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International audience; Gene Drives are regarded as future tools with a high potential for population control. Due to their inherent ability to overcome the rules of Mendelian inheritance, gene drives (GD) may spread genes rapidly through populations of sexually reproducing organisms. A release of organisms carrying a GD would constitute a paradigm shift in the handling of genetically modified organisms because gene drive organisms (GDO) are designed to drive their transgenes into wild populations and thereby increase the number of GDOs. The rapid development in this field and its focus on wild populations demand a prospective risk assessment with a focus on exposure related aspects. Presently, it is unclear how adequate risk management could be guaranteed to limit the spread of GDs in time and space, in order to avoid potential adverse effects in socio-ecological systems. The recent workshop on the “Evaluation of Spatial and Temporal Control of Gene Drives” hosted by the Institute of Safety/Security and Risk Sciences (ISR) in Vienna aimed at gaining some insight into the potential population dynamic behavior of GDs and appropriate measures of control. Scientists from France, Germany, England, and the USA discussed both topics in this meeting on April 4–5, 2019. This article summarizes results of the workshop.

We show that very weak topological assumptions are enough to ensure the existence of a Helly-type theorem. More precisely, we show that for any non-negative integers $b$ and $d$ there exists an integer $h(b,d)$ such that the following holds. If $\mathcal F$ is a finite family of subsets of $\mathbb R^d$ such that $\tilde\beta_i\left(\bigcap\mathcal G\right) \le b$ for any $\mathcal G \subsetneq \mathcal F$ and every $0 \le i \le \lceil d/2 \rceil-1$ then $\mathcal F$ has Helly number at most $h(b,d)$. Here $\tilde\beta_i$ denotes the reduced $\mathbb Z_2$-Betti numbers (with singular homology). These topological conditions are sharp: not controlling any of these $\lceil d/2 \rceil$ first Betti numbers allow for families with unbounded Helly number. Our proofs combine homological non-embeddability results with a Ramsey-based approach to build, given an arbitrary simplicial complex $K$, some well-behaved chain map $C_*(K) \to C_*(\mathbb R^d)$., Comment: 29 pages, 8 figures

International audience; To control morphogenesis, molecular regulatory networks have to interfere with the mechanical properties of the indi-vidual cells of developing organs and tissues, but how this is achieved is not well known. We study this issue here in the shoot meristem of higher plants, a group of undifferenti-ated cells where complex changes in growth rates and direc-tions lead to the continuous formation of new organs [1, 2]. Here, we show that the plant hormone auxin plays an impor-tant role in this process via a dual, local effect on the extracellular matrix, the cell wall, which determines cell shape. Our study reveals that auxin not only causes a limited reduction in wall stiffness but also directly interferes with wall anisotropy via the regulation of cortical microtubule dy-namics. We further show that to induce growth isotropy and organ outgrowth, auxin somehow interferes with the cortical microtubule-ordering activity of a network of proteins, in-cluding AUXIN BINDING PROTEIN 1 and KATANIN 1. Numer-ical simulations further indicate that the induced isotropy is sufficient to amplify the effects of the relatively minor changes in wall stiffness to promote organogenesis and the establishment of new growth axes in a robust manner.

International audience; In the past decade carbon nanotubes (CNTs) have been widely studied as a potential drug-delivery system, especially with functionality for cellular targeting. Yet, little is known about the actual process of docking to cell receptors and transport dynamics after internalization. Here we performed single-particle studies of folic acid (FA) mediated CNT binding to human carcinoma cells and their transport inside the cytosol. In particular, we employed molecular recognition force spectroscopy, an atomic force microscopy based method, to visualize and quantify docking of FA functionalized CNTs to FA binding receptors in terms of binding probability and binding force. We then traced individual fluorescently labeled, FA functionalized CNTs after specific uptake, and created a dynamic 'roadmap' that clearly showed trajectories of directed diffusion and areas of nanotube confinement in the cytosol. Our results demonstrate the potential of a single-molecule approach for investigation of drug-delivery vehicles and their targeting capacity.

Neurons extend axons to form the complex circuitry of the mature brain. This depends on the coordinated response and continuous remodelling of the microtubule and F-actin networks in the axonal growth cone. Growth cone architecture remains poorly understood at nanoscales. We therefore investigated mouse hippocampal neuron growth cones using cryo-electron tomography to directly visualise their three-dimensional subcellular architecture with molecular detail. Our data showed that the hexagonal arrays of actin bundles that form filopodia penetrate and terminate deep within the growth cone interior. We directly observed the modulation of these and other growth cone actin bundles by alteration of individual F-actin helical structures. Microtubules with blunt, slightly flared or gently curved ends predominated in the growth cone, frequently contained lumenal particles and exhibited lattice defects. Investigation of the effect of absence of doublecortin, a neurodevelopmental cytoskeleton regulator, on growth cone cytoskeleton showed no major anomalies in overall growth cone organisation or in F-actin subpopulations. However, our data suggested that microtubules sustained more structural defects, highlighting the importance of microtubule integrity during growth cone migration.

We provide an inductive algorithm computing Gromov-Witten invariants in all genera with arbitrary insertions of all smooth complete intersections in projective space. We also prove that all Gromov-Witten classes of all smooth complete intersections in projective space belong to the tautological ring of the moduli space of stable curves. The main idea is to show that invariants with insertions of primitive cohomology classes are controlled by their monodromy and by invariants defined without primitive insertions but with imposed nodes in the domain curve. To compute these nodal Gromov-Witten invariants, we introduce the new notion of nodal relative Gromov-Witten invariants. We then prove a nodal degeneration formula and a relative splitting formula. These results for nodal relative Gromov-Witten theory are stated in complete generality and are of independent interest., 90 pages, 15 figures. Revision which includes an algorithm for the exceptional cases of even dimensional complete intersections of two quadrics

International audience; Molecular chaperones are central to cellular protein homeostasis. Dynamic disorder is a key feature of the complexes of molecular chaperones and their client proteins, and it facilitates the client release towards a folded state or the handover to downstream components. The dynamic nature also implies that a given chaperone can interact with many different client proteins, based on physico-chemical sequence properties rather than on structural complementarity of their (folded) 3D structure. Yet, the balance between this promiscuity and some degree of client specificity is poorly understood. Here, we review recent atomic-level descriptions of chaperones with client proteins, including chaperones in complex with intrinsically disordered proteins, with membrane-protein precursors, or partially folded client proteins. We focus hereby on chaperone-client interactions that are independent of ATP. The picture emerging from these studies highlights the importance of dynamics in these complexes, whereby several interaction types, not only hydrophobic ones, contribute to the complex formation. We discuss these features of chaperone-client complexes and possible factors that may contribute to this balance of promiscuity and specificity.

International audience

Suppose that Alice plans to buy a physical good from Bob over a programmable Blockchain. Alice does not trust Bob, so she is not willing to pay before the good is delivered off-chain. Similarly, Bob does not trust Alice, so he is not willing to deliver the good before getting paid on-chain. Moreover, they are not inclined to use the services of a trusted third-party. Traditionally, such scenarios are handled by game-theoretic escrow smart contracts, such as BitHalo. In this work, we first show that the common method for this problem suffers from a major flaw which can be exploited by Bob in order to extort Alice. We also show that, unlike the case of auctions, this flaw cannot be addressed by a commitment-scheme-based approach. We then provide a much more general result: assuming that the two sides are rational actors and the smart contract language is Turing-complete, there is no escrow smart contract that can facilitate this exchange without either relying on third parties or enabling at least one side to extort the other.

Probabilistic recurrence relations (PRRs) are a standard formalism to analyze the runtime of randomized algorithms. In this work, we consider the classical problem of obtaining concentration bounds on the runtime of randomized algorithms modeled as PRRs. More specifically, given a time limit k, we study the probability Pr[ T ≥ k ] that the runtime of the algorithm reaches or exceeds the time limit. The key research question in concentration bound analysis is to find an upper-bound function upper(n) ≥ Pr[ T ≥ k ] such that upper(n) converges rapidly to zero as n tends to infinity. The classical approach to this problem is the "cookbook" method by Karp (J. ACM 1994). For the past three decades, finding an approach to improve Karp's classical bounds has been a major open problem. In this work, we first demonstrate a method to obtain such upper-bound functions from a special family of supermartingale functions through the well-known Optional Stopping Theorem (OST). We then provide automated algorithmic approaches to synthesize such supermartingale functions in exponential and polynomial form. Our algorithms are based on the Taylor expansion and tight approximations of the expectation of moments that involve logarithmic terms. Compared with Karp's method, our algorithmic approaches find significantly tighter concentration bounds for several classical randomized algorithms. Moreover, our algorithmic approaches can also find concentration bounds for several randomized algorithms in computational geometry which adopt techniques such as randomized incremental construction. To the best of our knowledge, no previous method was applicable in these cases. Finally, we present experimental results demonstrating the practical versatility and efficiency of our approach..

Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. manifolds defined as the zero set of some multivariate vector-valued smooth function f: ℝ^d → ℝ^(d-n). A natural (and efficient) way to approximate an isomanifold is to consider its Piecewise-Linear (PL) approximation based on a triangulation 𝒯 of the ambient space ℝ^d. In this paper, we give conditions under which the PL-approximation of an isomanifold is topologically equivalent to the isomanifold. The conditions are easy to satisfy in the sense that they can always be met by taking a sufficiently fine triangulation 𝒯. This contrasts with previous results on the triangulation of manifolds where, in arbitrary dimensions, delicate perturbations are needed to guarantee topological correctness, which leads to strong limitations in practice. We further give a bound on the Fréchet distance between the original isomanifold and its PL-approximation. Finally we show analogous results for the PL-approximation of an isomanifold with boundary., LIPIcs, Vol. 164, 36th International Symposium on Computational Geometry (SoCG 2020), pages 20:1-20:18

Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group. Keywords: sex chromosomes, evolutionary strata, W-linked gene, sex determining gene, schistosome parasites.

Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. submanifolds of ℝ^d defined as the zero set of some multivariate multivalued smooth function f: ℝ^d → ℝ^{d-n}, where n is the intrinsic dimension of the manifold. A natural way to approximate a smooth isomanifold M is to consider its Piecewise-Linear (PL) approximation M̂ based on a triangulation 𝒯 of the ambient space ℝ^d. In this paper, we describe a simple algorithm to trace isomanifolds from a given starting point. The algorithm works for arbitrary dimensions n and d, and any precision D. Our main result is that, when f (or M) has bounded complexity, the complexity of the algorithm is polynomial in d and δ = 1/D (and unavoidably exponential in n). Since it is known that for δ = Ω (d^{2.5}), M̂ is O(D²)-close and isotopic to M, our algorithm produces a faithful PL-approximation of isomanifolds of bounded complexity in time polynomial in d. Combining this algorithm with dimensionality reduction techniques, the dependency on d in the size of M̂ can be completely removed with high probability. We also show that the algorithm can handle isomanifolds with boundary and, more generally, isostratifolds. The algorithm for isomanifolds with boundary has been implemented and experimental results are reported, showing that it is practical and can handle cases that are far ahead of the state-of-the-art., LIPIcs, Vol. 189, 37th International Symposium on Computational Geometry (SoCG 2021), pages 17:1-17:16

International audience; Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. submanifolds of $R^d$ defined as the zero set of some multivariate multivalued smooth function f from $R^d$ to $R^{d-n}$, where n is the intrinsic dimension of the manifold. A natural way to approximate a smooth isomanifold M is to consider its Piecewise-Linear (PL) approximation M' based on a triangulation T of the ambient space $R^d$. In this paper, we describe a simple algorithm to trace isomanifolds from a given starting point. The algorithm works for arbitrary dimensions n and d, and any precision D. Our main result is that, when f (or M) has bounded complexity, the complexity of the algorithm is polynomial in d and 1/D (and unavoidably exponential in n). Since it is known that for $1/D = \Omega (d^{2.5})$, M' is $O(D^2)$-close andisotopic to M, our algorithm produces a faithful PL-approximation of isomanifolds of bounded complexity in time polynomial in d. Combining this algorithm with dimensionality reduction techniques, the dependency on d in the size of M' can be completely removed with high probability. We also show that the algorithm can handle isomanifolds with boundary and, more generally, isostratifolds. The algorithm for isomanifolds with boundary has been implemented and experimental results are reported, showing that it is practical and can handle cases that are far ahead of the state-of-the-art.

The way in which interactions between mechanics and biochemistry lead to the emergence of complex cell and tissue organization is an old question that has recently attracted renewed interest from biologists, physicists, mathematicians and computer scientists. Rapid advances in optical physics, microscopy and computational image analysis have greatly enhanced our ability to observe and quantify spatiotemporal patterns of signalling, force generation, deformation, and flow in living cells and tissues. Powerful new tools for genetic, biophysical and optogenetic manipulation are allowing us to perturb the underlying machinery that generates these patterns in increasingly sophisticated ways. Rapid advances in theory and computing have made it possible to construct predictive models that describe how cell and tissue organization and dynamics emerge from the local coupling of biochemistry and mechanics. Together, these advances have opened up a wealth of new opportunities to explore how mechanochemical patterning shapes organismal development. In this roadmap, we present a series of forward-looking case studies on mechanochemical patterning in development, written by scientists working at the interface between the physical and biological sciences, and covering a wide range of spatial and temporal scales, organisms, and modes of development. Together, these contributions highlight the many ways in which the dynamic coupling of mechanics and biochemistry shapes biological dynamics: from mechanoenzymes that sense force to tune their activity and motor output, to collectives of cells in tissues that flow and redistribute biochemical signals during development.

When the ranges of closely-related lineages are large, and overlapping, we can often study introgression at many “replicated” contacts, with different locations and spatial scales. Here we analysed multiple contact zones of the M. edulis complex of marine mussel species, which represent a mosaic distribution of heterogeneously differentiated, semi-isolated genomes. Our aim was to contrast ongoing introgression at the heart of hybrid zones, with past introgression between similar parental populations, at increasing distance from the contact. Using a panel of ancestry-informative SNPs derived from a previous genomic study, we first confirm, with a broader sampling, that local introgression, affecting one but not all of the populations compared, is both widespread and heterogeneous across the genome. Some outlier loci show patterns of complete introgression in certain populations, and an absence of introgression in others. Genomic cline analyses reveal a globally high concordance among loci at a local scale, albeit with signals of asymmetric introgression at a few loci. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants, or less loaded alleles. Given the mosaic structure of the M. edulis complex, with a succession of genetic barriers to gene flow, variants with enhanced introgression through one barrier can be trapped, maybe transiently, at the next barrier, confining introgression locally. This makes the Mytilus complex an ideal model of the heterogeneous porosity of species barriers.

International audience; Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a "protracted period" of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available.

Half a century after Lewis Wolpert's seminal conceptual advance on how cellular fates distribute in space, we provide a brief historical perspective on how the concept of positional information emerged and influenced the field of developmental biology and beyond. We focus on a modern interpretation of this concept in terms of information theory, largely centered on its application to cell specification in the early Drosophila embryo. We argue that a true physical variable (position) is encoded in local concentrations of patterning molecules, that this mapping is stochastic, and that the processes by which positions and corresponding cell fates are determined based on these concentrations need to take such stochasticity into account. With this approach, we shift the focus from biological mechanisms, molecules, genes and pathways to quantitative systems-level questions: where does positional information reside, how it is transformed and accessed during development, and what fundamental limits it is subject to?

International audience; We quantize Whitney's construction to prove the existence of a triangulation for any C^2 manifold, so that we get an algorithm with explicit bounds. We also give a new elementary proof, which is completely geometric.

In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.We use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades.; Dans cette thèse, nous considérons plusieurs des problèmes les plus classiques et fondamentaux de l'analyse statique et de la vérification formelle, y compris la génération d'invariants, l'analyse d'accessibilité, l'analyse de terminaison de programmes probabilistes et l'analyse quantitative des chaînes de Markov et des processus de décision de Markov.Nous utilisons des techniques issues de la théorie de la complexité paramétrée, de la géométrie polyédrique et de la géométrie algébrique réelle. Dans certains cas, nos résultats sont les premières améliorations théoriques des problèmes respectifs en deux ou trois décennies.

We consider a family of highly regular triangulations of Rd that can be stored and queried efficiently in high dimensions. This family consists of Freudenthal-Kuhn triangulations and their images through affine mappings, among which are the celebrated Coxeter triangulations of type Ãd. Those triangulations have major advantages over grids in applications in high dimensions like interpolation of functions and manifold sampling and meshing. We introduce an elegant and very compact data structure to implicitly store the full facial structure of such triangulations. This data structure allows to locate a point and to retrieve the faces or the cofaces of a simplex of any dimension in an output sensitive way. The data structure has been implemented and experimental 9 results are presented.

Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. submanifolds of R d defined as the zero set of some multivariate multivalued smooth function $f : R^d → R^{d−n}$ , where n is the intrinsic dimension of the manifold. A natural way to approximate a smooth isomanifold M is to consider its Piecewise-Linear (PL) approximationM based on a triangulation T of the ambient space $R^d$. In this paper, we describe a simple algorithm to trace isomanifolds from a given starting point. The algorithm works for arbitrary dimensions n and d, and any precision D. Our main result is that, when f (or M) has bounded complexity, the complexity of the algorithm is polynomial in d and $δ = 1/D$ (and unavoidably exponential in n). Since it is known that for $δ = Ω(d^{2.5}),$M is $O(D^2)$-close and isotopic to M, our algorithm produces a faithful PL-approximation of isomanifolds of bounded complexity in time polynomial in d. Combining this algorithm with dimensionality reduction techniques, the dependency on d in the size of M can be completely removed with high probability. We also show that the algorithm can handle isomanifolds with boundary and, more generally, isostratifolds. The algorithm has been implemented and experimental results are reported, showing that it is practical and can handle cases that are far ahead of the state-of-the-art.

Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding., As protein synthesis takes place, newly synthesized polypeptide chain passes through the ribosomal exit tunnel, which can accommodate up to 70 residues in the case of a helical peptide. Here the authors show that oxidation of cysteine residues in the nascent chain can occur within the ribosome exit tunnel, where sufficient space exists for the formation of disulfide bonds.

Resting-state brain activity is characterized by the presence of neuronal avalanches showing absence of characteristic size. Such evidence has been interpreted in the context of criticality and associated with the normal functioning of the brain. A distinctive attribute of systems at criticality is the presence of long-range correlations. Thus, to verify the hypothesis that the brain operates close to a critical point and consequently assess deviations from criticality for diagnostic purposes, it is of primary importance to robustly and reliably characterize correlations in resting-state brain activity. Recent works focused on the analysis of narrow-band electroencephalography (EEG) and magnetoencephalography (MEG) signal amplitude envelope, showing evidence of long-range temporal correlations (LRTC) in neural oscillations. However, brain activity is a broadband phenomenon, and a significant piece of information useful to precisely discriminate between normal (critical) and pathological behavior (non-critical), may be encoded in the broadband spatio-temporal cortical dynamics. Here we propose to characterize the temporal correlations in the broadband brain activity through the lens of neuronal avalanches. To this end, we consider resting-state EEG and long-term MEG recordings, extract the corresponding neuronal avalanche sequences, and study their temporal correlations. We demonstrate that the broadband resting-state brain activity consistently exhibits long-range power-law correlations in both EEG and MEG recordings, with similar values of the scaling exponents. Importantly, although we observe that the avalanche size distribution depends on scale parameters, scaling exponents characterizing long-range correlations are quite robust. In particular, they are independent of the temporal binning (scale of analysis), indicating that our analysis captures intrinsic characteristics of the underlying dynamics. Because neuronal avalanches constitute a fundamental feature of neural systems with universal characteristics, the proposed approach may serve as a general, systems- and experiment-independent procedure to infer the existence of underlying long-range correlations in extended neural systems, and identify pathological behaviors in the complex spatio-temporal interplay of cortical rhythms.

Clathrin-mediated endocytosis (CME) and its core endocytic machinery are evolutionarily conserved across all eukaryotes. In mammals, the heterotetrameric adaptor protein complex-2 (AP-2) sorts plasma membrane (PM) cargoes into vesicles via the recognition of motifs based on Tyr or di-Leu in their cytoplasmic tails. However, in plants, very little is known about how PM proteins are sorted for CME and whether similar motifs are required. In Arabidopsis (Arabidopsis thaliana), the brassinosteroid (BR) receptor BR INSENSITIVE1 (BRI1) undergoes endocytosis, which depends on clathrin and AP-2. Here, we demonstrate that BRI1 binds directly to the medium AP-2 subunit (AP2M). The cytoplasmic domain of BRI1 contains five putative canonical surface-exposed Tyr-based endocytic motifs. The Tyr-to-Phe substitution in Y898KAI reduced BRI1 internalization without affecting its kinase activity. Consistently, plants carrying the BRI1Y898F mutation were hypersensitive to BRs. Our study demonstrates that AP-2–dependent internalization of PM proteins via the recognition of functional Tyr motifs also operates in plants.

International audience; Statement: We present detailed novel quantitative imaging protocols and review 15 pharmacological and genetic manipulation to provide standardized experimental approaches 16 for the investigation of plant clathrin-mediated endocytosis at multiple scales. Abstract 18 Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects 19 of plant growth, development, intra-and inter-cellular signaling, nutrient uptake and 20 pathogen defense. Despite these significant roles, little is known about the precise molecular 21 details of how it functions in planta. In order to facilitate the direct quantitative study of plant 22 CME, here we review current routinely used methods and present refined, standardized 23 quantitative imaging protocols which allow the detailed characterization of CME at multiple 24 scales in plant tissues. These include: (i) an efficient electron microscopy protocol for the 25 imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed 26 characterization of the ultra-structure of clathrin-coated vesicles; (ii) a detailed protocol and 27 analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal 28 interplay of endocytosis components during single CME events; (iii) a semi-automated 29 analysis to allow the quantitative characterization of global internalization of cargos in whole 30 plant tissues; and (iv) an overview and validation of useful genetic and pharmacological tools 31 to interrogate the molecular mechanisms and function of CME in intact plant samples. 32 2

We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2020. This year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. These tools are applied to solve reachability analysis problems on six benchmark problems, two of them featuring hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools.

Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. submanifolds of R d defined as the zero set of some multivariate multivalued smooth function f : R^d → R^{d−m} where m is the intrinsic dimension of the manifold. A natural way to approximate a smooth isomanifold M is to consider its Piecewise-Linear (PL) approximation or meshM based on a triangulation T of the ambient space R d. In this paper, we present a simple algorithm to construct such an approximation for arbitrary m and d up to a given precision D. The complexity of our algorithm is polynomial in d and δ, and exponential in m. Since, by previous results,M is O(D 2)-close and isotopic to M when δ = Ω(d 2.5), our algorithm constructs a geometrically close and topologically correct PL-approximation of isomanifolds of low dimensions in polynomial time. The algorithm is practical and can handle cases that are far ahead of the state-of-the-art. Combining this algorithm with dimensionality reduction techniques, the dependency on d in the sizes of the output sample and mesh can be completely removed with high probability. The crux of our algorithm is to use for the ambient triangulation T a regular triangulation from a particular family. This family consists of Freudenthal-Kuhn triangulations and their images through affine mappings. It also includes Coxeter triangulations of typeà d. We introduce an elegant and very compact data structure to implicitly store the full facial structure of such triangulations. This data structure allows to retrieve the faces or the cofaces of a simplex of any dimension in an output sensitive way, which is essential for our application and is of independent interest.

In the recent study of crossing numbers, drawings of graphs that can be extended to an arrangement of pseudolines (pseudolinear drawings) have played an important role as they are a natural combinatorial extension of rectilinear (or straight-line) drawings. A characterization of the pseudolinear drawings of $K_n$ was found recently. We extend this characterization to all graphs, by describing the set of minimal forbidden subdrawings for pseudolinear drawings. Our characterization also leads to a polynomial-time algorithm to recognize pseudolinear drawings and construct the pseudolines when it is possible., Journal of Computational Geometry, Vol. 12 No. 2 (2021)

Nitrogen is an essential macronutrient and its availability in soil plays a critical role in plant growth, development and impacts agricultural productivity. Plants have evolved different strategies to sense and respond to heterogeneous nitrogen distribution. Modulating root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to varying nitrogen sources are poorly understood. Here, using a combination of physiological, live in vivo high- and super resolution imaging, we describe a novel adaptation strategy of root growth on available nitrogen source. We show that growth, i.e. tissue-specific cell division and elongation rates are fine-tuned by modulating auxin flux within and between tissues. Changes in auxin redistribution are achieved by nitrogen source dependent post-translational modification of PIN2, a major auxin efflux carrier, at an uncharacterized, evolutionary conserved phosphosite. Further, we generate a computer model based on our results which successfully recapitulate our experimental observations and creates new predictions that could broaden our understanding of root growth mechanisms in the dynamic environment.

International audience; In agricultural systems, nitrate is the main source of nitrogen available for plants. Besides its role as a nutrient, nitrate has been shown to act as a signal molecule for plant growth, development and stress responses. In Arabidopsis, the NRT1.1 nitrate transceptor represses lateral root (LR) development at low nitrate availability by promoting auxin basipetal transport out of the LR primordia (LRPs). In addition, our present study shows that NRT1.1 acts as a negative regulator of the TAR2 auxin biosynthetic gene expression in the root stele. This is expected to repress local auxin biosynthesis and thus to reduce acropetal auxin supply to the LRPs. Moreover, NRT1.1 also negatively affects expression of the LAX3 auxin influx carrier, thus preventing cell wall remodeling required for overlying tissues separation during LRP emergence. Both NRT1.1-mediated repression of TAR2 and LAX3 are suppressed at high nitrate availability, resulting in the nitrate induction of TAR2 and LAX3 expression that is required for optimal stimulation of LR development by nitrate. Altogether, our results indicate that the NRT1.1 transceptor coordinately controls several crucial auxin-associated processes required for LRP development, and as a consequence that NRT1.1 plays a much more integrated role than previously anticipated in regulating the nitrate response of root system architecture.

There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but interacting sites are embedded in a liquid droplet of proteins which condenses out of the surrounding solution. We argue that droplet-mediated interactions can account for crucial features of gene regulation only if the droplet is poised at a non-generic point in its phase diagram. We explore a minimal model that embodies this idea, show that this model has a natural mechanism for self-tuning, and suggest direct experimental tests.

This paper presents a rather simple tracing algorithm to sample and mesh an m-dimensional sub-manifold of Rd for arbitrary m and d. We extend the work of Dobkin et al. to submanifolds of arbitrary dimension and codimension. The algorithm is practical and has been thoroughly investigated from both theoretical and experimental perspectives. The paper provides a full description and analysis of the data structure and of the tracing algorithm. The main contributions are : 1. We unify and complement the knowledge about Coxeter and Freudenthal-Kuhn triangulations. 2. We introduce an elegant and compact data structure to store Coxeter or Freudenthal-Kuhn triangulations and describe output sensitive algorithms to compute faces and cofaces or any simplex in the triangulation. 3. We present a manifold tracing algorithm based on the above data structure. We provide a detailled complexity analysis along with experimental results that show that the algorithm can handle cases that are far ahead of the state-of-the-art.

To validate a French translation of the Pain Sensitivity Questionnaire (PSQ), which is a valuable tool to predict an individual’s natural disposition to feel pain that could be used after surgery. We studied content validity, internal consistency, convergent validity (anxiety, depression and catastrophism) and test-retest reliability of the French version of the PSQ (PSQ-F) in 146 patients either before scheduled surgery or during pregnancy; then, convergent and concurrent validity in 85 healthy volunteers submitted to nociceptive tests. Internal consistency of the PSQ-F was found to be excellent, with Cronbach’s α at 0.866, 0.886, and 0.927, respectively for its “minor”, “moderate” and “total” scores. Test-retest reliability was significant, with intraclass correlation coefficients at 0.629, 0.629, and 0.635, respectively for the above- mentioned scores. These three scores correlated with anxiety, depression and catastrophizing scores in patients, but not in healthy volunteers, possibly because of low and few variant psychometric scores in this group. They were inversely correlated to the temperature needed to evoke heat pain rated 6 out of 10, but not to the mechanical pain threshold (electronic von Frey), nor to the heat pain threshold. Finally, they directly correlated to the pain induced by the cold pressor test (minor and total scores only). This validated version can now be used by French-speaking researchers and physicians. www.ClinicalTrials.gov (NCT03113903); 14 April, 2017.

The mitochondrial respiratory chain formed by five protein complexes utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains fragmentary due to bottlenecks arising from large conformational transitions and their interplay with the hydrated proton pathways. A recent study has reported the crystallographic structure of complex I from Thermus thermophilus, encasing 16 subunits with 9 iron-sulfur clusters, which are reduced by electrons from NADH. Here, we have used large-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron-sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol form – a design essential for menaquinol release. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the TM subunits are found to be responsible for proton pumping. Random insertion of molecular oxygen in reduced complex I illuminates an enhanced access to the iron-sulfur clusters, conducive to the formation of reactive oxygen species. Our simulations reveal molecular design principles linking redox reactions and proton translocation in complex I.

Mathematical models have been used successfully at diverse scales of biological organization, ranging from ecology and population dynamics to stochastic reaction events occurring between individual molecules in single cells. Generally, many biological processes unfold across multiple scales, with mutations being the best studied example of how stochasticity at the molecular scale can influence outcomes at the population scale. In many other contexts, however, an analogous link between micro- and macro-scale remains elusive, primarily due to the challenges involved in setting up and analyzing multi-scale models. Here, we employ such a model to investigate how stochasticity propagates from individual biochemical reaction events in the bacterial innate immune system to the ecology of bacteria and bacterial viruses. We show analytically how the dynamics of bacterial populations are shaped by the activities of immunity-conferring enzymes in single cells and how the ecological consequences imply optimal bacterial defense strategies against viruses. Our results suggest that bacterial populations in the presence of viruses can either optimize their initial growth rate or their population size, with the first strategy favoring simple immunity featuring a single restriction modification system and the second strategy favoring complex bacterial innate immunity featuring several simultaneously active restriction modification systems., Author summary Mathematical understanding of how randomness at the molecular scale, also known as molecular noise, ultimately affects the fate of organisms and whole populations is widely recognized as a challenging problem in multi-scale modeling. Here, we develop an analytical framework for analyzing how the randomness of individual reaction events in single cells propagates to higher levels of biological organization and affects population and ecology scale dynamics. We deploy our mathematical results to study an example from the ecology of bacteria and bacteriophage viruses. Bacteria defend themselves against viruses by a simple innate immune system composed of a pair of enzymes. Due to molecular noise, however, viruses sometimes escape this immunity, causing bacterial populations to plummet. Noise can also cause the immune system to turn against its own host. By analyzing how such costs and benefits of bacterial immunity balance at the ecological level, we predict the optimal parameters for bacterial innate immune systems. While the focus of this work is on bacteria-phage ecologies, we expect that our results will generally help to better understand population and ecology scale consequences of stochastic cell fate decisions in diverse biological domains ranging from cell differentiation in developmental biology to studies of the microbiome and consequences of stochasticity in apoptotic responses for anti-cancer therapies.

We consider the following setting: suppose that we are given a manifold M in $${\mathbb {R}}^d$$ R d with positive reach. Moreover assume that we have an embedded simplical complex $${\mathcal {A}}$$ A without boundary, whose vertex set lies on the manifold, is sufficiently dense and such that all simplices in $${\mathcal {A}}$$ A have sufficient quality. We prove that if, locally, interiors of the projection of the simplices onto the tangent space do not intersect, then $${\mathcal {A}}$$ A is a triangulation of the manifold, that is, they are homeomorphic.

The subject of this paper is the big quantum cohomology rings of symplectic isotropic Grassmannians $\text{IG}(2, 2n)$. We show that these rings are regular. In particular, by "generic smoothness", we obtain a conceptual proof of generic semisimplicity of the big quantum cohomology for $\text{IG}(2, 2n)$. Further, by a general result of Claus Hertling, the regularity of these rings implies that they have a description in terms of isolated hypersurface singularities, which we show in this case to be of type $A_{n-1}$. By the homological mirror symmetry conjecture, these results suggest the existence of a very special full exceptional collection in the derived category of coherent sheaves on $\text{IG}(2, 2n)$. Such a collection is constructed in the appendix by Alexander Kuznetsov., Comment: Appendix by Alexander Kuznetsov. The paper incorporates the results of the earlier preprint arXiv:1510.07903. Comments are welcome

In developing organisms, spatially prescribed cell identities are thought to be determined by the expression levels of multiple genes. Quantitative tests of this idea, however, require a theoretical framework capable of exposing the rules and precision of cell specification over developmental time. Using the gap gene network in the early fly embryo as an example, we use such a framework to show how expression levels of the four gap genes can be jointly decoded into an optimal specification of position with 1% accuracy. The decoder correctly predicts, with no free parameters, the dynamics of pair-rule expression patterns at different developmental time points and in various mutant backgrounds. Precise cellular identities are thus available at the earliest stages of development, contrasting the prevailing view of positional information being slowly refined across successive layers of the patterning network. Our results suggest that developmental enhancers closely approximate a mathematically optimal decoding strategy.

Despite their different origins,Drosophilaglia and hemocytes are related cell populations that provide an immune function.Drosophilahemocytes patrol the body cavity and act as macrophages outside the nervous system, whereas glia originate from the neuroepithelium and provide the scavenger population of the nervous system.Drosophilaglia are hence the functional orthologs of vertebrate microglia, even though the latter are cells of immune origin that subsequently move into the brain during development. Interestingly, theDrosophilaimmune cells within (glia) and outside (hemocytes) the nervous system require the same transcription factor glial cells deficient/glial cells missing (Glide/Gcm) for their development. This raises the issue of how do glia specifically differentiate in the nervous system, and hemocytes in the procephalic mesoderm. The Repo homeodomain transcription factor and panglial direct target of Glide/Gcm is known to ensure glial terminal differentiation. Here we show that Repo also takes center stage in the process that discriminates between glia and hemocytes. First, Repo expression is repressed in the hemocyte anlagen by mesoderm-specific factors. Second, Repo ectopic activation in the procephalic mesoderm is sufficient to repress the expression of hemocyte-specific genes. Third, the lack of Repo triggers the expression of hemocyte markers in glia. Thus, a complex network of tissue-specific cues biases the potential of Glide/Gcm. These data allow us to revise the concept of fate determinants and help us to understand the bases of cell specification. Both sexes were analyzed.SIGNIFICANCE STATEMENTDistinct cell types often require the same pioneer transcription factor, raising the issue of how one factor triggers different fates. InDrosophila, glia and hemocytes provide a scavenger activity within and outside the nervous system, respectively. While they both require the glial cells deficient/glial cells missing (Glide/Gcm) transcription factor, glia originate from the ectoderm, and hemocytes from the mesoderm. Here we show that tissue-specific factors inhibit the gliogenic potential of Glide/Gcm in the mesoderm by repressing the expression of the homeodomain protein Repo, a major glial-specific target of Glide/Gcm. Repo expression in turn inhibits the expression of hemocyte-specific genes in the nervous system. These cell-specific networks secure the establishment of the glial fate only in the nervous system and allow cell diversification.

We consider the problem of bounding large deviations for non-i.i.d. random variables that are allowed to have arbitrary dependencies. Previous works typically assumed a specific dependence structure, namely the existence of independent components. Bounds that depend on the degree of dependence between the observations have only been studied in the theory of mixing processes, where variables are time-ordered. Here, we introduce a new way of measuring dependences within an unordered set of variables. We prove concentration inequalities, that apply to any set of random variables, but benefit from the presence of weak dependencies. We also discuss applications and extensions of our results to related problems of machine learning and large deviations.

International audience; This paper presents a reliable method to verify the existence of loops along the uncertain trajectory of a robot, based on proprioceptive measurements only, within a bounded-error context. The loop closure detection is one of the key points in SLAM methods, especially in homogeneous environments with difficult scenes recognitions. The proposed approach is generic and could be coupled with conventional SLAM algorithms to reliably reduce their computing burden, thus improving the localization and mapping processes in the most challenging environments such as unexplored underwater extents. To prove that a robot performed a loop whatever the uncertainties in its evolution, we employ the notion of topological degree that originates in the field of differential topology. We show that a verification tool based on the topological degree is an optimal method for proving robot loops. This is demonstrated both on datasets from real missions involving autonomous underwater vehicles, and by a mathematical discussion.

International audience; Formalizing properties of systems with continuous dynamics is a challenging task. In this paper, we propose a formal framework for specifying and monitoring rich temporal properties of real-valued signals. We introduce signal first-order logic (SFO) as a specification language that combines first-order logic with linear-real arithmetic and unary function symbols interpreted as piecewise-linear signals. We first show that while the satisfiability problem for SFO is undecidable, its membership and monitoring problems are decidable. We develop an offline monitoring procedure for SFO that has polynomial complexity in the size of the input trace and the specification, for a fixed number of quantifiers and function symbols. We show that the algorithm has computation time linear in the size of the input trace for the important fragment of bounded-response specifications interpreted over input traces with finite variability. We can use our results to extend signal temporal logic with first-order quantifiers over time and value parameters, while preserving its efficient monitoring. We finally demonstrate the practical appeal of our logic through a case study in the microelectronics domain.

International audience; We provide a procedure for detecting the sub-segments of an incrementally observed Boolean signal w that match a given temporal pattern phi. As a pattern specification language, we use timed regular expressions, a formalism well-suited for expressing properties of concurrent asynchronous behaviors embedded in metric time. We construct a timed automaton accepting the timed language denoted by phi and modify it slightly for the purpose of matching. We then apply zone-based reachability computation to this automaton while it reads w, and retrieve all the matching segments from the results. Since the procedure is automaton based, it can be applied to patterns specified by other formalisms such as timed temporal logics reducible to timed automata or directly encoded as timed automata. The procedure has been implemented and its performance on synthetic examples is demonstrated.

XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno's classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes., eLife digest The DNA inside cells is organized in structures called chromosomes, some of which can control whether individuals develop as males or females. For instance, female mammals have two X chromosomes, whereas male mammals have one X and one Y chromosome. A mechanism called ‘dosage compensation’ makes sure that females do not produce double the number of transcripts from genes on the X-chromosome as males. In other organisms, including the parasitic flatworms called Schistosomes, females have ZW sex chromosomes, whereas males have two Z chromosomes. In these parasites, males do create more transcripts from genes on the Z chromosome than females do, suggesting they do not have the same kind of compensation mechanisms as mammals. Among Schistosome parasites, the Z chromosome has only been studied in detail in the model organism Schistosoma mansoni. Investigating other closely related species can shed light on how the Z and W chromosomes evolved. Picard et al. studied the Z chromosome in two additional species of Schistosome parasites: the African S. haematobium and the Asian S. japonicum. Using a technique called DNA sequencing, Picard et al. were able to analyse their genes, focusing on a part of the Z chromosome known to have been lost from the W chromosome. The results revealed that this region was different in the African and Asian species. In addition, females of both species expressed genes on their single Z chromosome at fairly high levels. The males did not need to express these genes at a high level because they have two copies – but they did so anyway. This could be because this high expression is a by-product of the way the females have evolved to boost their Z chromosome gene expression. A next step will be to investigate the molecular mechanisms underlying this regulation. Schistosomiasis – a disease caused by this type of flatworm parasite – is one of the deadliest neglected tropical diseases, according to the US Centers of Disease Control. It kills more than 200,000 people a year. Better understanding of the reproductive biology of this parasite could eventually help to develop ways to control it by interfering with its reproduction.

International audience; A standard design pattern found in many concurrent data structures , such as hash tables or ordered containers, is an alternation of parallelizable sections that incur no data conflicts and critical sections that must run sequentially and are protected with locks. A lock can be viewed as a queue that arbitrates the order in which the critical sections are executed, and a natural question is whether we can use stochastic analysis to predict the resulting throughput. As a preliminary evidence to the affirmative, we describe a simple model that can be used to predict the throughput of coarse-grained lock-based algorithms. We show that our model works well for CLH lock, and we expect it to work for other popular lock designs such as TTAS, MCS, etc.

International audience; We describe a new algorithm for the parametric identification problem for signal temporal logic (STL), stated as follows. Given a dense-time real-valued signal w and a parameterized temporal logic formula phi, compute the subset of the parameter space that renders the formula satisfied by the signal. Unlike previous solutions, which were based on search in the parameter space or quantifier elimination, our procedure works recursively on phi and computes the evolution over time of the set of valid parameter assignments. This procedure is similar to that of monitoring or computing the robustness of phi relative to w. Our implementation and experiments demonstrate that this approach can work well in practice.

Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymous mutations computed either from exome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the joint site frequency spectrum, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e. periodic connectivity) and across genes (i.e. genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding site frequency spectrum, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed.

The evolution of assortative mating is a key part of the speciation process. Stronger assortment, or greater divergence in mating traits, between species pairs with overlapping ranges is commonly observed, but possible causes of this pattern of reproductive character displacement are difficult to distinguish. We use a multidisciplinary approach to provide a rare example where it is possible to distinguish among hypotheses concerning the evolution of reproductive character displacement. We build on an earlier comparative analysis that illustrated a strong pattern of greater divergence in penis form between pairs of sister species with overlapping ranges than between allopatric sister-species pairs, in a large clade of marine gastropods (Littorinidae). We investigate both assortative mating and divergence in male genitalia in one of the sister-species pairs, discriminating among three contrasting processes each of which can generate a pattern of reproductive character displacement: reinforcement, reproductive interference and the Templeton effect. We demonstrate reproductive character displacement in assortative mating, but not in genital form between this pair of sister species and use demographic models to distinguish among the different processes. Our results support a model with no gene flow since secondary contact and thus favor reproductive interference as the cause of reproductive character displacement for mate choice, rather than reinforcement. High gene flow within species argues against the Templeton effect. Secondary contact appears to have had little impact on genital divergence.

The draft genome of Chara braunii reveals many plant-like features important for colonization of land that evolved in charophytic algae and therefore prior to the earliest land plants. Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote. © 2018 Elsevier Inc.