@article{20757, abstract = {We report the utilisation of an iodine(III) reagent to access α,β-unsaturated carbonyls from the corresponding silyl enol ethers and enol phosphates. The transformation can also be carried out in one pot, directly dehydrogenating carbonyls.}, author = {Botlik, Bence B. and Finkelstein, Patrick and Paschke, Ann-Sophie K. and Reisenbauer, Julia and Morandi, Bill}, issn = {1364-548X}, journal = {Chemical Communications}, number = {69}, pages = {9254--9257}, publisher = {Royal Society of Chemistry}, title = {{Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent}}, doi = {10.1039/d4cc02609h}, volume = {60}, year = {2024}, } @article{20807, abstract = {Human glutamate carboxypeptidase 2 (GCP2) from the M28B metalloprotease group is an important target for therapy in neurological disorders and an established tumor marker. However, its physiological functions remain unclear. To better understand general roles, we used the model organism Caenorhabditis elegans to genetically manipulate its three existing orthologous genes and evaluate the impact on worm physiology. The results of gene knockout studies showed that C. elegans GCP2 orthologs affect the pharyngeal physiology, reproduction, and structural integrity of the organism. Promoter-driven GFP expression revealed distinct localization for each of the three gene paralogs, with gcp-2.1 being most abundant in muscles, intestine, and pharyngeal interneurons, gcp-2.2 restricted to the phasmid neurons, and gcp-2.3 located in the excretory cell. The present study provides new insight into the unique phenotypic effects of GCP2 gene knockouts in C. elegans, and the specific tissue localizations. We believe that elucidation of particular roles in a non-mammalian organism can help to explain important questions linked to physiology of this protease group and in extension to human GCP2 involvement in pathophysiological processes.}, author = {Panska, Lucie and Nedvedova, Stepanka and Vacek, Vojtech and Krivska, Daniela and Konecny, Lukas and Knop, Filip and Kutil, Zsofia and Skultetyova, Lubica and Leontovyc, Adrian and Ulrychova, Lenka and Sakanari, Judy and Asahina, Masako and Barinka, Cyril and Macurkova, Marie and Dvorak, Jan}, issn = {1573-4935}, journal = {Bioscience Reports}, number = {1}, publisher = {Portland Press}, title = {{Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans}}, doi = {10.1042/bsr20230502}, volume = {44}, year = {2024}, } @article{20808, abstract = {During Caenorhabditis elegans development, multiple cells migrate long distances or extend processes to reach their final position and/or attain proper shape. The Wnt signalling pathway stands out as one of the major coordinators of cell migration or cell outgrowth along the anterior-posterior body axis. The outcome of Wnt signalling is fine-tuned by various mechanisms including endocytosis. In this study, we show that SEL-5, the C. elegans orthologue of mammalian AP2-associated kinase AAK1, acts together with the retromer complex as a positive regulator of EGL-20/Wnt signalling during the migration of QL neuroblast daughter cells. At the same time, SEL-5 in cooperation with the retromer complex is also required during excretory canal cell outgrowth. Importantly, SEL-5 kinase activity is not required for its role in neuronal migration or excretory cell outgrowth, and neither of these processes is dependent on DPY-23/AP2M1 phosphorylation. We further establish that the Wnt proteins CWN-1 and CWN-2, together with the Frizzled receptor CFZ-2, positively regulate excretory cell outgrowth, while LIN-44/Wnt and LIN-17/Frizzled together generate a stop signal inhibiting its extension.}, author = {Knop, Filip and Zounarová, Apolena and Šabata, Vojtěch and Middelkoop, Teije Corneel and Macůrková, Marie}, issn = {2050-084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity}}, doi = {10.7554/elife.91054}, volume = {13}, year = {2024}, } @article{9651, abstract = {We introduce a hierachy of equivalence relations on the set of separated nets of a given Euclidean space, indexed by concave increasing functions ϕ:(0,∞)→(0,∞). Two separated nets are called ϕ-displacement equivalent if, roughly speaking, there is a bijection between them which, for large radii R, displaces points of norm at most R by something of order at most ϕ(R). We show that the spectrum of ϕ-displacement equivalence spans from the established notion of bounded displacement equivalence, which corresponds to bounded ϕ, to the indiscrete equivalence relation, coresponding to ϕ(R)∈Ω(R), in which all separated nets are equivalent. In between the two ends of this spectrum, the notions of ϕ-displacement equivalence are shown to be pairwise distinct with respect to the asymptotic classes of ϕ(R) for R→∞. We further undertake a comparison of our notion of ϕ-displacement equivalence with previously studied relations on separated nets. Particular attention is given to the interaction of the notions of ϕ-displacement equivalence with that of bilipschitz equivalence.}, author = {Dymond, Michael and Kaluza, Vojtech}, issn = {1572-9168}, journal = {Geometriae Dedicata}, publisher = {Springer Nature}, title = {{Divergence of separated nets with respect to displacement equivalence}}, doi = {10.1007/s10711-023-00862-3}, volume = {218}, year = {2024}, } @article{17202, abstract = {Gate-tunable transmons (gatemons) employing semiconductor Josephson junctions have recently emerged as building blocks for hybrid quantum circuits. In this study, we present a gatemon fabricated in planar Germanium. We induce superconductivity in a two-dimensional hole gas by evaporating aluminum atop a thin spacer, which separates the superconductor from the Ge quantum well. The Josephson junction is then integrated into an Xmon circuit and capacitively coupled to a transmission line resonator. We showcase the qubit tunability in a broad frequency range with resonator and two-tone spectroscopy. Time-domain characterizations reveal energy relaxation and coherence times up to 75 ns. Our results, combined with the recent advances in the spin qubit field, pave the way towards novel hybrid and protected qubits in a group IV, CMOS-compatible material.}, author = {Sagi, Oliver and Crippa, Alessandro and Valentini, Marco and Janik, Marian and Baghumyan, Levon and Fabris, Giorgio and Kapoor, Lucky and Hassani, Farid and Fink, Johannes M and Calcaterra, Stefano and Chrastina, Daniel and Isella, Giovanni and Katsaros, Georgios}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{A gate tunable transmon qubit in planar Ge}}, doi = {10.1038/s41467-024-50763-6}, volume = {15}, year = {2024}, } @article{17203, abstract = {The behavior of a rigid body primarily depends on its mass moments, which consist of the mass, center of mass, and moments of inertia. It is possible to manipulate these quantities without altering the geometric appearance of an object by introducing cavities in its interior. Algorithms that find cavities of suitable shapes and sizes have enabled the computational design of spinning tops, yo-yos, wheels, buoys, and statically balanced objects. Previous work is based, for example, on topology optimization on voxel grids, which introduces a large number of optimization variables and box constraints, or offset surface computation, which cannot guarantee that solutions to a feasible problem will always be found. In this work, we provide a mathematical analysis of constrained topology optimization problems that depend only on mass moments. This class of problems covers, among others, all applications mentioned above. Our main result is to show that no matter the outer shape of the rigid body to be optimized or the optimization objective and constraints considered, the optimal solution always features a quadric-shaped interface between material and cavities. This proves that optimal interfaces are always ellipsoids, hyperboloids, paraboloids, or one of a few degenerate cases, such as planes. This insight lets us replace a difficult topology optimization problem with a provably equivalent non-linear equation system in a small number (<10) of variables, which represent the coefficients of the quadric. This system can be solved in a few seconds for most examples, provides insights into the geometric structure of many specific applications, and lets us describe their solution properties. Finally, our method integrates seamlessly into modern fabrication workflows because our solutions are analytical surfaces that are native to the CAD domain.}, author = {Hafner, Christian and Ly, Mickaël and Wojtan, Christopher J}, issn = {1557-7368}, journal = {Transactions on Graphics}, keywords = {Topology Optimization, Mass Moments, Computational Geometry}, location = {Denver, Colorado}, number = {4}, publisher = {Association for Computing Machinery}, title = {{Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments}}, doi = {10.1145/3658194}, volume = {43}, year = {2024}, } @article{17207, author = {Fouqueau, Louise and Polechova, Jitka}, issn = {1420-9101}, journal = {Journal of evolutionary biology}, number = {6}, pages = {579--587}, publisher = {Oxford University Press}, title = {{Eco-evolutionary dynamics in changing environments: Integrating theory with data}}, doi = {10.1093/jeb/voae067}, volume = {37}, year = {2024}, } @phdthesis{17208, abstract = {Can current quantum computers provide a speedup over their classical counterparts for some kinds of problems? In this thesis, with a focus on ground state search/preparation, we address some of the challenges that both quantum annealing and variational quantum algorithms suffer from, hindering any possible practical speedup in comparison to the best classical counterparts. In the first part of the thesis, we study the performance of quantum annealing for solving a particular combinatorial optimization problem called 3-XOR satisfability (3-XORSAT). The classical problem is mapped into a ground state search of a 3-local classical Hamiltonian $H_C$. We consider how modifying the initial problem, by adding more interaction terms to the corresponding Hamiltonian, leads to the emergence of a first-order phase transition during the annealing process. This phenomenon causes the total annealing duration, $T$, required to prepare the ground state of $H_C$ with a high probability to increase exponentially with the size of the problem. Our findings indicate that with the growing complexity of problem instances, the likelihood of encountering first-order phase transitions also increases, making quantum annealing an impractical solution for these types of combinatorial optimization problems. In the second part, we focus on the problem of barren plateaus in generic variational quantum algorithms. Barren plateaus correspond to flat regions in the parameter space where the gradient of the cost function is zero in expectation, and with the variance decaying exponentially with the system size, thus obstructing an efficient parameter optimization. We propose an algorithm to circumvent Barren Plateaus by monitoring the entanglement entropy of k-local reduced density matrices, alongside a method for estimating entanglement entropy via classical shadow tomography. We illustrate the approach with the paradigmatic example of the variational quantum eigensolver, and show that our algorithm effectively avoids barren plateaus in the initialization as well as during the optimization stage. Lastly, in the last two Chapters of this thesis, we focus on the quantum approximate optimization algorithm (QAOA), originally introduced as an algorithm for solving generic combinatorial optimization problems in near-term quantum devices. Specifically, we focus on how to develop rigorous initialization strategies with guarantee improvement. Our motivation for this study lies in that for random initialization, the optimization typically leads to local minima with poor performance. Our main result corresponds to the analytical construction of index-1 saddle points or transition states, stationary points with a single direction of descent, as a tool for systematically exploring the QAOA optimization landscape. This leads us to propose a novel greedy parameter initialization strategy that guarantees for the energy to decrease with an increasing number of circuit layers. Furthermore, with precise estimates for the negative Hessian eigenvalue and its eigenvector, we establish a lower bound for energy improvement following a QAOA iteration.}, author = {Medina Ramos, Raimel A}, issn = {2663-337X}, keywords = {Quantum computing, Variational Quantum Algorithms, Optimization}, pages = {133}, publisher = {Institute of Science and Technology Austria}, title = {{Exploring the optimization landscape of variational quantum algorithms}}, doi = {10.15479/at:ista:17208}, year = {2024}, } @inproceedings{17214, abstract = {Current numerical algorithms for simulating friction fall in one of two camps: smooth solvers sacrifice the stable treatment of static friction in exchange for fast convergence, and non-smooth solvers accurately compute friction at convergence rates that are often prohibitive for large graphics applications. We introduce a novel bridge between these two ideas that computes static and dynamic friction stably and efficiently. Our key idea is to convert the highly constrained non-smooth problem into an unconstrained smooth problem using logarithmic barriers that converges to the exact solution as accuracy increases. We phrase the problem as an interior point primal-dual problem that can be solved efficiently with Newton iteration. We observe quadratic convergence despite the non-smooth nature of the original problem, and our method is well-suited for large systems of tightly packed objects with many contact points. We demonstrate the efficacy of our method with stable piles of grains and stacks of objects, complex granular flows, and robust interlocking assemblies of rigid bodies.}, author = {Chen, Yi-Lu and Ly, Mickaël and Wojtan, Christopher J}, booktitle = {Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers '24}, isbn = {9798400705250}, keywords = {physical simulation, frictional contact, rigid body mechanics, non-smooth dynamics}, location = {Denver, United States}, publisher = {Association for Computing Machinery}, title = {{Primal-dual non-smooth friction for rigid body animation}}, doi = {10.1145/3641519.3657485}, year = {2024}, } @article{17219, abstract = {We introduce a multi-material non-manifold mesh-based surface tracking algorithm that converts self-intersections into topological changes. Our algorithm generalizes prior work on manifold surface tracking with topological changes: it preserves surface features like mesh-based methods, and it robustly handles topological changes like level set methods. Our method also offers improved efficiency and robustness over the state of the art. We demonstrate the effectiveness of the approach on a range of examples, including complex soap film simulations with thousands of interacting bubbles, and boolean unions of non-manifold meshes consisting of millions of triangles.}, author = {Synak, Peter and Kalinov, Aleksei and Strugaru, Irina-Malina and Etemadihaghighi, Arian and Yang, Huidong and Wojtan, Christopher J}, issn = {1557-7368}, journal = {ACM Transactions on Graphics}, keywords = {surface tracking, topology change, non- manifold meshes, multi-material flows, solid modeling}, number = {4}, publisher = {Association for Computing Machinery}, title = {{Multi-material mesh-based surface tracking with implicit topology changes}}, doi = {10.1145/3658223}, volume = {43}, year = {2024}, } @unpublished{17222, abstract = {The quantum approximate optimization algorithm (QAOA) uses a quantum computer to implement a variational method with $2p$ layers of alternating unitary operators, optimized by a classical computer to minimize a cost function. While rigorous performance guarantees exist for the QAOA at small depths $p$, the behavior at large depths remains less clear, though simulations suggest exponentially fast convergence for certain problems. In this work, we gain insights into the deep QAOA using an analytic expansion of the cost function around transition states. Transition states are constructed in a recursive manner: from the local minima of the QAOA with $p$ layers we obtain transition states of the QAOA with $p+1$ layers, which are stationary points characterized by a unique direction of negative curvature. We construct an analytic estimate of the negative curvature and the corresponding direction in parameter space at each transition state. The expansion of the QAOA cost function along the negative direction to the quartic order gives a lower bound of the QAOA cost function improvement. We provide physical intuition behind the analytic expressions for the local curvature and quartic expansion coefficient. Our numerical study confirms the accuracy of our approximations and reveals that the obtained bound and the true value of the QAOA cost function gain have a characteristic exponential decrease with the number of layers $p$, with the bound decreasing more rapidly. Our study establishes an analytical method for recursively studying the QAOA that is applicable in the regime of high circuit depth.}, author = {Medina Ramos, Raimel A and Serbyn, Maksym}, booktitle = {arXiv}, title = {{A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm}}, doi = {10.48550/arXiv.2405.10125}, year = {2024}, } @article{17232, abstract = {The lineage relationship of clonally-related cells offers important insights into the ontogeny and cytoarchitecture of the brain in health and disease. Here, we provide a protocol to concurrently assess cell lineage relationship and cell-type identity among clonally-related cells in situ. We first describe the preparation and screening of acute brain slices containing clonally-related cells labeled using mosaic analysis with double markers (MADM). We then outline steps to collect RNA from individual cells for downstream applications and cell-type identification using RNA sequencing. For complete details on the use and execution of this protocol, please refer to Cheung et al. 1}, author = {Cheung, Giselle T and Pauler, Florian and Koppensteiner, Peter and Hippenmeyer, Simon}, issn = {2666-1667}, journal = {STAR Protocols}, number = {3}, publisher = {Elsevier}, title = {{Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq}}, doi = {10.1016/j.xpro.2024.103168}, volume = {5}, year = {2024}, } @article{17233, abstract = {CRISPR-Cas9 technology has become an essential tool for plant genome editing. Recent advancements have significantly improved the ability to target multiple genes simultaneously within the same genetic background through various strategies. Additionally, there has been significant progress in developing methods for inducible or tissue-specific editing. These advancements offer numerous possibilities for tailored genome modifications. Building upon existing research, we have developed an optimized and modular strategy allowing the targeting of several genes simultaneously in combination with the synchronized expression of the Cas9 endonuclease in the egg cell. This system allows significant editing efficiency while avoiding mosaicism. In addition, the versatile system we propose allows adaptation to inducible and/or tissue-specific edition according to the promoter chosen to drive the expression of the Cas9 gene. Here, we describe a step-by-step protocol for generating the binary vector necessary for establishing Arabidopsis edited lines using a versatile cloning strategy that combines Gateway® and Golden Gate technologies. We describe a versatile system that allows the cloning of as many guides as needed to target DNA, which can be multiplexed into a polycistronic gene and combined in the same construct with sequences for the expression of the Cas9 endonuclease. The expression of Cas9 is controlled by selecting from among a collection of promoters, including constitutive, inducible, ubiquitous, or tissue-specific promoters. Only one vector containing the polycistronic gene (tRNA-sgRNA) needs to be constructed. For that, sgRNA (composed of protospacers chosen to target the gene of interest and sgRNA scaffold) is cloned in tandem with the pre-tRNA sequence. Then, a single recombination reaction is required to assemble the promoter, the zCas9 coding sequence, and the tRNA-gRNA polycistronic gene. Each element is cloned in an entry vector and finally assembled according to the Multisite Gateway® Technology. Here, we detail the process to express zCas9 under the control of egg cell promoter fused to enhancer sequence (EC1.2en-EC1.1p) and to simultaneously target two multiple C2 domains and transmembrane region protein genes (MCTP3 and MCTP4, respectively at3g57880 and at1g51570), using one or two sgRNA per gene.}, author = {Li, Ziqiang and Huard, Jennifer and Bayer, Emmanuelle M. and Wattelet-Boyer, Valérie}, issn = {2331-8325}, journal = {Bio-protocol}, number = {13}, publisher = {Bio-Protocol}, title = {{Versatile cloning strategy for efficient multigene editing in Arabidopsis}}, doi = {10.21769/BioProtoc.5029}, volume = {14}, year = {2024}, } @article{17234, abstract = {The identification of red, apparently massive galaxies at z > 7 in early James Webb Space Telescope (JWST) photometry suggests a strongly accelerated time line compared to standard models of galaxy growth. A major uncertainty in the interpretation is whether the red colors are caused by evolved stellar populations, dust, or other effects such as emission lines or active galactic nuclei (AGNs). Here we show that three of the massive galaxy candidates at z = 6.7–8.4 have prominent Balmer breaks in JWST/NIRSpec spectroscopy from the RUBIES program. The Balmer breaks demonstrate unambiguously that stellar emission dominates at λrest = 0.4 μm and require formation histories extending hundreds of millions of years into the past in galaxies only 600–800 Myr after the big bang. Two of the three galaxies also show broad Balmer lines, with Hβ FWHM > 2500 km s−1, suggesting that dust-reddened AGNs contribute to, or even dominate, the spectral energy distributions of these galaxies at λrest ≳ 0.6 μm. All three galaxies have relatively narrow [O iii] lines, seemingly ruling out a high-mass interpretation if the lines arise in dynamically relaxed, inclined disks. Yet the inferred masses also remain highly uncertain. We model the high-quality spectra using Prospector to decompose the continuum into stellar and AGN components and explore limiting cases in stellar/AGN contribution. This produces a wide range of possible stellar masses, spanning M⋆ ∼ 109−1011M⊙. Nevertheless, all fits suggest a very early and rapid formation, most of which follow with a truncation in star formation. Potential origins and evolutionary tracks for these objects are discussed, from the cores of massive galaxies to low-mass galaxies with overmassive black holes. Intriguingly, we find all of these explanations to be incomplete; deeper and redder data are needed to understand the physics of these systems.}, author = {Wang, Bingjie and Leja, Joel and De Graaff, Anna and Brammer, Gabriel B. and Weibel, Andrea and Van Dokkum, Pieter and Baggen, Josephine F.W. and Suess, Katherine A. and Greene, Jenny E. and Bezanson, Rachel and Cleri, Nikko J. and Hirschmann, Michaela and Labbé, Ivo and Matthee, Jorryt J and Mcconachie, Ian and Naidu, Rohan P. and Nelson, Erica and Oesch, Pascal A. and Setton, David J. and Williams, Christina C.}, issn = {2041-8213}, journal = {Astrophysical Journal Letters}, number = {1}, publisher = {IOP Publishing}, title = {{RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec}}, doi = {10.3847/2041-8213/ad55f7}, volume = {969}, year = {2024}, } @article{17235, abstract = {We demonstrate ion irradiation by argon or gallium as a wafer-scale post-processing method to increase disorder in superconducting thin films. We study several widely used superconductors, both single-elements and compounds. We show that ion irradiation increases normal-state resistivity in all our films, which is expected to enable tuning their superconducting properties, for example, toward a higher kinetic inductance. We observe an increase in superconducting transition temperature for Al and MoSi and a decrease for Nb, NbN, and TiN. In MoSi, ion irradiation also improves the mixing of the two materials. We demonstrate the fabrication of an amorphous and homogeneous film of MoSi with uniform thickness, which is promising, for example, for superconducting nanowire single-photon detectors.}, author = {Kohopää, Katja and Ronzani, Alberto and Jabdaraghi, Robab Najafi and Bera, Arijit and Ribeiro, Mário and Hazra, Dibyendu and Senior, Jorden L and Prunnila, Mika and Govenius, Joonas and Lehtinen, Janne S. and Kemppinen, Antti}, issn = {2166-532X}, journal = {APL Materials}, number = {7}, publisher = {AIP Publishing}, title = {{Effect of ion irradiation on superconducting thin films}}, doi = {10.1063/5.0202851}, volume = {12}, year = {2024}, } @inproceedings{17236, abstract = {Currently, the best known tradeoff between approximation ratio and complexity for the Sparsest Cut problem is achieved by the algorithm in [Sherman, FOCS 2009]: it computes O(√(log n)/ε)-approximation using O(nε logO(1) n) maxflows for any ε∈[Θ(1/log n),Θ(1)]. It works by solving the SDP relaxation of [Arora-Rao-Vazirani, STOC 2004] using the Multiplicative Weights Update algorithm (MW) of [Arora-Kale, JACM 2016]. To implement one MW step, Sherman approximately solves a multicommodity flow problem using another application of MW. Nested MW steps are solved via a certain "chaining" algorithm that combines results of multiple calls to the maxflow algorithm. We present an alternative approach that avoids solving the multicommodity flow problem and instead computes "violating paths". This simplifies Sherman's algorithm by removing a need for a nested application of MW, and also allows parallelization: we show how to compute O(√(log n)/ε)-approximation via O(logO(1) n) maxflows using O(nε) processors. We also revisit Sherman's chaining algorithm, and present a simpler version together with a new analysis.}, author = {Kolmogorov, Vladimir}, booktitle = {Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures}, isbn = {9798400704161}, issn = {1548-6109}, location = {Nantes, France}, pages = {403--414}, publisher = {Association for Computing Machinery}, title = {{A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut}}, doi = {10.1145/3626183.3659969}, year = {2024}, } @article{17237, abstract = {The impact of climate change on populations will be contingent upon their contemporary adaptive evolution. In this study, we investigated the contemporary evolution of 4 populations of the cold-water kelp Laminaria digitata by analyzing their spatial and temporal genomic variations using ddRAD-sequencing. These populations were sampled from the center to the southern margin of its north-eastern Atlantic distribution at 2 time points, spanning at least 2 generations. Through genome scans for local adaptation at a single time point, we identified candidate loci that showed clinal variation correlated with changes in sea surface temperature (SST) along latitudinal gradients. This finding suggests that SST may drive the adaptive response of these kelp populations, although factors such as species’ demographic history should also be considered. Additionally, we performed a simulation approach to distinguish the effect of selection from genetic drift in allele frequency changes over time. This enabled the detection of loci in the southernmost population that exhibited temporal differentiation beyond what would be expected from genetic drift alone: these are candidate loci which could have evolved under selection over time. In contrast, we did not detect any outlier locus based on temporal differentiation in the population from the North Sea, which also displayed low and decreasing levels of genetic diversity. The diverse evolutionary scenarios observed among populations can be attributed to variations in the prevalence of selection relative to genetic drift across different environments. Therefore, our study highlights the potential of temporal genomics to offer valuable insights into the contemporary evolution of marine foundation species facing climate change.}, author = {Reynes, Lauric and Fouqueau, Louise and Aurelle, Didier and Mauger, Stephane and Destombe, Christophe and Valero, Myriam}, issn = {1420-9101}, journal = {Journal of Evolutionary Biology}, number = {6}, pages = {677--692}, publisher = {Oxford University Press}, title = {{Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations}}, doi = {10.1093/jeb/voae048}, volume = {37}, year = {2024}, } @article{17238, abstract = {We know that heritable variation is abundant, and that selection causes all but the smallest populations to rapidly shift beyond their original trait distribution. So then, what limits the range of a species? There are physical constraints and also population genetic limits to the effectiveness of selection, ultimately set by population size. Global adaptation, where the same genotype is favoured over the whole range, is most efficient when based on a multitude of weakly selected alleles and is effective even when local demes are small, provided that there is some gene flow. In contrast, local adaptation is sensitive to gene flow and may require alleles with substantial effect. How can populations combine the advantages of large effective size with the ability to specialise into local niches? To what extent does reproductive isolation help resolve this tension? I address these questions using eco-evolutionary models of polygenic adaptation, contrasting discrete demes with continuousspace.}, author = {Barton, Nicholas H}, issn = {1420-9101}, journal = {Journal of Evolutionary Biology}, number = {6}, pages = {605--615}, publisher = {Oxford University Press}, title = {{Limits to species' range: The tension between local and global adaptation}}, doi = {10.1093/jeb/voae052}, volume = {37}, year = {2024}, } @article{17239, abstract = {Collagen is the most abundant protein in tissue scaffolds in live organisms. Collagen can self-assemble in vitro, which has led to a number of biotechnological and biomedical applications. To understand the dominant factors that participate in the formation of collagen nanostructures, here we study in real time and with nanoscale resolution the disassembly and reassembly of collagens. We implement a high-speed force microscope, which provides in situ high spatiotemporal resolution images of collagen nanostructures under changing pH conditions. The disassembly and reassembly are dominated by the electrostatic interactions among amino-acid residues of different molecules. Acidic conditions favor disassembly by neutralizing negatively charged residues. The process sets a net repulsive force between collagen molecules. A neutral pH favors the presence of negative and positively charged residues along the collagen molecules, which promotes their electrostatic attraction. Molecular dynamics simulations reproduce the experimental behavior and validate the electrostatic-based model of the disassembly and reassembly processes.}, author = {Garcia-Sacristan, Clara and Gisbert, Victor G. and Klein, Kevin and Šarić, Anđela and Garcia, Ricardo}, issn = {1936-086X}, journal = {ACS Nano}, number = {28}, pages = {18485--18492}, publisher = {American Chemical Society}, title = {{In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures}}, doi = {10.1021/acsnano.4c03839}, volume = {18}, year = {2024}, } @article{17269, abstract = {The directed migration of epithelial cell collectives through coordinated movements plays a crucial role in various physiological processes and is increasingly understood at the level of large confluent monolayers. However, numerous processes rely on the migration of small groups of polarized epithelial clusters in complex environments, and their responses to external geometries remain poorly understood. To address this, we cultivate primary epithelial keratocyte tissues on adhesive microstripes to create autonomous epithelial clusters with well-defined geometries. We show that their migration efficiency is strongly influenced by the contact geometry and the orientation of cell–cell contacts with respect to the direction of migration. A combination of velocity and polarity alignment with contact regulation of locomotion in an active matter model captures quantitatively the experimental data. Furthermore, we predict that this combination of rules enables efficient navigation in complex geometries, which we confirm experimentally. Altogether, our findings provide a conceptual framework for extracting the interaction rules of active systems from their interaction with physical boundaries, as well as design principles for collective navigation in complex microenvironments.}, author = {Vercruysse, Eléonore and Brückner, David and Gómez-González, Manuel and Remson, Alexandre and Luciano, Marine and Kalukula, Yohalie and Rossetti, Leone and Trepat, Xavier and Hannezo, Edouard B and Gabriele, Sylvain}, issn = {1745-2481}, journal = {Nature Physics}, pages = {1492--1500}, publisher = {Springer Nature}, title = {{Geometry-driven migration efficiency of autonomous epithelial cell clusters}}, doi = {10.1038/s41567-024-02532-x}, volume = {20}, year = {2024}, }