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Autism is Associated with in vivo Changes in Gray Matter Neurite Architecture. biorxiv.org/content/10.1101/20

Autism is Associated with in vivo Changes in Gray Matter Neurite Architecture.

Postmortem investigations in autism have identified anomalies in neural cytoarchitecture across limbic, cerebellar, and neocortical networks. These anomalies include narrow cell mini-columns and variable neuron density. However, difficulty obtaining sufficient post-mortem samples has often prevented investigations from converging on reproducible measures. Recent advances in processing magnetic resonance diffusion weighted images (DWI) make in vivo characterization of neuronal cytoarchitecture a potential alternative to post-mortem studies. Using extensive DWI data from the Adolescent Brain Cognitive (ABCD) study 142 individuals with an Autism diagnosis were compared with 8971 controls using a restriction spectrum imaging (RSI) framework that characterized total neurite density (TND), its component restricted normalized directional diffusion (RND), and restricted normalized isotropic diffusion (RNI). A significant decrease in TND was observed in Autism in the right cerebellar cortex (β=-0.005, SE =0.0015, p=0.0267), with significant decreases in RNI and significant increases in RND found diffusely throughout posterior and anterior aspects of the brain, respectively. Furthermore, these regions remained significant in post-hoc analysis when the ASD sample was compared against a subset of 1404 individuals with other psychiatric conditions (pulled from the original 8971). These findings highlight the importance of characterizing neuron cytoarchitecture in Autism and the significance of their incorporation as physiological covariates in future studies. ### Competing Interest Statement The authors have declared no competing interest.

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Cell-type-specificity of isoform diversity in the developing human neocortex informs mechanisms of neurodevelopmental disorders biorxiv.org/content/10.1101/20

Cell-type-specificity of isoform diversity in the developing human neocortex informs mechanisms of neurodevelopmental disorders

Human brain development is under tight molecular genetic control and the recent advent of single-cell genomics has revolutionized our ability to elucidate the diverse underlying cell-types and states. Although RNA splicing is highly prevalent in the brain and has strong links to neuropsychiatric disorders, previous work has not systematically investigated the role of cell-type-specific splicing or transcript-isoform diversity during human brain development. Here, we leverage single molecule long-read sequencing to deeply profile the full-length transcriptome of the germinal zone (GZ) and cortical plate (CP) regions of the developing human neocortex at tissue and single-cell resolution. We identify 214,516 unique isoforms, corresponding to 22,391 genes. Remarkably, we find that 72.6% of these are novel and together with >7,000 novel-spliced exons expands the proteome by 92,422 proteoforms. We uncover myriad novel isoform switches during cortical neurogenesis, implicating previously-uncharacterized RNA-binding protein-mediated and other regulatory mechanisms in cellular identity and disease. Early-stage excitatory neurons exhibit the greatest isoform diversity and isoform-based single-cell clustering identifies previously uncharacterized cell states. Leveraging this resource, we re-prioritize thousands of rare de novo risk variants associated with neurodevelopmental disorders (NDDs) and reveal that risk genes are strongly associated with the number of unique isoforms observed per gene. Altogether, this work uncovers a substantial contribution of transcript-isoform diversity in cellular identity in the developing neocortex, elucidates novel genetic risk mechanisms for neurodevelopmental and neuropsychiatric disorders, and provides a comprehensive isoform-centric gene annotation for the developing human brain. ### Competing Interest Statement M.J.G. receives grant funding from Mitsubishi Tanabe Pharma America that is unrelated to this current project.

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The spatial arrangement of laminar thickness profiles in the human cortex scaffolds processing hierarchy biorxiv.org/content/10.1101/20

The spatial arrangement of laminar thickness profiles in the human cortex scaffolds processing hierarchy

The human neocortex consists of tangentially organized layers with unique cytoarchitectural properties. These layers show spatial variations in thickness and cytoarchitecture across the neocortex, which is thought to support brain function through enabling targeted corticocortical connections. Here, leveraging maps of the six cortical layers in 3D human brain histology, we aimed to quantitatively characterize the systematic covariation of laminar structure in the cortex and its functional consequences. After correcting for the effect of cortical curvature, we identified a spatial pattern of changes in laminar thickness covariance from lateral frontal to posterior occipital regions, which differentiated the dominance of infra- versus supragranular layer thickness. Corresponding to the laminar regularities of cortical connections along cortical hierarchy, the infragranular-dominant pattern of laminar thickness was associated with higher hierarchical positions of regions, mapped based on resting-state effective connectivity in humans and tract-tracing of structural connections in macaques. Moreover, we show that regions with comparable laminar thickness patterns correspond to inter-regional structural covariance, maturational coupling, and transcriptomic patterning, indicating developmental relevance. In sum, here we characterize the association between organization of laminar thickness and processing hierarchy, anchored in ontogeny. As such, we illustrate how laminar organization may provide a foundational principle ultimately supporting human cognitive functioning. ### Competing Interest Statement The authors have declared no competing interest.

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Dual roles for nucleus accumbens core dopamine D1-expressing neurons projecting to the substantia nigra pars reticulata in limbic and motor control biorxiv.org/content/10.1101/20

Dual roles for nucleus accumbens core dopamine D1-expressing neurons projecting to the substantia nigra pars reticulata in limbic and motor control

The nucleus accumbens (NAc) is a critical component of a limbic basal ganglia circuit that is thought to play an important role in decision-making and the processing of rewarding stimuli. As part of this circuit, dopamine D1 receptor-expressing medium spiny neurons (D1-MSNs) of the NAc core are known to send a major projection to the substantia nigra pars reticulata (SNr). However, the functional role of this SNr-projecting NAc D1-MSNs (NAcD1-MSN-SNr) pathway is still largely uncharacterized. Moreover, as the SNr is thought to belong to both limbic and motor information processing basal ganglia loops, it is possible that the NAcD1-MSN-SNr pathway may be able to influence both limbic and motor functions. In this study we investigated the effect of optogenetic activation of the NAcD1-MSN-SNr pathway on reward-learning and locomotor behavior. Stimulation of the axon terminals of NAc core D1-MSNs in the SNr induced a preference for a laser-paired location, self-stimulation via a laser-paired lever, and augmented instrumental responding for a liquid reward-paired lever. Additionally, stimulation was observed to increase locomotor behavior when delivered bilaterally and induced contralateral turning behavior when delivered unilaterally. These findings indicate that the NAcD1-MSN-SNr pathway is able to control both reward learning and motor behaviors. ### Competing Interest Statement The authors have declared no competing interest.

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Unravelling individual rhythmic abilities using machine learning biorxiv.org/content/10.1101/20

Unravelling individual rhythmic abilities using machine learning

Humans can easily extract the rhythm of a complex sound, like music, and move to its regular beat, for example in dance. These abilities are modulated by musical training and vary significantly in untrained individuals. The causes of this variability are multidimensional and typically hard to grasp with single tasks. To date we lack a comprehensive model capturing the rhythmic fingerprints of both musicians and non-musicians. Here we harnessed machine learning to extract a parsimonious model of rhythmic abilities, based on the behavioral testing (with perceptual and motor tasks) of individuals with and without formal musical training (n = 79). We demonstrate that the variability of rhythmic abilities, and their link with formal and informal music experience, can be successfully captured by profiles including a minimal set of behavioral measures. These profiles can shed light on individual variability in healthy and clinical populations, and provide guidelines for personalizing rhythm-based interventions. ### Competing Interest Statement Simone Dalla Bella is on the board of the BeatHealth company dedicated to the design and commercialization of technological tools for assessing rhythm capacities (e.g. BAASTA), and implementing rhythm-based interventions.

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Likelihood-ratio test statistic for the finite-sample case in nonlinear ordinary differential equation models biorxiv.org/content/10.1101/20

Likelihood-ratio test statistic for the finite-sample case in nonlinear ordinary differential equation models

Likelihood ratios are frequently utilized as basis for statistical tests, for model selection criteria and for assessing parameter and prediction uncertainties, e.g. using the profile likelihood. However, translating these likelihood ratios into p-values or confidence intervals requires the exact form of the test statistic's distribution. The lack of knowledge about this distribution for nonlinear ordinary differential equation (ODE) models requires an approximation which assumes the so-called asymptotic setting, i.e. a sufficiently large amount of data. Since the amount of data from quantitative molecular biology is typically limited in applications, this finite-sample case regularly occurs for mechanistic models of dynamical systems, e.g. biochemical reaction networks or infectious disease models. Thus, it is unclear whether the standard approach of using statistical thresholds derived for the asymptotic large-sample setting in realistic applications results in valid conclusions. In this study, empirical likelihood ratios for parameters from 19 published nonlinear ODE benchmark models are investigated using a resampling approach for the original data designs. Their distributions are compared to the asymptotic approximation and statistical thresholds are checked for conservativeness. It turns out, that corrections of the likelihood ratios in such finite-sample applications are required in order to avoid anti-conservative results. ### Competing Interest Statement The authors have declared no competing interest.

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Evidence for ancient selective sweeps followed by differentiation among three species of Sphyrapicus sapsuckers biorxiv.org/content/10.1101/20

Evidence for ancient selective sweeps followed by differentiation among three species of Sphyrapicus sapsuckers

Speciation occurs when gene pools differentiate between populations, but that differentiation is heterogeneous across the genome. Understanding what parts of the genome are more prone to differentiation is a key mission in evolutionary biology because it can identify genomic regions and evolutionary processes central to the speciation process. Here, we study genomic variation among three closely related species of North American woodpecker: red-breasted, red-naped, and yellow-bellied sapsuckers. We construct a new sapsucker reference genome and use whole genome resequencing to measure genetic variation among these species and to quantify how the level of differentiation between these forms varies across the genome. We find that regions of high relative differentiation between species ( FST ) tend to have low absolute differentiation between species (πB), indicating that regions of high relative differentiation often have more recent between-population coalescence times than regions of low relative differentiation do. Most of the high- FST genomic windows are found on the Z chromosome, indicating this sex chromosome is particularly important in sapsucker speciation. We show that LD is high across the Z chromosome and that each species tends to have a unique Z haploblock, a pattern suggestive of chromosomal inversions. These results are consistent with a model of speciation in which selective sweeps of globally advantageous variants spread among partly differentiated populations, followed by differential local adaptation of those same genomic regions. We propose that sapsucker speciation may occur primarily via this process occurring on the Z chromosomes, followed by epistatic interactions between Z haploblocks. ### Competing Interest Statement The authors have declared no competing interest.

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RB loss sensitizes cells to replication-associated DNA damage by PARP inhibition biorxiv.org/content/10.1101/20

RB loss sensitizes cells to replication-associated DNA damage by PARP inhibition

The retinoblastoma tumor suppressor protein (RB) interacts physically and functionally with a number of epigenetic modifying enzymes to control transcriptional regulation, respond to replication stress, promote DNA damage response and repair pathways, and regulate genome stability. To better understand how disruption of RB function impacts epigenetic regulation of genome stability and determine whether such changes may represent exploitable weaknesses of RB-deficient cancer cells, we performed an imaging-based screen to identify epigenetic inhibitors that promote DNA damage and compromise viability of RB-deficient cells. We found that loss of RB alone leads to high levels of replication-dependent poly-ADP ribosylation (PARylation) and that preventing PARylation through inhibition of PARP enzymes enables RB-deficient cells to progress to mitosis with unresolved replication stress and under-replicated DNA. These defects contribute to high levels of DNA damage, decreased proliferation, and compromised cell viability. We demonstrate this sensitivity is conserved across a panel of inhibitors that target both PARP1 and PARP2 and can be suppressed by re-expression of the RB protein. Together, these data indicate that inhibitors of PARP1 and PARP2 may be clinically relevant for RB-deficient cancers. ### Competing Interest Statement The authors have declared no competing interest.

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Genome-wide characterization of T cell responses to Bordetella pertussis reveals broad reactivity and similar polarization irrespective of childhood vaccination profiles. biorxiv.org/content/10.1101/20

Genome-wide characterization of T cell responses to Bordetella pertussis reveals broad reactivity and similar polarization irrespective of childhood vaccination profiles.

The incidence of whooping cough (pertussis), the respiratory disease caused by Bordetella pertussis (BP) has increased in recent years, and it is suspected that the switch from whole-cell pertussis (wP) to acellular pertussis (aP) vaccines may be a contributing factor to the rise in morbidity. While a growing body of evidence indicates that T cells play a role in the control and prevention of symptomatic disease, nearly all data on human BP-specific T cells is related to the four antigens contained in the aP vaccines, and data detailing T cell responses to additional non-aP antigens, are lacking. Here, we derived a full-genome map of human BP-specific CD4+ T cell responses using a high-throughput ex vivo Activation Induced Marker (AIM) assay, to screen a peptide library spanning over 3000 different BP ORFs. First, our data show that BP specific-CD4+ T cells are associated with a large and previously unrecognized breadth of responses, including hundreds of targets. Notably, fifteen distinct non-aP vaccine antigens were associated with reactivity comparable to that of the aP vaccine antigens. Second, the overall pattern and magnitude of CD4+ T cell reactivity to aP and non-aP vaccine antigens was similar regardless of aP vs wP childhood vaccination history, suggesting that the profile of T cell reactivity in adults is not driven by vaccination, but rather is likely driven by subsequent asymptomatic or sub-clinical infections. Finally, while aP vaccine responses were Th1/Th2 polarized as a function of childhood vaccination, CD4+ T cell responses to non-aP BP antigens vaccine responses were not, suggesting that these antigens could be used to avoid the Th2 bias associated with aP vaccination. Overall, these findings enhance our understanding of human T cell responses against BP and suggest potential targets for designing next-generation pertussis vaccines. ### Competing Interest Statement The authors have declared no competing interest.

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Metabolic benefits of 17α-estradiol in liver are partially mediated by ERβ in male mice biorxiv.org/content/10.1101/20

Metabolic benefits of 17α-estradiol in liver are partially mediated by ERβ in male mice

Metabolic dysfunction underlies several chronic diseases. Dietary interventions can reverse metabolic declines and slow aging but remaining compliant is difficult. 17α-estradiol (17α-E2) treatment improves metabolic parameters and slows aging in male mice without inducing significant feminization. We recently reported that estrogen receptor α is required for the majority of 17α-E2-mediated benefits in male mice, but that 17α-E2 also attenuates fibrogenesis in liver, which is regulated by estrogen receptor β (ERβ)-expressing hepatic stellate cells (HSC). The current studies sought to determine if 17α-E2-mediated benefits on systemic and hepatic metabolism are ERβ-dependent. We found that 17α-E2 treatment reversed obesity and related systemic metabolic sequela in both male and female mice, but this was partially blocked in female, but not male, ERβKO mice. ERβ ablation in male mice attenuated 17α-E2-mediated benefits on hepatic stearoyl-coenyzme A desaturase 1 (SCD1) and transforming growth factor β1 (TGF-β1) production, which play critical roles in HSC activation and liver fibrosis. We also found that 17α-E2 treatment suppresses SCD1 production in cultured hepatocytes and hepatic stellate cells, indicating that 17α-E2 directly signals in both cell-types to suppress drivers of steatosis and fibrosis. We conclude that ERβ partially controls 17α-E2-mediated benefits on systemic metabolic regulation in female, but not male, mice, and that 17α-E2 likely signals through ERβ in HSCs to attenuate pro-fibrotic mechanisms. ### Competing Interest Statement The authors have declared no competing interest.

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Modulation of pore opening of Eukaryotic sodium channels by π-helices in S6 biorxiv.org/content/10.1101/20

Modulation of pore opening of Eukaryotic sodium channels by π-helices in S6

Voltage-gated sodium channels are heterotetrameric sodium selective ion channels that play a central role in electrical signaling in excitable cells. With recent advances in structural biology, structures of eukaryotic sodium channels have been captured in several distinct conformations corresponding to different functional states. The secondary structure of the pore lining S6 helices of subunit DI, DII, and DIV has been captured with both short 𝜋-helix stretches and in fully α-helical conformations. The relevance of these secondary structure elements for pore gating is not yet understood. Here, we propose that a 𝜋 helix in at least DI-S6, DIII-S6, and DIV-S6 results in a fully conductive state. On the other hand, the absence of 𝜋-helix in either DI-S6 or DIV-S6 yields a sub-conductance state, and its absence from both DI-S6 and DIV-S6 yields a non-conducting state. This work highlights the impact of the presence of a 𝜋-helix in the different S6 helices of an expanded pore on pore conductance, thus opening new doors towards reconstructing the entire conformational landscape along the functional cycle of Nav Channels and paving the way to the design of state-dependent modulators. ### Competing Interest Statement The authors have declared no competing interest.

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An open-source FACS automation system for high-throughput cell biology biorxiv.org/content/10.1101/20

An open-source FACS automation system for high-throughput cell biology

Recent advances in gene editing are enabling the engineering of cells with an unprecedented level of scale. To capitalize on this opportunity, new methods are needed to accelerate the different steps required to manufacture and handle engineered cells. Here, we describe the development of an integrated software and hardware platform to automate Fluorescence-Activated Cell Sorting (FACS), a central step for the selection of cells displaying desired molecular attributes. Sorting large numbers of samples is laborious, and, to date, no automated system exists to sequentially manage FACS samples, likely owing to the need to tailor sorting conditions ("gating") to each individual sample. Our platform is built around a commercial instrument and integrates the handling and transfer of samples to and from the instrument, autonomous control of the instrument's software, and the algorithmic generation of sorting gates, resulting in walkaway functionality. Automation eliminates operator errors, standardizes gating conditions by eliminating operator-to-operator variations, and reduces hands-on labor by 93%. Moreover, our strategy for automating the operation of a commercial instrument control software in the absence of an Application Program Interface (API) exemplifies a universal solution for other instruments that lack an API. Our software and hardware designs are fully open-source and include step-by-step build documentation to contribute to a growing open ecosystem of tools for high-throughput cell biology. ### Competing Interest Statement The authors have declared no competing interest.

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Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments biorxiv.org/content/10.1101/20

Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments

The release of inorganic phosphate (Pi) from actin filaments constitutes a key step in their regulated turnover, which is fundamental to many cellular functions. However, the molecular mechanisms underlying Pi release from both the core and barbed end of actin filaments remain unclear. Here, we combine cryo-EM with molecular dynamics simulations and in vitro reconstitution to demonstrate how actin releases Pi through a molecular backdoor. While constantly open at the barbed end, the backdoor is predominantly closed in filament-core subunits and only opens transiently through concerted backbone movements and rotameric rearrangements of residues close to the nucleotide binding pocket. This mechanism explains why Pi escapes rapidly from the filament end and yet slowly from internal actin subunits. In an actin variant associated with nemaline myopathy, the backdoor is predominantly open in filament-core subunits, resulting in greatly accelerated Pi release after polymerization and filaments with drastically shortened ADP-Pi caps. This demonstrates that the Pi release rate from F-actin is controlled by steric hindrance through the backdoor rather than by the disruption of the ionic bond between Pi and Mg2+ at the nucleotide-binding site. Our results provide the molecular basis for Pi release from actin and exemplify how a single, disease-linked point mutation distorts the nucleotide state distribution and atomic structure of the actin filament. ### Competing Interest Statement The authors have declared no competing interest.

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Multiple mechanisms of self-association of chemokine receptors CXCR4 and CCR5 demonstrated by deep mutagenesis biorxiv.org/content/10.1101/20

Multiple mechanisms of self-association of chemokine receptors CXCR4 and CCR5 demonstrated by deep mutagenesis

Chemokine receptors are members of the rhodopsin-like class A GPCRs whose signaling through G proteins drives the directional movement of cells in response to a chemokine gradient. Chemokine receptors CXCR4 and CCR5 have been extensively studied due to their roles in white blood cell development and inflammation and their status as coreceptors for HIV-1 infection, among other functions. Both receptors form dimers or oligomers but the function/s of self-associations are unclear. While CXCR4 has been crystallized in a dimeric arrangement, available atomic resolution structures of CCR5 are monomeric. To investigate the dimerization interfaces of these chemokine receptors, we used a bimolecular fluorescence complementation (BiFC)-based screen and deep mutational scanning to find mutations that modify receptor self-association. Many disruptive mutations promoted self-associations nonspecifically, suggesting they aggregated in the membrane. A mutationally intolerant region was found on CXCR4 that matched the crystallographic dimer interface, supporting this dimeric arrangement in living cells. A mutationally intolerant region was also observed on the surface of CCR5 by transmembrane helices 3 and 4. Mutations from the deep mutational scan that reduce BiFC were validated and were localized in the transmembrane domains as well as the C-terminal cytoplasmic tails where they reduced lipid microdomain localization. The reduced self-association mutants of CXCR4 had increased binding to the ligand CXCL12 but diminished calcium signaling. There was no change in syncytia formation with cells expressing HIV-1 Env. The data highlight that multiple mechanisms are involved in self-association of chemokine receptor chains. ### Competing Interest Statement E.P. is an employee and shareholder of Cyrus Biotechnology, Inc. The work described in this manuscript was conducted at the University of Illinois. Cyrus Biotechnology had no role in the project's design, execution, and analysis/interpretation. The views expressed in the manuscript are solely those of the authors, and they do not represent official views or opinions of the University of Illinois or Cyrus Biotechnology.

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Evidence for adaptive evolution towards high magnetic sensitivity of potential magnetoreceptor in songbirds biorxiv.org/content/10.1101/20

Evidence for adaptive evolution towards high magnetic sensitivity of potential magnetoreceptor in songbirds

Migratory birds possess remarkable accuracy in orientation and navigation, which involves various compass systems including the magnetic compass. Identifying the primary magnetosensor remains a fundamental open question. Cryptochromes (Cry) have been shown to be magnetically sensitive, specifically Cry4 shows enhanced magnetic sensitivity in migratory songbirds compared to resident species. Here, we investigate cryptochromes and their potential involvement in magnetoreception in a phylogenetic framework, integrating molecular evolutionary analyses with protein dynamics modeling. We base our analysis on 363 bird genomes and associate different selection regimes with migratory behaviour. We show that Cry4 is characterized by strong positive selection and high variability, typical characteristics of sensor proteins. We identify key sites that likely facilitated the evolution of a highly optimized sensory protein for night time compass orientation in songbirds and a potential functional shift or specialisation. Additionally, we show that Cry4 was lost in hummingbirds, parrots and Tyranni (Suboscines) and thus identified a natural comparative gene knockout, which can be used to test the function of Cry4 in birds. In contrast, the other two cryptochromes Cry1 and Cry2, were highly conserved in all species, indicating basal, non-sensory functions. Our results strengthen the hypothesised role of Cry4 as sensor protein in (night)-migratory songbirds. ### Competing Interest Statement The authors have declared no competing interest.

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Gut-associated functions are favored during microbiome assembly across C. elegans life biorxiv.org/content/10.1101/20

Gut-associated functions are favored during microbiome assembly across C. elegans life

The microbiome expresses a variety of functions that influence host biology. The range of functions depends on composition of the microbiome, which itself can change during the lifetime of the host as a consequence of neutral assembly processes, host-mediated selection, and/or environmental conditions. To date, the exact dynamics of microbiome assembly, the underlying determinants as well as the resulting effects on host-associated functions are not always well understood. Here, we used the nematode Caenorhabditis elegans and a defined community of fully sequenced, naturally associated bacteria to study microbiome dynamics and functions across the lifetime of individual hosts under controlled experimental conditions. By applying the neutral and null models, we demonstrate that bacterial community composition initially shows strongly declining levels of stochasticity, which, however, increase during late worm life, suggesting the action of random assembly processes in aged hosts following first colonization of C. elegans. The adult microbiome is enriched in strains of the genera Ochrobactrum and Enterobacter in comparison to the direct substrate and a host-free control environment. Using pathway analysis, metabolic, and ecological modelling, we further found that the lifetime assembly dynamics lead to an increase in gut-associated functions in the host-associated microbiome, possibly indicating that the initially colonizing bacteria are beneficial for the worm. Overall, our study introduces a framework for studying microbiome assembly dynamics based on the stochastic models and inference of functions, yielding new insights into the processes determining host-associated microbiome composition and function. ### Competing Interest Statement The authors have declared no competing interest.

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Learning the functional landscape of microbial communities biorxiv.org/content/10.1101/20

Learning the functional landscape of microbial communities

Microbial consortia exhibit complex functional properties in contexts ranging from soils to bioreactors to human hosts. Understanding how community composition determines emergent function is a major goal of microbial ecology. Here we address this challenge using the concept of community-function landscapes -- analogs to fitness landscapes -- that capture how changes in community composition alter collective function. Using datasets that represent a broad set of community functions, from production/degradation of specific compounds to biomass generation, we show that statistically-inferred landscapes quantitatively predict community functions from knowledge of strain presence or absence. Crucially, community-function landscapes allow prediction without explicit knowledge of abundance dynamics or interactions between species, and can be accurately trained using measurements from a small subset of all possible community compositions. The success of our approach arises from the fact that empirical community-function landscapes are typically not rugged, meaning that they largely lack high-order epistatic contributions that would be difficult to fit with limited data. Finally, we show this observation is generic across many ecological models, suggesting community-function landscapes can be applied broadly across many contexts. Our results open the door to the rational design of consortia without detailed knowledge of abundance dynamics or interactions. ### Competing Interest Statement The authors have declared no competing interest.

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Inducible protein degradation as a strategy to identify Phosphoprotein Phosphatase 6 substrates in RAS-mutant colorectal cancer cells biorxiv.org/content/10.1101/20

Inducible protein degradation as a strategy to identify Phosphoprotein Phosphatase 6 substrates in RAS-mutant colorectal cancer cells

Protein phosphorylation is an essential regulatory mechanism that controls most cellular processes, including cell cycle progression, cell division, and response to extracellular stimuli, among many others, and is deregulated in many diseases. Protein phosphorylation is coordinated by the opposing activities of protein kinases and protein phosphatases. In eukaryotic cells, most serine/threonine phosphorylation sites are dephosphorylated by members of the Phosphoprotein Phosphatase (PPP) family. However, we only know for a few phosphorylation sites which specific PPP dephosphorylates them. Although natural compounds such as calyculin A and okadaic acid inhibit PPPs at low nanomolar concentrations, no selective chemical PPP inhibitors exist. Here, we demonstrate the utility of endogenous tagging of genomic loci with an auxin-inducible degron (AID) as a strategy to investigate specific PPP signaling. Using Protein Phosphatase 6 (PP6) as an example, we demonstrate how rapidly inducible protein degradation can be employed to identify dephosphorylation SITES and elucidate PP6 biology. Using genome editing, we introduce AID-tags into each allele of the PP6 catalytic subunit (PP6c) in DLD-1 cells expressing the auxin receptor Tir1. Upon rapid auxin-induced degradation of PP6c, we perform quantitative mass spectrometry-based proteomics and phosphoproteomics to identify PP6 substrates in mitosis. PP6 is an essential enzyme with conserved roles in mitosis and growth signaling. Consistently, we identify candidate PP6c-dependent phosphorylation sites on proteins implicated in coordinating the mitotic cell cycle, cytoskeleton, gene expression, and mitogen-activated protein kinase (MAPK) and Hippo signaling. Finally, we demonstrate that PP6c opposes the activation of large tumor suppressor 1 (LATS1) by dephosphorylating Threonine 35 (T35) on Mps One Binder (MOB1), thereby blocking the interaction of MOB1 and LATS1. Our analyses highlight the utility of combining genome engineering, inducible degradation, and multiplexed phosphoproteomics to investigate signaling by individual PPPs on a global level, which is currently limited by the lack of tools for specific interrogation. ### Competing Interest Statement The authors have declared no competing interest.

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