@article{12226, abstract = {Background: Biases of DNA repair can shape the nucleotide landscape of genomes at evolutionary timescales. The molecular mechanisms of those biases are still poorly understood because it is difficult to isolate the contributions of DNA repair from those of DNA damage. Results: Here, we develop a genome-wide assay whereby the same DNA lesion is repaired in different genomic contexts. We insert thousands of barcoded transposons carrying a reporter of DNA mismatch repair in the genome of mouse embryonic stem cells. Upon inducing a double-strand break between tandem repeats, a mismatch is generated if the break is repaired through single-strand annealing. The resolution of the mismatch showed a 60–80% bias in favor of the strand with the longest 3′ flap. The location of the lesion in the genome and the type of mismatch had little influence on the bias. Instead, we observe a complete reversal of the bias when the longest 3′ flap is moved to the opposite strand by changing the position of the double-strand break in the reporter. Conclusions: These results suggest that the processing of the double-strand break has a major influence on the repair of mismatches during single-strand annealing.}, author = {Pokusaeva, Victoria and Diez, Aránzazu Rosado and Espinar, Lorena and Pérez, Albert Torelló and Filion, Guillaume J.}, issn = {1474-760X}, journal = {Genome Biology}, publisher = {Springer Nature}, title = {{Strand asymmetry influences mismatch resolution during single-strand annealing}}, doi = {10.1186/s13059-022-02665-3}, volume = {23}, year = {2022}, } @article{12227, abstract = {Polydicyclopentadiene (pDCPD), a thermoset with excellent mechanical properties, has enormous potential as a lightweight, tough, and stable matrix material owing to its highly cross-linked macromolecular network. This work describes generating pDCPD-based foams and hierarchically porous carbons derived therefrom by combining ring-opening metathesis polymerization (ROMP) of DCPD, high internal phase emulsions (HIPEs) as structural templates, and subsequent carbonization. The structure and function of the carbon foams were characterized and discussed in detail using scanning electron, transmission electron, or atomic force microscopy (SEM, TEM, AFM), electron energy-loss spectroscopy (TEM-EELS), N2 sorption, and analyses of electrical conductivity as well as mechanical properties. The resulting materials exhibited uniform, shape-retaining shrinkage of only ∼1/3 after carbonization. No structural failure was observed even when the pDCPD precursor foams were heated to 1400 °C. Instead, the high porosity, void size, and 3D interconnectivity were fully preserved, and the void diameters could be adjusted between 87 and 2.5 μm. Moreover, foams have a carbon content >97%, an electronic conductivity of up to 2800 S·m–1, a Young’s modulus of up to 2.1 GPa, and a specific surface area of up to 1200 m2·g–1. Surprisingly, the pDCPD foams were carbonized into shapes other than monoliths, such as 10’s of micron thick membranes or foamy coatings adhered to a metal foil or grid substrate. The latter coatings even adhere upon bending. Finally, as a use case, carbonized foams were applied as porous cathodes for Li–O2 batteries where the foams show a favorable combination of porosity, active surface area, and pore size for outstanding capacity.}, author = {Kovačič, Sebastijan and Schafzahl, Bettina and Matsko, Nadejda B. and Gruber, Katharina and Schmuck, Martin and Koller, Stefan and Freunberger, Stefan Alexander and Slugovc, Christian}, issn = {2574-0962}, journal = {ACS Applied Energy Materials}, keywords = {Electrical and Electronic Engineering, Materials Chemistry, Electrochemistry, Energy Engineering and Power Technology, Chemical Engineering (miscellaneous)}, number = {11}, pages = {14381--14390}, publisher = {American Chemical Society}, title = {{Carbon foams via ring-opening metathesis polymerization of emulsion templates: A facile method to make carbon current collectors for battery applications}}, doi = {10.1021/acsaem.2c02787}, volume = {5}, year = {2022}, } @article{12228, abstract = {The question of how RNA, as the principal carrier of genetic information evolved is fundamentally important for our understanding of the origin of life. The RNA molecule is far too complex to have formed in one evolutionary step, suggesting that ancestral proto-RNAs (first ancestor of RNA) may have existed, which evolved over time into the RNA of today. Here we show that isoxazole nucleosides, which are quickly formed from hydroxylamine, cyanoacetylene, urea and ribose, are plausible precursors for RNA. The isoxazole nucleoside can rearrange within an RNA-strand to give cytidine, which leads to an increase of pairing stability. If the proto-RNA contains a canonical seed-nucleoside with defined stereochemistry, the seed-nucleoside can control the configuration of the anomeric center that forms during the in-RNA transformation. The results demonstrate that RNA could have emerged from evolutionarily primitive precursor isoxazole ribosides after strand formation.}, author = {Xu, Felix and Crisp, Antony and Schinkel, Thea and Dubini, Romeo C. A. and Hübner, Sarah and Becker, Sidney and Schelter, Florian and Rovo, Petra and Carell, Thomas}, issn = {1521-3773}, journal = {Angewandte Chemie International Edition}, keywords = {General Chemistry, Catalysis}, number = {45}, publisher = {Wiley}, title = {{Isoxazole nucleosides as building blocks for a plausible proto‐RNA}}, doi = {10.1002/anie.202211945}, volume = {61}, year = {2022}, } @inproceedings{12229, abstract = {We present Bullshark, the first directed acyclic graph (DAG) based asynchronous Byzantine Atomic Broadcast protocol that is optimized for the common synchronous case. Like previous DAG-based BFT protocols [19, 25], Bullshark requires no extra communication to achieve consensus on top of building the DAG. That is, parties can totally order the vertices of the DAG by interpreting their local view of the DAG edges. Unlike other asynchronous DAG-based protocols, Bullshark provides a practical low latency fast-path that exploits synchronous periods and deprecates the need for notoriously complex view-change and view-synchronization mechanisms. Bullshark achieves this while maintaining all the desired properties of its predecessor DAG-Rider [25]. Namely, it has optimal amortized communication complexity, it provides fairness and asynchronous liveness, and safety is guaranteed even under a quantum adversary. In order to show the practicality and simplicity of our approach, we also introduce a standalone partially synchronous version of Bullshark, which we evaluate against the state of the art. The implemented protocol is embarrassingly simple (200 LOC on top of an existing DAG-based mempool implementation). It is highly efficient, achieving for example, 125,000 transactions per second with a 2 seconds latency for a deployment of 50 parties. In the same setting, the state of the art pays a steep 50% latency increase as it optimizes for asynchrony.}, author = {Spiegelman, Alexander and Giridharan, Neil and Sonnino, Alberto and Kokoris Kogias, Eleftherios}, booktitle = {Proceedings of the 2022 ACM SIGSAC Conference on Computer and Communications Security}, isbn = {9781450394505}, location = {Los Angeles, CA, United States}, pages = {2705–2718}, publisher = {Association for Computing Machinery}, title = {{Bullshark: DAG BFT protocols made practical}}, doi = {10.1145/3548606.3559361}, year = {2022}, } @article{12231, abstract = {Ventral tail bending, which is transient but pronounced, is found in many chordate embryos and constitutes an interesting model of how tissue interactions control embryo shape. Here, we identify one key upstream regulator of ventral tail bending in embryos of the ascidian Ciona. We show that during the early tailbud stages, ventral epidermal cells exhibit a boat-shaped morphology (boat cell) with a narrow apical surface where phosphorylated myosin light chain (pMLC) accumulates. We further show that interfering with the function of the BMP ligand Admp led to pMLC localizing to the basal instead of the apical side of ventral epidermal cells and a reduced number of boat cells. Finally, we show that cutting ventral epidermal midline cells at their apex using an ultraviolet laser relaxed ventral tail bending. Based on these results, we propose a previously unreported function for Admp in localizing pMLC to the apical side of ventral epidermal cells, which causes the tail to bend ventrally by resisting antero-posterior notochord extension at the ventral side of the tail.}, author = {Kogure, Yuki S. and Muraoka, Hiromochi and Koizumi, Wataru C. and Gelin-alessi, Raphaël and Godard, Benoit G and Oka, Kotaro and Heisenberg, Carl-Philipp J and Hotta, Kohji}, issn = {1477-9129}, journal = {Development}, keywords = {Developmental Biology, Molecular Biology}, number = {21}, publisher = {The Company of Biologists}, title = {{Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona}}, doi = {10.1242/dev.200215}, volume = {149}, year = {2022}, } @article{12232, abstract = {We derive a precise asymptotic formula for the density of the small singular values of the real Ginibre matrix ensemble shifted by a complex parameter z as the dimension tends to infinity. For z away from the real axis the formula coincides with that for the complex Ginibre ensemble we derived earlier in Cipolloni et al. (Prob Math Phys 1:101–146, 2020). On the level of the one-point function of the low lying singular values we thus confirm the transition from real to complex Ginibre ensembles as the shift parameter z becomes genuinely complex; the analogous phenomenon has been well known for eigenvalues. We use the superbosonization formula (Littelmann et al. in Comm Math Phys 283:343–395, 2008) in a regime where the main contribution comes from a three dimensional saddle manifold.}, author = {Cipolloni, Giorgio and Erdös, László and Schröder, Dominik J}, issn = {1424-0661}, journal = {Annales Henri Poincaré}, keywords = {Mathematical Physics, Nuclear and High Energy Physics, Statistical and Nonlinear Physics}, number = {11}, pages = {3981--4002}, publisher = {Springer Nature}, title = {{Density of small singular values of the shifted real Ginibre ensemble}}, doi = {10.1007/s00023-022-01188-8}, volume = {23}, year = {2022}, } @article{12233, abstract = {A novel recursive list decoding (RLD) algorithm for Reed-Muller (RM) codes based on successive permutations (SP) of the codeword is presented. A low-complexity SP scheme applied to a subset of the symmetry group of RM codes is first proposed to carefully select a good codeword permutation on the fly. Then, the proposed SP technique is integrated into an improved RLD algorithm that initializes different decoding paths with random codeword permutations, which are sampled from the full symmetry group of RM codes. Finally, efficient latency and complexity reduction schemes are introduced that virtually preserve the error-correction performance of the proposed decoder. Simulation results demonstrate that at the target frame error rate of 10−3 for the RM code of length 256 with 163 information bits, the proposed decoder reduces 6% of the computational complexity and 22% of the decoding latency of the state-of-the-art semi-parallel simplified successive-cancellation decoder with fast Hadamard transform (SSC-FHT) that uses 96 permutations from the full symmetry group of RM codes, while relatively maintaining the error-correction performance and memory consumption of the semi-parallel permuted SSC-FHT decoder.}, author = {Doan, Nghia and Hashemi, Seyyed Ali and Mondelli, Marco and Gross, Warren J.}, issn = {1558-0857}, journal = {IEEE Transactions on Communications}, number = {11}, pages = {7134--7145}, publisher = {Institute of Electrical and Electronics Engineers}, title = {{Decoding Reed-Muller codes with successive codeword permutations}}, doi = {10.1109/tcomm.2022.3211101}, volume = {70}, year = {2022}, } @article{12234, abstract = {Hybrid speciation—the origin of new species resulting from the hybridization of genetically divergent lineages—was once considered rare, but genomic data suggest that it may occur more often than once thought. In this study, Noguerales and Ortego found genomic evidence supporting the hybrid origin of a grasshopper that is able to exploit a broader range of host plants than either of its putative parents.}, author = {Stankowski, Sean}, issn = {1558-5646}, journal = {Evolution}, keywords = {General Agricultural and Biological Sciences, Genetics, Ecology, Evolution, Behavior and Systematics}, number = {11}, pages = {2784--2785}, publisher = {Wiley}, title = {{Digest: On the origin of a possible hybrid species}}, doi = {10.1111/evo.14632}, volume = {76}, year = {2022}, } @article{12235, abstract = {Background: About 800 women die every day worldwide from pregnancy-related complications, including excessive blood loss, infections and high-blood pressure (World Health Organization, 2019). To improve screening for high-risk pregnancies, we set out to identify patterns of maternal hematological changes associated with future pregnancy complications. Methods: Using mixed effects models, we established changes in 14 complete blood count (CBC) parameters for 1710 healthy pregnancies and compared them to measurements from 98 pregnancy-induced hypertension, 106 gestational diabetes and 339 postpartum hemorrhage cases. Results: Results show interindividual variations, but good individual repeatability in CBC values during physiological pregnancies, allowing the identification of specific alterations in women with obstetric complications. For example, in women with uncomplicated pregnancies, haemoglobin count decreases of 0.12 g/L (95% CI −0.16, −0.09) significantly per gestation week (p value <.001). Interestingly, this decrease is three times more pronounced in women who will develop pregnancy-induced hypertension, with an additional decrease of 0.39 g/L (95% CI −0.51, −0.26). We also confirm that obstetric complications and white CBC predict the likelihood of giving birth earlier during pregnancy. Conclusion: We provide a comprehensive description of the associations between haematological changes through pregnancy and three major obstetric complications to support strategies for prevention, early-diagnosis and maternal care.}, author = {Patxot, Marion and Stojanov, Miloš and Ojavee, Sven Erik and Gobert, Rosanna Pescini and Kutalik, Zoltán and Gavillet, Mathilde and Baud, David and Robinson, Matthew Richard}, issn = {1600-0609}, journal = {European Journal of Haematology}, keywords = {Hematology, General Medicine}, number = {5}, pages = {566--575}, publisher = {Wiley}, title = {{Haematological changes from conception to childbirth: An indicator of major pregnancy complications}}, doi = {10.1111/ejh.13844}, volume = {109}, year = {2022}, } @article{12236, abstract = {High-entropy materials offer numerous advantages as catalysts, including a flexible composition to tune the catalytic activity and selectivity and a large variety of adsorption/reaction sites for multistep or multiple reactions. Herein, we report on the synthesis, properties, and electrocatalytic performance of an amorphous high-entropy boride based on abundant transition metals, CoFeNiMnZnB. This metal boride provides excellent performance toward the oxygen evolution reaction (OER), including a low overpotential of 261 mV at 10 mA cm–2, a reduced Tafel slope of 56.8 mV dec–1, and very high stability. The outstanding OER performance of CoFeNiMnZnB is attributed to the synergistic interactions between the different metals, the leaching of Zn ions, the generation of oxygen vacancies, and the in situ formation of an amorphous oxyhydroxide at the CoFeNiMnZnB surface during the OER.}, author = {Wang, Xiang and Zuo, Yong and Horta, Sharona and He, Ren and Yang, Linlin and Ostovari Moghaddam, Ahmad and Ibáñez, Maria and Qi, Xueqiang and Cabot, Andreu}, issn = {1944-8252}, journal = {ACS Applied Materials & Interfaces}, keywords = {General Materials Science}, number = {42}, pages = {48212--48219}, publisher = {American Chemical Society}, title = {{CoFeNiMnZnB as a high-entropy metal boride to boost the oxygen evolution reaction}}, doi = {10.1021/acsami.2c11627}, volume = {14}, year = {2022}, } @article{12237, abstract = {Thermoelectric technology requires synthesizing complex materials where not only the crystal structure but also other structural features such as defects, grain size and orientation, and interfaces must be controlled. To date, conventional solid-state techniques are unable to provide this level of control. Herein, we present a synthetic approach in which dense inorganic thermoelectric materials are produced by the consolidation of well-defined nanoparticle powders. The idea is that controlling the characteristics of the powder allows the chemical transformations that take place during consolidation to be guided, ultimately yielding inorganic solids with targeted features. Different from conventional methods, syntheses in solution can produce particles with unprecedented control over their size, shape, crystal structure, composition, and surface chemistry. However, to date, most works have focused only on the low-cost benefits of this strategy. In this perspective, we first cover the opportunities that solution processing of the powder offers, emphasizing the potential structural features that can be controlled by precisely engineering the inorganic core of the particle, the surface, and the organization of the particles before consolidation. We then discuss the challenges of this synthetic approach and more practical matters related to solution processing. Finally, we suggest some good practices for adequate knowledge transfer and improving reproducibility among different laboratories.}, author = {Fiedler, Christine and Kleinhanns, Tobias and Garcia, Maria and Lee, Seungho and Calcabrini, Mariano and Ibáñez, Maria}, issn = {1520-5002}, journal = {Chemistry of Materials}, keywords = {Materials Chemistry, General Chemical Engineering, General Chemistry}, number = {19}, pages = {8471--8489}, publisher = {American Chemical Society}, title = {{Solution-processed inorganic thermoelectric materials: Opportunities and challenges}}, doi = {10.1021/acs.chemmater.2c01967}, volume = {34}, year = {2022}, } @article{12238, abstract = {Upon the initiation of collective cell migration, the cells at the free edge are specified as leader cells; however, the mechanism underlying the leader cell specification remains elusive. Here, we show that lamellipodial extension after the release from mechanical confinement causes sustained extracellular signal-regulated kinase (ERK) activation and underlies the leader cell specification. Live-imaging of Madin-Darby canine kidney (MDCK) cells and mouse epidermis through the use of Förster resonance energy transfer (FRET)-based biosensors showed that leader cells exhibit sustained ERK activation in a hepatocyte growth factor (HGF)-dependent manner. Meanwhile, follower cells exhibit oscillatory ERK activation waves in an epidermal growth factor (EGF) signaling-dependent manner. Lamellipodial extension at the free edge increases the cellular sensitivity to HGF. The HGF-dependent ERK activation, in turn, promotes lamellipodial extension, thereby forming a positive feedback loop between cell extension and ERK activation and specifying the cells at the free edge as the leader cells. Our findings show that the integration of physical and biochemical cues underlies the leader cell specification during collective cell migration.}, author = {Hino, Naoya and Matsuda, Kimiya and Jikko, Yuya and Maryu, Gembu and Sakai, Katsuya and Imamura, Ryu and Tsukiji, Shinya and Aoki, Kazuhiro and Terai, Kenta and Hirashima, Tsuyoshi and Trepat, Xavier and Matsuda, Michiyuki}, issn = {1534-5807}, journal = {Developmental Cell}, keywords = {Developmental Biology, Cell Biology, General Biochemistry, Genetics and Molecular Biology, Molecular Biology}, number = {19}, pages = {2290--2304.e7}, publisher = {Elsevier}, title = {{A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration}}, doi = {10.1016/j.devcel.2022.09.003}, volume = {57}, year = {2022}, } @article{12239, abstract = {Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs.}, author = {Johnson, Alexander J and Kaufmann, Walter and Sommer, Christoph M and Costanzo, Tommaso and Dahhan, Dana A. and Bednarek, Sebastian Y. and Friml, Jiří}, issn = {1674-2052}, journal = {Molecular Plant}, keywords = {Plant Science, Molecular Biology}, number = {10}, pages = {1533--1542}, publisher = {Elsevier}, title = {{Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution}}, doi = {10.1016/j.molp.2022.09.003}, volume = {15}, year = {2022}, } @article{12243, abstract = {We consider the eigenvalues of a large dimensional real or complex Ginibre matrix in the region of the complex plane where their real parts reach their maximum value. This maximum follows the Gumbel distribution and that these extreme eigenvalues form a Poisson point process as the dimension asymptotically tends to infinity. In the complex case, these facts have already been established by Bender [Probab. Theory Relat. Fields 147, 241 (2010)] and in the real case by Akemann and Phillips [J. Stat. Phys. 155, 421 (2014)] even for the more general elliptic ensemble with a sophisticated saddle point analysis. The purpose of this article is to give a very short direct proof in the Ginibre case with an effective error term. Moreover, our estimates on the correlation kernel in this regime serve as a key input for accurately locating [Formula: see text] for any large matrix X with i.i.d. entries in the companion paper [G. Cipolloni et al., arXiv:2206.04448 (2022)]. }, author = {Cipolloni, Giorgio and Erdös, László and Schröder, Dominik J and Xu, Yuanyuan}, issn = {1089-7658}, journal = {Journal of Mathematical Physics}, keywords = {Mathematical Physics, Statistical and Nonlinear Physics}, number = {10}, publisher = {AIP Publishing}, title = {{Directional extremal statistics for Ginibre eigenvalues}}, doi = {10.1063/5.0104290}, volume = {63}, year = {2022}, } @article{12244, abstract = {Environmental cues influence the highly dynamic morphology of microglia. Strategies to characterize these changes usually involve user-selected morphometric features, which preclude the identification of a spectrum of context-dependent morphological phenotypes. Here we develop MorphOMICs, a topological data analysis approach, which enables semiautomatic mapping of microglial morphology into an atlas of cue-dependent phenotypes and overcomes feature-selection biases and biological variability. We extract spatially heterogeneous and sexually dimorphic morphological phenotypes for seven adult mouse brain regions. This sex-specific phenotype declines with maturation but increases over the disease trajectories in two neurodegeneration mouse models, with females showing a faster morphological shift in affected brain regions. Remarkably, microglia morphologies reflect an adaptation upon repeated exposure to ketamine anesthesia and do not recover to control morphologies. Finally, we demonstrate that both long primary processes and short terminal processes provide distinct insights to morphological phenotypes. MorphOMICs opens a new perspective to characterize microglial morphology.}, author = {Colombo, Gloria and Cubero, Ryan J and Kanari, Lida and Venturino, Alessandro and Schulz, Rouven and Scolamiero, Martina and Agerberg, Jens and Mathys, Hansruedi and Tsai, Li-Huei and Chachólski, Wojciech and Hess, Kathryn and Siegert, Sandra}, issn = {1546-1726}, journal = {Nature Neuroscience}, keywords = {General Neuroscience}, number = {10}, pages = {1379--1393}, publisher = {Springer Nature}, title = {{A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes}}, doi = {10.1038/s41593-022-01167-6}, volume = {25}, year = {2022}, } @article{12245, abstract = {MicroRNAs (miRs) have an important role in tuning dynamic gene expression. However, the mechanism by which they are quantitatively controlled is unknown. We show that the amount of mature miR-9, a key regulator of neuronal development, increases during zebrafish neurogenesis in a sharp stepwise manner. We characterize the spatiotemporal profile of seven distinct microRNA primary transcripts (pri-mir)-9s that produce the same mature miR-9 and show that they are sequentially expressed during hindbrain neurogenesis. Expression of late-onset pri-mir-9-1 is added on to, rather than replacing, the expression of early onset pri-mir-9-4 and -9-5 in single cells. CRISPR/Cas9 mutation of the late-onset pri-mir-9-1 prevents the developmental increase of mature miR-9, reduces late neuronal differentiation and fails to downregulate Her6 at late stages. Mathematical modelling shows that an adaptive network containing Her6 is insensitive to linear increases in miR-9 but responds to stepwise increases of miR-9. We suggest that a sharp stepwise increase of mature miR-9 is created by sequential and additive temporal activation of distinct loci. This may be a strategy to overcome adaptation and facilitate a transition of Her6 to a new dynamic regime or steady state.}, author = {Soto, Ximena and Burton, Joshua and Manning, Cerys S. and Minchington, Thomas and Lea, Robert and Lee, Jessica and Kursawe, Jochen and Rattray, Magnus and Papalopulu, Nancy}, issn = {1477-9129}, journal = {Development}, keywords = {Developmental Biology, Molecular Biology}, number = {19}, publisher = {The Company of Biologists}, title = {{Sequential and additive expression of miR-9 precursors control timing of neurogenesis}}, doi = {10.1242/dev.200474}, volume = {149}, year = {2022}, } @article{12246, abstract = {The Lieb–Oxford inequality provides a lower bound on the Coulomb energy of a classical system of N identical charges only in terms of their one-particle density. We prove here a new estimate on the best constant in this inequality. Numerical evaluation provides the value 1.58, which is a significant improvement to the previously known value 1.64. The best constant has recently been shown to be larger than 1.44. In a second part, we prove that the constant can be reduced to 1.25 when the inequality is restricted to Hartree–Fock states. This is the first proof that the exchange term is always much lower than the full indirect Coulomb energy.}, author = {Lewin, Mathieu and Lieb, Elliott H. and Seiringer, Robert}, issn = {1573-0530}, journal = {Letters in Mathematical Physics}, keywords = {Mathematical Physics, Statistical and Nonlinear Physics}, number = {5}, publisher = {Springer Nature}, title = {{Improved Lieb–Oxford bound on the indirect and exchange energies}}, doi = {10.1007/s11005-022-01584-5}, volume = {112}, year = {2022}, } @article{12247, abstract = {Chromosomal inversions have been shown to play a major role in a local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence.}, author = {Koch, Eva L. and Ravinet, Mark and Westram, Anja M and Johannesson, Kerstin and Butlin, Roger K.}, issn = {1558-5646}, journal = {Evolution}, keywords = {General Agricultural and Biological Sciences, Genetics, Ecology, Evolution, Behavior and Systematics}, number = {10}, pages = {2332--2346}, publisher = {Wiley}, title = {{Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution}}, doi = {10.1111/evo.14602}, volume = {76}, year = {2022}, } @article{12248, abstract = {Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species Artemia sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species Artemia sp. Kazakhstan and several asexual lineages of Artemia parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.}, author = {Elkrewi, Marwan N and Khauratovich, Uladzislava and Toups, Melissa A and Bett, Vincent K and Mrnjavac, Andrea and Macon, Ariana and Fraisse, Christelle and Sax, Luca and Huylmans, Ann K and Hontoria, Francisco and Vicoso, Beatriz}, issn = {1943-2631}, journal = {Genetics}, keywords = {Genetics}, number = {2}, publisher = {Oxford University Press}, title = {{ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp}}, doi = {10.1093/genetics/iyac123}, volume = {222}, year = {2022}, } @article{12249, abstract = {The chemical potential of a component in a solution is defined as the free energy change as the amount of that component changes. Computing this fundamental thermodynamic property from atomistic simulations is notoriously difficult because of the convergence issues involved in free energy methods and finite size effects. This Communication presents the so-called S0 method, which can be used to obtain chemical potentials from static structure factors computed from equilibrium molecular dynamics simulations under the isothermal–isobaric ensemble. This new method is demonstrated on the systems of binary Lennard-Jones particles, urea–water mixtures, a NaCl aqueous solution, and a high-pressure carbon–hydrogen mixture. }, author = {Cheng, Bingqing}, issn = {1089-7690}, journal = {The Journal of Chemical Physics}, keywords = {Physical and Theoretical Chemistry, General Physics and Astronomy}, number = {12}, publisher = {AIP Publishing}, title = {{Computing chemical potentials of solutions from structure factors}}, doi = {10.1063/5.0107059}, volume = {157}, year = {2022}, }