower the 1,6-hex concentration, check the WTAP phosphorylation status after 1,6-hex treatment, and discuss them in the discussion part.

A considerable number of proteins undergo phase separation via interactions between intrinsically disordered regions (IDRs). IDR contains more charged and polar amino acids to present multiple weakly interacting elements, while lacking hydrophobic amino acids to show flexible conformations7. In our article, we used PLAAC websites (http://plaac.wi.mit.edu/) to predict IDR domain of WTAP, and a fragment (234-249 amino acids) was predicted as prion-like domain. However, deletion of this fragment failed to abolish the phase separation properties of WTAP, which might be the main confusion to reviewers. To explain this issue, we checked the WTAP structure (within part of MTC complex) from protein data bank (https://www.rcsb.org/structure/7VF2) and found that prediction of IDR has been renewed due to the update of different algorithm. IDR of WTAP has expanded to 245-396 amino acids, containing the whole CTD region. According to our results, lack of CTD inhibited WTAP liquid-liquid phase separation both in vitro and in cells, while the phosphorylation status on CTD had dramatic impact on WTAP phase transition, which was consistent with the LLPS-regulating function of IDR. Therefore, we will revise our description on WTAP IDR, and performed further experiment to test its function.

Taken together, given the highly association between WTAP phosphorylation with phase separation status and its function during IFN-β stimulation, it is necessary to involve WTAP phase separation in our mechanism. We will perform further experiments to propose more convincing evidence and perfect our project.

Reviewer #2 (Public review):

In this study, Cai and colleagues investigate how one component of the m6A methyltransferase complex, the WTAP protein, responds to IFNb stimulation. They find that viral infection or IFNb stimulation induces the transition of WTAP from aggregates to liquid droplets through dephosphorylation by PPP4. This process affects the m6A modification levels of ISG mRNAs and modulates their stability. In addition, the WTAP droplets interact with the transcription factor STAT1 to recruit the methyltransferase complex to ISG promoters and enhance m6A modification during transcription. The investigation dives into a previously unexplored area of how viral infection or IFNb stimulation affects m6A modification on ISGs. The observation that WTAP undergoes a phase transition is significant in our understanding of the mechanisms underlying m6A's function in immunity. However, there are still key gaps that should be addressed to fully accept the model presented.

Major points:

(1) More detailed analyses on the effects of WTAP sgRNA on the m6A modification of ISGs:

a. A comprehensive summary of the ISGs, including the percentage of ISGs that are m6A-modified. merip-isg percentage

b. The distribution of m6A modification across the ISGs. topology

c. A comparison of the m6A modification distribution in ISGs with non-ISGs. topology

In addition, since the authors propose a novel mechanism where the interaction between phosphorylated STAT1 and WTAP directs the MTC to the promoter regions of ISGs to facilitate co-transcriptional m6A modification, it is critical to analyze whether the m6A modification distribution holds true in the data.

We appreciate the reviewer‘s summary of our manuscript and the constructive assessment. We plan to perform the related analysis accordingly to present the m6A modification in ISGs in our model. 

(2) Since a key part of the model includes the cytosol-localized STAT1 protein undergoing phosphorylation to translocate to the nucleus to mediate gene expression, the authors should focus on the interaction between phosphorylated STAT1 and WTAP in Figure 4, rather than the unphosphorylated STAT1. Only phosphorylated STAT1 localizes to the nucleus, so the presence of pSTAT1 in the immunoprecipitate is critical for establishing a functional link between STAT1 activation and its interaction with WTAP.

We plan to repeat the immunoprecipitation experiments to clarify the function of pSTAT1 in WTAP interaction and m6A modification as the reviewer suggested.

(3) The authors should include pSTAT1 ChIP-seq and WTAP ChIP-seq on IFNb-treated samples in Figure 5 to allow for a comprehensive and unbiased genomic analysis for comparing the overlaps of peaks from both ChIP-seq datasets. These results should further support their hypothesis that WTAP interacts with pSTAT1 to enhance m6A modifications on ISGs.

We first performed the MeRIP-seq and RNA-seq and explored the critical role of WTAP in ISGs m6A modification and expression. By immunoprecipitation and immunofluorescence experiments, we found phase transition of WTAP enhanced its interaction to pSTAT1. These results indicate that WTAP mediated ISGs m6A modification and expression by enhanced its interaction with pSTAT1 during virus infection and IFN-β stimulation. However, we were still not sure how WTAP-mediated m6A modification related to pSTAT1-mediated transcription. By analyzing METTL3 ChIP-seq data or caPAR-CLIP-seq data, several researches have revealed the recruitment of m6A methylation complex (MTC) to transcription start sites (TSS) of coding genes and R-loop structure by interacting with transcriptional factors STAT5B or DNA helicase DDX21, indicating the engagement of MTC mediated m6A modification on nascent transcripts at the very beginning of transcription 8-10. Thus, we proposed that phase transition of WTAP could be recruited to the ISGs promoter region by pSTAT1, and verified this hypothesis by pSTAT1/WTAP-ChIP-qPCR. We believe ChIP-seq experiment is a good idea to explore the mechanism in depth, but the results in this article for now are enough to explain our mechanism. We will continuously focus on the whole genome chromatin distribution of WTAP and explore more functional effect of transcriptional factor-dependent WTAP-promoter region interaction in t.

Minor points:

(1) Since IFNb is primarily known for modulating biological processes through gene transcription, it would be informative if the authors discussed the mechanism of how IFNb would induce the interaction between WTAP and PPP4.

(2) The authors should include mCherry alone controls in Figure 1D to demonstrate that mCherry does not contribute to the phase separation of WTAP. Does mCherry have or lack a PLD?

(3) The authors should clarify the immunoprecipitation assays in the methods. For example, the labeling in Figure 2A suggests that antibodies against WTAP and pan-p were used for two immunoprecipitations. Is that accurate?

(4) The authors should include overall m6A modification levels quantified of GFPsgRNA and WTAPsgRNA cells, either by mass spectrometry (preferably) or dot blot.

We thank reviewer for raising these useful suggestions. We will perform related experiments and revised the manuscript carefully the as reviewer suggested.

Reviewer #3 (Public review):

Summary:

This study presents a valuable finding on the mechanism used by WTAP to modulate the IFN-β stimulation. It describes the phase transition of WTAP driven by IFN-β-induced dephosphorylation. The evidence supporting the claims of the authors is solid, although major analysis and controls would strengthen the impact of the findings. Additionally, more attention to the figure design and to the text would help the reader to understand the major findings.

Strength:

The key finding is the revelation that WTAP undergoes phase separation during virus infection or IFN-β treatment. The authors conducted a series of precise experiments to uncover the mechanism behind WTAP phase separation and identified the regulatory role of 5 phosphorylation sites. They also succeeded in pinpointing the phosphatase involved.

Weaknesses:

However, as the authors acknowledge, it is already widely known in the field that IFN and viral infection regulate m6A mRNAs and ISGs. Therefore, a more detailed discussion could help the reader interpret the obtained findings in light of previous research.

It is well-known that protein concentration drives phase separation events. Similarly, previous studies and some of the figures presented by the authors show an increase in WTAP expression upon IFN treatment. The authors do not discuss the contribution of WTAP expression levels to the phase separation event observed upon IFN treatment. Similarly, METTL3 and METTL14, as well as other proteins of the MTC are upregulated upon IFN treatment. How does the MTC protein concentration contribute to the observed phase separation event?

How is PP4 related to the IFN signaling cascade?

In general, it is very confusing to talk about WTAP KO as WTAPgRNA.

We are grateful for the positive comments and the unbiased advice by reviewer. To interpret the findings in previous research, we will revise the manuscript carefully and preform more detailed discussion on ISGs m6A modification during virus infection or IFN stimulation. As previous reported, WTAP protein level will be induced by long time IFN-β stimulation or LPS stimulation, while LPS-induced WTAP expression promoted its phase separation ability2,11. Although there was no significant upregulation of WTAP expression level in our short time treatment, we hypothesized that WTAP phase separation will be promoted due to higher protein concentration after long time IFN stimulation, enhancing m6A modification deposition on ISGs mRNA, revealing a feedback loop between WTAP phase separation and m6A modification during specific stimulation. To discuss the effect of MTC protein concentration in our proposed event, we will perform immunoblotting experiments of MTC proteins and check the phase separation effect in different WTAP concentration.

Protein phosphatase 4 (PP4) is a multi-subunit Ser/Thr phosphatase complex that participate in diverse cellular pathways including DDR, cell cycle progression, and apoptosis12. Protein phosphatase 4 catalytic subunit 4C (PPP4C) is one of the components of PP4 complex. Previous research showed that knockout of PPP4C enhanced IFN-β downstream signaling and gene expression, which was consistent with our findings that knockdown of PPP4C impaired WTAP-mediated m6A modification, enhanced the ISGs expression. Since there was no significant enhancement in PPP4C expression level during IFN-β stimulation in our results, we will consider to explore the post-translation modification that may influence the protein-protein interaction, such as ubiquitination.

In this project, all the WTAP-deficient THP-1 cells were bulk cells treated with WTAPsgRNA, but not monoclonal knockout cells. We confirmed that WTAP expression was efficiently knockdown in WTAPsgRNA THP-1 cells, and the m6A modification level has been impaired, avoiding the compensatory effect on m6A modification by other possible proteins. Thus, we prefer to call it WTAPsgRNA THP-1 cells rather than WTAP KO THP-1 cells.  

References

(1) Raja, R., Wu, C., Bassoy, E.Y., Rubino, T.E., Jr., Utagawa, E.C., Magtibay, P.M., Butler, K.A., and Curtis, M. (2022). PP4 inhibition sensitizes ovarian cancer to NK cell-mediated cytotoxicity via STAT1 activation and inflammatory signaling. J Immunother Cancer 10. 10.1136/jitc-2022-005026.

(2) Ge, Y., Chen, R., Ling, T., Liu, B., Huang, J., Cheng, Y., Lin, Y., Chen, H., Xie, X., Xia, G., et al. (2024). Elevated WTAP promotes hyperinflammation by increasing m6A modification in inflammatory disease models. J Clin Invest 134. 10.1172/JCI177932.

(3) Duster, R., Kaltheuner, I.H., Schmitz, M., and Geyer, M. (2021). 1,6-Hexanediol, commonly used to dissolve liquid-liquid phase separated condensates, directly impairs kinase and phosphatase activities. J Biol Chem 296, 100260. 10.1016/j.jbc.2021.100260.

(4) Wegmann, S., Eftekharzadeh, B., Tepper, K., Zoltowska, K.M., Bennett, R.E., Dujardin, S., Laskowski, P.R., MacKenzie, D., Kamath, T., Commins, C., et al. (2018). Tau protein liquid-liquid phase separation can initiate tau aggregation. The EMBO journal 37. 10.15252/embj.201798049.

(5) Lu, Y., Wu, T., Gutman, O., Lu, H., Zhou, Q., Henis, Y.I., and Luo, K. (2020). Phase separation of TAZ compartmentalizes the transcription machinery to promote gene expression. Nat Cell Biol 22, 453-464. 10.1038/s41556-020-0485-0.

(6) Zhang, H., Shao, S., Zeng, Y., Wang, X., Qin, Y., Ren, Q., Xiang, S., Wang, Y., Xiao, J., and Sun, Y. (2022). Reversible phase separation of HSF1 is required for an acute transcriptional response during heat shock. Nat Cell Biol 24, 340-352. 10.1038/s41556-022-00846-7.

(7) Hou, S., Hu, J., Yu, Z., Li, D., Liu, C., and Zhang, Y. (2024). Machine learning predictor PSPire screens for phase-separating proteins lacking intrinsically disordered regions. Nat Commun 15, 2147. 10.1038/s41467-024-46445-y.

(8) Hao, J.D., Liu, Q.L., Liu, M.X., Yang, X., Wang, L.M., Su, S.Y., Xiao, W., Zhang, M.Q., Zhang, Y.C., Zhang, L., et al. (2024). DDX21 mediates co-transcriptional RNA m(6)A modification to promote transcription termination and genome stability. Mol Cell 84, 1711-1726 e1711. 10.1016/j.molcel.2024.03.006.

(9) Barbieri, I., Tzelepis, K., Pandolfini, L., Shi, J., Millan-Zambrano, G., Robson, S.C., Aspris, D., Migliori, V., Bannister, A.J., Han, N., et al. (2017). Promoter-bound METTL3 maintains myeloid leukaemia by m(6)A-dependent translation control. Nature 552, 126-131. 10.1038/nature24678.

(10) Bhattarai, P.Y., Kim, G., Lim, S.C., and Choi, H.S. (2024). METTL3-STAT5B interaction facilitates the co-transcriptional m(6)A modification of mRNA to promote breast tumorigenesis. Cancer Lett 603, 217215. 10.1016/j.canlet.2024.217215.

(11) Ge, Y., Ling, T., Wang, Y., Jia, X., Xie, X., Chen, R., Chen, S., Yuan, S., and Xu, A. (2021). Degradation of WTAP blocks antiviral responses by reducing the m(6) A levels of IRF3 and IFNAR1 mRNA. EMBO Rep 22, e52101. 10.15252/embr.202052101.

(12) Dong, M.Z., Ouyang, Y.C., Gao, S.C., Ma, X.S., Hou, Y., Schatten, H., Wang, Z.B., and Sun, Q.Y. (2022). PPP4C facilitates homologous recombination DNA repair by dephosphorylating PLK1 during early embryo development. Development 149. 10.1242/dev.200351.

eLife assessment

This important study demonstrates that interferon beta stimulation induces WTAP transition from aggregates to liquid droplets, coordinating m6A modification of a subset of mRNAs that encode interferon-stimulated genes and restricting their expression. The evidence presented is solid, supported by microscopy, immunoprecipitations, m6A sequencing, and ChIP, to show that WTAP phosphorylation controls phase transition and its interaction with STAT1 and the methyltransferase complex.

Reviewer #1 (Public review):

Summary:

This study puts forth the model that under IFN-B stimulation, liquid-phase WTAP coordinates with the transcription factor STAT1 to recruit MTC to the promoter region of interferon-stimulated genes (ISGs), mediating the installation of m6A on newly synthesized ISG mRNAs. This model is supported by strong evidence that the phosphorylation state of WTAP, regulated by PPP4, is regulated by IFN-B stimulation, and that this results in interactions between WTAP, the m6A methyltransferase complex, and STAT1, a transcription factor that mediates activation of ISGs. This was demonstrated via a combination of microscopy, immunoprecipitations, m6A sequencing, and ChIP. These experiments converge on a set of experiments that nicely demonstrate that IFN-B stimulation increases the interaction between WTAP, METTL3, and STAT1, that this interaction is lost with the knockdown of WTAP (even in the presence of IFN-B), and that this IFN-B stimulation also induces METTL3-ISG interactions.

Strengths:

The evidence for the IFN-B stimulated interaction between METTL3 and STAT1, mediated by WTAP, is quite strong. Removal of WTAP in this system seems to be sufficient to reduce these interactions and the concomitant m6A methylation of ISGs. The conclusion that the phosphorylation state of WTAP is important in this process is also quite well supported.

Weaknesses:

The evidence that the above mechanism is fundamentally driven by different phase-separated pools of WTAP (regulated by its phosphorylation state) is weaker. These experiments rely relatively heavily on the treatment of cells with 1,6-hexanediol, which has been shown to have some off-target effects on phosphatases and kinases (PMID 33814344). Given that the model invoked in this study depends on the phosphorylation (or lack thereof) of WTAP, this is a particularly relevant concern. Related to this point, it is also interesting (and potentially concerning for the proposed model) that the initial region of WTAP that was predicted to be disordered is in fact not the region that the authors demonstrate is important for the different phase-separated states. Taking all the data together, it is also not clear to me that one has to invoke phase separation in the proposed mechanism.

Reviewer #2 (Public review):

In this study, Cai and colleagues investigate how one component of the m6A methyltransferase complex, the WTAP protein, responds to IFNb stimulation. They find that viral infection or IFNb stimulation induces the transition of WTAP from aggregates to liquid droplets through dephosphorylation by PPP4. This process affects the m6A modification levels of ISG mRNAs and modulates their stability. In addition, the WTAP droplets interact with the transcription factor STAT1 to recruit the methyltransferase complex to ISG promoters and enhance m6A modification during transcription. The investigation dives into a previously unexplored area of how viral infection or IFNb stimulation affects m6A modification on ISGs. The observation that WTAP undergoes a phase transition is significant in our understanding of the mechanisms underlying m6A's function in immunity. However, there are still key gaps that should be addressed to fully accept the model presented.

Major points:

(1) More detailed analyses on the effects of WTAP sgRNA on the m6A modification of ISGs:<br /> a. A comprehensive summary of the ISGs, including the percentage of ISGs that are m6A-modified.<br /> b. The distribution of m6A modification across the ISGs.<br /> c. A comparison of the m6A modification distribution in ISGs with non-ISGs.

In addition, since the authors propose a novel mechanism where the interaction between phosphorylated STAT1 and WTAP directs the MTC to the promoter regions of ISGs to facilitate co-transcriptional m6A modification, it is critical to analyze whether the m6A modification distribution holds true in the data.

(2) Since a key part of the model includes the cytosol-localized STAT1 protein undergoing phosphorylation to translocate to the nucleus to mediate gene expression, the authors should focus on the interaction between phosphorylated STAT1 and WTAP in Figure 4, rather than the unphosphorylated STAT1. Only phosphorylated STAT1 localizes to the nucleus, so the presence of pSTAT1 in the immunoprecipitate is critical for establishing a functional link between STAT1 activation and its interaction with WTAP.

(3) The authors should include pSTAT1 ChIP-seq and WTAP ChIP-seq on IFNb-treated samples in Figure 5 to allow for a comprehensive and unbiased genomic analysis for comparing the overlaps of peaks from both ChIP-seq datasets. These results should further support their hypothesis that WTAP interacts with pSTAT1 to enhance m6A modifications on ISGs.

Minor points:

(1) Since IFNb is primarily known for modulating biological processes through gene transcription, it would be informative if the authors discussed the mechanism of how IFNb would induce the interaction between WTAP and PPP4.

(2) The authors should include mCherry alone controls in Figure 1D to demonstrate that mCherry does not contribute to the phase separation of WTAP. Does mCherry have or lack a PLD?

(3) The authors should clarify the immunoprecipitation assays in the methods. For example, the labeling in Figure 2A suggests that antibodies against WTAP and pan-p were used for two immunoprecipitations. Is that accurate?

(4) The authors should include overall m6A modification levels quantified of GFPsgRNA and WTAPsgRNA cells, either by mass spectrometry (preferably) or dot blot.

Reviewer #3 (Public review):

Summary:

This study presents a valuable finding on the mechanism used by WTAP to modulate the IFN-β stimulation. It describes the phase transition of WTAP driven by IFN-β-induced dephosphorylation. The evidence supporting the claims of the authors is solid, although major analysis and controls would strengthen the impact of the findings. Additionally, more attention to the figure design and to the text would help the reader to understand the major findings.

Strength:

The key finding is the revelation that WTAP undergoes phase separation during virus infection or IFN-β treatment. The authors conducted a series of precise experiments to uncover the mechanism behind WTAP phase separation and identified the regulatory role of 5 phosphorylation sites. They also succeeded in pinpointing the phosphatase involved.

Weaknesses:

However, as the authors acknowledge, it is already widely known in the field that IFN and viral infection regulate m6A mRNAs and ISGs. Therefore, a more detailed discussion could help the reader interpret the obtained findings in light of previous research.

It is well-known that protein concentration drives phase separation events. Similarly, previous studies and some of the figures presented by the authors show an increase in WTAP expression upon IFN treatment. The authors do not discuss the contribution of WTAP expression levels to the phase separation event observed upon IFN treatment. Similarly, METTL3 and METTL14, as well as other proteins of the MTC are upregulated upon IFN treatment. How does the MTC protein concentration contribute to the observed phase separation event?

How is PP4 related to the IFN signaling cascade?

In general, it is very confusing to talk about WTAP KO as WTAPgRNA.

ggg

Hoe kan verzuim eindigen?

Wat zijn de eisen van ingebrekestelling?

Wat staat er in art 6:82 lid 2 BW

Wat is het doel van ingebrekestelling

количество занятых мест в массиве

так как у нас, по сути, в stringBuilder массив chars. уже имеет фиксированную длину. то есть, это не лист и он не может расширяться. но нам нужно знать сколько уже точно занято мест в массиве.

для этого он и нужен.

сам массив chars, куда помещаются данные.

зачему, что это весь длина всего массива в нём есть и индекусы на пустые символы. другими словами, m_ChunkChars.lenght - это capacity данного stringBuilder.

сколько осталось после добавление в прошлый чанк

сколько свободно в этом чанке

смотрим, а если мы создадим новый чанк, с новыми данными, он будет ли меньше чем, то что уже занято в этой чанке

ссылка на прошлый StringBuilder

Should we use "If" instead of "IF"?

I think scrolling is not performed by default. But user can still enable the scrolling for verify steps.

.from: https://hypothes.is/a/_YXugnsSEe-8SCtXFT3E2Q

https://hypothes.is/a/QhoGREFwEeyzOi8fzklbJw

.definition

Aphanipoiesis (n.) combines two words from ancient Greek to describe this way in which life coalesces toward vitality in unseen ways. (Aphanis comes from a Greek root meaning obscured, unseen, unnoticed; poiesis is from one meaning to bring forth, to make.) Other words which also carry the root aphanis include phantom, diaphanous, and phenomenon, while the root poiesis is familiar from the word poetry, along with Maturana and Varela’s autopoiesis.

https://hypothes.is/a/juRkSmqgEe-f0-u6YIKvvw

I believe that when editing the steps, we are unable to select the alternative texts. So I think this sentence is not relevant for editing step section.

It seems that we missed the "Enter" step

I believe that "Text" has already been updated to "Identification Text".

.4 hyperpost

https://hypothes.is/a/t3LmpKh2Ee2V1v9DBNPdrA

Dan Whaley | The Revolution Will Be Annotated | PDF13 HD

Det här är tilltalande, att förståelse är beroende av möjligheten till kontrast

The English and the Continent: “Dwelling In” and“Breaking Out”

Christopher P. Goodman

.title

= Francis.Bacon

well yes that is standardisation. If you exclude intended users from its creation it won't be one. A standard gets created by the intended field of users, who commit to adopting it once created. It's not idealism or altruism, it's industry.

This entire piece gave me nothing to understand 'what's the problem' other han a personal beef with a key figure, a dislike for organisation and not understanding standardisation as an industry effort. So I see the author's problems, but still don't know anything about Social Web Foundation, other than that many people seem to feel left out.

This entire thing indeed seems to be about the author's personal perspective on Evan Prodromou

organising is suspect by def then?

a standard is only a standard if it is adopted by those in the user group. Creating your 'own' by definition isn't a standard, at most it's a method or protocol.

мы как бы говорим, что хотим работать с этими данными. не изменять или, а только работать с ними