@article{18479, abstract = {The dominance of beneficial mutations is a key evolutionary parameter affecting the rate and genetic basis of adaptation, yet it is notoriously difficult to estimate. A leading method to infer it is to compare the relative rates of adaptive substitution for X-linked and autosomal genes, which—according to a classic model by Charlesworth et al. (1987)—is a simple function of the dominance of new beneficial mutations. Recent evidence that rates of adaptive substitution are faster for X-linked genes implies, accordingly, that beneficial mutations are usually recessive. However, this conclusion is incompatible with leading theories of dominance, which predict that beneficial mutations tend to be dominant or overdominant with respect to fitness. To address this incompatibility, we use Fisher’s geometric model to predict the distribution of fitness effects of new mutations and the relative rates of positively selected substitution on the X and autosomes. Previous predictions of faster-X theory emerge as a special case of our model in which the phenotypic effects of mutations are small relative to the distance to the phenotypic optimum. But as mutational effects become large relative to the optimum, we observe an elevated tempo of positively selected substitutions on the X relative to the autosomes across a broader range of dominance conditions, including those predicted by theories of dominance. Our results imply that, contrary to previous models, dominant and overdominant beneficial mutations can plausibly generate patterns of faster-X adaptation. We discuss resulting implications for genomic studies of adaptation and inferences of dominance.}, author = {Mcdonough, Yasmine and Ruzicka, Filip and Connallon, Tim}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {44}, publisher = {National Academy of Sciences}, title = {{Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes}}, doi = {10.1073/pnas.2406335121}, volume = {121}, year = {2024}, } @article{18761, abstract = {Termites, together with cockroaches, belong to the Blattodea. They possess an XX/XY sex determination system which has evolved from an XX/X0 system present in other Blattodean species, such as cockroaches and wood roaches. Little is currently known about the sex chromosomes of termites, their gene content, or their evolution. We here investigate the X chromosome of multiple termite species and compare them with the X chromosome of cockroaches using genomic and transcriptomic data. We find that the X chromosome of the termite Macrotermes natalensis is large and differentiated showing hall marks of sex chromosome evolution such as dosage compensation, while this does not seem to be the case in the other two termite species investigated here where sex chromosomes may be evolutionary younger. Furthermore, the X chromosome in M. natalensis is different from the X chromosome found in the cockroach Blattella germanica indicating that sex chromosome turn-over events may have happened during termite evolution.}, author = {Fraser, Roxanne and Moraa, Ruth and Djolai, Annika and Meisenheimer, Nils and Laube, Sophie and Vicoso, Beatriz and Huylmans, Ann K}, issn = {1759-6653}, journal = {Genome Biology and Evolution}, number = {12}, publisher = {Oxford University Press}, title = {{Evidence for a novel X chromosome in termites}}, doi = {10.1093/gbe/evae265}, volume = {16}, year = {2024}, } @misc{17362, abstract = {This is the supplementary data for the paper titled "Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome", where we described the generation and analysis of single-nucleus expression and chromatin-accessibility data from the female reproductive system of Artemia franciscana. We compared our dataset to the published Drosophila single-nucleus data (over 400 million years of divergence) and highlighted the extreme conservation of several of the molecular pathways of oogenesis and meiosis. We found evidence of global transcriptional quiescence and chromatin condensation in late germ cells, highlighting the conserved role of this repressive stage in arthropod oogenesis. Additionally, we explored the expression patterns of the ZW sex chromosomes during oogenesis. Our data shows that the Z-chromosome is consistently downregulated in germline cells. While this is partly driven by a lack of dosage compensation in the germline, a subset of cells show stronger repression of the Z chromosome.}, author = {Elkrewi, Marwan N and Vicoso, Beatriz}, publisher = {Institute of Science and Technology Austria}, title = {{Data for: "Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome"}}, doi = {10.15479/AT:ISTA:17362}, year = {2024}, } @article{18952, abstract = {A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern. The use of CSP in the prediction of likely cocrystal stoichiometry was also explored, demonstrating multiple possible approaches. Crystallographic disorder emerged as an important theme throughout the test as both a challenge for analysis and a major achievement where two groups blindly predicted the existence of disorder for the first time. Additionally, large-scale comparisons of the sets of predicted crystal structures also showed that some methods yield sets that largely contain the same crystal structures.}, author = {Hunnisett, Lily M. and Nyman, Jonas and Francia, Nicholas and Abraham, Nathan S. and Adjiman, Claire S. and Aitipamula, Srinivasulu and Alkhidir, Tamador and Almehairbi, Mubarak and Anelli, Andrea and Anstine, Dylan M. and Anthony, John E. and Arnold, Joseph E. and Bahrami, Faezeh and Bellucci, Michael A. and Bhardwaj, Rajni M. and Bier, Imanuel and Bis, Joanna A. and Boese, A. Daniel and Bowskill, David H. and Bramley, James and Brandenburg, Jan Gerit and Braun, Doris E. and Butler, Patrick W. V. and Cadden, Joseph and Carino, Stephen and Chan, Eric J. and Chang, Chao and Cheng, Bingqing and Clarke, Sarah M. and Coles, Simon J. and Cooper, Richard I. and Couch, Ricky and Cuadrado, Ramon and Darden, Tom and Day, Graeme M. and Dietrich, Hanno and Ding, Yiming and DiPasquale, Antonio and Dhokale, Bhausaheb and van Eijck, Bouke P. and Elsegood, Mark R. J. and Firaha, Dzmitry and Fu, Wenbo and Fukuzawa, Kaori and Glover, Joseph and Goto, Hitoshi and Greenwell, Chandler and Guo, Rui and Harter, Jürgen and Helfferich, Julian and Hofmann, Detlef W. M. and Hoja, Johannes and Hone, John and Hong, Richard and Hutchison, Geoffrey and Ikabata, Yasuhiro and Isayev, Olexandr and Ishaque, Ommair and Jain, Varsha and Jin, Yingdi and Jing, Aling and Johnson, Erin R. and Jones, Ian and Jose, K. V. Jovan and Kabova, Elena A. and Keates, Adam and Kelly, Paul F. and Khakimov, Dmitry and Konstantinopoulos, Stefanos and Kuleshova, Liudmila N. and Li, He and Lin, Xiaolu and List, Alexander and Liu, Congcong and Liu, Yifei Michelle and Liu, Zenghui and Liu, Zhi-Pan and Lubach, Joseph W. and Marom, Noa and Maryewski, Alexander A. and Matsui, Hiroyuki and Mattei, Alessandra and Mayo, R. Alex and Melkumov, John W. and Mohamed, Sharmarke and Momenzadeh Abardeh, Zahrasadat and Muddana, Hari S. and Nakayama, Naofumi and Nayal, Kamal Singh and Neumann, Marcus A. and Nikhar, Rahul and Obata, Shigeaki and O'Connor, Dana and Oganov, Artem R. and Okuwaki, Koji and Otero-de-la-Roza, Alberto and Pantelides, Constantinos C. and Parkin, Sean and Pickard, Chris J. and Pilia, Luca and Pivina, Tatyana and Podeszwa, Rafał and Price, Alastair J. A. and Price, Louise S. and Price, Sarah L. and Probert, Michael R. and Pulido, Angeles and Ramteke, Gunjan Rajendra and Rehman, Atta Ur and Reutzel-Edens, Susan M. and Rogal, Jutta and Ross, Marta J. and Rumson, Adrian F. and Sadiq, Ghazala and Saeed, Zeinab M. and Salimi, Alireza and Salvalaglio, Matteo and Sanders de Almada, Leticia and Sasikumar, Kiran and Sekharan, Sivakumar and Shang, Cheng and Shankland, Kenneth and Shinohara, Kotaro and Shi, Baimei and Shi, Xuekun and Skillman, A. Geoffrey and Song, Hongxing and Strasser, Nina and van de Streek, Jacco and Sugden, Isaac J. and Sun, Guangxu and Szalewicz, Krzysztof and Tan, Benjamin I. and Tan, Lu and Tarczynski, Frank and Taylor, Christopher R. and Tkatchenko, Alexandre and Tom, Rithwik and Tuckerman, Mark E. and Utsumi, Yohei and Vogt-Maranto, Leslie and Weatherston, Jake and Wilkinson, Luke J. and Willacy, Robert D. and Wojtas, Lukasz and Woollam, Grahame R. and Yang, Zhuocen and Yonemochi, Etsuo and Yue, Xin and Zeng, Qun and Zhang, Yizu and Zhou, Tian and Zhou, Yunfei and Zubatyuk, Roman and Cole, Jason C.}, issn = {2052-5206}, journal = {Acta Crystallographica Section B}, number = {6}, pages = {517--547}, publisher = {International Union of Crystallography}, title = {{The seventh blind test of crystal structure prediction: Structure generation methods}}, doi = {10.1107/s2052520624007492}, volume = {80}, year = {2024}, } @article{15311, abstract = {Materials with low thermal conductivity usually have complex crystal structures. Herein we experimentally find that a simple crystal structure material AgTlI2 (I4/mcm) owns an extremely low thermal conductivity of 0.25 W/mK at room temperature. To understand this anomaly, we perform in-depth theoretical studies based on ab initio molecular dynamics simulations and anharmonic lattice dynamics. We find that the unique atomic arrangement and weak chemical bonding provide a permissive environment for strong oscillations of Ag atoms, leading to a considerable rattling behaviour and giant lattice anharmonicity. This feature is also verified by the experimental probability density function refinement of single-crystal diffraction. The particularly strong anharmonicity breaks down the conventional phonon gas model, giving rise to non-negligible wavelike phonon behaviours in AgTlI2 at 300 K. Intriguingly, unlike many strongly anharmonic materials where a small propagative thermal conductivity is often accompanied by a large diffusive thermal conductivity, we find an unusual coexistence of ultralow propagative and diffusive thermal conductivities in AgTlI2 based on the thermal transport unified theory. This study underscores the potential of simple crystal structures in achieving low thermal conductivity and encourages further experimental research to enrich the family of materials with ultralow thermal conductivity.}, author = {Zeng, Zezhu and Shen, Xingchen and Cheng, Ruihuan and Perez, Olivier and Ouyang, Niuchang and Fan, Zheyong and Lemoine, Pierric and Raveau, Bernard and Guilmeau, Emmanuel and Chen, Yue}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Pushing thermal conductivity to its lower limit in crystals with simple structures}}, doi = {10.1038/s41467-024-46799-3}, volume = {15}, year = {2024}, } @article{18452, abstract = {Diffusion models have recently emerged as powerful tools for the generation of new molecular and material structures. The key insight is that the noise in these models is related to the response of the atoms to displacement, and the denoising step is thus analogous to the geometry relaxation of atomistic systems starting from a random structure. Building on this, we present a generative method called Response Matching (RM), which leverages the fact that each stable material or molecule exists at the minimum of its potential energy surface. Any perturbation induces a response in energy and stress, driving the structure back to equilibrium. Matching this response is closely related to score matching in diffusion models. Another important aspect of state-of-the-art diffusion models is the incorporation of physical symmetries such as translation, rotation, and periodicity. RM employs a machine learning interatomic potential and random structure search as the denoising model, inherently respecting these symmetries and exploiting the locality of atomic interactions. RM handles both molecules and bulk materials under the same framework. Its efficiency and generalization are demonstrated on three systems: a small organic molecular data set, stable crystals from the Materials Project, and one-shot learning on a single diamond configuration.}, author = {Cheng, Bingqing}, issn = {1549-9626}, journal = {Journal of Chemical Theory and Computation}, number = {20}, pages = {9259--9266}, publisher = {American Chemical Society}, title = {{Response matching for generating materials and molecules}}, doi = {10.1021/acs.jctc.4c00998}, volume = {20}, year = {2024}, } @article{17322, abstract = {Machine learning interatomic potentials are revolutionizing large-scale, accurate atomistic modeling in material science and chemistry. Many potentials use atomic cluster expansion or equivariant message-passing frameworks. Such frameworks typically use spherical harmonics as angular basis functions, followed by Clebsch-Gordan contraction to maintain rotational symmetry. We propose a mathematically equivalent and simple alternative that performs all operations in the Cartesian coordinates. This approach provides a complete set of polynormially independent features of atomic environments while maintaining interaction body orders. Additionally, we integrate low-dimensional embeddings of various chemical elements, trainable radial channel coupling, and inter-atomic message passing. The resulting potential, named Cartesian Atomic Cluster Expansion (CACE), exhibits good accuracy, stability, and generalizability. We validate its performance in diverse systems, including bulk water, small molecules, and 25-element high-entropy alloys.}, author = {Cheng, Bingqing}, issn = {2057-3960}, journal = {npj Computational Materials}, publisher = {Springer Nature}, title = {{Cartesian atomic cluster expansion for machine learning interatomic potentials}}, doi = {10.1038/s41524-024-01332-4}, volume = {10}, year = {2024}, } @article{15052, abstract = {Substrate induces mechanical strain on perovskite devices, which can result in alterations to its lattice dynamics and thermal transport. Herein, we have performed a theoretical investigation on the anharmonic lattice dynamics and thermal property of perovskite Rb2SnBr6 and Cs2SnBr6 under strains using perturbation theory up to the fourth-order terms and the unified thermal transport theory. We demonstrate a pronounced hardening of low-frequency optical phonons as temperature increases, indicating strong lattice anharmonicity and the necessity of adopting temperature-dependent interatomic force constants in the lattice thermal conductivity ( κL) calculations. It is found that the low-lying optical phonon modes of Rb2SnBr6 are extremely soft and their phonon energies are almost strain independent, which ultimately lead to a lower κL and a weaker strain dependence than Cs2SnBr6. We further reveal that the strain dependence of these phonon modes in the A2XB6-type perovskites weakens as their ibrational frequency decreases. This study deepens the understanding of lattice thermal transport in perovskites A2XB6 and provides a perspective on the selection of materials that meet the expected thermal behaviors in practical applications.}, author = {Cheng, Ruihuan and Zeng, Zezhu and Wang, Chen and Ouyang, Niuchang and Chen, Yue}, issn = {2469-9969}, journal = {Physical Review B}, number = {5}, publisher = {American Physical Society}, title = {{Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites}}, doi = {10.1103/physrevb.109.054305}, volume = {109}, year = {2024}, } @article{18553, abstract = {Transcription-coupled nucleotide excision repair (TC-NER) efficiently eliminates DNA damage that impedes gene transcription by RNA polymerase II (RNA Pol II). TC-NER is initiated by the recognition of lesion-stalled RNA Pol II by CSB, which recruits the CRL4CSA ubiquitin ligase and UVSSA. RNA Pol II ubiquitylation at RPB1-K1268 by CRL4CSA serves as a critical TC-NER checkpoint, governing RNA Pol II stability and initiating DNA damage excision by TFIIH recruitment. However, the precise regulatory mechanisms of CRL4CSA activity and TFIIH recruitment remain elusive. Here, we reveal human serine/threonine-protein kinase 19 (STK19) as a TC-NER factor, which is essential for correct DNA damage removal and subsequent transcription restart. Cryogenic electron microscopy (cryo-EM) studies demonstrate that STK19 is an integral part of the RNA Pol II-TC-NER complex, bridging CSA, UVSSA, RNA Pol II, and downstream DNA. STK19 stimulates TC-NER complex stability and CRL4CSA activity, resulting in efficient RNA Pol II ubiquitylation and correct UVSSA and TFIIH binding. These findings underscore the crucial role of STK19 as a core TC-NER component.}, author = {Ramadhin, Anisha R. and Lee, Shun-Hsiao and Zhou, Di and Testa Salmazo, Anita P and Gonzalo-Hansen, Camila and van Sluis, Marjolein and Blom, Cindy M.A. and Janssens, Roel C. and Raams, Anja and Dekkers, Dick and Bezstarosti, Karel and Slade, Dea and Vermeulen, Wim and Pines, Alex and Demmers, Jeroen A.A. and Bernecky, Carrie A and Sixma, Titia K. and Marteijn, Jurgen A.}, issn = {1097-2765}, journal = {Molecular Cell}, number = {24}, pages = {4740--4757.e12}, publisher = {Elsevier}, title = {{STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment}}, doi = {10.1016/j.molcel.2024.10.030}, volume = {84}, year = {2024}, } @article{18945, abstract = {Vaccinia-related kinase 1 (VRK1) and the δ and ε isoforms of casein kinase 1 (CK1) are linked to various disease-relevant pathways. However, the lack of tool compounds for these kinases has significantly hampered our understanding of their cellular functions and therapeutic potential. Here, we describe the structure-based development of potent inhibitors of VRK1, a kinase highly expressed in various tumor types and crucial for cell proliferation and genome integrity. Kinome-wide profiling revealed that our compounds also inhibit CK1δ and CK1ε. We demonstrate that dihydropteridinones 35 and 36 mimic the cellular outcomes of VRK1 depletion. Complementary studies with existing CK1δ and CK1ε inhibitors suggest that these kinases may play overlapping roles in cell proliferation and genome instability. Together, our findings highlight the potential of VRK1 inhibition in treating p53-deficient tumors and possibly enhancing the efficacy of existing cancer therapies that target DNA stability or cell division.}, author = {de Souza Gama, Fernando H. and Dutra, Luiz A. and Hawgood, Michael and dos Reis, Caio Vinícius and Serafim, Ricardo A. M. and Ferreira, Marcos A. and Teodoro, Bruno V. M. and Takarada, Jéssica Emi and Santiago, André S. and Balourdas, Dimitrios-Ilias and Nilsson, Ann-Sofie and Urien, Bruno and Almeida, Vitor M. and Gileadi, Carina and Ramos, Priscila Z. and Testa Salmazo, Anita P and Vasconcelos, Stanley N. S. and Cunha, Micael R. and Mueller, Susanne and Knapp, Stefan and Massirer, Katlin B. and Elkins, Jonathan M. and Gileadi, Opher and Mascarello, Alessandra and Lemmens, Bennie B. L. G. and Guimarães, Cristiano R. W. and Azevedo, Hatylas and Couñago, Rafael M.}, issn = {1520-4804}, journal = {Journal of Medicinal Chemistry}, number = {11}, pages = {8609--8629}, publisher = {American Chemical Society}, title = {{Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε}}, doi = {10.1021/acs.jmedchem.3c02250}, volume = {67}, year = {2024}, } @article{17407, abstract = {The ability to control forces between sub-micron-scale building blocks offers significant potential for designing new materials through self-assembly. Traditionally, this involves identifying a crystal structure with a desired property and then designing building-block interactions so that it assembles spontaneously. However, this paradigm fails for structurally disordered solids, which lack a well-defined structure. Here, we show that disordered solids can still be treated from an inverse self-assembly perspective by bypassing structure and directly targeting material properties. Using the Poisson’s ratio as a primary example, we demonstrate how differentiable programming links interaction parameters with emergent behavior, enabling iterative training to achieve the desired Poisson’s ratio. We also tune other properties, including pressure and local 8-fold structural order, and can even control multiple properties simultaneously. This robust, transferable, and scalable approach can handle a wide variety of systems and properties, demonstrating the utility of disordered solids as a practical avenue for self-assembly platforms.}, author = {Zu, Mengjie and Goodrich, Carl Peter}, issn = {2662-4443}, journal = {Communications Materials}, publisher = {Springer Nature}, title = {{Designing athermal disordered solids with automatic differentiation}}, doi = {10.1038/s43246-024-00583-4}, volume = {5}, year = {2024}, } @article{17325, abstract = {Bacterial ion fluxes are involved in the generation of energy, transport, and motility. As such, bacterial electrophysiology is fundamentally important for the bacterial life cycle, but it is often neglected and consequently, by and large, not understood. Arguably, the two main reasons for this are the complexity of measuring relevant variables in small cells with a cell envelope that contains the cell wall and the fact that, in a unicellular organism, relevant variables become intertwined in a nontrivial manner. To help give bacterial electrophysiology studies a firm footing, in this review, we go back to basics. We look first at the biophysics of bacterial membrane potential, and then at the approaches and models developed mostly for the study of neurons and eukaryotic mitochondria. We discuss their applicability to bacterial cells. Finally, we connect bacterial membrane potential with other relevant (electro)physiological variables and summarize methods that can be used to both measure and influence bacterial electrophysiology.}, author = {Lo, Wei Chang and Krasnopeeva, Ekaterina and Pilizota, Teuta}, issn = {1936-1238}, journal = {Annual Review of Biophysics}, pages = {487--510}, publisher = {Annual Reviews}, title = {{Bacterial Electrophysiology}}, doi = {10.1146/annurev-biophys-030822-032215}, volume = {53}, year = {2024}, } @article{17128, abstract = {The onset of turbulence in pipe flow has defied detailed understanding ever since the first observations of the spatially heterogeneous nature of the transition. Recent theoretical studies and experiments in simpler, shear-driven flows suggest that the onset of turbulence is a directed-percolation non-equilibrium phase transition, but whether these findings are generic and also apply to open or pressure-driven flows is unknown. In pipe flow, the extremely long time scales near the transition make direct observations of critical behaviour virtually impossible. Here we find a technical solution to that limitation and show that the universality class of the transition is directed percolation, from which a jammed phase of puffs emerges above the critical point. Our method is to experimentally characterize all pairwise interactions between localized patches of turbulence puffs and use these interactions as input for renormalization group and computer simulations of minimal models that extrapolate to long length and time scales. The strong interactions in the jamming regime enable us to explicitly measure the turbulent fraction and confirm model predictions. Our work shows that directed-percolation scaling applies beyond simple closed shear flows and underscores how statistical mechanics can lead to profound, quantitative and predictive insights on turbulent flows and their phases.}, author = {Lemoult, Grégoire M and Vasudevan, Mukund and Shih, Hong Yan and Linga, Gaute and Mathiesen, Joachim and Goldenfeld, Nigel and Hof, Björn}, issn = {1745-2481}, journal = {Nature Physics}, pages = {1339--1345}, publisher = {Springer Nature}, title = {{Directed percolation and puff jamming near the transition to pipe turbulence}}, doi = {10.1038/s41567-024-02513-0}, volume = {20}, year = {2024}, } @article{18651, abstract = {Embryo axis formation begins with the localized expression of biochemical signals, which organize cell movements and determine cell fate. A quail study finds that tissue contraction and resulting long-range changes in tissue tension restrict the area where these biochemical signals are expressed.}, author = {Hino, Naoya and Santos Fernandes Lasbarrères Camelo, Carolina and Heisenberg, Carl-Philipp J}, issn = {1879-0445}, journal = {Current Biology}, number = {24}, pages = {R1230--R1232}, publisher = {Elsevier}, title = {{Development: Turing mechanics}}, doi = {10.1016/j.cub.2024.10.065}, volume = {34}, year = {2024}, } @misc{23013, abstract = {Raw data of figures in our manuscript 'Study of STK19 drives Transcription-Coupled Repair by stimulating repair complex stability, Pol II ubiquitylation and TFIIH recruitment' by Ramadhin et al. }, author = {Marteijn, Jurgen}, publisher = {Mendeley Data}, title = {{Study of STK19 drives Transcription-Coupled Repair by stimulating repair complex stability, Pol II ubiquitylation and TFIIH recruitment by Ramadhin et al.}}, doi = {10.17632/wp9sf6sp4z.1}, year = {2024}, } @article{14846, abstract = {Contraction and flow of the actin cell cortex have emerged as a common principle by which cells reorganize their cytoplasm and take shape. However, how these cortical flows interact with adjacent cytoplasmic components, changing their form and localization, and how this affects cytoplasmic organization and cell shape remains unclear. Here we show that in ascidian oocytes, the cooperative activities of cortical actomyosin flows and deformation of the adjacent mitochondria-rich myoplasm drive oocyte cytoplasmic reorganization and shape changes following fertilization. We show that vegetal-directed cortical actomyosin flows, established upon oocyte fertilization, lead to both the accumulation of cortical actin at the vegetal pole of the zygote and compression and local buckling of the adjacent elastic solid-like myoplasm layer due to friction forces generated at their interface. Once cortical flows have ceased, the multiple myoplasm buckles resolve into one larger buckle, which again drives the formation of the contraction pole—a protuberance of the zygote’s vegetal pole where maternal mRNAs accumulate. Thus, our findings reveal a mechanism where cortical actomyosin network flows determine cytoplasmic reorganization and cell shape by deforming adjacent cytoplasmic components through friction forces.}, author = {Caballero Mancebo, Silvia and Shinde, Rushikesh and Bolger-Munro, Madison and Peruzzo, Matilda and Szep, Gregory and Steccari, Irene and Labrousse Arias, David and Zheden, Vanessa and Merrin, Jack and Callan-Jones, Andrew and Voituriez, Raphaël and Heisenberg, Carl-Philipp J}, issn = {1745-2481}, journal = {Nature Physics}, pages = {310--321}, publisher = {Springer Nature}, title = {{Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization}}, doi = {10.1038/s41567-023-02302-1}, volume = {20}, year = {2024}, } @article{14795, abstract = {Metazoan development relies on the formation and remodeling of cell-cell contacts. Dynamic reorganization of adhesion receptors and the actomyosin cell cortex in space and time plays a central role in cell-cell contact formation and maturation. Nevertheless, how this process is mechanistically achieved when new contacts are formed remains unclear. Here, by building a biomimetic assay composed of progenitor cells adhering to supported lipid bilayers functionalized with E-cadherin ectodomains, we show that cortical F-actin flows, driven by the depletion of myosin-2 at the cell contact center, mediate the dynamic reorganization of adhesion receptors and cell cortex at the contact. E-cadherin-dependent downregulation of the small GTPase RhoA at the forming contact leads to both a depletion of myosin-2 and a decrease of F-actin at the contact center. At the contact rim, in contrast, myosin-2 becomes enriched by the retraction of bleb-like protrusions, resulting in a cortical tension gradient from the contact rim to its center. This tension gradient, in turn, triggers centrifugal F-actin flows, leading to further accumulation of F-actin at the contact rim and the progressive redistribution of E-cadherin from the contact center to the rim. Eventually, this combination of actomyosin downregulation and flows at the contact determines the characteristic molecular organization, with E-cadherin and F-actin accumulating at the contact rim, where they are needed to mechanically link the contractile cortices of the adhering cells.}, author = {Arslan, Feyza N and Hannezo, Edouard B and Merrin, Jack and Loose, Martin and Heisenberg, Carl-Philipp J}, issn = {1879-0445}, journal = {Current Biology}, number = {1}, pages = {171--182.e8}, publisher = {Elsevier}, title = {{Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts}}, doi = {10.1016/j.cub.2023.11.067}, volume = {34}, year = {2024}, } @article{15048, abstract = {Embryogenesis results from the coordinated activities of different signaling pathways controlling cell fate specification and morphogenesis. In vertebrate gastrulation, both Nodal and BMP signaling play key roles in germ layer specification and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis is still insufficiently understood. Here, we took a reductionist approach using zebrafish embryonic explants to study the coordination of Nodal and BMP signaling for embryo patterning and morphogenesis. We show that Nodal signaling triggers explant elongation by inducing mesendodermal progenitors but also suppressing BMP signaling activity at the site of mesendoderm induction. Consistent with this, ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm intercalations, key processes during explant elongation. Translating these ex vivo observations to the intact embryo showed that, similar to explants, Nodal signaling suppresses the effect of BMP signaling on cell intercalations in the dorsal domain, thus allowing robust embryonic axis elongation. These findings suggest a dual function of Nodal signaling in embryonic axis elongation by both inducing mesendoderm and suppressing BMP effects in the dorsal portion of the mesendoderm.}, author = {Schauer, Alexandra and Pranjic-Ferscha, Kornelija and Hauschild, Robert and Heisenberg, Carl-Philipp J}, issn = {1477-9129}, journal = {Development}, number = {4}, pages = {1--18}, publisher = {Company of Biologists}, title = {{Robust axis elongation by Nodal-dependent restriction of BMP signaling}}, doi = {10.1242/dev.202316}, volume = {151}, year = {2024}, } @article{15047, abstract = {Tropical precipitation extremes and their changes with surface warming are investigated using global storm resolving simulations and high-resolution observations. The simulations demonstrate that the mesoscale organization of convection, a process that cannot be physically represented by conventional global climate models, is important for the variations of tropical daily accumulated precipitation extremes. In both the simulations and observations, daily precipitation extremes increase in a more organized state, in association with larger, but less frequent, storms. Repeating the simulations for a warmer climate results in a robust increase in monthly-mean daily precipitation extremes. Higher precipitation percentiles have a greater sensitivity to convective organization, which is predicted to increase with warming. Without changes in organization, the strongest daily precipitation extremes over the tropical oceans increase at a rate close to Clausius-Clapeyron (CC) scaling. Thus, in a future warmer state with increased organization, the strongest daily precipitation extremes over oceans increase at a faster rate than CC scaling.}, author = {Bao, Jiawei and Stevens, Bjorn and Kluft, Lukas and Muller, Caroline J}, issn = {2375-2548}, journal = {Science Advances}, number = {8}, publisher = {American Association for the Advancement of Science}, title = {{Intensification of daily tropical precipitation extremes from more organized convection}}, doi = {10.1126/sciadv.adj6801}, volume = {10}, year = {2024}, } @article{17396, abstract = {Wildfire intensity and severity have been increasing in the Iberian Peninsula in recent years, particularly in the Galicia region, due to rising temperatures and accumulating drier combustible vegetation in unmanaged lands. This leads to substantial emissions of air pollutants, notably fine particles (PM2.5), posing a risk to public health. This study aims to assess the impact of local and regional wildfires on PM2.5 levels in Galicia's main cities and their implications for air quality and public health. Over a decade (2013–2022), PM2.5 data during wildfire seasons were analyzed using statistical methods and Lagrangian tracking to monitor smoke plume evolution. The results reveal a notable increase in PM2.5 concentration during the wildfire season (June–November) in Galicia, surpassing health guidelines during extreme events and posing a significant health risk to the population. Regional wildfire analyses indicate that smoke plumes from Northern Portugal contribute to pollution in Galician cities, influencing the seasonality of heightened PM2.5 levels. During extensive wildfires, elevated PM2.5 concentration values persisted for several days, potentially exacerbating health concerns in Galicia. These findings underscore the urgency of implementing air pollution prevention and management measures in the region, including developing effective alerts for large-scale events and improved wildfire management strategies to mitigate their impact on air quality in Galician cities.}, author = {Quishpe-Vásquez, César and Oliva, Patricia and López-Barrera, Ellie Anne and Casallas Garcia, Alejandro}, issn = {0301-4797}, journal = {Journal of Environmental Management}, publisher = {Elsevier}, title = {{Wildfires impact on PM2.5 concentration in galicia Spain}}, doi = {10.1016/j.jenvman.2024.122093}, volume = {367}, year = {2024}, }